Multiple sequence alignment - TraesCS7A01G071600

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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 TraesCS7A01G071600 chr7A 100.000 3038 0 0 1 3038 37362783 37359746 0.000000e+00 5611.0
1 TraesCS7A01G071600 chr7A 87.151 895 60 27 1491 2374 37930395 37931245 0.000000e+00 965.0
2 TraesCS7A01G071600 chr7A 84.211 209 28 4 2834 3038 37931775 37931982 6.640000e-47 198.0
3 TraesCS7A01G071600 chr7A 89.231 130 9 2 2418 2546 37931335 37931460 1.130000e-34 158.0
4 TraesCS7A01G071600 chr7A 92.079 101 4 1 2630 2730 37931584 37931680 4.080000e-29 139.0
5 TraesCS7A01G071600 chr4A 90.575 1740 79 36 686 2373 686529108 686530814 0.000000e+00 2226.0
6 TraesCS7A01G071600 chr4A 92.442 344 26 0 323 666 490857771 490857428 2.720000e-135 492.0
7 TraesCS7A01G071600 chr4A 78.625 669 58 29 2418 3038 686530914 686531545 6.190000e-97 364.0
8 TraesCS7A01G071600 chr4A 78.689 366 43 18 2685 3038 686560467 686560809 8.530000e-51 211.0
9 TraesCS7A01G071600 chr4A 91.228 57 3 2 2828 2882 642909240 642909184 3.250000e-10 76.8
10 TraesCS7A01G071600 chr4A 94.737 38 0 2 2828 2863 642908683 642908646 1.180000e-04 58.4
11 TraesCS7A01G071600 chr7D 91.252 1646 83 28 804 2419 38077566 38075952 0.000000e+00 2185.0
12 TraesCS7A01G071600 chr7D 85.629 668 35 17 2418 3038 38075873 38075220 0.000000e+00 645.0
13 TraesCS7A01G071600 chr7D 91.570 344 29 0 324 667 451263631 451263288 2.740000e-130 475.0
14 TraesCS7A01G071600 chr7D 90.303 330 19 7 4 326 38078218 38077895 1.300000e-113 420.0
15 TraesCS7A01G071600 chr7D 83.448 435 42 13 2620 3038 38196864 38197284 7.950000e-101 377.0
16 TraesCS7A01G071600 chr7D 87.640 89 4 1 686 767 38077872 38077784 2.490000e-16 97.1
17 TraesCS7A01G071600 chr5B 92.442 344 26 0 323 666 498294861 498295204 2.720000e-135 492.0
18 TraesCS7A01G071600 chr5B 92.625 339 25 0 326 664 26850842 26850504 3.520000e-134 488.0
19 TraesCS7A01G071600 chr6D 92.375 341 26 0 324 664 459199508 459199168 1.270000e-133 486.0
20 TraesCS7A01G071600 chr5A 92.128 343 27 0 324 666 321903711 321903369 4.550000e-133 484.0
21 TraesCS7A01G071600 chr3D 92.128 343 27 0 324 666 491617118 491616776 4.550000e-133 484.0
22 TraesCS7A01G071600 chr2B 91.837 343 28 0 324 666 550068898 550069240 2.120000e-131 479.0
23 TraesCS7A01G071600 chr2B 90.909 352 30 2 324 674 780179882 780179532 3.550000e-129 472.0


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 TraesCS7A01G071600 chr7A 37359746 37362783 3037 True 5611.000 5611 100.000 1 3038 1 chr7A.!!$R1 3037
1 TraesCS7A01G071600 chr7A 37930395 37931982 1587 False 365.000 965 88.168 1491 3038 4 chr7A.!!$F1 1547
2 TraesCS7A01G071600 chr4A 686529108 686531545 2437 False 1295.000 2226 84.600 686 3038 2 chr4A.!!$F2 2352
3 TraesCS7A01G071600 chr7D 38075220 38078218 2998 True 836.775 2185 88.706 4 3038 4 chr7D.!!$R2 3034

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
44 45 0.234884 CGCGTCACTCCTTTTGTTCC 59.765 55.0 0.0 0.0 0.0 3.62 F
829 1057 0.239347 CAAAAGTGCCGAGCCAAGAG 59.761 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2174 0.736325 CGCCGTTGAGGTTGTAGGAG 60.736 60.0 0.0 0.0 43.70 3.69 R
2752 3218 0.033699 GAGAAAGCAGGCCCATCCTT 60.034 55.0 0.0 0.0 44.75 3.36 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
28 29 6.918123 ACTAAAAAGTTCAAATTTTGACGCG 58.082 32.000 11.30 3.53 39.87 6.01
43 44 0.935196 ACGCGTCACTCCTTTTGTTC 59.065 50.000 5.58 0.00 0.00 3.18
44 45 0.234884 CGCGTCACTCCTTTTGTTCC 59.765 55.000 0.00 0.00 0.00 3.62
85 86 7.048512 GGCAATATAGGAGTACTGTCTTTTGT 58.951 38.462 0.00 0.00 0.00 2.83
90 91 3.387050 AGGAGTACTGTCTTTTGTTCCGT 59.613 43.478 0.00 0.00 0.00 4.69
161 162 2.750350 CGGCCTTCCCACTTGACT 59.250 61.111 0.00 0.00 0.00 3.41
162 163 1.672356 CGGCCTTCCCACTTGACTG 60.672 63.158 0.00 0.00 0.00 3.51
163 164 1.303643 GGCCTTCCCACTTGACTGG 60.304 63.158 0.00 0.00 0.00 4.00
230 231 2.643933 GCCAAATGCTTTCACTCTCC 57.356 50.000 0.00 0.00 36.87 3.71
241 242 4.742138 GCTTTCACTCTCCTCACTGACTTT 60.742 45.833 0.00 0.00 0.00 2.66
254 255 4.980434 TCACTGACTTTACTGCGAAACTAC 59.020 41.667 0.00 0.00 0.00 2.73
255 256 4.150098 CACTGACTTTACTGCGAAACTACC 59.850 45.833 0.00 0.00 0.00 3.18
257 258 2.998670 GACTTTACTGCGAAACTACCCC 59.001 50.000 0.00 0.00 0.00 4.95
277 285 1.910688 CGGAGAAGACCGTAAAGCTC 58.089 55.000 0.00 0.00 46.70 4.09
289 297 5.557866 ACCGTAAAGCTCTATTTTTCCACT 58.442 37.500 0.00 0.00 0.00 4.00
308 316 2.690653 TAGCCCATGCGCCCATTACC 62.691 60.000 4.18 0.00 44.33 2.85
312 320 2.515991 ATGCGCCCATTACCCACG 60.516 61.111 4.18 0.00 0.00 4.94
326 334 2.711542 ACCCACGGCAATCTTTCTTAG 58.288 47.619 0.00 0.00 0.00 2.18
327 335 2.304761 ACCCACGGCAATCTTTCTTAGA 59.695 45.455 0.00 0.00 37.28 2.10
328 336 2.939103 CCCACGGCAATCTTTCTTAGAG 59.061 50.000 0.00 0.00 36.02 2.43
329 337 2.352960 CCACGGCAATCTTTCTTAGAGC 59.647 50.000 0.00 0.00 36.02 4.09
330 338 3.002791 CACGGCAATCTTTCTTAGAGCA 58.997 45.455 0.00 0.00 36.02 4.26
331 339 3.624861 CACGGCAATCTTTCTTAGAGCAT 59.375 43.478 0.00 0.00 36.02 3.79
332 340 3.873952 ACGGCAATCTTTCTTAGAGCATC 59.126 43.478 0.00 0.00 36.02 3.91
352 360 9.734620 GAGCATCTCTAATAGCTTGTCTATATG 57.265 37.037 0.00 0.00 37.01 1.78
353 361 9.473007 AGCATCTCTAATAGCTTGTCTATATGA 57.527 33.333 0.00 0.00 37.01 2.15
385 393 2.640375 GTTTTTCACGACGTGACCTC 57.360 50.000 29.22 15.89 42.60 3.85
386 394 1.928503 GTTTTTCACGACGTGACCTCA 59.071 47.619 29.22 12.94 42.60 3.86
387 395 2.296831 TTTTCACGACGTGACCTCAA 57.703 45.000 29.22 18.08 42.60 3.02
388 396 2.296831 TTTCACGACGTGACCTCAAA 57.703 45.000 29.22 17.72 42.60 2.69
389 397 2.296831 TTCACGACGTGACCTCAAAA 57.703 45.000 29.22 11.05 42.60 2.44
390 398 1.563111 TCACGACGTGACCTCAAAAC 58.437 50.000 26.04 0.00 37.67 2.43
391 399 1.135053 TCACGACGTGACCTCAAAACA 60.135 47.619 26.04 0.36 37.67 2.83
392 400 1.257936 CACGACGTGACCTCAAAACAG 59.742 52.381 23.39 0.00 35.23 3.16
393 401 0.859232 CGACGTGACCTCAAAACAGG 59.141 55.000 0.00 0.00 39.80 4.00
402 410 3.426615 ACCTCAAAACAGGTGTTCAACA 58.573 40.909 0.00 0.00 45.80 3.33
403 411 3.443681 ACCTCAAAACAGGTGTTCAACAG 59.556 43.478 0.00 0.00 45.80 3.16
404 412 3.438360 CTCAAAACAGGTGTTCAACAGC 58.562 45.455 11.98 11.98 46.20 4.40
418 426 9.413048 GGTGTTCAACAGCTTATCTATATAGTC 57.587 37.037 12.62 0.00 42.83 2.59
419 427 9.119329 GTGTTCAACAGCTTATCTATATAGTCG 57.881 37.037 9.58 0.00 0.00 4.18
420 428 8.847196 TGTTCAACAGCTTATCTATATAGTCGT 58.153 33.333 9.58 0.91 0.00 4.34
421 429 9.332301 GTTCAACAGCTTATCTATATAGTCGTC 57.668 37.037 9.58 0.00 0.00 4.20
422 430 8.850007 TCAACAGCTTATCTATATAGTCGTCT 57.150 34.615 9.58 0.34 0.00 4.18
423 431 9.939802 TCAACAGCTTATCTATATAGTCGTCTA 57.060 33.333 9.58 0.00 0.00 2.59
439 447 9.742144 ATAGTCGTCTAAATATACACATCCTCT 57.258 33.333 0.00 0.00 0.00 3.69
441 449 9.570468 AGTCGTCTAAATATACACATCCTCTAA 57.430 33.333 0.00 0.00 0.00 2.10
449 457 8.423906 AATATACACATCCTCTAAATCGACCT 57.576 34.615 0.00 0.00 0.00 3.85
450 458 4.657436 ACACATCCTCTAAATCGACCTC 57.343 45.455 0.00 0.00 0.00 3.85
451 459 3.066900 ACACATCCTCTAAATCGACCTCG 59.933 47.826 0.00 0.00 41.45 4.63
463 471 1.332686 TCGACCTCGACAATATCCACG 59.667 52.381 0.00 0.00 44.22 4.94
464 472 1.065102 CGACCTCGACAATATCCACGT 59.935 52.381 0.00 0.00 43.02 4.49
465 473 2.728922 GACCTCGACAATATCCACGTC 58.271 52.381 0.00 0.00 0.00 4.34
466 474 2.358267 GACCTCGACAATATCCACGTCT 59.642 50.000 0.00 0.00 0.00 4.18
467 475 2.099263 ACCTCGACAATATCCACGTCTG 59.901 50.000 0.00 0.00 0.00 3.51
468 476 2.543861 CCTCGACAATATCCACGTCTGG 60.544 54.545 0.00 0.00 39.23 3.86
476 484 3.605013 TCCACGTCTGGACAATGTG 57.395 52.632 0.00 1.83 42.15 3.21
477 485 1.044611 TCCACGTCTGGACAATGTGA 58.955 50.000 0.00 0.00 42.15 3.58
478 486 1.414550 TCCACGTCTGGACAATGTGAA 59.585 47.619 0.00 0.00 42.15 3.18
479 487 1.800586 CCACGTCTGGACAATGTGAAG 59.199 52.381 0.00 0.00 40.55 3.02
480 488 1.800586 CACGTCTGGACAATGTGAAGG 59.199 52.381 0.00 0.00 32.39 3.46
481 489 0.798776 CGTCTGGACAATGTGAAGGC 59.201 55.000 0.00 0.00 0.00 4.35
482 490 1.877680 CGTCTGGACAATGTGAAGGCA 60.878 52.381 0.00 0.00 0.00 4.75
483 491 2.440409 GTCTGGACAATGTGAAGGCAT 58.560 47.619 0.00 0.00 0.00 4.40
484 492 2.821969 GTCTGGACAATGTGAAGGCATT 59.178 45.455 0.00 0.00 39.42 3.56
493 501 6.017400 CAATGTGAAGGCATTGTCTAAACT 57.983 37.500 9.78 0.00 46.24 2.66
494 502 5.886960 ATGTGAAGGCATTGTCTAAACTC 57.113 39.130 0.00 0.00 0.00 3.01
495 503 4.713553 TGTGAAGGCATTGTCTAAACTCA 58.286 39.130 0.00 0.00 0.00 3.41
496 504 4.756642 TGTGAAGGCATTGTCTAAACTCAG 59.243 41.667 0.00 0.00 0.00 3.35
497 505 4.757149 GTGAAGGCATTGTCTAAACTCAGT 59.243 41.667 0.00 0.00 0.00 3.41
498 506 5.239525 GTGAAGGCATTGTCTAAACTCAGTT 59.760 40.000 0.00 0.00 0.00 3.16
499 507 5.239306 TGAAGGCATTGTCTAAACTCAGTTG 59.761 40.000 0.00 0.00 0.00 3.16
500 508 3.503748 AGGCATTGTCTAAACTCAGTTGC 59.496 43.478 0.00 0.00 0.00 4.17
501 509 3.253188 GGCATTGTCTAAACTCAGTTGCA 59.747 43.478 0.00 0.00 0.00 4.08
502 510 4.470462 GCATTGTCTAAACTCAGTTGCAG 58.530 43.478 0.00 0.00 0.00 4.41
503 511 4.023707 GCATTGTCTAAACTCAGTTGCAGT 60.024 41.667 0.00 0.00 0.00 4.40
504 512 5.683859 CATTGTCTAAACTCAGTTGCAGTC 58.316 41.667 0.00 0.00 0.00 3.51
505 513 4.400529 TGTCTAAACTCAGTTGCAGTCA 57.599 40.909 0.00 0.00 0.00 3.41
506 514 4.960938 TGTCTAAACTCAGTTGCAGTCAT 58.039 39.130 0.00 0.00 0.00 3.06
507 515 4.751600 TGTCTAAACTCAGTTGCAGTCATG 59.248 41.667 0.00 0.00 0.00 3.07
508 516 4.991056 GTCTAAACTCAGTTGCAGTCATGA 59.009 41.667 0.00 0.00 0.00 3.07
509 517 5.641209 GTCTAAACTCAGTTGCAGTCATGAT 59.359 40.000 0.00 0.00 0.00 2.45
510 518 6.148480 GTCTAAACTCAGTTGCAGTCATGATT 59.852 38.462 0.00 0.00 0.00 2.57
511 519 5.779529 AAACTCAGTTGCAGTCATGATTT 57.220 34.783 0.00 0.00 0.00 2.17
512 520 5.368256 AACTCAGTTGCAGTCATGATTTC 57.632 39.130 0.00 0.00 0.00 2.17
513 521 4.649692 ACTCAGTTGCAGTCATGATTTCT 58.350 39.130 0.00 0.00 0.00 2.52
514 522 5.068636 ACTCAGTTGCAGTCATGATTTCTT 58.931 37.500 0.00 0.00 0.00 2.52
515 523 5.180868 ACTCAGTTGCAGTCATGATTTCTTC 59.819 40.000 0.00 0.00 0.00 2.87
516 524 5.311265 TCAGTTGCAGTCATGATTTCTTCT 58.689 37.500 0.00 0.00 0.00 2.85
517 525 5.766670 TCAGTTGCAGTCATGATTTCTTCTT 59.233 36.000 0.00 0.00 0.00 2.52
518 526 6.072838 TCAGTTGCAGTCATGATTTCTTCTTC 60.073 38.462 0.00 0.00 0.00 2.87
519 527 6.002704 AGTTGCAGTCATGATTTCTTCTTCT 58.997 36.000 0.00 0.00 0.00 2.85
520 528 6.489361 AGTTGCAGTCATGATTTCTTCTTCTT 59.511 34.615 0.00 0.00 0.00 2.52
521 529 6.492007 TGCAGTCATGATTTCTTCTTCTTC 57.508 37.500 0.00 0.00 0.00 2.87
522 530 6.236409 TGCAGTCATGATTTCTTCTTCTTCT 58.764 36.000 0.00 0.00 0.00 2.85
523 531 6.370994 TGCAGTCATGATTTCTTCTTCTTCTC 59.629 38.462 0.00 0.00 0.00 2.87
524 532 6.370994 GCAGTCATGATTTCTTCTTCTTCTCA 59.629 38.462 0.00 0.00 0.00 3.27
525 533 7.413219 GCAGTCATGATTTCTTCTTCTTCTCAG 60.413 40.741 0.00 0.00 0.00 3.35
526 534 6.594937 AGTCATGATTTCTTCTTCTTCTCAGC 59.405 38.462 0.00 0.00 0.00 4.26
527 535 5.579904 TCATGATTTCTTCTTCTTCTCAGCG 59.420 40.000 0.00 0.00 0.00 5.18
528 536 5.139435 TGATTTCTTCTTCTTCTCAGCGA 57.861 39.130 0.00 0.00 0.00 4.93
529 537 4.926238 TGATTTCTTCTTCTTCTCAGCGAC 59.074 41.667 0.00 0.00 0.00 5.19
530 538 2.620779 TCTTCTTCTTCTCAGCGACG 57.379 50.000 0.00 0.00 0.00 5.12
531 539 1.200252 TCTTCTTCTTCTCAGCGACGG 59.800 52.381 0.00 0.00 0.00 4.79
532 540 0.388649 TTCTTCTTCTCAGCGACGGC 60.389 55.000 0.00 0.00 40.37 5.68
533 541 1.807573 CTTCTTCTCAGCGACGGCC 60.808 63.158 0.00 0.00 41.24 6.13
534 542 3.296709 TTCTTCTCAGCGACGGCCC 62.297 63.158 0.00 0.00 41.24 5.80
535 543 4.069232 CTTCTCAGCGACGGCCCA 62.069 66.667 0.00 0.00 41.24 5.36
536 544 4.373116 TTCTCAGCGACGGCCCAC 62.373 66.667 0.00 0.00 41.24 4.61
543 551 4.082523 CGACGGCCCACCTGTCAT 62.083 66.667 0.00 0.00 38.56 3.06
544 552 2.436646 GACGGCCCACCTGTCATG 60.437 66.667 0.00 0.00 38.53 3.07
545 553 3.976701 GACGGCCCACCTGTCATGG 62.977 68.421 0.00 0.00 38.53 3.66
546 554 4.033776 CGGCCCACCTGTCATGGT 62.034 66.667 0.00 0.00 41.77 3.55
547 555 2.440599 GGCCCACCTGTCATGGTT 59.559 61.111 0.00 0.00 38.45 3.67
548 556 1.678970 GGCCCACCTGTCATGGTTC 60.679 63.158 0.00 0.00 38.45 3.62
549 557 1.678970 GCCCACCTGTCATGGTTCC 60.679 63.158 0.00 0.00 38.45 3.62
550 558 2.078452 CCCACCTGTCATGGTTCCT 58.922 57.895 0.00 0.00 38.45 3.36
551 559 0.322816 CCCACCTGTCATGGTTCCTG 60.323 60.000 0.00 0.00 38.45 3.86
552 560 0.401738 CCACCTGTCATGGTTCCTGT 59.598 55.000 0.00 0.00 38.45 4.00
553 561 1.628340 CCACCTGTCATGGTTCCTGTA 59.372 52.381 0.00 0.00 38.45 2.74
554 562 2.239654 CCACCTGTCATGGTTCCTGTAT 59.760 50.000 0.00 0.00 38.45 2.29
555 563 3.454447 CCACCTGTCATGGTTCCTGTATA 59.546 47.826 0.00 0.00 38.45 1.47
556 564 4.103153 CCACCTGTCATGGTTCCTGTATAT 59.897 45.833 0.00 0.00 38.45 0.86
557 565 5.306937 CCACCTGTCATGGTTCCTGTATATA 59.693 44.000 0.00 0.00 38.45 0.86
558 566 6.459066 CACCTGTCATGGTTCCTGTATATAG 58.541 44.000 0.00 0.00 38.45 1.31
559 567 6.267699 CACCTGTCATGGTTCCTGTATATAGA 59.732 42.308 0.00 0.00 38.45 1.98
560 568 6.267928 ACCTGTCATGGTTCCTGTATATAGAC 59.732 42.308 0.00 0.00 36.89 2.59
561 569 6.267699 CCTGTCATGGTTCCTGTATATAGACA 59.732 42.308 0.00 0.00 0.00 3.41
562 570 7.038729 CCTGTCATGGTTCCTGTATATAGACAT 60.039 40.741 0.00 0.00 32.62 3.06
563 571 8.262601 TGTCATGGTTCCTGTATATAGACATT 57.737 34.615 0.00 0.00 0.00 2.71
564 572 8.367911 TGTCATGGTTCCTGTATATAGACATTC 58.632 37.037 0.00 0.00 0.00 2.67
565 573 8.589338 GTCATGGTTCCTGTATATAGACATTCT 58.411 37.037 0.00 0.00 0.00 2.40
566 574 9.822727 TCATGGTTCCTGTATATAGACATTCTA 57.177 33.333 0.00 0.00 32.87 2.10
570 578 9.372369 GGTTCCTGTATATAGACATTCTAATGC 57.628 37.037 0.00 0.00 40.04 3.56
571 579 9.929180 GTTCCTGTATATAGACATTCTAATGCA 57.071 33.333 0.00 0.00 40.04 3.96
579 587 9.851686 ATATAGACATTCTAATGCAAAACTGGA 57.148 29.630 2.60 0.00 40.04 3.86
580 588 6.899393 AGACATTCTAATGCAAAACTGGAA 57.101 33.333 2.60 0.00 40.04 3.53
581 589 6.917533 AGACATTCTAATGCAAAACTGGAAG 58.082 36.000 2.60 0.00 40.04 3.46
582 590 6.491403 AGACATTCTAATGCAAAACTGGAAGT 59.509 34.615 2.60 0.00 45.20 3.01
583 591 6.449698 ACATTCTAATGCAAAACTGGAAGTG 58.550 36.000 2.60 0.00 43.39 3.16
584 592 6.040842 ACATTCTAATGCAAAACTGGAAGTGT 59.959 34.615 2.60 0.00 43.39 3.55
585 593 7.230510 ACATTCTAATGCAAAACTGGAAGTGTA 59.769 33.333 2.60 0.00 43.39 2.90
653 661 9.006839 AGACATCCAAATATACACATGCTATTG 57.993 33.333 0.00 0.00 0.00 1.90
654 662 8.114331 ACATCCAAATATACACATGCTATTGG 57.886 34.615 0.00 0.00 0.00 3.16
655 663 7.944000 ACATCCAAATATACACATGCTATTGGA 59.056 33.333 12.85 12.85 0.00 3.53
656 664 7.984422 TCCAAATATACACATGCTATTGGAG 57.016 36.000 0.00 0.00 0.00 3.86
657 665 7.744733 TCCAAATATACACATGCTATTGGAGA 58.255 34.615 0.00 0.00 0.00 3.71
658 666 8.385491 TCCAAATATACACATGCTATTGGAGAT 58.615 33.333 0.00 0.00 0.00 2.75
659 667 8.456471 CCAAATATACACATGCTATTGGAGATG 58.544 37.037 0.00 0.00 0.00 2.90
660 668 7.621428 AATATACACATGCTATTGGAGATGC 57.379 36.000 0.00 0.00 0.00 3.91
661 669 3.572632 ACACATGCTATTGGAGATGCT 57.427 42.857 0.00 0.00 0.00 3.79
662 670 3.474600 ACACATGCTATTGGAGATGCTC 58.525 45.455 0.00 0.00 0.00 4.26
663 671 3.136077 ACACATGCTATTGGAGATGCTCT 59.864 43.478 0.00 0.00 0.00 4.09
664 672 4.135306 CACATGCTATTGGAGATGCTCTT 58.865 43.478 0.00 0.00 0.00 2.85
665 673 5.163269 ACACATGCTATTGGAGATGCTCTTA 60.163 40.000 0.00 0.00 0.00 2.10
666 674 5.178996 CACATGCTATTGGAGATGCTCTTAC 59.821 44.000 0.00 0.00 0.00 2.34
667 675 5.071519 ACATGCTATTGGAGATGCTCTTACT 59.928 40.000 0.00 0.00 0.00 2.24
668 676 6.268617 ACATGCTATTGGAGATGCTCTTACTA 59.731 38.462 0.00 0.00 0.00 1.82
669 677 6.338214 TGCTATTGGAGATGCTCTTACTAG 57.662 41.667 0.00 0.00 0.00 2.57
677 685 6.319152 TGGAGATGCTCTTACTAGTACTCAAC 59.681 42.308 0.91 0.00 0.00 3.18
684 692 7.024768 GCTCTTACTAGTACTCAACTTGTCAG 58.975 42.308 0.91 0.00 42.22 3.51
696 710 4.082190 TCAACTTGTCAGGTAGATTCGGAG 60.082 45.833 0.00 0.00 0.00 4.63
715 729 5.105106 TCGGAGGCAGTAGAATGAATGTTAA 60.105 40.000 0.00 0.00 0.00 2.01
783 999 6.831353 TCTTCTTAATCCACAGACAAAACCAA 59.169 34.615 0.00 0.00 0.00 3.67
790 1006 0.934436 CAGACAAAACCAAAGCCGCG 60.934 55.000 0.00 0.00 0.00 6.46
816 1044 1.488812 GGCCAAAGAAACCCCAAAAGT 59.511 47.619 0.00 0.00 0.00 2.66
820 1048 0.750249 AAGAAACCCCAAAAGTGCCG 59.250 50.000 0.00 0.00 0.00 5.69
828 1056 1.172180 CCAAAAGTGCCGAGCCAAGA 61.172 55.000 0.00 0.00 0.00 3.02
829 1057 0.239347 CAAAAGTGCCGAGCCAAGAG 59.761 55.000 0.00 0.00 0.00 2.85
830 1058 1.518903 AAAAGTGCCGAGCCAAGAGC 61.519 55.000 0.00 0.00 44.25 4.09
869 1097 0.252012 CCTCTCCACTCCACTCCACT 60.252 60.000 0.00 0.00 0.00 4.00
871 1099 0.251832 TCTCCACTCCACTCCACTCC 60.252 60.000 0.00 0.00 0.00 3.85
872 1100 0.542938 CTCCACTCCACTCCACTCCA 60.543 60.000 0.00 0.00 0.00 3.86
899 1133 4.161189 TCTCACTCTCACTCCATGGATTTC 59.839 45.833 16.63 0.00 0.00 2.17
901 1135 4.081254 TCACTCTCACTCCATGGATTTCAG 60.081 45.833 16.63 10.24 0.00 3.02
914 1148 2.303022 GGATTTCAGACTCTCACCACCA 59.697 50.000 0.00 0.00 0.00 4.17
926 1161 4.653888 CCACCACCGTTCCCCACC 62.654 72.222 0.00 0.00 0.00 4.61
958 1193 4.778143 CCCGGCCAAGAACCTCCG 62.778 72.222 2.24 0.00 41.41 4.63
1530 1771 2.669240 GGGGTGTACCTGGTGCTC 59.331 66.667 15.99 12.02 40.03 4.26
2040 2282 4.485554 CTCGACCAGCACTAGCAC 57.514 61.111 0.00 0.00 45.49 4.40
2108 2351 4.610844 GCGCTAGCGGTAGTAGTG 57.389 61.111 35.86 7.67 40.19 2.74
2116 2359 1.005687 AGCGGTAGTAGTGTTCCTCCT 59.994 52.381 0.00 0.00 0.00 3.69
2117 2360 1.823610 GCGGTAGTAGTGTTCCTCCTT 59.176 52.381 0.00 0.00 0.00 3.36
2118 2361 2.159268 GCGGTAGTAGTGTTCCTCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
2177 2424 1.604378 CCATGGGAGCGTTTCCTCT 59.396 57.895 2.85 0.00 45.98 3.69
2178 2425 0.462759 CCATGGGAGCGTTTCCTCTC 60.463 60.000 2.85 0.00 45.98 3.20
2179 2426 0.539051 CATGGGAGCGTTTCCTCTCT 59.461 55.000 0.00 0.00 45.98 3.10
2180 2427 0.827368 ATGGGAGCGTTTCCTCTCTC 59.173 55.000 0.00 0.00 45.98 3.20
2181 2428 0.251832 TGGGAGCGTTTCCTCTCTCT 60.252 55.000 0.00 0.00 45.98 3.10
2205 2452 2.491675 TAGAGTCAGTGAGCCGAAGA 57.508 50.000 0.00 0.00 0.00 2.87
2206 2453 1.621992 AGAGTCAGTGAGCCGAAGAA 58.378 50.000 0.00 0.00 0.00 2.52
2207 2454 1.543802 AGAGTCAGTGAGCCGAAGAAG 59.456 52.381 0.00 0.00 0.00 2.85
2220 2467 0.036388 GAAGAAGCATGGTGGTCCGA 60.036 55.000 0.00 0.00 36.30 4.55
2235 2482 3.461773 CGATCCGGTGAGCCCAGT 61.462 66.667 0.00 0.00 0.00 4.00
2257 2538 1.027357 CTGGCTCATGGTTGGTATGC 58.973 55.000 0.00 0.00 0.00 3.14
2296 2577 8.905660 ATGTTTTGGATGTTCAAATTTGATGA 57.094 26.923 21.10 11.27 36.63 2.92
2313 2594 6.669125 TTGATGACATTTTGTCCATTTCCT 57.331 33.333 5.27 0.00 46.40 3.36
2315 2596 6.690530 TGATGACATTTTGTCCATTTCCTTC 58.309 36.000 5.27 0.00 46.40 3.46
2317 2598 4.283212 TGACATTTTGTCCATTTCCTTCCC 59.717 41.667 5.27 0.00 46.40 3.97
2319 2600 1.917872 TTTGTCCATTTCCTTCCCCG 58.082 50.000 0.00 0.00 0.00 5.73
2320 2601 0.610785 TTGTCCATTTCCTTCCCCGC 60.611 55.000 0.00 0.00 0.00 6.13
2321 2602 1.303282 GTCCATTTCCTTCCCCGCT 59.697 57.895 0.00 0.00 0.00 5.52
2322 2603 0.748367 GTCCATTTCCTTCCCCGCTC 60.748 60.000 0.00 0.00 0.00 5.03
2323 2604 1.819632 CCATTTCCTTCCCCGCTCG 60.820 63.158 0.00 0.00 0.00 5.03
2343 2625 4.541779 TCGGGTTCGTTCAAATTTGATTG 58.458 39.130 21.10 15.85 34.38 2.67
2350 2632 7.064490 GGTTCGTTCAAATTTGATTGGCATTAT 59.936 33.333 21.10 0.00 37.00 1.28
2354 2636 9.086336 CGTTCAAATTTGATTGGCATTATTACT 57.914 29.630 21.10 0.00 37.00 2.24
2378 2664 9.046296 ACTAGTAGCATATTTGAAACATGTAGC 57.954 33.333 0.00 0.00 0.00 3.58
2380 2666 7.923888 AGTAGCATATTTGAAACATGTAGCAG 58.076 34.615 0.00 0.00 0.00 4.24
2382 2668 7.395190 AGCATATTTGAAACATGTAGCAGAA 57.605 32.000 0.00 0.00 0.00 3.02
2383 2669 7.253422 AGCATATTTGAAACATGTAGCAGAAC 58.747 34.615 0.00 0.00 0.00 3.01
2384 2670 7.028962 GCATATTTGAAACATGTAGCAGAACA 58.971 34.615 0.00 0.00 0.00 3.18
2385 2671 7.703621 GCATATTTGAAACATGTAGCAGAACAT 59.296 33.333 0.00 0.00 40.75 2.71
2386 2672 9.577110 CATATTTGAAACATGTAGCAGAACATT 57.423 29.630 0.00 0.00 38.01 2.71
2387 2673 7.878477 ATTTGAAACATGTAGCAGAACATTG 57.122 32.000 0.00 0.00 38.01 2.82
2388 2674 5.375417 TGAAACATGTAGCAGAACATTGG 57.625 39.130 0.00 0.00 38.01 3.16
2389 2675 4.218200 TGAAACATGTAGCAGAACATTGGG 59.782 41.667 0.00 0.00 38.01 4.12
2390 2676 3.719268 ACATGTAGCAGAACATTGGGA 57.281 42.857 0.00 0.00 38.01 4.37
2549 2923 2.594013 TGCTGTGCGGCATCAACA 60.594 55.556 5.72 5.32 37.29 3.33
2550 2924 2.192187 TGCTGTGCGGCATCAACAA 61.192 52.632 5.72 0.00 37.29 2.83
2551 2925 1.730547 GCTGTGCGGCATCAACAAC 60.731 57.895 5.72 0.00 0.00 3.32
2559 2933 2.480555 CATCAACAACGGAGCGCC 59.519 61.111 2.29 0.00 0.00 6.53
2596 2970 1.802365 GTCGCCATTTTGTTCCGTAGT 59.198 47.619 0.00 0.00 0.00 2.73
2597 2971 2.995258 GTCGCCATTTTGTTCCGTAGTA 59.005 45.455 0.00 0.00 0.00 1.82
2598 2972 3.061697 GTCGCCATTTTGTTCCGTAGTAG 59.938 47.826 0.00 0.00 0.00 2.57
2601 2992 4.626604 CGCCATTTTGTTCCGTAGTAGTAA 59.373 41.667 0.00 0.00 0.00 2.24
2625 3071 0.396278 CCCTTCCTTGGATTGGAGCC 60.396 60.000 9.70 0.00 34.76 4.70
2631 3077 2.275547 CTTGGATTGGAGCCGCTTGC 62.276 60.000 0.00 0.00 41.71 4.01
2650 3102 0.243907 CTACTCCGTGGTCACCAGTG 59.756 60.000 0.00 0.00 32.34 3.66
2726 3178 0.806868 ATTGCTGCACAGTCGAATGG 59.193 50.000 18.14 7.36 0.00 3.16
2752 3218 1.270785 CCATGATGGCTGCACCGTATA 60.271 52.381 0.00 0.00 43.94 1.47
2755 3221 1.202639 TGATGGCTGCACCGTATAAGG 60.203 52.381 2.81 2.81 43.94 2.69
2776 3242 1.271840 TGGGCCTGCTTTCTCCGTAT 61.272 55.000 4.53 0.00 0.00 3.06
2877 3354 8.455903 TTCCTTCTAGGCATAGAAATTCAATG 57.544 34.615 20.29 8.03 45.25 2.82
2903 3383 7.014449 CCCATGGCCATTCATATTATGGATAT 58.986 38.462 17.92 7.22 44.36 1.63
2966 3450 2.674220 GCCTCCCACCTCTCCCTTG 61.674 68.421 0.00 0.00 0.00 3.61
2979 3463 3.827302 CTCTCCCTTGTACATATACCGCT 59.173 47.826 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.525071 CGCGTCAAAATTTGAACTTTTTAGTTA 58.475 29.630 10.27 0.00 42.15 2.24
10 11 3.789224 GTGACGCGTCAAAATTTGAACTT 59.211 39.130 40.60 0.00 42.15 2.66
11 12 3.064820 AGTGACGCGTCAAAATTTGAACT 59.935 39.130 40.60 26.68 42.15 3.01
16 17 2.218603 AGGAGTGACGCGTCAAAATTT 58.781 42.857 40.60 23.76 41.85 1.82
18 19 1.878953 AAGGAGTGACGCGTCAAAAT 58.121 45.000 40.60 29.06 41.85 1.82
28 29 1.617322 GGGGGAACAAAAGGAGTGAC 58.383 55.000 0.00 0.00 0.00 3.67
85 86 0.321564 CATGTTGCCTCTCCACGGAA 60.322 55.000 0.00 0.00 0.00 4.30
90 91 0.250858 CACCACATGTTGCCTCTCCA 60.251 55.000 0.00 0.00 0.00 3.86
161 162 0.883153 CTGCATTTGTACTGCTGCCA 59.117 50.000 7.07 0.00 40.34 4.92
162 163 0.883833 ACTGCATTTGTACTGCTGCC 59.116 50.000 10.96 0.00 40.87 4.85
163 164 1.973138 CACTGCATTTGTACTGCTGC 58.027 50.000 10.96 9.00 40.87 5.25
212 213 3.190118 GTGAGGAGAGTGAAAGCATTTGG 59.810 47.826 0.00 0.00 39.27 3.28
229 230 2.724977 TCGCAGTAAAGTCAGTGAGG 57.275 50.000 0.00 0.00 0.00 3.86
230 231 4.051922 AGTTTCGCAGTAAAGTCAGTGAG 58.948 43.478 0.00 0.00 0.00 3.51
241 242 1.606885 CCGGGGGTAGTTTCGCAGTA 61.607 60.000 0.00 0.00 0.00 2.74
277 285 3.003689 CGCATGGGCTAGTGGAAAAATAG 59.996 47.826 0.00 0.00 38.10 1.73
289 297 1.228124 GTAATGGGCGCATGGGCTA 60.228 57.895 30.72 21.29 41.87 3.93
302 310 3.016736 AGAAAGATTGCCGTGGGTAATG 58.983 45.455 2.61 0.00 38.09 1.90
308 316 2.352960 GCTCTAAGAAAGATTGCCGTGG 59.647 50.000 0.00 0.00 32.41 4.94
312 320 5.367302 AGAGATGCTCTAAGAAAGATTGCC 58.633 41.667 0.00 0.00 39.28 4.52
326 334 9.734620 CATATAGACAAGCTATTAGAGATGCTC 57.265 37.037 0.00 0.00 40.30 4.26
327 335 9.473007 TCATATAGACAAGCTATTAGAGATGCT 57.527 33.333 0.00 0.00 40.30 3.79
366 374 1.928503 TGAGGTCACGTCGTGAAAAAC 59.071 47.619 28.48 16.72 44.49 2.43
367 375 2.296831 TGAGGTCACGTCGTGAAAAA 57.703 45.000 28.48 12.55 44.49 1.94
368 376 2.296831 TTGAGGTCACGTCGTGAAAA 57.703 45.000 28.48 17.21 44.49 2.29
369 377 2.296831 TTTGAGGTCACGTCGTGAAA 57.703 45.000 28.48 16.68 44.49 2.69
370 378 1.928503 GTTTTGAGGTCACGTCGTGAA 59.071 47.619 28.48 11.41 44.49 3.18
371 379 1.135053 TGTTTTGAGGTCACGTCGTGA 60.135 47.619 23.70 23.70 40.50 4.35
372 380 1.257936 CTGTTTTGAGGTCACGTCGTG 59.742 52.381 19.38 19.38 34.45 4.35
373 381 1.567504 CTGTTTTGAGGTCACGTCGT 58.432 50.000 0.00 0.00 0.00 4.34
374 382 0.859232 CCTGTTTTGAGGTCACGTCG 59.141 55.000 0.00 0.00 0.00 5.12
375 383 1.597663 CACCTGTTTTGAGGTCACGTC 59.402 52.381 0.00 0.00 45.15 4.34
376 384 1.065709 ACACCTGTTTTGAGGTCACGT 60.066 47.619 0.00 0.00 45.15 4.49
377 385 1.663695 ACACCTGTTTTGAGGTCACG 58.336 50.000 0.00 0.00 45.15 4.35
378 386 3.013921 TGAACACCTGTTTTGAGGTCAC 58.986 45.455 0.00 0.00 45.15 3.67
379 387 3.358111 TGAACACCTGTTTTGAGGTCA 57.642 42.857 0.00 0.00 45.15 4.02
380 388 3.442273 TGTTGAACACCTGTTTTGAGGTC 59.558 43.478 0.00 0.00 45.15 3.85
382 390 3.734902 GCTGTTGAACACCTGTTTTGAGG 60.735 47.826 0.00 0.00 38.56 3.86
383 391 3.129287 AGCTGTTGAACACCTGTTTTGAG 59.871 43.478 0.00 0.00 38.56 3.02
384 392 3.088532 AGCTGTTGAACACCTGTTTTGA 58.911 40.909 0.00 0.00 38.56 2.69
385 393 3.508744 AGCTGTTGAACACCTGTTTTG 57.491 42.857 0.00 0.00 38.56 2.44
386 394 5.594317 AGATAAGCTGTTGAACACCTGTTTT 59.406 36.000 0.00 0.00 38.56 2.43
387 395 5.133221 AGATAAGCTGTTGAACACCTGTTT 58.867 37.500 0.00 0.00 38.56 2.83
388 396 4.718961 AGATAAGCTGTTGAACACCTGTT 58.281 39.130 0.00 0.00 41.64 3.16
389 397 4.357918 AGATAAGCTGTTGAACACCTGT 57.642 40.909 0.00 0.00 0.00 4.00
390 398 9.416794 CTATATAGATAAGCTGTTGAACACCTG 57.583 37.037 3.44 0.00 0.00 4.00
391 399 9.148879 ACTATATAGATAAGCTGTTGAACACCT 57.851 33.333 16.79 0.00 0.00 4.00
392 400 9.413048 GACTATATAGATAAGCTGTTGAACACC 57.587 37.037 16.79 0.00 0.00 4.16
393 401 9.119329 CGACTATATAGATAAGCTGTTGAACAC 57.881 37.037 16.79 0.00 0.00 3.32
394 402 8.847196 ACGACTATATAGATAAGCTGTTGAACA 58.153 33.333 16.79 0.00 0.00 3.18
395 403 9.332301 GACGACTATATAGATAAGCTGTTGAAC 57.668 37.037 16.79 0.00 0.00 3.18
396 404 9.286170 AGACGACTATATAGATAAGCTGTTGAA 57.714 33.333 16.79 0.00 0.00 2.69
397 405 8.850007 AGACGACTATATAGATAAGCTGTTGA 57.150 34.615 16.79 0.00 0.00 3.18
413 421 9.742144 AGAGGATGTGTATATTTAGACGACTAT 57.258 33.333 0.00 0.00 0.00 2.12
415 423 9.570468 TTAGAGGATGTGTATATTTAGACGACT 57.430 33.333 0.00 0.00 0.00 4.18
423 431 8.871125 AGGTCGATTTAGAGGATGTGTATATTT 58.129 33.333 0.00 0.00 0.00 1.40
424 432 8.423906 AGGTCGATTTAGAGGATGTGTATATT 57.576 34.615 0.00 0.00 0.00 1.28
425 433 7.148222 CGAGGTCGATTTAGAGGATGTGTATAT 60.148 40.741 0.00 0.00 43.02 0.86
426 434 6.148976 CGAGGTCGATTTAGAGGATGTGTATA 59.851 42.308 0.00 0.00 43.02 1.47
427 435 5.048643 CGAGGTCGATTTAGAGGATGTGTAT 60.049 44.000 0.00 0.00 43.02 2.29
428 436 4.275196 CGAGGTCGATTTAGAGGATGTGTA 59.725 45.833 0.00 0.00 43.02 2.90
429 437 3.066900 CGAGGTCGATTTAGAGGATGTGT 59.933 47.826 0.00 0.00 43.02 3.72
430 438 3.315470 TCGAGGTCGATTTAGAGGATGTG 59.685 47.826 0.00 0.00 44.22 3.21
431 439 3.552875 TCGAGGTCGATTTAGAGGATGT 58.447 45.455 0.00 0.00 44.22 3.06
444 452 1.065102 ACGTGGATATTGTCGAGGTCG 59.935 52.381 0.00 0.00 41.45 4.79
445 453 2.358267 AGACGTGGATATTGTCGAGGTC 59.642 50.000 0.00 9.23 45.23 3.85
446 454 2.099263 CAGACGTGGATATTGTCGAGGT 59.901 50.000 0.00 0.00 36.55 3.85
447 455 2.732366 CAGACGTGGATATTGTCGAGG 58.268 52.381 0.00 0.00 37.69 4.63
459 467 1.800586 CTTCACATTGTCCAGACGTGG 59.199 52.381 0.00 0.00 46.63 4.94
460 468 1.800586 CCTTCACATTGTCCAGACGTG 59.199 52.381 0.00 0.00 0.00 4.49
461 469 1.878102 GCCTTCACATTGTCCAGACGT 60.878 52.381 0.00 0.00 0.00 4.34
462 470 0.798776 GCCTTCACATTGTCCAGACG 59.201 55.000 0.00 0.00 0.00 4.18
463 471 1.896220 TGCCTTCACATTGTCCAGAC 58.104 50.000 0.00 0.00 0.00 3.51
464 472 2.885135 ATGCCTTCACATTGTCCAGA 57.115 45.000 0.00 0.00 0.00 3.86
471 479 5.769662 TGAGTTTAGACAATGCCTTCACATT 59.230 36.000 0.00 0.00 40.90 2.71
472 480 5.316167 TGAGTTTAGACAATGCCTTCACAT 58.684 37.500 0.00 0.00 0.00 3.21
473 481 4.713553 TGAGTTTAGACAATGCCTTCACA 58.286 39.130 0.00 0.00 0.00 3.58
474 482 4.757149 ACTGAGTTTAGACAATGCCTTCAC 59.243 41.667 0.00 0.00 0.00 3.18
475 483 4.973168 ACTGAGTTTAGACAATGCCTTCA 58.027 39.130 0.00 0.00 0.00 3.02
476 484 5.693814 CAACTGAGTTTAGACAATGCCTTC 58.306 41.667 0.00 0.00 0.00 3.46
477 485 4.022849 GCAACTGAGTTTAGACAATGCCTT 60.023 41.667 0.00 0.00 0.00 4.35
478 486 3.503748 GCAACTGAGTTTAGACAATGCCT 59.496 43.478 0.00 0.00 0.00 4.75
479 487 3.253188 TGCAACTGAGTTTAGACAATGCC 59.747 43.478 0.00 0.00 32.07 4.40
480 488 4.023707 ACTGCAACTGAGTTTAGACAATGC 60.024 41.667 11.87 4.39 32.98 3.56
481 489 5.237127 TGACTGCAACTGAGTTTAGACAATG 59.763 40.000 11.87 0.00 0.00 2.82
482 490 5.368145 TGACTGCAACTGAGTTTAGACAAT 58.632 37.500 11.87 0.00 0.00 2.71
483 491 4.765273 TGACTGCAACTGAGTTTAGACAA 58.235 39.130 11.87 0.00 0.00 3.18
484 492 4.400529 TGACTGCAACTGAGTTTAGACA 57.599 40.909 11.87 9.41 0.00 3.41
485 493 4.991056 TCATGACTGCAACTGAGTTTAGAC 59.009 41.667 11.87 7.36 0.00 2.59
486 494 5.213891 TCATGACTGCAACTGAGTTTAGA 57.786 39.130 11.87 0.00 0.00 2.10
487 495 6.492007 AATCATGACTGCAACTGAGTTTAG 57.508 37.500 0.00 0.00 0.00 1.85
488 496 6.712095 AGAAATCATGACTGCAACTGAGTTTA 59.288 34.615 0.00 0.00 0.00 2.01
489 497 5.533903 AGAAATCATGACTGCAACTGAGTTT 59.466 36.000 0.00 0.00 0.00 2.66
490 498 5.068636 AGAAATCATGACTGCAACTGAGTT 58.931 37.500 0.00 0.00 0.00 3.01
491 499 4.649692 AGAAATCATGACTGCAACTGAGT 58.350 39.130 0.00 0.00 0.00 3.41
492 500 5.411977 AGAAGAAATCATGACTGCAACTGAG 59.588 40.000 0.00 0.00 0.00 3.35
493 501 5.311265 AGAAGAAATCATGACTGCAACTGA 58.689 37.500 0.00 0.00 0.00 3.41
494 502 5.624344 AGAAGAAATCATGACTGCAACTG 57.376 39.130 0.00 0.00 0.00 3.16
495 503 6.002704 AGAAGAAGAAATCATGACTGCAACT 58.997 36.000 0.00 0.00 0.00 3.16
496 504 6.251655 AGAAGAAGAAATCATGACTGCAAC 57.748 37.500 0.00 0.00 0.00 4.17
497 505 6.713903 AGAAGAAGAAGAAATCATGACTGCAA 59.286 34.615 0.00 0.00 0.00 4.08
498 506 6.236409 AGAAGAAGAAGAAATCATGACTGCA 58.764 36.000 0.00 0.00 0.00 4.41
499 507 6.370994 TGAGAAGAAGAAGAAATCATGACTGC 59.629 38.462 0.00 0.00 0.00 4.40
500 508 7.413219 GCTGAGAAGAAGAAGAAATCATGACTG 60.413 40.741 0.00 0.00 0.00 3.51
501 509 6.594937 GCTGAGAAGAAGAAGAAATCATGACT 59.405 38.462 0.00 0.00 0.00 3.41
502 510 6.455380 CGCTGAGAAGAAGAAGAAATCATGAC 60.455 42.308 0.00 0.00 0.00 3.06
503 511 5.579904 CGCTGAGAAGAAGAAGAAATCATGA 59.420 40.000 0.00 0.00 0.00 3.07
504 512 5.579904 TCGCTGAGAAGAAGAAGAAATCATG 59.420 40.000 0.00 0.00 0.00 3.07
505 513 5.580297 GTCGCTGAGAAGAAGAAGAAATCAT 59.420 40.000 0.00 0.00 0.00 2.45
506 514 4.926238 GTCGCTGAGAAGAAGAAGAAATCA 59.074 41.667 0.00 0.00 0.00 2.57
507 515 4.031201 CGTCGCTGAGAAGAAGAAGAAATC 59.969 45.833 0.00 0.00 0.00 2.17
508 516 3.923461 CGTCGCTGAGAAGAAGAAGAAAT 59.077 43.478 0.00 0.00 0.00 2.17
509 517 3.309388 CGTCGCTGAGAAGAAGAAGAAA 58.691 45.455 0.00 0.00 0.00 2.52
510 518 2.351835 CCGTCGCTGAGAAGAAGAAGAA 60.352 50.000 0.00 0.00 0.00 2.52
511 519 1.200252 CCGTCGCTGAGAAGAAGAAGA 59.800 52.381 0.00 0.00 0.00 2.87
512 520 1.623359 CCGTCGCTGAGAAGAAGAAG 58.377 55.000 0.00 0.00 0.00 2.85
513 521 0.388649 GCCGTCGCTGAGAAGAAGAA 60.389 55.000 0.00 0.00 0.00 2.52
514 522 1.213013 GCCGTCGCTGAGAAGAAGA 59.787 57.895 0.00 0.00 0.00 2.87
515 523 1.807573 GGCCGTCGCTGAGAAGAAG 60.808 63.158 0.00 0.00 34.44 2.85
516 524 2.261671 GGCCGTCGCTGAGAAGAA 59.738 61.111 0.00 0.00 34.44 2.52
517 525 3.760035 GGGCCGTCGCTGAGAAGA 61.760 66.667 0.00 0.00 34.44 2.87
518 526 4.069232 TGGGCCGTCGCTGAGAAG 62.069 66.667 0.00 0.00 34.44 2.85
519 527 4.373116 GTGGGCCGTCGCTGAGAA 62.373 66.667 0.00 0.00 34.44 2.87
526 534 4.082523 ATGACAGGTGGGCCGTCG 62.083 66.667 0.00 0.00 39.45 5.12
527 535 2.436646 CATGACAGGTGGGCCGTC 60.437 66.667 0.00 0.00 40.50 4.79
528 536 4.033776 CCATGACAGGTGGGCCGT 62.034 66.667 0.00 0.00 40.50 5.68
529 537 3.567579 AACCATGACAGGTGGGCCG 62.568 63.158 0.00 0.00 42.25 6.13
530 538 1.678970 GAACCATGACAGGTGGGCC 60.679 63.158 0.00 0.00 42.25 5.80
531 539 1.678970 GGAACCATGACAGGTGGGC 60.679 63.158 0.00 0.00 42.25 5.36
532 540 0.322816 CAGGAACCATGACAGGTGGG 60.323 60.000 0.00 0.00 42.25 4.61
533 541 0.401738 ACAGGAACCATGACAGGTGG 59.598 55.000 0.00 0.00 42.25 4.61
534 542 3.634397 ATACAGGAACCATGACAGGTG 57.366 47.619 0.00 0.00 42.25 4.00
535 543 6.267928 GTCTATATACAGGAACCATGACAGGT 59.732 42.308 0.00 0.00 45.91 4.00
536 544 6.267699 TGTCTATATACAGGAACCATGACAGG 59.732 42.308 0.00 0.00 0.00 4.00
537 545 7.290110 TGTCTATATACAGGAACCATGACAG 57.710 40.000 0.00 0.00 0.00 3.51
538 546 7.855784 ATGTCTATATACAGGAACCATGACA 57.144 36.000 0.00 0.00 35.63 3.58
539 547 8.589338 AGAATGTCTATATACAGGAACCATGAC 58.411 37.037 0.00 0.00 31.70 3.06
540 548 8.727100 AGAATGTCTATATACAGGAACCATGA 57.273 34.615 0.00 0.00 31.70 3.07
544 552 9.372369 GCATTAGAATGTCTATATACAGGAACC 57.628 37.037 4.27 0.00 38.65 3.62
545 553 9.929180 TGCATTAGAATGTCTATATACAGGAAC 57.071 33.333 4.27 0.00 38.65 3.62
553 561 9.851686 TCCAGTTTTGCATTAGAATGTCTATAT 57.148 29.630 4.27 0.00 38.65 0.86
554 562 9.679661 TTCCAGTTTTGCATTAGAATGTCTATA 57.320 29.630 4.27 0.00 38.65 1.31
555 563 8.579850 TTCCAGTTTTGCATTAGAATGTCTAT 57.420 30.769 4.27 0.00 38.65 1.98
556 564 7.665559 ACTTCCAGTTTTGCATTAGAATGTCTA 59.334 33.333 4.27 0.00 38.65 2.59
557 565 6.491403 ACTTCCAGTTTTGCATTAGAATGTCT 59.509 34.615 4.27 0.00 38.65 3.41
558 566 6.583806 CACTTCCAGTTTTGCATTAGAATGTC 59.416 38.462 4.27 0.00 38.65 3.06
559 567 6.040842 ACACTTCCAGTTTTGCATTAGAATGT 59.959 34.615 4.27 0.00 38.65 2.71
560 568 6.449698 ACACTTCCAGTTTTGCATTAGAATG 58.550 36.000 0.00 0.00 39.40 2.67
561 569 6.655078 ACACTTCCAGTTTTGCATTAGAAT 57.345 33.333 0.00 0.00 0.00 2.40
562 570 7.759489 ATACACTTCCAGTTTTGCATTAGAA 57.241 32.000 0.00 0.00 0.00 2.10
563 571 8.892723 CATATACACTTCCAGTTTTGCATTAGA 58.107 33.333 0.00 0.00 0.00 2.10
564 572 8.892723 TCATATACACTTCCAGTTTTGCATTAG 58.107 33.333 0.00 0.00 0.00 1.73
565 573 8.800370 TCATATACACTTCCAGTTTTGCATTA 57.200 30.769 0.00 0.00 0.00 1.90
566 574 7.611467 TCTCATATACACTTCCAGTTTTGCATT 59.389 33.333 0.00 0.00 0.00 3.56
567 575 7.112122 TCTCATATACACTTCCAGTTTTGCAT 58.888 34.615 0.00 0.00 0.00 3.96
568 576 6.472016 TCTCATATACACTTCCAGTTTTGCA 58.528 36.000 0.00 0.00 0.00 4.08
569 577 6.818644 TCTCTCATATACACTTCCAGTTTTGC 59.181 38.462 0.00 0.00 0.00 3.68
570 578 8.777865 TTCTCTCATATACACTTCCAGTTTTG 57.222 34.615 0.00 0.00 0.00 2.44
571 579 9.606631 GATTCTCTCATATACACTTCCAGTTTT 57.393 33.333 0.00 0.00 0.00 2.43
572 580 8.986991 AGATTCTCTCATATACACTTCCAGTTT 58.013 33.333 0.00 0.00 0.00 2.66
573 581 8.546083 AGATTCTCTCATATACACTTCCAGTT 57.454 34.615 0.00 0.00 0.00 3.16
574 582 8.546083 AAGATTCTCTCATATACACTTCCAGT 57.454 34.615 0.00 0.00 0.00 4.00
575 583 9.829507 AAAAGATTCTCTCATATACACTTCCAG 57.170 33.333 0.00 0.00 0.00 3.86
588 596 9.354673 AGACAATGGTTTAAAAAGATTCTCTCA 57.645 29.630 0.00 0.00 0.00 3.27
627 635 9.006839 CAATAGCATGTGTATATTTGGATGTCT 57.993 33.333 0.00 0.00 0.00 3.41
628 636 8.239314 CCAATAGCATGTGTATATTTGGATGTC 58.761 37.037 0.00 0.00 0.00 3.06
629 637 7.944000 TCCAATAGCATGTGTATATTTGGATGT 59.056 33.333 0.00 0.00 0.00 3.06
630 638 8.339344 TCCAATAGCATGTGTATATTTGGATG 57.661 34.615 0.00 0.00 0.00 3.51
631 639 8.385491 TCTCCAATAGCATGTGTATATTTGGAT 58.615 33.333 0.00 0.00 0.00 3.41
632 640 7.744733 TCTCCAATAGCATGTGTATATTTGGA 58.255 34.615 0.00 0.00 0.00 3.53
633 641 7.984422 TCTCCAATAGCATGTGTATATTTGG 57.016 36.000 0.00 0.00 0.00 3.28
634 642 7.966753 GCATCTCCAATAGCATGTGTATATTTG 59.033 37.037 0.00 0.00 0.00 2.32
635 643 7.886970 AGCATCTCCAATAGCATGTGTATATTT 59.113 33.333 0.00 0.00 0.00 1.40
636 644 7.400439 AGCATCTCCAATAGCATGTGTATATT 58.600 34.615 0.00 0.00 0.00 1.28
637 645 6.955364 AGCATCTCCAATAGCATGTGTATAT 58.045 36.000 0.00 0.00 0.00 0.86
638 646 6.364568 AGCATCTCCAATAGCATGTGTATA 57.635 37.500 0.00 0.00 0.00 1.47
639 647 5.238624 AGCATCTCCAATAGCATGTGTAT 57.761 39.130 0.00 0.00 0.00 2.29
640 648 4.635223 GAGCATCTCCAATAGCATGTGTA 58.365 43.478 0.00 0.00 0.00 2.90
641 649 3.474600 GAGCATCTCCAATAGCATGTGT 58.525 45.455 0.00 0.00 0.00 3.72
652 660 7.801430 AGTTGAGTACTAGTAAGAGCATCTCCA 60.801 40.741 3.61 0.00 39.39 3.86
653 661 6.544564 AGTTGAGTACTAGTAAGAGCATCTCC 59.455 42.308 3.61 0.00 39.39 3.71
654 662 7.562454 AGTTGAGTACTAGTAAGAGCATCTC 57.438 40.000 3.61 5.90 39.39 2.75
655 663 7.394923 ACAAGTTGAGTACTAGTAAGAGCATCT 59.605 37.037 10.54 0.00 42.31 2.90
656 664 7.540299 ACAAGTTGAGTACTAGTAAGAGCATC 58.460 38.462 10.54 0.91 35.54 3.91
657 665 7.176865 TGACAAGTTGAGTACTAGTAAGAGCAT 59.823 37.037 10.54 0.00 35.54 3.79
658 666 6.489022 TGACAAGTTGAGTACTAGTAAGAGCA 59.511 38.462 10.54 0.00 35.54 4.26
659 667 6.910995 TGACAAGTTGAGTACTAGTAAGAGC 58.089 40.000 10.54 0.00 35.54 4.09
660 668 7.175293 ACCTGACAAGTTGAGTACTAGTAAGAG 59.825 40.741 10.54 0.00 35.54 2.85
661 669 7.002879 ACCTGACAAGTTGAGTACTAGTAAGA 58.997 38.462 10.54 0.00 35.54 2.10
662 670 7.216973 ACCTGACAAGTTGAGTACTAGTAAG 57.783 40.000 10.54 0.00 35.54 2.34
663 671 8.159447 TCTACCTGACAAGTTGAGTACTAGTAA 58.841 37.037 10.54 0.00 35.54 2.24
664 672 7.683578 TCTACCTGACAAGTTGAGTACTAGTA 58.316 38.462 10.54 0.00 35.54 1.82
665 673 6.540995 TCTACCTGACAAGTTGAGTACTAGT 58.459 40.000 10.54 0.00 35.54 2.57
666 674 7.633193 ATCTACCTGACAAGTTGAGTACTAG 57.367 40.000 10.54 3.08 35.54 2.57
667 675 7.148289 CGAATCTACCTGACAAGTTGAGTACTA 60.148 40.741 10.54 0.00 35.54 1.82
668 676 6.349445 CGAATCTACCTGACAAGTTGAGTACT 60.349 42.308 10.54 0.00 39.32 2.73
669 677 5.800941 CGAATCTACCTGACAAGTTGAGTAC 59.199 44.000 10.54 0.00 0.00 2.73
677 685 2.482142 GCCTCCGAATCTACCTGACAAG 60.482 54.545 0.00 0.00 0.00 3.16
684 692 2.584236 TCTACTGCCTCCGAATCTACC 58.416 52.381 0.00 0.00 0.00 3.18
696 710 6.038603 TGCTCATTAACATTCATTCTACTGCC 59.961 38.462 0.00 0.00 0.00 4.85
715 729 8.601047 TCCTGCTAATAATCTATACTGCTCAT 57.399 34.615 0.00 0.00 0.00 2.90
755 778 7.363431 GTTTTGTCTGTGGATTAAGAAGAAGG 58.637 38.462 0.00 0.00 0.00 3.46
828 1056 1.878656 GACACGGGACAGTGCTAGCT 61.879 60.000 17.23 0.00 45.45 3.32
829 1057 1.446272 GACACGGGACAGTGCTAGC 60.446 63.158 8.10 8.10 45.45 3.42
830 1058 0.603569 AAGACACGGGACAGTGCTAG 59.396 55.000 0.00 0.00 45.45 3.42
831 1059 0.601558 GAAGACACGGGACAGTGCTA 59.398 55.000 0.00 0.00 45.45 3.49
869 1097 2.509569 GAGTGAGAGTGAGAGTGTGGA 58.490 52.381 0.00 0.00 0.00 4.02
871 1099 2.234143 TGGAGTGAGAGTGAGAGTGTG 58.766 52.381 0.00 0.00 0.00 3.82
872 1100 2.666272 TGGAGTGAGAGTGAGAGTGT 57.334 50.000 0.00 0.00 0.00 3.55
899 1133 1.290324 CGGTGGTGGTGAGAGTCTG 59.710 63.158 0.00 0.00 0.00 3.51
901 1135 0.319641 GAACGGTGGTGGTGAGAGTC 60.320 60.000 0.00 0.00 0.00 3.36
914 1148 0.638292 TATAGAGGGTGGGGAACGGT 59.362 55.000 0.00 0.00 0.00 4.83
926 1161 1.339151 GCCGGGGATGCTTTATAGAGG 60.339 57.143 2.18 0.00 0.00 3.69
958 1193 2.769893 TGTCGCCTGGTTTACTTTACC 58.230 47.619 0.00 0.00 36.17 2.85
1200 1441 2.812499 CCGTACCAGATCGGGTGG 59.188 66.667 25.72 16.09 42.39 4.61
1395 1636 2.811317 GCGTCGCACTTCTCCTGG 60.811 66.667 13.44 0.00 0.00 4.45
1461 1702 2.028484 GTCACCGCGTCCTTGACA 59.972 61.111 17.46 0.00 39.60 3.58
1512 1753 2.933834 AGCACCAGGTACACCCCC 60.934 66.667 0.00 0.00 36.42 5.40
1545 1786 3.016474 GCAGAAGTTCTCCACGCGC 62.016 63.158 5.73 0.00 0.00 6.86
1779 2020 2.511600 GGGTTGGACGCCATCTCG 60.512 66.667 0.00 0.00 31.53 4.04
1893 2135 4.087892 AGCAGCTGGCCGGTGTAG 62.088 66.667 17.12 5.76 46.50 2.74
1932 2174 0.736325 CGCCGTTGAGGTTGTAGGAG 60.736 60.000 0.00 0.00 43.70 3.69
2034 2276 2.096174 ACGAAAGAGACGCTAGTGCTAG 59.904 50.000 2.40 2.04 36.97 3.42
2040 2282 2.476519 GGTGAGACGAAAGAGACGCTAG 60.477 54.545 0.00 0.00 0.00 3.42
2047 2290 4.170723 GGCGGTGAGACGAAAGAG 57.829 61.111 0.00 0.00 35.47 2.85
2089 2332 1.224075 CACTACTACCGCTAGCGCTA 58.776 55.000 31.35 20.95 38.24 4.26
2090 2333 0.747283 ACACTACTACCGCTAGCGCT 60.747 55.000 31.35 20.95 38.24 5.92
2091 2334 0.100146 AACACTACTACCGCTAGCGC 59.900 55.000 31.35 0.00 38.24 5.92
2092 2335 1.268437 GGAACACTACTACCGCTAGCG 60.268 57.143 29.93 29.93 39.44 4.26
2093 2336 2.022934 AGGAACACTACTACCGCTAGC 58.977 52.381 4.06 4.06 0.00 3.42
2179 2426 3.628032 CGGCTCACTGACTCTATACAAGA 59.372 47.826 0.00 0.00 0.00 3.02
2180 2427 3.628032 TCGGCTCACTGACTCTATACAAG 59.372 47.826 0.00 0.00 0.00 3.16
2181 2428 3.617284 TCGGCTCACTGACTCTATACAA 58.383 45.455 0.00 0.00 0.00 2.41
2205 2452 1.224592 GGATCGGACCACCATGCTT 59.775 57.895 0.00 0.00 35.59 3.91
2206 2453 2.911143 GGATCGGACCACCATGCT 59.089 61.111 0.00 0.00 35.59 3.79
2207 2454 2.588877 CGGATCGGACCACCATGC 60.589 66.667 0.00 0.00 35.59 4.06
2235 2482 1.496444 TACCAACCATGAGCCAGCCA 61.496 55.000 0.00 0.00 0.00 4.75
2242 2523 1.027357 GCAGGCATACCAACCATGAG 58.973 55.000 0.00 0.00 39.06 2.90
2247 2528 3.051392 GCACGCAGGCATACCAACC 62.051 63.158 0.00 0.00 39.06 3.77
2257 2538 2.128853 AAACATTGTCCGCACGCAGG 62.129 55.000 0.00 0.00 0.00 4.85
2296 2577 3.582647 GGGGAAGGAAATGGACAAAATGT 59.417 43.478 0.00 0.00 0.00 2.71
2317 2598 1.296056 ATTTGAACGAACCCGAGCGG 61.296 55.000 1.06 1.06 39.50 5.52
2319 2600 2.031508 TCAAATTTGAACGAACCCGAGC 60.032 45.455 18.45 0.00 34.05 5.03
2320 2601 3.889196 TCAAATTTGAACGAACCCGAG 57.111 42.857 18.45 0.00 34.05 4.63
2321 2602 4.541779 CAATCAAATTTGAACGAACCCGA 58.458 39.130 23.91 0.00 41.13 5.14
2322 2603 3.672867 CCAATCAAATTTGAACGAACCCG 59.327 43.478 23.91 7.12 41.13 5.28
2323 2604 3.431912 GCCAATCAAATTTGAACGAACCC 59.568 43.478 23.91 6.41 41.13 4.11
2354 2636 8.956533 TGCTACATGTTTCAAATATGCTACTA 57.043 30.769 2.30 0.00 33.79 1.82
2355 2637 7.770433 TCTGCTACATGTTTCAAATATGCTACT 59.230 33.333 2.30 0.00 33.79 2.57
2363 2649 6.869913 CCAATGTTCTGCTACATGTTTCAAAT 59.130 34.615 2.30 0.00 38.69 2.32
2378 2664 3.981071 TGTACTCCTCCCAATGTTCTG 57.019 47.619 0.00 0.00 0.00 3.02
2380 2666 7.201821 CCAATAATTGTACTCCTCCCAATGTTC 60.202 40.741 0.00 0.00 0.00 3.18
2382 2668 6.069088 TCCAATAATTGTACTCCTCCCAATGT 60.069 38.462 0.00 0.00 0.00 2.71
2383 2669 6.364701 TCCAATAATTGTACTCCTCCCAATG 58.635 40.000 0.00 0.00 0.00 2.82
2384 2670 6.389869 TCTCCAATAATTGTACTCCTCCCAAT 59.610 38.462 0.00 0.00 0.00 3.16
2385 2671 5.729229 TCTCCAATAATTGTACTCCTCCCAA 59.271 40.000 0.00 0.00 0.00 4.12
2386 2672 5.130477 GTCTCCAATAATTGTACTCCTCCCA 59.870 44.000 0.00 0.00 0.00 4.37
2387 2673 5.612351 GTCTCCAATAATTGTACTCCTCCC 58.388 45.833 0.00 0.00 0.00 4.30
2388 2674 5.068723 TCGTCTCCAATAATTGTACTCCTCC 59.931 44.000 0.00 0.00 0.00 4.30
2389 2675 6.145338 TCGTCTCCAATAATTGTACTCCTC 57.855 41.667 0.00 0.00 0.00 3.71
2390 2676 5.069251 CCTCGTCTCCAATAATTGTACTCCT 59.931 44.000 0.00 0.00 0.00 3.69
2549 2923 2.514592 CCATCATGGCGCTCCGTT 60.515 61.111 7.64 0.00 34.14 4.44
2550 2924 3.740128 GACCATCATGGCGCTCCGT 62.740 63.158 7.64 0.00 42.67 4.69
2551 2925 2.969238 GACCATCATGGCGCTCCG 60.969 66.667 7.64 0.00 42.67 4.63
2559 2933 1.224069 GACGCCCATCGACCATCATG 61.224 60.000 0.00 0.00 41.67 3.07
2598 2972 4.010349 CAATCCAAGGAAGGGACACTTAC 58.990 47.826 0.00 0.00 40.21 2.34
2601 2992 1.355720 CCAATCCAAGGAAGGGACACT 59.644 52.381 3.96 0.00 37.23 3.55
2625 3071 1.805945 GACCACGGAGTAGCAAGCG 60.806 63.158 0.00 0.00 41.61 4.68
2631 3077 0.243907 CACTGGTGACCACGGAGTAG 59.756 60.000 0.00 0.00 41.61 2.57
2650 3102 1.061421 TCAATAATTCGTTCGGTGCGC 59.939 47.619 0.00 0.00 0.00 6.09
2739 3205 1.512926 CATCCTTATACGGTGCAGCC 58.487 55.000 10.90 2.64 0.00 4.85
2744 3210 1.056660 AGGCCCATCCTTATACGGTG 58.943 55.000 0.00 0.00 44.75 4.94
2745 3211 1.056660 CAGGCCCATCCTTATACGGT 58.943 55.000 0.00 0.00 44.75 4.83
2752 3218 0.033699 GAGAAAGCAGGCCCATCCTT 60.034 55.000 0.00 0.00 44.75 3.36
2755 3221 1.821332 CGGAGAAAGCAGGCCCATC 60.821 63.158 0.00 0.00 0.00 3.51
2776 3242 1.327303 AGCAGGGCAAATGAAACGAA 58.673 45.000 0.00 0.00 0.00 3.85
2925 3405 4.827284 CCATCATTCACCCCAAGTATAACC 59.173 45.833 0.00 0.00 0.00 2.85
2966 3450 3.979495 CGAAGTTGGAGCGGTATATGTAC 59.021 47.826 0.00 0.00 0.00 2.90
2979 3463 3.695830 ATCTACTTTGGCGAAGTTGGA 57.304 42.857 24.39 20.93 46.34 3.53


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

AutoCloner maintained by Alex Coulton.