Multiple sequence alignment - TraesCS3D01G367600

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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 TraesCS3D01G367600 chr3D 100.000 2383 0 0 410 2792 481526191 481528573 0.000000e+00 4401.0
1 TraesCS3D01G367600 chr3D 96.308 325 12 0 410 734 607009920 607009596 4.090000e-148 534.0
2 TraesCS3D01G367600 chr3D 95.399 326 15 0 410 735 465513504 465513179 1.150000e-143 520.0
3 TraesCS3D01G367600 chr3D 94.345 336 17 2 410 744 501269497 501269163 5.330000e-142 514.0
4 TraesCS3D01G367600 chr3D 100.000 129 0 0 1 129 481525782 481525910 3.590000e-59 239.0
5 TraesCS3D01G367600 chr3B 90.341 1905 116 32 781 2626 642818729 642820624 0.000000e+00 2436.0
6 TraesCS3D01G367600 chr3A 89.030 1896 117 45 783 2626 624532700 624534556 0.000000e+00 2265.0
7 TraesCS3D01G367600 chr3A 95.200 125 6 0 5 129 37621236 37621360 6.100000e-47 198.0
8 TraesCS3D01G367600 chr3A 97.297 37 1 0 2756 2792 624534760 624534796 2.320000e-06 63.9
9 TraesCS3D01G367600 chr5D 95.758 330 14 0 410 739 538364664 538364335 1.470000e-147 532.0
10 TraesCS3D01G367600 chr5D 95.166 331 16 0 410 740 45649982 45650312 8.860000e-145 523.0
11 TraesCS3D01G367600 chr5D 95.200 125 6 0 5 129 479574088 479574212 6.100000e-47 198.0
12 TraesCS3D01G367600 chr1D 94.864 331 16 1 410 740 431094199 431094528 1.480000e-142 516.0
13 TraesCS3D01G367600 chr1D 94.545 330 18 0 410 739 45395687 45395358 6.900000e-141 510.0
14 TraesCS3D01G367600 chr1D 95.082 122 6 0 8 129 45395841 45395720 2.840000e-45 193.0
15 TraesCS3D01G367600 chr4D 95.092 326 15 1 410 735 8158727 8158403 1.920000e-141 512.0
16 TraesCS3D01G367600 chr4D 95.200 125 6 0 5 129 53880520 53880644 6.100000e-47 198.0
17 TraesCS3D01G367600 chr2D 93.510 339 21 1 410 747 401552247 401552585 1.150000e-138 503.0
18 TraesCS3D01G367600 chr2D 96.000 125 5 0 5 129 492994389 492994513 1.310000e-48 204.0
19 TraesCS3D01G367600 chr2D 96.000 125 5 0 5 129 557686848 557686972 1.310000e-48 204.0
20 TraesCS3D01G367600 chr2D 95.200 125 6 0 5 129 390402426 390402550 6.100000e-47 198.0
21 TraesCS3D01G367600 chrUn 95.902 122 5 0 8 129 28927763 28927642 6.100000e-47 198.0
22 TraesCS3D01G367600 chr7D 95.868 121 5 0 9 129 43217583 43217463 2.190000e-46 196.0


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 TraesCS3D01G367600 chr3D 481525782 481528573 2791 False 2320.00 4401 100.0000 1 2792 2 chr3D.!!$F1 2791
1 TraesCS3D01G367600 chr3B 642818729 642820624 1895 False 2436.00 2436 90.3410 781 2626 1 chr3B.!!$F1 1845
2 TraesCS3D01G367600 chr3A 624532700 624534796 2096 False 1164.45 2265 93.1635 783 2792 2 chr3A.!!$F2 2009

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
732 733 0.037326 TGCGGGTTCTGCTAGAGTTG 60.037 55.0 0.0 0.0 0.0 3.16 F
1508 1566 0.108585 AGCCGGCGATATGGTTTGAT 59.891 50.0 23.2 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1842 0.179215 GTCAAACTCGCGCAATCTGG 60.179 55.0 8.75 0.00 0.0 3.86 R
2749 2903 0.392461 TTAGTGGCATGGCGGAGTTC 60.392 55.0 15.27 1.06 0.0 3.01 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
21 22 0.179062 CCACTAGTGGCCAGATGAGC 60.179 60.000 28.48 0.00 44.73 4.26
22 23 0.829333 CACTAGTGGCCAGATGAGCT 59.171 55.000 15.49 0.00 0.00 4.09
23 24 1.118838 ACTAGTGGCCAGATGAGCTC 58.881 55.000 5.11 6.82 0.00 4.09
24 25 0.392336 CTAGTGGCCAGATGAGCTCC 59.608 60.000 5.11 0.00 0.00 4.70
25 26 1.050988 TAGTGGCCAGATGAGCTCCC 61.051 60.000 5.11 4.25 0.00 4.30
26 27 3.092511 TGGCCAGATGAGCTCCCC 61.093 66.667 12.15 2.55 0.00 4.81
27 28 4.247380 GGCCAGATGAGCTCCCCG 62.247 72.222 12.15 0.00 0.00 5.73
28 29 4.925861 GCCAGATGAGCTCCCCGC 62.926 72.222 12.15 1.88 39.57 6.13
29 30 4.598894 CCAGATGAGCTCCCCGCG 62.599 72.222 12.15 0.00 45.59 6.46
30 31 4.598894 CAGATGAGCTCCCCGCGG 62.599 72.222 21.04 21.04 45.59 6.46
31 32 4.841617 AGATGAGCTCCCCGCGGA 62.842 66.667 30.73 6.52 45.59 5.54
32 33 4.593864 GATGAGCTCCCCGCGGAC 62.594 72.222 30.73 13.26 45.59 4.79
38 39 4.760047 CTCCCCGCGGACCAGTTG 62.760 72.222 30.73 7.66 33.32 3.16
45 46 4.760047 CGGACCAGTTGGCGGAGG 62.760 72.222 0.00 0.00 39.32 4.30
46 47 3.319198 GGACCAGTTGGCGGAGGA 61.319 66.667 0.00 0.00 39.32 3.71
47 48 2.266055 GACCAGTTGGCGGAGGAG 59.734 66.667 0.00 0.00 39.32 3.69
48 49 3.316573 GACCAGTTGGCGGAGGAGG 62.317 68.421 0.00 0.00 39.32 4.30
49 50 4.785453 CCAGTTGGCGGAGGAGGC 62.785 72.222 0.00 0.00 37.19 4.70
94 95 2.940007 GAACTCGTCGAGCTCGCG 60.940 66.667 32.47 32.47 39.60 5.87
426 427 2.887568 GGCGTCAGATCTGGCACG 60.888 66.667 26.10 25.44 34.22 5.34
427 428 2.887568 GCGTCAGATCTGGCACGG 60.888 66.667 28.07 15.19 34.22 4.94
428 429 2.887568 CGTCAGATCTGGCACGGC 60.888 66.667 26.10 0.00 34.22 5.68
429 430 2.265739 GTCAGATCTGGCACGGCA 59.734 61.111 22.39 0.00 34.82 5.69
430 431 1.812922 GTCAGATCTGGCACGGCAG 60.813 63.158 22.39 14.07 34.82 4.85
431 432 3.200593 CAGATCTGGCACGGCAGC 61.201 66.667 15.38 3.19 32.53 5.25
432 433 4.827087 AGATCTGGCACGGCAGCG 62.827 66.667 15.31 0.00 34.64 5.18
449 450 4.554036 GGTGCTCCGCCTCATCCC 62.554 72.222 0.00 0.00 0.00 3.85
450 451 4.554036 GTGCTCCGCCTCATCCCC 62.554 72.222 0.00 0.00 0.00 4.81
456 457 3.917760 CGCCTCATCCCCCGAGTC 61.918 72.222 0.00 0.00 0.00 3.36
457 458 3.917760 GCCTCATCCCCCGAGTCG 61.918 72.222 5.29 5.29 0.00 4.18
459 460 3.917760 CTCATCCCCCGAGTCGGC 61.918 72.222 26.60 0.00 46.86 5.54
462 463 4.880426 ATCCCCCGAGTCGGCCAT 62.880 66.667 26.60 13.55 46.86 4.40
466 467 4.838152 CCCGAGTCGGCCATGGTG 62.838 72.222 26.60 6.70 46.86 4.17
467 468 4.838152 CCGAGTCGGCCATGGTGG 62.838 72.222 20.50 5.69 41.17 4.61
468 469 4.082523 CGAGTCGGCCATGGTGGT 62.083 66.667 14.67 0.00 40.46 4.16
469 470 2.351276 GAGTCGGCCATGGTGGTT 59.649 61.111 14.67 0.00 40.46 3.67
470 471 1.745489 GAGTCGGCCATGGTGGTTC 60.745 63.158 14.67 1.77 40.46 3.62
471 472 2.033448 GTCGGCCATGGTGGTTCA 59.967 61.111 14.67 0.00 40.46 3.18
472 473 1.602323 GTCGGCCATGGTGGTTCAA 60.602 57.895 14.67 0.00 40.46 2.69
473 474 1.303236 TCGGCCATGGTGGTTCAAG 60.303 57.895 14.67 0.00 40.46 3.02
474 475 1.303236 CGGCCATGGTGGTTCAAGA 60.303 57.895 14.67 0.00 40.46 3.02
475 476 1.586154 CGGCCATGGTGGTTCAAGAC 61.586 60.000 14.67 0.00 40.46 3.01
476 477 0.251341 GGCCATGGTGGTTCAAGACT 60.251 55.000 14.67 0.00 40.46 3.24
477 478 1.168714 GCCATGGTGGTTCAAGACTC 58.831 55.000 14.67 0.00 40.46 3.36
478 479 1.442769 CCATGGTGGTTCAAGACTCG 58.557 55.000 2.57 0.00 31.35 4.18
479 480 0.798776 CATGGTGGTTCAAGACTCGC 59.201 55.000 0.00 0.00 0.00 5.03
480 481 0.321653 ATGGTGGTTCAAGACTCGCC 60.322 55.000 0.00 0.00 32.78 5.54
481 482 2.027625 GGTGGTTCAAGACTCGCCG 61.028 63.158 0.00 0.00 0.00 6.46
482 483 2.027625 GTGGTTCAAGACTCGCCGG 61.028 63.158 0.00 0.00 0.00 6.13
483 484 3.119096 GGTTCAAGACTCGCCGGC 61.119 66.667 19.07 19.07 0.00 6.13
484 485 3.479269 GTTCAAGACTCGCCGGCG 61.479 66.667 42.13 42.13 41.35 6.46
485 486 4.735132 TTCAAGACTCGCCGGCGG 62.735 66.667 44.95 35.79 40.25 6.13
496 497 4.865761 CCGGCGGCGAGAAATCGA 62.866 66.667 34.49 0.00 34.64 3.59
497 498 3.323136 CGGCGGCGAGAAATCGAG 61.323 66.667 29.19 0.00 34.64 4.04
498 499 3.631127 GGCGGCGAGAAATCGAGC 61.631 66.667 12.98 5.99 37.49 5.03
499 500 3.977568 GCGGCGAGAAATCGAGCG 61.978 66.667 12.98 0.00 34.64 5.03
500 501 3.323136 CGGCGAGAAATCGAGCGG 61.323 66.667 0.00 0.00 34.64 5.52
501 502 3.631127 GGCGAGAAATCGAGCGGC 61.631 66.667 1.17 0.00 41.85 6.53
502 503 3.977568 GCGAGAAATCGAGCGGCG 61.978 66.667 0.51 0.51 42.69 6.46
503 504 3.977568 CGAGAAATCGAGCGGCGC 61.978 66.667 26.86 26.86 40.61 6.53
504 505 3.977568 GAGAAATCGAGCGGCGCG 61.978 66.667 27.59 20.10 40.61 6.86
518 519 2.824041 CGCGGTGGGGAATTGGAG 60.824 66.667 0.00 0.00 0.00 3.86
519 520 2.440247 GCGGTGGGGAATTGGAGG 60.440 66.667 0.00 0.00 0.00 4.30
520 521 2.275418 CGGTGGGGAATTGGAGGG 59.725 66.667 0.00 0.00 0.00 4.30
521 522 2.689813 GGTGGGGAATTGGAGGGG 59.310 66.667 0.00 0.00 0.00 4.79
522 523 1.933812 GGTGGGGAATTGGAGGGGA 60.934 63.158 0.00 0.00 0.00 4.81
523 524 1.514864 GGTGGGGAATTGGAGGGGAA 61.515 60.000 0.00 0.00 0.00 3.97
524 525 0.636647 GTGGGGAATTGGAGGGGAAT 59.363 55.000 0.00 0.00 0.00 3.01
525 526 0.636101 TGGGGAATTGGAGGGGAATG 59.364 55.000 0.00 0.00 0.00 2.67
526 527 0.933700 GGGGAATTGGAGGGGAATGA 59.066 55.000 0.00 0.00 0.00 2.57
527 528 1.133356 GGGGAATTGGAGGGGAATGAG 60.133 57.143 0.00 0.00 0.00 2.90
528 529 1.133356 GGGAATTGGAGGGGAATGAGG 60.133 57.143 0.00 0.00 0.00 3.86
529 530 1.697284 GAATTGGAGGGGAATGAGGC 58.303 55.000 0.00 0.00 0.00 4.70
530 531 0.106519 AATTGGAGGGGAATGAGGCG 60.107 55.000 0.00 0.00 0.00 5.52
531 532 1.999634 ATTGGAGGGGAATGAGGCGG 62.000 60.000 0.00 0.00 0.00 6.13
532 533 4.570874 GGAGGGGAATGAGGCGGC 62.571 72.222 0.00 0.00 0.00 6.53
533 534 4.918201 GAGGGGAATGAGGCGGCG 62.918 72.222 0.51 0.51 0.00 6.46
537 538 4.918201 GGAATGAGGCGGCGGGAG 62.918 72.222 9.78 0.00 0.00 4.30
538 539 4.918201 GAATGAGGCGGCGGGAGG 62.918 72.222 9.78 0.00 0.00 4.30
541 542 3.828083 ATGAGGCGGCGGGAGGATA 62.828 63.158 9.78 0.00 0.00 2.59
542 543 3.686045 GAGGCGGCGGGAGGATAG 61.686 72.222 9.78 0.00 0.00 2.08
546 547 2.842936 CGGCGGGAGGATAGGGTT 60.843 66.667 0.00 0.00 0.00 4.11
547 548 2.440817 CGGCGGGAGGATAGGGTTT 61.441 63.158 0.00 0.00 0.00 3.27
548 549 1.450642 GGCGGGAGGATAGGGTTTC 59.549 63.158 0.00 0.00 0.00 2.78
549 550 1.069258 GCGGGAGGATAGGGTTTCG 59.931 63.158 0.00 0.00 0.00 3.46
550 551 1.397390 GCGGGAGGATAGGGTTTCGA 61.397 60.000 0.00 0.00 0.00 3.71
551 552 0.388294 CGGGAGGATAGGGTTTCGAC 59.612 60.000 0.00 0.00 0.00 4.20
552 553 0.757512 GGGAGGATAGGGTTTCGACC 59.242 60.000 0.00 0.00 0.00 4.79
559 560 2.267961 GGGTTTCGACCCGCATCT 59.732 61.111 0.00 0.00 40.59 2.90
560 561 2.106683 GGGTTTCGACCCGCATCTG 61.107 63.158 0.00 0.00 40.59 2.90
561 562 2.750888 GGTTTCGACCCGCATCTGC 61.751 63.158 0.00 0.00 37.78 4.26
562 563 2.435938 TTTCGACCCGCATCTGCC 60.436 61.111 0.00 0.00 37.91 4.85
563 564 3.969250 TTTCGACCCGCATCTGCCC 62.969 63.158 0.00 0.00 37.91 5.36
570 571 4.481112 CGCATCTGCCCCGCAAAC 62.481 66.667 0.00 0.00 38.41 2.93
571 572 4.133796 GCATCTGCCCCGCAAACC 62.134 66.667 0.00 0.00 38.41 3.27
572 573 2.361610 CATCTGCCCCGCAAACCT 60.362 61.111 0.00 0.00 38.41 3.50
573 574 2.361610 ATCTGCCCCGCAAACCTG 60.362 61.111 0.00 0.00 38.41 4.00
584 585 2.825086 GCAAACCTGCGGTTATAGTG 57.175 50.000 12.33 8.74 46.20 2.74
585 586 1.400494 GCAAACCTGCGGTTATAGTGG 59.600 52.381 12.33 0.00 46.20 4.00
586 587 1.400494 CAAACCTGCGGTTATAGTGGC 59.600 52.381 12.33 0.00 46.20 5.01
587 588 0.909623 AACCTGCGGTTATAGTGGCT 59.090 50.000 10.62 0.00 44.94 4.75
588 589 0.464452 ACCTGCGGTTATAGTGGCTC 59.536 55.000 0.00 0.00 27.29 4.70
589 590 0.597637 CCTGCGGTTATAGTGGCTCG 60.598 60.000 0.00 0.00 0.00 5.03
590 591 0.597637 CTGCGGTTATAGTGGCTCGG 60.598 60.000 0.00 0.00 0.00 4.63
591 592 1.300697 GCGGTTATAGTGGCTCGGG 60.301 63.158 0.00 0.00 0.00 5.14
592 593 1.366366 CGGTTATAGTGGCTCGGGG 59.634 63.158 0.00 0.00 0.00 5.73
593 594 1.752833 GGTTATAGTGGCTCGGGGG 59.247 63.158 0.00 0.00 0.00 5.40
594 595 1.052694 GGTTATAGTGGCTCGGGGGT 61.053 60.000 0.00 0.00 0.00 4.95
595 596 0.835276 GTTATAGTGGCTCGGGGGTT 59.165 55.000 0.00 0.00 0.00 4.11
596 597 0.834612 TTATAGTGGCTCGGGGGTTG 59.165 55.000 0.00 0.00 0.00 3.77
597 598 1.692173 TATAGTGGCTCGGGGGTTGC 61.692 60.000 0.00 0.00 0.00 4.17
602 603 4.038080 GCTCGGGGGTTGCGTTTG 62.038 66.667 0.00 0.00 0.00 2.93
603 604 4.038080 CTCGGGGGTTGCGTTTGC 62.038 66.667 0.00 0.00 43.20 3.68
637 638 1.812235 AAAATTACGGGTCGGACACC 58.188 50.000 10.76 7.91 45.97 4.16
653 654 4.899239 CCGATGCGGGCTCTGGTC 62.899 72.222 0.00 0.00 44.15 4.02
654 655 3.842923 CGATGCGGGCTCTGGTCT 61.843 66.667 0.00 0.00 0.00 3.85
655 656 2.202987 GATGCGGGCTCTGGTCTG 60.203 66.667 0.00 0.00 0.00 3.51
656 657 3.746949 GATGCGGGCTCTGGTCTGG 62.747 68.421 0.00 0.00 0.00 3.86
668 669 1.631405 TGGTCTGGCCAGAAAAATGG 58.369 50.000 36.66 7.62 43.61 3.16
669 670 0.897621 GGTCTGGCCAGAAAAATGGG 59.102 55.000 36.66 6.78 40.97 4.00
673 674 3.693411 GCCAGAAAAATGGGCCGA 58.307 55.556 0.00 0.00 41.90 5.54
674 675 1.512694 GCCAGAAAAATGGGCCGAG 59.487 57.895 0.00 0.00 41.90 4.63
675 676 1.512694 CCAGAAAAATGGGCCGAGC 59.487 57.895 0.00 0.00 36.64 5.03
686 687 3.123674 GGCCGAGCCTGTATAATCG 57.876 57.895 7.58 0.00 46.69 3.34
687 688 1.014564 GGCCGAGCCTGTATAATCGC 61.015 60.000 7.58 0.00 46.69 4.58
688 689 1.014564 GCCGAGCCTGTATAATCGCC 61.015 60.000 0.00 0.00 33.94 5.54
689 690 0.732880 CCGAGCCTGTATAATCGCCG 60.733 60.000 0.00 0.00 33.94 6.46
690 691 0.732880 CGAGCCTGTATAATCGCCGG 60.733 60.000 0.00 0.00 0.00 6.13
691 692 0.601558 GAGCCTGTATAATCGCCGGA 59.398 55.000 5.05 0.00 0.00 5.14
692 693 1.000506 GAGCCTGTATAATCGCCGGAA 59.999 52.381 5.05 0.00 0.00 4.30
693 694 1.623811 AGCCTGTATAATCGCCGGAAT 59.376 47.619 5.05 0.00 0.00 3.01
694 695 2.038557 AGCCTGTATAATCGCCGGAATT 59.961 45.455 5.05 6.70 0.00 2.17
695 696 3.259876 AGCCTGTATAATCGCCGGAATTA 59.740 43.478 5.05 9.02 0.00 1.40
696 697 4.081087 AGCCTGTATAATCGCCGGAATTAT 60.081 41.667 20.06 20.06 0.00 1.28
697 698 4.034048 GCCTGTATAATCGCCGGAATTATG 59.966 45.833 22.93 12.91 0.00 1.90
698 699 4.034048 CCTGTATAATCGCCGGAATTATGC 59.966 45.833 22.93 21.95 0.00 3.14
706 707 3.250220 CGGAATTATGCGGGTTTGC 57.750 52.632 0.00 0.00 36.66 3.68
707 708 0.591236 CGGAATTATGCGGGTTTGCG 60.591 55.000 0.00 0.00 36.66 4.85
708 709 0.869880 GGAATTATGCGGGTTTGCGC 60.870 55.000 0.00 0.00 37.81 6.09
709 710 0.869880 GAATTATGCGGGTTTGCGCC 60.870 55.000 4.18 0.00 37.81 6.53
710 711 2.606155 AATTATGCGGGTTTGCGCCG 62.606 55.000 4.18 0.75 37.81 6.46
725 726 4.473520 CCGGATGCGGGTTCTGCT 62.474 66.667 19.27 0.00 0.00 4.24
726 727 2.499205 CGGATGCGGGTTCTGCTA 59.501 61.111 0.00 0.00 0.00 3.49
727 728 1.592669 CGGATGCGGGTTCTGCTAG 60.593 63.158 0.00 0.00 0.00 3.42
728 729 1.823295 GGATGCGGGTTCTGCTAGA 59.177 57.895 0.00 0.00 0.00 2.43
729 730 0.249657 GGATGCGGGTTCTGCTAGAG 60.250 60.000 0.00 0.00 0.00 2.43
730 731 0.461961 GATGCGGGTTCTGCTAGAGT 59.538 55.000 0.00 0.00 0.00 3.24
731 732 0.905357 ATGCGGGTTCTGCTAGAGTT 59.095 50.000 0.00 0.00 0.00 3.01
732 733 0.037326 TGCGGGTTCTGCTAGAGTTG 60.037 55.000 0.00 0.00 0.00 3.16
733 734 1.362406 GCGGGTTCTGCTAGAGTTGC 61.362 60.000 0.00 0.00 0.00 4.17
734 735 0.247736 CGGGTTCTGCTAGAGTTGCT 59.752 55.000 0.00 0.00 0.00 3.91
735 736 1.338200 CGGGTTCTGCTAGAGTTGCTT 60.338 52.381 0.00 0.00 0.00 3.91
736 737 2.784347 GGGTTCTGCTAGAGTTGCTTT 58.216 47.619 0.00 0.00 0.00 3.51
737 738 3.149981 GGGTTCTGCTAGAGTTGCTTTT 58.850 45.455 0.00 0.00 0.00 2.27
738 739 4.324267 GGGTTCTGCTAGAGTTGCTTTTA 58.676 43.478 0.00 0.00 0.00 1.52
739 740 4.760204 GGGTTCTGCTAGAGTTGCTTTTAA 59.240 41.667 0.00 0.00 0.00 1.52
740 741 5.106515 GGGTTCTGCTAGAGTTGCTTTTAAG 60.107 44.000 0.00 0.00 0.00 1.85
741 742 5.106515 GGTTCTGCTAGAGTTGCTTTTAAGG 60.107 44.000 0.00 0.00 0.00 2.69
742 743 4.579869 TCTGCTAGAGTTGCTTTTAAGGG 58.420 43.478 0.00 0.00 0.00 3.95
743 744 3.686016 TGCTAGAGTTGCTTTTAAGGGG 58.314 45.455 0.00 0.00 0.00 4.79
744 745 3.073946 TGCTAGAGTTGCTTTTAAGGGGT 59.926 43.478 0.00 0.00 0.00 4.95
745 746 4.287585 TGCTAGAGTTGCTTTTAAGGGGTA 59.712 41.667 0.00 0.00 0.00 3.69
746 747 4.634883 GCTAGAGTTGCTTTTAAGGGGTAC 59.365 45.833 0.00 0.00 0.00 3.34
765 766 6.291648 GGTACCCTTAGTTAGTTAGTTGCT 57.708 41.667 0.00 0.00 0.00 3.91
766 767 6.336566 GGTACCCTTAGTTAGTTAGTTGCTC 58.663 44.000 0.00 0.00 0.00 4.26
767 768 6.154192 GGTACCCTTAGTTAGTTAGTTGCTCT 59.846 42.308 0.00 0.00 0.00 4.09
768 769 6.283544 ACCCTTAGTTAGTTAGTTGCTCTC 57.716 41.667 0.00 0.00 0.00 3.20
769 770 5.105837 ACCCTTAGTTAGTTAGTTGCTCTCG 60.106 44.000 0.00 0.00 0.00 4.04
770 771 5.125097 CCCTTAGTTAGTTAGTTGCTCTCGA 59.875 44.000 0.00 0.00 0.00 4.04
771 772 6.259638 CCTTAGTTAGTTAGTTGCTCTCGAG 58.740 44.000 5.93 5.93 0.00 4.04
772 773 4.705337 AGTTAGTTAGTTGCTCTCGAGG 57.295 45.455 13.56 4.50 0.00 4.63
773 774 4.333690 AGTTAGTTAGTTGCTCTCGAGGA 58.666 43.478 13.56 0.00 0.00 3.71
774 775 4.396790 AGTTAGTTAGTTGCTCTCGAGGAG 59.603 45.833 13.56 9.83 44.49 3.69
819 822 3.838795 CGCGGTCGCTAGTTGCAC 61.839 66.667 13.51 0.00 43.06 4.57
820 823 3.838795 GCGGTCGCTAGTTGCACG 61.839 66.667 8.20 0.00 43.06 5.34
924 928 1.654023 GCAGGTTAATCGGGTGCACC 61.654 60.000 28.57 28.57 34.18 5.01
936 940 1.974343 GTGCACCCATTAACCGGCA 60.974 57.895 5.22 0.00 0.00 5.69
1005 1013 3.568538 CCAGAAAGAAAAGAACATGGCG 58.431 45.455 0.00 0.00 0.00 5.69
1045 1053 2.567169 CTGTTGGTCCACAGGATCACTA 59.433 50.000 0.00 0.00 43.19 2.74
1158 1166 1.065410 TCCCCAGTTTCAGGGCAAGA 61.065 55.000 0.00 0.00 45.39 3.02
1170 1178 0.534203 GGGCAAGAGTGTCCGTGAAA 60.534 55.000 0.00 0.00 40.47 2.69
1310 1323 6.769512 TCTTTCAGGTCAGTAGTAAGCATTT 58.230 36.000 0.00 0.00 0.00 2.32
1333 1391 3.360867 TGGTCTTCTCTCTCAGCTTAGG 58.639 50.000 0.00 0.00 0.00 2.69
1341 1399 1.138661 CTCTCAGCTTAGGCCTTCAGG 59.861 57.143 12.58 0.00 39.73 3.86
1356 1414 3.100545 CAGGTGAACTGCTTGGTGT 57.899 52.632 0.00 0.00 40.97 4.16
1357 1415 2.254546 CAGGTGAACTGCTTGGTGTA 57.745 50.000 0.00 0.00 40.97 2.90
1358 1416 2.783135 CAGGTGAACTGCTTGGTGTAT 58.217 47.619 0.00 0.00 40.97 2.29
1359 1417 3.149196 CAGGTGAACTGCTTGGTGTATT 58.851 45.455 0.00 0.00 40.97 1.89
1360 1418 4.323417 CAGGTGAACTGCTTGGTGTATTA 58.677 43.478 0.00 0.00 40.97 0.98
1361 1419 4.393062 CAGGTGAACTGCTTGGTGTATTAG 59.607 45.833 0.00 0.00 40.97 1.73
1362 1420 4.041691 AGGTGAACTGCTTGGTGTATTAGT 59.958 41.667 0.00 0.00 0.00 2.24
1363 1421 5.247564 AGGTGAACTGCTTGGTGTATTAGTA 59.752 40.000 0.00 0.00 0.00 1.82
1364 1422 5.350640 GGTGAACTGCTTGGTGTATTAGTAC 59.649 44.000 0.00 0.00 0.00 2.73
1380 1438 9.607988 TGTATTAGTACAATTCAATACACCCAG 57.392 33.333 0.00 0.00 38.36 4.45
1381 1439 9.052759 GTATTAGTACAATTCAATACACCCAGG 57.947 37.037 0.00 0.00 35.11 4.45
1397 1455 4.935808 CACCCAGGTAGAACTGATGTTTAC 59.064 45.833 0.00 0.00 40.97 2.01
1413 1471 4.972201 TGTTTACGTTGAACCTGTTTGTC 58.028 39.130 0.00 0.00 0.00 3.18
1416 1474 2.980568 ACGTTGAACCTGTTTGTCTGA 58.019 42.857 0.00 0.00 0.00 3.27
1425 1483 1.140852 CTGTTTGTCTGACAGTGGGGA 59.859 52.381 10.77 0.00 39.66 4.81
1434 1492 2.632996 CTGACAGTGGGGAAACAGTCTA 59.367 50.000 0.00 0.00 37.45 2.59
1477 1535 1.912731 TGCCAGTGCCTATCAAGGTAA 59.087 47.619 0.00 0.00 45.64 2.85
1506 1564 0.532862 AGAGCCGGCGATATGGTTTG 60.533 55.000 23.20 0.00 0.00 2.93
1508 1566 0.108585 AGCCGGCGATATGGTTTGAT 59.891 50.000 23.20 0.00 0.00 2.57
1516 1585 6.100004 CGGCGATATGGTTTGATATACTTCT 58.900 40.000 0.00 0.00 0.00 2.85
1575 1644 2.034221 GTGGACAAGGTGGAGGGC 59.966 66.667 0.00 0.00 0.00 5.19
1773 1842 0.391661 TGGCGCTTCAGAAGTCCATC 60.392 55.000 17.34 0.00 31.56 3.51
1808 1877 4.276926 AGTTTGACAAGCCTGTTCAGATTC 59.723 41.667 1.00 0.00 35.30 2.52
1822 1918 4.818534 TCAGATTCTGCAAGTTTGACAC 57.181 40.909 8.89 0.00 33.76 3.67
1834 1930 5.221126 GCAAGTTTGACACTGAAGAAGGAAT 60.221 40.000 0.00 0.00 35.12 3.01
1846 1942 4.577693 TGAAGAAGGAATATGATGCAGCAC 59.422 41.667 6.89 0.00 0.00 4.40
1851 1947 3.501062 AGGAATATGATGCAGCACGATTG 59.499 43.478 16.29 0.00 0.00 2.67
2071 2173 2.223089 ACACGCACACGGTAAAGAAAAC 60.223 45.455 0.00 0.00 46.04 2.43
2098 2200 5.973565 GTCAATATAACAACTGGAGCATTGC 59.026 40.000 0.00 0.00 0.00 3.56
2248 2351 1.135960 GCCTCTAGCTTTGGGAGGAT 58.864 55.000 21.06 0.00 46.82 3.24
2297 2400 4.837896 AGCTAACTTTGCTTGACCTTTC 57.162 40.909 0.00 0.00 37.52 2.62
2427 2530 1.081641 CTGGCTGCTTTCAACTGCG 60.082 57.895 0.00 0.00 33.24 5.18
2463 2566 6.477360 ACAAAACACCGGTCAAACAAATTATC 59.523 34.615 2.59 0.00 0.00 1.75
2484 2587 2.171567 CATTCACAATTTCTGCTCGCG 58.828 47.619 0.00 0.00 0.00 5.87
2488 2591 1.349627 CAATTTCTGCTCGCGCGAT 59.650 52.632 34.86 14.23 39.65 4.58
2493 2598 0.591659 TTCTGCTCGCGCGATATAGT 59.408 50.000 34.86 0.00 39.65 2.12
2503 2608 4.678287 TCGCGCGATATAGTTCCTTAAAAG 59.322 41.667 31.40 0.00 0.00 2.27
2568 2673 4.836825 TCTCAGGGTTCATGAACTTCATC 58.163 43.478 31.81 18.02 40.94 2.92
2589 2694 8.256611 TCATCTTTTCACTGCAGTAAGAATAC 57.743 34.615 26.35 0.00 0.00 1.89
2615 2720 8.338259 CGATGAGAAAATTTCCAGGTAATAGTG 58.662 37.037 1.57 0.00 0.00 2.74
2618 2723 7.450014 TGAGAAAATTTCCAGGTAATAGTGCAA 59.550 33.333 1.57 0.00 0.00 4.08
2626 2731 8.410673 TTCCAGGTAATAGTGCAAAATAAACA 57.589 30.769 0.00 0.00 0.00 2.83
2628 2733 8.465999 TCCAGGTAATAGTGCAAAATAAACATG 58.534 33.333 0.00 0.00 0.00 3.21
2629 2734 8.465999 CCAGGTAATAGTGCAAAATAAACATGA 58.534 33.333 0.00 0.00 0.00 3.07
2630 2735 9.507280 CAGGTAATAGTGCAAAATAAACATGAG 57.493 33.333 0.00 0.00 0.00 2.90
2635 2740 6.741992 AGTGCAAAATAAACATGAGATCGA 57.258 33.333 0.00 0.00 0.00 3.59
2636 2741 6.546395 AGTGCAAAATAAACATGAGATCGAC 58.454 36.000 0.00 0.00 0.00 4.20
2638 2743 6.249260 GTGCAAAATAAACATGAGATCGACAC 59.751 38.462 0.00 0.00 0.00 3.67
2642 2747 6.668541 AATAAACATGAGATCGACACAAGG 57.331 37.500 0.00 0.00 0.00 3.61
2644 2749 4.478206 AACATGAGATCGACACAAGGAT 57.522 40.909 0.00 0.00 0.00 3.24
2646 2751 5.598416 ACATGAGATCGACACAAGGATTA 57.402 39.130 0.00 0.00 0.00 1.75
2650 2804 2.434702 AGATCGACACAAGGATTACCCC 59.565 50.000 0.00 0.00 36.73 4.95
2661 2815 1.271926 GGATTACCCCTGTGTTGTGCT 60.272 52.381 0.00 0.00 0.00 4.40
2678 2832 8.386606 GTGTTGTGCTAAGAGATTAGAGATTTG 58.613 37.037 0.00 0.00 0.00 2.32
2710 2864 7.885297 TGACTCTGGAATTTTCAAATTGGTAG 58.115 34.615 2.17 0.00 38.64 3.18
2722 2876 2.713828 ATTGGTAGGGCCCAGTTTTT 57.286 45.000 27.56 3.89 35.49 1.94
2725 2879 3.837399 TGGTAGGGCCCAGTTTTTATT 57.163 42.857 27.56 1.16 36.04 1.40
2762 2942 0.169009 GTGAAAGAACTCCGCCATGC 59.831 55.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.829333 AGCTCATCTGGCCACTAGTG 59.171 55.000 16.34 16.34 0.00 2.74
4 5 1.118838 GAGCTCATCTGGCCACTAGT 58.881 55.000 9.40 0.00 0.00 2.57
5 6 0.392336 GGAGCTCATCTGGCCACTAG 59.608 60.000 17.19 0.00 0.00 2.57
6 7 1.050988 GGGAGCTCATCTGGCCACTA 61.051 60.000 17.19 0.00 0.00 2.74
7 8 2.373707 GGGAGCTCATCTGGCCACT 61.374 63.158 17.19 0.00 0.00 4.00
8 9 2.191641 GGGAGCTCATCTGGCCAC 59.808 66.667 17.19 0.00 0.00 5.01
9 10 3.092511 GGGGAGCTCATCTGGCCA 61.093 66.667 17.19 4.71 0.00 5.36
10 11 4.247380 CGGGGAGCTCATCTGGCC 62.247 72.222 17.19 5.95 0.00 5.36
11 12 4.925861 GCGGGGAGCTCATCTGGC 62.926 72.222 17.19 7.36 44.04 4.85
12 13 4.598894 CGCGGGGAGCTCATCTGG 62.599 72.222 17.19 0.55 45.59 3.86
13 14 4.598894 CCGCGGGGAGCTCATCTG 62.599 72.222 20.10 12.90 45.59 2.90
14 15 4.841617 TCCGCGGGGAGCTCATCT 62.842 66.667 27.83 0.00 45.59 2.90
15 16 4.593864 GTCCGCGGGGAGCTCATC 62.594 72.222 27.83 5.02 44.97 2.92
21 22 4.760047 CAACTGGTCCGCGGGGAG 62.760 72.222 27.83 20.12 44.97 4.30
28 29 4.760047 CCTCCGCCAACTGGTCCG 62.760 72.222 0.00 0.00 37.57 4.79
29 30 3.316573 CTCCTCCGCCAACTGGTCC 62.317 68.421 0.00 0.00 37.57 4.46
30 31 2.266055 CTCCTCCGCCAACTGGTC 59.734 66.667 0.00 0.00 37.57 4.02
31 32 3.322466 CCTCCTCCGCCAACTGGT 61.322 66.667 0.00 0.00 37.57 4.00
32 33 4.785453 GCCTCCTCCGCCAACTGG 62.785 72.222 0.00 0.00 38.53 4.00
77 78 2.940007 CGCGAGCTCGACGAGTTC 60.940 66.667 38.74 26.27 43.02 3.01
409 410 2.887568 CGTGCCAGATCTGACGCC 60.888 66.667 24.62 11.98 0.00 5.68
410 411 2.887568 CCGTGCCAGATCTGACGC 60.888 66.667 24.62 18.11 31.90 5.19
411 412 2.887568 GCCGTGCCAGATCTGACG 60.888 66.667 24.62 23.80 32.69 4.35
412 413 1.812922 CTGCCGTGCCAGATCTGAC 60.813 63.158 24.62 13.69 34.77 3.51
413 414 2.580815 CTGCCGTGCCAGATCTGA 59.419 61.111 24.62 1.64 34.77 3.27
414 415 3.200593 GCTGCCGTGCCAGATCTG 61.201 66.667 16.24 16.24 34.77 2.90
415 416 4.827087 CGCTGCCGTGCCAGATCT 62.827 66.667 0.00 0.00 34.77 2.75
439 440 3.917760 GACTCGGGGGATGAGGCG 61.918 72.222 0.00 0.00 37.79 5.52
440 441 3.917760 CGACTCGGGGGATGAGGC 61.918 72.222 0.00 0.00 38.16 4.70
441 442 3.227276 CCGACTCGGGGGATGAGG 61.227 72.222 9.85 0.00 44.15 3.86
451 452 3.605749 AACCACCATGGCCGACTCG 62.606 63.158 13.04 0.00 42.67 4.18
452 453 1.745489 GAACCACCATGGCCGACTC 60.745 63.158 13.04 0.00 42.67 3.36
453 454 2.063015 TTGAACCACCATGGCCGACT 62.063 55.000 13.04 0.00 42.67 4.18
454 455 1.586154 CTTGAACCACCATGGCCGAC 61.586 60.000 13.04 0.44 42.67 4.79
455 456 1.303236 CTTGAACCACCATGGCCGA 60.303 57.895 13.04 0.00 42.67 5.54
456 457 1.303236 TCTTGAACCACCATGGCCG 60.303 57.895 13.04 4.10 42.67 6.13
457 458 0.251341 AGTCTTGAACCACCATGGCC 60.251 55.000 13.04 0.00 42.67 5.36
458 459 1.168714 GAGTCTTGAACCACCATGGC 58.831 55.000 13.04 0.00 42.67 4.40
459 460 1.442769 CGAGTCTTGAACCACCATGG 58.557 55.000 11.19 11.19 45.02 3.66
460 461 0.798776 GCGAGTCTTGAACCACCATG 59.201 55.000 0.00 0.00 0.00 3.66
461 462 0.321653 GGCGAGTCTTGAACCACCAT 60.322 55.000 0.00 0.00 0.00 3.55
462 463 1.070786 GGCGAGTCTTGAACCACCA 59.929 57.895 0.00 0.00 0.00 4.17
463 464 2.027625 CGGCGAGTCTTGAACCACC 61.028 63.158 0.00 0.00 0.00 4.61
464 465 2.027625 CCGGCGAGTCTTGAACCAC 61.028 63.158 9.30 0.00 0.00 4.16
465 466 2.342279 CCGGCGAGTCTTGAACCA 59.658 61.111 9.30 0.00 0.00 3.67
466 467 3.119096 GCCGGCGAGTCTTGAACC 61.119 66.667 12.58 0.00 0.00 3.62
467 468 3.479269 CGCCGGCGAGTCTTGAAC 61.479 66.667 44.86 0.00 42.83 3.18
479 480 4.865761 TCGATTTCTCGCCGCCGG 62.866 66.667 0.00 0.00 44.65 6.13
480 481 3.323136 CTCGATTTCTCGCCGCCG 61.323 66.667 0.00 0.00 44.65 6.46
481 482 3.631127 GCTCGATTTCTCGCCGCC 61.631 66.667 0.00 0.00 44.65 6.13
482 483 3.977568 CGCTCGATTTCTCGCCGC 61.978 66.667 0.00 0.00 44.65 6.53
483 484 3.323136 CCGCTCGATTTCTCGCCG 61.323 66.667 0.00 0.00 44.65 6.46
484 485 3.631127 GCCGCTCGATTTCTCGCC 61.631 66.667 0.00 0.00 44.65 5.54
485 486 3.977568 CGCCGCTCGATTTCTCGC 61.978 66.667 0.00 0.00 44.65 5.03
486 487 3.977568 GCGCCGCTCGATTTCTCG 61.978 66.667 0.00 0.00 46.41 4.04
487 488 3.977568 CGCGCCGCTCGATTTCTC 61.978 66.667 7.78 0.00 41.67 2.87
501 502 2.824041 CTCCAATTCCCCACCGCG 60.824 66.667 0.00 0.00 0.00 6.46
502 503 2.440247 CCTCCAATTCCCCACCGC 60.440 66.667 0.00 0.00 0.00 5.68
503 504 2.275418 CCCTCCAATTCCCCACCG 59.725 66.667 0.00 0.00 0.00 4.94
504 505 1.514864 TTCCCCTCCAATTCCCCACC 61.515 60.000 0.00 0.00 0.00 4.61
505 506 0.636647 ATTCCCCTCCAATTCCCCAC 59.363 55.000 0.00 0.00 0.00 4.61
506 507 0.636101 CATTCCCCTCCAATTCCCCA 59.364 55.000 0.00 0.00 0.00 4.96
507 508 0.933700 TCATTCCCCTCCAATTCCCC 59.066 55.000 0.00 0.00 0.00 4.81
508 509 1.133356 CCTCATTCCCCTCCAATTCCC 60.133 57.143 0.00 0.00 0.00 3.97
509 510 1.755621 GCCTCATTCCCCTCCAATTCC 60.756 57.143 0.00 0.00 0.00 3.01
510 511 1.697284 GCCTCATTCCCCTCCAATTC 58.303 55.000 0.00 0.00 0.00 2.17
511 512 0.106519 CGCCTCATTCCCCTCCAATT 60.107 55.000 0.00 0.00 0.00 2.32
512 513 1.533711 CGCCTCATTCCCCTCCAAT 59.466 57.895 0.00 0.00 0.00 3.16
513 514 2.679342 CCGCCTCATTCCCCTCCAA 61.679 63.158 0.00 0.00 0.00 3.53
514 515 3.089874 CCGCCTCATTCCCCTCCA 61.090 66.667 0.00 0.00 0.00 3.86
515 516 4.570874 GCCGCCTCATTCCCCTCC 62.571 72.222 0.00 0.00 0.00 4.30
516 517 4.918201 CGCCGCCTCATTCCCCTC 62.918 72.222 0.00 0.00 0.00 4.30
520 521 4.918201 CTCCCGCCGCCTCATTCC 62.918 72.222 0.00 0.00 0.00 3.01
521 522 4.918201 CCTCCCGCCGCCTCATTC 62.918 72.222 0.00 0.00 0.00 2.67
523 524 3.828083 TATCCTCCCGCCGCCTCAT 62.828 63.158 0.00 0.00 0.00 2.90
524 525 4.533124 TATCCTCCCGCCGCCTCA 62.533 66.667 0.00 0.00 0.00 3.86
525 526 3.686045 CTATCCTCCCGCCGCCTC 61.686 72.222 0.00 0.00 0.00 4.70
529 530 2.379030 GAAACCCTATCCTCCCGCCG 62.379 65.000 0.00 0.00 0.00 6.46
530 531 1.450642 GAAACCCTATCCTCCCGCC 59.549 63.158 0.00 0.00 0.00 6.13
531 532 1.069258 CGAAACCCTATCCTCCCGC 59.931 63.158 0.00 0.00 0.00 6.13
532 533 0.388294 GTCGAAACCCTATCCTCCCG 59.612 60.000 0.00 0.00 0.00 5.14
533 534 0.757512 GGTCGAAACCCTATCCTCCC 59.242 60.000 0.00 0.00 39.93 4.30
543 544 2.750888 GCAGATGCGGGTCGAAACC 61.751 63.158 0.00 0.00 45.65 3.27
544 545 2.750888 GGCAGATGCGGGTCGAAAC 61.751 63.158 0.00 0.00 43.26 2.78
545 546 2.435938 GGCAGATGCGGGTCGAAA 60.436 61.111 0.00 0.00 43.26 3.46
546 547 4.467084 GGGCAGATGCGGGTCGAA 62.467 66.667 0.00 0.00 43.26 3.71
553 554 4.481112 GTTTGCGGGGCAGATGCG 62.481 66.667 0.00 0.00 40.61 4.73
554 555 4.133796 GGTTTGCGGGGCAGATGC 62.134 66.667 0.00 0.00 40.61 3.91
555 556 2.361610 AGGTTTGCGGGGCAGATG 60.362 61.111 0.00 0.00 40.61 2.90
556 557 2.361610 CAGGTTTGCGGGGCAGAT 60.362 61.111 0.00 0.00 40.61 2.90
571 572 0.597637 CCGAGCCACTATAACCGCAG 60.598 60.000 0.00 0.00 0.00 5.18
572 573 1.440060 CCGAGCCACTATAACCGCA 59.560 57.895 0.00 0.00 0.00 5.69
573 574 1.300697 CCCGAGCCACTATAACCGC 60.301 63.158 0.00 0.00 0.00 5.68
574 575 1.366366 CCCCGAGCCACTATAACCG 59.634 63.158 0.00 0.00 0.00 4.44
575 576 1.052694 ACCCCCGAGCCACTATAACC 61.053 60.000 0.00 0.00 0.00 2.85
576 577 0.835276 AACCCCCGAGCCACTATAAC 59.165 55.000 0.00 0.00 0.00 1.89
577 578 0.834612 CAACCCCCGAGCCACTATAA 59.165 55.000 0.00 0.00 0.00 0.98
578 579 1.692173 GCAACCCCCGAGCCACTATA 61.692 60.000 0.00 0.00 0.00 1.31
579 580 3.043999 GCAACCCCCGAGCCACTAT 62.044 63.158 0.00 0.00 0.00 2.12
580 581 3.712907 GCAACCCCCGAGCCACTA 61.713 66.667 0.00 0.00 0.00 2.74
585 586 4.038080 CAAACGCAACCCCCGAGC 62.038 66.667 0.00 0.00 0.00 5.03
586 587 4.038080 GCAAACGCAACCCCCGAG 62.038 66.667 0.00 0.00 0.00 4.63
592 593 4.999939 CAGCCCGCAAACGCAACC 63.000 66.667 0.00 0.00 38.22 3.77
617 618 2.153645 GGTGTCCGACCCGTAATTTTT 58.846 47.619 0.00 0.00 39.10 1.94
618 619 1.812235 GGTGTCCGACCCGTAATTTT 58.188 50.000 0.00 0.00 39.10 1.82
619 620 3.538379 GGTGTCCGACCCGTAATTT 57.462 52.632 0.00 0.00 39.10 1.82
632 633 4.148825 AGAGCCCGCATCGGTGTC 62.149 66.667 0.00 0.86 46.80 3.67
633 634 4.457496 CAGAGCCCGCATCGGTGT 62.457 66.667 0.00 0.00 46.80 4.16
637 638 3.842923 AGACCAGAGCCCGCATCG 61.843 66.667 0.00 0.00 0.00 3.84
638 639 2.202987 CAGACCAGAGCCCGCATC 60.203 66.667 0.00 0.00 0.00 3.91
639 640 3.790437 CCAGACCAGAGCCCGCAT 61.790 66.667 0.00 0.00 0.00 4.73
650 651 0.897621 CCCATTTTTCTGGCCAGACC 59.102 55.000 35.26 0.00 37.14 3.85
651 652 0.247460 GCCCATTTTTCTGGCCAGAC 59.753 55.000 35.26 17.07 39.30 3.51
652 653 2.669878 GCCCATTTTTCTGGCCAGA 58.330 52.632 32.00 32.00 39.30 3.86
656 657 1.512694 CTCGGCCCATTTTTCTGGC 59.487 57.895 0.00 0.00 44.59 4.85
657 658 1.512694 GCTCGGCCCATTTTTCTGG 59.487 57.895 0.00 0.00 35.95 3.86
658 659 1.512694 GGCTCGGCCCATTTTTCTG 59.487 57.895 0.00 0.00 44.06 3.02
659 660 4.018409 GGCTCGGCCCATTTTTCT 57.982 55.556 0.00 0.00 44.06 2.52
669 670 1.014564 GGCGATTATACAGGCTCGGC 61.015 60.000 1.69 1.69 46.78 5.54
670 671 0.732880 CGGCGATTATACAGGCTCGG 60.733 60.000 0.00 0.00 0.00 4.63
671 672 0.732880 CCGGCGATTATACAGGCTCG 60.733 60.000 9.30 0.00 0.00 5.03
672 673 0.601558 TCCGGCGATTATACAGGCTC 59.398 55.000 9.30 0.00 0.00 4.70
673 674 1.045407 TTCCGGCGATTATACAGGCT 58.955 50.000 9.30 0.00 0.00 4.58
674 675 2.094762 ATTCCGGCGATTATACAGGC 57.905 50.000 9.30 0.00 0.00 4.85
675 676 4.034048 GCATAATTCCGGCGATTATACAGG 59.966 45.833 9.30 9.92 30.59 4.00
676 677 5.143916 GCATAATTCCGGCGATTATACAG 57.856 43.478 9.30 10.16 30.59 2.74
686 687 0.248866 CAAACCCGCATAATTCCGGC 60.249 55.000 0.00 0.00 43.05 6.13
687 688 0.248866 GCAAACCCGCATAATTCCGG 60.249 55.000 0.00 0.00 43.97 5.14
688 689 0.591236 CGCAAACCCGCATAATTCCG 60.591 55.000 0.00 0.00 0.00 4.30
689 690 3.250220 CGCAAACCCGCATAATTCC 57.750 52.632 0.00 0.00 0.00 3.01
709 710 1.592669 CTAGCAGAACCCGCATCCG 60.593 63.158 0.00 0.00 0.00 4.18
710 711 0.249657 CTCTAGCAGAACCCGCATCC 60.250 60.000 0.00 0.00 0.00 3.51
711 712 0.461961 ACTCTAGCAGAACCCGCATC 59.538 55.000 0.00 0.00 0.00 3.91
712 713 0.905357 AACTCTAGCAGAACCCGCAT 59.095 50.000 0.00 0.00 0.00 4.73
713 714 0.037326 CAACTCTAGCAGAACCCGCA 60.037 55.000 0.00 0.00 0.00 5.69
714 715 1.362406 GCAACTCTAGCAGAACCCGC 61.362 60.000 0.00 0.00 0.00 6.13
715 716 0.247736 AGCAACTCTAGCAGAACCCG 59.752 55.000 0.00 0.00 0.00 5.28
716 717 2.481289 AAGCAACTCTAGCAGAACCC 57.519 50.000 0.00 0.00 0.00 4.11
717 718 5.106515 CCTTAAAAGCAACTCTAGCAGAACC 60.107 44.000 0.00 0.00 0.00 3.62
718 719 5.106515 CCCTTAAAAGCAACTCTAGCAGAAC 60.107 44.000 0.00 0.00 0.00 3.01
719 720 5.003804 CCCTTAAAAGCAACTCTAGCAGAA 58.996 41.667 0.00 0.00 0.00 3.02
720 721 4.565652 CCCCTTAAAAGCAACTCTAGCAGA 60.566 45.833 0.00 0.00 0.00 4.26
721 722 3.691609 CCCCTTAAAAGCAACTCTAGCAG 59.308 47.826 0.00 0.00 0.00 4.24
722 723 3.073946 ACCCCTTAAAAGCAACTCTAGCA 59.926 43.478 0.00 0.00 0.00 3.49
723 724 3.687125 ACCCCTTAAAAGCAACTCTAGC 58.313 45.455 0.00 0.00 0.00 3.42
724 725 5.183969 GGTACCCCTTAAAAGCAACTCTAG 58.816 45.833 0.00 0.00 0.00 2.43
725 726 5.169992 GGTACCCCTTAAAAGCAACTCTA 57.830 43.478 0.00 0.00 0.00 2.43
726 727 4.030314 GGTACCCCTTAAAAGCAACTCT 57.970 45.455 0.00 0.00 0.00 3.24
743 744 7.167924 AGAGCAACTAACTAACTAAGGGTAC 57.832 40.000 0.00 0.00 0.00 3.34
744 745 6.094603 CGAGAGCAACTAACTAACTAAGGGTA 59.905 42.308 0.00 0.00 0.00 3.69
745 746 5.105837 CGAGAGCAACTAACTAACTAAGGGT 60.106 44.000 0.00 0.00 0.00 4.34
746 747 5.125097 TCGAGAGCAACTAACTAACTAAGGG 59.875 44.000 0.00 0.00 0.00 3.95
747 748 6.192234 TCGAGAGCAACTAACTAACTAAGG 57.808 41.667 0.00 0.00 0.00 2.69
748 749 6.093771 TCCTCGAGAGCAACTAACTAACTAAG 59.906 42.308 15.71 0.00 0.00 2.18
749 750 5.942236 TCCTCGAGAGCAACTAACTAACTAA 59.058 40.000 15.71 0.00 0.00 2.24
750 751 5.494724 TCCTCGAGAGCAACTAACTAACTA 58.505 41.667 15.71 0.00 0.00 2.24
751 752 4.333690 TCCTCGAGAGCAACTAACTAACT 58.666 43.478 15.71 0.00 0.00 2.24
752 753 4.664188 CTCCTCGAGAGCAACTAACTAAC 58.336 47.826 15.71 0.00 35.31 2.34
753 754 4.966965 CTCCTCGAGAGCAACTAACTAA 57.033 45.455 15.71 0.00 35.31 2.24
764 765 1.181786 GATATGGGGCTCCTCGAGAG 58.818 60.000 15.71 10.58 46.29 3.20
765 766 0.780637 AGATATGGGGCTCCTCGAGA 59.219 55.000 15.71 0.00 0.00 4.04
766 767 1.638529 AAGATATGGGGCTCCTCGAG 58.361 55.000 3.07 5.13 0.00 4.04
767 768 2.992847 TAAGATATGGGGCTCCTCGA 57.007 50.000 3.07 0.00 0.00 4.04
768 769 5.677319 TTATTAAGATATGGGGCTCCTCG 57.323 43.478 3.07 0.00 0.00 4.63
769 770 8.885693 AAATTTATTAAGATATGGGGCTCCTC 57.114 34.615 3.07 0.00 0.00 3.71
819 822 0.318699 TCTTGTCTCGTGGTTCAGCG 60.319 55.000 0.00 0.00 0.00 5.18
820 823 1.795286 CTTCTTGTCTCGTGGTTCAGC 59.205 52.381 0.00 0.00 0.00 4.26
879 883 4.202090 GGATGAGAAATGAATGGACAAGCC 60.202 45.833 0.00 0.00 37.10 4.35
919 923 1.974343 GTGCCGGTTAATGGGTGCA 60.974 57.895 1.90 0.00 0.00 4.57
924 928 2.341846 ATACCAGTGCCGGTTAATGG 57.658 50.000 20.73 20.73 40.67 3.16
936 940 3.618507 GCTTGAGAGAGCACAATACCAGT 60.619 47.826 0.00 0.00 42.25 4.00
1158 1166 2.280592 GGCGGTTTCACGGACACT 60.281 61.111 0.00 0.00 0.00 3.55
1310 1323 2.897271 AGCTGAGAGAGAAGACCAGA 57.103 50.000 0.00 0.00 0.00 3.86
1333 1391 0.595095 CAAGCAGTTCACCTGAAGGC 59.405 55.000 0.00 4.25 44.49 4.35
1341 1399 5.929992 TGTACTAATACACCAAGCAGTTCAC 59.070 40.000 0.00 0.00 36.34 3.18
1355 1413 9.052759 CCTGGGTGTATTGAATTGTACTAATAC 57.947 37.037 0.00 0.00 36.83 1.89
1356 1414 8.774183 ACCTGGGTGTATTGAATTGTACTAATA 58.226 33.333 0.00 0.00 0.00 0.98
1357 1415 7.639378 ACCTGGGTGTATTGAATTGTACTAAT 58.361 34.615 0.00 0.00 0.00 1.73
1358 1416 7.023171 ACCTGGGTGTATTGAATTGTACTAA 57.977 36.000 0.00 0.00 0.00 2.24
1359 1417 6.630203 ACCTGGGTGTATTGAATTGTACTA 57.370 37.500 0.00 0.00 0.00 1.82
1360 1418 5.514500 ACCTGGGTGTATTGAATTGTACT 57.486 39.130 0.00 0.00 0.00 2.73
1361 1419 6.646267 TCTACCTGGGTGTATTGAATTGTAC 58.354 40.000 2.07 0.00 0.00 2.90
1362 1420 6.877668 TCTACCTGGGTGTATTGAATTGTA 57.122 37.500 2.07 0.00 0.00 2.41
1363 1421 5.772393 TCTACCTGGGTGTATTGAATTGT 57.228 39.130 2.07 0.00 0.00 2.71
1364 1422 6.094048 CAGTTCTACCTGGGTGTATTGAATTG 59.906 42.308 2.07 3.54 0.00 2.32
1380 1438 6.347160 GGTTCAACGTAAACATCAGTTCTACC 60.347 42.308 13.74 0.00 36.84 3.18
1381 1439 6.423001 AGGTTCAACGTAAACATCAGTTCTAC 59.577 38.462 13.74 0.00 36.84 2.59
1397 1455 2.675844 TGTCAGACAAACAGGTTCAACG 59.324 45.455 0.00 0.00 0.00 4.10
1413 1471 1.417890 AGACTGTTTCCCCACTGTCAG 59.582 52.381 11.83 0.00 44.18 3.51
1416 1474 2.290323 GCATAGACTGTTTCCCCACTGT 60.290 50.000 0.00 0.00 0.00 3.55
1425 1483 1.453155 CGCCTTGGCATAGACTGTTT 58.547 50.000 12.45 0.00 0.00 2.83
1492 1550 6.035005 CAGAAGTATATCAAACCATATCGCCG 59.965 42.308 0.00 0.00 0.00 6.46
1494 1552 8.709386 ATCAGAAGTATATCAAACCATATCGC 57.291 34.615 0.00 0.00 0.00 4.58
1516 1585 3.198417 TGCAGTATCAGCTGAGGAAATCA 59.802 43.478 22.96 12.11 38.70 2.57
1523 1592 4.397103 TGGAAAATTGCAGTATCAGCTGAG 59.603 41.667 22.96 9.46 38.70 3.35
1536 1605 3.058777 CCTGTTTGCACATGGAAAATTGC 60.059 43.478 0.00 0.00 37.12 3.56
1575 1644 1.048724 TGAACCCTAGCCTGATCCCG 61.049 60.000 0.00 0.00 0.00 5.14
1732 1801 0.831288 AGGAGGCTCCTCATGATCCG 60.831 60.000 30.46 0.00 45.66 4.18
1773 1842 0.179215 GTCAAACTCGCGCAATCTGG 60.179 55.000 8.75 0.00 0.00 3.86
1808 1877 4.497006 CCTTCTTCAGTGTCAAACTTGCAG 60.497 45.833 0.00 0.00 36.83 4.41
1822 1918 4.820173 TGCTGCATCATATTCCTTCTTCAG 59.180 41.667 0.00 0.00 0.00 3.02
1846 1942 4.631377 TGTATCAACAGAGAAAGGCAATCG 59.369 41.667 0.00 0.00 0.00 3.34
1851 1947 6.681777 ACAAATTGTATCAACAGAGAAAGGC 58.318 36.000 0.00 0.00 36.83 4.35
1884 1981 6.607198 AGAACATGAAAGGAGACCTTGAAAAA 59.393 34.615 0.00 0.00 43.92 1.94
1949 2051 3.838244 AGACAGTGGAGTTGTTTAGCA 57.162 42.857 0.00 0.00 0.00 3.49
2071 2173 6.682423 TGCTCCAGTTGTTATATTGACATG 57.318 37.500 0.00 0.00 0.00 3.21
2098 2200 7.332430 TCATGTATACTTAAAAGTGACGGTTGG 59.668 37.037 4.17 0.00 40.07 3.77
2267 2370 7.018235 GTCAAGCAAAGTTAGCTAAAGACATC 58.982 38.462 7.99 0.00 42.53 3.06
2270 2373 5.470437 AGGTCAAGCAAAGTTAGCTAAAGAC 59.530 40.000 7.99 0.00 42.53 3.01
2297 2400 2.256174 CTTGCATTCCATGAGTTTGCG 58.744 47.619 0.00 0.00 36.11 4.85
2427 2530 5.103687 ACCGGTGTTTTGTTGTGAATAAAC 58.896 37.500 6.12 0.00 0.00 2.01
2463 2566 2.523015 GCGAGCAGAAATTGTGAATGG 58.477 47.619 0.00 0.00 0.00 3.16
2568 2673 6.706055 TCGTATTCTTACTGCAGTGAAAAG 57.294 37.500 29.57 23.06 0.00 2.27
2589 2694 8.338259 CACTATTACCTGGAAATTTTCTCATCG 58.662 37.037 0.00 2.67 0.00 3.84
2615 2720 6.314018 TGTGTCGATCTCATGTTTATTTTGC 58.686 36.000 0.00 0.00 0.00 3.68
2618 2723 6.878923 TCCTTGTGTCGATCTCATGTTTATTT 59.121 34.615 0.00 0.00 0.00 1.40
2626 2731 4.202264 GGGTAATCCTTGTGTCGATCTCAT 60.202 45.833 0.00 0.00 0.00 2.90
2628 2733 3.492829 GGGGTAATCCTTGTGTCGATCTC 60.493 52.174 0.00 0.00 35.33 2.75
2629 2734 2.434702 GGGGTAATCCTTGTGTCGATCT 59.565 50.000 0.00 0.00 35.33 2.75
2630 2735 2.434702 AGGGGTAATCCTTGTGTCGATC 59.565 50.000 0.00 0.00 32.13 3.69
2632 2737 1.553248 CAGGGGTAATCCTTGTGTCGA 59.447 52.381 0.00 0.00 37.79 4.20
2633 2738 2.024176 CAGGGGTAATCCTTGTGTCG 57.976 55.000 0.00 0.00 37.79 4.35
2638 2743 2.819608 CACAACACAGGGGTAATCCTTG 59.180 50.000 0.00 0.00 46.90 3.61
2642 2747 2.200373 AGCACAACACAGGGGTAATC 57.800 50.000 0.00 0.00 0.00 1.75
2644 2749 2.706723 TCTTAGCACAACACAGGGGTAA 59.293 45.455 0.00 0.00 0.00 2.85
2646 2751 1.072331 CTCTTAGCACAACACAGGGGT 59.928 52.381 0.00 0.00 0.00 4.95
2650 2804 6.625362 TCTCTAATCTCTTAGCACAACACAG 58.375 40.000 0.00 0.00 35.32 3.66
2686 2840 7.315890 CCTACCAATTTGAAAATTCCAGAGTC 58.684 38.462 0.00 0.00 36.52 3.36
2690 2844 5.178061 GCCCTACCAATTTGAAAATTCCAG 58.822 41.667 0.00 0.00 36.52 3.86
2700 2854 1.937191 AACTGGGCCCTACCAATTTG 58.063 50.000 25.70 4.23 40.68 2.32
2710 2864 8.582437 GGATAATAACTAATAAAAACTGGGCCC 58.418 37.037 17.59 17.59 0.00 5.80
2749 2903 0.392461 TTAGTGGCATGGCGGAGTTC 60.392 55.000 15.27 1.06 0.00 3.01
2751 2905 1.221840 CTTAGTGGCATGGCGGAGT 59.778 57.895 15.27 3.45 0.00 3.85
2752 2906 2.182842 GCTTAGTGGCATGGCGGAG 61.183 63.158 15.27 10.19 0.00 4.63
2753 2907 2.124736 GCTTAGTGGCATGGCGGA 60.125 61.111 15.27 0.00 0.00 5.54
2762 2942 4.876107 AGTTCCATATTTCGTGCTTAGTGG 59.124 41.667 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.