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locus

locus. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 a 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0

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locus

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  1. locus 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 a 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 b 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 c 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 1 d 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 0 1 1 1 e 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 1 1 0 0 0 0 0 1 1 1 f 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 g 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 1 0 h 1 1 ? 1 1 1 1 1 1 1 ? 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 0 0 0 1 0 i 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 j 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 k 1 1 1 1 1 1 1 1 1 1 0 ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 l 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 m 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ? 0 0 ? 0 0 0 0 0 0 0 0 0 0 0 n 1 1 1 ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ? ? 0 0 0 0 0 0 0 0 0 0 ? 0 0 0 o 0 0 0 0 0 0 0 0 0 0 0 0 ? ? 0 ? ? 0 0 ? 0 ? ? ? 0 0 0 0 0 ? ? 0 0 ? 0 0 species 1 Hump 17 2 Hump 49 3 sNR 99 4 SR 3 5 GRY20 6 BLU 47 7 BRY 50 8 Hump 9 9 Hump 55 10 Sei 8-2 11 BRY 82 12 Fin 12 13 Nag 41 14 Mnk 38 15 Sir 49 16 Hump 38 17 Mnk 55 18 Sei 17 a; humpback b; fin c; blue d; sei e; bryde’s f; gray g; common minke h; Antarctic minke i ; pygmy right j; right k; bowhead l ; sperm m; beaked n; bottle-nosed dolphin o; hippopotamus 19 Sei 19 20 Sei 47 21 Fin 9 22 Hump 46 23 Hump 53 24 BRY 24 25Sei 26 26 Sei 20 27 Sei 35 28 Sei 37 29 Ac 144 30 Mnk 1 31 NM 35 32 SEM 3 33 SEM 15 34 IWA31 35 BRY28 36 Sei23 Supplementaｌ table 3. Nikaido et al.

  2. d 98 e 88 c 59 f g 99 98 h a 100 93 b 99 i j 87 k 97 l n m o sei bryde's blue gray common minke Ant. minke hump fin pygmy right right bowhead sperm bottlenosed dolphin beaked hippo Supplemental figure 2

  3. IWA31 humpback AAGAGTAGTCAAATTCACAAGCTGC IWA31 fin .......A................. IWA31 blue .-....CA................. IWA31 sei .......A................. IWA31 Bryde's .......A................T IWA31 gray .......A................. IWA31 common minke .......A................. IWA31 Ant. minke .......A................. IWA31 right .......A...G............. IWA31 sperm .......A................. ----------------------------- ---------------TCCACCTAGA ---------------.......... AAATTCACAAGCTGC.......... AAATTCACAAGCTGC.......... AAATTCACAAGCTGC.......... AAATTCACAAGCTGC.......... ---------------.......... ---------------.......... ---------------.......... ---------------.......... ----------------------------- CHR-2 (CD) ----------------------------- ----------------------------- ----------------------------- ----------------------------- BRY28 humpback TGAATAAATTAAAAAGAACTG BRY28 fin ..................... BRY28 blue ..................... BRY28 sei ..................... BRY28 Bryde's ..................... BRY28 gray ..................... BRY28 common minke ..................... BRY28 Ant. minke ..................... BRY28 right ..................... BRY28 sperm ..................... ----------------------------- -----------AAGAAAATAT AAAAAGAACTG.......... AAAAAGAACTG.......... AAAAAGAACTG.......... AAAAAGAACTG.......... -----------.......... -----------.......... -----------.......... -----------.......... -----------.......... CHR-2 (CD) ----------------------------- ----------------------------- ----------------------------- ----------------------------- ----------------------------- Sei23 hump TGTTGTGATTAAGAACAAGAGCTTCA Sei23 fin .........................G Sei23 blue .......................... Sei23 sei .......................... Sei23 Bryde‘s .......................... Sei23 gray .......................... Sei23 common minke .......................... Sei23 Ant. minke .......................... Sei23 right .......................... Sei23 sperm .......................... ----------------AAATTAATAG ----------------.......... ----------------.......... AAGAATAAGAGCTTCA.......... AAGAATAAGAGCTTCA.......... ----------------.......... AAGAACAAGAGCTTCA.......... AAGAACAAGAGCTTCA.......... ----------------.......... ----------------.......... ----------------------------- ----------------------------- ----------------------------- CHR-2 (CD) ----------------------------- CHR-2 (CD) ----------------------------- ----------------------------- Supplemental figure 3 Nikaido et al.

  4. A B X speciation in a short period (not enough time to fix a SINEallele) Y The loci will be fixed SINE + or – almost at random gene tree (deduced by SINE insertion) species tree a c b d Fixed to + Fixed to + Fixed to - Fixed to - a a b c c b d d Supplemental figure 4 Nikaido et al.

  5. Hump17-1.nuc 1:-------------GGGAATTTCTTGGGGAAACATGACATTAGAAAAATATTCCAGGACTTCCCTGGTGGTGCAGT--GGC 65 Hump17-2.nuc 1:ATCTCATAGAAATA..G.A..TC.T...G..............................................--..T 78 Hump17-3.NUC 1:-------------------..TC.T...G..............................................--... 59 Hump17-4.NUC 1:----------------------------------NNNNNNNNNNNNNNNNNNNN.....................--... 44 Hump17-5.NUC 1:-------------------------------............................................--... 47 Hump17-6.NUC 1:-------------------------------............................................--... 47 Hump17-7.NUC 1:-------------------------------NNNNNNNNNNNNNNNNNN............A.......C.....--... 47 Hump17-8.NUC 1:-------------------..TC.T...G................................A.......C.....--... 59 Hump17-9.NUC 1:-------------------..TC.T...G..........GG....................A.......C.....--... 59 Hump17-10.NUC 1:-------------------------------------------..........................C.....GT... 37 Hump17-11.NUC 1:-------------------------------------------..........................C.....--... 35 Hump17-12.NUC 1:----------------G.A..TCCT...G........................................C.....--..T 62 Hump17-13.NUC 1:---------------.G.A..TCCT...G.........................A..............C.....--..T 63 Hump17-14.nuc 1:------------------------------------------............A..............C.....--..T 36 Hump17-15.NUC 1:--TCTCATAGAAATA.GGA..TC.T...GNNNCN..NNNN.A.....A......A------------------------- 53 Hump17-1.nuc 66:TAAGAATCCGCCTGCCAATTCAGGGGXXXXXXXXXX-AGCCAAATAAATAAATAAATAAATACATTAAAAATTAAAAATT 144 Hump17-2.nuc 79:....................................-.....................C.............A....... 157 Hump17-3.NUC 60:........T...........................-..T.......................-......-.A....-.. 135 Hump17-4.NUC 45:....................................-..T................................A....... 123 Hump17-5.NUC 48:....................................-..T................................A....... 126 Hump17-6.NUC 48:....................................-..T................................A....... 126 Hump17-7.NUC 48:....................................-...................................A....... 126 Hump17-8.NUC 60:....................................-............................A......A....... 138 Hump17-9.NUC 60:....................................-............................A......A....... 138 Hump17-10.NUC 38:.........A.......G..................-...................................A....... 116 Hump17-11.NUC 36:.........A.......G..................-...................................A....... 114 Hump17-12.NUC 63:.........T...A.....G................-....---------..A...A...............A....... 132 Hump17-13.NUC 64:.........A.........G................-....--------..T....................A....... 134 Hump17-14.nuc 37:...................G................-....--------............................... 107 Hump17-15.NUC 54:-------------------------------------------------------------------------------- 54 Hump17-1.nuc 145:CCAATAAATAAATATTCTAGAAAATAGAATCCAATTTTAAACCAAATCAGTTGTGGTTGGTAAGGTATCACTGTTTAACA 224 Hump17-2.nuc 158:....................................................T........................... 237 Hump17-3.NUC 136:.........G.............-.-.......-......-....-......T.......A.G.A..C 198 Hump17-4.NUC 124:....................................................T........................... 203 Hump17-5.NUC 127:....................................................T........................... 206 Hump17-6.NUC 127:....................................................T........................... 206 Hump17-7.NUC 127:....................................................T.......C.....G............. 206 Hump17-8.NUC 139:....................................................T.......C................... 218 Hump17-9.NUC 139:T.................C..................A..............T.......C................... 218 Hump17-10.NUC 117:......................................T.............T........................... 196 Hump17-11.NUC 115:....................................................T........................... 194 Hump17-12.NUC 133:....................................................T.................T......... 212 Hump17-13.NUC 135:....................................................T...............T........... 214 Hump17-14.nuc 108:G.............G...................................G.T-...C.-.....-.........-.... 183 Hump17-15.NUC 54:----.CCC........A..............T.G....G..A..........T..................C........ 129 Supplemental figure 5 Nikaido et al.

  6. Hump49-1 1:-------------NNNNNNNNNNNNNNNNNNNNGTGACTGCAAAATAGAGGGGG-TCAAGGCTTCCCTGGTGGCGCAGTG 66 Hump49-2 1:---ACTCAGTTCCTTGATTGATGGATAAGATAA.....................-......................... 76 Hump49-3 1:-----TCAGTTCCTTGATTGATGGATAAGATAA.....................-......................... 74 Hump49-4 1:CAATCTCAGTTCCTTGATTGATGAATAAGATAA.....................-......................... 79 Hump49-5 1:-----------CCTTGATTGATGAATAAGATAA.....................-..C...................... 68 Hump49-6 1:-----------CCTTGATTGATGAATAAGATAA.......G.............-..C...................... 68 Hump49-7 1:--------------..............GATAA.......G............A-..CC...........A......... 65 Hump49-8 1:--------------...................NNNN.......-.........-......................... 64 Hump49-10 1:-----------CCTTGATTGATGAATAAGATAA.....................-..........T.............. 68 Hump49-11.NUC 1:-----------CCTTGATTGATGAATAAGATAA.....A...............-..C.......T.............. 68 Hump49-12.NUC 1:NNNNNNNNNNNNN..GATTGATTGATAAGATAA.....................-...................T..... 79 Hump49-13 1:-----------------................N..........-.........G...................T..... 62 Hump49-14.NUC 1:ATCTGCAGTTCACTTGATTGATTGATAAGATAA.....................-...................T..... 79 Hump49-15 1:TTCGATCTCGTTCCTTGATTGATGTA.AGATAA....................--...---------------------- 56 Hump49-1 67:GTTXXXXXXXXXXGCTCGCTGCAACTAGAGGAAGCCTGCGCGCAGCAACATGGACCCAATGCAGCCAAAAATAAATAAAA 146 Hump49-2 77:.................................................G.............................. 156 Hump49-3 75:...................C...G......A.........T.........AA...........A................ 154 Hump49-4 80:...................C..........A...................AA............................ 159 Hump49-5 69:...................C..........A...................AA............................ 148 Hump49-6 69:...................C..........A...................AA............................ 148 Hump49-7 66:.................A.C....................T.........AA............................ 145 Hump49-8 65:...................C..........A.........T.........AA............................ 144 Hump49-10 69:...................C..........A...................GA............................ 148 Hump49-11.NUC 69:...................C..........A...................GA............................ 148 Hump49-12.NUC 80:................T.............A...................AA.................T.......... 159 Hump49-13 63:.............NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--C..CC.....T.. 140 Hump49-14.NUC 80:................T.............A..................GAA.................T.......... 159 Hump49-15 57:-------------------------------------------------------------------------------- 57 Hump49-1 147:ATAAAAATAAGTAAATTATTAAAAAAAAA--------------CAACAGAGGGGTCAGTTTGGGAAA-GTTTTCTCCCTT 211 Hump49-2 157:.............................--------------........................-............ 221 Hump49-3 155:.......A.TTATT.AA.AA...--------------------........................-............ 213 Hump49-4 160:..........A..................--------------.....A..................-............ 224 Hump49-5 149:..........A..................--------------.....A..................-............ 213 Hump49-6 149:..........A..................A-------------.....A..................A............ 215 Hump49-7 146:..........A..................--------------........................-............ 210 Hump49-8 145:.........TT.CT.........C..C..ACAACAAAGAAAAA........................-.A.......... 223 Hump49-10 149:..........A..................--------------.....A..................-T........... 213 Hump49-11.NUC 149:..........A..................--------------.....A..................-T........... 213 Hump49-12.NUC 160:..........A..............------------------...A.A..................-............ 220 Hump49-13 141:..........A.C................--------------........................-............ 205 Hump49-14.NUC 160:.......ATTA.T..GA.AA..---------------------........................-.C.......... 217 Hump49-15 57:---------------------------------------------------------..........-ACG......T.. 78 Supplemental figure 5 Nikaido et al. continued

  7. sNR99-1.nuc 81:ATAAATATACAAAACAGGGGCTTCCCCAGTGGCGCAGTGGTTAAGAATCTGCCTGCCAATGCAGGGGXXXXXXXXXXGCC 160 sNR99-2.NUC 81:.........................................................C...................... 160 sNR99-3.NUC 78:................................................................................ 157 sNR99-4.nuc 81:.................................................C.............................. 160 sNR99-5.NUC 81:.................................................C.............................. 160 sNR99-6.NUC 81:.................................................C.............................. 160 sNR99-7.NUC 81:......................................A..........C.............................. 160 sNR99-9.NUC 81:.................................................C.............................. 160 sNR99-10.NUC 81:....................------------.A...............C.............................. 148 sNR99-11.NUC 81:....................------------.A...............C.............................. 148 sNR99-12.nuc 76:.................................A...............CA............................. 155 sNR99-13.nuc 81:................................T................C.............................. 160 sNR99-14.nuc 80:.................................................C.............................. 159 sNR99-15.NUC 80:......C..........--------------------------------------------------------------- 96 sNR99-1.nuc 161:CACGTGCAGCAACGAAGACCCAACACAGCCAAAAATAAATAAATATAAACAAATAAATTAAAAATACATATATACAAAAC 240 sNR99-2.NUC 161:................................................................................ 240 sNR99-3.NUC 158:................................................................................ 237 sNR99-4.nuc 161:................................................................................ 240 sNR99-5.NUC 161:................................................................................ 240 sNR99-6.NUC 161:................................................................................ 240 sNR99-7.NUC 161:............................G................................................... 240 sNR99-9.NUC 161:................................................................................ 240 sNR99-10.NUC 149:................................................................................ 228 sNR99-11.NUC 149:................................................................................ 228 sNR99-12.nuc 156:...ACAT......A...G......G....................A.................................. 235 sNR99-13.nuc 161:....CAT......A...G......G....................A.........T........................ 240 sNR99-14.nuc 160:....C.T.A....A...G......G....................A.................................. 239 sNR99-15.NUC 97:-------------------------------------------------------------------------------- 97 sNR99-1.nuc 241:AGATCATGAGTAAATTCTTAGATG 264 sNR99-2.NUC 241:........-T...... 255 sNR99-3.NUC 238:..............A......... 261 sNR99-4.nuc 241:..............-......... 263 sNR99-5.NUC 241:..............A.........A 265 sNR99-6.NUC 241:..............A.........A 265 sNR99-7.NUC 241:..............-.........A 264 sNR99-9.NUC 241:..............-......... 263 sNR99-10.NUC 229:..............-......... 251 sNR99-11.NUC 229:..............-......... 251 sNR99-12.nuc 236:..............-......... 258 sNR99-13.nuc 241:..............-......... 263 sNR99-14.nuc 240:..............A......... 263 sNR99-15.NUC 97:--............-.........A 118 Supplemental figure 5 Nikaido et al. continued

  8. SR3-1 76:ACAGACTAGGTTTAAAAAAGAGCACACTGGACTTCCCTGGTGGCACAGTGGGTAAGAAXXXXXXXXXXACTGGAGAAACC 155 SR3-2 65:................................................................................ 144 SR3-3 46:..C.N..T.....T.....N.N.N.N........N.....N..NN.NNNNNNNNNNNNNNNNNNNNNN............ 125 SR3-4 75:................................................G......A........................ 154 SR3-5 71:......C........................................A................................ 150 SR3-7 71:.......................................................................A........ 150 SR3-8 71:.......................................................................A........ 150 SR3-9 61:......C................................A.............T...T.............A........ 140 SR3-10 58:......C................................A....G..........................A........ 137 SR3-11 57:.......................................................................A........ 136 SR3-12 46:.......................................................A...............A........ 125 SR3-13 46:.......................................................A...............A........ 125 SR3-15.NUC 57:............................---------------------------------------------------- 94 SR3-1 156:CTGTGCAGCAACGAAGACCCAACACAACCAAAAATTTAAAAAA--TTAAATCTTTTGACTTCTGA-GATGACTCACT-CA 231 SR3-2 145:........................................C..--....................T..........G-.. 221 SR3-3 126:...................................A.......--....................-...........-.. 201 SR3-4 155:...........................................--....................-...........-.. 230 SR3-5 151:................................C..........--....................-...........-.. 226 SR3-7 151:...G..................TG....G...--.AA.T....--....................-...........-.. 224 SR3-8 151:...G..................TG....G...--.AA.T....--....................-...........-.. 224 SR3-9 141:.........G............TG...........AA......AA...........A........-...........-.. 218 SR3-10 138:.........G............TG...........AA......--...........A........-...........-.. 213 SR3-11 137:.......................G...........AA.T....--....................-...........A.. 213 SR3-12 126:...G.G.........A.......G...........AA.T....--....TCT........NNNNNNNNNNNNNNNNNNNN 203 SR3-13 126:T..G.G....T....A.......G...........AA.T....--....TCT.............ANNNNNNNNNNNNNN 203 SR3-15.NUC 95:------------------------------------------------------------------------------.. 96 SR3-1 232:CGTGGCTGTAGGTAAGAGGCCTCAGT 257 SR3-2 222:....................-.....CT 248 SR3-3 202:...........-........-.....CT 227 SR3-4 231:..........................TCCTTGCCACATGGATCTCTCCTTA 281 SR3-5 227:..........................TCCTTGCCACATGGATCTCTCCTTA 277 SR3-7 225:.A........................TCCTTGCCACATGGATCTCTCCTTA 275 SR3-8 225:.A........................TCCTTGCCACATGGATCTCTCCTTA 275 SR3-9 219:...........NNNNNNNNNNN 240 SR3-10 214:...........NNNNNNNNNNNNN 237 SR3-11 214:........-..NNNNNNNNNN 233 SR3-12 204:NNNNNNNNNNNNNNNNNNNNNNNN 227 SR3-13 204:NNNNNNNNNNNNNNNNNNNNNNNN 227 SR3-15.NUC 97:.A...................... 120 Supplemental figure 5 Nikaido et al. continued

  9. GRY20-1 1:-GAACATAAGGGGCTT-CCCTGGTGGNACAGTGGTTGGGAATCC-GCCTXXXXXXXXXXGCCCCCGCT-TGCTGCAACTA 76 GRY20-2 1:NNNNNNNNNNNNNNNNNNNNNNNNNN.NNN-.............T...................T...-........... 78 GRY20-3 1:-...............-.........C.................-.......................-C.......... 76 GRY20-4 1:-...............-.........C.................-.......................-C.......... 76 GRY20-5 1:-...............-.........C.................-.......................-C.......... 76 GRY20-6 1:-....G..........G.........C.................-.......................-C.......... 77 GRY20-7 1:-...............-...........................-.......................-........... 76 GRY20-8 1:T...............-........N..................-.......................-........... 77 GRY20-9.NUC 1:N...............-......A....................-..............C........-........... 77 GRY20-11.NUC 1:NNN.............-......A....................-..............C........C........... 78 GRY20-12 1:NNNNNNNNNNNNNNNNNNNNNNNNNN.NNN..............-.......................-........... 78 GRY20-15.NUC 1:N........----------------------------------------------------------------------- 9 GRY20-1 77:GAGAAAGCCAGTGCACAGCAGCGAAGACCCAACGCAGCCATAAATAAATAAATAAATAAATAAATAAAATTAAAAACAAC 156 GRY20-2 79:........................................A.............................-...--.... 155 GRY20-3 77:........................................A...........AT..A...----------------.... 140 GRY20-4 77:...........C............................A.......................AT...AA.----.... 152 GRY20-5 77:...........C......................G.....A.......................AT...AA.----.... 152 GRY20-6 78:...........C............................A...................AT..A...--------.... 149 GRY20-7 77:........................................A.......................AT...AA.----.... 152 GRY20-8 78:........................................A.......................AT...AA.----..C. 153 GRY20-9.NUC 78:....................T...................A.......................A....AA...--..C. 155 GRY20-11.NUC 79:.....--NN...........T...................A.......................A.TT.AA...--..C. 154 GRY20-12 79:...........C.........T.G.........A..................................TAA.----.... 154 GRY20-15.NUC 10:-------------------------------------------------------------------------------- 10 GRY20-1 157:AACAACAAA-GTGAACATAATCTTTGCCTGGGACTGTCCTAGTTAGCCTCAAACTAGGTTCAATTATTGA 225 GRY20-2 156:........CAAAT............................ 196 GRY20-3 141:.........-.............................................G..... 200 GRY20-4 153:.........-.....................-................................. 215 GRY20-5 153:.........-................................................ 209 GRY20-6 150:.........-.................................................-.......... 217 GRY20-7 153:.........-............................................................ 221 GRY20-8 154:.........-.................................. 196 GRY20-9.NUC 156:.........-.................................. 198 GRY20-11.NUC 155:.C.......-.................................. 197 GRY20-12 155:.......C.-.....T..............A............................-.......... 222 GRY20-15.NUC 10:--------------------.........................T............NN... 52 Supplemental figure 5 Nikaido et al. continued

  10. BLU47-1.NUC 80:AGGCTTACTGTTAAGAAGAGCAGGATATGGGCTTCCCTGGTGGTGCAGTGGTTGAGAAXXXXXXXXXXNNNNNNNNNNNN 159 BLU47-2 81:...........................................C....G........G..........GCCCTCGCACAG 160 BLU47-3 80:...........................................C........................GCCCTCGCCCGG 159 BLU47-4 80:...........................................C........................GCCCTCGCCCGG 159 BLU47-5 80:...........................................C........................GCCCTCGCCCGG 159 BLU47-6 80:...................................T.......C........................ACCCTCGCCCGG 159 BLU47-7 42:...........................................CA.......................GCCCTCGTGTGG 121 BLU47-8 80:...........................................CA.......................GTCCTCGTGCGG 159 BLU47-9 66:.......-..................................CC..........GA............GCCCTCGTGCGG 144 BLU47-10 71:...........................................G...........A............GCCCTCGTGCGG 150 BLU47-11 62:...........................................G...........A............GCCCTCGTGCGG 141 BLU47-12 80:.........................G.G---------------------------------------------------- 107 BLU47-13 80:................---........G---------------------------------------------------- 104 BLU47-14 80:....C...C..................G---------------------------------------------------- 107 BLU47-15 80:..........................GG---------------------------------------------------- 107 BLU47-1.NUC 160:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATTAATTANTTACTTAAAAAATAATAATAAAAATAAAATAAAT 239 BLU47-2 161:AAACGAAGACCCAACACAGCCTAGAATGGATAGATT.........A...................C.............. 240 BLU47-3 160:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........A...AA............................. 239 BLU47-4 160:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........A...AA............................. 239 BLU47-5 160:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........AA..AAA..T..TA.TA..A.T...AT.......A 239 BLU47-6 160:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........AA..AAA..T..TA.TA..A.T...AT.......A 239 BLU47-7 122:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........A...AA............................. 201 BLU47-8 160:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........A...A.................T............ 239 BLU47-9 145:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........AA..AAA..T..TA.TA..A.T..TA...TA..TA 224 BLU47-10 151:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........AA.TAAA..T..TA.TA.TA.T...AT.....T.A 230 BLU47-11 142:AGGCGAGGACCCAACACAGCCAAGAATGGATAAATA.........AA.TAAA..T..TA.TA.TA.T...AT.....T.A 221 BLU47-12 108:-------------------------------------------------------------------------------- 108 BLU47-13 105:-------------------------------------------------------------------------------- 105 BLU47-14 108:-------------------------------------------------------------------------------- 108 BLU47-15 108:-------------------------------------------------------------------------------- 108 BLU47-1.NUC 240:AAAATAAAATAAAAGAAGAGCAGTATAGTAAGTAGTCTGCCACGTCACAGAAGCCTGACCAGTCATGCCTCATTACAGAC 319 BLU47-2 241:.......................G........................................................ 320 BLU47-3 240:.......................G........................................................ 319 BLU47-4 240:.......................G...................A.................................... 319 BLU47-5 240:T...AT...A----.........G........................................................ 315 BLU47-6 240:T...AT...A..--.........G........................................................ 317 BLU47-7 202:.......................G........................................................ 281 BLU47-8 240:.......................G........................................................ 319 BLU47-9 225:T..TA...------.........C........................................................ 298 BLU47-10 231:T...A---------.........G........C............................................... 301 BLU47-11 222:T...A---------.........G........C............................................... 292 BLU47-12 108:----------------------------........................CA......G................... 159 BLU47-13 105:----------------------------...................T....C............C..T........... 156 BLU47-14 108:----------------------------........................C............C..T........... 159 BLU47-15 108:----------------------------....C.........T.........C............CA............. 159 Supplemental figure 5 Nikaido et al. continued

  11. BRY50-1 1:CTCATTAAATTTTCAGGC-TGGGGCTTCCCTGGTGGCACAGATGGTTGAAAGTCTGCCT-GC-CGATGCAXXXXXXXXXX 77 BRY50-2 1:..................-......................-.......G.........-..-.......XXXXXXXXXX 76 BRY50-3 1:NNNN..G...........A-.....................-.......G.........-..-.......XXXXXXXXXX 76 BRY50-4 1:NNN.....-.........A......................-.......G.........-..-.......XXXXXXXXXX 76 BRY50-5 1:..................A..................G...-.......G.........-..-.......XXXXXXXXXX 77 BRY50-6 1:..................A......................-.......G.........-..-T......XXXXXXXXXX 77 BRY50-7 1:..................A......................-.......G.........-..-T......XXXXXXXXXX 77 BRY50-8 1:NNNN....G.........A......................-.......G.........-..-T......XXXXXXXXXX 77 BRY50-9 1:NNNN..............A......................-.......G..G......TTT-T......XXXXXXXXXX 78 BRY50-10 1:NNNN..............A......................-.......G.........-..CT......XXXXXXXXXX 78 BRY50-11 1:NNNN..............A......................-.......G.........-..CT......XXXXXXXXXX 78 BRY50-12 1:NNNTA..CTA......---------------------------------------------------------------- 16 BRY50-13 1:NNTTA.G..A......---------------------------------------------------------------- 16 BRY50-14 1:NNATA...TA......---------------------------------------------------------------- 16 BRY50-15 1:NNNTA.GCTA....CA---------------------------------------------------------------- 16 BRY50-1 78:ACCAACACAGCCAAAAATAAATAAATAAATAAAA---TTTAATTAAAAAAAAA-TTTTTTTTCAGGCAAA-GAATTAAA- 151 BRY50-2 77:.....................A............---.......T........-................-........- 150 BRY50-3 77:..................................---.......T........--...............-........- 149 BRY50-4 77:C.....G...........................---..A....T........A.............C..-........- 151 BRY50-5 78:C...C.C..C..TT..T...T...T..TTA....---..A.-..T.......--................-T.......- 149 BRY50-6 78:........C.........................---.......T......TTT.....C..........-........- 152 BRY50-7 78:..................................---.......T......TTT.....C..........-........- 152 BRY50-8 78:..................................---.......T........T................-........- 152 BRY50-9 79:.............................A....AAA..A....T........-.....C..-.......-........- 154 BRY50-10 79:.............................A....---..A....T........-........-.......-........- 151 BRY50-11 79:.............................A....---..A....T........-........-.......-........- 151 BRY50-12 17:-----------------------------------------------------------------.....-........A 30 BRY50-13 17:-----------------------------------------------------------------.....-........- 29 BRY50-14 17:-----------------------------------------------------------------.G...-........- 30 BRY50-15 17:-----------------------------------------------------------------.GC..A........- 30 BRY50-1 152:-CGGTT-GTTTATCTTTTTGGAGAAAATGCGACCTTGAGGCAAAGGTAAAAAGCGTGAAC 209 BRY50-2 151:-.....-.....................................................A. 210 BRY50-3 150:-.....-......................................TA....GCGTGA.C 206 BRY50-4 152:-.....-..................................................... 209 BRY50-5 150:-T....-........................ 178 BRY50-6 153:-.....-...............A..............................GCGTG.AC 211 BRY50-7 153:-.....-...............A..............................GCGTG.AC 211 BRY50-8 153:-.....-........A..NNNNNNNNNNN 179 BRY50-9 155:-.T...T........A.GCNNNNNNNNNN 182 BRY50-10 152:-T....-........A.GCNNNNN 173 BRY50-11 152:CT....-........A.GCNNNNNN. 176 BRY50-12 31:AT....-....G...................TA.CCTGA.GC..A.GT............C 90 BRY50-13 30:-T....-....T......-..........A....CC.....C.GA......GCGTGA.C 85 BRY50-14 31:-T..G.T....G......A.AGA...TGAGAC.T.GAG.CA.GG.......GCGTGA.CACTA 92 BRY50-15 31:--C.G.T..G.G...............C.T................GT............ACAT 92 Supplemental figure 5 Nikaido et al. continued

  12. Hump9 1 (clone) 1:TAATAATCATGCTTGTTGTAGCTATGCAACTACCTCTGCAAAATAAGTAACAGCGTTAAAACAAACAGAAATATGGGGCT 80 Hump9 1 1:-------------------------------........................................N........ 49 Hump9 2 1:-------------------------------.................T............................... 49 Hump9 3 1:-------------------------------.................................-............... 48 Hump9 4 1:-------------------------------................................................. 49 Hump9 5 1:-------------------------------................................................. 49 Hump9 6 1:-------------------------------......................A.......................... 49 Hump9 7 1:-------------------------------................................................. 49 Hump9 8 1:-------------------------------................................................. 49 Hump9 9 1:-------------------------------.........................................T......A 49 Hump9 10 1:-------------------------------.........................................T......A 49 Hump9 11 1:-------------------------------...............C....TTA.CGTTN.AC..........C...... 49 Hump9 12 1:-------------------------------....................GAT...................------- 42 Hump9 13 1:-------------------------------.............G.C.TT..A.......-............------- 41 Hump9 14 1:-------------------------------.............G.C.T....T......-............------- 41 Hump9 15 1:-------------------------------..................TGG.TTGA..C.G...T.A.....------- 42 Hump9 1 (clone) 81:TCCCTGGTGGCGCAGTGGTTGAGAATCTGCCTGCTAATGCAGGGGACACGGGTTTGAGCCCTGCTCTGGGXXXXXXXXXX 160 Hump9 1 50:.........................................NNNNNNNNNNNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 2 50:...............................................NNNNNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 3 49:........................G.........C..............NNNNNNNNNNNNNNNNNNNNN.......... 128 Hump9 4 50:..................C...........................NNNNNNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 5 50:..................C...............................NNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 6 50:............................................NNNNNNNNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 7 50:..................................NC....NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 8 50:...................................................NNNNNNNNNNNNNNNNNNN.......... 129 Hump9 9 50:N.................C...N...............................C........GNNNNNN.......... 129 Hump9 10 50:.T..CATG.CACG.....................................NNNNNNNNNNNNNNNNNNNN.......... 129 Hump9 11 50:............................................C.........C....NNNNNNNNNNN.......... 129 Hump9 12 43:-------------------------------------------------------------------------------- 43 Hump9 13 42:-------------------------------------------------------------------------------- 42 Hump9 14 42:-------------------------------------------------------------------------------- 42 Hump9 15 43:-------------------------------------------------------------------------------- 43 Hump9 1(clone) 395:TGTAAAGTTATATTAAAAAAAAACCAAACAGAAATAAAACTATAAAAGTAGCTCTTGTTT-CAATCTTTCTAAAATGTTT 473 Hump9 1 366:-.GNN.NG....................................................-................... 443 Hump9 2 366:-.....-G.T.T..T.............................................-..............G.... 442 Hump9 3 369:......A.......-.............................................-................... 446 Hump9 4 365:......A.......--....................................C.......-.........G......... 441 Hump9 5 365:......A.......--....................................C.......-.........G......... 441 Hump9 6 365:......A.......--............................................-................... 441 Hump9 7 370:......A.......--.....G-..C...C.....T.......T.....TN......G..T.C...C...CT.....G.. 446 Hump9 8 365:-.....A..N...ACTT.N.-NC.A..CAGNC.TAN..CTATA...GTANCTCT.GT..-C.NTNT..CTA.NNTGN..A 441 Hump9 9 363:NA.GTT.NAT....TTTTTT......CC...N.NN..T.....T.T......C......G-.NNC...NN.NN..N.N.G 441 Hump9 10 366:ATGT..AA.TATA.T............N.....N...N................N.....-................... 444 Hump9 11 370:......A-.TATAA.........N.N...C...........N..................-..............N.... 447 Hump9 12 43:------------------------------------........................-..............C.... 85 Hump9 13 42:------------------------------------...............T........-................... 84 Hump9 13 42:------------------------------------........................-...........G....... 84 Hump9 14 43:------------------------------------........T.N..G..........-TG.....C........... 85 Supplemental figure 5 Nikaido et al. continued

  13. Hump55-1.nuc 1:--------------------------------GGACGAGGAACATTAAAAAATA-CTACAGGGCTTCCCTGGTGGCACAG 47 Hump55-2.nuc 1:TTTTCTACCCCAATTTATAGGAAA-TATGGAG.ACA..................-.....................G... 78 Hump55-3.nuc 1:---------------TTTAGGAAA-TATGGAG.ACA..................-.....................G... 63 Hump55-4.nuc 1:--------------------------------.ACG..................-.....................G... 47 Hump55-5.nuc 1:-------------------------------------------........-..-....C................G... 35 Hump55-6.nuc 1:-------------------------------------------........-..-....C...........T.T..G... 35 Hump55-7.nuc 1:-------------------------------------------........-..-....C................G... 35 Hump55-8.nuc 1:--------------------------------.ACA..................-.....................G... 47 Hump55-9.nuc 1:--------------------------------.ACA..................-.............T.......G... 47 Hump55-10.nuc 1:--------------------------------.ACG..................-.............T.......G... 47 Hump55-11.nuc 1:-----------------------------------A..................-.............T.......G... 44 Hump55-12.nuc 1:--------------TTTATAGGAA-TATNNAG.ACA..................-..G..-------------------- 41 Hump55-13.nuc 1:--CTTTCTACACCATTTATAGGAA-TATGNAG.ACA..................-.....-------------------- 53 Hump55-14.nuc 1:-TTTCTACCACCAATTTATAGGAAATATGCAG.ACA..................-.....-------------------- 55 Hump55-15.nuc 1:--------CCACCAATTTGTAGGAATATNNAG.ACA.................GG...T.-------------------- 49 Hump55-1.nuc 48:TGGTTGAGAATXXXXXXXXXXGAAGACCCAACACAGCCATAAATAAATAAAAATTAAAAAAAAATTTTTTTAAAAA--CT 125 Hump55-2.nuc 79:.......................................................TTT......A-..........--.. 155 Hump55-3.nuc 64:................................................................AA...AA.....A-.. 142 Hump55-4.nuc 48:................................................................A.AAAAA....aA-.. 126 Hump55-5.nuc 36:..............................T........AT..AT..AT....A.T........A.AAAAA.....--.. 113 Hump55-6.nuc 36:..............................T........AT..AT..AT....A.T........A.AAAAA.....--.. 113 Hump55-7.nuc 36:.......................................................TTTT.....A...AAA.....A-.. 114 Hump55-8.nuc 48:.......................................................TTT......A...AAA.....--.. 125 Hump55-9.nuc 48:...............................................A.T.....TTTTT....AAA...A.....AA.. 127 Hump55-10.nuc 48:..-N..............................N....................TTTT.......AAAAA...-----. 121 Hump55-11.nuc 45:..AN..............................N....................TTTT.......AAAAA...-----. 119 Hump55-12.nuc 42:-------------------------------------------------------------------------------- 42 Hump55-13.nuc 54:-------------------------------------------------------------------------------- 54 Hump55-14.nuc 56:-------------------------------------------------------------------------------- 56 Hump55-15.nuc 50:-------------------------------------------------------------------------------- 50 Hump55-1.nuc 126:GCTACAGAGATGCAGAAAGCAAAA-TCC-AGACTATTGATATTCTACAGGATAAACAAGCAAAATTTCTTCA 195 Hump55-2.nuc 156:........................-...-........................................... 225 Hump55-3.nuc 143:.................-......-...-...........................................AA 213 Hump55-4.nuc 127:........................-...-........................................... 196 Hump55-5.nuc 114:.....T........T......C..A...C.N................................T..CT.CA 184 Hump55-6.nuc 114:.....T.C......TT.....C..A...C.N................................T..CT.CA 184 Hump55-7.nuc 115:........................-...-........................................... 184 Hump55-8.nuc 126:........................-...-..................................T..CT.CA 194 Hump55-9.nuc 128:........................-...-..................................T..CT.CA 196 Hump55-10.nuc 122:A.............N.....C.C.-...-...A................... 171 Hump55-11.nuc 120:A...................C.C.-...-...A..................... 171 Hump55-12.nuc 42:------..................-...-.......G..........................T..CT.CA 107 Hump55-13.nuc 54:------........A.........-...-.......G..........................T..CT.CA 119 Hump55-14.nuc 56:------........A.........-...-.......G..........................T..CT.CA 121 Hump55-15.nuc 50:------........A.........-...-.......A..........................T..CT.CA 115 Supplemental figure 5 Nikaido et al. continued

  14. Sei8-2-1.nuc 1:NNNNNNNNNNNNNCAAAAT-GCCTACAGGAGGGCTTCCCTGGTGGCGCAGTGGTTGAGAATCTXXXXXXXXXXACGAAGA 79 Sei8-2-2.nuc 1:ATTCTAAGCCTTC....-.-............................................................ 78 Sei8-2-3.nuc 1:ATTCTAAGCCTTC....-.-....................................G....................... 78 Sei8-2-4.nuc 1:ATTCTAAGCCTTC......-............................................................ 79 Sei8-2-5.nuc 1:ATTCTAAGCCTTC....-.-..........................A....C............................ 78 Sei8-2-6.nuc 1:ATTCTAAGCCTTC....-.-..........................A....C............................ 78 Sei8-2-7.nuc 1:ATTCTAAGCCTTC......-.........................T.................................. 79 Sei8-2-8.nuc 1:ATTCTAAGCCTTC....-N-.N.......................................................... 78 Sei8-2-9.nuc 1:ATTCTAAGCCTTC.....A-......................................................T..... 79 Sei8-2-10.nuc 1:ATTCTAAGCCTTC......-..........A...........................................T..... 79 Sei8-2-11.nuc 1:ATTCTAAGCCTTC......-......................................................T..... 79 Sei8-2-12.nuc 1:-TTCTAAGCCTTC......A..........-------------------------------------------------- 29 Sei8-2-13.nuc 1:ATTCTAAGCCTTC....-.-..........-------------------------------------------------- 28 Sei8-2-14.nuc 1:ATTCTAAGCCTTC....-.-..........-------------------------------------------------- 28 Sei8-2-15.nuc 1:ATTCTAAGCCTTC....-.-..........-------------------------------------------------- 28 Sei8-2-1.nuc 80:CCCAACACAGCCATAAATTTAAAAAAAAAAAAAA---------TGCCTACAGGAAAGAAATCGCTAGACAAACCCCAATA 150 Sei8-2-2.nuc 79:..................................AAAA-----.......G.....A....-....A.........G... 152 Sei8-2-3.nuc 79:..................................AAA------A....C.T.....A....G.................. 152 Sei8-2-4.nuc 80:...................A..............AAAA-----..................-....A............. 153 Sei8-2-5.nuc 79:...................A..............AAA------..................-.................. 151 Sei8-2-6.nuc 79:...................A..............AAA------..................-.................. 151 Sei8-2-7.nuc 80:..................................AAAAA----..................................... 155 Sei8-2-8.nuc 79:...................A...........------------.............C..T.-....A............. 145 Sei8-2-9.nuc 80:....................TT............AAAAAAAAA..G..........A....-....C.A.......C... 159 Sei8-2-10.nuc 80:....................T.............AAAAAAA--..G....N.....A....G.T..C.A.......C... 157 Sei8-2-11.nuc 80:..................................AAAAAAA--..G..........A....G.T..C.A.......C... 157 Sei8-2-12.nuc 30:------------------------------------------------------.......-....C............. 54 Sei8-2-13.nuc 29:------------------------------------------------------.......-....C............. 53 Sei8-2-14.nuc 29:------------------------------------------------------.......-.................. 53 Sei8-2-15.nuc 29:------------------------------------------------------.......-.AG.CNA..NAN...... 53 Sei8-2-1.nuc 151:AAGA---TATGTGTATAGATTTCTGTACTTGGAATGTTAATGGCCCTTGACTCAAA 203 Sei8-2-2.nuc 153:....---..........A.............A..........C..T..TGGA 201 Sei8-2-3.nuc 153:....---............................... 187 Sei8-2-4.nuc 154:....---.......................CC......... 191 Sei8-2-5.nuc 152:....---....................................G........... 203 Sei8-2-6.nuc 152:....---....................................G........... 203 Sei8-2-7.nuc 156:....---................................. 192 Sei8-2-8.nuc 146:..A.TCTCTGTGTA...........ATAC.T 176 Sei8-2-9.nuc 160:....---.................... 183 Sei8-2-10.nuc 158:....---.................... 181 Sei8-2-11.nuc 158:....---.................... 181 Sei8-2-12.nuc 55:....---......C..........A..................G..........G.A 108 Sei8-2-13.nuc 54:....---........C........A..................G..........G.A 107 Sei8-2-14.nuc 54:....---..............C..A..................G..........G.A 107 Sei8-2-15.nuc 54:....GTA..GA.............A..................G..........G. 109 Supplemental figure 5 Nikaido et al. continued

  15. BRY82-1 1:TATTGTAAAATAGAATATTATTTTATATGTGCACATATAAAAATAACTGTTGGGCTTCCCTGGTGGCACAGXXXXXXXXX 80 BRY82-2 1:.......................................................................XXXXXXXXX 80 BRY82-3 1:--------------------NNNNNNNNNN.........................................XXXXXXXXX 50 BRY82-4 1:-------...A............................................................XXXXXXXXX 73 BRY82-5 1:-......................................................................XXXXXXXXX 79 BRY82-7 1:------------------NNNNNNNNNNNN.........................................XXXXXXXXX 50 BRY82-9 1:.......................................................................XXXXXXXXX 80 BRY82-10 1:----------------NNNNNNNNNNNNN......................--------------------XXXXXXXXX 22 BRY82-11 1:-----------------------NNNNNN......................--------------------XXXXXXXXX 22 BRY82-12 1:---------------NNNNNNNNNNNNNN......................--------------------XXXXXXXXX 22 BRY82-13 1:------------------NNNNNNNNNNN......................--------------------XXXXXXXXX 22 BRY82-14 1:.......G....A......................................--------------------XXXXXXXXX 51 BRY82-15 1:.G.....G....A...........................GG.........--------------------XXXXXXXXX BRY82-1 81:XAAATTTAACTGAGCATCCTGGAATTAAAAAATAAAAATAAATATAAAACGGTTATGGGAACAGTTATTTGCCTCTTTTC 160 BRY82-2 81:X...........T................................................................... 160 BRY82-3 51:X.........................................A.......T............................. 130 BRY82-4 74:X...............C.........................A.......T............................. 153 BRY82-5 80:X.........................................A.......T............................. 159 BRY82-7 51:X.........................................A.......T............................T 130 BRY82-9 81:X.........................T...............A.......T............................T 160 BRY82-10 23:X-----------------------------------------------------.........................T 48 BRY82-11 23:X-----------------------------------------------------.........................T 48 BRY82-12 23:X-----------------------------------------------------.........................T 48 BRY82-13 23:X-----------------------------------------------------.........................T 48 BRY82-14 52:X-----------------------------------------------------.........................T 77 BRY82-15 52:X-----------------------------------------------------......................AA.T 77 BRY82-1 161:ATACATTTATTTTCCTTTGTATAATTCTCATAGCTTTTTTATTTCGCAGCATTTCCCCCCTTCA 224 BRY82-2 161:................................................................ 224 BRY82-3 131:................................................................ 194 BRY82-4 154:...................A............................................ 217 BRY82-5 160:................................................................ 223 BRY82-7 131:................................C............................... 194 BRY82-9 161:................................................................ 224 BRY82-10 49:.....................G.......................................... 112 BRY82-11 49:.....................G.......................................... 112 BRY82-12 49:.......................................A....T................... 112 BRY82-13 49:...TT....................................A..T................... 112 BRY82-14 78:................................................................ 141 BRY82-15 78:................................................................ 141 Supplemental figure 5 Nikaido et al. continued

  16. Fin12-1 1:---------------CATTGCTGAAAGACATT-AAACAAGACCTAGGGA---CTTTC-TGGTGGCGCAGTGGTTGAGAGT 60 Fin12-2 1:----TGAACTAAA-T.................-................---.....-.................G.... 70 Fin12-3 1:----TGAACTAAAAT.................-.....---....CC.TAACG....T.TC...T.GCTGA....G.NNN 72 Fin12-4 1:----TGAACTAAA-T.............-...-................---.....-.................G.... 69 Fin12-5 1:-------ACTAAA-T.............-...-................---.....-.................G.... 66 Fin12-6 1:-------ACTAAA-T............T-...-................---.....-.................G.... 66 Fin12-7 1:-----GAACTAAA-T.................-...............G---...C.C.................G.... 70 Fin12-9.nuc 1:-------ACTAAA-T.............-...-................---.....-...........A.....G.... 66 Fin12-10 1:GTCATGAACTAAA-T..........-......C............----------------------------------- 43 Fin12-12 1:----TGAACTAAA-A..........-....NN-........NN..----------------------------------- 38 Fin12-14 1:GTCATGGACTAAA-A..........-.....NN............----------------------------------- 43 Fin12-1 61:CTGCCTGCCGGTGCAGGGGXXXXXXXXXXGCCCTCACACAGAAACGAAGTACCAACACAGCCAATAAACAAACAAACAAA 140 Fin12-2 71:........T...A......................G...G....T..G.ACA...........TA..TA..TA..TA..T 150 Fin12-3 73:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.TA..T 152 Fin12-4 70:........T...A......................G........T..G.ACA...........TA..TG..TG..TG..T 149 Fin12-5 67:........T...A......................G........T..G.ACA...........TA..TA..TG..TG..T 146 Fin12-6 67:........T...A......................G........T..G.ACA...........TA.TTA..TG..TG..T 146 Fin12-7 71:.........AA........................G.............AC............TA..TA..TA..TA..T 150 Fin12-9.nuc 67:....T...T...A......................G...........G.ACA...........TA.TTA..TG..TG..T 146 Fin12-10 44:-------------------------------------------------------------------------------- 44 Fin12-12 39:-------------------------------------------------------------------------------- 39 Fin12-14 44:-------------------------------------------------------------------------------- 44 Fin12-1 141:CAAACAAACAAACAAATAAATAAATAAA--TGGATCATCGCATTATCAAATTAAAAAAACCTAACTATCCGAGAAATTGT 218 Fin12-2 151:A..TA..TA..TA.T.A.TGG.TCATC.CA.........A.....------------G......A...AGANNT..A... 218 Fin12-3 153:A..TA..TA..TA..TGG.TC.TCAC.TTAAAA.AA.AAAA.---------------G......A...AA......A... 217 Fin12-4 150:G..TG..TG..TGG.----TC.TCACCTTAAAA.AA.AAAA.A--------------G......A...AA......A... 211 Fin12-5 147:G..TG..TG..TG..TGG.TC.TCAC.TTAAAA.AA.AAAA.A--------------G......A...AAA.....A... 212 Fin12-6 147:G..TG..TG..TG..TGG.TC.TCAC.TTAAAA.AA.AAAA.A--------------G......A...AAA.A...A... 212 Fin12-7 151:A..TA..--------TGG.TC.TCAC.TTAAAA.AA.AAAA.AA.AA.---------G......T...AAA.....A... 213 Fin12-9.nuc 147:G..TG..TG..TG..TGG.TC.TCAC.TTAAAA.AA.AAA-----------------G......A...AAA.A...A... 209 Fin12-10 44:---------------------------------------------------------------.A...AA......A... 60 Fin12-12 39:---------------------------------------------------------------.A...AA......A... 55 Fin12-14 44:---------------------------------------------------------------.A...AA......A... 60 Fin12-1 219:TGATAACNTGGACTTCATGCAAAATTTANAACTTTTGTTTTTTG 262 Fin12-2 219:.......A...NNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNN 262 Fin12-3 218:.......C..........-.........A.....GN......GAAAGAC 265 Fin12-4 212:.......C..........-.........A.....GN........AAAGACAACATAAGA 269 Fin12-5 213:.......C..........-.........A............... 255 Fin12-6 213:.......C..........-.........A............... 255 Fin12-7 214:.......C..........-.........A............... 256 Fin12-9.nuc 210:.......C..........-.........A...............A 253 Fin12-10 61:.......C..........-.C.......A............... 103 Fin12-12 56:.......C..........-......G..A.....C......... 98 Fin12-14 61:.......C..........-......G..A.....C........T 103 Supplemental figure 5 Nikaido et al. continued

  17. Mnk38-1 1:GAGGGTTGTTTTCAAGTTTTTAAGAGAAGATCTGGGGCTTCCCTGGTGGCGCAGTGGTTGAGAATCTGCCTXXXXXXXXX 80 Mnk38-2 1:................................................................................ 80 Mnk38-3 1:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN............. 80 Mnk38-4 1:.....-N..........C.............................................................. 79 Mnk38-5 1:.................C.............................................................. 80 Mnk38-6 1:.............G...C........T..................................................... 80 Mnk38-7 1:......GN........................................................................ 80 Mnk38-8 1:................................................................................ 80 Mnk38-9 1:................................................................................ 80 Mnk38-10 1:...C..............................---------------------------------------------- 34 Mnk38-11 1:...C..............................---------------------------------------------- 34 Mnk38-12 1:..................................---------------------------------------------- 34 Mnk38-13 1:..............G...................---------------------------------------------- 34 Mnk38-14 1:..................................---------------------------------------------- 34 Mnk38-1 81:XACAGAAACGAAGACCCAACACAGCCAAAAGTAAAAATAAATAAATTAATTAATTAAAATATATATATATATATATATAT 160 Mnk38-2 81:..............................................A....T..AT.T...................... 160 Mnk38-3 81:...........................................................A...............----- 155 Mnk38-4 80:..........................................T................A...............----- 154 Mnk38-5 81:..........................................T................A.ATATATATATATATA---- 156 Mnk38-6 81:..........................................T................A.ATATATATATATATATA-- 158 Mnk38-7 81:..........................................T............T-..A.ATATATATATATA------ 153 Mnk38-8 81:..........................................T............T-..A.ATATATATATATA------ 153 Mnk38-9 81:......................C...................T............T-..A.ATATATATATATA------ 153 Mnk38-10 35:-------------------------------------------------------------------------------- 35 Mnk38-11 35:-------------------------------------------------------------------------------- 35 Mnk38-12 35:-------------------------------------------------------------------------------- 35 Mnk38-13 35:-------------------------------------------------------------------------------- 35 Mnk38-14 35:-------------------------------------------------------------------------------- 35 Mnk38-1 161:ATATATATATATATATATATATAGTCCCTACAAGATTAAAAAAAAAAAAA---GATCTGGAGTAGCTTTGGTCTAATGGT 237 Mnk38-2 161:.....------------------..........................----...........T..........G.... 218 Mnk38-3 156:-----------------------...........................A--.........N.T.........GN.... 210 Mnk38-4 155:-----------------------...........................---......A.................... 208 Mnk38-5 157:-----------------------...........................A--........................... 211 Mnk38-6 159:-----------------------..............T............-GA........................... 214 Mnk38-7 154:-----------------------...........................AAA---.N......A......G.N.....G 207 Mnk38-8 154:-----------------------T......NCNN.....G.TT.......A--.....A....................G 208 Mnk38-9 154:-----------------------.......AC.A.....G.TT.......A--.....A....................G 208 Mnk38-10 35:-----------------------------------------------------------..................... 55 Mnk38-11 35:-----------------------------------------------------------..................... 55 Mnk38-12 35:-----------------------------------------------------------.................C... 55 Mnk38-13 35:-----------------------------------------------------------..................... 55 Mnk38-14 35:-----------------------------------------------------------..................... 55 Supplemental figure 5 Nikaido et al. continued

  18. Nag41-1.nuc 1:TCTTTCTATTGAAAATTATTTCAGGCTTAATTTATTAAGAGAGCTACTCTTGGGCTTCCCTGGTGGCGCAGTGGTTGAGA 80 Nag41-2.NUC 1:................................................................................ 80 Nag41-3.NUC 1:................................................................................ 80 Nag41-4.NUC 1:................................................................................ 80 Nag41-5.NUC 1:.........................................................................T...... 80 Nag41-6.NUC 1:..............T..............T...........................................T...... 80 Nag41-7.nuc 1:NNNNNNNNNNNNNNNNNNNNNNNN...........................................A....T....... 80 Nag41-8.NUC 1:........C..........................................................A....T....... 80 Nag41-9.NUC 1:........C...............................................................TT...... 80 Nag41-10.nuc 1:.................................................------------------------------- 49 Nag41-11.nuc 1:.................................................------------------------------- 49 Nag41-12.nuc 1:.................................................------------------------------- 49 Nag41-13.nuc 1:..............................C..................------------------------------- 49 Nag41-14.nuc 1:....CT...........................................------------------------------- 49 Nag41-1.nuc 81:ATCXXXXXXXXXXTCATTTTTTAAAAAAAAGAAAAGAAAAAAAA-------GGACTTTAAAAAAAAA------------- 140 Nag41-2.NUC 81:.....................A.....................--------..GAC.CTTT......AAA---------- 142 Nag41-3.NUC 81:.....................CTTTT....A....A.G....G.AAAAAAA.....AA.......--------------- 145 Nag41-4.NUC 81:.....................A.....................--------.....CA.......--------------- 137 Nag41-5.NUC 81:.....................A.......GA...GA.......--------.....C.TTT......AAAGAAAAGAAAA 152 Nag41-6.NUC 81:............................................-------.....C.TTT......A------------ 141 Nag41-7.nuc 81:....................CA........AG...AG.......A------.....C.TT.......------------- 141 Nag41-8.NUC 81:....................CA......................-------.....C.TT.......AA----------- 142 Nag41-9.NUC 81:............................................-------.....C.TT.......AA----------- 142 Nag41-10.nuc 50:-------------------------------------------------------------------------------- 50 Nag41-11.nuc 50:-------------------------------------------------------------------------------- 50 Nag41-12.nuc 50:-------------------------------------------------------------------------------- 50 Nag41-13.nuc 50:-------------------------------------------------------------------------------- 50 Nag41-14.nuc 50:-------------------------------------------------------------------------------- 50 Nag41-1.nuc 141:-----------------------AGAGAGAGCTACTCAATATTAAAAAAAATATGTCTGTTTTATGAGCCATTTGTTTCA 197 Nag41-2.NUC 143:-----------------------..T.....................G................................ 199 Nag41-3.NUC 146:-----------------------........................G..........A..................... 202 Nag41-4.NUC 138:-----------------------........................G................................ 194 Nag41-5.NUC 153:AAAAGGACTCTTTAAAAAAAAAA........................G................................ 232 Nag41-6.NUC 142:-----------------------........................G................................ 198 Nag41-7.nuc 142:-----------------------........................G..........................A..... 198 Nag41-8.NUC 143:-----------------------........................G..........................A..... 199 Nag41-9.NUC 143:-----------------------........................G..........................A..... 199 Nag41-10.nuc 50:-------------------------------------..........G..........................A..... 92 Nag41-11.nuc 50:-------------------------------------..........G..........................A..... 92 Nag41-12.nuc 50:-------------------------------------..........G..........................A..... 92 Nag41-13.nuc 50:-------------------------------------..........G.....................G.C..A..... 92 Nag41-14.nuc 50:-------------------------------------..........G............C.............A..... 92 Supplemental figure 5 Nikaido et al. continued

  19. Sir49-1 78:AAATATAATTTCCATGAACCCCATCACCCCAGGACAATCCCTCTTAAAATTGTCATGGGGCTTCCCTGGTGGCGCAGTGG 157 Sir49-2 45:................................................................................ 124 Sir49-3.nuc 68:................................................................................ 147 Sir49-4.NUC 71:................................................................................ 150 Sir49-5 59:................................................................................ 138 Sir49-6 67:................................................................................ 146 Sir49-7.NUC 71:......................--................................C................A...... 148 Sir49-8 77:...AT........................................................................... 156 Sir49-9 78:................................................................................ 157 Sir49-10 80:....................................................GT...----------------------- 136 Sir49-11 80:.....................................................T...----------------------- 136 Sir49-12 80:.....................................................T...----------------------- 136 Sir49-13 80:G....................................................T...----------------------- 136 Sir49-14 80:......................G..............................T...----------------------- 136 Sir49-15 81:.G................T................C...T.............T.CA----------------------- 137 Sir49-1 158:TTGXXXXXXXXXXGCCCTCGCACAGAAACGAAGACCCAACACAGCCAAAAATAAATACATAAATAAATAAAAATTTAAAA 237 Sir49-2 125:..................T.........T...............T......AT..ATACAT..AT..AT....A...... 204 Sir49-3.nuc 148:..................T.........T...............T......AT..ATACAT..AT..AT....A...... 227 Sir49-4.NUC 151:..................T.NG..N...T..NN..A..C...G...TC...AT.TATT.AC.TA..TA.----------- 219 Sir49-5 139:..................T.........T.............G........AT..A------------------...... 200 Sir49-6 147:..................T.........T.............G........AT..ATT.A...A...A..---------- 216 Sir49-7.NUC 149:..................T.........T...............T......AT..ATACAT..AT..AT....A...... 228 Sir49-8 157:..................T.........T......................AT..ATA.AT..AT..AT..T.A..TT.. 236 Sir49-9 158:..................T.........T......................AT..A.A.A...AT..AT..T.AAATT.. 237 Sir49-10 137:-------------------------------------------------------------------------------- 137 Sir49-11 137:-------------------------------------------------------------------------------- 137 Sir49-12 137:-------------------------------------------------------------------------------- 137 Sir49-13 137:-------------------------------------------------------------------------------- 137 Sir49-14 137:-------------------------------------------------------------------------------- 137 Sir49-15 138:-------------------------------------------------------------------------------- 138 Sir49-1 238:AAAA----TTAAAAAGATAAAACCTTCAAAAAAA---TTGTCATGTTTTCTAGTCTTTT-CTCTGTGTTTGTTGTATATG 309 Sir49-2 205:....----..T......AT.....C.TT......---.........G......A.....T.................... 277 Sir49-3.nuc 228:....----..T......AT...A.C.TT......AA-......................-............GTATA 298 Sir49-4.NUC 220:--------..................T.......AA-.....C................-...........C.TGTACAN 289 Sir49-5 201:....AAAA..................T.......AA-......................-.................... 278 Sir49-6 217:--------..................T.......AA-...C..................-.................... 286 Sir49-7.NUC 229:....----..................A.......---......................-.................... 300 Sir49-8 237:....A---..................T.......A--......................-.................... 310 Sir49-9 238:..------......-........T..T.....-----......................-.................... 304 Sir49-10 137:---------------------------------------------..............-.................... 170 Sir49-11 137:---------------------------------------------..............-.................... 170 Sir49-12 137:---------------------------------------------..............-...................A 170 Sir49-13 137:---------------------------------------------..............-.................... 170 Sir49-14 137:---------------------------------------------..............-......T.G.TG.A..--.. 168 Sir49-15 138:---------------------------------------------..............-.C....T.G.TG.AC.--.. 169 Supplemental figure 5 Nikaido et al. continued

  20. Hump38-1 81:AGATACCACATGACATGAGGCACAGCCAAAAAATACTGATAAAAATAATTAAATAA-TTTTTTTAAAAAAGGGGGCTTCC 159 Hump38-2 81:.........................A..........................-----....................... 155 Hump38-3 79:....................................................-----.......TTT........G...N 153 Hump38-4 76:....C..............................T................T...-....................... 154 Hump38-5 81:....C..............................T................T...-....................... 159 Hump38-6 81:....C..........G...................T................T...-....................... 159 Hump38-7 75:....C..............................T................-----.......T............... 149 Hump38-8 79:.........................A..........................-----....................... 153 Hump38-9 77:....C..........CA..............T....................T.-.A.....AATT...G.--------- 146 Hump38-10 77:....C..........CA..............T....................T.T.A.....AA.....G.--------- 147 Hump38-11 79:....C..........CA..............T....................T.T.A.....AA.....G.--------- 149 Hump38-13 81:..G.C.............................GT................T.----GGGCTTCCCTGGTGGCGCAGTG 156 Hump38-14 81:....C..........C................C...................TC----GGGCTTCCCTGGTGGTGCAGTG 156 Hump38-1 160:CTGGTGGCGCAGTGGTTXXXXXXXXXXGCCCTCACACAGAAACGAAGACCCAGCACAGCAATCAATCAATCAATCAATCA 239 Hump38-2 156:.................................G.........................C..A...A...AG..AG..AG 235 Hump38-3 154:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.C..A...A...A...A...A. 233 Hump38-4 155:...........................................................C..A.G.A...A...A...A. 234 Hump38-5 160:...........................................................C..A...AC..A...A...A. 239 Hump38-6 160:...........................................................C..A...AC..A...A...A. 239 Hump38-7 150:.................................G.............................................. 229 Hump38-8 154:.................................G.............................................. 233 Hump38-9 147:-------------------------------------------------------------------------------- 147 Hump38-10 148:-------------------------------------------------------------------------------- 148 Hump38-11 150:-------------------------------------------------------------------------------- 150 Hump38-13 157:G.TXXXXXXXXXXGGGAGAGGCCACAACAGTGAGAGGCCCGCGTACCACAAAAAAAAAAAAAAAAAAATTTAATTAATTA 236 Hump38-14 157:G.TXXXXXXXXXXGGGAGAGGCCACAGCAGTGAGAGGCCCACGTACCGCAAAAAAAA--------ATAATTAATTAATTA 228 Hump38-1 240:ATCAATCAAT--------------------GGGCCTCCCACATTCTGAGGCCAACTTCCATTTCAACATGGGTCTTACTG 299 Hump38-2 236:..AG..AG..AGATCGATAGATAGAAAAAA.................................................. 315 Hump38-3 234:..A...A...AATAAACAAACAAACAAACAA-..............................-................. 311 Hump38-4 235:..A...A...AATAAACAAACAAACAAACAA-................................................ 313 Hump38-5 240:..A...A...AATAAACTAACTAACTAACTA-.....T........... 287 Hump38-6 240:..A...A...AATTAACTAACTAACTAACTA-.....T.......................................... 318 Hump38-7 230:......A...AAT-----------------.................................. 276 Hump38-8 234:......A...--------------------.................................................. 293 Hump38-9 147:---------------------------------............................................... 195 Hump38-10 148:-------------------------------................................................. 196 Hump38-11 150:-------------------------------................................................. 198 Hump38-13 237:AAAAAAAAAGG---------------------..............................-..G.....NNNNNNNNN 292 Hump38-14 229:TTTTAAAAAGG---------------------................................................ 287 Supplemental figure 5 Nikaido et al. continued

  21. Mnk55-1 1:--GCACAAAGCAAGAAGAAAAATATTGATACATTTTGCTACATTAAGATACAAAA--CATGTAGGATAAAAGATGACAAA 76 Mnk55-2 1:AA.............-.......................................CTT...................... 79 Mnk55-3 1:------------------------.......C....................G..CTTC..................... 56 Mnk55-4 1:----...................................................CTT...................... 76 Mnk55-5 1:-----..................................................CTT...................... 75 Mnk55-6 1:-----..................................................CTT...................... 75 Mnk55-7 1:--.....................................................CTT...................... 78 Mnk55-8 1:-----.........................T........................CTT...................... 75 Mnk55-9 1:-----..................................................CTT...................... 75 Mnk55-10 1:-A................................A....................CTTC.............G....... 79 Mnk55-11 1:-A......-.........................A....................CTTC.............G....... 78 Mnk55-12 1:-A......-.......................................C......CTTC.............G....... 78 Mnk55-13 1:--..............................................C....G.CTTCC.................... 78 Mnk55-14 1:AA..............................................C......CTTC..................... 80 Mnk55-1 77:AATGAAAATACAGGGCTTCCCTGGTGGCGCAGTGGTTGAGAXXXXXXXXXXGCCCCCACTCGCCACAACTAGAGAAAGCC 156 Mnk55-2 80:.......................................A........................................ 159 Mnk55-3 57:...........................N...........................G........G............... 136 Mnk55-4 77:...........................N....................................G............... 156 Mnk55-5 76:............................A...................................G............... 155 Mnk55-6 76:................................................................G............... 155 Mnk55-7 79:.........................................................G......G............... 158 Mnk55-8 76:.........................................................G..T................... 155 Mnk55-9 76:............-------------------------------------------------------------------- 87 Mnk55-10 80:............-------------------------------------------------------------------- 91 Mnk55-11 79:............-------------------------------------------------------------------- 90 Mnk55-12 79:............-------------------------------------------------------------------- 90 Mnk55-13 79:............-------------------------------------------------------------------- 90 Mnk55-14 81:............-------------------------------------------------------------------- 92 Mnk55-1 157:CTCGCACAGAAACGAAGGCCCAACACAGCCAAAAATAAATAAATAAATTTTTAAAAAAATGAAAATACAAGTTTATAGAC 236 Mnk55-2 160:....................................................T........................... 239 Mnk55-3 137:..........................T........................A...---...................... 213 Mnk55-4 157:................................................................................ 236 Mnk55-5 156:....................................................TT.......................... 235 Mnk55-6 156:................................................................................ 235 Mnk55-7 159:.............................................G.....A............................ 238 Mnk55-8 156:.............................................G...AAA............................ 235 Mnk55-9 88:---------------------------------------------------------------------........... 98 Mnk55-10 92:---------------------------------------------------------------------...GG...... 102 Mnk55-11 91:---------------------------------------------------------------------...GG...... 101 Mnk55-12 91:---------------------------------------------------------------------....A...... 101 Mnk55-13 91:---------------------------------------------------------------------........... 101 Mnk55-14 93:---------------------------------------------------------------------........... 103 Supplemental figure 5 Nikaido et al. continued

  22. Sei17-1 1:-----------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTCCCTGGTGGCGCAGTG 63 Sei17-2.NUC 1:--GTTGAACGTGAAAATTATATTGAT------------------------------CGGGG................... 48 Sei17-3 1:--GTTGAACATGAA-TATCTATTGATCTATTTTGAA-CA-TGAAAATTATATTGATCGGGG............T...... 75 Sei17-4 1:--GTTGAACATGAA-TATCTATTGATCTATTTTGAA-CA-TGAAAATTATAT..ATCGGGG............T...... 75 Sei17-5 1:--GTTGAACATGANNTATCTATTGATCTA.TT........TGAAAATTATATTGATCGGGG................... 78 Sei17-7 1:--NNNNNNNNNNNNNNN................GAA-CA-TGAAAATTATATTGATTGGGG................... 76 Sei17-8 1:--GTTGAACATGANNTATCTATTGATCTA.TT........TGAAAATTATATTGATTGGGG................... 78 Sei17-9 1:------------NNNNN................GTT-CAGTGAAAA---------------------------------- 33 Sei17-10 1:--GTTGAACANNNNNNN.CTATTGATCTATTTTGTT-CAGTGAAAA---------------------------------- 43 Sei17-11 1:--GTTGAACATGAA-TATCTATTGATCTA.TTTGTT-CAGTGAAAA---------------------------------- 42 Sei17-12.nuc 1:GAAACCATGAAAAATTTCTTATTGATCAATTTGTTA-CAGTGAAAA---------------------------------- 45 Sei17-13 1:--GTTGAACATGAA-TATCTATTGATCTA.TTTGTTACAGGGAAAA---------------------------------- 43 Sei17-14 1:--GTTGAACATGAAAATTCTATTGA--C..TTTGTTACAGTGAAAA---------------------------------- 42 Sei17-15 1:CAGTTGAACATGAAA-TTCTAT-GA..A--TTTGTTACAGTGAAAA---------------------------------- 42 Sei17-1 64:GTTXXXXXXXXXXGCCCTCGCACAGAAACGAAGACCCAACACAGCCATAAATAAATAAATAAATAAAATTTAAAAAATTT 143 Sei17-2.NUC 49:...................A.........................................................C.. 128 Sei17-3 76:...................A............................................................ 155 Sei17-4 76:.............................A.........................................T...C.... 155 Sei17-5 79:.............................A.........................................T........ 158 Sei17-7 77:...................................................................T............ 156 Sei17-8 79:...................................................................T............ 158 Sei17-9 34:-------------------------------------------------------------------------------- 34 Sei17-10 44:-------------------------------------------------------------------------------- 44 Sei17-11 43:-------------------------------------------------------------------------------- 43 Sei17-12.nuc 46:-------------------------------------------------------------------------------- 46 Sei17-13 44:-------------------------------------------------------------------------------- 44 Sei17-14 43:-------------------------------------------------------------------------------- 43 Sei17-15 43:-------------------------------------------------------------------------------- 43 Sei17-1 144:ATTAAAAAAAAAAAAA-GTGCCCTACAAAA-GTTAAAAAAAAAAAA-TTATATTGATCATTTT-GTTACA-GTGAAAAGG 218 Sei17-2.NUC 129:...T..........G.A..TG..CTGCTT.A...............A.............A..T......C......... 208 Sei17-3 156:................A...G...GG....-T.A..........---...A............-......-......... 229 Sei17-4 156:................-.G.....G.....-...............-............A...-.A....-.G....... 230 Sei17-5 159:................-.......G.....-..............-T..T.T...........-......-......... 233 Sei17-7 157:................-.......G.....-T.A...........-T............A...-......-......... 231 Sei17-8 159:................-.......G.....-T.A...........-T............A...-......-.....T... 233 Sei17-9 34:------------------------------------------------------------------------------.. 35 Sei17-10 44:------------------------------------------------------------------------------.. 45 Sei17-11 43:------------------------------------------------------------------------------.. 44 Sei17-12.nuc 46:------------------------------------------------------------------------------.. 47 Sei17-13 44:------------------------------------------------------------------------------.. 45 Sei17-14 43:------------------------------------------------------------------------------.. 44 Sei17-15 43:------------------------------------------------------------------------------.. 44 Sei17-1 219:TTTTGAGATTTGGGGCAGGCAAA--CAAA-CTG-TACTC 253 Sei17-2.NUC 209:...-......---..... 222 Sei17-3 230:.......................--....-...-..... 264 Sei17-4 231:.....................N.AC.. 257 Sei17-5 234:......A............. 253 Sei17-7 232:......A................AC..G.A...-.....CA 271 Sei17-8 234:......A...........C....AC..G.A...-.....CA 273 Sei17-9 36:.....................G.AC..G.-...G.....CAA 76 Sei17-10 46:.....................G.AC..G.-...G.....CAA 86 Sei17-11 45:.....................G.AC..G.-...G.....CAA 85 Sei17-12.nuc 48:.....................G.AC..G.-...TACTC.CAA 88 Sei17-13 46:.....................G.AC..G.-...-..... 82 Sei17-14 45:.....................G.AC..G.-...-.....CA 83 Sei17-15 45:.....................G.AC..G.-...-.....CAAT 85 Supplemental figure 5 Nikaido et al. continued

  23. Sei19-1.nuc 1:GACGACCTGAAGTATCC-TT-GAGGGGCTTCC-TGGTGGTGCNGTGGTTGAGAATCTGCCTGCCAATGCAGGGGXXXXXX 77 Sei19-2.nuc 1:.................A..A...........C.........A..................................... 80 Sei19-3.nuc 1:NNNNNNNNNNNNNNNNNNNNNNNNNNN.....-.........A.....C........................T...... 79 Sei19-4.nuc 1:NNNNNNNNNNNNNNNNNNNNN...........-.........A..................................... 79 Sei19-5.nuc 1:.................-..A...........-.........A..................................... 78 Sei19-6.nuc 1:.................-..A...........-.........A..................................... 78 Sei19-7.nuc 1:.................A..A...........C.........A.....................C............... 80 Sei19-8.NUC 1:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN.NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 80 Sei19-9.nuc 1:................TA..AA..-------------------------------------------------------- 24 Sei19-10.nuc 1:................TA..AA..-------------------------------------------------------- 24 Sei19-11.nuc 1:................TA..AA..-------------------------------------------------------- 24 Sei19-12.nuc 1:----GA........-.TA..AA..-------------------------------------------------------- 19 Sei19-13.nuc 1:................TA..AA..-------------------------------------------------------- 24 Sei19-14.NUC 1:---...........-.TA..AA..-------------------------------------------------------- 20 Sei19-1.nuc 78:XXXXACCCAAAACAGCCAAAAATAAATAAATAAATAGATAAATAAA-TTTTTAAAATTACCTTTCTCTTAAAAAAAAAAA 156 Sei19-2.nuc 81:....................................A.........-................................. 159 Sei19-3.nuc 80:....................................A.........-................................. 158 Sei19-4.nuc 80:....................................A.........A.....TT.-..............CTT....... 158 Sei19-5.nuc 79:....................................A.........-................................. 157 Sei19-6.nuc 79:....................................A.........-................................. 157 Sei19-7.nuc 81:.....................C..............A.---------...................T.A........... 151 Sei19-8.NUC 81:NNNN.................C..............A.---------...................T............. 151 Sei19-9.nuc 25:-------------------------------------------------------------------------------- 25 Sei19-10.nuc 25:-------------------------------------------------------------------------------- 25 Sei19-11.nuc 25:-------------------------------------------------------------------------------- 25 Sei19-12.nuc 20:-------------------------------------------------------------------------------- 20 Sei19-13.nuc 25:-------------------------------------------------------------------------------- 25 Sei19-14.NUC 21:-------------------------------------------------------------------------------- 21 Sei19-1.nuc 157:---CAAGCATTAGAGGAAAAGGGGGA--TTG-TGTGAGC-AAC-ATGATAA--CAGGAAAA-TAGAAGA-TAGGTTCTAG 224 Sei19-2.nuc 160:---.......................--...-.......-...-.......--........-.....A.-.......... 227 Sei19-3.nuc 159:---.C...C..TA.............--A..-....T..-...-.......--. 202 Sei19-4.nuc 159:A--........CA.T....GA.....--...-.......-...-.......--.......T-.......-.......... 227 Sei19-5.nuc 158:A--.......................--...-.......-...-...G...--........-.......-....... 223 Sei19-6.nuc 158:A--.......................--...-.......-...-...G...--........-.......-....... 223 Sei19-7.nuc 152:AAA................C......--...-.......-...-.......--........-......--...T.C 217 Sei19-8.NUC 152:AAA.....T...A.............--...-.......-...-T......--........-..A...G-.......... 222 Sei19-9.nuc 25:------C.C..........-......--...-.......C...-......---........-......G-.......... 88 Sei19-10.nuc 25:------C.C..........-......--...G.......CCC.-......---........-......GG.......... 90 Sei19-11.nuc 25:------C.C..........-......--...G.......CCC.-......---........-......GG.......... 90 Sei19-12.nuc 20:------C.C.................-A...G.....-TT...-.......--........-......G-.......... 86 Sei19-13.nuc 25:------C.................A.--...-.......C...C......CAC........-......G-...-...... 92 Sei19-14.NUC 21:------C...................--...-.......C...C.......-C........CC.....G-...-C..... 88 Supplemental figure 5 Nikaido et al. continued

  24. Sei47-1 1:-------NNNNNNNNNNNNNNNGACCCTCCAGAGA-TCACTAAAGAGTGAAGGTGAGGGGCTTCCCTGGTGGCGCAGTGG 72 Sei47-2 1:GAAAGTCTAGCGAACCCA-CCC.............-.....................................T...... 78 Sei47-3 1:-------...............N............-....................................T....... 72 Sei47-4 1:------N...............NNNNNNNNNN...-............................................ 73 Sei47-5 1:----------............NNNNNNNNNNNNN-.....................................A...... 69 Sei47-6 1:--------------........NNNNNNNNNN...-.....................................A...... 65 Sei47-7 1:---------------.......NNNNNNNNNNNNN-.....................................A...... 64 Sei47-8.nuc 1:----NTC-AGCGACCCCAACCC...........AGA....................................T....... 75 Sei47-9 1:--------------........NNNNNNNNNNN..-..............G......----------------------- 42 Sei47-10 1:-----------...........N............-..............G.N....----------------------- 45 Sei47-11 1:-----------...........NNNNNNNNNNN..-..............G..--------------------------- 41 Sei47-12 1:-------TAGCAACCCCA-CCC..........T..-NN...................----------------------- 48 Sei47-13 1:----GTCTAGCAACCCCAACCCA...........G-.....G...............----------------------- 52 Sei47-14 1:-GAAGTCTAGCAACCCCA-CCC...G...T.....-...........G.....C...----------------------- 54 Sei47-1 73:TTGAGAATCCGCCTGCCXXXXXXXXXXCCCTCGCACAGAAACGAAGACCCAACACAGCCAAAAATAAATTAGTTAATTAA 152 Sei47-2 79:.........A...........................................................A.A.A...A.. 158 Sei47-3 73:.........................................T...........................A.A........ 152 Sei47-4 74:.................................................................C...A.A.A...... 153 Sei47-5 70:.....................................................................A.A.A...A.. 149 Sei47-6 66:.....................................................................A.A.A...A.. 145 Sei47-7 65:.........................................T....G......................A.A.A...A.. 144 Sei47-8.nuc 76:.........T.....TT....................................................A.A........ 155 Sei47-9 43:-------------------------------------------------------------------------------- 43 Sei47-10 46:-------------------------------------------------------------------------------- 46 Sei47-11 42:-------------------------------------------------------------------------------- 42 Sei47-12 49:-------------------------------------------------------------------------------- 49 Sei47-13 53:-------------------------------------------------------------------------------- 53 Sei47-14 55:-------------------------------------------------------------------------------- 55 Sei47-1 153:TTAATTAAAAAAAAAGATTTCCCACTGCTCAACTTATTTCTAAAAAAAAAA-GAAAAGAGTGAAGGTGAGGAATCAGGGG 231 Sei47-2 159:.A..............................................C..-............................ 237 Sei47-3 153:...............................T.A...C....G......---..G..................C...... 229 Sei47-4 154:.......G...........................................G.............A.............. 233 Sei47-5 150:.......G..........................................--.....................C...... 227 Sei47-6 146:..................................................--............................ 223 Sei47-7 145:...................................................A............................ 224 Sei47-8.nuc 156:...................................................A............................ 235 Sei47-9 43:----------------------------------------------------------------------.......... 52 Sei47-10 46:----------------------------------------------------------------------.......... 55 Sei47-11 42:------------------------------------------------------------------------........ 49 Sei47-12 49:----------------------------------------------------------------------.......... 58 Sei47-13 53:----------------------------------------------------------------------.......... 62 Sei47-14 55:----------------------------------------------------------------------.......... 64 Sei47-1 232:CAATCTTTCTCACAAATGTGCCTCTCCCCCTCGCTCCACCTAGGGGC-ACATTGCCCATCCTCAAACCCCACTGGCCCCC 310 Sei47-2 238:..............................A................-......................G........T 316 Sei47-3 230:......................C..................G....GC............T.G................. 309 Sei47-4 234:......................C........................-..............G........T........ 312 Sei47-5 228:......................C..................G....GC..............G................. 307 Sei47-6 224:......................C........G.........G.....-..............G................. 302 Sei47-7 225:...............................................-................................ 303 Sei47-8.nuc 236:...............................................-................................ 314 Sei47-9 53:.......C.......................................-................................ 131 Sei47-10 56:.......C.......................................-................................ 134 Sei47-11 50:.......C................................C......-................................ 128 Sei47-12 59:..C...............................C............-........................C....... 137 Sei47-13 63:...............................................-............. 122 Sei47-14 65:.C............................---------------------------.... 98 Supplemental figure 5 Nikaido et al. continued

  25. Ac144-1 1:GAGCANGACTTAACATATTTGATATCTTCAGAGCCACTTCTAAAAAAAAAAAAAAAAA--CAAATCCCCATGCGACATTT 78 Ac144-2 1:AGAGCA....................................................A--C..........GC...... 78 Ac144-3 1:....NA..................................................--CC...TC..A....G....... 78 Ac144-4 1:-GAGCA...................................................--C.C..AT.A....G....... 77 Ac144-5 1:-GAGCA....................................................A-.C..AT.A....G....... 78 Ac144-6 1:tGAGCA...........................T........................A-.C..AT.A....G....... 79 Ac144-7 1:AGATCA..........................T......................-----.C..AT.A....G....... 75 Ac144-8 1:-------------...................T.....................NNNNNNNNNNNNNNNNNNNNNNNNNN 67 Ac144-9 1:-GAGCA....................................................AA.C..AT.A...TG....... 79 Ac144-10 1:AGAGCA....................................................AA.C..AT.A...TG....... 80 Ac144-11 1:AGAGCA....................................................AA.C..AT.A...TG....... 80 Ac144-12 1:AGAGCA...............................................C....CA.C..AT.A....G....... 80 Ac144-13 1:-GAGCA...............................................C....CA.C..AT.A....G....... 79 Ac144-14 1:----CA.........................................T...---------.C..AT.A....G....... 67 Ac144-15 1:AGAGCA.................G............T............-----------GC..AT.A....G..T.... 69 Ac144-1 79:TAGCTTACAAATAGTGATTAAGAAGTATGT-------------------------------------------------- 108 Ac144-2 79:..............................-------------------------------------------------- 108 Ac144-3 79:..............................-------------------------------------------------- 108 Ac144-4 78:..............................-------------------------------------------------- 107 Ac144-5 79:..............................-------------------------------------------------- 108 Ac144-6 80:.........GG...................-------------------------------------------------- 109 Ac144-7 76:..............................AGGGGCTTCCCTGGTGGTGCAGTGGTTGAGAGTTTXXXXXXXXXXATAAA 155 Ac144-8 68:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 147 Ac144-9 80:..............................-------------------------------------------------- 109 Ac144-10 81:..............................-------------------------------------------------- 110 Ac144-11 81:..............................-------------------------------------------------- 110 Ac144-12 81:..............................-------------------------------------------------- 110 Ac144-13 80:..............................-------------------------------------------------- 109 Ac144-14 68:..............................-------------------------------------------------- 97 Ac144-15 70:...............C..C...........-------------------------------------------------- 99 Ac144-1 109:------------------------------------------AAAACCATTT--TACCATGGTGTATCTGAAATCTCAGA 144 Ac144-2 109:------------------------------------------..........--.......................... 144 Ac144-3 109:------------------------------------------..........--.......................... 144 Ac144-4 108:------------------------------------------..........--.......................... 143 Ac144-5 109:------------------------------------------..........--.......................... 144 Ac144-6 110:------------------------------------------..........--.......................... 145 Ac144-7 156:TTAATAAATAAATTAATTAATTAAAAAAAAAAAGAAGTATGT..........--.......................... 233 Ac144-8 148:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGAAGTATGT..........--.......................... 225 Ac144-9 110:------------------------------------------..........--.......................... 145 Ac144-10 111:------------------------------------------..........--.......................... 146 Ac144-11 111:------------------------------------------..........--.......................... 146 Ac144-12 111:------------------------------------------G.........--........G...............A. 146 Ac144-13 110:------------------------------------------G.........--........G...............A. 145 Ac144-14 98:------------------------------------------G.........CT........G................. 135 Ac144-15 100:------------------------------------------G....N....--......AAG........NN..... 133 Supplemental figure 5 Nikaido et al. continued

  26. Mnk1-1.nuc 1:TAAATCATCATTTTTATT--NACCCTATGAAAAATGTTCCAGGATCAAAAACTACCATGA-------------------- 58 Mnk1-2.nuc 1:AT................TCA.......................................-------------------- 60 Mnk1-3.nuc 1:-----.............T-CC......................................-------------------- 54 Mnk1-4.nuc 1:AT................T-C.......................................-------------------- 59 Mnk1-5.nuc 1:AT................T-C.......................................-------------------- 59 Mnk1-6.nuc 1:AT.....G..........T-C....C..................................-------------------- 59 Mnk1-7.nuc 1:AT................T-C.......................................GGGCTTCCCTGGTGGTGTGG 79 Mnk1-8.nuc 1:AT................T-C.......................................GGGCTTCCCTGGTGGTGTGG 79 Mnk1-9.nuc 1:-----------.......T-C.........................T.............-------------------- 48 Mnk1-10.nuc 1:-----------.......T-C.........................TC.-..........-------------------- 47 Mnk1-11.nuc 1:--------------------C-........................TC.-..........-------------------- 38 Mnk1-12.nuc 1:GT.TAA.....NA..T..A-T.........................N.............-------------------- 59 Mnk1-13.nuc 1:..T...............--C.............................G.........-------------------- 58 Mnk1-14.nuc 1:AC................T-C.............................C.........-------------------- 59 Mnk1-1.nuc 59:-------------------------------------------------------------------------------- 59 Mnk1-2.nuc 61:-------------------------------------------------------------------------------- 61 Mnk1-3.nuc 55:-------------------------------------------------------------------------------- 55 Mnk1-4.nuc 60:-------------------------------------------------------------------------------- 60 Mnk1-5.nuc 60:-------------------------------------------------------------------------------- 60 Mnk1-6.nuc 60:-------------------------------------------------------------------------------- 60 Mnk1-7.nuc 80:TGGTTGAGAATXXXXXXXXXXACATACATACATAAATAAAAAGAATGTAAGCAGACAAGAATAGCATTAAAAAAAAAAAA 159 Mnk1-8.nuc 80:TGGTTGAGAATXXXXXXXXXXACATACATACATAAATAAAAAGAATGTAAGCAGACAAGAATAGCATTAAAAAAAAAAAA 159 Mnk1-9.nuc 49:-------------------------------------------------------------------------------- 49 Mnk1-10.nuc 48:-------------------------------------------------------------------------------- 48 Mnk1-11.nuc 39:-------------------------------------------------------------------------------- 39 Mnk1-12.nuc 60:-------------------------------------------------------------------------------- 60 Mnk1-13.nuc 59:-------------------------------------------------------------------------------- 59 Mnk1-14.nuc 60:-------------------------------------------------------------------------------- 60 Mnk1-1.nuc 59:-----------AAGCATGTCTCAAAAGAGTCCACTCTCT-AAAAGGTGGCAAGAAAGATTATATATGAAACTCGAAGCCT 126 Mnk1-2.nuc 61:-----------............................-........................................ 128 Mnk1-3.nuc 55:-----------.............G..............-........................................ 122 Mnk1-4.nuc 60:-----------............................-........................................ 127 Mnk1-5.nuc 60:-----------............................-........................................ 127 Mnk1-6.nuc 60:-----------............................-..........T............................. 127 Mnk1-7.nuc 160:AACTACCATGA............................-................................. 231 Mnk1-8.nuc 160:AACTACCATGA............................-................................. 231 Mnk1-9.nuc 49:-----------...................A........A...G.............G...................... 117 Mnk1-10.nuc 48:-----------...................A........-........................................ 115 Mnk1-11.nuc 39:-----------...................A........-........................................ 106 Mnk1-12.nuc 60:-----------............................--...................G................... 126 Mnk1-13.nuc 59:-----------.............--.............-........................................ 124 Mnk1-14.nuc 60:-----------............................-........................................ 127 Supplemental figure 5 Nikaido et al. continued

  27. NM35-1.nuc 1:TAAAACATACAGA-GAACGATCTTTTATTAACTTAAAACTGCTCTAAAAAAATAGTCTACTA------------------ 61 NM35-2.NUC 1:.............-................................................------------------ 61 NM35-3.NUC 1:.............-................................................------------------ 61 NM35-4.nuc 1:.............-................................................------------------ 61 NM35-5.nuc 1:.............-................................................------------------ 61 NM35-6.nuc 1:.............-.......T.......................T................------------------ 61 NM35-7.NUC 1:.............-................................................GGGCTTCCCTGGTGGCGC 79 NM35-8.NUC 1:.............T................................................GGGCTTCCCTGGTGGCGC 80 NM35-9.NUC 1:.............-................................................------------------ 61 NM35-10.NUC 1:.............-................................................------------------ 61 NM35-11.NUC 1:NNNNNNNNN....-................................................------------------ 61 NM35-12.nuc 1:............C-.....................................-.......T..------------------ 60 NM35-13.NUC 1:.............-....A......C..................G..............T..------------------ 61 NM35-14.nuc 1:.............-....T........................................T..------------------ 61 NM35-1.nuc 62:-------------------------------------------------------------------------------- 62 NM35-2.NUC 62:-------------------------------------------------------------------------------- 62 NM35-3.NUC 62:-------------------------------------------------------------------------------- 62 NM35-4.nuc 62:-------------------------------------------------------------------------------- 62 NM35-5.nuc 62:-------------------------------------------------------------------------------- 62 NM35-6.nuc 62:-------------------------------------------------------------------------------- 62 NM35-7.NUC 80:AGTGGTTGAGAATCTGCCTGCCAATGCAGGGGACACGGGXXXXXXXXXXGCCCTCGCACAGAAACCAAGACCCAACACAT 159 NM35-8.NUC 81:AGTGGTTGAGAATCTGCCTGCCAATGCAGGGGACACGGGXXXXXXXXXXGCCCTCGCACAGAAACCAAGACCCAACACAT 160 NM35-9.NUC 62:-------------------------------------------------------------------------------- 62 NM35-10.NUC 62:-------------------------------------------------------------------------------- 62 NM35-11.NUC 62:-------------------------------------------------------------------------------- 62 NM35-12.nuc 61:-------------------------------------------------------------------------------- 61 NM35-13.NUC 62:-------------------------------------------------------------------------------- 62 NM35-14.nuc 62:-------------------------------------------------------------------------------- 62 NM35-1.nuc 62:-----------------------------------------------AAAAACAAAAAACTGAGACAACCAATAAACA-G 93 NM35-2.NUC 62:-----------------------------------------------................A..............A. 94 NM35-3.NUC 62:-----------------------------------------------......C........GA..C...C..T....-. 93 NM35-4.nuc 62:-----------------------------------------------................A..............-. 93 NM35-5.nuc 62:-----------------------------------------------......C.........A..............-. 93 NM35-6.nuc 62:-----------------------------------------------...C..C.........A..............-. 93 NM35-7.NUC 160:GCAAAAATAAATAAATAATTAATTT---AAAAAAAAACAGTCTACTA................A..............-. 235 NM35-8.NUC 161:GCAAAAATAAATAAATAATTAATTAATTAAAAAAAAA---TCTACTA................A..............-. 236 NM35-9.NUC 62:-----------------------------------------------................A....T.........-. 93 NM35-10.NUC 62:-----------------------------------------------................A....T.........-- 92 NM35-11.NUC 62:-----------------------------------------------................A....T.........-- 92 NM35-12.nuc 61:-----------------------------------------------................A..............-. 92 NM35-13.NUC 62:-----------------------------------------------......G.........A..............-. 93 NM35-14.nuc 62:-----------------------------------------------................A..............-. 93 Supplemental figure 5 Nikaido et al. continued

  28. Sei20-1 1:-----TGTATGAGCCA-GTA-CTTCAAA---------------------------------------------------- 21 Sei20-2 1:ATATT...........A...-.......A--------------------------------------------------- 28 Sei20-3 1:----T...........A...-.......A--------------------------------------------------- 24 Sei20-4 1:-----...........A...-......NNNNCTTCCCATGGTGGCGCAGTGGTTGAGAGTCTGCCTGCCAGTGCAGGGGX 74 Sei20-5 1:-----...........A...-.......GGGCTTCCCATGGNGGCGCACTGGTTGAGAGTCTGCCTGCCAGTGCAGGGGX 74 Sei20-6 1:------..........-...-.......---------------------------------------------------- 20 Sei20-7 1:------..........-...-.......---------------------------------------------------- 20 Sei20-8 1:------..........-...-.......---------------------------------------------------- 20 Sei20-9 1:-TATT...........-...-.......---------------------------------------------------- 25 Sei20-10 1:-TATT...........-...-.......---------------------------------------------------- 25 Sei20-11 1:-TATT...........-...-.......---------------------------------------------------- 25 Sei20-12.NUC 1:TAATT...........A...A.......A--------------------------------------------------- 29 Sei20-14 1:------..........-...-.......---------------------------------------------------- 20 Sei20-15.NUC 1:TAATT...TGAG....A...A.......A--------------------------------------------------- 29 Sei20-1 22:-------------------------------------------------------------------------------- 22 Sei20-2 29:-------------------------------------------------------------------------------- 29 Sei20-3 25:-------------------------------------------------------------------------------- 25 Sei20-4 75:XXXXXXXXXGCCCTCGCACAGGAACGAAGATCCAACACAGCCATAAATAAACAAATAAATAAATAAATTTAAAAACAAAA 154 Sei20-5 75:XXXXXXXXXGCCCTCGCACAGGAACGAAGATCCAACACAGCCATAAATAAACAAATAAATAAATAAATTTAAAAAAAAAA 154 Sei20-6 21:-------------------------------------------------------------------------------- 21 Sei20-7 21:-------------------------------------------------------------------------------- 21 Sei20-8 21:-------------------------------------------------------------------------------- 21 Sei20-9 26:-------------------------------------------------------------------------------- 26 Sei20-10 26:-------------------------------------------------------------------------------- 26 Sei20-11 26:-------------------------------------------------------------------------------- 26 Sei20-12.NUC 30:-------------------------------------------------------------------------------- 30 Sei20-14 21:-------------------------------------------------------------------------------- 21 Sei20-15.NUC 30:-------------------------------------------------------------------------------- 30 Sei20-1 22:-----------TGGCTCATCTTAAAGCTCAT--GGTGCTACTATCTAAACTGA-TTCAACTAATTATTTATTCATTAGTA 87 Sei20-2 29:-----------..C.-...............--....................-.......................... 93 Sei20-3 25:-----------..C-A...............--.-.................GA.......................... 89 Sei20-4 155:CAAAACAAAA-..C-A...............--.-..................-.......................... 228 Sei20-5 155:CAAAACAAAA-..C-A...............--.-..................-.......................... 228 Sei20-6 21:-----------..CAA...............--.-..................-.......................... 85 Sei20-7 21:-----------..C-A...............--.-..................-.......................... 84 Sei20-8 21:-----------NNN-A.......G.......--.-.................GA.......................... 85 Sei20-9 26:-----------.T.-A...............--.-..................-.......................... 89 Sei20-10 26:-----------.T.-A...............--.-..................-.......................... 89 Sei20-11 26:-----------.NN-A...............--.-..................-.......................... 89 Sei20-12.NUC 30:-----------..C-A...............--.-............C.....-.......................T.. 93 Sei20-14 21:-----------NN--A...............--....................-.......................... 84 Sei20-15.NUC 30:-----------..C-A...........A...CATA............G.T...-..A................G...... 96 Supplemental figure 5 Nikaido et al. continued

  29. Sei35-1.nuc 1:ACGGTATAGAGGAGATTCATCAAAAAAGCCCCTGCCT------------------------------------------- 37 Sei35-2.nuc 1:.....................................------------------------------------------- 37 Sei35-3.nuc 1:------..TGA..........................------------------------------------------- 31 Sei35-4.nuc 1:------.T...A..............-....-..TT.TGGGCTTCCCTGGTGGCGCGGTCATTGAGAGTCTGCCTGXXXX 72 Sei35-5.nuc 1:------GTTGA...............-....-..TT.TGGGCTTCCCTGGTGGCGCGGTCATTGAGAGTCTGCCTGXXXX 72 Sei35-6.nuc 1:---------G.A.A.......................T------------------------------------------ 29 Sei35-7.nuc 1:---------G.A.A.......................T------------------------------------------ 29 Sei35-8.nuc 1:-...GG.T.......G...............--TAT.T------------------------------------------ 35 Sei35-9.nuc 1:-------.TGA..........................------------------------------------------- 30 Sei35-10.nuc 1:-------.TGA..........................------------------------------------------- 30 Sei35-11.nuc 1:-------.TGA..........................------------------------------------------- 30 Sei35-13.nuc 1:------------..............-....-.A.NNN------------------------------------------ 24 Sei35-14.nuc 1:----.CAGAG.....A..........-....-.A-NNN------------------------------------------ 31 Sei35-15.nuc 1:----.G.....AGA..C.........-....-A.TT.------------------------------------------- 31 Sei35-1.nuc 38:-------------------------------------------------------------------------------- 38 Sei35-2.nuc 38:-------------------------------------------------------------------------------- 38 Sei35-3.nuc 32:-------------------------------------------------------------------------------- 32 Sei35-4.nuc 73:XXXXXXCAGAAACAAAGACCCAACACAGCCATAAATAAATAAATAAATAAATAATATTAAAAAAAAAAAAAAAAAAAA-- 150 Sei35-5.nuc 73:XXXXXXCAGAAACAAAGACCCAACACAGCCATAAATAAATAAATAAATAAATAATATTAAAAAAAAAAAAAAAAAAAAAA 152 Sei35-6.nuc 30:-------------------------------------------------------------------------------- 30 Sei35-7.nuc 30:-------------------------------------------------------------------------------- 30 Sei35-8.nuc 36:-------------------------------------------------------------------------------- 36 Sei35-9.nuc 31:-------------------------------------------------------------------------------- 31 Sei35-10.nuc 31:-------------------------------------------------------------------------------- 31 Sei35-11.nuc 31:-------------------------------------------------------------------------------- 31 Sei35-13.nuc 25:-------------------------------------------------------------------------------- 25 Sei35-14.nuc 32:-------------------------------------------------------------------------------- 32 Sei35-15.nuc 32:-------------------------------------------------------------------------------- 32 Sei35-1.nuc 38:-----GTTTTCCCAAC-AGATGGTTCCCTAATCCAGCTTTATGGG-AAGTAAGAAACCCATTGAAT 96 Sei35-2.nuc 38:-----...........-............................-.................... 96 Sei35-3.nuc 32:-------.........-..-.......-....-...........--............-.......TA 85 Sei35-4.nuc 151:GCCCT.....T.....-..-..-....-....-..N........--.........CN.........T 210 Sei35-5.nuc 153:GCCCT.....T.....-..-..-....-....-..N........--......A..C..TT.GAT.. 211 Sei35-6.nuc 30:-------...T.....-...............-............-.................G.ATTAA 89 Sei35-7.nuc 30:-------...T.....-...............-............-.................G.ATTAA 89 Sei35-8.nuc 36:-------.........-..-.......-....-.......CAT..G............-....G.ATTAA 93 Sei35-9.nuc 31:-------...T.....-..-......T-....-............-............-.......TA 85 Sei35-10.nuc 31:-------C..T.....-..-......T-....-............-............-.......TA 85 Sei35-11.nuc 31:-------C..T.....-..-......T-....-............-............-.......TA 85 Sei35-13.nuc 25:-------...T.....-.ATA..C...-....-...........--............-.......TAA 80 Sei35-14.nuc 32:-------...T.....-.ATA.-C...-....-............-............-....G.ATTAA 88 Sei35-15.nuc 32:-------.......-.-.A-C..C........-...T........-.................G.ATTACA 90 Supplemental figure 5 Nikaido et al. continued

  30. Sei37-1.nuc 1:ACCCGATTGATT--CGTAATGAGGAAAAAAAAA---T-ACTAAGTTTTCAAAAAAAACTTTTTT-AAAAAAA---TTCTC 70 Sei37-2.nuc 1:............TC...................A--.-.......C.NN.......-.......T......----..... 72 Sei37-3.nuc 1:NNNNNNNNNNNNNNN-A...AGA.G........A--.-........CC-.....---.ACC...T.......A--..... 70 Sei37-4.nuc 1:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN....CA......-----C...T......----..... 71 Sei37-5.nuc 1:NNNNCGA.TGGATT.-GT.AT-.AGG.......AAA.-.........CA......-----C...T......----..... 68 Sei37-6.nuc 1:NNNNN...TCCGTAATA...AGA.G........A--.-........-C......---.ACC...T.......A--..... 71 Sei37-7.nuc 1:NNNNNNNNNNN.AAATA...AGA.G........A--.-........-C......---.ACC...T.......A--..... 71 Sei37-8.nuc 1:NNNNNNNNNNNNNNNNA...AGA.G........A--.-........-C......---.ACC...T.......A--..... 71 Sei37-9.nuc 1:............TC-........--........A--.-.........C.......------...T......----..A.. 64 Sei37-10.nuc 1:............TC-........--........A--.-.........C.......-----GCN.A.....-----..A.. 64 Sei37-11.nuc 1:............TC-........--........A--.-.........C.......-----GCN.A.....-----..A.. 64 Sei37-12.nuc 1:............TC-........--........A--.C.........CA......-----CNN.A......----.CTCT 66 Sei37-13.nuc 1:............TC.........--........A--.-.........C.......----.CCG.A.....----CCATC. 67 Sei37-14.nuc 1:............TC.........AG-.......G--.-.........C.....---TAACCNC.A......----..... 69 Sei37-1.nuc 71:TC------------------------------------------------------------------------------ 72 Sei37-2.nuc 73:..------------------------------------------------------------------------------ 74 Sei37-3.nuc 71:..------------------------------------------------------------------------------ 72 Sei37-4.nuc 72:..GGGCTTCCCTGGTGGTGCAGTGGTTGGGAATCTGCCTGCCXXXXXXXXXX-----------------TTTAAAAAATA 134 Sei37-5.nuc 69:..GGGCTTCCCTGGTGGCGCAGTGGTTGGGAATCTGCCTGCCXXXXXXXXXXAATAAATAAATAAAATATTTAAAATATA 148 Sei37-6.nuc 72:..------------------------------------------------------------------------------ 73 Sei37-7.nuc 72:..------------------------------------------------------------------------------ 73 Sei37-8.nuc 72:..------------------------------------------------------------------------------ 73 Sei37-9.nuc 65:..------------------------------------------------------------------------------ 66 Sei37-10.nuc 65:..------------------------------------------------------------------------------ 66 Sei37-11.nuc 65:..------------------------------------------------------------------------------ 66 Sei37-12.nuc 67:C------------------------------------------------------------------------------- 67 Sei37-13.nuc 68:..------------------------------------------------------------------------------ 69 Sei37-14.nuc 70:..------------------------------------------------------------------------------ 71 Sei37-1.nuc 73:--------------ATTTCTGGTGGGCTCAATTTAACAAATTCTACAGCCCAC 111 Sei37-2.nuc 75:--------------...-................................... 112 Sei37-3.nuc 73:--------------....................................... 111 Sei37-4.nuc 135:TATTTATATTATAA......CTCA-T................NNNNN 180 Sei37-5.nuc 149:TATATATATTAAAA.A....CTCA-T.......NN.......NNNNNN 195 Sei37-6.nuc 74:--------------....................................... 112 Sei37-7.nuc 74:--------------....................................... 112 Sei37-8.nuc 74:--------------....................................... 112 Sei37-9.nuc 67:--------------................-..-................... 103 Sei37-10.nuc 67:-------------C...CT-------....-..-................... 97 Sei37-11.nuc 67:-------------C...CT-------....-..-................... 97 Sei37-12.nuc 68:-------------------------A...GG.G-................... 94 Sei37-13.nuc 70:-------------C.C...------------C--................... 95 Sei37-14.nuc 72:-------------------------A.CTTT.G-................... 98 Supplemental figure 5 Nikaido et al. continued

  31. Fin9-1 1:CACTAGTT-GGAATCACTACTCTAAAATACCACGAGGGCTTCCCTGGTGGCGCAGCGGTTGAGAATCTXXXXXXXXXXAA 79 Fin9-2 1:........-......................................................................G 79 Fin9-3 1:----....T......-..................---------------------------------------------- 29 Fin9-4 1:----....T......-..........-.......---------------------------------------------- 28 Fin9-5 1:----....T......-..................---------------------------------------------- 29 Fin9-6 1:----....T......-..................---------------------------------------------- 29 Fin9-7 1:-------.T......-..................---------------------------------------------- 26 Fin9-8 1:---.G...T.........................---------------------------------------------- 31 Fin9-10 1:----....T......-..................---------------------------------------------- 29 Fin9-11 1:----....T......-..................---------------------------------------------- 29 Fin9-12 1:-C..C...T....-............-.-.....---------------------------------------------- 30 Fin9-13 1:..-.....G.A-..............-.......---------------------------------------------- 31 Fin9-1 80:AAAGCCCTCGCACAGAAACGAAGACCCAACACAGCCAAAAATAAATAAATAAATAAAATTTAAAATACCACGAATACATG 159 Fin9-2 80:.....................................T.......................................... 159 Fin9-3 30:-----------------------------------------------------------------------TC....... 38 Fin9-4 29:------------------------------------------------------------------------N....... 36 Fin9-5 30:------------------------------------------------------------------------........ 37 Fin9-6 30:------------------------------------------------------------------------.......N 37 Fin9-7 27:------------------------------------------------------------------------........ 34 Fin9-8 32:------------------------------------------------------------------------........ 39 Fin9-10 30:-----------------------------------------------------------------------TC....... 38 Fin9-11 30:-----------------------------------------------------------------------TC....... 38 Fin9-12 31:------------------------------------------------------------------------...-.... 37 Fin9-13 32:------------------------------------------------------------------------........ 39 Fin9-1 160:TAAGGACTGCTTAAAACAGTCACAAGATTAATAGTCCACTTAGGGAGATATTAATAACCCTACTATTT-CAAGTTTTGGA 238 Fin9-2 160:....................................................................-........... 238 Fin9-3 39:..........................................................A.........-........... 117 Fin9-4 37:....................................................................-........... 115 Fin9-5 38:....................................................................-........... 116 Fin9-6 38:N...................................................................-......G.... 116 Fin9-7 35:....................................................................-........... 113 Fin9-8 40:....................................................................-........... 118 Fin9-10 39:..............C.AC..A.................T.............................T........... 118 Fin9-11 39:..............C.ACN.N.................T.............................-........... 117 Fin9-12 38:...............-..............C..A....T.............................-........... 115 Fin9-13 40:....................................................................-........... 118 Supplemental figure 5 Nikaido et al. continued

  32. Hump46-1 1:----------------GTTATAGTAGTTTTCTGCTCTGTTCAGATATATCAGATCTTAGACCCATTTGGC-AGATTTAAA 63 Hump46-2 1:TAAGTCATAGTCTTTGT.ATA.................................................-......... 79 Hump46-3 1:-------------------------------.............................T......A..-......... 48 Hump46-4 1:---------TCTTTGTA.ATA.......NN.....................................A..-......... 70 Hump46-5 1:TAGTCATAGTCTTTGTA.ATA..............................................A..-G........ 79 Hump46-6 1:TAGTCATAGTCTTTGTA.ATA......C.......................................A..-G........ 79 Hump46-7 1:-------ATAGTCTTT.............NNN......................................-......... 72 Hump46-8 1:-------ATAGTCTTT......................................................-......... 72 Hump46-9 1:----------------------------------------..............................A......... 40 Hump46-10 1:----------------------------------------..................C...........-......... 39 Hump46-11 1:-----------------------------------TCTG...................C...........-......... 44 Hump46-14 1:----CAATAGTCTTTGT.ATA............GGGGGGGCTTCCCTGGTGGCGCAGTGGGTGGGXXXXXXXXXXXCAAA 76 Hump46-1 64:AGAGTGGCCTCAAAAAGGATCATTCTTGGGGCTTCCCTGGTGGCGCAGTGGTTGAGAGTCTXXXXXXXXXXGCCCTCGCA 143 Hump46-2 80:...........................................T.................................... 159 Hump46-3 49:...........................----------------------------------------------------- 75 Hump46-4 71:...........................----------------------------------------------------- 97 Hump46-5 80:...........................----------------------------------------------------- 106 Hump46-6 80:...............G...........----------------------------------------------------- 106 Hump46-7 73:...........................----------------------------------------------------- 99 Hump46-8 73:...........................----------------------------------------------------- 99 Hump46-9 41:...........................----------------------------------------------------- 67 Hump46-10 40:...........................----------------------------------------------------- 66 Hump46-11 45:...........................----------------------------------------------------- 71 Hump46-14 77:GACCCAACACAGCCAAAAATAAAAACAAATAAATAAATACATCTAGTAAAAAAAAAAAAAATAGAAAGTAGTTTTCTGCT 156 Hump46-1 144:CAGAAACTAAGACCCAACACAGCCAAAAAATAAAAAA------------------AAAAAGGATCATTCTT-TTTGG--A 202 Hump46-2 160:......................T..................TAAAAA--------................-.....--. 228 Hump46-3 76:------------------------------------------------------------------------.....--. 81 Hump46-4 98:------------------------------------------------------------------------.....--. 103 Hump46-5 107:------------------------------------------------------------------------.....--. 112 Hump46-6 107:------------------------------------------------------------------------.....--. 112 Hump46-7 100:------------------------------------------------------------------------.....--. 105 Hump46-8 100:------------------------------------------------------------------------.....--. 105 Hump46-9 68:------------------------------------------------------------------------.....--. 73 Hump46-10 67:------------------------------------------------------------------------.....--. 72 Hump46-11 72:------------------------------------------------------------------------.....--. 77 Hump46-14 157:CTCTTCAGATATATCAGATCTTAGACCCATTTGGCAGATTTAAAAGAGTGACCTC................T.....GG. 236 Hump46-1 203:TACACTGTATAAAA--CTACTGTGGACTGGTCTGCTTTGTGGCTCTATTATATAGGACAGATGAGATCTTTAACAACCCA 280 Hump46-2 229:..............--..............................T.................A............... 306 Hump46-3 82:..T...........--....................................... 134 Hump46-4 104:...C..........--....................................... 156 Hump46-5 113:..............--....................................... 165 Hump46-6 113:.............--C.........................C............. 165 Hump46-7 106:..............--...................................G............................ 183 Hump46-8 106:..............--...................................G............................ 183 Hump46-9 74:........CAT..--C...................................G... 126 Hump46-10 73:........CAT...AC...................................G... 127 Hump46-11 78:........CAT...AC...................................G... 132 Hump46-14 237:..............--...................................G..................-......... 313 Supplemental figure 5 Nikaido et al. continued

  33. Hump53-1 1:TGGAGAGCAAAATTGGCTATTTGTGGATCTGTCAAGAAGAGCCCTGGTAGAGACCACGG-ATTTCAGTTAAAAATTAAGG 79 Hump53-2 1:---G..............G........................................-.................... 76 Hump53-3 1:--------------.............................................C.................... 66 Hump53-4 1:----.......-...............................................-.................... 74 Hump53-5 1:----.......-...............................................-.................... 74 Hump53-6 1:----.......-........................G......................-.................... 74 Hump53-7 1:----.......-...............................................-.................... 74 Hump53-8 1:----------.-....N...........T.CC.........ANN...N........TN.C.................N.. 69 Hump53-9 1:----------.-....................-.......................T..-.................... 67 Hump53-10 1:----------.-....................-.......................T..-.................... 67 Hump53-11 1:----------.-...............NNN..-.......................T..-.................... 67 Hump53-12.nuc 1:AAAGACAA...-...............................................-.................... 78 Hump53-13 1:----.......-..........................A......A..........T..T.................... 75 Hump53-14 1:----.......-.............T.A..........A....................C.................... 75 Hump53-1 80:CAGGGGCTTCCCTGGTGGCGCAGTGGTTGAGAGTCXXXXXXXXXXCCCAACACAGCAATCAATCAATCAA----TAAATA 155 Hump53-2 77:......................................................................TCAA...... 156 Hump53-3 67:...----------------------------------------------------------------------------- 69 Hump53-4 75:...----------------------------------------------------------------------------- 77 Hump53-5 75:...----------------------------------------------------------------------------- 77 Hump53-6 75:...----------------------------------------------------------------------------- 77 Hump53-7 75:...----------------------------------------------------------------------------- 77 Hump53-8 70:.N.----------------------------------------------------------------------------- 72 Hump53-9 68:...----------------------------------------------------------------------------- 70 Hump53-10 68:...----------------------------------------------------------------------------- 70 Hump53-11 68:...----------------------------------------------------------------------------- 70 Hump53-12.nuc 79:...----------------------------------------------------------------------------- 81 Hump53-13 76:...----------------------------------------------------------------------------- 78 Hump53-14 76:...----------------------------------------------------------------------------- 78 Hump53-1 156:AGAATGTGAATTTCTAAAAAAAAAAAATTAAAAAAATAAAAATTAAGGCAGGATATAATATAGGAGTAAGCACTAATAAA 235 Hump53-2 157:.........................-------T............................................... 229 Hump53-3 70:---------------------------------------------------............................. 98 Hump53-4 78:---------------------------------------------------...........C................. 106 Hump53-5 78:---------------------------------------------------............................. 106 Hump53-6 78:---------------------------------------------------......T...................... 106 Hump53-7 78:---------------------------------------------------............................. 106 Hump53-8 73:---------------------------------------------------...............A....N........ 101 Hump53-9 71:---------------------------------------------------............................. 99 Hump53-10 71:---------------------------------------------------............................. 99 Hump53-11 71:---------------------------------------------------............................. 99 Hump53-12.nuc 82:---------------------------------------------------............................. 110 Hump53-13 79:---------------------------------------------------A....C..................G.... 107 Hump53-14 79:---------------------------------------------------............C................ 107 Supplemental figure 5 Nikaido et al. continued

  34. SEM4-1 71:GAATACAAAGTAATTTTAAAAA--GTATATGTT----------------------------------------------- 101 SEM4-2 78:......................--.C.......----------------------------------------------- 108 SEM4-3 76:................A.....--..G......----------------------------------------------- 106 SEM4-4 73:......................--.C.......----------------------------------------------- 103 SEM4-5 73:......................--.C.......----------------------------------------------- 103 SEM4-6 73:......................--.C.......----------------------------------------------- 103 SEM4-7 74:......................--.C.......----------------------------------------------- 104 SEM4-8 72:......................--.C.......----------------------------------------------- 102 SEM4-9 73:......................--.C.......----------------------------------------------- 103 SEM4-10.NUC 73:......................--.C.......GGGCTTCCCTGGTGGCGCAGTGGTTGAGAATCTGCCXXXXXXXXXXG 150 SEM4-11.NUC 73:...................T..--.C......GGGGCTTCTCTGGTGGCGCAGTGGTTGAGAATCTGCCXXXXXXXXXXG 150 SEM4-12.nuc 71:.....T...........T....--.C.......----------------------------------------------- 101 SEM4-13 74:.....T....A...........--.C.......----------------------------------------------- 104 SEM4-14 74:.....T.......G...T....AT.C.......----------------------------------------------- 106 SEM4-15 76:.....T................AA.C.......----------------------------------------------- 108 SEM4-1 102:-------------------------------------------------------------------------------- 102 SEM4-2 109:-------------------------------------------------------------------------------- 109 SEM4-3 107:-------------------------------------------------------------------------------- 107 SEM4-4 104:-------------------------------------------------------------------------------- 104 SEM4-5 104:-------------------------------------------------------------------------------- 104 SEM4-6 104:-------------------------------------------------------------------------------- 104 SEM4-7 105:-------------------------------------------------------------------------------- 105 SEM4-8 103:-------------------------------------------------------------------------------- 103 SEM4-9 104:-------------------------------------------------------------------------------- 104 SEM4-10.NUC 151:CCAGAAAAATTTTTTAAAAA--TAAATAAATAAATTTTTTTAAAAAAGGAATTTACACTTGTTACTACTATTAAAAAAAA 228 SEM4-11.NUC 151:CCAGAAAAATTTTTTAAAAAAATAAATAAATAAATTTTTTTAAAAAAGGAATTTACACTTGTTACTACTATTAAAAAAAA 230 SEM4-12.nuc 102:-------------------------------------------------------------------------------- 102 SEM4-13 105:-------------------------------------------------------------------------------- 105 SEM4-14 107:-------------------------------------------------------------------------------- 107 SEM4-15 109:-------------------------------------------------------------------------------- 109 SEM4-1 102:------------GTGCTACTCTTTCAGAAGACTACTAATTCCTCAGAGGAGAAGGTGTATTTA 152 SEM4-2 109:------------...................T..T...........G..G-............ 158 SEM4-3 107:------------.....................................G-............ 156 SEM4-4 104:------------...................T..T...........-..G-............A 153 SEM4-5 104:------------...................T..T...........-..G-............AAA 155 SEM4-6 104:------------...................T..T...........-..G-............AAA 155 SEM4-7 105:------------..................................-..G-............ 153 SEM4-8 103:------------..................................-..G-............A 152 SEM4-9 104:------------..................................-..G-............A 153 SEM4-10.NUC 229:AAAGCATATGTT..............C....T..T...........G...A.G.......... 291 SEM4-11.NUC 231:AAAGCATATGTT..............C....T..T...........G...A.G.......... 293 SEM4-12.nuc 102:------------.....T...........A.T..T...........G...AGGT..A.T.AA 151 SEM4-13 105:------------...................T..T...........-..G-............A 154 SEM4-14 107:------------......G............T..T...........-..G-............ 155 SEM4-15 109:------------...................A..T...........-..G-............AAACC 162 Supplemental figure 5 Nikaido et al. continued

  35. SEM15-1 63:TTCTTTCAGACTCAATCAATAGTTCATCCTG------------------------------------------------- 93 SEM15-2 76:..............................T------------------------------------------------- 106 SEM15-3 58:..............................T------------------------------------------------- 88 SEM15-4 67:..............................T------------------------------------------------- 97 SEM15-5 68:..............................T------------------------------------------------- 98 SEM15-6 68:..............................T------------------------------------------------- 98 SEM15-7 67:.............T................T------------------------------------------------- 97 SEM15-8 64:.............T................T------------------------------------------------- 94 SEM15-9 64:..............................T------------------------------------------------- 94 SEM15-10 68:...................C..........TGGGGCTTCCCTGGTGGCGTAGTGGTTGAGAATCTGCCTGCCAATGCAGG 147 SEM15-11 67:...................C..........TGGGGCTTCCCTGGTGGCGTAGTGGTTGAGAATCTGCCTGCCAATGCAGG 146 SEM15-12.NUC 67:..............................T------------------------------------------------- 97 SEM15-13 68:..............................T------------------------------------------------- 98 SEM15-15 76:......G...A...................T------------------------------------------------- 106 SEM15-1 94:-------------------------------------------------------------------------------- 94 SEM15-2 107:-------------------------------------------------------------------------------- 107 SEM15-3 89:-------------------------------------------------------------------------------- 89 SEM15-4 98:-------------------------------------------------------------------------------- 98 SEM15-5 99:-------------------------------------------------------------------------------- 99 SEM15-6 99:-------------------------------------------------------------------------------- 99 SEM15-7 98:-------------------------------------------------------------------------------- 98 SEM15-8 95:-------------------------------------------------------------------------------- 95 SEM15-9 95:-------------------------------------------------------------------------------- 95 SEM15-10 148:GGXXXXXXXXXXAATAAATTAATTAATTAATTAAAAAAAAAAAAAAAAAACTGATTCTTCTAAAAAAATCTTTACATTGA 227 SEM15-11 147:GGXXXXXXXXXXAATAAATTAATTAATTAATTTAAAAAAAAAAAAAAAAACTGATTCTTCTAAAAAAATCTTTACATTGA 226 SEM15-12.NUC 98:-------------------------------------------------------------------------------- 98 SEM15-13 99:-------------------------------------------------------------------------------- 99 SEM15-15 107:-------------------------------------------------------------------------------- 107 SEM15-1 94:-------------------------------AAACATTAAGTGGCCCAAATGTTTTACAATAGGTAAGCAAAATTGGAGT 142 SEM15-2 107:-------------------------------................................................. 155 SEM15-3 89:-------------------------------.............................................A... 137 SEM15-4 98:-------------------------------................................................. 146 SEM15-5 99:-------------------------------................................................. 147 SEM15-6 99:-------------------------------................................................. 147 SEM15-7 98:-------------------------------................................................. 146 SEM15-8 95:-------------------------------................................................. 143 SEM15-9 95:-------------------------------................................................. 143 SEM15-10 228:TAAATCTTTAAAAAACAAATANTTCATCCTT....................................A............ 307 SEM15-11 227:TAAATCTTTAAAAAACAAATATTTCATCCTT....................................A............ 306 SEM15-12.NUC 98:-------------------------------....................................A............ 146 SEM15-13 99:-------------------------------....................................A............ 147 SEM15-15 107:-------------------------------....................A.....TG..G.A...A............ 155 Supplemental figure 5 Nikaido et al. continued

  36. BRY24-1 71:AGAAATAATATTTGGCTTATGTGTATGTGAATAATGTGAGATGATGTCTAAGAAAGCATCTA------------------ 132 BRY24-2 79:..............................................................------------------ 140 BRY24-3 78:...................C..........................................GGGCTTCCCTGGTGGCAC 157 BRY24-4 80:..............................................................GGGCTTCCCTGGTGGCGC 159 BRY24-5 70:..................NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 149 BRY24-6 80:..............................................C...............------------------ 141 BRY24-7 80:..............................................C...............------------------ 141 BRY24-8 80:..............................................C...............------------------ 141 BRY24-9 79:..............................................C...............------------------ 140 BRY24-10 62:..............................................................------------------ 123 BRY24-11 62:..............................................................------------------ 123 BRY24-12.NUC 80:..................G...........................................------------------ 141 BRY24-13 64:NNNNNNNNNNNNN.....G...........................................------------------ 125 BRY24-14 80:..................G...........................................------------------ 141 BRY24-1 133:-------------------------------------------------------------------------------- 133 BRY24-2 141:-------------------------------------------------------------------------------- 141 BRY24-3 158:AGTGGTTXXXXXXXXXXAAAACCCAACACAGCAATAAATAAATAAATAATTAATTCCCATTTAAAAAAACAAACAAAAAC 237 BRY24-4 160:AGTGGTTXXXXXXXXXXAAAACCCAACACAGCAATAAATAAATAAATAAGTAATTCCCATTTAAAAAAACAAACAAAAAC 239 BRY24-5 150:NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATAAATAAATAAATAAGTAATTCCCCTTTAAAAAAACAAACAAAAAC 229 BRY24-6 142:-------------------------------------------------------------------------------- 142 BRY24-7 142:-------------------------------------------------------------------------------- 142 BRY24-8 142:-------------------------------------------------------------------------------- 142 BRY24-9 141:-------------------------------------------------------------------------------- 141 BRY24-10 124:-------------------------------------------------------------------------------- 124 BRY24-11 124:-------------------------------------------------------------------------------- 124 BRY24-12.NUC 142:-------------------------------------------------------------------------------- 142 BRY24-13 126:-------------------------------------------------------------------------------- 126 BRY24-14 142:-------------------------------------------------------------------------------- 142 BRY24-1 133:-----------------------------------------------------ACCCAGGCACTTGATAAACACTGAAGA 159 BRY24-2 141:-----------------------------------------------------........................... 167 BRY24-3 238:AAAACAAAAAAAACACATAGTTTCCTTTAAAAAAAAAAAAAAAAAAGCATCTA.........................A. 317 BRY24-4 240:AAAACAAAAAAACCACATAGTTTCCTTTAAAAAAAAAAAAAAGAAAGCATCTA........................... 319 BRY24-5 230:AAAACAAAAAAACCCCATAGTTTCCTTTAAAAAAAAAAAAAAGAAAGCATCTA........................... 309 BRY24-6 142:-----------------------------------------------------........................... 168 BRY24-7 142:-----------------------------------------------------........................... 168 BRY24-8 142:-----------------------------------------------------........................... 168 BRY24-9 141:-----------------------------------------------------........................... 167 BRY24-10 124:-----------------------------------------------------........................... 150 BRY24-11 124:-----------------------------------------------------........................... 150 BRY24-12.NUC 142:-----------------------------------------------------..........G.C.............. 168 BRY24-13 126:-----------------------------------------------------........................... 152 BRY24-14 142:-----------------------------------------------------........................... 168 Supplemental figure 5 Nikaido et al. continued

  37. Sei26-1.nuc 1:----CTAATCTTATTGNATATCT-TAATCGCNAA-TGTATGGTTCTG--------------------------------- 41 Sei26-2.nuc 1:-TAT............T......C.....AGC..-............--------------------------------- 45 Sei26-3.nuc 1:----............T......-.....AAGN.A............GGCATTCCCTGGTGGCGCAGTGGTTGAGAATCT 75 Sei26-4.nuc 1:----............T......-.....NN.N.A............GGGCTTCCCTGGTGGCGCAGTGGTTGAGAATCT 75 Sei26-5.nuc 1:----............T......-.....AAG..-............GGGCTTCCCTGGTGGCGCAGTGGTTGAGAATCT 74 Sei26-6.nuc 1:-TAT............T......-.....NG.CN-............--------------------------------- 44 Sei26-7.nuc 1:-TAT............T......-.....-G.CN-............--------------------------------- 43 Sei26-8.nuc 1:-TAT............T......-.....AGC..-............--------------------------------- 44 Sei26-9.nuc 1:----------......T......-.....AGCG.-............--------------------------------- 35 Sei26-10.nuc 1:----------......T......-.....AGCG.C............--------------------------------- 36 Sei26-11.nuc 1:----------......T......-.....AGCG.C............--------------------------------- 36 Sei26-13.nuc 1:TATC-...........T......-.....ANGC.-............--------------------------------- 44 Sei26-14.nuc 1:TATC............T......-.....AAG..-.A..........--------------------------------- 45 Sei26-1.nuc 42:-------------------------------------------------------------------------------- 42 Sei26-2.nuc 46:-------------------------------------------------------------------------------- 46 Sei26-3.nuc 76:GXXXXXXXXXXCCCAACACAGCCGTAAATAATTAAATAAATAAGTCATTAAAAAAAAAAAAACTTTCTTTAAAAAAAAAA 155 Sei26-4.nuc 76:GXXXXXXXXXXCCCAACACAGCCGTAAATAATTAAATAAATAAGTCATTAAAAAAAAAAAA-GTCATTAAAAAAAAAAAA 154 Sei26-5.nuc 75:GXXXXXXXXXXCCCAACACAGCCGTAAATAATTAAATAAATAAGTCATTAAAAAAAAAAAAGTCTTTAAAAAAAAAAAAA 154 Sei26-6.nuc 45:-------------------------------------------------------------------------------- 45 Sei26-7.nuc 44:-------------------------------------------------------------------------------- 44 Sei26-8.nuc 45:-------------------------------------------------------------------------------- 45 Sei26-9.nuc 36:-------------------------------------------------------------------------------- 36 Sei26-10.nuc 37:-------------------------------------------------------------------------------- 37 Sei26-11.nuc 37:-------------------------------------------------------------------------------- 37 Sei26-13.nuc 45:-------------------------------------------------------------------------------- 45 Sei26-14.nuc 46:-------------------------------------------------------------------------------- 46 Sei26-1.nuc 42:-------------------ACAAATACATGGTACC-TAGCAGGGTAGTACTTAGTTTAGTTTGAAAAGAAGTAA-CCAAC 100 Sei26-2.nuc 46:-------------------...........-....-.......-..............................A..... 103 Sei26-3.nuc 156:AAAAAA-TGGATGGGTCTG.A......C...-...T..NNNNNNNNNNNNNNNNNNNNNNNNN 216 Sei26-4.nuc 155:AAAAAA-TGTATGGTTCTG........N..-....-.......-.........T....T...............A.A 227 Sei26-5.nuc 155:AAAAGAATGTATGGTTCTG........N..-....-.......-..NNNNNNNNNNNNNNNNNNN 216 Sei26-6.nuc 45:-------------------G..........-..T.C.......-..............................A-.... 102 Sei26-7.nuc 44:-------------------G..........-....-.......-..............................A-.... 101 Sei26-8.nuc 45:-------------------G..........-....-.......-..............................A-.... 101 Sei26-9.nuc 36:-------------------...........-....-.......-..............................A-.... 92 Sei26-10.nuc 37:-------------------...........-....-.......-..............................A-.... 93 Sei26-11.nuc 37:-------------------...........-....-.......-..............................A-.... 93 Sei26-13.nuc 45:-------------------...........-...A-.......-....G.................G.......A-.... 101 Sei26-14.nuc 46:-------------------.........C.-...G-.......-..............................A-.C.A 102 Supplemental figure 5 Nikaido et al. continued

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