Multiple sequence alignment - TraesCS7D01G535100

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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 TraesCS7D01G535100 chr7D 100.000 2798 0 0 1 2798 627297319 627300116 0.000000e+00 5168
1 TraesCS7D01G535100 chr7D 80.420 429 46 17 812 1207 627304920 627305343 2.730000e-75 292
2 TraesCS7D01G535100 chr7D 90.351 114 11 0 1219 1332 627305326 627305439 1.740000e-32 150
3 TraesCS7D01G535100 chr7A 91.918 2054 104 23 804 2798 722792662 722794712 0.000000e+00 2817
4 TraesCS7D01G535100 chr7A 91.866 2053 106 23 804 2798 722877197 722879246 0.000000e+00 2809
5 TraesCS7D01G535100 chr7A 82.914 1668 181 53 1219 2797 722898728 722900380 0.000000e+00 1406
6 TraesCS7D01G535100 chr7A 83.041 1651 175 53 1219 2784 723074961 723076591 0.000000e+00 1400
7 TraesCS7D01G535100 chr7A 84.790 1407 141 37 1219 2566 722988239 722989631 0.000000e+00 1345
8 TraesCS7D01G535100 chr7A 79.436 958 132 37 1892 2797 722938568 722939512 3.960000e-173 617
9 TraesCS7D01G535100 chr7A 78.706 958 139 37 1892 2797 723031378 723032322 1.870000e-161 579
10 TraesCS7D01G535100 chr7A 95.765 307 11 1 2 306 722792287 722792593 6.960000e-136 494
11 TraesCS7D01G535100 chr7A 95.114 307 13 1 2 306 722876822 722877128 1.510000e-132 483
12 TraesCS7D01G535100 chr7A 80.597 469 60 14 2346 2784 722794709 722795176 1.610000e-87 333
13 TraesCS7D01G535100 chr7A 87.162 296 23 6 1219 1499 723031082 723031377 3.480000e-84 322
14 TraesCS7D01G535100 chr7A 95.556 180 7 1 1028 1207 723030921 723031099 1.270000e-73 287
15 TraesCS7D01G535100 chr7A 96.023 176 6 1 1032 1207 722936628 722936802 4.560000e-73 285
16 TraesCS7D01G535100 chr7A 95.429 175 8 0 1028 1202 722898567 722898741 2.120000e-71 279
17 TraesCS7D01G535100 chr7A 94.444 180 9 1 1028 1207 723074800 723074978 2.750000e-70 276
18 TraesCS7D01G535100 chr7A 84.074 270 30 7 163 429 722798962 722799221 5.980000e-62 248
19 TraesCS7D01G535100 chr7A 94.074 135 8 0 1365 1499 722938433 722938567 3.650000e-49 206
20 TraesCS7D01G535100 chr7A 88.506 174 11 6 579 745 711669411 711669240 4.730000e-48 202
21 TraesCS7D01G535100 chr7A 87.006 177 16 4 579 748 23794154 23793978 2.840000e-45 193
22 TraesCS7D01G535100 chr7B 90.639 2051 122 30 804 2798 728005465 728007501 0.000000e+00 2660
23 TraesCS7D01G535100 chr7B 83.725 1659 166 58 1219 2789 728012978 728014620 0.000000e+00 1472
24 TraesCS7D01G535100 chr7B 88.339 566 44 10 2 561 728004887 728005436 0.000000e+00 660
25 TraesCS7D01G535100 chr7B 94.554 202 10 1 1006 1207 728012795 728012995 7.530000e-81 311
26 TraesCS7D01G535100 chr7B 87.448 239 17 9 2346 2580 728007498 728007727 2.140000e-66 263
27 TraesCS7D01G535100 chr7B 88.235 85 8 1 2715 2797 728007869 728007953 1.770000e-17 100
28 TraesCS7D01G535100 chr4D 88.235 187 14 5 573 751 64349626 64349440 1.690000e-52 217
29 TraesCS7D01G535100 chr1A 90.062 161 12 2 579 739 588910457 588910301 3.650000e-49 206
30 TraesCS7D01G535100 chr3D 88.554 166 14 2 579 739 606630689 606630854 2.200000e-46 196
31 TraesCS7D01G535100 chr1D 87.571 177 13 3 578 745 6789453 6789277 2.200000e-46 196
32 TraesCS7D01G535100 chr3A 86.228 167 18 2 578 739 555649114 555648948 2.860000e-40 176
33 TraesCS7D01G535100 chr3A 86.228 167 18 2 578 739 555681640 555681474 2.860000e-40 176
34 TraesCS7D01G535100 chr5A 89.706 136 14 0 581 716 642714831 642714966 1.030000e-39 174


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 TraesCS7D01G535100 chr7D 627297319 627300116 2797 False 5168.000000 5168 100.000000 1 2798 1 chr7D.!!$F1 2797
1 TraesCS7D01G535100 chr7D 627304920 627305439 519 False 221.000000 292 85.385500 812 1332 2 chr7D.!!$F2 520
2 TraesCS7D01G535100 chr7A 722876822 722879246 2424 False 1646.000000 2809 93.490000 2 2798 2 chr7A.!!$F3 2796
3 TraesCS7D01G535100 chr7A 722988239 722989631 1392 False 1345.000000 1345 84.790000 1219 2566 1 chr7A.!!$F1 1347
4 TraesCS7D01G535100 chr7A 722792287 722799221 6934 False 973.000000 2817 88.088500 2 2798 4 chr7A.!!$F2 2796
5 TraesCS7D01G535100 chr7A 722898567 722900380 1813 False 842.500000 1406 89.171500 1028 2797 2 chr7A.!!$F4 1769
6 TraesCS7D01G535100 chr7A 723074800 723076591 1791 False 838.000000 1400 88.742500 1028 2784 2 chr7A.!!$F7 1756
7 TraesCS7D01G535100 chr7A 723030921 723032322 1401 False 396.000000 579 87.141333 1028 2797 3 chr7A.!!$F6 1769
8 TraesCS7D01G535100 chr7A 722936628 722939512 2884 False 369.333333 617 89.844333 1032 2797 3 chr7A.!!$F5 1765
9 TraesCS7D01G535100 chr7B 728004887 728007953 3066 False 920.750000 2660 88.665250 2 2798 4 chr7B.!!$F1 2796
10 TraesCS7D01G535100 chr7B 728012795 728014620 1825 False 891.500000 1472 89.139500 1006 2789 2 chr7B.!!$F2 1783

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
722 731 0.040336 GCTATAGCGTGCTCGTGCTA 60.04 55.0 9.4 6.18 46.75 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 3680 0.318869 TGCGTGCAAAATTGAGCTGG 60.319 50.0 0.0 0.0 0.0 4.85 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
128 130 1.557371 AGGGAAGCTTCCTAGTTGAGC 59.443 52.381 37.72 22.07 46.72 4.26
206 208 4.878971 TGGAACAACCAACGTCATATATGG 59.121 41.667 12.78 0.11 46.75 2.74
288 292 3.305720 TCTGGATTAATAGTGAGGGCGT 58.694 45.455 0.00 0.00 0.00 5.68
334 339 8.286097 GCCTGTTATATTGAAAAAGCTAGCTAG 58.714 37.037 19.70 16.84 0.00 3.42
343 348 4.951963 GCTAGCTAGCGGTGCGGG 62.952 72.222 28.89 0.00 39.82 6.13
346 351 2.955751 CTAGCTAGCGGTGCGGGTTC 62.956 65.000 8.05 0.00 35.28 3.62
353 358 1.301401 CGGTGCGGGTTCTCTTCAA 60.301 57.895 0.00 0.00 0.00 2.69
404 412 6.756542 ACTTGAACTAATTTTGCAGGTTTGAC 59.243 34.615 0.00 0.00 0.00 3.18
412 420 2.356665 TGCAGGTTTGACTTTAGCCA 57.643 45.000 0.00 0.00 0.00 4.75
490 499 6.597280 GGTAAAAATCAGCTCTGAGACTTGAT 59.403 38.462 9.28 10.71 43.61 2.57
497 506 4.099113 CAGCTCTGAGACTTGATGGTATGA 59.901 45.833 9.28 0.00 0.00 2.15
499 508 4.340666 GCTCTGAGACTTGATGGTATGAGA 59.659 45.833 9.28 0.00 0.00 3.27
500 509 5.507817 GCTCTGAGACTTGATGGTATGAGAG 60.508 48.000 9.28 0.00 40.12 3.20
501 510 4.892345 TCTGAGACTTGATGGTATGAGAGG 59.108 45.833 0.00 0.00 0.00 3.69
502 511 3.963374 TGAGACTTGATGGTATGAGAGGG 59.037 47.826 0.00 0.00 0.00 4.30
503 512 3.964031 GAGACTTGATGGTATGAGAGGGT 59.036 47.826 0.00 0.00 0.00 4.34
504 513 5.141182 GAGACTTGATGGTATGAGAGGGTA 58.859 45.833 0.00 0.00 0.00 3.69
511 520 2.319747 TGGTATGAGAGGGTAAGGGGAA 59.680 50.000 0.00 0.00 0.00 3.97
515 524 2.674420 TGAGAGGGTAAGGGGAATACG 58.326 52.381 0.00 0.00 0.00 3.06
560 569 9.847224 AGTAAACAAACTATTTCTCTCTTTCCA 57.153 29.630 0.00 0.00 0.00 3.53
562 571 8.980481 AAACAAACTATTTCTCTCTTTCCAGA 57.020 30.769 0.00 0.00 0.00 3.86
563 572 9.579932 AAACAAACTATTTCTCTCTTTCCAGAT 57.420 29.630 0.00 0.00 0.00 2.90
564 573 8.558973 ACAAACTATTTCTCTCTTTCCAGATG 57.441 34.615 0.00 0.00 0.00 2.90
565 574 8.160106 ACAAACTATTTCTCTCTTTCCAGATGT 58.840 33.333 0.00 0.00 0.00 3.06
566 575 9.007901 CAAACTATTTCTCTCTTTCCAGATGTT 57.992 33.333 0.00 0.00 0.00 2.71
567 576 9.579932 AAACTATTTCTCTCTTTCCAGATGTTT 57.420 29.630 0.00 0.00 0.00 2.83
568 577 8.785329 ACTATTTCTCTCTTTCCAGATGTTTC 57.215 34.615 0.00 0.00 0.00 2.78
569 578 8.378565 ACTATTTCTCTCTTTCCAGATGTTTCA 58.621 33.333 0.00 0.00 0.00 2.69
570 579 9.393512 CTATTTCTCTCTTTCCAGATGTTTCAT 57.606 33.333 0.00 0.00 0.00 2.57
572 581 9.917887 ATTTCTCTCTTTCCAGATGTTTCATAT 57.082 29.630 0.00 0.00 0.00 1.78
578 587 9.160496 CTCTTTCCAGATGTTTCATATATAGGC 57.840 37.037 0.00 0.00 0.00 3.93
579 588 8.659527 TCTTTCCAGATGTTTCATATATAGGCA 58.340 33.333 0.00 0.00 0.00 4.75
580 589 9.288576 CTTTCCAGATGTTTCATATATAGGCAA 57.711 33.333 0.00 0.00 0.00 4.52
581 590 9.639563 TTTCCAGATGTTTCATATATAGGCAAA 57.360 29.630 0.00 0.00 0.00 3.68
582 591 8.853077 TCCAGATGTTTCATATATAGGCAAAG 57.147 34.615 0.00 0.00 0.00 2.77
583 592 8.439971 TCCAGATGTTTCATATATAGGCAAAGT 58.560 33.333 0.00 0.00 0.00 2.66
584 593 9.071276 CCAGATGTTTCATATATAGGCAAAGTT 57.929 33.333 0.00 0.00 0.00 2.66
596 605 3.498082 AGGCAAAGTTTTAAATAGCGCG 58.502 40.909 0.00 0.00 0.00 6.86
597 606 2.027569 GGCAAAGTTTTAAATAGCGCGC 59.972 45.455 26.66 26.66 0.00 6.86
598 607 2.914838 GCAAAGTTTTAAATAGCGCGCT 59.085 40.909 38.01 38.01 0.00 5.92
599 608 4.092816 GCAAAGTTTTAAATAGCGCGCTA 58.907 39.130 39.72 39.72 0.00 4.26
600 609 4.555747 GCAAAGTTTTAAATAGCGCGCTAA 59.444 37.500 40.90 26.03 31.73 3.09
601 610 5.275280 GCAAAGTTTTAAATAGCGCGCTAAG 60.275 40.000 40.90 16.80 31.73 2.18
602 611 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
603 612 3.033873 GTTTTAAATAGCGCGCTAAGCC 58.966 45.455 40.90 21.36 44.76 4.35
604 613 2.234300 TTAAATAGCGCGCTAAGCCT 57.766 45.000 40.90 26.65 44.76 4.58
605 614 1.779569 TAAATAGCGCGCTAAGCCTC 58.220 50.000 40.90 6.44 44.76 4.70
606 615 0.105039 AAATAGCGCGCTAAGCCTCT 59.895 50.000 40.90 23.18 44.76 3.69
607 616 0.105039 AATAGCGCGCTAAGCCTCTT 59.895 50.000 40.90 27.25 44.76 2.85
608 617 0.959553 ATAGCGCGCTAAGCCTCTTA 59.040 50.000 40.90 20.62 44.76 2.10
609 618 0.311165 TAGCGCGCTAAGCCTCTTAG 59.689 55.000 36.77 8.76 44.76 2.18
610 619 2.590401 GCGCGCTAAGCCTCTTAGC 61.590 63.158 26.67 22.09 44.76 3.09
614 623 2.874709 GCTAAGCCTCTTAGCGTCG 58.125 57.895 18.95 0.00 38.12 5.12
615 624 0.595310 GCTAAGCCTCTTAGCGTCGG 60.595 60.000 18.95 0.00 38.12 4.79
616 625 1.022735 CTAAGCCTCTTAGCGTCGGA 58.977 55.000 0.00 0.00 38.01 4.55
617 626 0.737219 TAAGCCTCTTAGCGTCGGAC 59.263 55.000 0.00 0.00 38.01 4.79
618 627 1.946475 AAGCCTCTTAGCGTCGGACC 61.946 60.000 1.91 0.00 38.01 4.46
619 628 2.416432 GCCTCTTAGCGTCGGACCT 61.416 63.158 1.91 3.67 0.00 3.85
620 629 1.728672 CCTCTTAGCGTCGGACCTC 59.271 63.158 1.91 0.00 0.00 3.85
621 630 0.748729 CCTCTTAGCGTCGGACCTCT 60.749 60.000 1.91 2.89 0.00 3.69
622 631 1.096416 CTCTTAGCGTCGGACCTCTT 58.904 55.000 1.91 0.00 0.00 2.85
623 632 1.064357 CTCTTAGCGTCGGACCTCTTC 59.936 57.143 1.91 0.00 0.00 2.87
624 633 1.096416 CTTAGCGTCGGACCTCTTCT 58.904 55.000 1.91 0.00 0.00 2.85
625 634 2.093288 TCTTAGCGTCGGACCTCTTCTA 60.093 50.000 1.91 0.00 0.00 2.10
626 635 2.408271 TAGCGTCGGACCTCTTCTAA 57.592 50.000 1.91 0.00 0.00 2.10
627 636 1.542492 AGCGTCGGACCTCTTCTAAA 58.458 50.000 1.91 0.00 0.00 1.85
628 637 2.100989 AGCGTCGGACCTCTTCTAAAT 58.899 47.619 1.91 0.00 0.00 1.40
629 638 2.159226 AGCGTCGGACCTCTTCTAAATG 60.159 50.000 1.91 0.00 0.00 2.32
630 639 2.194271 CGTCGGACCTCTTCTAAATGC 58.806 52.381 1.91 0.00 0.00 3.56
631 640 2.159226 CGTCGGACCTCTTCTAAATGCT 60.159 50.000 1.91 0.00 0.00 3.79
632 641 3.066342 CGTCGGACCTCTTCTAAATGCTA 59.934 47.826 1.91 0.00 0.00 3.49
633 642 4.261656 CGTCGGACCTCTTCTAAATGCTAT 60.262 45.833 1.91 0.00 0.00 2.97
634 643 5.048921 CGTCGGACCTCTTCTAAATGCTATA 60.049 44.000 1.91 0.00 0.00 1.31
635 644 6.383415 GTCGGACCTCTTCTAAATGCTATAG 58.617 44.000 0.00 0.00 0.00 1.31
636 645 5.047943 TCGGACCTCTTCTAAATGCTATAGC 60.048 44.000 18.18 18.18 42.50 2.97
637 646 5.164954 GGACCTCTTCTAAATGCTATAGCG 58.835 45.833 19.55 5.29 45.83 4.26
638 647 5.279056 GGACCTCTTCTAAATGCTATAGCGT 60.279 44.000 19.55 16.84 45.83 5.07
639 648 5.533482 ACCTCTTCTAAATGCTATAGCGTG 58.467 41.667 20.02 8.19 45.83 5.34
640 649 4.387256 CCTCTTCTAAATGCTATAGCGTGC 59.613 45.833 20.02 0.00 45.83 5.34
641 650 5.201713 TCTTCTAAATGCTATAGCGTGCT 57.798 39.130 20.02 12.62 45.83 4.40
642 651 6.327279 TCTTCTAAATGCTATAGCGTGCTA 57.673 37.500 20.02 13.04 45.83 3.49
643 652 6.925211 TCTTCTAAATGCTATAGCGTGCTAT 58.075 36.000 20.02 17.65 45.83 2.97
644 653 7.378966 TCTTCTAAATGCTATAGCGTGCTATT 58.621 34.615 20.02 12.57 45.83 1.73
645 654 7.872993 TCTTCTAAATGCTATAGCGTGCTATTT 59.127 33.333 20.02 19.10 45.83 1.40
646 655 9.140286 CTTCTAAATGCTATAGCGTGCTATTTA 57.860 33.333 20.02 19.18 45.83 1.40
647 656 9.483916 TTCTAAATGCTATAGCGTGCTATTTAA 57.516 29.630 20.02 8.78 45.83 1.52
648 657 9.483916 TCTAAATGCTATAGCGTGCTATTTAAA 57.516 29.630 20.02 8.03 45.83 1.52
651 660 8.955061 AATGCTATAGCGTGCTATTTAAAATG 57.045 30.769 20.02 3.98 45.83 2.32
652 661 7.490962 TGCTATAGCGTGCTATTTAAAATGT 57.509 32.000 18.62 0.00 45.83 2.71
653 662 7.925993 TGCTATAGCGTGCTATTTAAAATGTT 58.074 30.769 18.62 0.00 45.83 2.71
654 663 8.402472 TGCTATAGCGTGCTATTTAAAATGTTT 58.598 29.630 18.62 0.00 45.83 2.83
655 664 8.682016 GCTATAGCGTGCTATTTAAAATGTTTG 58.318 33.333 18.62 0.00 39.65 2.93
656 665 5.761818 AGCGTGCTATTTAAAATGTTTGC 57.238 34.783 0.00 0.00 0.00 3.68
657 666 5.469479 AGCGTGCTATTTAAAATGTTTGCT 58.531 33.333 0.00 0.00 0.00 3.91
658 667 5.572896 AGCGTGCTATTTAAAATGTTTGCTC 59.427 36.000 0.00 0.00 0.00 4.26
659 668 5.344665 GCGTGCTATTTAAAATGTTTGCTCA 59.655 36.000 0.00 0.00 0.00 4.26
660 669 6.128956 GCGTGCTATTTAAAATGTTTGCTCAA 60.129 34.615 0.00 0.00 0.00 3.02
661 670 7.439490 CGTGCTATTTAAAATGTTTGCTCAAG 58.561 34.615 0.00 0.00 0.00 3.02
662 671 7.114811 CGTGCTATTTAAAATGTTTGCTCAAGT 59.885 33.333 0.00 0.00 0.00 3.16
663 672 8.216453 GTGCTATTTAAAATGTTTGCTCAAGTG 58.784 33.333 0.00 0.00 0.00 3.16
664 673 7.925483 TGCTATTTAAAATGTTTGCTCAAGTGT 59.075 29.630 0.00 0.00 0.00 3.55
665 674 8.764287 GCTATTTAAAATGTTTGCTCAAGTGTT 58.236 29.630 0.00 0.00 0.00 3.32
668 677 8.539770 TTTAAAATGTTTGCTCAAGTGTTTGA 57.460 26.923 0.00 0.00 40.92 2.69
669 678 8.539770 TTAAAATGTTTGCTCAAGTGTTTGAA 57.460 26.923 0.00 0.00 42.48 2.69
670 679 6.407475 AAATGTTTGCTCAAGTGTTTGAAC 57.593 33.333 0.00 0.00 42.48 3.18
671 680 4.511617 TGTTTGCTCAAGTGTTTGAACA 57.488 36.364 0.00 0.00 42.48 3.18
672 681 4.876125 TGTTTGCTCAAGTGTTTGAACAA 58.124 34.783 0.00 2.89 43.77 2.83
676 685 5.384063 TGCTCAAGTGTTTGAACAAAAGA 57.616 34.783 1.47 0.00 42.48 2.52
677 686 5.160641 TGCTCAAGTGTTTGAACAAAAGAC 58.839 37.500 1.47 2.88 42.48 3.01
684 693 6.786207 AGTGTTTGAACAAAAGACTCTTAGC 58.214 36.000 1.47 0.00 46.48 3.09
685 694 5.677178 GTGTTTGAACAAAAGACTCTTAGCG 59.323 40.000 1.47 0.00 41.21 4.26
686 695 4.468095 TTGAACAAAAGACTCTTAGCGC 57.532 40.909 0.00 0.00 0.00 5.92
687 696 3.462982 TGAACAAAAGACTCTTAGCGCA 58.537 40.909 11.47 0.00 0.00 6.09
688 697 3.494626 TGAACAAAAGACTCTTAGCGCAG 59.505 43.478 11.47 0.00 0.00 5.18
689 698 2.417719 ACAAAAGACTCTTAGCGCAGG 58.582 47.619 11.47 0.00 0.00 4.85
690 699 2.037251 ACAAAAGACTCTTAGCGCAGGA 59.963 45.455 11.47 3.25 0.00 3.86
691 700 2.371910 AAAGACTCTTAGCGCAGGAC 57.628 50.000 11.47 0.00 0.00 3.85
692 701 0.533032 AAGACTCTTAGCGCAGGACC 59.467 55.000 11.47 0.00 0.00 4.46
693 702 0.323908 AGACTCTTAGCGCAGGACCT 60.324 55.000 11.47 0.00 0.00 3.85
694 703 0.533032 GACTCTTAGCGCAGGACCTT 59.467 55.000 11.47 0.00 0.00 3.50
695 704 0.977395 ACTCTTAGCGCAGGACCTTT 59.023 50.000 11.47 0.00 0.00 3.11
696 705 1.348036 ACTCTTAGCGCAGGACCTTTT 59.652 47.619 11.47 0.00 0.00 2.27
697 706 2.003301 CTCTTAGCGCAGGACCTTTTC 58.997 52.381 11.47 0.00 0.00 2.29
698 707 1.623811 TCTTAGCGCAGGACCTTTTCT 59.376 47.619 11.47 0.00 0.00 2.52
699 708 2.829720 TCTTAGCGCAGGACCTTTTCTA 59.170 45.455 11.47 0.00 0.00 2.10
700 709 3.259876 TCTTAGCGCAGGACCTTTTCTAA 59.740 43.478 11.47 0.00 0.00 2.10
701 710 2.561478 AGCGCAGGACCTTTTCTAAA 57.439 45.000 11.47 0.00 0.00 1.85
702 711 3.073274 AGCGCAGGACCTTTTCTAAAT 57.927 42.857 11.47 0.00 0.00 1.40
703 712 2.749621 AGCGCAGGACCTTTTCTAAATG 59.250 45.455 11.47 0.00 0.00 2.32
704 713 2.732282 GCGCAGGACCTTTTCTAAATGC 60.732 50.000 0.30 0.00 0.00 3.56
705 714 2.749621 CGCAGGACCTTTTCTAAATGCT 59.250 45.455 0.00 0.00 0.00 3.79
706 715 3.938963 CGCAGGACCTTTTCTAAATGCTA 59.061 43.478 0.00 0.00 0.00 3.49
707 716 4.576463 CGCAGGACCTTTTCTAAATGCTAT 59.424 41.667 0.00 0.00 0.00 2.97
708 717 5.758296 CGCAGGACCTTTTCTAAATGCTATA 59.242 40.000 0.00 0.00 0.00 1.31
709 718 6.073548 CGCAGGACCTTTTCTAAATGCTATAG 60.074 42.308 0.00 0.00 0.00 1.31
710 719 6.293680 GCAGGACCTTTTCTAAATGCTATAGC 60.294 42.308 18.18 18.18 42.50 2.97
711 720 5.992217 AGGACCTTTTCTAAATGCTATAGCG 59.008 40.000 19.55 5.29 45.83 4.26
712 721 5.758784 GGACCTTTTCTAAATGCTATAGCGT 59.241 40.000 19.55 16.84 45.83 5.07
713 722 6.292919 GGACCTTTTCTAAATGCTATAGCGTG 60.293 42.308 20.02 8.19 45.83 5.34
714 723 5.007724 ACCTTTTCTAAATGCTATAGCGTGC 59.992 40.000 20.02 0.00 45.83 5.34
715 724 5.237344 CCTTTTCTAAATGCTATAGCGTGCT 59.763 40.000 20.02 12.62 45.83 4.40
716 725 5.907197 TTTCTAAATGCTATAGCGTGCTC 57.093 39.130 20.02 0.00 45.83 4.26
717 726 3.565516 TCTAAATGCTATAGCGTGCTCG 58.434 45.455 20.02 3.31 45.83 5.03
718 727 2.225068 AAATGCTATAGCGTGCTCGT 57.775 45.000 20.02 1.12 45.83 4.18
719 728 1.491670 AATGCTATAGCGTGCTCGTG 58.508 50.000 20.02 0.00 45.83 4.35
720 729 0.941463 ATGCTATAGCGTGCTCGTGC 60.941 55.000 18.70 1.71 45.83 5.34
721 730 1.299468 GCTATAGCGTGCTCGTGCT 60.299 57.895 9.40 4.06 45.04 4.40
722 731 0.040336 GCTATAGCGTGCTCGTGCTA 60.040 55.000 9.40 6.18 46.75 3.49
726 735 0.040336 TAGCGTGCTCGTGCTATAGC 60.040 55.000 18.18 18.18 42.48 2.97
727 736 2.639926 GCGTGCTCGTGCTATAGCG 61.640 63.158 19.55 6.76 41.77 4.26
728 737 2.011349 CGTGCTCGTGCTATAGCGG 61.011 63.158 19.55 13.84 45.83 5.52
729 738 1.661821 GTGCTCGTGCTATAGCGGG 60.662 63.158 19.55 13.49 45.83 6.13
731 740 3.043419 CTCGTGCTATAGCGGGCT 58.957 61.111 19.55 0.00 45.83 5.19
732 741 2.254471 CTCGTGCTATAGCGGGCTA 58.746 57.895 19.55 2.42 45.83 3.93
733 742 0.811915 CTCGTGCTATAGCGGGCTAT 59.188 55.000 19.55 16.61 45.83 2.97
734 743 1.202582 CTCGTGCTATAGCGGGCTATT 59.797 52.381 19.55 3.74 45.83 1.73
735 744 1.616865 TCGTGCTATAGCGGGCTATTT 59.383 47.619 19.55 0.00 45.83 1.40
736 745 2.821378 TCGTGCTATAGCGGGCTATTTA 59.179 45.455 19.55 1.23 45.83 1.40
737 746 3.256383 TCGTGCTATAGCGGGCTATTTAA 59.744 43.478 19.55 0.55 45.83 1.52
738 747 3.991773 CGTGCTATAGCGGGCTATTTAAA 59.008 43.478 19.55 0.21 45.83 1.52
739 748 4.091509 CGTGCTATAGCGGGCTATTTAAAG 59.908 45.833 19.55 10.34 45.83 1.85
740 749 4.000988 TGCTATAGCGGGCTATTTAAAGC 58.999 43.478 19.55 18.49 45.83 3.51
754 763 8.340230 GCTATTTAAAGCCATGTATGTCAAAC 57.660 34.615 0.00 0.00 36.45 2.93
755 764 7.973388 GCTATTTAAAGCCATGTATGTCAAACA 59.027 33.333 0.00 0.00 36.45 2.83
756 765 9.289303 CTATTTAAAGCCATGTATGTCAAACAC 57.711 33.333 0.00 0.00 0.00 3.32
757 766 6.641169 TTAAAGCCATGTATGTCAAACACA 57.359 33.333 0.00 0.00 40.18 3.72
782 791 0.471617 ATAGGATGGCACCTGCACTC 59.528 55.000 15.94 0.00 44.36 3.51
783 792 0.909133 TAGGATGGCACCTGCACTCA 60.909 55.000 15.94 0.00 44.36 3.41
784 793 2.042831 GGATGGCACCTGCACTCAC 61.043 63.158 0.00 0.00 44.36 3.51
785 794 1.002868 GATGGCACCTGCACTCACT 60.003 57.895 0.00 0.00 44.36 3.41
786 795 1.303074 ATGGCACCTGCACTCACTG 60.303 57.895 0.00 0.00 44.36 3.66
839 865 7.736893 TGTTTCTTAGAAAAGCTTAGTCTCCT 58.263 34.615 14.22 2.64 32.36 3.69
974 1033 3.525537 CAGTCCCAAGCCGCTATATATG 58.474 50.000 0.00 0.00 0.00 1.78
1004 1079 1.827969 ACAGTGCATCTAGAGTGTCCC 59.172 52.381 0.00 0.00 0.00 4.46
1284 1374 1.577328 CTTCCGCATGTTCGCCACTT 61.577 55.000 0.00 0.00 0.00 3.16
1394 3001 0.872881 GTTACCCGTATGCGTGCGAT 60.873 55.000 18.47 8.08 35.29 4.58
1473 3080 0.036388 TGGTAAGAAAGGCTGCTCCG 60.036 55.000 0.00 0.00 40.77 4.63
1576 3189 0.179936 GAGGCAGATCAGGAACAGGG 59.820 60.000 0.00 0.00 0.00 4.45
1858 3492 6.674694 ACTTTGATGCAGCTAGAACTAATG 57.325 37.500 2.53 0.00 0.00 1.90
1991 3650 5.132897 TCCAGCAATTTTGTATGGTGAAC 57.867 39.130 6.54 0.00 45.40 3.18
2007 3672 9.202545 GTATGGTGAACGAAATTATTTAACGAC 57.797 33.333 5.92 1.77 0.00 4.34
2008 3673 6.601264 TGGTGAACGAAATTATTTAACGACC 58.399 36.000 5.92 4.33 0.00 4.79
2010 3675 6.957635 GGTGAACGAAATTATTTAACGACCTC 59.042 38.462 5.92 1.71 0.00 3.85
2011 3676 6.675747 GTGAACGAAATTATTTAACGACCTCG 59.324 38.462 5.92 0.00 46.33 4.63
2101 3780 1.959710 TCCCAGGTGTTGTGCCTATA 58.040 50.000 0.00 0.00 34.45 1.31
2151 3838 3.822735 AGGGTCACAATGTATATGCATGC 59.177 43.478 11.82 11.82 0.00 4.06
2177 3864 7.172532 CGATTAATGGATGATAAAAGGGTCGAA 59.827 37.037 0.00 0.00 0.00 3.71
2267 3958 4.335082 AAAAAGTGGCTTTGCGAAAAAC 57.665 36.364 0.00 0.00 33.64 2.43
2353 4044 8.608185 ACATACCATTTCCCAAGTTAATGATT 57.392 30.769 0.00 0.00 32.36 2.57
2379 4070 7.984422 TGCTTCACAATGTATATATTGGAGG 57.016 36.000 21.79 16.96 41.29 4.30
2414 4105 5.922544 GGCATCATTGGAGTAATTAATGCAC 59.077 40.000 6.62 0.00 33.10 4.57
2420 4111 9.851686 TCATTGGAGTAATTAATGCACTCTATT 57.148 29.630 21.17 13.53 38.95 1.73
2425 4116 9.042008 GGAGTAATTAATGCACTCTATTTCGAA 57.958 33.333 21.17 0.00 38.95 3.71
2448 4614 8.132362 CGAATCTATATGCTATAAGAGTGTCCC 58.868 40.741 0.00 0.00 0.00 4.46
2453 4619 4.737855 TGCTATAAGAGTGTCCCTGTTC 57.262 45.455 0.00 0.00 0.00 3.18
2594 4790 3.804518 TTACAATGTAGCGCACAACAG 57.195 42.857 11.47 8.76 41.55 3.16
2602 4798 0.798776 AGCGCACAACAGAGCATTAC 59.201 50.000 11.47 0.00 36.73 1.89
2608 4804 3.607775 GCACAACAGAGCATTACACACAG 60.608 47.826 0.00 0.00 0.00 3.66
2609 4805 3.058708 CACAACAGAGCATTACACACAGG 60.059 47.826 0.00 0.00 0.00 4.00
2661 4857 5.075493 GGATGTCTAATTTGGCCATCAGAT 58.925 41.667 6.09 0.00 34.89 2.90
2690 4886 3.378427 GCATAGTGGAAGACAATTGGACC 59.622 47.826 10.83 7.79 0.00 4.46
2700 4896 5.041191 AGACAATTGGACCTGGATATGTC 57.959 43.478 10.83 6.25 36.95 3.06
2705 4901 4.927267 TTGGACCTGGATATGTCTGTTT 57.073 40.909 0.00 0.00 0.00 2.83
2753 4951 5.221823 TGGGTATGACTGAGTTTGACATGAA 60.222 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.523464 CGAAAGTGTTTGTAATTTCAGTTTCTG 58.477 33.333 16.61 9.99 42.79 3.02
128 130 7.624360 TGCAACCTACTTTATATGGTTTGAG 57.376 36.000 0.00 0.00 40.39 3.02
263 267 5.419155 CGCCCTCACTATTAATCCAGATAGA 59.581 44.000 0.00 0.00 31.75 1.98
281 285 0.313672 TTTGCAATCACAACGCCCTC 59.686 50.000 0.00 0.00 0.00 4.30
313 317 6.990349 ACCGCTAGCTAGCTTTTTCAATATAA 59.010 34.615 36.02 0.00 46.85 0.98
334 339 3.119096 GAAGAGAACCCGCACCGC 61.119 66.667 0.00 0.00 0.00 5.68
336 341 1.314730 TTTTGAAGAGAACCCGCACC 58.685 50.000 0.00 0.00 0.00 5.01
463 472 6.859112 AGTCTCAGAGCTGATTTTTACCTA 57.141 37.500 0.00 0.00 39.13 3.08
464 473 5.753721 AGTCTCAGAGCTGATTTTTACCT 57.246 39.130 0.00 0.00 39.13 3.08
490 499 1.941682 TCCCCTTACCCTCTCATACCA 59.058 52.381 0.00 0.00 0.00 3.25
497 506 3.036819 GTTCGTATTCCCCTTACCCTCT 58.963 50.000 0.00 0.00 0.00 3.69
499 508 2.770232 CAGTTCGTATTCCCCTTACCCT 59.230 50.000 0.00 0.00 0.00 4.34
500 509 2.767960 TCAGTTCGTATTCCCCTTACCC 59.232 50.000 0.00 0.00 0.00 3.69
501 510 4.476628 TTCAGTTCGTATTCCCCTTACC 57.523 45.455 0.00 0.00 0.00 2.85
502 511 6.806388 TTTTTCAGTTCGTATTCCCCTTAC 57.194 37.500 0.00 0.00 0.00 2.34
537 546 8.980481 TCTGGAAAGAGAGAAATAGTTTGTTT 57.020 30.769 0.00 0.00 0.00 2.83
538 547 9.007901 CATCTGGAAAGAGAGAAATAGTTTGTT 57.992 33.333 0.00 0.00 0.00 2.83
539 548 8.160106 ACATCTGGAAAGAGAGAAATAGTTTGT 58.840 33.333 0.00 0.00 0.00 2.83
542 551 9.225436 GAAACATCTGGAAAGAGAGAAATAGTT 57.775 33.333 0.00 0.00 0.00 2.24
570 579 8.225107 CGCGCTATTTAAAACTTTGCCTATATA 58.775 33.333 5.56 0.00 0.00 0.86
571 580 7.075741 CGCGCTATTTAAAACTTTGCCTATAT 58.924 34.615 5.56 0.00 0.00 0.86
572 581 6.423862 CGCGCTATTTAAAACTTTGCCTATA 58.576 36.000 5.56 0.00 0.00 1.31
573 582 5.270853 CGCGCTATTTAAAACTTTGCCTAT 58.729 37.500 5.56 0.00 0.00 2.57
574 583 4.654015 CGCGCTATTTAAAACTTTGCCTA 58.346 39.130 5.56 0.00 0.00 3.93
575 584 3.498082 CGCGCTATTTAAAACTTTGCCT 58.502 40.909 5.56 0.00 0.00 4.75
576 585 2.027569 GCGCGCTATTTAAAACTTTGCC 59.972 45.455 26.67 0.00 0.00 4.52
577 586 2.914838 AGCGCGCTATTTAAAACTTTGC 59.085 40.909 35.79 0.00 0.00 3.68
578 587 5.275280 GCTTAGCGCGCTATTTAAAACTTTG 60.275 40.000 38.51 15.49 0.00 2.77
579 588 4.791676 GCTTAGCGCGCTATTTAAAACTTT 59.208 37.500 38.51 13.72 0.00 2.66
580 589 4.340263 GCTTAGCGCGCTATTTAAAACTT 58.660 39.130 38.51 13.94 0.00 2.66
581 590 3.242641 GGCTTAGCGCGCTATTTAAAACT 60.243 43.478 38.51 14.50 40.44 2.66
582 591 3.033873 GGCTTAGCGCGCTATTTAAAAC 58.966 45.455 38.51 21.47 40.44 2.43
583 592 2.940410 AGGCTTAGCGCGCTATTTAAAA 59.060 40.909 38.51 24.43 40.44 1.52
584 593 2.542595 GAGGCTTAGCGCGCTATTTAAA 59.457 45.455 38.51 25.16 40.44 1.52
585 594 2.132762 GAGGCTTAGCGCGCTATTTAA 58.867 47.619 38.51 25.53 40.44 1.52
586 595 1.340248 AGAGGCTTAGCGCGCTATTTA 59.660 47.619 38.51 24.25 40.44 1.40
587 596 0.105039 AGAGGCTTAGCGCGCTATTT 59.895 50.000 38.51 24.06 40.44 1.40
588 597 0.105039 AAGAGGCTTAGCGCGCTATT 59.895 50.000 38.51 26.01 40.44 1.73
589 598 0.959553 TAAGAGGCTTAGCGCGCTAT 59.040 50.000 38.51 25.42 40.44 2.97
590 599 0.311165 CTAAGAGGCTTAGCGCGCTA 59.689 55.000 35.48 35.48 40.44 4.26
591 600 1.066587 CTAAGAGGCTTAGCGCGCT 59.933 57.895 38.01 38.01 40.44 5.92
592 601 2.590401 GCTAAGAGGCTTAGCGCGC 61.590 63.158 26.66 26.66 38.12 6.86
593 602 3.619054 GCTAAGAGGCTTAGCGCG 58.381 61.111 19.61 0.00 38.12 6.86
596 605 0.595310 CCGACGCTAAGAGGCTTAGC 60.595 60.000 22.75 22.75 42.82 3.09
597 606 1.022735 TCCGACGCTAAGAGGCTTAG 58.977 55.000 9.30 9.30 0.00 2.18
598 607 0.737219 GTCCGACGCTAAGAGGCTTA 59.263 55.000 0.00 0.00 0.00 3.09
599 608 1.511768 GTCCGACGCTAAGAGGCTT 59.488 57.895 0.00 0.00 0.00 4.35
600 609 2.416432 GGTCCGACGCTAAGAGGCT 61.416 63.158 0.00 0.00 0.00 4.58
601 610 2.104530 GGTCCGACGCTAAGAGGC 59.895 66.667 0.00 0.00 0.00 4.70
602 611 0.748729 AGAGGTCCGACGCTAAGAGG 60.749 60.000 0.00 0.00 0.00 3.69
603 612 1.064357 GAAGAGGTCCGACGCTAAGAG 59.936 57.143 0.00 0.00 0.00 2.85
604 613 1.093159 GAAGAGGTCCGACGCTAAGA 58.907 55.000 0.00 0.00 0.00 2.10
605 614 1.096416 AGAAGAGGTCCGACGCTAAG 58.904 55.000 0.00 0.00 0.00 2.18
606 615 2.408271 TAGAAGAGGTCCGACGCTAA 57.592 50.000 0.00 0.00 0.00 3.09
607 616 2.408271 TTAGAAGAGGTCCGACGCTA 57.592 50.000 0.00 0.00 0.00 4.26
608 617 1.542492 TTTAGAAGAGGTCCGACGCT 58.458 50.000 0.00 0.00 0.00 5.07
609 618 2.194271 CATTTAGAAGAGGTCCGACGC 58.806 52.381 0.00 0.00 0.00 5.19
610 619 2.159226 AGCATTTAGAAGAGGTCCGACG 60.159 50.000 0.00 0.00 0.00 5.12
611 620 3.528597 AGCATTTAGAAGAGGTCCGAC 57.471 47.619 0.00 0.00 0.00 4.79
612 621 5.047943 GCTATAGCATTTAGAAGAGGTCCGA 60.048 44.000 20.01 0.00 41.59 4.55
613 622 5.164954 GCTATAGCATTTAGAAGAGGTCCG 58.835 45.833 20.01 0.00 41.59 4.79
614 623 5.164954 CGCTATAGCATTTAGAAGAGGTCC 58.835 45.833 23.99 0.00 42.21 4.46
615 624 5.631512 CACGCTATAGCATTTAGAAGAGGTC 59.368 44.000 23.99 0.00 42.21 3.85
616 625 5.533482 CACGCTATAGCATTTAGAAGAGGT 58.467 41.667 23.99 6.60 42.21 3.85
617 626 4.387256 GCACGCTATAGCATTTAGAAGAGG 59.613 45.833 23.99 5.98 42.21 3.69
618 627 5.226396 AGCACGCTATAGCATTTAGAAGAG 58.774 41.667 23.99 6.48 42.21 2.85
619 628 5.201713 AGCACGCTATAGCATTTAGAAGA 57.798 39.130 23.99 0.00 42.21 2.87
620 629 7.588143 AATAGCACGCTATAGCATTTAGAAG 57.412 36.000 23.99 7.87 42.21 2.85
621 630 7.962964 AAATAGCACGCTATAGCATTTAGAA 57.037 32.000 23.99 3.88 42.21 2.10
622 631 9.483916 TTTAAATAGCACGCTATAGCATTTAGA 57.516 29.630 23.99 16.17 42.21 2.10
625 634 9.398170 CATTTTAAATAGCACGCTATAGCATTT 57.602 29.630 23.99 20.76 42.21 2.32
626 635 8.567948 ACATTTTAAATAGCACGCTATAGCATT 58.432 29.630 23.99 12.61 42.21 3.56
627 636 8.099364 ACATTTTAAATAGCACGCTATAGCAT 57.901 30.769 23.99 6.50 42.21 3.79
628 637 7.490962 ACATTTTAAATAGCACGCTATAGCA 57.509 32.000 23.99 4.83 42.21 3.49
629 638 8.682016 CAAACATTTTAAATAGCACGCTATAGC 58.318 33.333 15.09 15.09 38.20 2.97
630 639 8.682016 GCAAACATTTTAAATAGCACGCTATAG 58.318 33.333 11.80 0.00 38.20 1.31
631 640 8.402472 AGCAAACATTTTAAATAGCACGCTATA 58.598 29.630 11.80 0.00 38.20 1.31
632 641 7.257722 AGCAAACATTTTAAATAGCACGCTAT 58.742 30.769 5.72 5.72 40.63 2.97
633 642 6.616947 AGCAAACATTTTAAATAGCACGCTA 58.383 32.000 0.39 0.39 0.00 4.26
634 643 5.469479 AGCAAACATTTTAAATAGCACGCT 58.531 33.333 0.00 0.00 0.00 5.07
635 644 5.344665 TGAGCAAACATTTTAAATAGCACGC 59.655 36.000 0.00 0.00 0.00 5.34
636 645 6.926280 TGAGCAAACATTTTAAATAGCACG 57.074 33.333 0.00 0.00 0.00 5.34
637 646 8.216453 CACTTGAGCAAACATTTTAAATAGCAC 58.784 33.333 0.00 0.00 0.00 4.40
638 647 7.925483 ACACTTGAGCAAACATTTTAAATAGCA 59.075 29.630 0.00 0.00 0.00 3.49
639 648 8.298030 ACACTTGAGCAAACATTTTAAATAGC 57.702 30.769 0.00 0.00 0.00 2.97
642 651 9.160496 TCAAACACTTGAGCAAACATTTTAAAT 57.840 25.926 0.00 0.00 36.62 1.40
643 652 8.539770 TCAAACACTTGAGCAAACATTTTAAA 57.460 26.923 0.00 0.00 36.62 1.52
644 653 8.439286 GTTCAAACACTTGAGCAAACATTTTAA 58.561 29.630 0.00 0.00 42.48 1.52
645 654 7.600375 TGTTCAAACACTTGAGCAAACATTTTA 59.400 29.630 2.42 0.00 46.13 1.52
646 655 6.426328 TGTTCAAACACTTGAGCAAACATTTT 59.574 30.769 2.42 0.00 46.13 1.82
647 656 5.931146 TGTTCAAACACTTGAGCAAACATTT 59.069 32.000 2.42 0.00 46.13 2.32
648 657 5.477510 TGTTCAAACACTTGAGCAAACATT 58.522 33.333 2.42 0.00 46.13 2.71
649 658 5.070770 TGTTCAAACACTTGAGCAAACAT 57.929 34.783 2.42 0.00 46.13 2.71
650 659 4.511617 TGTTCAAACACTTGAGCAAACA 57.488 36.364 2.42 0.00 46.13 2.83
655 664 5.402398 AGTCTTTTGTTCAAACACTTGAGC 58.598 37.500 0.00 0.00 42.48 4.26
656 665 6.846350 AGAGTCTTTTGTTCAAACACTTGAG 58.154 36.000 0.00 0.62 42.48 3.02
657 666 6.817765 AGAGTCTTTTGTTCAAACACTTGA 57.182 33.333 0.00 0.00 39.87 3.02
658 667 7.218963 GCTAAGAGTCTTTTGTTCAAACACTTG 59.781 37.037 11.40 0.00 38.92 3.16
659 668 7.251281 GCTAAGAGTCTTTTGTTCAAACACTT 58.749 34.615 11.40 6.95 38.92 3.16
660 669 6.456988 CGCTAAGAGTCTTTTGTTCAAACACT 60.457 38.462 11.40 8.10 38.92 3.55
661 670 5.677178 CGCTAAGAGTCTTTTGTTCAAACAC 59.323 40.000 11.40 0.00 38.92 3.32
662 671 5.729454 GCGCTAAGAGTCTTTTGTTCAAACA 60.729 40.000 11.40 0.00 37.08 2.83
663 672 4.671068 GCGCTAAGAGTCTTTTGTTCAAAC 59.329 41.667 11.40 0.00 0.00 2.93
664 673 4.334203 TGCGCTAAGAGTCTTTTGTTCAAA 59.666 37.500 11.40 0.00 0.00 2.69
665 674 3.874543 TGCGCTAAGAGTCTTTTGTTCAA 59.125 39.130 11.40 0.00 0.00 2.69
666 675 3.462982 TGCGCTAAGAGTCTTTTGTTCA 58.537 40.909 11.40 1.03 0.00 3.18
667 676 3.120511 CCTGCGCTAAGAGTCTTTTGTTC 60.121 47.826 11.40 0.00 0.00 3.18
668 677 2.808543 CCTGCGCTAAGAGTCTTTTGTT 59.191 45.455 11.40 0.00 0.00 2.83
669 678 2.037251 TCCTGCGCTAAGAGTCTTTTGT 59.963 45.455 11.40 0.00 0.00 2.83
670 679 2.413453 GTCCTGCGCTAAGAGTCTTTTG 59.587 50.000 11.40 6.00 0.00 2.44
671 680 2.613223 GGTCCTGCGCTAAGAGTCTTTT 60.613 50.000 11.40 0.00 0.00 2.27
672 681 1.066787 GGTCCTGCGCTAAGAGTCTTT 60.067 52.381 11.40 0.00 0.00 2.52
673 682 0.533032 GGTCCTGCGCTAAGAGTCTT 59.467 55.000 9.73 10.87 0.00 3.01
674 683 0.323908 AGGTCCTGCGCTAAGAGTCT 60.324 55.000 9.73 0.84 0.00 3.24
675 684 0.533032 AAGGTCCTGCGCTAAGAGTC 59.467 55.000 9.73 0.00 0.00 3.36
676 685 0.977395 AAAGGTCCTGCGCTAAGAGT 59.023 50.000 9.73 0.00 0.00 3.24
677 686 2.003301 GAAAAGGTCCTGCGCTAAGAG 58.997 52.381 9.73 0.00 0.00 2.85
678 687 1.623811 AGAAAAGGTCCTGCGCTAAGA 59.376 47.619 9.73 0.00 0.00 2.10
679 688 2.100605 AGAAAAGGTCCTGCGCTAAG 57.899 50.000 9.73 0.00 0.00 2.18
680 689 3.688694 TTAGAAAAGGTCCTGCGCTAA 57.311 42.857 9.73 0.00 0.00 3.09
681 690 3.688694 TTTAGAAAAGGTCCTGCGCTA 57.311 42.857 9.73 0.00 0.00 4.26
682 691 2.561478 TTTAGAAAAGGTCCTGCGCT 57.439 45.000 9.73 0.00 0.00 5.92
683 692 2.732282 GCATTTAGAAAAGGTCCTGCGC 60.732 50.000 0.00 0.00 0.00 6.09
684 693 2.749621 AGCATTTAGAAAAGGTCCTGCG 59.250 45.455 0.00 0.00 33.76 5.18
685 694 6.293680 GCTATAGCATTTAGAAAAGGTCCTGC 60.294 42.308 20.01 0.00 41.59 4.85
686 695 6.073548 CGCTATAGCATTTAGAAAAGGTCCTG 60.074 42.308 23.99 0.00 42.21 3.86
687 696 5.992217 CGCTATAGCATTTAGAAAAGGTCCT 59.008 40.000 23.99 0.00 42.21 3.85
688 697 5.758784 ACGCTATAGCATTTAGAAAAGGTCC 59.241 40.000 23.99 0.00 42.21 4.46
689 698 6.650372 CACGCTATAGCATTTAGAAAAGGTC 58.350 40.000 23.99 0.00 42.21 3.85
690 699 5.007724 GCACGCTATAGCATTTAGAAAAGGT 59.992 40.000 23.99 6.60 42.21 3.50
691 700 5.237344 AGCACGCTATAGCATTTAGAAAAGG 59.763 40.000 23.99 5.98 42.21 3.11
692 701 6.292389 AGCACGCTATAGCATTTAGAAAAG 57.708 37.500 23.99 6.48 42.21 2.27
693 702 5.051039 CGAGCACGCTATAGCATTTAGAAAA 60.051 40.000 23.99 0.00 42.21 2.29
694 703 4.444388 CGAGCACGCTATAGCATTTAGAAA 59.556 41.667 23.99 0.00 42.21 2.52
695 704 3.981416 CGAGCACGCTATAGCATTTAGAA 59.019 43.478 23.99 0.00 42.21 2.10
696 705 3.004419 ACGAGCACGCTATAGCATTTAGA 59.996 43.478 23.99 0.00 43.96 2.10
697 706 3.120286 CACGAGCACGCTATAGCATTTAG 59.880 47.826 23.99 9.98 43.96 1.85
698 707 3.049912 CACGAGCACGCTATAGCATTTA 58.950 45.455 23.99 0.00 43.96 1.40
699 708 1.860950 CACGAGCACGCTATAGCATTT 59.139 47.619 23.99 6.63 43.96 2.32
700 709 1.491670 CACGAGCACGCTATAGCATT 58.508 50.000 23.99 7.75 43.96 3.56
701 710 0.941463 GCACGAGCACGCTATAGCAT 60.941 55.000 23.99 6.50 43.96 3.79
702 711 1.588932 GCACGAGCACGCTATAGCA 60.589 57.895 23.99 0.00 43.96 3.49
703 712 0.040336 TAGCACGAGCACGCTATAGC 60.040 55.000 15.09 15.09 45.49 2.97
704 713 2.620779 ATAGCACGAGCACGCTATAG 57.379 50.000 7.77 0.00 46.90 1.31
705 714 2.159558 GCTATAGCACGAGCACGCTATA 60.160 50.000 20.01 9.36 46.90 1.31
707 716 0.040336 GCTATAGCACGAGCACGCTA 60.040 55.000 20.01 1.00 44.40 4.26
708 717 1.299468 GCTATAGCACGAGCACGCT 60.299 57.895 20.01 0.00 45.49 5.07
709 718 2.639926 CGCTATAGCACGAGCACGC 61.640 63.158 23.99 2.84 45.49 5.34
710 719 2.011349 CCGCTATAGCACGAGCACG 61.011 63.158 23.99 0.76 45.49 5.34
711 720 1.661821 CCCGCTATAGCACGAGCAC 60.662 63.158 23.99 0.00 45.49 4.40
712 721 2.728180 CCCGCTATAGCACGAGCA 59.272 61.111 23.99 0.00 45.49 4.26
713 722 1.863662 TAGCCCGCTATAGCACGAGC 61.864 60.000 23.99 18.51 42.21 5.03
714 723 0.811915 ATAGCCCGCTATAGCACGAG 59.188 55.000 23.99 10.19 42.21 4.18
715 724 1.254026 AATAGCCCGCTATAGCACGA 58.746 50.000 23.99 9.67 42.21 4.35
716 725 2.080286 AAATAGCCCGCTATAGCACG 57.920 50.000 23.99 13.71 42.21 5.34
717 726 4.142881 GCTTTAAATAGCCCGCTATAGCAC 60.143 45.833 23.99 12.65 38.20 4.40
718 727 4.000988 GCTTTAAATAGCCCGCTATAGCA 58.999 43.478 23.99 4.83 38.20 3.49
719 728 4.601621 GCTTTAAATAGCCCGCTATAGC 57.398 45.455 15.09 15.09 38.20 2.97
729 738 7.973388 TGTTTGACATACATGGCTTTAAATAGC 59.027 33.333 0.00 0.00 36.54 2.97
730 739 9.289303 GTGTTTGACATACATGGCTTTAAATAG 57.711 33.333 1.94 0.00 36.54 1.73
731 740 8.797438 TGTGTTTGACATACATGGCTTTAAATA 58.203 29.630 1.94 0.00 36.54 1.40
732 741 7.598493 GTGTGTTTGACATACATGGCTTTAAAT 59.402 33.333 1.94 0.00 39.59 1.40
733 742 6.920758 GTGTGTTTGACATACATGGCTTTAAA 59.079 34.615 1.94 0.00 39.59 1.52
734 743 6.039829 TGTGTGTTTGACATACATGGCTTTAA 59.960 34.615 6.56 0.00 43.66 1.52
735 744 5.532779 TGTGTGTTTGACATACATGGCTTTA 59.467 36.000 6.56 0.00 43.66 1.85
736 745 4.340666 TGTGTGTTTGACATACATGGCTTT 59.659 37.500 6.56 0.00 43.66 3.51
737 746 3.888323 TGTGTGTTTGACATACATGGCTT 59.112 39.130 6.56 0.00 43.66 4.35
738 747 3.485394 TGTGTGTTTGACATACATGGCT 58.515 40.909 6.56 0.00 43.66 4.75
739 748 3.913548 TGTGTGTTTGACATACATGGC 57.086 42.857 6.56 0.00 43.66 4.40
744 753 9.935682 CATCCTATTTATGTGTGTTTGACATAC 57.064 33.333 0.00 1.61 40.13 2.39
745 754 9.119418 CCATCCTATTTATGTGTGTTTGACATA 57.881 33.333 0.00 0.00 36.78 2.29
746 755 7.416664 GCCATCCTATTTATGTGTGTTTGACAT 60.417 37.037 0.00 0.00 36.78 3.06
747 756 6.127758 GCCATCCTATTTATGTGTGTTTGACA 60.128 38.462 0.00 0.00 0.00 3.58
748 757 6.127758 TGCCATCCTATTTATGTGTGTTTGAC 60.128 38.462 0.00 0.00 0.00 3.18
749 758 5.948758 TGCCATCCTATTTATGTGTGTTTGA 59.051 36.000 0.00 0.00 0.00 2.69
750 759 6.035843 GTGCCATCCTATTTATGTGTGTTTG 58.964 40.000 0.00 0.00 0.00 2.93
751 760 5.127031 GGTGCCATCCTATTTATGTGTGTTT 59.873 40.000 0.00 0.00 0.00 2.83
752 761 4.644685 GGTGCCATCCTATTTATGTGTGTT 59.355 41.667 0.00 0.00 0.00 3.32
753 762 4.079787 AGGTGCCATCCTATTTATGTGTGT 60.080 41.667 0.00 0.00 35.87 3.72
754 763 4.276678 CAGGTGCCATCCTATTTATGTGTG 59.723 45.833 0.00 0.00 35.87 3.82
755 764 4.464008 CAGGTGCCATCCTATTTATGTGT 58.536 43.478 0.00 0.00 35.87 3.72
756 765 3.254166 GCAGGTGCCATCCTATTTATGTG 59.746 47.826 0.00 0.00 35.87 3.21
757 766 3.117550 TGCAGGTGCCATCCTATTTATGT 60.118 43.478 0.00 0.00 41.18 2.29
839 865 6.971726 AATCTATATTAGTGTCACCGGTGA 57.028 37.500 33.23 33.23 37.24 4.02
1004 1079 2.869801 TGCCGTTTCTGTCTTTGTGTAG 59.130 45.455 0.00 0.00 0.00 2.74
1013 1088 1.444119 TTGTGGCTGCCGTTTCTGTC 61.444 55.000 14.98 0.00 0.00 3.51
1095 1185 2.821366 TCCCGCGACGAGGTAGTC 60.821 66.667 16.70 0.00 37.76 2.59
1473 3080 1.142965 GCTCCTCTCTTTCGAGCCC 59.857 63.158 0.00 0.00 42.59 5.19
1576 3189 4.279145 TGTTGATCACTCCTACTACTCCC 58.721 47.826 0.00 0.00 0.00 4.30
1831 3465 5.363939 AGTTCTAGCTGCATCAAAGTATCC 58.636 41.667 1.02 0.00 0.00 2.59
1880 3514 8.078596 GCACTAAATCAGATCAAGAAACAAAGT 58.921 33.333 0.00 0.00 0.00 2.66
1894 3528 8.445275 TTCAAGTAAAACAGCACTAAATCAGA 57.555 30.769 0.00 0.00 0.00 3.27
1902 3540 6.447162 GGCTAATTTCAAGTAAAACAGCACT 58.553 36.000 0.00 0.00 38.64 4.40
2007 3672 1.813513 AAATTGAGCTGGACACGAGG 58.186 50.000 0.00 0.00 0.00 4.63
2008 3673 2.666619 GCAAAATTGAGCTGGACACGAG 60.667 50.000 0.00 0.00 0.00 4.18
2010 3675 1.001487 TGCAAAATTGAGCTGGACACG 60.001 47.619 0.00 0.00 0.00 4.49
2011 3676 2.397549 GTGCAAAATTGAGCTGGACAC 58.602 47.619 0.00 0.00 32.27 3.67
2012 3677 1.001487 CGTGCAAAATTGAGCTGGACA 60.001 47.619 0.00 0.00 31.52 4.02
2013 3678 1.689959 CGTGCAAAATTGAGCTGGAC 58.310 50.000 0.00 0.00 0.00 4.02
2015 3680 0.318869 TGCGTGCAAAATTGAGCTGG 60.319 50.000 0.00 0.00 0.00 4.85
2016 3681 1.705256 ATGCGTGCAAAATTGAGCTG 58.295 45.000 0.00 0.00 0.00 4.24
2085 3764 9.809096 CTCTATATAATATAGGCACAACACCTG 57.191 37.037 0.00 0.00 38.26 4.00
2101 3780 9.635284 TTCCTCCTTTTCCCATCTCTATATAAT 57.365 33.333 0.00 0.00 0.00 1.28
2114 3801 2.158370 TGACCCTTTTCCTCCTTTTCCC 60.158 50.000 0.00 0.00 0.00 3.97
2151 3838 6.649141 TCGACCCTTTTATCATCCATTAATCG 59.351 38.462 0.00 0.00 0.00 3.34
2177 3864 8.220898 TGAGAGTATATCATACTAGGACTGGT 57.779 38.462 0.00 0.00 0.00 4.00
2353 4044 8.849168 CCTCCAATATATACATTGTGAAGCAAA 58.151 33.333 3.17 0.00 40.91 3.68
2422 4113 8.132362 GGGACACTCTTATAGCATATAGATTCG 58.868 40.741 0.00 0.00 0.00 3.34
2425 4116 8.119246 ACAGGGACACTCTTATAGCATATAGAT 58.881 37.037 0.00 0.00 0.00 1.98
2577 4772 1.464687 GCTCTGTTGTGCGCTACATTG 60.465 52.381 14.73 11.28 39.48 2.82
2594 4790 1.522668 TGTGCCTGTGTGTAATGCTC 58.477 50.000 0.00 0.00 0.00 4.26
2602 4798 1.775039 CGGACAGTTGTGCCTGTGTG 61.775 60.000 0.00 0.00 45.46 3.82
2608 4804 1.635663 CGGATTCGGACAGTTGTGCC 61.636 60.000 0.00 0.00 32.36 5.01
2609 4805 0.669318 TCGGATTCGGACAGTTGTGC 60.669 55.000 0.00 0.00 36.95 4.57
2661 4857 4.746535 TGTCTTCCACTATGCGGAAATA 57.253 40.909 0.00 0.00 41.93 1.40
2690 4886 6.128445 GCGATGGATTAAACAGACATATCCAG 60.128 42.308 0.00 0.00 45.62 3.86
2700 4896 5.991606 TCTAGGAATGCGATGGATTAAACAG 59.008 40.000 0.00 0.00 0.00 3.16
2705 4901 4.416516 TCCTCTAGGAATGCGATGGATTA 58.583 43.478 0.00 0.00 42.18 1.75
2753 4951 6.826668 TGTATCCATGTCCGACTGATAATTT 58.173 36.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.