Multiple sequence alignment - TraesCS4A01G030800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G030800 chr4A 100.000 2618 0 0 1 2618 24105097 24107714 0.000000e+00 4835.0
1 TraesCS4A01G030800 chr4D 91.247 1508 53 21 654 2110 443742707 443741228 0.000000e+00 1980.0
2 TraesCS4A01G030800 chr4D 91.006 467 31 9 2154 2612 443740948 443740485 1.030000e-173 619.0
3 TraesCS4A01G030800 chr4B 93.167 1361 51 13 654 1995 553339218 553337881 0.000000e+00 1960.0
4 TraesCS4A01G030800 chr4B 84.843 607 39 11 2047 2613 553337651 553337058 1.760000e-156 562.0
5 TraesCS4A01G030800 chr4B 90.107 374 34 3 1 373 553339930 553339559 1.410000e-132 483.0
6 TraesCS4A01G030800 chr1D 85.854 205 17 2 406 599 449273669 449273872 9.500000e-50 207.0
7 TraesCS4A01G030800 chr3A 85.294 204 17 4 406 597 48665358 48665560 5.720000e-47 198.0
8 TraesCS4A01G030800 chr3A 77.586 174 21 7 440 598 554082173 554082003 3.590000e-14 89.8
9 TraesCS4A01G030800 chr2B 80.247 243 25 8 377 598 209823929 209824169 7.500000e-36 161.0
10 TraesCS4A01G030800 chr7D 79.757 247 29 10 375 601 27667200 27666955 2.700000e-35 159.0
11 TraesCS4A01G030800 chr5B 80.435 184 20 6 426 598 656929090 656929268 2.740000e-25 126.0
12 TraesCS4A01G030800 chr5D 79.891 184 26 3 426 598 520913084 520913267 9.840000e-25 124.0
13 TraesCS4A01G030800 chr2A 77.366 243 34 13 376 598 150491279 150491038 9.840000e-25 124.0
14 TraesCS4A01G030800 chr1A 89.024 82 9 0 517 598 492802172 492802091 4.610000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G030800 chr4A 24105097 24107714 2617 False 4835.000000 4835 100.000000 1 2618 1 chr4A.!!$F1 2617
1 TraesCS4A01G030800 chr4D 443740485 443742707 2222 True 1299.500000 1980 91.126500 654 2612 2 chr4D.!!$R1 1958
2 TraesCS4A01G030800 chr4B 553337058 553339930 2872 True 1001.666667 1960 89.372333 1 2613 3 chr4B.!!$R1 2612

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
418 420 0.031721 CGTTAGGTGATACCGGCTCC 59.968 60.0 0.0 0.0 44.9 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 2232 0.037975 CAGATGCCCCAACACAAAGC 60.038 55.0 0.0 0.0 0.0 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.852853 GCATACAAAATTATCACTGGTCATCG 59.147 38.462 0.00 0.00 0.00 3.84
41 42 2.880890 GTCATCGGGATTTCATTCCAGG 59.119 50.000 0.00 0.00 37.53 4.45
56 57 3.398694 CAGGACTGGCATGGATCTG 57.601 57.895 0.00 0.00 0.00 2.90
75 76 5.560966 TCTGGAAAACTTGTTGTCAACTC 57.439 39.130 16.45 4.78 0.00 3.01
111 112 9.852091 ATTTTCTTCTGATTGCTTCTTCATAAC 57.148 29.630 0.00 0.00 0.00 1.89
113 114 8.571461 TTCTTCTGATTGCTTCTTCATAACAT 57.429 30.769 0.00 0.00 0.00 2.71
115 116 7.825761 TCTTCTGATTGCTTCTTCATAACATGA 59.174 33.333 0.00 0.00 37.55 3.07
135 136 4.211125 TGAAAAACACAAGACCCATGCTA 58.789 39.130 0.00 0.00 0.00 3.49
138 139 2.479566 ACACAAGACCCATGCTACAG 57.520 50.000 0.00 0.00 0.00 2.74
142 143 2.203070 GACCCATGCTACAGCGGG 60.203 66.667 11.42 11.42 44.28 6.13
166 167 9.408648 GGGAAAACTTCTTCATTCCTGATTATA 57.591 33.333 3.67 0.00 40.90 0.98
172 173 9.606631 ACTTCTTCATTCCTGATTATACTTGTC 57.393 33.333 0.00 0.00 0.00 3.18
189 190 2.627945 TGTCTTTTATGCGGCCTACAG 58.372 47.619 0.00 0.00 0.00 2.74
192 193 1.670811 CTTTTATGCGGCCTACAGGTG 59.329 52.381 0.00 0.00 37.57 4.00
203 204 3.003480 GCCTACAGGTGCTTGAAACTAG 58.997 50.000 0.00 0.00 37.57 2.57
232 234 5.186797 CACCTTTTCCTACATTGCCCATTTA 59.813 40.000 0.00 0.00 0.00 1.40
281 283 1.807814 ACATGGACTCCTACATCCCC 58.192 55.000 0.00 0.00 33.69 4.81
294 296 3.358932 ATCCCCGGGCATCCAACAC 62.359 63.158 17.73 0.00 0.00 3.32
318 320 5.390991 CGAGATCAACAACTTAAAAGCCCTC 60.391 44.000 0.00 0.00 0.00 4.30
322 324 4.959839 TCAACAACTTAAAAGCCCTCCTTT 59.040 37.500 0.00 0.00 45.49 3.11
332 334 1.177401 GCCCTCCTTTGTGTTCCATC 58.823 55.000 0.00 0.00 0.00 3.51
354 356 3.512329 CCTCTCTGGAGATCATCATCCTG 59.488 52.174 0.48 0.00 41.86 3.86
355 357 2.898612 TCTCTGGAGATCATCATCCTGC 59.101 50.000 0.00 0.00 36.50 4.85
376 378 3.960571 CCTTCTTGGGCTATATGGATGG 58.039 50.000 0.00 0.00 0.00 3.51
377 379 3.308688 CCTTCTTGGGCTATATGGATGGG 60.309 52.174 0.00 0.00 0.00 4.00
378 380 3.290039 TCTTGGGCTATATGGATGGGA 57.710 47.619 0.00 0.00 0.00 4.37
381 383 3.290039 TGGGCTATATGGATGGGAAGA 57.710 47.619 0.00 0.00 0.00 2.87
382 384 3.819187 TGGGCTATATGGATGGGAAGAT 58.181 45.455 0.00 0.00 0.00 2.40
384 386 4.971282 TGGGCTATATGGATGGGAAGATAG 59.029 45.833 0.00 0.00 0.00 2.08
385 387 4.202409 GGGCTATATGGATGGGAAGATAGC 60.202 50.000 0.00 0.00 40.55 2.97
387 389 5.454471 GGCTATATGGATGGGAAGATAGCAG 60.454 48.000 12.33 0.00 42.20 4.24
388 390 5.454471 GCTATATGGATGGGAAGATAGCAGG 60.454 48.000 6.78 0.00 40.82 4.85
389 391 2.196742 TGGATGGGAAGATAGCAGGT 57.803 50.000 0.00 0.00 0.00 4.00
390 392 1.770658 TGGATGGGAAGATAGCAGGTG 59.229 52.381 0.00 0.00 0.00 4.00
394 396 4.323104 GGATGGGAAGATAGCAGGTGATAC 60.323 50.000 0.00 0.00 0.00 2.24
395 397 2.972713 TGGGAAGATAGCAGGTGATACC 59.027 50.000 0.00 0.00 38.99 2.73
396 398 2.028930 GGGAAGATAGCAGGTGATACCG 60.029 54.545 0.00 0.00 44.90 4.02
397 399 2.028930 GGAAGATAGCAGGTGATACCGG 60.029 54.545 0.00 0.00 44.90 5.28
398 400 1.633774 AGATAGCAGGTGATACCGGG 58.366 55.000 6.32 0.00 44.90 5.73
399 401 0.037232 GATAGCAGGTGATACCGGGC 60.037 60.000 6.32 8.88 44.90 6.13
400 402 1.816863 ATAGCAGGTGATACCGGGCG 61.817 60.000 6.32 0.00 44.90 6.13
401 403 4.157120 GCAGGTGATACCGGGCGT 62.157 66.667 6.32 0.00 44.90 5.68
402 404 2.582436 CAGGTGATACCGGGCGTT 59.418 61.111 6.32 0.00 44.90 4.84
403 405 1.817881 CAGGTGATACCGGGCGTTA 59.182 57.895 6.32 0.00 44.90 3.18
404 406 0.249322 CAGGTGATACCGGGCGTTAG 60.249 60.000 6.32 0.00 44.90 2.34
405 407 1.068585 GGTGATACCGGGCGTTAGG 59.931 63.158 6.32 0.00 0.00 2.69
407 409 0.529119 GTGATACCGGGCGTTAGGTG 60.529 60.000 6.32 0.00 41.51 4.00
408 410 0.683828 TGATACCGGGCGTTAGGTGA 60.684 55.000 6.32 0.00 41.51 4.02
409 411 0.677842 GATACCGGGCGTTAGGTGAT 59.322 55.000 6.32 0.00 41.51 3.06
410 412 1.888512 GATACCGGGCGTTAGGTGATA 59.111 52.381 6.32 0.00 41.51 2.15
412 414 1.068585 CCGGGCGTTAGGTGATACC 59.931 63.158 0.00 0.00 38.99 2.73
413 415 1.299620 CGGGCGTTAGGTGATACCG 60.300 63.158 0.00 0.00 44.90 4.02
414 416 1.068585 GGGCGTTAGGTGATACCGG 59.931 63.158 0.00 0.00 44.90 5.28
415 417 1.593479 GGCGTTAGGTGATACCGGC 60.593 63.158 0.00 0.00 44.90 6.13
416 418 1.440476 GCGTTAGGTGATACCGGCT 59.560 57.895 0.00 0.00 44.90 5.52
417 419 0.596859 GCGTTAGGTGATACCGGCTC 60.597 60.000 0.00 0.00 44.90 4.70
418 420 0.031721 CGTTAGGTGATACCGGCTCC 59.968 60.000 0.00 0.00 44.90 4.70
419 421 0.391966 GTTAGGTGATACCGGCTCCC 59.608 60.000 0.00 2.77 44.90 4.30
420 422 1.111116 TTAGGTGATACCGGCTCCCG 61.111 60.000 0.00 0.00 44.90 5.14
431 433 3.200522 GCTCCCGAAAGCCATTGG 58.799 61.111 0.00 0.00 36.22 3.16
432 434 1.378514 GCTCCCGAAAGCCATTGGA 60.379 57.895 6.95 0.00 36.22 3.53
433 435 0.753111 GCTCCCGAAAGCCATTGGAT 60.753 55.000 6.95 0.00 36.22 3.41
434 436 1.312815 CTCCCGAAAGCCATTGGATC 58.687 55.000 6.95 0.24 0.00 3.36
435 437 0.918983 TCCCGAAAGCCATTGGATCT 59.081 50.000 6.95 0.00 0.00 2.75
436 438 1.134098 TCCCGAAAGCCATTGGATCTC 60.134 52.381 6.95 0.00 0.00 2.75
437 439 1.133976 CCCGAAAGCCATTGGATCTCT 60.134 52.381 6.95 0.00 0.00 3.10
438 440 1.945394 CCGAAAGCCATTGGATCTCTG 59.055 52.381 6.95 0.00 0.00 3.35
439 441 2.420547 CCGAAAGCCATTGGATCTCTGA 60.421 50.000 6.95 0.00 0.00 3.27
440 442 3.474600 CGAAAGCCATTGGATCTCTGAT 58.525 45.455 6.95 0.00 0.00 2.90
441 443 3.497640 CGAAAGCCATTGGATCTCTGATC 59.502 47.826 6.95 0.00 0.00 2.92
442 444 3.505480 AAGCCATTGGATCTCTGATCC 57.495 47.619 17.12 17.12 38.66 3.36
443 445 2.415624 AGCCATTGGATCTCTGATCCA 58.584 47.619 21.32 21.32 45.71 3.41
448 450 2.945080 TGGATCTCTGATCCAATGGC 57.055 50.000 22.49 0.83 44.54 4.40
449 451 2.415624 TGGATCTCTGATCCAATGGCT 58.584 47.619 22.49 0.00 44.54 4.75
450 452 2.371179 TGGATCTCTGATCCAATGGCTC 59.629 50.000 22.49 0.00 44.54 4.70
451 453 2.290197 GGATCTCTGATCCAATGGCTCC 60.290 54.545 18.57 0.00 38.09 4.70
452 454 1.135094 TCTCTGATCCAATGGCTCCC 58.865 55.000 0.18 0.00 0.00 4.30
453 455 0.250209 CTCTGATCCAATGGCTCCCG 60.250 60.000 0.18 0.00 0.00 5.14
454 456 1.228063 CTGATCCAATGGCTCCCGG 60.228 63.158 0.18 0.00 0.00 5.73
455 457 2.113986 GATCCAATGGCTCCCGGG 59.886 66.667 16.85 16.85 0.00 5.73
456 458 2.368192 ATCCAATGGCTCCCGGGA 60.368 61.111 25.06 25.06 0.00 5.14
457 459 2.403132 GATCCAATGGCTCCCGGGAG 62.403 65.000 41.29 41.29 44.56 4.30
465 467 3.713650 CTCCCGGGAGCTCTTGAA 58.286 61.111 36.90 4.87 35.31 2.69
466 468 1.219393 CTCCCGGGAGCTCTTGAAC 59.781 63.158 36.90 0.00 35.31 3.18
467 469 1.535444 TCCCGGGAGCTCTTGAACA 60.535 57.895 22.63 0.00 0.00 3.18
468 470 0.909610 TCCCGGGAGCTCTTGAACAT 60.910 55.000 22.63 0.00 0.00 2.71
469 471 0.035056 CCCGGGAGCTCTTGAACATT 60.035 55.000 18.48 0.00 0.00 2.71
470 472 1.614317 CCCGGGAGCTCTTGAACATTT 60.614 52.381 18.48 0.00 0.00 2.32
471 473 2.162681 CCGGGAGCTCTTGAACATTTT 58.837 47.619 14.64 0.00 0.00 1.82
472 474 2.095059 CCGGGAGCTCTTGAACATTTTG 60.095 50.000 14.64 0.00 0.00 2.44
473 475 2.669391 CGGGAGCTCTTGAACATTTTGC 60.669 50.000 14.64 0.00 0.00 3.68
474 476 2.297033 GGGAGCTCTTGAACATTTTGCA 59.703 45.455 14.64 0.00 0.00 4.08
475 477 3.243839 GGGAGCTCTTGAACATTTTGCAA 60.244 43.478 14.64 0.00 0.00 4.08
476 478 4.370917 GGAGCTCTTGAACATTTTGCAAA 58.629 39.130 14.64 8.05 0.00 3.68
477 479 4.810491 GGAGCTCTTGAACATTTTGCAAAA 59.190 37.500 25.76 25.76 0.00 2.44
478 480 5.294060 GGAGCTCTTGAACATTTTGCAAAAA 59.706 36.000 27.10 8.85 0.00 1.94
479 481 6.017687 GGAGCTCTTGAACATTTTGCAAAAAT 60.018 34.615 27.10 16.12 0.00 1.82
480 482 6.721321 AGCTCTTGAACATTTTGCAAAAATG 58.279 32.000 27.10 24.03 41.91 2.32
482 484 6.630045 GCTCTTGAACATTTTGCAAAAATGTC 59.370 34.615 27.10 21.76 46.62 3.06
483 485 7.606858 TCTTGAACATTTTGCAAAAATGTCA 57.393 28.000 27.10 23.69 46.62 3.58
484 486 8.211116 TCTTGAACATTTTGCAAAAATGTCAT 57.789 26.923 27.10 16.40 46.62 3.06
485 487 8.336806 TCTTGAACATTTTGCAAAAATGTCATC 58.663 29.630 27.10 22.00 46.62 2.92
486 488 6.957150 TGAACATTTTGCAAAAATGTCATCC 58.043 32.000 27.10 18.18 46.62 3.51
487 489 5.594724 ACATTTTGCAAAAATGTCATCCG 57.405 34.783 27.10 10.29 44.83 4.18
488 490 5.295950 ACATTTTGCAAAAATGTCATCCGA 58.704 33.333 27.10 1.37 44.83 4.55
489 491 5.757320 ACATTTTGCAAAAATGTCATCCGAA 59.243 32.000 27.10 1.16 44.83 4.30
490 492 6.259608 ACATTTTGCAAAAATGTCATCCGAAA 59.740 30.769 27.10 0.70 44.83 3.46
491 493 5.903764 TTTGCAAAAATGTCATCCGAAAG 57.096 34.783 10.02 0.00 0.00 2.62
492 494 4.582701 TGCAAAAATGTCATCCGAAAGT 57.417 36.364 0.00 0.00 0.00 2.66
493 495 4.545610 TGCAAAAATGTCATCCGAAAGTC 58.454 39.130 0.00 0.00 0.00 3.01
494 496 4.278170 TGCAAAAATGTCATCCGAAAGTCT 59.722 37.500 0.00 0.00 0.00 3.24
495 497 5.221224 TGCAAAAATGTCATCCGAAAGTCTT 60.221 36.000 0.00 0.00 0.00 3.01
496 498 5.343325 GCAAAAATGTCATCCGAAAGTCTTC 59.657 40.000 0.00 0.00 0.00 2.87
497 499 6.437928 CAAAAATGTCATCCGAAAGTCTTCA 58.562 36.000 0.00 0.00 0.00 3.02
498 500 6.633500 AAAATGTCATCCGAAAGTCTTCAA 57.367 33.333 0.00 0.00 0.00 2.69
499 501 6.633500 AAATGTCATCCGAAAGTCTTCAAA 57.367 33.333 0.00 0.00 0.00 2.69
500 502 6.824305 AATGTCATCCGAAAGTCTTCAAAT 57.176 33.333 0.00 0.00 0.00 2.32
501 503 6.824305 ATGTCATCCGAAAGTCTTCAAATT 57.176 33.333 0.00 0.00 0.00 1.82
502 504 6.633500 TGTCATCCGAAAGTCTTCAAATTT 57.367 33.333 0.00 0.00 0.00 1.82
503 505 6.668323 TGTCATCCGAAAGTCTTCAAATTTC 58.332 36.000 0.00 0.00 0.00 2.17
504 506 6.262049 TGTCATCCGAAAGTCTTCAAATTTCA 59.738 34.615 0.00 0.00 33.50 2.69
505 507 6.578919 GTCATCCGAAAGTCTTCAAATTTCAC 59.421 38.462 0.00 0.00 33.50 3.18
506 508 6.262049 TCATCCGAAAGTCTTCAAATTTCACA 59.738 34.615 0.00 0.00 33.50 3.58
507 509 6.060028 TCCGAAAGTCTTCAAATTTCACAG 57.940 37.500 0.00 0.00 33.50 3.66
508 510 5.820423 TCCGAAAGTCTTCAAATTTCACAGA 59.180 36.000 0.00 0.00 33.50 3.41
509 511 6.486657 TCCGAAAGTCTTCAAATTTCACAGAT 59.513 34.615 0.00 0.00 33.50 2.90
510 512 7.013274 TCCGAAAGTCTTCAAATTTCACAGATT 59.987 33.333 0.00 0.00 33.50 2.40
511 513 7.649306 CCGAAAGTCTTCAAATTTCACAGATTT 59.351 33.333 0.00 0.00 33.50 2.17
512 514 8.685536 CGAAAGTCTTCAAATTTCACAGATTTC 58.314 33.333 0.00 3.02 33.50 2.17
513 515 9.520204 GAAAGTCTTCAAATTTCACAGATTTCA 57.480 29.630 0.00 0.00 33.97 2.69
514 516 9.874205 AAAGTCTTCAAATTTCACAGATTTCAA 57.126 25.926 0.00 0.00 0.00 2.69
515 517 9.874205 AAGTCTTCAAATTTCACAGATTTCAAA 57.126 25.926 0.00 0.00 0.00 2.69
516 518 9.525409 AGTCTTCAAATTTCACAGATTTCAAAG 57.475 29.630 0.00 0.00 0.00 2.77
517 519 9.520204 GTCTTCAAATTTCACAGATTTCAAAGA 57.480 29.630 0.00 0.00 30.59 2.52
518 520 9.740239 TCTTCAAATTTCACAGATTTCAAAGAG 57.260 29.630 0.00 0.00 30.15 2.85
519 521 7.935338 TCAAATTTCACAGATTTCAAAGAGC 57.065 32.000 0.00 0.00 0.00 4.09
520 522 6.925165 TCAAATTTCACAGATTTCAAAGAGCC 59.075 34.615 0.00 0.00 0.00 4.70
521 523 4.488126 TTTCACAGATTTCAAAGAGCCG 57.512 40.909 0.00 0.00 0.00 5.52
522 524 3.126001 TCACAGATTTCAAAGAGCCGT 57.874 42.857 0.00 0.00 0.00 5.68
523 525 3.067106 TCACAGATTTCAAAGAGCCGTC 58.933 45.455 0.00 0.00 0.00 4.79
524 526 2.069273 ACAGATTTCAAAGAGCCGTCG 58.931 47.619 0.00 0.00 0.00 5.12
525 527 1.394917 CAGATTTCAAAGAGCCGTCGG 59.605 52.381 6.99 6.99 0.00 4.79
526 528 1.275291 AGATTTCAAAGAGCCGTCGGA 59.725 47.619 17.49 0.00 0.00 4.55
527 529 2.093447 AGATTTCAAAGAGCCGTCGGAT 60.093 45.455 17.49 9.33 0.00 4.18
528 530 1.722011 TTTCAAAGAGCCGTCGGATC 58.278 50.000 21.82 21.82 38.56 3.36
536 538 2.405172 GAGCCGTCGGATCTTAAATCC 58.595 52.381 22.03 0.00 34.95 3.01
537 539 1.760613 AGCCGTCGGATCTTAAATCCA 59.239 47.619 17.49 3.07 38.08 3.41
538 540 2.169769 AGCCGTCGGATCTTAAATCCAA 59.830 45.455 17.49 0.00 38.08 3.53
539 541 2.287103 GCCGTCGGATCTTAAATCCAAC 59.713 50.000 17.49 7.26 38.08 3.77
540 542 2.538449 CCGTCGGATCTTAAATCCAACG 59.462 50.000 4.91 16.62 45.35 4.10
541 543 3.184541 CGTCGGATCTTAAATCCAACGT 58.815 45.455 15.88 0.00 42.02 3.99
542 544 3.242248 CGTCGGATCTTAAATCCAACGTC 59.758 47.826 15.88 3.86 42.02 4.34
543 545 4.430908 GTCGGATCTTAAATCCAACGTCT 58.569 43.478 13.60 0.00 38.08 4.18
544 546 4.503370 GTCGGATCTTAAATCCAACGTCTC 59.497 45.833 13.60 0.00 38.08 3.36
545 547 4.158949 TCGGATCTTAAATCCAACGTCTCA 59.841 41.667 13.60 0.00 38.08 3.27
546 548 4.504461 CGGATCTTAAATCCAACGTCTCAG 59.496 45.833 13.60 0.00 38.08 3.35
547 549 5.661458 GGATCTTAAATCCAACGTCTCAGA 58.339 41.667 10.18 0.00 38.09 3.27
548 550 6.106673 GGATCTTAAATCCAACGTCTCAGAA 58.893 40.000 10.18 0.00 38.09 3.02
549 551 6.256757 GGATCTTAAATCCAACGTCTCAGAAG 59.743 42.308 10.18 0.00 38.09 2.85
550 552 4.929808 TCTTAAATCCAACGTCTCAGAAGC 59.070 41.667 0.00 0.00 0.00 3.86
551 553 2.100605 AATCCAACGTCTCAGAAGCC 57.899 50.000 0.00 0.00 0.00 4.35
552 554 0.250513 ATCCAACGTCTCAGAAGCCC 59.749 55.000 0.00 0.00 0.00 5.19
553 555 1.738099 CCAACGTCTCAGAAGCCCG 60.738 63.158 0.00 0.00 0.00 6.13
554 556 1.006102 CAACGTCTCAGAAGCCCGT 60.006 57.895 0.00 0.00 33.18 5.28
555 557 0.242825 CAACGTCTCAGAAGCCCGTA 59.757 55.000 0.00 0.00 32.06 4.02
556 558 1.135083 CAACGTCTCAGAAGCCCGTAT 60.135 52.381 0.00 0.00 32.06 3.06
557 559 0.739561 ACGTCTCAGAAGCCCGTATC 59.260 55.000 0.00 0.00 31.04 2.24
558 560 0.738975 CGTCTCAGAAGCCCGTATCA 59.261 55.000 0.00 0.00 0.00 2.15
559 561 1.534175 CGTCTCAGAAGCCCGTATCAC 60.534 57.143 0.00 0.00 0.00 3.06
560 562 0.738975 TCTCAGAAGCCCGTATCACG 59.261 55.000 0.00 0.00 42.11 4.35
575 577 4.852104 CGTATCACGGTATCATCTAAGTGC 59.148 45.833 0.00 0.00 38.08 4.40
576 578 5.334957 CGTATCACGGTATCATCTAAGTGCT 60.335 44.000 0.00 0.00 38.08 4.40
577 579 4.307443 TCACGGTATCATCTAAGTGCTG 57.693 45.455 0.00 0.00 0.00 4.41
578 580 3.068165 TCACGGTATCATCTAAGTGCTGG 59.932 47.826 0.00 0.00 0.00 4.85
579 581 3.031736 ACGGTATCATCTAAGTGCTGGT 58.968 45.455 0.00 0.00 0.00 4.00
580 582 4.037565 CACGGTATCATCTAAGTGCTGGTA 59.962 45.833 0.00 0.00 0.00 3.25
581 583 4.278669 ACGGTATCATCTAAGTGCTGGTAG 59.721 45.833 0.00 0.00 0.00 3.18
582 584 4.561105 GGTATCATCTAAGTGCTGGTAGC 58.439 47.826 0.00 0.00 42.82 3.58
596 598 5.175090 GCTGGTAGCACTTGATATTTTCC 57.825 43.478 0.00 0.00 41.89 3.13
605 607 8.870075 AGCACTTGATATTTTCCCCTATATTC 57.130 34.615 0.00 0.00 0.00 1.75
637 642 5.767168 AGGATATTTAAAGAGATGCACTGGC 59.233 40.000 0.00 0.00 41.68 4.85
639 644 6.072783 GGATATTTAAAGAGATGCACTGGCTC 60.073 42.308 0.00 0.00 41.91 4.70
645 650 0.829333 AGATGCACTGGCTCACCTAG 59.171 55.000 0.00 0.00 41.91 3.02
705 949 1.300233 GGAAGCCGCATCTACTCCG 60.300 63.158 0.00 0.00 0.00 4.63
730 974 3.118298 TGTTAATTAGGCCGGGGAGTAAC 60.118 47.826 2.18 5.68 0.00 2.50
799 1045 4.154195 GCACTGAACTCAATACGTCCAATT 59.846 41.667 0.00 0.00 0.00 2.32
848 1094 2.029844 GGCGCCACTCACTTCACTC 61.030 63.158 24.80 0.00 0.00 3.51
890 1136 2.512515 GCATCCACCACGCTCTCC 60.513 66.667 0.00 0.00 0.00 3.71
934 1180 2.284921 CCCCACTCTCTCCAGCCA 60.285 66.667 0.00 0.00 0.00 4.75
957 1208 2.727544 GCTAGAGAGCGAGCCCAG 59.272 66.667 0.00 0.00 39.39 4.45
1148 1408 2.510238 CTCCGCCCGCTTCAAGAG 60.510 66.667 0.00 0.00 0.00 2.85
1606 1866 4.700365 CCGACGACGAGCAGCACA 62.700 66.667 9.28 0.00 42.66 4.57
1678 1938 3.994392 GAGCTCAACACTTTCGTCCATTA 59.006 43.478 9.40 0.00 0.00 1.90
1679 1939 4.579869 AGCTCAACACTTTCGTCCATTAT 58.420 39.130 0.00 0.00 0.00 1.28
1681 1941 5.473504 AGCTCAACACTTTCGTCCATTATTT 59.526 36.000 0.00 0.00 0.00 1.40
1682 1942 5.795441 GCTCAACACTTTCGTCCATTATTTC 59.205 40.000 0.00 0.00 0.00 2.17
1684 1944 7.129109 TCAACACTTTCGTCCATTATTTCTC 57.871 36.000 0.00 0.00 0.00 2.87
1685 1945 6.708502 TCAACACTTTCGTCCATTATTTCTCA 59.291 34.615 0.00 0.00 0.00 3.27
1686 1946 7.390440 TCAACACTTTCGTCCATTATTTCTCAT 59.610 33.333 0.00 0.00 0.00 2.90
1687 1947 8.664798 CAACACTTTCGTCCATTATTTCTCATA 58.335 33.333 0.00 0.00 0.00 2.15
1766 2027 6.732531 TGCATCTGATCTGACTGTAAAAAG 57.267 37.500 4.21 0.00 0.00 2.27
1792 2053 2.050533 GTGTGCAATTTCGCGGCA 60.051 55.556 6.13 4.18 34.70 5.69
1793 2054 1.659954 GTGTGCAATTTCGCGGCAA 60.660 52.632 6.13 0.00 39.57 4.52
1794 2055 1.066422 TGTGCAATTTCGCGGCAAA 59.934 47.368 6.13 0.00 39.57 3.68
1827 2088 0.820074 TACCTTTGTGTGGGCGTTGG 60.820 55.000 0.00 0.00 0.00 3.77
1828 2089 2.027460 CTTTGTGTGGGCGTTGGC 59.973 61.111 0.00 0.00 38.90 4.52
1829 2090 2.441164 TTTGTGTGGGCGTTGGCT 60.441 55.556 0.00 0.00 39.81 4.75
1830 2091 2.682256 CTTTGTGTGGGCGTTGGCTG 62.682 60.000 0.00 0.00 39.81 4.85
1890 2151 3.579151 AGACGGGGAATATCTTAGCTTCC 59.421 47.826 0.00 0.00 38.16 3.46
1937 2198 5.641709 TGTGTAATTGCGTTTGTCTTTTCA 58.358 33.333 0.00 0.00 0.00 2.69
1957 2218 4.697756 CACCTCCCCGCGCTTTCA 62.698 66.667 5.56 0.00 0.00 2.69
1964 2232 1.644786 CCCCGCGCTTTCACCTTTAG 61.645 60.000 5.56 0.00 0.00 1.85
1969 2237 2.319472 GCGCTTTCACCTTTAGCTTTG 58.681 47.619 0.00 0.00 32.80 2.77
2029 2322 1.458398 TGGTTATGCCGTGACCATTG 58.542 50.000 0.00 0.00 41.19 2.82
2038 2493 1.136085 CCGTGACCATTGCTTTGTACG 60.136 52.381 0.00 0.00 0.00 3.67
2039 2494 1.529438 CGTGACCATTGCTTTGTACGT 59.471 47.619 0.00 0.00 0.00 3.57
2040 2495 2.732500 CGTGACCATTGCTTTGTACGTA 59.267 45.455 0.00 0.00 0.00 3.57
2041 2496 3.181534 CGTGACCATTGCTTTGTACGTAG 60.182 47.826 0.00 0.00 0.00 3.51
2042 2497 3.991773 GTGACCATTGCTTTGTACGTAGA 59.008 43.478 0.00 0.00 0.00 2.59
2043 2498 3.991773 TGACCATTGCTTTGTACGTAGAC 59.008 43.478 0.00 0.00 0.00 2.59
2044 2499 3.991773 GACCATTGCTTTGTACGTAGACA 59.008 43.478 0.00 0.00 0.00 3.41
2045 2500 3.744426 ACCATTGCTTTGTACGTAGACAC 59.256 43.478 0.00 0.00 0.00 3.67
2061 2516 6.908588 CGTAGACACGTAGTAAATGTGAATG 58.091 40.000 4.46 0.00 46.40 2.67
2110 2566 2.031683 CGAGTAATTTTGGGATCGCCAC 59.968 50.000 7.38 0.00 35.15 5.01
2111 2567 3.013921 GAGTAATTTTGGGATCGCCACA 58.986 45.455 7.38 0.00 35.15 4.17
2132 2603 2.492090 CTTGAGACGGGCGAGAGG 59.508 66.667 0.00 0.00 0.00 3.69
2159 2851 1.880340 GTCTTCGGATCCAGCAGCG 60.880 63.158 13.41 0.00 0.00 5.18
2249 2964 1.079127 ACACATGGCCGCTGTACTC 60.079 57.895 10.19 0.00 0.00 2.59
2275 2995 4.418993 CGTCGACGGATAGATCGC 57.581 61.111 29.70 0.00 38.24 4.58
2316 3036 0.171007 CCATCACGCGCCAATCTTTT 59.829 50.000 5.73 0.00 0.00 2.27
2323 3043 1.466360 CGCGCCAATCTTTTTCCTCTG 60.466 52.381 0.00 0.00 0.00 3.35
2336 3056 1.095600 TCCTCTGGTTCGAGATCACG 58.904 55.000 6.17 6.17 32.74 4.35
2356 3076 2.022520 GGCCGGCCGAAATTAAGAG 58.977 57.895 33.60 7.40 0.00 2.85
2366 3086 5.180304 GGCCGAAATTAAGAGGATTGAGATC 59.820 44.000 0.00 0.00 0.00 2.75
2378 3102 4.465660 AGGATTGAGATCTATCATGGACCG 59.534 45.833 0.00 0.00 32.66 4.79
2379 3103 4.221703 GGATTGAGATCTATCATGGACCGT 59.778 45.833 0.00 0.00 32.66 4.83
2380 3104 4.855715 TTGAGATCTATCATGGACCGTC 57.144 45.455 0.00 0.00 0.00 4.79
2381 3105 4.105754 TGAGATCTATCATGGACCGTCT 57.894 45.455 0.00 0.00 0.00 4.18
2406 3130 4.332543 TCTCCCCCGTGCCTTCCT 62.333 66.667 0.00 0.00 0.00 3.36
2407 3131 3.787001 CTCCCCCGTGCCTTCCTC 61.787 72.222 0.00 0.00 0.00 3.71
2436 3160 4.759096 CAAAAAGAGCCGGCCGCG 62.759 66.667 26.15 14.87 44.76 6.46
2534 3258 3.127533 GATCGTGGCCGCTTTGCT 61.128 61.111 15.69 0.00 0.00 3.91
2573 3297 1.444895 GACGCAGGCAGGCAAAATG 60.445 57.895 0.00 0.00 0.00 2.32
2584 3308 0.388659 GGCAAAATGTGTGTGCTCCA 59.611 50.000 0.00 0.00 38.36 3.86
2613 3337 0.108186 TGCGTGATTACCCTGCTGAG 60.108 55.000 0.00 0.00 0.00 3.35
2614 3338 0.108138 GCGTGATTACCCTGCTGAGT 60.108 55.000 0.00 0.00 0.00 3.41
2615 3339 1.645034 CGTGATTACCCTGCTGAGTG 58.355 55.000 0.00 0.00 0.00 3.51
2616 3340 1.373570 GTGATTACCCTGCTGAGTGC 58.626 55.000 0.00 0.00 43.25 4.40
2617 3341 1.065854 GTGATTACCCTGCTGAGTGCT 60.066 52.381 0.00 0.00 43.37 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.771114 TCCCGATGACCAGTGATAATTT 57.229 40.909 0.00 0.00 0.00 1.82
12 13 3.709141 TGAAATCCCGATGACCAGTGATA 59.291 43.478 0.00 0.00 0.00 2.15
13 14 2.505407 TGAAATCCCGATGACCAGTGAT 59.495 45.455 0.00 0.00 0.00 3.06
41 42 2.424956 GTTTTCCAGATCCATGCCAGTC 59.575 50.000 0.00 0.00 0.00 3.51
56 57 6.308041 GTCTTTGAGTTGACAACAAGTTTTCC 59.692 38.462 20.08 0.00 39.43 3.13
75 76 7.866393 AGCAATCAGAAGAAAATCTTGTCTTTG 59.134 33.333 0.00 1.94 36.73 2.77
111 112 3.742369 GCATGGGTCTTGTGTTTTTCATG 59.258 43.478 0.00 0.00 35.30 3.07
113 114 3.030291 AGCATGGGTCTTGTGTTTTTCA 58.970 40.909 0.00 0.00 0.00 2.69
115 116 3.957497 TGTAGCATGGGTCTTGTGTTTTT 59.043 39.130 0.00 0.00 0.00 1.94
117 118 3.149196 CTGTAGCATGGGTCTTGTGTTT 58.851 45.455 0.00 0.00 0.00 2.83
119 120 1.611673 GCTGTAGCATGGGTCTTGTGT 60.612 52.381 0.00 0.00 41.59 3.72
120 121 1.089920 GCTGTAGCATGGGTCTTGTG 58.910 55.000 0.00 0.00 41.59 3.33
122 123 1.091771 CCGCTGTAGCATGGGTCTTG 61.092 60.000 4.59 0.00 42.21 3.02
127 128 0.679640 TTTTCCCGCTGTAGCATGGG 60.680 55.000 9.75 9.75 41.36 4.00
135 136 2.341846 TGAAGAAGTTTTCCCGCTGT 57.658 45.000 0.00 0.00 0.00 4.40
138 139 2.820197 AGGAATGAAGAAGTTTTCCCGC 59.180 45.455 0.52 0.00 38.73 6.13
166 167 2.200373 AGGCCGCATAAAAGACAAGT 57.800 45.000 0.00 0.00 0.00 3.16
172 173 1.670811 CACCTGTAGGCCGCATAAAAG 59.329 52.381 0.00 0.00 39.32 2.27
180 181 0.605319 TTTCAAGCACCTGTAGGCCG 60.605 55.000 0.00 0.00 39.32 6.13
189 190 3.010420 GTGATCCCTAGTTTCAAGCACC 58.990 50.000 0.00 0.00 0.00 5.01
192 193 3.636153 AGGTGATCCCTAGTTTCAAGC 57.364 47.619 1.23 0.00 43.87 4.01
203 204 3.381590 GCAATGTAGGAAAAGGTGATCCC 59.618 47.826 0.00 0.00 36.31 3.85
232 234 8.646900 ACATAAATAAGTCCAACAACATTTGGT 58.353 29.630 1.94 0.00 45.60 3.67
265 267 1.075525 CCGGGGATGTAGGAGTCCA 60.076 63.158 12.86 0.00 36.19 4.02
268 270 2.446036 GCCCGGGGATGTAGGAGT 60.446 66.667 25.28 0.00 0.00 3.85
281 283 1.153369 ATCTCGTGTTGGATGCCCG 60.153 57.895 0.00 0.00 34.29 6.13
294 296 4.455877 AGGGCTTTTAAGTTGTTGATCTCG 59.544 41.667 0.00 0.00 0.00 4.04
318 320 6.090253 TCCAGAGAGGATGGAACACAAAGG 62.090 50.000 0.00 0.00 43.87 3.11
322 324 2.325661 TCCAGAGAGGATGGAACACA 57.674 50.000 0.00 0.00 43.87 3.72
332 334 3.512329 CAGGATGATGATCTCCAGAGAGG 59.488 52.174 11.65 0.00 38.80 3.69
355 357 3.308688 CCCATCCATATAGCCCAAGAAGG 60.309 52.174 0.00 0.00 37.03 3.46
373 375 3.584848 GGTATCACCTGCTATCTTCCCAT 59.415 47.826 0.00 0.00 34.73 4.00
375 377 2.028930 CGGTATCACCTGCTATCTTCCC 60.029 54.545 0.00 0.00 35.66 3.97
376 378 2.028930 CCGGTATCACCTGCTATCTTCC 60.029 54.545 0.00 0.00 35.66 3.46
377 379 2.028930 CCCGGTATCACCTGCTATCTTC 60.029 54.545 0.00 0.00 35.66 2.87
378 380 1.971357 CCCGGTATCACCTGCTATCTT 59.029 52.381 0.00 0.00 35.66 2.40
381 383 1.816863 CGCCCGGTATCACCTGCTAT 61.817 60.000 0.00 0.00 35.66 2.97
382 384 2.495409 CGCCCGGTATCACCTGCTA 61.495 63.158 0.00 0.00 35.66 3.49
384 386 2.300850 TAACGCCCGGTATCACCTGC 62.301 60.000 0.00 0.00 35.66 4.85
385 387 0.249322 CTAACGCCCGGTATCACCTG 60.249 60.000 0.00 0.00 35.66 4.00
387 389 1.068585 CCTAACGCCCGGTATCACC 59.931 63.158 0.00 0.00 34.05 4.02
388 390 0.529119 CACCTAACGCCCGGTATCAC 60.529 60.000 0.00 0.00 30.91 3.06
389 391 0.683828 TCACCTAACGCCCGGTATCA 60.684 55.000 0.00 0.00 30.91 2.15
390 392 0.677842 ATCACCTAACGCCCGGTATC 59.322 55.000 0.00 0.00 30.91 2.24
394 396 1.068585 GGTATCACCTAACGCCCGG 59.931 63.158 0.00 0.00 34.73 5.73
395 397 1.299620 CGGTATCACCTAACGCCCG 60.300 63.158 0.00 0.00 35.66 6.13
396 398 1.068585 CCGGTATCACCTAACGCCC 59.931 63.158 0.00 0.00 39.28 6.13
397 399 1.593479 GCCGGTATCACCTAACGCC 60.593 63.158 1.90 0.00 39.28 5.68
398 400 0.596859 GAGCCGGTATCACCTAACGC 60.597 60.000 1.90 0.00 39.28 4.84
399 401 0.031721 GGAGCCGGTATCACCTAACG 59.968 60.000 1.90 0.00 40.34 3.18
400 402 0.391966 GGGAGCCGGTATCACCTAAC 59.608 60.000 1.90 0.00 35.66 2.34
401 403 1.111116 CGGGAGCCGGTATCACCTAA 61.111 60.000 1.90 0.00 44.15 2.69
402 404 1.529948 CGGGAGCCGGTATCACCTA 60.530 63.158 1.90 0.00 44.15 3.08
403 405 2.838225 CGGGAGCCGGTATCACCT 60.838 66.667 1.90 0.00 44.15 4.00
414 416 0.753111 ATCCAATGGCTTTCGGGAGC 60.753 55.000 0.00 2.79 41.96 4.70
415 417 1.133976 AGATCCAATGGCTTTCGGGAG 60.134 52.381 0.00 0.00 0.00 4.30
416 418 0.918983 AGATCCAATGGCTTTCGGGA 59.081 50.000 0.00 0.00 0.00 5.14
417 419 1.133976 AGAGATCCAATGGCTTTCGGG 60.134 52.381 0.00 0.00 0.00 5.14
418 420 1.945394 CAGAGATCCAATGGCTTTCGG 59.055 52.381 0.00 0.00 0.00 4.30
419 421 2.910199 TCAGAGATCCAATGGCTTTCG 58.090 47.619 0.00 0.00 0.00 3.46
420 422 3.819902 GGATCAGAGATCCAATGGCTTTC 59.180 47.826 18.63 0.00 38.09 2.62
421 423 3.203710 TGGATCAGAGATCCAATGGCTTT 59.796 43.478 22.72 0.00 44.54 3.51
422 424 2.781757 TGGATCAGAGATCCAATGGCTT 59.218 45.455 22.72 0.00 44.54 4.35
423 425 2.415624 TGGATCAGAGATCCAATGGCT 58.584 47.619 22.72 0.00 44.54 4.75
424 426 2.945080 TGGATCAGAGATCCAATGGC 57.055 50.000 22.72 0.09 44.54 4.40
429 431 2.371179 GAGCCATTGGATCAGAGATCCA 59.629 50.000 21.50 21.50 45.71 3.41
430 432 2.290197 GGAGCCATTGGATCAGAGATCC 60.290 54.545 21.72 17.12 40.28 3.36
431 433 2.290197 GGGAGCCATTGGATCAGAGATC 60.290 54.545 21.72 3.91 40.28 2.75
432 434 1.704070 GGGAGCCATTGGATCAGAGAT 59.296 52.381 21.72 0.00 40.28 2.75
433 435 1.135094 GGGAGCCATTGGATCAGAGA 58.865 55.000 21.72 0.00 40.28 3.10
434 436 0.250209 CGGGAGCCATTGGATCAGAG 60.250 60.000 21.72 8.87 40.28 3.35
435 437 1.699054 CCGGGAGCCATTGGATCAGA 61.699 60.000 21.72 0.00 40.28 3.27
436 438 1.228063 CCGGGAGCCATTGGATCAG 60.228 63.158 21.72 14.44 40.28 2.90
437 439 2.756042 CCCGGGAGCCATTGGATCA 61.756 63.158 18.48 0.00 40.28 2.92
438 440 2.113986 CCCGGGAGCCATTGGATC 59.886 66.667 18.48 12.62 37.39 3.36
439 441 2.368192 TCCCGGGAGCCATTGGAT 60.368 61.111 22.63 0.00 0.00 3.41
440 442 3.089874 CTCCCGGGAGCCATTGGA 61.090 66.667 36.90 4.87 35.31 3.53
448 450 1.219393 GTTCAAGAGCTCCCGGGAG 59.781 63.158 41.29 41.29 44.56 4.30
449 451 0.909610 ATGTTCAAGAGCTCCCGGGA 60.910 55.000 25.06 25.06 0.00 5.14
450 452 0.035056 AATGTTCAAGAGCTCCCGGG 60.035 55.000 16.85 16.85 0.00 5.73
451 453 1.826385 AAATGTTCAAGAGCTCCCGG 58.174 50.000 10.93 0.00 0.00 5.73
452 454 2.669391 GCAAAATGTTCAAGAGCTCCCG 60.669 50.000 10.93 1.25 0.00 5.14
453 455 2.297033 TGCAAAATGTTCAAGAGCTCCC 59.703 45.455 10.93 0.00 0.00 4.30
454 456 3.648339 TGCAAAATGTTCAAGAGCTCC 57.352 42.857 10.93 0.00 0.00 4.70
455 457 5.971895 TTTTGCAAAATGTTCAAGAGCTC 57.028 34.783 20.46 5.27 0.00 4.09
456 458 6.316890 ACATTTTTGCAAAATGTTCAAGAGCT 59.683 30.769 24.39 0.00 45.52 4.09
457 459 6.488817 ACATTTTTGCAAAATGTTCAAGAGC 58.511 32.000 24.39 0.00 45.52 4.09
466 468 5.842619 TCGGATGACATTTTTGCAAAATG 57.157 34.783 24.39 22.96 41.91 2.32
467 469 6.482973 ACTTTCGGATGACATTTTTGCAAAAT 59.517 30.769 24.39 10.72 0.00 1.82
468 470 5.814705 ACTTTCGGATGACATTTTTGCAAAA 59.185 32.000 20.46 20.46 0.00 2.44
469 471 5.355596 ACTTTCGGATGACATTTTTGCAAA 58.644 33.333 8.05 8.05 0.00 3.68
470 472 4.942852 ACTTTCGGATGACATTTTTGCAA 58.057 34.783 0.00 0.00 0.00 4.08
471 473 4.278170 AGACTTTCGGATGACATTTTTGCA 59.722 37.500 0.00 0.00 0.00 4.08
472 474 4.798574 AGACTTTCGGATGACATTTTTGC 58.201 39.130 0.00 0.00 0.00 3.68
473 475 6.437928 TGAAGACTTTCGGATGACATTTTTG 58.562 36.000 0.00 0.00 36.04 2.44
474 476 6.633500 TGAAGACTTTCGGATGACATTTTT 57.367 33.333 0.00 0.00 36.04 1.94
475 477 6.633500 TTGAAGACTTTCGGATGACATTTT 57.367 33.333 0.00 0.00 36.04 1.82
476 478 6.633500 TTTGAAGACTTTCGGATGACATTT 57.367 33.333 0.00 0.00 36.04 2.32
477 479 6.824305 ATTTGAAGACTTTCGGATGACATT 57.176 33.333 0.00 0.00 36.04 2.71
478 480 6.824305 AATTTGAAGACTTTCGGATGACAT 57.176 33.333 0.00 0.00 36.04 3.06
479 481 6.262049 TGAAATTTGAAGACTTTCGGATGACA 59.738 34.615 0.00 0.00 36.04 3.58
480 482 6.578919 GTGAAATTTGAAGACTTTCGGATGAC 59.421 38.462 0.00 0.00 36.04 3.06
481 483 6.262049 TGTGAAATTTGAAGACTTTCGGATGA 59.738 34.615 0.00 0.00 36.04 2.92
482 484 6.437928 TGTGAAATTTGAAGACTTTCGGATG 58.562 36.000 0.00 0.00 36.04 3.51
483 485 6.486657 TCTGTGAAATTTGAAGACTTTCGGAT 59.513 34.615 0.00 0.00 36.04 4.18
484 486 5.820423 TCTGTGAAATTTGAAGACTTTCGGA 59.180 36.000 0.00 0.00 36.04 4.55
485 487 6.060028 TCTGTGAAATTTGAAGACTTTCGG 57.940 37.500 0.00 0.00 36.04 4.30
486 488 8.566008 AAATCTGTGAAATTTGAAGACTTTCG 57.434 30.769 0.00 0.00 36.04 3.46
487 489 9.520204 TGAAATCTGTGAAATTTGAAGACTTTC 57.480 29.630 0.00 8.20 0.00 2.62
488 490 9.874205 TTGAAATCTGTGAAATTTGAAGACTTT 57.126 25.926 0.00 0.07 0.00 2.66
489 491 9.874205 TTTGAAATCTGTGAAATTTGAAGACTT 57.126 25.926 0.00 0.00 0.00 3.01
490 492 9.525409 CTTTGAAATCTGTGAAATTTGAAGACT 57.475 29.630 0.00 0.00 0.00 3.24
491 493 9.520204 TCTTTGAAATCTGTGAAATTTGAAGAC 57.480 29.630 0.00 0.00 29.27 3.01
492 494 9.740239 CTCTTTGAAATCTGTGAAATTTGAAGA 57.260 29.630 0.00 0.00 31.27 2.87
493 495 8.485591 GCTCTTTGAAATCTGTGAAATTTGAAG 58.514 33.333 0.00 0.00 0.00 3.02
494 496 7.439056 GGCTCTTTGAAATCTGTGAAATTTGAA 59.561 33.333 0.00 0.00 0.00 2.69
495 497 6.925165 GGCTCTTTGAAATCTGTGAAATTTGA 59.075 34.615 0.00 0.00 0.00 2.69
496 498 6.129009 CGGCTCTTTGAAATCTGTGAAATTTG 60.129 38.462 0.00 0.00 0.00 2.32
497 499 5.922544 CGGCTCTTTGAAATCTGTGAAATTT 59.077 36.000 0.00 0.00 0.00 1.82
498 500 5.010012 ACGGCTCTTTGAAATCTGTGAAATT 59.990 36.000 0.00 0.00 0.00 1.82
499 501 4.520492 ACGGCTCTTTGAAATCTGTGAAAT 59.480 37.500 0.00 0.00 0.00 2.17
500 502 3.882888 ACGGCTCTTTGAAATCTGTGAAA 59.117 39.130 0.00 0.00 0.00 2.69
501 503 3.476552 ACGGCTCTTTGAAATCTGTGAA 58.523 40.909 0.00 0.00 0.00 3.18
502 504 3.067106 GACGGCTCTTTGAAATCTGTGA 58.933 45.455 0.00 0.00 0.00 3.58
503 505 2.159787 CGACGGCTCTTTGAAATCTGTG 60.160 50.000 0.00 0.00 0.00 3.66
504 506 2.069273 CGACGGCTCTTTGAAATCTGT 58.931 47.619 0.00 0.00 0.00 3.41
505 507 1.394917 CCGACGGCTCTTTGAAATCTG 59.605 52.381 0.00 0.00 0.00 2.90
506 508 1.275291 TCCGACGGCTCTTTGAAATCT 59.725 47.619 9.66 0.00 0.00 2.40
507 509 1.722011 TCCGACGGCTCTTTGAAATC 58.278 50.000 9.66 0.00 0.00 2.17
508 510 2.093447 AGATCCGACGGCTCTTTGAAAT 60.093 45.455 14.39 0.00 0.00 2.17
509 511 1.275291 AGATCCGACGGCTCTTTGAAA 59.725 47.619 14.39 0.00 0.00 2.69
510 512 0.895530 AGATCCGACGGCTCTTTGAA 59.104 50.000 14.39 0.00 0.00 2.69
511 513 0.895530 AAGATCCGACGGCTCTTTGA 59.104 50.000 23.76 0.00 34.97 2.69
512 514 2.579207 TAAGATCCGACGGCTCTTTG 57.421 50.000 31.37 0.00 38.78 2.77
513 515 3.604875 TTTAAGATCCGACGGCTCTTT 57.395 42.857 31.37 18.49 38.78 2.52
514 516 3.492829 GGATTTAAGATCCGACGGCTCTT 60.493 47.826 29.72 29.72 40.61 2.85
515 517 2.036089 GGATTTAAGATCCGACGGCTCT 59.964 50.000 14.39 14.39 28.42 4.09
516 518 2.223971 TGGATTTAAGATCCGACGGCTC 60.224 50.000 9.66 9.70 41.03 4.70
517 519 1.760613 TGGATTTAAGATCCGACGGCT 59.239 47.619 9.66 0.00 41.03 5.52
518 520 2.234300 TGGATTTAAGATCCGACGGC 57.766 50.000 9.66 0.00 41.03 5.68
521 523 4.430908 AGACGTTGGATTTAAGATCCGAC 58.569 43.478 18.19 18.19 45.12 4.79
522 524 4.158949 TGAGACGTTGGATTTAAGATCCGA 59.841 41.667 0.00 7.12 41.03 4.55
523 525 4.430007 TGAGACGTTGGATTTAAGATCCG 58.570 43.478 0.00 0.00 41.03 4.18
524 526 5.661458 TCTGAGACGTTGGATTTAAGATCC 58.339 41.667 0.00 8.79 38.66 3.36
525 527 6.237969 GCTTCTGAGACGTTGGATTTAAGATC 60.238 42.308 0.00 0.00 0.00 2.75
526 528 5.582665 GCTTCTGAGACGTTGGATTTAAGAT 59.417 40.000 0.00 0.00 0.00 2.40
527 529 4.929808 GCTTCTGAGACGTTGGATTTAAGA 59.070 41.667 0.00 0.00 0.00 2.10
528 530 4.093556 GGCTTCTGAGACGTTGGATTTAAG 59.906 45.833 0.00 0.00 0.00 1.85
529 531 4.000988 GGCTTCTGAGACGTTGGATTTAA 58.999 43.478 0.00 0.00 0.00 1.52
530 532 3.596214 GGCTTCTGAGACGTTGGATTTA 58.404 45.455 0.00 0.00 0.00 1.40
531 533 2.427506 GGCTTCTGAGACGTTGGATTT 58.572 47.619 0.00 0.00 0.00 2.17
532 534 1.339151 GGGCTTCTGAGACGTTGGATT 60.339 52.381 0.00 0.00 0.00 3.01
533 535 0.250513 GGGCTTCTGAGACGTTGGAT 59.749 55.000 0.00 0.00 0.00 3.41
534 536 1.671742 GGGCTTCTGAGACGTTGGA 59.328 57.895 0.00 0.00 0.00 3.53
535 537 1.738099 CGGGCTTCTGAGACGTTGG 60.738 63.158 0.00 0.00 0.00 3.77
536 538 0.242825 TACGGGCTTCTGAGACGTTG 59.757 55.000 1.24 0.00 38.42 4.10
537 539 1.134560 GATACGGGCTTCTGAGACGTT 59.865 52.381 1.24 0.00 38.42 3.99
538 540 0.739561 GATACGGGCTTCTGAGACGT 59.260 55.000 1.60 1.60 39.90 4.34
539 541 0.738975 TGATACGGGCTTCTGAGACG 59.261 55.000 0.00 0.00 0.00 4.18
540 542 1.534175 CGTGATACGGGCTTCTGAGAC 60.534 57.143 0.00 0.00 38.08 3.36
541 543 0.738975 CGTGATACGGGCTTCTGAGA 59.261 55.000 0.00 0.00 38.08 3.27
542 544 3.258225 CGTGATACGGGCTTCTGAG 57.742 57.895 0.00 0.00 38.08 3.35
552 554 4.852104 GCACTTAGATGATACCGTGATACG 59.148 45.833 0.00 0.00 42.11 3.06
553 555 5.859114 CAGCACTTAGATGATACCGTGATAC 59.141 44.000 0.00 0.00 35.00 2.24
554 556 5.048013 CCAGCACTTAGATGATACCGTGATA 60.048 44.000 0.00 0.00 35.00 2.15
555 557 4.262207 CCAGCACTTAGATGATACCGTGAT 60.262 45.833 0.00 0.00 35.00 3.06
556 558 3.068165 CCAGCACTTAGATGATACCGTGA 59.932 47.826 0.00 0.00 35.00 4.35
557 559 3.181475 ACCAGCACTTAGATGATACCGTG 60.181 47.826 0.00 0.00 35.00 4.94
558 560 3.031736 ACCAGCACTTAGATGATACCGT 58.968 45.455 0.00 0.00 35.00 4.83
559 561 3.735237 ACCAGCACTTAGATGATACCG 57.265 47.619 0.00 0.00 35.00 4.02
560 562 4.561105 GCTACCAGCACTTAGATGATACC 58.439 47.826 0.00 0.00 41.89 2.73
574 576 4.036852 GGGAAAATATCAAGTGCTACCAGC 59.963 45.833 0.00 0.00 42.82 4.85
575 577 4.580580 GGGGAAAATATCAAGTGCTACCAG 59.419 45.833 0.00 0.00 0.00 4.00
576 578 4.229582 AGGGGAAAATATCAAGTGCTACCA 59.770 41.667 0.00 0.00 0.00 3.25
577 579 4.793201 AGGGGAAAATATCAAGTGCTACC 58.207 43.478 0.00 0.00 0.00 3.18
578 580 9.740710 AATATAGGGGAAAATATCAAGTGCTAC 57.259 33.333 0.00 0.00 0.00 3.58
579 581 9.959721 GAATATAGGGGAAAATATCAAGTGCTA 57.040 33.333 0.00 0.00 0.00 3.49
580 582 8.673251 AGAATATAGGGGAAAATATCAAGTGCT 58.327 33.333 0.00 0.00 0.00 4.40
581 583 8.870075 AGAATATAGGGGAAAATATCAAGTGC 57.130 34.615 0.00 0.00 0.00 4.40
589 591 9.112658 CCTCCTACAAGAATATAGGGGAAAATA 57.887 37.037 0.00 0.00 41.05 1.40
590 592 7.799583 TCCTCCTACAAGAATATAGGGGAAAAT 59.200 37.037 0.00 0.00 41.05 1.82
591 593 7.143741 TCCTCCTACAAGAATATAGGGGAAAA 58.856 38.462 0.00 0.00 41.05 2.29
592 594 6.699688 TCCTCCTACAAGAATATAGGGGAAA 58.300 40.000 0.00 0.00 41.05 3.13
593 595 6.303427 TCCTCCTACAAGAATATAGGGGAA 57.697 41.667 0.00 0.00 41.05 3.97
594 596 5.961399 TCCTCCTACAAGAATATAGGGGA 57.039 43.478 0.00 1.98 41.05 4.81
595 597 8.862091 AATATCCTCCTACAAGAATATAGGGG 57.138 38.462 0.00 0.00 38.61 4.79
605 607 9.213799 GCATCTCTTTAAATATCCTCCTACAAG 57.786 37.037 0.00 0.00 0.00 3.16
609 611 8.370940 CAGTGCATCTCTTTAAATATCCTCCTA 58.629 37.037 0.00 0.00 0.00 2.94
610 612 7.222872 CAGTGCATCTCTTTAAATATCCTCCT 58.777 38.462 0.00 0.00 0.00 3.69
637 642 6.206634 CCTAGATTAGTTGCTCTCTAGGTGAG 59.793 46.154 13.82 8.64 46.52 3.51
639 644 6.325919 CCTAGATTAGTTGCTCTCTAGGTG 57.674 45.833 13.82 0.00 46.52 4.00
645 650 5.596845 CAGGTTCCTAGATTAGTTGCTCTC 58.403 45.833 0.00 0.00 0.00 3.20
652 657 6.726490 TTATTCGCAGGTTCCTAGATTAGT 57.274 37.500 0.00 0.00 0.00 2.24
662 906 1.604278 GCAGGGATTATTCGCAGGTTC 59.396 52.381 4.73 0.00 37.28 3.62
730 974 2.025898 GTCCGAGAAGAGAAGGGGTAG 58.974 57.143 0.00 0.00 0.00 3.18
764 1010 1.942657 GTTCAGTGCAGAGCTGACAAA 59.057 47.619 5.07 0.00 42.00 2.83
799 1045 1.432024 GGTAGGAGGGGCTCACCTATA 59.568 57.143 13.93 0.00 42.10 1.31
848 1094 2.442126 GGGGAGTTTATAGGGGAAGTGG 59.558 54.545 0.00 0.00 0.00 4.00
890 1136 3.499737 GTGCGCGGTGAATGGAGG 61.500 66.667 8.83 0.00 0.00 4.30
920 1166 1.981636 AGCTTGGCTGGAGAGAGTG 59.018 57.895 0.00 0.00 37.57 3.51
934 1180 2.114638 CTCGCTCTCTAGCCAGCTT 58.885 57.895 0.00 0.00 46.68 3.74
1184 1444 2.812542 CTTCGCGACGGTCACATCCA 62.813 60.000 9.15 0.00 0.00 3.41
1185 1445 2.126228 TTCGCGACGGTCACATCC 60.126 61.111 9.15 0.00 0.00 3.51
1188 1448 3.263503 CTCCTTCGCGACGGTCACA 62.264 63.158 28.34 10.70 0.00 3.58
1189 1449 2.504244 CTCCTTCGCGACGGTCAC 60.504 66.667 28.34 0.00 0.00 3.67
1190 1450 2.981909 ACTCCTTCGCGACGGTCA 60.982 61.111 28.34 11.76 0.00 4.02
1191 1451 2.504244 CACTCCTTCGCGACGGTC 60.504 66.667 28.34 0.00 0.00 4.79
1192 1452 4.719369 GCACTCCTTCGCGACGGT 62.719 66.667 28.34 10.13 0.00 4.83
1225 1485 4.148825 GGAGTCCACGGCGAGCAT 62.149 66.667 16.62 0.00 0.00 3.79
1766 2027 3.420417 GCGAAATTGCACACGAACAATTC 60.420 43.478 1.82 0.00 43.76 2.17
1794 2055 3.118920 ACAAAGGTACAAAGCGGCTTTTT 60.119 39.130 24.43 20.57 30.60 1.94
1827 2088 3.317603 TTCATAAAGGGCAAAAGCAGC 57.682 42.857 0.00 0.00 0.00 5.25
1890 2151 1.569708 AACAAAGCGGTGCAATTGTG 58.430 45.000 7.40 0.00 39.48 3.33
1951 2212 4.307443 ACACAAAGCTAAAGGTGAAAGC 57.693 40.909 12.21 0.00 35.33 3.51
1956 2217 2.035832 CCCCAACACAAAGCTAAAGGTG 59.964 50.000 0.00 0.00 37.29 4.00
1957 2218 2.316108 CCCCAACACAAAGCTAAAGGT 58.684 47.619 0.00 0.00 0.00 3.50
1964 2232 0.037975 CAGATGCCCCAACACAAAGC 60.038 55.000 0.00 0.00 0.00 3.51
1969 2237 1.598701 GCCTTCAGATGCCCCAACAC 61.599 60.000 0.00 0.00 0.00 3.32
2038 2493 6.309494 TGCATTCACATTTACTACGTGTCTAC 59.691 38.462 0.00 0.00 32.42 2.59
2039 2494 6.391537 TGCATTCACATTTACTACGTGTCTA 58.608 36.000 0.00 0.00 32.42 2.59
2040 2495 5.234752 TGCATTCACATTTACTACGTGTCT 58.765 37.500 0.00 0.00 32.42 3.41
2041 2496 5.524511 TGCATTCACATTTACTACGTGTC 57.475 39.130 0.00 0.00 32.42 3.67
2042 2497 5.933187 TTGCATTCACATTTACTACGTGT 57.067 34.783 0.00 0.00 32.42 4.49
2043 2498 7.216881 CAGAATTGCATTCACATTTACTACGTG 59.783 37.037 0.00 0.00 41.71 4.49
2044 2499 7.094805 ACAGAATTGCATTCACATTTACTACGT 60.095 33.333 0.00 0.00 41.71 3.57
2045 2500 7.243487 ACAGAATTGCATTCACATTTACTACG 58.757 34.615 10.26 0.00 41.71 3.51
2061 2516 7.025963 CCAAGAGAGTAAAATGACAGAATTGC 58.974 38.462 0.00 0.00 0.00 3.56
2077 2532 5.238583 CAAAATTACTCGGTCCAAGAGAGT 58.761 41.667 1.15 2.85 45.85 3.24
2110 2566 2.738521 CGCCCGTCTCAAGGTGTG 60.739 66.667 0.00 0.00 0.00 3.82
2111 2567 2.915659 TCGCCCGTCTCAAGGTGT 60.916 61.111 0.00 0.00 35.11 4.16
2159 2851 3.545426 GCGTCTGTTTATTATTGCGTCCC 60.545 47.826 0.00 0.00 0.00 4.46
2275 2995 2.356075 TGGTTTACCACGCGTCCG 60.356 61.111 9.86 4.75 42.01 4.79
2316 3036 1.472878 CGTGATCTCGAACCAGAGGAA 59.527 52.381 11.64 0.00 38.71 3.36
2323 3043 3.255379 GCCGCGTGATCTCGAACC 61.255 66.667 20.54 2.60 0.00 3.62
2343 3063 5.994668 AGATCTCAATCCTCTTAATTTCGGC 59.005 40.000 0.00 0.00 31.78 5.54
2356 3076 4.221703 ACGGTCCATGATAGATCTCAATCC 59.778 45.833 0.00 0.00 31.78 3.01
2366 3086 2.690497 AGTGACAGACGGTCCATGATAG 59.310 50.000 4.14 0.00 46.38 2.08
2378 3102 1.316706 CGGGGGAGAGAGTGACAGAC 61.317 65.000 0.00 0.00 0.00 3.51
2379 3103 1.000771 CGGGGGAGAGAGTGACAGA 60.001 63.158 0.00 0.00 0.00 3.41
2380 3104 1.304547 ACGGGGGAGAGAGTGACAG 60.305 63.158 0.00 0.00 0.00 3.51
2381 3105 1.606601 CACGGGGGAGAGAGTGACA 60.607 63.158 0.00 0.00 36.79 3.58
2406 3130 0.878416 CTTTTTGGATGGGTTCGCGA 59.122 50.000 3.71 3.71 0.00 5.87
2407 3131 0.878416 TCTTTTTGGATGGGTTCGCG 59.122 50.000 0.00 0.00 0.00 5.87
2408 3132 1.402852 GCTCTTTTTGGATGGGTTCGC 60.403 52.381 0.00 0.00 0.00 4.70
2436 3160 2.405191 GCTTCGCCTTTCGCCATC 59.595 61.111 0.00 0.00 38.27 3.51
2454 3178 2.125512 ACGCTCACCGGCTTGATC 60.126 61.111 0.00 0.00 42.52 2.92
2456 3180 3.573772 CTCACGCTCACCGGCTTGA 62.574 63.158 0.00 0.00 42.52 3.02
2457 3181 3.114616 CTCACGCTCACCGGCTTG 61.115 66.667 0.00 0.00 42.52 4.01
2534 3258 3.135994 CTGCATGTGATCCGATTCATGA 58.864 45.455 21.33 0.00 39.68 3.07
2595 3319 0.108138 ACTCAGCAGGGTAATCACGC 60.108 55.000 0.00 0.00 37.87 5.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.