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437_2

TA496. 437_2. G/A syn. 46. T/A syn. 52. 162. T/-. G/T. 179. A/-. 185. 212. C/A. T/C. 255. T/G. 335. S. arcanum. 395-429 complex indel. TA496 --CACA--------------------TTT------- other AGCA--TCGTAATGATGAAATTCTTGTTTTTGATTC. 491. 491. C/T. 435. 435. A/G. T/A. 460.

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437_2

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  1. TA496 437_2 G/A syn 46 T/A syn 52 162 T/- G/T 179 A/- 185 212 C/A T/C 255 T/G 335 S. arcanum 395-429 complex indel TA496 --CACA--------------------TTT------- other AGCA--TCGTAATGATGAAATTCTTGTTTTTGATTC 491 491 C/T 435 435 A/G T/A 460 T/- 185 185 A/- 462 591 489 -/T 162 162 G/- T/A ser/thr -/T 462 462 460 460 A/- noncoding (no shading) A/T 214 214 synonymous non-syn, conservative n = 32 non-syn, nonconservative

  2. noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative 3300_2 n = 4 C/T syn 293 293 n = 31

  3. 4301_3 n = 31 G/A syn 228 228 LR_011 T/C syn 273 273 T/C syn 240 240 T/C syn 96 96 G/A gly/ser 52 52 S. arcanum noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative

  4. LR_027 3155_3 330 330 T/C n = 3 n = 27 C/T syn 592 523 523 A/G LR_029 488 488 718 C/T A/G LR_018 809 809 G/A 756 756 C/T 425 425 -/T 334 334 T/C T/A 249 249 248 248 G/A 243 243 -/A noncoding (no shading) synonymous 219 219 A/T non-syn, conservative 119 119 A/T non-syn, nonconservative 26 26 C/- A/- 7 S. arcanum

  5. 1260_2 n = 32 G/A syn 210 210 MM G/T ala/ser 355 355 A/C syn 264 264 noncoding (no shading) C/T syn 246 246 synonymous non-syn, conservative A/T syn 60 60 non-syn, nonconservative S. arcanum

  6. 3332_3 S. arcanum G/- 163 158 -/C 157 A/- 151 151 C/T 138 C/T 129-132 microsat ATAT/- 73-75 microsat -/GCT n = 23 noncoding (no shading) 165 T/C 67-72 microsat -/GCTGCT synonymous n = 7 non-syn, conservative LR_024 -/GCT 64-66 microsat non-syn, nonconservative LR_011

  7. 2534_1b n = 25 TA496 C/A 64 553 T/C n = 3 96 489 T/C A/G n = 4 G/C 146 T/A 127 177 T/G 149 A/C G/T 572 515 T/A 594 594 A/G A/T 581 581 513-516 indel noncoding (no shading) ATGT/- synonymous 499 499 A/T S. lyc. AATTGTCAAACCC S. arc. - 153-165 indel non-syn, conservative 152 152 G/A non-syn, nonconservative C/T 81 S. arcanum

  8. 2325_3 n = 30 n = 2 T/C syn 174 C/G syn 327 214 214 C/A leu/met G/C val/leu 363 361 C/T val/leu G/T syn 390 390 T/C syn 331 331 G/C syn 258 258 noncoding (no shading) synonymous C/T syn 249 249 non-syn, conservative non-syn, nonconservative T/A syn 126 126 S. arcanum

  9. 1287_1 n = 18 C/A thr/lys 86 86 n = 18 C/T syn 60 60 noncoding (no shading) 49 49 A/C asn/his synonymous non-syn, conservative S. arcanum non-syn, nonconservative

  10. 1589_1 S. arcanum A/C 123 123 75 75 A/G n = 32 noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative

  11. 1675_1 S. arcanum 90 A/- 57 A/- 51 A/T 19 T/G 14 C/A noncoding (no shading) n = 31 synonymous non-syn, conservative non-syn, nonconservative

  12. S. arcanum 1724_1 6 C/T 56 56 G/C gly/ala 57 57 T/C G/A syn 78 78 C/T 103 103 125 125 C/T G/A 152 152 C/T 157 157 175 175 T/C leu/pro 176 176 C/T T/G T/C 96 107 LR_024 n = 2 96 96 107 107 T/G T/C noncoding (no shading) synonymous n = 23 non-syn, conservative G/T ala/ser non-syn, nonconservative 85 85 n = 9

  13. 175_1 n = 7 C/T syn 53 53 n = 9 C/G ala/gly 7 noncoding (no shading) n = 20 synonymous non-syn, conservative non-syn, nonconservative

  14. 1863_3 n = 5 229 229 A/G 456 456 C/T T/A 511 511 T/C 521 521 n = 26 noncoding (no shading) A/- 282 282 synonymous non-syn, conservative 536 536 A/G non-syn, nonconservative LR_024

  15. 1909_2 n = 6 T/C syn 54 54 n = 27 160 160 C/T 146 146 C/T noncoding (no shading) 126 126 -/A synonymous non-syn, conservative 92 T/C non-syn, nonconservative S. arcanum

  16. 2189_1 n = 21 103 103 T/A n = 6 C/T syn 164 164 T/C 56 n = 7 noncoding (no shading) synonymous non-syn, conservative 68 T/C non-syn, nonconservative S. arcanum

  17. 220_1 TA496 A/G syn 6 52 52 A/T met/leu n = 31 noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative

  18. S. arcanum 2280_1 131 131 A/T lys/met A/T lys/met 92 92 A/G syn 87 87 80-82 80 microsat ---/TGT T/C syn 73 73 C/T syn 45 45 noncoding (no shading) synonymous n = 32 non-syn, conservative non-syn, nonconservative

  19. 241_2b n = 2 n = 2 GATCTCTTGTTT other - 172 172-183 indel n = 4 T/C 249 249 60 60 C/T LR_001 n = 26 noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative

  20. 2486_1 TA496 36 36 T/C leu/ser n = 29 C/G thr/arg 117 117 T/G met/arg 132 69 69 T/C thr/met 200 200 G/T LR013hap2 133-138 indel -/GAGAAG n = 3 noncoding (no shading) synonymous 182 182 T/A non-syn, conservative S. arcanum non-syn, nonconservative

  21. 2582_1 n = 32 A/G syn 111 111 S. arcanum noncoding (no shading) synonymous non-syn, conservative non-syn, nonconservative

  22. 2719_1 n = 14 118 118 T/C n = 19 150 150 131 131 T/- 107 107 99 99 C/T S. arcanum noncoding (no shading) C/A synonymous non-syn, conservative A/C non-syn, nonconservative

  23. S. arcanum 2819_5 C/A 567 311 311 A/G C/- 628 566 (S. arcanum missing data) A/T (S. arcanum missing data) 627 183 183 G/T G/A G/T 618 166 166 G/A 539 539 T/C C/T syn n = 31 442 442 T/C 428 428 391 391 G/T 312 312 T/- 283 A/G 272 G/- 235 T/G 234 noncoding (no shading) G/C synonymous 156 T/A non-syn, conservative 146 C/G non-syn, nonconservative 111 G/T 107 A/T LR_024

  24. S. arcanum 2875_4b 561 G/C 546 -/T 543 G/C 468 T/C A/T 444 429 A/G 415 A/G 412 G/A 383 T/A 285 A/T 237 G/A 222 G/T 199 A/C 185 T/A 171 G/A S. arc. - S. lyc. AATGCATATGATAC 124-137 indel 69-91 indel -/C 77 77 -/A S. arc. - S. lyc. AAATTCTGCGGGGCTGTTATTGT n = 2 LR_018 77 412 A/G C/A 399 A/G 317 T/A noncoding (no shading) n = 8 137 A/C synonymous G/T A/T 371 205 non-syn, conservative other ACACAAGAAGCACATTC LR_029 - 92-108 indel n = 22 38 166 non-syn, nonconservative G/A G/A LR_029

  25. S. arcanum 296_1 95 G/A C/T 120 239 C/A TA496 n = 4 C/- (S. arcanum missing data) 107 448 A/T LR013hap1 (S. arcanum missing data) 537 T/C (S. arcanum missing data) 532 T/G noncoding (no shading) synonymous n = 26 non-syn, conservative non-syn, nonconservative

  26. S. arcanum U146140 522 C/T 481 G/T 449 A/G 441 G/C 382 G/C 377 T/C 336 A/- 303 T/C 261 T/A 254 254 -/A 225 T/C 222 T/C T/C syn 178 106 106 C/T -/T 100 100 58 58 A/T noncoding (no shading) 50-53 indel -/AAAA synonymous 25 A/- non-syn, conservative non-syn, nonconservative n = 33

  27. S. arcanum C2_At1g13380 168 168 T/A 194 194 G/A 201 201 A/T 256 256 G/C 305 305 A/G 323 323 T/A 327 327 T/A A/T 349 349 404-405 indel -/TT 406 406 T/G 414 414 G/A 461 461 G/A 514 514 C/G 543 543 T/A 584 584 A/C A/G 629 629 noncoding (no shading) synonymous n = 32 non-syn, conservative non-syn, nonconservative G/A gly/arg 42 LR_027

  28. C2_At1g14000 n = 30 G/A 530 530 T/C 606 606 G/A 657 657 n = 4 G/C 673 673 T/- 419 419 noncoding (no shading) 369 369 C/T synonymous 229 229 non-syn, conservative C/T non-syn, nonconservative 89 89 C/A S. arcanum

  29. S. arcanum C2_At1g20050 128 128 T/- 153 153 G/T 155 155 A/G 170 170 C/G S. arc. - S. lyc. AGTATCTTAGTCTTCATTTTTACTACTGCCTATTGCTTCATTTG 203-246 indel 313 313 C/T 344 344 T/C 379 379 T/C 428 428 T/G 449 449 G/A 461 461 C/T 126 510 C/T G/A 489 489 T/C 230 A/G n = 4 577 G/A 708 T/C noncoding (no shading) synonymous n = 22 non-syn, conservative non-syn, nonconservative CAT/- 718-720 indel n = 8

  30. C2_At1g32130 A/G n = 3 314 314 n = 31 428 428 C/T syn 322 322 254 254 G/T 136 136 G/T noncoding (no shading) S. arcanum synonymous G/C non-syn, conservative non-syn, nonconservative

  31. S. arcanum S. arc./S. lyc G/A syn 662 C2_At1g44575 A/C syn 632 C/T 608 T/C 575 A/G 574 G/A 565 T/C 562 A/T 560 G/A 522 G/T 507 A/G 471 -/A 464 G/A 460 G/A 459 G/A 453 A/G 451 C/T 438 A/G 434 G/A 421 C/T 411 G/A 408 n = 29 G/A 398 G/A 391 ATA/- 371-373 indel T/A 366 A/G 365 344 332 C/G 314 A/C 313 A/- 274 A/T 265 A/T 426 C/T 262 A/G 255 T/C LR_028 235 A/T 223 T/G 465 465 220 G/A T/G 219 G/A 218 C/T n = 2 217 G/- branch to S. arcanum 214 C/T 197 C/T 602 602 196 C/- G/C 57 G/T 179-180 indel C/T 165-167 indel noncoding (no shading) AA/- 439 439 153 C/T -/AAT 141 C/T G/C synonymous 135 C/- LR_014 68 130 G/A 114 T/A non-syn, conservative indel 67-114 LR_001 - other S. lyc. T(G/C)AATA 97 67-72 C/T 73-85 indel C/- 344 CAATTACATATAT/- 70 G/C non-syn, nonconservative LR_001 - other S. lyc. TATTTTTTCTT 86-96 T/A 68 A/C 65 A/C LR_001 64 LR_001 - other S. lyc. GATATCAGATACATTAT 98-114 C/A 60 T/C 57 G/T

  32. C2_At1g50020 S. arcanum C/G ala/gly 49 49 135 135 T/- A/- 159 159 227 227 A/T 255 A/C S. arc. TAAATCT S. lyc. - 276-282 indel 428 428 G/C 451 451 -/T T/C 470 470 A/T 512 512 n = 5 other - n = 30 CTGGTAA 378-384 indel -/G 1096 (S. arcanum missing data) noncoding (no shading) synonymous non-syn, conservative n = 30 non-syn, nonconservative

  33. n = 4 C2_At1g73180 A/C lys/thr 94 94 LR_029 C/T 245 245 C/T 243 243 other - n = 29 AA 200-201 indel other - n = 29 TTA 190 190-192 indel 184 184 A/G 181 181 A/T 180 180 A/G T/C syn 107 107 C/T syn 83 83 G/A 2 2 noncoding (no shading) synonymous non-syn, conservative n = 29 non-syn, nonconservative

  34. S. arcanum C2_At2g15890 35 35 G/A 137 137 C/T T/C 189 189 S. arc. TGTC S. lyc. - 265-268 indel C/A S. arc. AAT S. lyc. - 308 308 S. arc. - S. lyc. GCA 350-352 indel G/T 391 391 T/C 420 420 357-359 indel 458 458 G/A -/T 491 491 529 529 A/G G/A 553 553 715 715 G/C gly/ala LR_024 430 430 A/T noncoding (no shading) T/- 606 synonymous T/G 273 273 non-syn, conservative n = 2 n = 31 non-syn, nonconservative

  35. LR_021 C2_At2g22570 540 540 -/A C/T syn 325 T/C -/A n = 2 -/TA T/A 935 43 43 540 511-512 indel LR029hap2 LR_014 T/A c 935 325 T/C A/C 839 -/A 540 540 LR013hap2 CA/- 307-308 indel TCT/- 302-304 indel 302-304 indel TCT/- 110 T/C 839 307-308 indel G/C 287 -/C 122 A/C AC/- -/C 136 305-306 indel CG/- 221 A/G noncoding (no shading) 275 A/T synonymous non-syn, conservative 280 A/T n = 29 282 A/T non-syn, nonconservative S. arcanum

  36. C2_At2g36930 n = 31 221 221 -/A LR_029 TT/- 234-235 indel LR_024 T/- 233 233 200 200 T/A -/TT 197-198 indel noncoding (no shading) synonymous 178 178 C/T non-syn, conservative non-syn, nonconservative C/T 172 172 S. arcanum

  37. S. arcanum U221402 9 9 T/C T/A syn 97 C/T 208 208 C/T 255 255 284 284 T/C 323-326 indel -/TTTT T/- 336 336 382 382 A/G A/- 395 395 593 593 C/A A/- 327 C/T 482 LR_029 T/C 456 noncoding (no shading) synonymous non-syn, conservative n = 32 non-syn, nonconservative

  38. S. arcanum U318882 584 A/T -/TTTT 435-438 indel 434 C/T C/- 423 404 C/T 326 T/C 287 C/T 285 A/G -/A 230 361 361 A/C A/G n = 3 n = 3 361 G/C T/- noncoding (no shading) 422 422 synonymous non-syn, conservative n = 27 non-syn, nonconservative

  39. U146437 S. arcanum T/C syn 27 27 G/A val/ile 79 79 110 110 A/G 128 128 T/C 131-132 indel -/TA -/T 153 153 G/T 160 160 195 195 A/T 152 -/T 161 161 T/C n = 26 LR_024 noncoding (no shading) C/T syn 162 54 C/T synonymous C/T syn non-syn, conservative 57 174 174 G/A LR_010 LR_028 non-syn, nonconservative T/- 152 152 n = 4

  40. hp2 exon 2 n = 30 G/A val/ile 11 11 n = 2 A/G syn 223 223 A/C glu/asp 163 163 G/A syn noncoding (no shading) 121 121 synonymous non-syn, conservative A/T ile/leu 29 29 non-syn, nonconservative S. arcanum

  41. Pds A/G -/T T/A A/T S. arcanum A/T 14 14 87 87 A/G 177 177 A/T 179 179 227 227 S. arc. TACTTTTT S. lyc. - 324 324 420 423-430 indel noncoding (no shading) synonymous n = 29 non-syn, conservative non-syn, nonconservative T/A 519 519 LR_029

  42. S. arcanum Psy1 S. arc. TATATATATATATATATA S. lyc. - 69-86 microsat A/T 386 A/T 472 472 n = 30 C/T 250 250 noncoding (no shading) C/A 352 352 synonymous non-syn, conservative 464 464 A/T non-syn, nonconservative LR_029

  43. S. arcanum Cyc-B 5' region 436-437 indel -/CT S. arc. CCAAATAT S. lyc. - 434-435 indel TT/- 427 -/A 417 T/- 363 T/G 351 A/G 299 -/T 157 A/C 156 C/A 143 G/A C/T 141 125-132 indel 114 A/G C/T 95 80 A/G T/C 78 G/A 74 noncoding (no shading) T/C 31 synonymous 28 A/G 4 A/C non-syn, conservative non-syn, nonconservative n = 31

  44. S. arcanum hp2 3' region 80 80 T/G 90 90 G/A G/T 95 95 97 97 T/A 158 158 C/A 167 167 T/C G/A syn 199 199 T/A syn 256 256 A/G syn 277 277 346 346 T/G C/T 380 380 400 400 G/A 444 444 C/T C/T 459 459 LR_024 163 163 T/A noncoding (no shading) -/T 84 84 synonymous non-syn, conservative non-syn, nonconservative n = 30

  45. S. arcanum fw 2.2 11 C/T C/T 120 120 T/C 133 133 142 142 G/A G/T 154 154 156 156 T/C 193 193 A/G 216 216 A/G 254 254 T/C 255 255 G/A 278 278 A/C 288 288 A/G G/- 392 392 452 452 C/T -/T 453 453 C/T 90 71 G/A 8 A/T 124 A/G n = 2 130 A/G 154 T/A noncoding (no shading) 468 C/A pro/gln synonymous n = 28 non-syn, conservative non-syn, nonconservative T/- 169 283 G/A n = 4

  46. LR_022 TG11 210 210 C/T n = 22 189 T/G n = 2 245 A/C 136 136 G/A n = 7 517 517 A/C 481 481 C/G T/C 467 467 359 359 A/G 307 307 C/A C/A 301 301 A/G 295 295 T/A 250 250 237 237 T/C T/C 202 202 S. arcanum unknown annotation

  47. CRTISO n = 29 (S. arcanum missing data) 9 C/T 116 116 C/A C/T 27 n = 2 n = 3 (S. arcanum missing data) 27 C/? 27 T/? 430 425 T/C 425 425 G/C 341 341 A/G -/G 339 339 299 299 A/C noncoding (no shading) 237 237 C/A synonymous T/C 65 65 non-syn, conservative 55 55 A/T non-syn, nonconservative A/C 50 50 S. arcanum

  48. S. arcanum rin 65 T/G 70 C/A ATATTAACGTATCAGTGTAACCTCACAAGTAGGATATGAAAAGAGTGATG TACGTATCAGCGTTACCTTTAATTAATTCGTGAAGATAGAAAAGTTGTTT ATATTAACGTATCAGTGTAACCTCACAAGTAGGATATGAAAAGAGCGATG TACGTATCAGCGTTACCTTTAGTTAATTCGTGAAGATAGAAAAGTTATTT 87-286 indel 200 nt insertion in S. arcanum 318 318 A/G 321 321 T/C 333 333 A/G 334 334 A/G 348 348 G/A 352 352 C/T T/C 353 353 358 358 A/G 365 365 T/C 383 383 A/G 393 393 A/G 449 449 G/A C/T 468 468 484 484 A/T n = 7 noncoding (no shading) 336 G/A 519 G/A LR_027 LR_029 synonymous C/T 339 34 T/- (S. arcanum missing data) non-syn, conservative n = 20 n = 4 non-syn, nonconservative C/T 339 T/- 34 n = 3

  49. n = 2 PTOX 147 -/C 148 -/A n = 28 LR_014 154 40 40 G/C G/T A/G syn 286 286 LR024hap2 LR013hap2 199 162 162 A/C T/C T/C syn 241 241 noncoding (no shading) T/C 89 89 synonymous T/A 78 78 non-syn, conservative non-syn, nonconservative 37 37 T/G S. arcanum

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