Multiple sequence alignment - TraesCS2B01G152500

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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 TraesCS2B01G152500 chr2B 100.000 2670 0 0 453 3122 119183039 119185708 0.000000e+00 4931.0
1 TraesCS2B01G152500 chr2B 100.000 65 0 0 1 65 119182587 119182651 1.520000e-23 121.0
2 TraesCS2B01G152500 chr2D 93.875 1551 68 9 834 2379 77183474 77185002 0.000000e+00 2313.0
3 TraesCS2B01G152500 chr2D 88.108 740 84 2 2382 3121 386839721 386840456 0.000000e+00 876.0
4 TraesCS2B01G152500 chr2D 87.500 128 15 1 696 823 77182200 77182326 2.510000e-31 147.0
5 TraesCS2B01G152500 chr2A 90.553 741 63 2 1329 2068 78190098 78190832 0.000000e+00 974.0
6 TraesCS2B01G152500 chr2A 90.785 586 43 6 710 1284 78189501 78190086 0.000000e+00 773.0
7 TraesCS2B01G152500 chr2A 83.486 218 23 6 2056 2271 78216228 78216434 1.140000e-44 191.0
8 TraesCS2B01G152500 chr2A 89.899 99 10 0 2281 2379 78216697 78216795 9.090000e-26 128.0
9 TraesCS2B01G152500 chr2A 97.436 39 1 0 1658 1696 191899210 191899172 2.010000e-07 67.6
10 TraesCS2B01G152500 chr6D 89.623 742 70 5 2382 3122 137122353 137121618 0.000000e+00 937.0
11 TraesCS2B01G152500 chr6D 88.472 746 79 6 2378 3122 351928361 351929100 0.000000e+00 894.0
12 TraesCS2B01G152500 chr4D 88.799 741 78 4 2382 3122 32771405 32770670 0.000000e+00 904.0
13 TraesCS2B01G152500 chr4D 88.769 739 72 10 2386 3122 431621046 431621775 0.000000e+00 894.0
14 TraesCS2B01G152500 chr4D 88.498 739 74 9 2386 3122 431674408 431675137 0.000000e+00 883.0
15 TraesCS2B01G152500 chr4D 88.363 739 75 10 2386 3122 431555281 431556010 0.000000e+00 878.0
16 TraesCS2B01G152500 chr4D 88.227 739 76 9 2386 3122 431733947 431734676 0.000000e+00 872.0
17 TraesCS2B01G152500 chr6B 87.701 748 82 8 2378 3122 76862672 76861932 0.000000e+00 863.0
18 TraesCS2B01G152500 chr7D 77.167 473 85 16 1649 2105 574759135 574759600 1.440000e-63 254.0
19 TraesCS2B01G152500 chr7B 72.170 751 153 30 1387 2109 634559436 634560158 8.900000e-41 178.0
20 TraesCS2B01G152500 chr1B 82.787 122 18 1 1160 1281 92551060 92551178 4.260000e-19 106.0
21 TraesCS2B01G152500 chr1A 81.600 125 18 3 1158 1281 56600582 56600702 7.130000e-17 99.0
22 TraesCS2B01G152500 chr1A 97.436 39 1 0 1658 1696 309700229 309700191 2.010000e-07 67.6
23 TraesCS2B01G152500 chr1A 97.436 39 1 0 1658 1696 456472603 456472565 2.010000e-07 67.6
24 TraesCS2B01G152500 chr7A 97.436 39 1 0 1658 1696 577689902 577689940 2.010000e-07 67.6
25 TraesCS2B01G152500 chr5A 97.436 39 1 0 1658 1696 648814218 648814256 2.010000e-07 67.6


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 TraesCS2B01G152500 chr2B 119182587 119185708 3121 False 2526.0 4931 100.0000 1 3122 2 chr2B.!!$F1 3121
1 TraesCS2B01G152500 chr2D 77182200 77185002 2802 False 1230.0 2313 90.6875 696 2379 2 chr2D.!!$F2 1683
2 TraesCS2B01G152500 chr2D 386839721 386840456 735 False 876.0 876 88.1080 2382 3121 1 chr2D.!!$F1 739
3 TraesCS2B01G152500 chr2A 78189501 78190832 1331 False 873.5 974 90.6690 710 2068 2 chr2A.!!$F1 1358
4 TraesCS2B01G152500 chr6D 137121618 137122353 735 True 937.0 937 89.6230 2382 3122 1 chr6D.!!$R1 740
5 TraesCS2B01G152500 chr6D 351928361 351929100 739 False 894.0 894 88.4720 2378 3122 1 chr6D.!!$F1 744
6 TraesCS2B01G152500 chr4D 32770670 32771405 735 True 904.0 904 88.7990 2382 3122 1 chr4D.!!$R1 740
7 TraesCS2B01G152500 chr4D 431621046 431621775 729 False 894.0 894 88.7690 2386 3122 1 chr4D.!!$F2 736
8 TraesCS2B01G152500 chr4D 431674408 431675137 729 False 883.0 883 88.4980 2386 3122 1 chr4D.!!$F3 736
9 TraesCS2B01G152500 chr4D 431555281 431556010 729 False 878.0 878 88.3630 2386 3122 1 chr4D.!!$F1 736
10 TraesCS2B01G152500 chr4D 431733947 431734676 729 False 872.0 872 88.2270 2386 3122 1 chr4D.!!$F4 736
11 TraesCS2B01G152500 chr6B 76861932 76862672 740 True 863.0 863 87.7010 2378 3122 1 chr6B.!!$R1 744

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
518 519 0.032267 GTGTAGGGGCGAGTGCTATC 59.968 60.0 0.00 0.00 42.25 2.08 F
549 550 0.033228 TGTTTGCGCCAATGGAAAGG 59.967 50.0 2.05 0.00 29.41 3.11 F
652 653 0.105964 TTGGTGATCTATTCGGGCCG 59.894 55.0 22.51 22.51 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 2698 0.534203 AAGTCGAAATGTGGTGCCGT 60.534 50.000 0.0 0.0 0.0 5.68 R
1606 2749 1.079819 CCTCAATCAGCACGTCCGT 60.080 57.895 0.0 0.0 0.0 4.69 R
2431 3579 1.110518 TCCTACTCACGCCACACACA 61.111 55.000 0.0 0.0 0.0 3.72 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
24 25 1.002624 TGGAACCAACCAGATCCGC 60.003 57.895 0.00 0.00 34.77 5.54
25 26 1.749258 GGAACCAACCAGATCCGCC 60.749 63.158 0.00 0.00 0.00 6.13
26 27 1.299976 GAACCAACCAGATCCGCCT 59.700 57.895 0.00 0.00 0.00 5.52
27 28 1.002134 AACCAACCAGATCCGCCTG 60.002 57.895 0.00 0.00 0.00 4.85
28 29 2.825836 CCAACCAGATCCGCCTGC 60.826 66.667 0.00 0.00 32.97 4.85
29 30 2.270205 CAACCAGATCCGCCTGCT 59.730 61.111 0.00 0.00 32.97 4.24
30 31 1.522092 CAACCAGATCCGCCTGCTA 59.478 57.895 0.00 0.00 32.97 3.49
31 32 0.811616 CAACCAGATCCGCCTGCTAC 60.812 60.000 0.00 0.00 32.97 3.58
32 33 1.264749 AACCAGATCCGCCTGCTACA 61.265 55.000 0.00 0.00 32.97 2.74
33 34 1.264749 ACCAGATCCGCCTGCTACAA 61.265 55.000 0.00 0.00 32.97 2.41
34 35 0.531532 CCAGATCCGCCTGCTACAAG 60.532 60.000 0.00 0.00 32.97 3.16
35 36 0.531532 CAGATCCGCCTGCTACAAGG 60.532 60.000 0.00 0.00 40.63 3.61
42 43 4.408821 CTGCTACAAGGCCCCGCA 62.409 66.667 0.00 0.00 0.00 5.69
43 44 4.715523 TGCTACAAGGCCCCGCAC 62.716 66.667 0.00 0.00 0.00 5.34
45 46 4.077184 CTACAAGGCCCCGCACGA 62.077 66.667 0.00 0.00 0.00 4.35
46 47 3.599285 CTACAAGGCCCCGCACGAA 62.599 63.158 0.00 0.00 0.00 3.85
47 48 3.599285 TACAAGGCCCCGCACGAAG 62.599 63.158 0.00 0.00 0.00 3.79
58 59 4.760047 CACGAAGCTCCGGGGTGG 62.760 72.222 1.62 0.00 40.09 4.61
469 470 3.650369 CGGGGACAACAAGAACGG 58.350 61.111 0.00 0.00 0.00 4.44
470 471 1.964373 CGGGGACAACAAGAACGGG 60.964 63.158 0.00 0.00 0.00 5.28
471 472 2.265904 GGGGACAACAAGAACGGGC 61.266 63.158 0.00 0.00 0.00 6.13
472 473 1.527380 GGGACAACAAGAACGGGCA 60.527 57.895 0.00 0.00 0.00 5.36
473 474 1.515521 GGGACAACAAGAACGGGCAG 61.516 60.000 0.00 0.00 0.00 4.85
474 475 1.515521 GGACAACAAGAACGGGCAGG 61.516 60.000 0.00 0.00 0.00 4.85
475 476 1.515521 GACAACAAGAACGGGCAGGG 61.516 60.000 0.00 0.00 0.00 4.45
476 477 1.228124 CAACAAGAACGGGCAGGGA 60.228 57.895 0.00 0.00 0.00 4.20
477 478 0.609131 CAACAAGAACGGGCAGGGAT 60.609 55.000 0.00 0.00 0.00 3.85
478 479 0.609131 AACAAGAACGGGCAGGGATG 60.609 55.000 0.00 0.00 0.00 3.51
479 480 2.044946 AAGAACGGGCAGGGATGC 60.045 61.111 0.00 0.00 0.00 3.91
480 481 2.606587 AAGAACGGGCAGGGATGCT 61.607 57.895 0.00 0.00 34.73 3.79
481 482 2.514824 GAACGGGCAGGGATGCTC 60.515 66.667 0.00 0.00 34.73 4.26
504 505 3.015145 CAGGGGGTGGGGGTGTAG 61.015 72.222 0.00 0.00 0.00 2.74
505 506 4.364686 AGGGGGTGGGGGTGTAGG 62.365 72.222 0.00 0.00 0.00 3.18
513 514 3.782443 GGGGTGTAGGGGCGAGTG 61.782 72.222 0.00 0.00 0.00 3.51
514 515 4.468689 GGGTGTAGGGGCGAGTGC 62.469 72.222 0.00 0.00 41.71 4.40
515 516 3.391382 GGTGTAGGGGCGAGTGCT 61.391 66.667 0.00 0.00 42.25 4.40
516 517 2.056223 GGTGTAGGGGCGAGTGCTA 61.056 63.158 0.00 0.00 42.25 3.49
517 518 1.400530 GGTGTAGGGGCGAGTGCTAT 61.401 60.000 0.00 0.00 42.25 2.97
518 519 0.032267 GTGTAGGGGCGAGTGCTATC 59.968 60.000 0.00 0.00 42.25 2.08
519 520 1.113517 TGTAGGGGCGAGTGCTATCC 61.114 60.000 0.00 0.00 42.25 2.59
520 521 1.113517 GTAGGGGCGAGTGCTATCCA 61.114 60.000 0.00 0.00 42.25 3.41
521 522 0.827925 TAGGGGCGAGTGCTATCCAG 60.828 60.000 0.00 0.00 42.25 3.86
532 533 1.668419 GCTATCCAGCGGAAATGTGT 58.332 50.000 1.44 0.00 38.22 3.72
533 534 2.017049 GCTATCCAGCGGAAATGTGTT 58.983 47.619 1.44 0.00 38.22 3.32
534 535 2.423538 GCTATCCAGCGGAAATGTGTTT 59.576 45.455 1.44 0.00 38.22 2.83
535 536 3.731867 GCTATCCAGCGGAAATGTGTTTG 60.732 47.826 1.44 0.00 38.22 2.93
536 537 0.313672 TCCAGCGGAAATGTGTTTGC 59.686 50.000 0.00 0.00 32.89 3.68
541 542 3.280920 GGAAATGTGTTTGCGCCAA 57.719 47.368 4.18 0.00 0.00 4.52
542 543 1.794512 GGAAATGTGTTTGCGCCAAT 58.205 45.000 4.18 0.00 0.00 3.16
543 544 1.460359 GGAAATGTGTTTGCGCCAATG 59.540 47.619 4.18 0.00 0.00 2.82
544 545 1.460359 GAAATGTGTTTGCGCCAATGG 59.540 47.619 4.18 0.00 0.00 3.16
545 546 0.678395 AATGTGTTTGCGCCAATGGA 59.322 45.000 2.05 0.00 0.00 3.41
546 547 0.678395 ATGTGTTTGCGCCAATGGAA 59.322 45.000 2.05 0.00 0.00 3.53
547 548 0.461548 TGTGTTTGCGCCAATGGAAA 59.538 45.000 2.05 0.00 0.00 3.13
548 549 1.139163 GTGTTTGCGCCAATGGAAAG 58.861 50.000 2.05 0.00 29.41 2.62
549 550 0.033228 TGTTTGCGCCAATGGAAAGG 59.967 50.000 2.05 0.00 29.41 3.11
550 551 0.670239 GTTTGCGCCAATGGAAAGGG 60.670 55.000 2.05 0.00 29.41 3.95
551 552 1.825281 TTTGCGCCAATGGAAAGGGG 61.825 55.000 2.05 0.00 40.51 4.79
552 553 2.362375 GCGCCAATGGAAAGGGGA 60.362 61.111 2.05 0.00 40.00 4.81
553 554 2.418083 GCGCCAATGGAAAGGGGAG 61.418 63.158 2.05 0.00 40.00 4.30
554 555 2.418083 CGCCAATGGAAAGGGGAGC 61.418 63.158 2.05 0.00 40.00 4.70
555 556 2.060383 GCCAATGGAAAGGGGAGCC 61.060 63.158 2.05 0.00 0.00 4.70
556 557 1.754234 CCAATGGAAAGGGGAGCCG 60.754 63.158 0.00 0.00 0.00 5.52
557 558 2.043953 AATGGAAAGGGGAGCCGC 60.044 61.111 0.00 0.00 0.00 6.53
558 559 3.662117 AATGGAAAGGGGAGCCGCC 62.662 63.158 0.00 0.74 36.67 6.13
560 561 4.360405 GGAAAGGGGAGCCGCCAA 62.360 66.667 10.21 0.00 39.05 4.52
561 562 2.282887 GAAAGGGGAGCCGCCAAA 60.283 61.111 10.21 0.00 39.05 3.28
562 563 1.906333 GAAAGGGGAGCCGCCAAAA 60.906 57.895 10.21 0.00 39.05 2.44
563 564 1.229177 AAAGGGGAGCCGCCAAAAT 60.229 52.632 10.21 0.00 39.05 1.82
564 565 1.257750 AAAGGGGAGCCGCCAAAATC 61.258 55.000 10.21 0.00 39.05 2.17
565 566 3.147595 GGGGAGCCGCCAAAATCC 61.148 66.667 3.83 0.00 38.95 3.01
566 567 3.147595 GGGAGCCGCCAAAATCCC 61.148 66.667 0.00 0.00 44.48 3.85
567 568 3.518068 GGAGCCGCCAAAATCCCG 61.518 66.667 0.00 0.00 36.34 5.14
568 569 2.750237 GAGCCGCCAAAATCCCGT 60.750 61.111 0.00 0.00 0.00 5.28
569 570 1.450669 GAGCCGCCAAAATCCCGTA 60.451 57.895 0.00 0.00 0.00 4.02
570 571 1.436983 GAGCCGCCAAAATCCCGTAG 61.437 60.000 0.00 0.00 0.00 3.51
571 572 1.450669 GCCGCCAAAATCCCGTAGA 60.451 57.895 0.00 0.00 0.00 2.59
572 573 0.818040 GCCGCCAAAATCCCGTAGAT 60.818 55.000 0.00 0.00 36.48 1.98
573 574 1.541670 GCCGCCAAAATCCCGTAGATA 60.542 52.381 0.00 0.00 33.66 1.98
574 575 2.874457 GCCGCCAAAATCCCGTAGATAT 60.874 50.000 0.00 0.00 33.66 1.63
575 576 2.742053 CCGCCAAAATCCCGTAGATATG 59.258 50.000 0.00 0.00 33.66 1.78
576 577 2.742053 CGCCAAAATCCCGTAGATATGG 59.258 50.000 10.65 10.65 41.70 2.74
577 578 3.556213 CGCCAAAATCCCGTAGATATGGA 60.556 47.826 15.81 0.45 41.48 3.41
578 579 4.003648 GCCAAAATCCCGTAGATATGGAG 58.996 47.826 15.81 0.00 41.48 3.86
579 580 4.579869 CCAAAATCCCGTAGATATGGAGG 58.420 47.826 9.90 0.00 41.48 4.30
580 581 4.286032 CCAAAATCCCGTAGATATGGAGGA 59.714 45.833 9.90 0.00 41.48 3.71
581 582 5.221843 CCAAAATCCCGTAGATATGGAGGAA 60.222 44.000 9.90 0.00 41.48 3.36
582 583 6.296026 CAAAATCCCGTAGATATGGAGGAAA 58.704 40.000 0.00 0.00 33.66 3.13
583 584 6.704056 AAATCCCGTAGATATGGAGGAAAT 57.296 37.500 0.00 0.00 33.66 2.17
584 585 5.683876 ATCCCGTAGATATGGAGGAAATG 57.316 43.478 0.00 0.00 34.17 2.32
585 586 3.838317 TCCCGTAGATATGGAGGAAATGG 59.162 47.826 0.00 0.00 34.17 3.16
586 587 3.600388 CCGTAGATATGGAGGAAATGGC 58.400 50.000 0.00 0.00 34.17 4.40
587 588 3.600388 CGTAGATATGGAGGAAATGGCC 58.400 50.000 0.00 0.00 0.00 5.36
588 589 3.261897 CGTAGATATGGAGGAAATGGCCT 59.738 47.826 3.32 0.00 42.17 5.19
593 594 4.225497 GAGGAAATGGCCTCGTGG 57.775 61.111 3.32 0.00 44.52 4.94
594 595 1.602237 GAGGAAATGGCCTCGTGGA 59.398 57.895 7.92 0.00 44.52 4.02
595 596 0.181350 GAGGAAATGGCCTCGTGGAT 59.819 55.000 7.92 0.00 44.52 3.41
596 597 0.625849 AGGAAATGGCCTCGTGGATT 59.374 50.000 7.92 0.00 30.76 3.01
597 598 1.025041 GGAAATGGCCTCGTGGATTC 58.975 55.000 7.92 5.61 34.57 2.52
598 599 1.681780 GGAAATGGCCTCGTGGATTCA 60.682 52.381 7.92 2.54 34.57 2.57
599 600 1.672881 GAAATGGCCTCGTGGATTCAG 59.327 52.381 7.92 0.00 34.57 3.02
600 601 0.911769 AATGGCCTCGTGGATTCAGA 59.088 50.000 7.92 0.00 34.57 3.27
601 602 0.911769 ATGGCCTCGTGGATTCAGAA 59.088 50.000 7.92 0.00 34.57 3.02
602 603 0.911769 TGGCCTCGTGGATTCAGAAT 59.088 50.000 7.92 0.00 34.57 2.40
603 604 1.134401 TGGCCTCGTGGATTCAGAATC 60.134 52.381 14.09 14.09 37.17 2.52
614 615 4.701956 GATTCAGAATCCCGCAGAAAAA 57.298 40.909 11.69 0.00 31.60 1.94
633 634 5.545063 AAAAATTCTGGGACGGTTGAATT 57.455 34.783 0.00 0.00 39.78 2.17
634 635 5.545063 AAAATTCTGGGACGGTTGAATTT 57.455 34.783 13.78 13.78 45.32 1.82
635 636 4.519540 AATTCTGGGACGGTTGAATTTG 57.480 40.909 0.00 0.00 36.19 2.32
636 637 1.904287 TCTGGGACGGTTGAATTTGG 58.096 50.000 0.00 0.00 35.30 3.28
637 638 1.144093 TCTGGGACGGTTGAATTTGGT 59.856 47.619 0.00 0.00 35.30 3.67
638 639 1.269448 CTGGGACGGTTGAATTTGGTG 59.731 52.381 0.00 0.00 0.00 4.17
639 640 1.133761 TGGGACGGTTGAATTTGGTGA 60.134 47.619 0.00 0.00 0.00 4.02
640 641 2.167662 GGGACGGTTGAATTTGGTGAT 58.832 47.619 0.00 0.00 0.00 3.06
641 642 2.163613 GGGACGGTTGAATTTGGTGATC 59.836 50.000 0.00 0.00 0.00 2.92
642 643 3.081804 GGACGGTTGAATTTGGTGATCT 58.918 45.455 0.00 0.00 0.00 2.75
643 644 4.258543 GGACGGTTGAATTTGGTGATCTA 58.741 43.478 0.00 0.00 0.00 1.98
644 645 4.881850 GGACGGTTGAATTTGGTGATCTAT 59.118 41.667 0.00 0.00 0.00 1.98
645 646 5.357032 GGACGGTTGAATTTGGTGATCTATT 59.643 40.000 0.00 0.00 0.00 1.73
646 647 6.436843 ACGGTTGAATTTGGTGATCTATTC 57.563 37.500 0.00 0.00 0.00 1.75
647 648 5.064707 ACGGTTGAATTTGGTGATCTATTCG 59.935 40.000 0.00 0.00 31.29 3.34
648 649 5.504010 CGGTTGAATTTGGTGATCTATTCGG 60.504 44.000 0.00 0.00 31.29 4.30
649 650 5.221048 GGTTGAATTTGGTGATCTATTCGGG 60.221 44.000 0.00 0.00 31.29 5.14
650 651 3.882888 TGAATTTGGTGATCTATTCGGGC 59.117 43.478 0.00 0.00 31.29 6.13
651 652 2.341846 TTTGGTGATCTATTCGGGCC 57.658 50.000 0.00 0.00 0.00 5.80
652 653 0.105964 TTGGTGATCTATTCGGGCCG 59.894 55.000 22.51 22.51 0.00 6.13
653 654 1.004918 GGTGATCTATTCGGGCCGG 60.005 63.158 27.98 10.15 0.00 6.13
654 655 1.469335 GGTGATCTATTCGGGCCGGA 61.469 60.000 27.98 20.48 0.00 5.14
655 656 0.608640 GTGATCTATTCGGGCCGGAT 59.391 55.000 25.39 25.39 0.00 4.18
656 657 1.002087 GTGATCTATTCGGGCCGGATT 59.998 52.381 27.35 7.44 0.00 3.01
657 658 1.697432 TGATCTATTCGGGCCGGATTT 59.303 47.619 27.35 10.95 0.00 2.17
658 659 2.901192 TGATCTATTCGGGCCGGATTTA 59.099 45.455 27.35 14.36 0.00 1.40
659 660 3.517901 TGATCTATTCGGGCCGGATTTAT 59.482 43.478 27.35 18.63 0.00 1.40
660 661 3.328382 TCTATTCGGGCCGGATTTATG 57.672 47.619 27.35 13.27 0.00 1.90
661 662 2.027561 TCTATTCGGGCCGGATTTATGG 60.028 50.000 27.35 12.91 0.00 2.74
662 663 0.251165 ATTCGGGCCGGATTTATGGG 60.251 55.000 27.98 0.00 0.00 4.00
665 666 4.081050 GGCCGGATTTATGGGCTC 57.919 61.111 5.05 0.00 46.62 4.70
666 667 1.603739 GGCCGGATTTATGGGCTCC 60.604 63.158 5.05 0.00 46.62 4.70
667 668 1.150536 GCCGGATTTATGGGCTCCA 59.849 57.895 5.05 0.00 43.52 3.86
668 669 0.251341 GCCGGATTTATGGGCTCCAT 60.251 55.000 5.05 10.96 46.99 3.41
669 670 1.826385 CCGGATTTATGGGCTCCATC 58.174 55.000 9.67 0.00 40.74 3.51
670 671 1.614317 CCGGATTTATGGGCTCCATCC 60.614 57.143 9.67 5.92 40.74 3.51
671 672 1.614317 CGGATTTATGGGCTCCATCCC 60.614 57.143 9.67 7.16 40.74 3.85
677 678 2.770130 GGGCTCCATCCCAACCAA 59.230 61.111 0.00 0.00 45.82 3.67
678 679 1.682344 GGGCTCCATCCCAACCAAC 60.682 63.158 0.00 0.00 45.82 3.77
679 680 2.046285 GGCTCCATCCCAACCAACG 61.046 63.158 0.00 0.00 0.00 4.10
680 681 1.002624 GCTCCATCCCAACCAACGA 60.003 57.895 0.00 0.00 0.00 3.85
681 682 0.394352 GCTCCATCCCAACCAACGAT 60.394 55.000 0.00 0.00 0.00 3.73
682 683 1.955208 GCTCCATCCCAACCAACGATT 60.955 52.381 0.00 0.00 0.00 3.34
683 684 2.682563 GCTCCATCCCAACCAACGATTA 60.683 50.000 0.00 0.00 0.00 1.75
684 685 3.820557 CTCCATCCCAACCAACGATTAT 58.179 45.455 0.00 0.00 0.00 1.28
685 686 4.207165 CTCCATCCCAACCAACGATTATT 58.793 43.478 0.00 0.00 0.00 1.40
686 687 4.605183 TCCATCCCAACCAACGATTATTT 58.395 39.130 0.00 0.00 0.00 1.40
687 688 5.020132 TCCATCCCAACCAACGATTATTTT 58.980 37.500 0.00 0.00 0.00 1.82
688 689 6.188407 TCCATCCCAACCAACGATTATTTTA 58.812 36.000 0.00 0.00 0.00 1.52
689 690 6.836527 TCCATCCCAACCAACGATTATTTTAT 59.163 34.615 0.00 0.00 0.00 1.40
690 691 7.013846 TCCATCCCAACCAACGATTATTTTATC 59.986 37.037 0.00 0.00 0.00 1.75
691 692 7.201866 CCATCCCAACCAACGATTATTTTATCA 60.202 37.037 0.00 0.00 0.00 2.15
692 693 7.704578 TCCCAACCAACGATTATTTTATCAA 57.295 32.000 0.00 0.00 0.00 2.57
693 694 7.767261 TCCCAACCAACGATTATTTTATCAAG 58.233 34.615 0.00 0.00 0.00 3.02
694 695 7.394923 TCCCAACCAACGATTATTTTATCAAGT 59.605 33.333 0.00 0.00 0.00 3.16
695 696 7.487829 CCCAACCAACGATTATTTTATCAAGTG 59.512 37.037 0.00 0.00 0.00 3.16
696 697 7.487829 CCAACCAACGATTATTTTATCAAGTGG 59.512 37.037 0.00 0.00 0.00 4.00
697 698 6.560711 ACCAACGATTATTTTATCAAGTGGC 58.439 36.000 0.00 0.00 0.00 5.01
698 699 6.151985 ACCAACGATTATTTTATCAAGTGGCA 59.848 34.615 0.00 0.00 0.00 4.92
699 700 6.472163 CCAACGATTATTTTATCAAGTGGCAC 59.528 38.462 10.29 10.29 0.00 5.01
700 701 5.806286 ACGATTATTTTATCAAGTGGCACG 58.194 37.500 12.71 0.00 0.00 5.34
701 702 5.204833 CGATTATTTTATCAAGTGGCACGG 58.795 41.667 12.71 9.00 0.00 4.94
702 703 5.220777 CGATTATTTTATCAAGTGGCACGGT 60.221 40.000 12.71 0.95 0.00 4.83
703 704 5.968528 TTATTTTATCAAGTGGCACGGTT 57.031 34.783 12.71 6.57 0.00 4.44
704 705 4.864704 ATTTTATCAAGTGGCACGGTTT 57.135 36.364 12.71 0.00 0.00 3.27
705 706 3.634568 TTTATCAAGTGGCACGGTTTG 57.365 42.857 12.71 11.61 0.00 2.93
726 727 3.965292 CAGGATGTGCTAGAAATGCTG 57.035 47.619 0.00 0.37 34.16 4.41
727 728 3.276857 CAGGATGTGCTAGAAATGCTGT 58.723 45.455 10.93 0.00 35.67 4.40
730 731 5.530171 CAGGATGTGCTAGAAATGCTGTAAT 59.470 40.000 10.93 0.00 35.67 1.89
823 829 3.507411 TCCTGGTCTGCCCTATACATAC 58.493 50.000 0.00 0.00 0.00 2.39
825 831 3.840666 CCTGGTCTGCCCTATACATACAT 59.159 47.826 0.00 0.00 0.00 2.29
826 832 4.287067 CCTGGTCTGCCCTATACATACATT 59.713 45.833 0.00 0.00 0.00 2.71
827 833 5.227569 TGGTCTGCCCTATACATACATTG 57.772 43.478 0.00 0.00 0.00 2.82
828 834 4.003648 GGTCTGCCCTATACATACATTGC 58.996 47.826 0.00 0.00 0.00 3.56
875 2018 5.293079 GCACTGATCTTACAGGTTGATCTTC 59.707 44.000 12.76 0.00 41.59 2.87
1028 2171 3.776347 TTTTGTCCGCCCTCCGCAA 62.776 57.895 0.00 0.00 37.30 4.85
1134 2277 3.474570 GCCAGGAGGACGATGCCT 61.475 66.667 0.00 0.00 42.17 4.75
1263 2406 2.360350 CTCAACCACGCCAGCCAT 60.360 61.111 0.00 0.00 0.00 4.40
1333 2476 2.607750 TGGACTGGGAGGAGCCAC 60.608 66.667 0.00 0.00 38.95 5.01
1371 2514 2.507324 GTGCGCCTCTTCTCGGAC 60.507 66.667 4.18 0.00 39.59 4.79
1422 2565 6.237595 CCGACTTCGTAAAACATGAGAATCTC 60.238 42.308 2.75 2.75 37.74 2.75
1425 2568 6.308282 ACTTCGTAAAACATGAGAATCTCGAC 59.692 38.462 5.73 0.00 34.92 4.20
1626 2769 0.670546 CGGACGTGCTGATTGAGGTT 60.671 55.000 5.27 0.00 0.00 3.50
1825 2968 3.358076 AACCAGCTAGAGACGGCGC 62.358 63.158 6.90 0.00 0.00 6.53
1897 3040 0.512085 GCTGAAGCAGATATGCGAGC 59.488 55.000 15.15 15.15 41.59 5.03
2016 3160 4.339247 CAGTTCATATCTTTTCCCGGCAAT 59.661 41.667 0.00 0.00 0.00 3.56
2115 3259 2.821366 CAGATGGTGCGGCTGGAC 60.821 66.667 8.99 8.99 35.37 4.02
2145 3290 0.454285 CCGGCGCAATGTACAACTTG 60.454 55.000 10.83 1.81 0.00 3.16
2152 3297 4.317769 GCGCAATGTACAACTTGTTTTTCC 60.318 41.667 0.30 0.00 0.00 3.13
2153 3298 4.800993 CGCAATGTACAACTTGTTTTTCCA 59.199 37.500 0.00 0.00 0.00 3.53
2221 3368 5.783111 ACCTAATCTTTCGCTTGCAAAAAT 58.217 33.333 0.00 0.00 0.00 1.82
2222 3369 5.634859 ACCTAATCTTTCGCTTGCAAAAATG 59.365 36.000 0.00 0.00 0.00 2.32
2223 3370 5.634859 CCTAATCTTTCGCTTGCAAAAATGT 59.365 36.000 0.00 0.00 0.00 2.71
2224 3371 5.580911 AATCTTTCGCTTGCAAAAATGTC 57.419 34.783 0.00 0.00 0.00 3.06
2225 3372 3.380142 TCTTTCGCTTGCAAAAATGTCC 58.620 40.909 0.00 0.00 0.00 4.02
2233 3380 4.021981 GCTTGCAAAAATGTCCTAGGAGTT 60.022 41.667 13.15 7.65 0.00 3.01
2237 3384 4.261994 GCAAAAATGTCCTAGGAGTTGCAA 60.262 41.667 24.91 0.00 39.82 4.08
2238 3385 5.738783 GCAAAAATGTCCTAGGAGTTGCAAA 60.739 40.000 24.91 6.20 39.82 3.68
2244 3391 5.841810 TGTCCTAGGAGTTGCAAATTTTTG 58.158 37.500 13.15 0.00 41.03 2.44
2254 3401 3.397482 TGCAAATTTTTGGGATGTTCCG 58.603 40.909 5.28 0.00 37.43 4.30
2255 3402 3.181461 TGCAAATTTTTGGGATGTTCCGT 60.181 39.130 5.28 0.00 37.43 4.69
2271 3418 6.189677 TGTTCCGTCCATGTAATTTGATTC 57.810 37.500 0.00 0.00 0.00 2.52
2273 3420 4.204012 TCCGTCCATGTAATTTGATTCCC 58.796 43.478 0.00 0.00 0.00 3.97
2342 3489 5.505654 CCAAACAGAACACATGTTGTACCTC 60.506 44.000 1.07 0.00 39.91 3.85
2349 3496 4.843728 ACACATGTTGTACCTCCCTAATG 58.156 43.478 0.00 0.00 36.32 1.90
2368 3516 7.124147 CCCTAATGTTTGAACCCATTATTGTCT 59.876 37.037 0.00 0.00 34.13 3.41
2375 3523 6.942532 TGAACCCATTATTGTCTCATTAGC 57.057 37.500 0.00 0.00 0.00 3.09
2379 3527 8.995027 AACCCATTATTGTCTCATTAGCATTA 57.005 30.769 0.00 0.00 0.00 1.90
2380 3528 8.396272 ACCCATTATTGTCTCATTAGCATTAC 57.604 34.615 0.00 0.00 0.00 1.89
2415 3563 1.640428 CACACGTGTGGCATACTAGG 58.360 55.000 35.65 10.61 42.10 3.02
2421 3569 1.140852 GTGTGGCATACTAGGCATCCA 59.859 52.381 7.17 0.00 46.23 3.41
2424 3572 2.304180 GTGGCATACTAGGCATCCATCT 59.696 50.000 0.00 0.00 46.23 2.90
2431 3579 6.705302 CATACTAGGCATCCATCTACACATT 58.295 40.000 0.00 0.00 0.00 2.71
2446 3594 0.463654 ACATTGTGTGTGGCGTGAGT 60.464 50.000 0.00 0.00 40.28 3.41
2453 3601 1.228769 TGTGGCGTGAGTAGGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
2464 3612 1.076024 AGTAGGAGGTAACCCACACGA 59.924 52.381 0.00 0.00 37.17 4.35
2465 3613 1.895131 GTAGGAGGTAACCCACACGAA 59.105 52.381 0.00 0.00 37.17 3.85
2492 3640 3.190535 GTGTGGGCGAACATTAGAATTGT 59.809 43.478 0.00 0.00 31.49 2.71
2525 3673 0.518355 CGCAGTTATTTCGTGCCACG 60.518 55.000 11.80 11.80 44.19 4.94
2542 3691 1.735571 CACGCGCCCAAAAAGTACTAT 59.264 47.619 5.73 0.00 0.00 2.12
2555 3704 7.611855 CCAAAAAGTACTATTCATCTTCACCCT 59.388 37.037 0.00 0.00 0.00 4.34
2642 3792 4.130118 GGATGACGATTTAGTTGCCATCT 58.870 43.478 0.00 0.00 32.10 2.90
2672 3823 5.104900 GGCAGATATAGTTATTCGGGATGGT 60.105 44.000 0.00 0.00 0.00 3.55
2689 3840 7.664731 TCGGGATGGTAAATGTAGTTGTAAAAA 59.335 33.333 0.00 0.00 0.00 1.94
2719 3870 7.078228 GCAACTCTATCTGTTTTGGTTAACTG 58.922 38.462 5.42 0.00 0.00 3.16
2728 3879 4.201930 TGTTTTGGTTAACTGTAGTTGCCG 60.202 41.667 5.42 0.00 38.90 5.69
2748 3900 6.876155 TGCCGTGTCTAATTTATGGTAGTTA 58.124 36.000 0.00 0.00 0.00 2.24
2749 3901 7.329499 TGCCGTGTCTAATTTATGGTAGTTAA 58.671 34.615 0.00 0.00 0.00 2.01
2842 3994 4.093472 TGTGTGTTTACCTAGTTGCCAT 57.907 40.909 0.00 0.00 0.00 4.40
2848 4000 4.069304 GTTTACCTAGTTGCCATGTGTGA 58.931 43.478 0.00 0.00 0.00 3.58
2850 4002 3.439857 ACCTAGTTGCCATGTGTGATT 57.560 42.857 0.00 0.00 0.00 2.57
2863 4015 6.039717 GCCATGTGTGATTCAACCATAGTTAT 59.960 38.462 0.00 0.00 33.27 1.89
2894 4046 5.767665 TGGTTAATCACAGTTGCTATGTGTT 59.232 36.000 13.63 10.60 46.49 3.32
2911 4063 3.701542 TGTGTTTTTATCTGGTTGCCACA 59.298 39.130 0.00 0.00 0.00 4.17
2917 4069 1.089481 ATCTGGTTGCCACATACGCG 61.089 55.000 3.53 3.53 0.00 6.01
2918 4070 1.739929 CTGGTTGCCACATACGCGA 60.740 57.895 15.93 0.00 0.00 5.87
2953 4105 2.471743 GCCGTCTAGCAACGAATCATAC 59.528 50.000 5.60 0.00 45.37 2.39
3024 4176 0.249573 CCAACAACGTACGGGTGTCT 60.250 55.000 22.17 12.57 0.00 3.41
3026 4178 1.935199 CAACAACGTACGGGTGTCTTT 59.065 47.619 22.17 8.67 0.00 2.52
3037 4189 1.137282 GGGTGTCTTTTGGGCGAAAAA 59.863 47.619 8.74 3.12 33.04 1.94
3042 4194 2.857748 GTCTTTTGGGCGAAAAACAGTG 59.142 45.455 8.74 0.00 33.04 3.66
3074 4226 1.758592 GTGGACTTGGTGGTGGCTA 59.241 57.895 0.00 0.00 0.00 3.93
3094 4246 3.788227 ATGTGGGCAGAAACTAGTTCA 57.212 42.857 8.95 0.03 38.86 3.18
3101 4253 4.385310 GGGCAGAAACTAGTTCACCCATAT 60.385 45.833 21.50 2.00 46.81 1.78
3105 4257 6.582636 CAGAAACTAGTTCACCCATATAGCA 58.417 40.000 8.95 0.00 38.86 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.749258 GGCGGATCTGGTTGGTTCC 60.749 63.158 3.14 0.00 0.00 3.62
8 9 1.026718 CAGGCGGATCTGGTTGGTTC 61.027 60.000 3.14 0.00 0.00 3.62
9 10 1.002134 CAGGCGGATCTGGTTGGTT 60.002 57.895 3.14 0.00 0.00 3.67
10 11 2.671070 CAGGCGGATCTGGTTGGT 59.329 61.111 3.14 0.00 0.00 3.67
11 12 1.971505 TAGCAGGCGGATCTGGTTGG 61.972 60.000 3.14 0.00 42.05 3.77
12 13 0.811616 GTAGCAGGCGGATCTGGTTG 60.812 60.000 3.14 0.00 42.05 3.77
13 14 1.264749 TGTAGCAGGCGGATCTGGTT 61.265 55.000 3.14 0.00 42.05 3.67
14 15 1.264749 TTGTAGCAGGCGGATCTGGT 61.265 55.000 3.14 8.17 45.86 4.00
15 16 0.531532 CTTGTAGCAGGCGGATCTGG 60.532 60.000 3.14 0.00 35.43 3.86
16 17 0.531532 CCTTGTAGCAGGCGGATCTG 60.532 60.000 0.00 0.00 37.79 2.90
17 18 1.826024 CCTTGTAGCAGGCGGATCT 59.174 57.895 0.00 0.00 0.00 2.75
18 19 4.445699 CCTTGTAGCAGGCGGATC 57.554 61.111 0.00 0.00 0.00 3.36
25 26 4.408821 TGCGGGGCCTTGTAGCAG 62.409 66.667 0.84 0.00 33.57 4.24
26 27 4.715523 GTGCGGGGCCTTGTAGCA 62.716 66.667 0.84 4.81 35.27 3.49
28 29 3.599285 TTCGTGCGGGGCCTTGTAG 62.599 63.158 0.84 0.00 0.00 2.74
29 30 3.599285 CTTCGTGCGGGGCCTTGTA 62.599 63.158 0.84 0.00 0.00 2.41
41 42 4.760047 CCACCCCGGAGCTTCGTG 62.760 72.222 14.59 0.52 36.56 4.35
452 453 1.964373 CCCGTTCTTGTTGTCCCCG 60.964 63.158 0.00 0.00 0.00 5.73
453 454 2.265904 GCCCGTTCTTGTTGTCCCC 61.266 63.158 0.00 0.00 0.00 4.81
454 455 1.515521 CTGCCCGTTCTTGTTGTCCC 61.516 60.000 0.00 0.00 0.00 4.46
455 456 1.515521 CCTGCCCGTTCTTGTTGTCC 61.516 60.000 0.00 0.00 0.00 4.02
456 457 1.515521 CCCTGCCCGTTCTTGTTGTC 61.516 60.000 0.00 0.00 0.00 3.18
457 458 1.528309 CCCTGCCCGTTCTTGTTGT 60.528 57.895 0.00 0.00 0.00 3.32
458 459 0.609131 ATCCCTGCCCGTTCTTGTTG 60.609 55.000 0.00 0.00 0.00 3.33
459 460 0.609131 CATCCCTGCCCGTTCTTGTT 60.609 55.000 0.00 0.00 0.00 2.83
460 461 1.002134 CATCCCTGCCCGTTCTTGT 60.002 57.895 0.00 0.00 0.00 3.16
461 462 2.409870 GCATCCCTGCCCGTTCTTG 61.410 63.158 0.00 0.00 42.88 3.02
462 463 2.044946 GCATCCCTGCCCGTTCTT 60.045 61.111 0.00 0.00 42.88 2.52
487 488 3.015145 CTACACCCCCACCCCCTG 61.015 72.222 0.00 0.00 0.00 4.45
488 489 4.364686 CCTACACCCCCACCCCCT 62.365 72.222 0.00 0.00 0.00 4.79
496 497 3.782443 CACTCGCCCCTACACCCC 61.782 72.222 0.00 0.00 0.00 4.95
497 498 4.468689 GCACTCGCCCCTACACCC 62.469 72.222 0.00 0.00 0.00 4.61
498 499 1.400530 ATAGCACTCGCCCCTACACC 61.401 60.000 0.00 0.00 39.83 4.16
499 500 0.032267 GATAGCACTCGCCCCTACAC 59.968 60.000 0.00 0.00 39.83 2.90
500 501 1.113517 GGATAGCACTCGCCCCTACA 61.114 60.000 0.00 0.00 39.83 2.74
501 502 1.113517 TGGATAGCACTCGCCCCTAC 61.114 60.000 0.00 0.00 39.83 3.18
502 503 0.827925 CTGGATAGCACTCGCCCCTA 60.828 60.000 0.00 0.00 39.83 3.53
503 504 2.041922 TGGATAGCACTCGCCCCT 60.042 61.111 0.00 0.00 39.83 4.79
504 505 2.423446 CTGGATAGCACTCGCCCC 59.577 66.667 0.00 0.00 39.83 5.80
513 514 1.668419 ACACATTTCCGCTGGATAGC 58.332 50.000 0.00 0.00 46.62 2.97
514 515 3.731867 GCAAACACATTTCCGCTGGATAG 60.732 47.826 0.00 0.00 0.00 2.08
515 516 2.163412 GCAAACACATTTCCGCTGGATA 59.837 45.455 0.00 0.00 0.00 2.59
516 517 1.067635 GCAAACACATTTCCGCTGGAT 60.068 47.619 0.00 0.00 0.00 3.41
517 518 0.313672 GCAAACACATTTCCGCTGGA 59.686 50.000 0.00 0.00 0.00 3.86
518 519 1.003262 CGCAAACACATTTCCGCTGG 61.003 55.000 0.00 0.00 0.00 4.85
519 520 1.608093 GCGCAAACACATTTCCGCTG 61.608 55.000 0.30 0.00 36.67 5.18
520 521 1.371635 GCGCAAACACATTTCCGCT 60.372 52.632 0.30 0.00 36.67 5.52
521 522 2.371923 GGCGCAAACACATTTCCGC 61.372 57.895 10.83 0.00 38.05 5.54
522 523 0.596083 TTGGCGCAAACACATTTCCG 60.596 50.000 10.83 0.00 0.00 4.30
523 524 1.460359 CATTGGCGCAAACACATTTCC 59.540 47.619 10.83 0.00 0.00 3.13
524 525 1.460359 CCATTGGCGCAAACACATTTC 59.540 47.619 10.83 0.00 0.00 2.17
525 526 1.069823 TCCATTGGCGCAAACACATTT 59.930 42.857 10.83 0.00 0.00 2.32
526 527 0.678395 TCCATTGGCGCAAACACATT 59.322 45.000 10.83 0.00 0.00 2.71
527 528 0.678395 TTCCATTGGCGCAAACACAT 59.322 45.000 10.83 0.00 0.00 3.21
528 529 0.461548 TTTCCATTGGCGCAAACACA 59.538 45.000 10.83 0.00 0.00 3.72
529 530 1.139163 CTTTCCATTGGCGCAAACAC 58.861 50.000 10.83 0.00 0.00 3.32
530 531 0.033228 CCTTTCCATTGGCGCAAACA 59.967 50.000 10.83 0.00 0.00 2.83
531 532 0.670239 CCCTTTCCATTGGCGCAAAC 60.670 55.000 10.83 0.00 0.00 2.93
532 533 1.670590 CCCTTTCCATTGGCGCAAA 59.329 52.632 10.83 3.91 0.00 3.68
533 534 2.282039 CCCCTTTCCATTGGCGCAA 61.282 57.895 10.83 0.00 0.00 4.85
534 535 2.679642 CCCCTTTCCATTGGCGCA 60.680 61.111 10.83 0.00 0.00 6.09
535 536 2.362375 TCCCCTTTCCATTGGCGC 60.362 61.111 0.00 0.00 0.00 6.53
536 537 2.418083 GCTCCCCTTTCCATTGGCG 61.418 63.158 0.00 0.00 0.00 5.69
537 538 2.060383 GGCTCCCCTTTCCATTGGC 61.060 63.158 0.00 0.00 0.00 4.52
538 539 1.754234 CGGCTCCCCTTTCCATTGG 60.754 63.158 0.00 0.00 0.00 3.16
539 540 2.418083 GCGGCTCCCCTTTCCATTG 61.418 63.158 0.00 0.00 0.00 2.82
540 541 2.043953 GCGGCTCCCCTTTCCATT 60.044 61.111 0.00 0.00 0.00 3.16
541 542 4.129148 GGCGGCTCCCCTTTCCAT 62.129 66.667 0.00 0.00 0.00 3.41
543 544 3.879180 TTTGGCGGCTCCCCTTTCC 62.879 63.158 11.43 0.00 0.00 3.13
544 545 1.257750 ATTTTGGCGGCTCCCCTTTC 61.258 55.000 11.43 0.00 0.00 2.62
545 546 1.229177 ATTTTGGCGGCTCCCCTTT 60.229 52.632 11.43 0.00 0.00 3.11
546 547 1.682344 GATTTTGGCGGCTCCCCTT 60.682 57.895 11.43 0.00 0.00 3.95
547 548 2.043953 GATTTTGGCGGCTCCCCT 60.044 61.111 11.43 0.00 0.00 4.79
548 549 3.147595 GGATTTTGGCGGCTCCCC 61.148 66.667 11.43 0.52 0.00 4.81
549 550 3.147595 GGGATTTTGGCGGCTCCC 61.148 66.667 16.79 16.79 40.60 4.30
550 551 2.879813 TACGGGATTTTGGCGGCTCC 62.880 60.000 11.43 8.61 0.00 4.70
551 552 1.436983 CTACGGGATTTTGGCGGCTC 61.437 60.000 11.43 0.00 0.00 4.70
552 553 1.451387 CTACGGGATTTTGGCGGCT 60.451 57.895 11.43 0.00 0.00 5.52
553 554 0.818040 ATCTACGGGATTTTGGCGGC 60.818 55.000 0.00 0.00 0.00 6.53
554 555 2.536761 TATCTACGGGATTTTGGCGG 57.463 50.000 0.00 0.00 35.98 6.13
555 556 2.742053 CCATATCTACGGGATTTTGGCG 59.258 50.000 0.00 0.00 35.98 5.69
556 557 4.003648 CTCCATATCTACGGGATTTTGGC 58.996 47.826 12.82 0.00 36.89 4.52
557 558 4.286032 TCCTCCATATCTACGGGATTTTGG 59.714 45.833 12.05 12.05 37.61 3.28
558 559 5.483685 TCCTCCATATCTACGGGATTTTG 57.516 43.478 0.00 0.00 35.98 2.44
559 560 6.509523 TTTCCTCCATATCTACGGGATTTT 57.490 37.500 0.00 0.00 35.98 1.82
560 561 6.476378 CATTTCCTCCATATCTACGGGATTT 58.524 40.000 0.00 0.00 35.98 2.17
561 562 5.045578 CCATTTCCTCCATATCTACGGGATT 60.046 44.000 0.00 0.00 35.98 3.01
562 563 4.471386 CCATTTCCTCCATATCTACGGGAT 59.529 45.833 0.00 0.00 38.38 3.85
563 564 3.838317 CCATTTCCTCCATATCTACGGGA 59.162 47.826 0.00 0.00 0.00 5.14
564 565 3.619979 GCCATTTCCTCCATATCTACGGG 60.620 52.174 0.00 0.00 0.00 5.28
565 566 3.600388 GCCATTTCCTCCATATCTACGG 58.400 50.000 0.00 0.00 0.00 4.02
566 567 3.261897 AGGCCATTTCCTCCATATCTACG 59.738 47.826 5.01 0.00 0.00 3.51
567 568 4.837972 GAGGCCATTTCCTCCATATCTAC 58.162 47.826 5.01 0.00 45.40 2.59
577 578 0.625849 AATCCACGAGGCCATTTCCT 59.374 50.000 5.01 0.00 39.67 3.36
578 579 1.025041 GAATCCACGAGGCCATTTCC 58.975 55.000 5.01 0.00 33.74 3.13
579 580 1.672881 CTGAATCCACGAGGCCATTTC 59.327 52.381 5.01 0.00 33.74 2.17
580 581 1.281867 TCTGAATCCACGAGGCCATTT 59.718 47.619 5.01 0.00 33.74 2.32
581 582 0.911769 TCTGAATCCACGAGGCCATT 59.088 50.000 5.01 0.00 33.74 3.16
582 583 0.911769 TTCTGAATCCACGAGGCCAT 59.088 50.000 5.01 0.00 33.74 4.40
583 584 0.911769 ATTCTGAATCCACGAGGCCA 59.088 50.000 5.01 0.00 33.74 5.36
584 585 1.587547 GATTCTGAATCCACGAGGCC 58.412 55.000 17.62 0.00 33.74 5.19
593 594 4.701956 TTTTTCTGCGGGATTCTGAATC 57.298 40.909 19.67 19.67 37.17 2.52
611 612 5.545063 AATTCAACCGTCCCAGAATTTTT 57.455 34.783 0.00 0.00 37.39 1.94
612 613 5.296748 CAAATTCAACCGTCCCAGAATTTT 58.703 37.500 8.71 0.00 44.01 1.82
613 614 4.262420 CCAAATTCAACCGTCCCAGAATTT 60.262 41.667 0.00 0.00 46.05 1.82
614 615 3.258123 CCAAATTCAACCGTCCCAGAATT 59.742 43.478 0.00 0.00 41.11 2.17
615 616 2.825532 CCAAATTCAACCGTCCCAGAAT 59.174 45.455 0.00 0.00 32.45 2.40
616 617 2.235016 CCAAATTCAACCGTCCCAGAA 58.765 47.619 0.00 0.00 0.00 3.02
617 618 1.144093 ACCAAATTCAACCGTCCCAGA 59.856 47.619 0.00 0.00 0.00 3.86
618 619 1.269448 CACCAAATTCAACCGTCCCAG 59.731 52.381 0.00 0.00 0.00 4.45
619 620 1.133761 TCACCAAATTCAACCGTCCCA 60.134 47.619 0.00 0.00 0.00 4.37
620 621 1.611519 TCACCAAATTCAACCGTCCC 58.388 50.000 0.00 0.00 0.00 4.46
621 622 3.081804 AGATCACCAAATTCAACCGTCC 58.918 45.455 0.00 0.00 0.00 4.79
622 623 6.436843 AATAGATCACCAAATTCAACCGTC 57.563 37.500 0.00 0.00 0.00 4.79
623 624 5.064707 CGAATAGATCACCAAATTCAACCGT 59.935 40.000 0.00 0.00 0.00 4.83
624 625 5.501715 CGAATAGATCACCAAATTCAACCG 58.498 41.667 0.00 0.00 0.00 4.44
625 626 5.221048 CCCGAATAGATCACCAAATTCAACC 60.221 44.000 0.00 0.00 0.00 3.77
626 627 5.733373 GCCCGAATAGATCACCAAATTCAAC 60.733 44.000 0.00 0.00 0.00 3.18
627 628 4.338118 GCCCGAATAGATCACCAAATTCAA 59.662 41.667 0.00 0.00 0.00 2.69
628 629 3.882888 GCCCGAATAGATCACCAAATTCA 59.117 43.478 0.00 0.00 0.00 2.57
629 630 3.253432 GGCCCGAATAGATCACCAAATTC 59.747 47.826 0.00 0.00 0.00 2.17
630 631 3.222603 GGCCCGAATAGATCACCAAATT 58.777 45.455 0.00 0.00 0.00 1.82
631 632 2.810400 CGGCCCGAATAGATCACCAAAT 60.810 50.000 0.00 0.00 0.00 2.32
632 633 1.474320 CGGCCCGAATAGATCACCAAA 60.474 52.381 0.00 0.00 0.00 3.28
633 634 0.105964 CGGCCCGAATAGATCACCAA 59.894 55.000 0.00 0.00 0.00 3.67
634 635 1.745890 CGGCCCGAATAGATCACCA 59.254 57.895 0.00 0.00 0.00 4.17
635 636 1.004918 CCGGCCCGAATAGATCACC 60.005 63.158 3.71 0.00 0.00 4.02
636 637 0.608640 ATCCGGCCCGAATAGATCAC 59.391 55.000 3.71 0.00 0.00 3.06
637 638 1.348064 AATCCGGCCCGAATAGATCA 58.652 50.000 3.71 0.00 0.00 2.92
638 639 2.474410 AAATCCGGCCCGAATAGATC 57.526 50.000 3.71 0.00 0.00 2.75
639 640 3.370527 CCATAAATCCGGCCCGAATAGAT 60.371 47.826 3.71 0.00 0.00 1.98
640 641 2.027561 CCATAAATCCGGCCCGAATAGA 60.028 50.000 3.71 0.00 0.00 1.98
641 642 2.356135 CCATAAATCCGGCCCGAATAG 58.644 52.381 3.71 0.00 0.00 1.73
642 643 1.003812 CCCATAAATCCGGCCCGAATA 59.996 52.381 3.71 0.00 0.00 1.75
643 644 0.251165 CCCATAAATCCGGCCCGAAT 60.251 55.000 3.71 0.00 0.00 3.34
644 645 1.149627 CCCATAAATCCGGCCCGAA 59.850 57.895 3.71 0.00 0.00 4.30
645 646 2.833227 CCCATAAATCCGGCCCGA 59.167 61.111 3.71 0.00 0.00 5.14
646 647 2.983592 GCCCATAAATCCGGCCCG 60.984 66.667 0.00 0.00 36.63 6.13
647 648 1.603739 GAGCCCATAAATCCGGCCC 60.604 63.158 0.00 0.00 44.13 5.80
648 649 1.603739 GGAGCCCATAAATCCGGCC 60.604 63.158 0.00 0.00 44.13 6.13
649 650 0.251341 ATGGAGCCCATAAATCCGGC 60.251 55.000 0.00 0.00 43.19 6.13
650 651 1.614317 GGATGGAGCCCATAAATCCGG 60.614 57.143 6.69 0.00 45.26 5.14
651 652 1.614317 GGGATGGAGCCCATAAATCCG 60.614 57.143 6.69 0.00 45.26 4.18
652 653 2.222227 GGGATGGAGCCCATAAATCC 57.778 55.000 6.69 5.20 45.26 3.01
661 662 2.046285 CGTTGGTTGGGATGGAGCC 61.046 63.158 0.00 0.00 0.00 4.70
662 663 0.394352 ATCGTTGGTTGGGATGGAGC 60.394 55.000 0.00 0.00 0.00 4.70
663 664 2.128771 AATCGTTGGTTGGGATGGAG 57.871 50.000 0.00 0.00 0.00 3.86
664 665 3.943671 ATAATCGTTGGTTGGGATGGA 57.056 42.857 0.00 0.00 0.00 3.41
665 666 5.337578 AAAATAATCGTTGGTTGGGATGG 57.662 39.130 0.00 0.00 0.00 3.51
666 667 7.711846 TGATAAAATAATCGTTGGTTGGGATG 58.288 34.615 0.00 0.00 0.00 3.51
667 668 7.889873 TGATAAAATAATCGTTGGTTGGGAT 57.110 32.000 0.00 0.00 0.00 3.85
668 669 7.394923 ACTTGATAAAATAATCGTTGGTTGGGA 59.605 33.333 0.00 0.00 0.00 4.37
669 670 7.487829 CACTTGATAAAATAATCGTTGGTTGGG 59.512 37.037 0.00 0.00 0.00 4.12
670 671 7.487829 CCACTTGATAAAATAATCGTTGGTTGG 59.512 37.037 0.00 0.00 0.00 3.77
671 672 7.009174 GCCACTTGATAAAATAATCGTTGGTTG 59.991 37.037 0.00 0.00 30.13 3.77
672 673 7.033185 GCCACTTGATAAAATAATCGTTGGTT 58.967 34.615 0.00 0.00 30.13 3.67
673 674 6.151985 TGCCACTTGATAAAATAATCGTTGGT 59.848 34.615 0.00 0.00 30.13 3.67
674 675 6.472163 GTGCCACTTGATAAAATAATCGTTGG 59.528 38.462 0.00 0.00 0.00 3.77
675 676 6.194508 CGTGCCACTTGATAAAATAATCGTTG 59.805 38.462 0.00 0.00 0.00 4.10
676 677 6.255215 CGTGCCACTTGATAAAATAATCGTT 58.745 36.000 0.00 0.00 0.00 3.85
677 678 5.220777 CCGTGCCACTTGATAAAATAATCGT 60.221 40.000 0.00 0.00 0.00 3.73
678 679 5.204833 CCGTGCCACTTGATAAAATAATCG 58.795 41.667 0.00 0.00 0.00 3.34
679 680 6.131544 ACCGTGCCACTTGATAAAATAATC 57.868 37.500 0.00 0.00 0.00 1.75
680 681 6.524101 AACCGTGCCACTTGATAAAATAAT 57.476 33.333 0.00 0.00 0.00 1.28
681 682 5.968528 AACCGTGCCACTTGATAAAATAA 57.031 34.783 0.00 0.00 0.00 1.40
682 683 5.704888 CAAACCGTGCCACTTGATAAAATA 58.295 37.500 0.00 0.00 0.00 1.40
683 684 4.555262 CAAACCGTGCCACTTGATAAAAT 58.445 39.130 0.00 0.00 0.00 1.82
684 685 3.971150 CAAACCGTGCCACTTGATAAAA 58.029 40.909 0.00 0.00 0.00 1.52
685 686 3.634568 CAAACCGTGCCACTTGATAAA 57.365 42.857 0.00 0.00 0.00 1.40
697 698 1.081242 GCACATCCTGCAAACCGTG 60.081 57.895 0.00 0.00 46.29 4.94
698 699 3.354678 GCACATCCTGCAAACCGT 58.645 55.556 0.00 0.00 46.29 4.83
706 707 3.276857 ACAGCATTTCTAGCACATCCTG 58.723 45.455 0.00 0.00 0.00 3.86
707 708 3.641434 ACAGCATTTCTAGCACATCCT 57.359 42.857 0.00 0.00 0.00 3.24
708 709 7.496529 TTATTACAGCATTTCTAGCACATCC 57.503 36.000 0.00 0.00 0.00 3.51
712 713 7.134815 CCACATTATTACAGCATTTCTAGCAC 58.865 38.462 0.00 0.00 0.00 4.40
713 714 6.238731 GCCACATTATTACAGCATTTCTAGCA 60.239 38.462 0.00 0.00 0.00 3.49
715 716 6.566564 CGGCCACATTATTACAGCATTTCTAG 60.567 42.308 2.24 0.00 0.00 2.43
726 727 0.466555 TGCCCCGGCCACATTATTAC 60.467 55.000 2.24 0.00 41.09 1.89
727 728 0.466555 GTGCCCCGGCCACATTATTA 60.467 55.000 15.95 0.00 41.09 0.98
730 731 4.434354 GGTGCCCCGGCCACATTA 62.434 66.667 20.56 0.00 41.09 1.90
827 833 2.419673 GGGTTTAGCATTTTTGCCATGC 59.580 45.455 0.00 0.00 46.39 4.06
828 834 3.672808 TGGGTTTAGCATTTTTGCCATG 58.327 40.909 0.00 0.00 34.90 3.66
927 2070 2.684843 CGTGGCTTGCAGGAGAAGC 61.685 63.158 0.00 0.00 44.32 3.86
1080 2223 2.420043 CGGAACACGTGTGACCCT 59.580 61.111 27.71 13.29 37.93 4.34
1134 2277 2.168521 CGAACTCATCTTCCAGCCCTTA 59.831 50.000 0.00 0.00 0.00 2.69
1263 2406 4.789075 GCGTCGCCGGTCTTGCTA 62.789 66.667 5.75 0.00 33.68 3.49
1333 2476 0.669077 CCGGAGAATCTAGTCCACGG 59.331 60.000 0.00 0.00 33.01 4.94
1445 2588 2.125912 CGAGGCAGTCGTCCTTGG 60.126 66.667 0.00 0.00 44.20 3.61
1554 2697 0.949105 AGTCGAAATGTGGTGCCGTC 60.949 55.000 0.00 0.00 0.00 4.79
1555 2698 0.534203 AAGTCGAAATGTGGTGCCGT 60.534 50.000 0.00 0.00 0.00 5.68
1556 2699 1.127951 GTAAGTCGAAATGTGGTGCCG 59.872 52.381 0.00 0.00 0.00 5.69
1557 2700 2.095919 GTGTAAGTCGAAATGTGGTGCC 60.096 50.000 0.00 0.00 0.00 5.01
1558 2701 2.411031 CGTGTAAGTCGAAATGTGGTGC 60.411 50.000 0.00 0.00 0.00 5.01
1559 2702 2.411031 GCGTGTAAGTCGAAATGTGGTG 60.411 50.000 0.00 0.00 0.00 4.17
1606 2749 1.079819 CCTCAATCAGCACGTCCGT 60.080 57.895 0.00 0.00 0.00 4.69
1719 2862 4.742201 CGTAGCACAGTGGCGGCT 62.742 66.667 11.43 10.44 41.51 5.52
1825 2968 3.190849 CCGCTCAGCCATCGTGTG 61.191 66.667 0.00 0.00 0.00 3.82
1921 3064 2.879233 TTGTCCCCACGGAGCTCAC 61.879 63.158 17.19 3.47 39.51 3.51
1965 3108 2.527951 CTTCCCTCAGTTCGGGGCAG 62.528 65.000 0.00 0.00 42.23 4.85
2016 3160 2.819608 GGTAGCCATGAGTGCTTTCAAA 59.180 45.455 0.09 0.00 40.23 2.69
2189 3336 5.857190 AAGCGAAAGATTAGGTCAAGTACCC 60.857 44.000 0.00 0.00 40.15 3.69
2190 3337 5.063564 CAAGCGAAAGATTAGGTCAAGTACC 59.936 44.000 0.00 0.00 43.56 3.34
2191 3338 5.446073 GCAAGCGAAAGATTAGGTCAAGTAC 60.446 44.000 0.00 0.00 37.83 2.73
2192 3339 4.630069 GCAAGCGAAAGATTAGGTCAAGTA 59.370 41.667 0.00 0.00 37.83 2.24
2193 3340 3.437049 GCAAGCGAAAGATTAGGTCAAGT 59.563 43.478 0.00 0.00 37.83 3.16
2209 3356 2.487762 TCCTAGGACATTTTTGCAAGCG 59.512 45.455 7.62 0.00 0.00 4.68
2221 3368 5.221422 CCAAAAATTTGCAACTCCTAGGACA 60.221 40.000 7.62 0.85 36.86 4.02
2222 3369 5.230182 CCAAAAATTTGCAACTCCTAGGAC 58.770 41.667 7.62 0.00 36.86 3.85
2223 3370 4.283212 CCCAAAAATTTGCAACTCCTAGGA 59.717 41.667 11.98 11.98 36.86 2.94
2224 3371 4.283212 TCCCAAAAATTTGCAACTCCTAGG 59.717 41.667 0.82 0.82 36.86 3.02
2225 3372 5.467035 TCCCAAAAATTTGCAACTCCTAG 57.533 39.130 0.00 0.00 36.86 3.02
2233 3380 3.181461 ACGGAACATCCCAAAAATTTGCA 60.181 39.130 0.29 0.00 36.86 4.08
2237 3384 3.235200 TGGACGGAACATCCCAAAAATT 58.765 40.909 0.00 0.00 41.87 1.82
2238 3385 2.883026 TGGACGGAACATCCCAAAAAT 58.117 42.857 0.00 0.00 41.87 1.82
2244 3391 2.702592 TTACATGGACGGAACATCCC 57.297 50.000 0.00 0.00 41.87 3.85
2254 3401 7.410120 AGAAAGGGAATCAAATTACATGGAC 57.590 36.000 0.00 0.00 0.00 4.02
2255 3402 9.540538 TTTAGAAAGGGAATCAAATTACATGGA 57.459 29.630 0.00 0.00 0.00 3.41
2317 3464 4.336993 GGTACAACATGTGTTCTGTTTGGA 59.663 41.667 6.23 0.00 41.98 3.53
2323 3470 3.074412 GGGAGGTACAACATGTGTTCTG 58.926 50.000 0.00 0.00 41.98 3.02
2342 3489 7.124147 AGACAATAATGGGTTCAAACATTAGGG 59.876 37.037 0.00 0.00 41.32 3.53
2349 3496 7.702348 GCTAATGAGACAATAATGGGTTCAAAC 59.298 37.037 0.00 0.00 0.00 2.93
2368 3516 3.430333 TCAGCGTCGTAATGCTAATGA 57.570 42.857 0.00 0.00 46.15 2.57
2375 3523 1.189446 GGCGTTATCAGCGTCGTAATG 59.811 52.381 0.00 0.00 35.00 1.90
2379 3527 2.202703 GGGCGTTATCAGCGTCGT 60.203 61.111 0.00 0.00 34.45 4.34
2380 3528 2.202690 TGGGCGTTATCAGCGTCG 60.203 61.111 0.00 0.00 34.45 5.12
2415 3563 4.282950 CACACAATGTGTAGATGGATGC 57.717 45.455 19.42 0.00 45.65 3.91
2431 3579 1.110518 TCCTACTCACGCCACACACA 61.111 55.000 0.00 0.00 0.00 3.72
2446 3594 2.307496 TTCGTGTGGGTTACCTCCTA 57.693 50.000 0.00 0.00 37.76 2.94
2464 3612 1.327303 ATGTTCGCCCACACACAATT 58.673 45.000 0.00 0.00 0.00 2.32
2465 3613 1.327303 AATGTTCGCCCACACACAAT 58.673 45.000 0.00 0.00 0.00 2.71
2525 3673 4.335594 AGATGAATAGTACTTTTTGGGCGC 59.664 41.667 0.00 0.00 0.00 6.53
2542 3691 1.741401 CGCGCAGGGTGAAGATGAA 60.741 57.895 8.75 0.00 34.98 2.57
2642 3792 6.406370 CCGAATAACTATATCTGCCATTCCA 58.594 40.000 0.00 0.00 0.00 3.53
2655 3805 8.877195 ACTACATTTACCATCCCGAATAACTAT 58.123 33.333 0.00 0.00 0.00 2.12
2672 3823 9.250624 GTTGCCATGTTTTTACAACTACATTTA 57.749 29.630 0.00 0.00 38.04 1.40
2689 3840 4.460382 CCAAAACAGATAGAGTTGCCATGT 59.540 41.667 0.00 0.00 0.00 3.21
2719 3870 5.583457 ACCATAAATTAGACACGGCAACTAC 59.417 40.000 0.00 0.00 0.00 2.73
2728 3879 7.009540 ACGCGTTAACTACCATAAATTAGACAC 59.990 37.037 5.58 0.00 0.00 3.67
2748 3900 3.998341 ACTATGGTTTGATTACACGCGTT 59.002 39.130 10.22 3.81 0.00 4.84
2749 3901 3.592059 ACTATGGTTTGATTACACGCGT 58.408 40.909 5.58 5.58 0.00 6.01
2811 3963 7.676947 ACTAGGTAAACACACATGACAACTAT 58.323 34.615 0.00 0.00 0.00 2.12
2842 3994 7.828717 ACATGATAACTATGGTTGAATCACACA 59.171 33.333 8.95 0.00 34.94 3.72
2863 4015 6.179756 AGCAACTGTGATTAACCATACATGA 58.820 36.000 0.00 0.00 0.00 3.07
2894 4046 3.127895 GCGTATGTGGCAACCAGATAAAA 59.872 43.478 5.15 0.00 40.61 1.52
2911 4063 1.348250 CTGCAATTGCGTCGCGTAT 59.652 52.632 24.58 5.77 45.83 3.06
2953 4105 4.072131 ACTAGGTAAACACACATGGCAAG 58.928 43.478 0.00 0.00 0.00 4.01
3024 4176 1.646189 GCACTGTTTTTCGCCCAAAA 58.354 45.000 0.00 0.00 31.73 2.44
3026 4178 1.064946 CGCACTGTTTTTCGCCCAA 59.935 52.632 0.00 0.00 0.00 4.12
3063 4215 3.086143 CCCACATAGCCACCACCA 58.914 61.111 0.00 0.00 0.00 4.17
3074 4226 3.412386 GTGAACTAGTTTCTGCCCACAT 58.588 45.455 10.02 0.00 34.97 3.21
3094 4246 0.109342 GCCAGCTGTGCTATATGGGT 59.891 55.000 13.81 0.00 36.40 4.51
3101 4253 1.965930 CGGTTTGCCAGCTGTGCTA 60.966 57.895 22.36 15.16 36.40 3.49


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

AutoCloner maintained by Alex Coulton.