Multiple sequence alignment - TraesCS4B01G237100

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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 TraesCS4B01G237100 chr4B 100.000 2183 0 0 1 2183 495075403 495077585 0.000000e+00 4032
1 TraesCS4B01G237100 chr4B 88.476 1293 144 5 877 2166 38776873 38778163 0.000000e+00 1557
2 TraesCS4B01G237100 chr4B 100.000 776 0 0 2392 3167 495077794 495078569 0.000000e+00 1434
3 TraesCS4B01G237100 chr4B 94.435 575 32 0 1 575 411750548 411751122 0.000000e+00 885
4 TraesCS4B01G237100 chr4B 91.478 575 34 5 1 575 66189780 66190339 0.000000e+00 776
5 TraesCS4B01G237100 chr1B 94.118 1309 77 0 875 2183 401558429 401559737 0.000000e+00 1991
6 TraesCS4B01G237100 chr1B 93.023 774 54 0 2394 3167 401559839 401560612 0.000000e+00 1131
7 TraesCS4B01G237100 chr1B 75.777 772 176 10 1000 1764 270324151 270324918 2.310000e-101 379
8 TraesCS4B01G237100 chr4A 90.972 1307 117 1 877 2183 26023176 26021871 0.000000e+00 1759
9 TraesCS4B01G237100 chr4A 89.318 777 77 4 2394 3167 26021770 26020997 0.000000e+00 970
10 TraesCS4B01G237100 chr6A 90.276 1306 122 5 879 2183 608223428 608224729 0.000000e+00 1703
11 TraesCS4B01G237100 chr6A 91.429 490 42 0 2394 2883 608233285 608233774 0.000000e+00 673
12 TraesCS4B01G237100 chr6A 83.806 599 57 10 1 570 612337563 612336976 1.670000e-147 532
13 TraesCS4B01G237100 chr5A 89.518 1307 135 2 877 2183 646996664 646997968 0.000000e+00 1653
14 TraesCS4B01G237100 chr5A 87.597 774 96 0 2394 3167 646998075 646998848 0.000000e+00 898
15 TraesCS4B01G237100 chr2A 89.478 1302 133 4 877 2177 41178191 41176893 0.000000e+00 1642
16 TraesCS4B01G237100 chr2A 87.597 774 96 0 2394 3167 41176605 41175832 0.000000e+00 898
17 TraesCS4B01G237100 chr5B 99.130 575 5 0 1 575 563792685 563792111 0.000000e+00 1035
18 TraesCS4B01G237100 chr5B 96.522 575 20 0 1 575 18329209 18328635 0.000000e+00 952
19 TraesCS4B01G237100 chr5B 92.696 575 34 4 1 575 68260275 68259709 0.000000e+00 822
20 TraesCS4B01G237100 chr5B 92.271 414 19 4 165 576 626495042 626494640 2.740000e-160 575
21 TraesCS4B01G237100 chr5B 95.294 340 16 0 236 575 147004269 147004608 9.990000e-150 540
22 TraesCS4B01G237100 chr3B 98.957 575 6 0 1 575 671012253 671012827 0.000000e+00 1029
23 TraesCS4B01G237100 chr3B 96.000 575 23 0 1 575 294645137 294644563 0.000000e+00 935
24 TraesCS4B01G237100 chr3B 93.011 186 13 0 573 758 104272272 104272087 4.030000e-69 272
25 TraesCS4B01G237100 chr3B 78.488 172 36 1 2013 2183 18783391 18783562 9.290000e-21 111
26 TraesCS4B01G237100 chr6B 79.939 1306 242 17 877 2170 573746900 573745603 0.000000e+00 942
27 TraesCS4B01G237100 chr6B 76.227 774 175 9 2395 3164 573745486 573744718 4.920000e-108 401
28 TraesCS4B01G237100 chr6B 90.957 188 17 0 573 760 655806245 655806058 1.460000e-63 254
29 TraesCS4B01G237100 chr2B 80.982 652 111 11 2523 3167 675501894 675502539 3.650000e-139 505
30 TraesCS4B01G237100 chr2B 75.389 772 179 9 1000 1764 217273683 217272916 2.320000e-96 363
31 TraesCS4B01G237100 chr2B 92.021 188 15 0 573 760 500705595 500705782 6.740000e-67 265
32 TraesCS4B01G237100 chr5D 94.681 188 10 0 573 760 398777816 398777629 3.090000e-75 292
33 TraesCS4B01G237100 chr5D 80.702 171 29 4 2015 2183 7614552 7614384 2.560000e-26 130
34 TraesCS4B01G237100 chr3D 94.681 188 10 0 573 760 297721219 297721406 3.090000e-75 292


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 TraesCS4B01G237100 chr4B 495075403 495078569 3166 False 2733.0 4032 100.0000 1 3167 2 chr4B.!!$F4 3166
1 TraesCS4B01G237100 chr4B 38776873 38778163 1290 False 1557.0 1557 88.4760 877 2166 1 chr4B.!!$F1 1289
2 TraesCS4B01G237100 chr4B 411750548 411751122 574 False 885.0 885 94.4350 1 575 1 chr4B.!!$F3 574
3 TraesCS4B01G237100 chr4B 66189780 66190339 559 False 776.0 776 91.4780 1 575 1 chr4B.!!$F2 574
4 TraesCS4B01G237100 chr1B 401558429 401560612 2183 False 1561.0 1991 93.5705 875 3167 2 chr1B.!!$F2 2292
5 TraesCS4B01G237100 chr1B 270324151 270324918 767 False 379.0 379 75.7770 1000 1764 1 chr1B.!!$F1 764
6 TraesCS4B01G237100 chr4A 26020997 26023176 2179 True 1364.5 1759 90.1450 877 3167 2 chr4A.!!$R1 2290
7 TraesCS4B01G237100 chr6A 608223428 608224729 1301 False 1703.0 1703 90.2760 879 2183 1 chr6A.!!$F1 1304
8 TraesCS4B01G237100 chr6A 612336976 612337563 587 True 532.0 532 83.8060 1 570 1 chr6A.!!$R1 569
9 TraesCS4B01G237100 chr5A 646996664 646998848 2184 False 1275.5 1653 88.5575 877 3167 2 chr5A.!!$F1 2290
10 TraesCS4B01G237100 chr2A 41175832 41178191 2359 True 1270.0 1642 88.5375 877 3167 2 chr2A.!!$R1 2290
11 TraesCS4B01G237100 chr5B 563792111 563792685 574 True 1035.0 1035 99.1300 1 575 1 chr5B.!!$R3 574
12 TraesCS4B01G237100 chr5B 18328635 18329209 574 True 952.0 952 96.5220 1 575 1 chr5B.!!$R1 574
13 TraesCS4B01G237100 chr5B 68259709 68260275 566 True 822.0 822 92.6960 1 575 1 chr5B.!!$R2 574
14 TraesCS4B01G237100 chr3B 671012253 671012827 574 False 1029.0 1029 98.9570 1 575 1 chr3B.!!$F2 574
15 TraesCS4B01G237100 chr3B 294644563 294645137 574 True 935.0 935 96.0000 1 575 1 chr3B.!!$R2 574
16 TraesCS4B01G237100 chr6B 573744718 573746900 2182 True 671.5 942 78.0830 877 3164 2 chr6B.!!$R2 2287
17 TraesCS4B01G237100 chr2B 675501894 675502539 645 False 505.0 505 80.9820 2523 3167 1 chr2B.!!$F2 644
18 TraesCS4B01G237100 chr2B 217272916 217273683 767 True 363.0 363 75.3890 1000 1764 1 chr2B.!!$R1 764

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
706 735 0.030235 GTGAAGTTTGGCGGGAACAC 59.970 55.0 0.00 0.0 0.0 3.32 F
707 736 0.106918 TGAAGTTTGGCGGGAACACT 60.107 50.0 1.95 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2154 0.320771 GGCCGCCGATATCTCATTGT 60.321 55.000 0.34 0.0 0.00 2.71 R
2504 2612 1.741732 CGGCTGCAAGAATCTAGCACT 60.742 52.381 0.50 0.0 37.89 4.40 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
61 62 2.080286 CAAGGTACGTGCAAGCTAGT 57.920 50.000 5.86 0.00 0.00 2.57
285 286 5.177696 GCATGTATTGTTAGCTAGGTACTGC 59.822 44.000 0.00 1.08 41.52 4.40
422 423 6.882140 TCACATACAACAGTAGGGGTAAAATG 59.118 38.462 0.00 0.00 0.00 2.32
575 604 7.560796 TTTAAGAATGGGCCAAATAAGGAAA 57.439 32.000 11.89 2.78 0.00 3.13
576 605 5.420725 AAGAATGGGCCAAATAAGGAAAC 57.579 39.130 11.89 0.00 0.00 2.78
577 606 3.447229 AGAATGGGCCAAATAAGGAAACG 59.553 43.478 11.89 0.00 0.00 3.60
578 607 2.296073 TGGGCCAAATAAGGAAACGT 57.704 45.000 2.13 0.00 0.00 3.99
579 608 3.436577 TGGGCCAAATAAGGAAACGTA 57.563 42.857 2.13 0.00 0.00 3.57
580 609 3.764218 TGGGCCAAATAAGGAAACGTAA 58.236 40.909 2.13 0.00 0.00 3.18
581 610 4.150359 TGGGCCAAATAAGGAAACGTAAA 58.850 39.130 2.13 0.00 0.00 2.01
582 611 4.022155 TGGGCCAAATAAGGAAACGTAAAC 60.022 41.667 2.13 0.00 0.00 2.01
583 612 4.022155 GGGCCAAATAAGGAAACGTAAACA 60.022 41.667 4.39 0.00 0.00 2.83
584 613 5.158494 GGCCAAATAAGGAAACGTAAACAG 58.842 41.667 0.00 0.00 0.00 3.16
585 614 5.278610 GGCCAAATAAGGAAACGTAAACAGT 60.279 40.000 0.00 0.00 0.00 3.55
586 615 5.854866 GCCAAATAAGGAAACGTAAACAGTC 59.145 40.000 0.00 0.00 0.00 3.51
587 616 6.293790 GCCAAATAAGGAAACGTAAACAGTCT 60.294 38.462 0.00 0.00 0.00 3.24
588 617 7.075741 CCAAATAAGGAAACGTAAACAGTCTG 58.924 38.462 0.00 0.00 0.00 3.51
589 618 7.041644 CCAAATAAGGAAACGTAAACAGTCTGA 60.042 37.037 6.91 0.00 0.00 3.27
590 619 7.653767 AATAAGGAAACGTAAACAGTCTGAG 57.346 36.000 6.91 0.00 0.00 3.35
591 620 3.391049 AGGAAACGTAAACAGTCTGAGC 58.609 45.455 6.91 0.00 0.00 4.26
592 621 2.479275 GGAAACGTAAACAGTCTGAGCC 59.521 50.000 6.91 0.00 0.00 4.70
593 622 1.779569 AACGTAAACAGTCTGAGCCG 58.220 50.000 6.91 5.73 0.00 5.52
594 623 0.672342 ACGTAAACAGTCTGAGCCGT 59.328 50.000 6.91 6.35 0.00 5.68
595 624 1.335689 ACGTAAACAGTCTGAGCCGTC 60.336 52.381 6.91 0.00 0.00 4.79
596 625 1.335597 CGTAAACAGTCTGAGCCGTCA 60.336 52.381 6.91 0.00 0.00 4.35
605 634 2.808598 TGAGCCGTCAGATCTACCC 58.191 57.895 0.00 0.00 0.00 3.69
606 635 0.033503 TGAGCCGTCAGATCTACCCA 60.034 55.000 0.00 0.00 0.00 4.51
607 636 1.333177 GAGCCGTCAGATCTACCCAT 58.667 55.000 0.00 0.00 0.00 4.00
608 637 2.158519 TGAGCCGTCAGATCTACCCATA 60.159 50.000 0.00 0.00 0.00 2.74
609 638 3.093057 GAGCCGTCAGATCTACCCATAT 58.907 50.000 0.00 0.00 0.00 1.78
610 639 3.093057 AGCCGTCAGATCTACCCATATC 58.907 50.000 0.00 0.00 0.00 1.63
611 640 2.159366 GCCGTCAGATCTACCCATATCG 60.159 54.545 0.00 0.00 0.00 2.92
612 641 3.344515 CCGTCAGATCTACCCATATCGA 58.655 50.000 0.00 0.00 0.00 3.59
613 642 3.127203 CCGTCAGATCTACCCATATCGAC 59.873 52.174 0.00 0.00 0.00 4.20
614 643 3.181519 CGTCAGATCTACCCATATCGACG 60.182 52.174 10.71 10.71 39.81 5.12
615 644 3.127203 GTCAGATCTACCCATATCGACGG 59.873 52.174 0.00 0.00 0.00 4.79
616 645 2.093106 AGATCTACCCATATCGACGGC 58.907 52.381 0.00 0.00 0.00 5.68
617 646 1.134560 GATCTACCCATATCGACGGCC 59.865 57.143 0.00 0.00 0.00 6.13
618 647 0.178984 TCTACCCATATCGACGGCCA 60.179 55.000 2.24 0.00 0.00 5.36
619 648 0.038526 CTACCCATATCGACGGCCAC 60.039 60.000 2.24 0.00 0.00 5.01
620 649 1.466025 TACCCATATCGACGGCCACC 61.466 60.000 2.24 0.00 0.00 4.61
621 650 2.507854 CCCATATCGACGGCCACCT 61.508 63.158 2.24 0.00 0.00 4.00
622 651 1.445942 CCATATCGACGGCCACCTT 59.554 57.895 2.24 0.00 0.00 3.50
623 652 0.179056 CCATATCGACGGCCACCTTT 60.179 55.000 2.24 0.00 0.00 3.11
624 653 1.217882 CATATCGACGGCCACCTTTC 58.782 55.000 2.24 0.00 0.00 2.62
625 654 1.120530 ATATCGACGGCCACCTTTCT 58.879 50.000 2.24 0.00 0.00 2.52
626 655 0.899720 TATCGACGGCCACCTTTCTT 59.100 50.000 2.24 0.00 0.00 2.52
627 656 0.036306 ATCGACGGCCACCTTTCTTT 59.964 50.000 2.24 0.00 0.00 2.52
628 657 0.179040 TCGACGGCCACCTTTCTTTT 60.179 50.000 2.24 0.00 0.00 2.27
629 658 0.040425 CGACGGCCACCTTTCTTTTG 60.040 55.000 2.24 0.00 0.00 2.44
630 659 1.314730 GACGGCCACCTTTCTTTTGA 58.685 50.000 2.24 0.00 0.00 2.69
631 660 1.886542 GACGGCCACCTTTCTTTTGAT 59.113 47.619 2.24 0.00 0.00 2.57
632 661 2.296190 GACGGCCACCTTTCTTTTGATT 59.704 45.455 2.24 0.00 0.00 2.57
633 662 2.296190 ACGGCCACCTTTCTTTTGATTC 59.704 45.455 2.24 0.00 0.00 2.52
634 663 2.295909 CGGCCACCTTTCTTTTGATTCA 59.704 45.455 2.24 0.00 0.00 2.57
635 664 3.653344 GGCCACCTTTCTTTTGATTCAC 58.347 45.455 0.00 0.00 0.00 3.18
636 665 3.321968 GGCCACCTTTCTTTTGATTCACT 59.678 43.478 0.00 0.00 0.00 3.41
637 666 4.550422 GCCACCTTTCTTTTGATTCACTC 58.450 43.478 0.00 0.00 0.00 3.51
638 667 4.559502 GCCACCTTTCTTTTGATTCACTCC 60.560 45.833 0.00 0.00 0.00 3.85
639 668 4.829492 CCACCTTTCTTTTGATTCACTCCT 59.171 41.667 0.00 0.00 0.00 3.69
640 669 5.302823 CCACCTTTCTTTTGATTCACTCCTT 59.697 40.000 0.00 0.00 0.00 3.36
641 670 6.442112 CACCTTTCTTTTGATTCACTCCTTC 58.558 40.000 0.00 0.00 0.00 3.46
642 671 6.264067 CACCTTTCTTTTGATTCACTCCTTCT 59.736 38.462 0.00 0.00 0.00 2.85
643 672 6.836007 ACCTTTCTTTTGATTCACTCCTTCTT 59.164 34.615 0.00 0.00 0.00 2.52
644 673 7.998964 ACCTTTCTTTTGATTCACTCCTTCTTA 59.001 33.333 0.00 0.00 0.00 2.10
645 674 8.510505 CCTTTCTTTTGATTCACTCCTTCTTAG 58.489 37.037 0.00 0.00 0.00 2.18
646 675 8.980481 TTTCTTTTGATTCACTCCTTCTTAGT 57.020 30.769 0.00 0.00 0.00 2.24
647 676 8.608844 TTCTTTTGATTCACTCCTTCTTAGTC 57.391 34.615 0.00 0.00 0.00 2.59
648 677 7.162082 TCTTTTGATTCACTCCTTCTTAGTCC 58.838 38.462 0.00 0.00 0.00 3.85
649 678 4.720649 TGATTCACTCCTTCTTAGTCCG 57.279 45.455 0.00 0.00 0.00 4.79
650 679 4.087182 TGATTCACTCCTTCTTAGTCCGT 58.913 43.478 0.00 0.00 0.00 4.69
651 680 4.527038 TGATTCACTCCTTCTTAGTCCGTT 59.473 41.667 0.00 0.00 0.00 4.44
652 681 3.936372 TCACTCCTTCTTAGTCCGTTG 57.064 47.619 0.00 0.00 0.00 4.10
653 682 2.561419 TCACTCCTTCTTAGTCCGTTGG 59.439 50.000 0.00 0.00 0.00 3.77
654 683 2.561419 CACTCCTTCTTAGTCCGTTGGA 59.439 50.000 0.00 0.00 0.00 3.53
655 684 3.195825 CACTCCTTCTTAGTCCGTTGGAT 59.804 47.826 0.00 0.00 32.73 3.41
656 685 3.447944 ACTCCTTCTTAGTCCGTTGGATC 59.552 47.826 0.00 0.00 32.73 3.36
657 686 3.702045 CTCCTTCTTAGTCCGTTGGATCT 59.298 47.826 0.00 0.00 32.73 2.75
658 687 3.447586 TCCTTCTTAGTCCGTTGGATCTG 59.552 47.826 0.00 0.00 32.73 2.90
659 688 2.961526 TCTTAGTCCGTTGGATCTGC 57.038 50.000 0.00 0.00 32.73 4.26
660 689 2.176045 TCTTAGTCCGTTGGATCTGCA 58.824 47.619 0.00 0.00 32.73 4.41
661 690 2.166459 TCTTAGTCCGTTGGATCTGCAG 59.834 50.000 7.63 7.63 32.73 4.41
662 691 1.847328 TAGTCCGTTGGATCTGCAGA 58.153 50.000 20.79 20.79 32.73 4.26
663 692 0.976641 AGTCCGTTGGATCTGCAGAA 59.023 50.000 22.50 0.40 32.73 3.02
664 693 1.556911 AGTCCGTTGGATCTGCAGAAT 59.443 47.619 22.50 9.47 32.73 2.40
665 694 1.936547 GTCCGTTGGATCTGCAGAATC 59.063 52.381 22.50 17.40 32.73 2.52
666 695 0.933097 CCGTTGGATCTGCAGAATCG 59.067 55.000 22.50 18.59 0.00 3.34
667 696 1.471501 CCGTTGGATCTGCAGAATCGA 60.472 52.381 22.50 12.62 0.00 3.59
668 697 1.857217 CGTTGGATCTGCAGAATCGAG 59.143 52.381 22.50 7.26 0.00 4.04
669 698 2.208431 GTTGGATCTGCAGAATCGAGG 58.792 52.381 22.50 0.00 0.00 4.63
670 699 1.780503 TGGATCTGCAGAATCGAGGA 58.219 50.000 22.50 0.00 0.00 3.71
671 700 1.410517 TGGATCTGCAGAATCGAGGAC 59.589 52.381 22.50 5.55 0.00 3.85
672 701 1.686052 GGATCTGCAGAATCGAGGACT 59.314 52.381 22.50 0.00 0.00 3.85
673 702 2.288152 GGATCTGCAGAATCGAGGACTC 60.288 54.545 22.50 10.03 0.00 3.36
674 703 1.839424 TCTGCAGAATCGAGGACTCA 58.161 50.000 15.67 0.00 0.00 3.41
675 704 1.474478 TCTGCAGAATCGAGGACTCAC 59.526 52.381 15.67 0.00 0.00 3.51
676 705 1.203287 CTGCAGAATCGAGGACTCACA 59.797 52.381 8.42 0.00 0.00 3.58
677 706 1.067565 TGCAGAATCGAGGACTCACAC 60.068 52.381 0.00 0.00 0.00 3.82
678 707 1.203523 GCAGAATCGAGGACTCACACT 59.796 52.381 0.00 0.00 0.00 3.55
679 708 2.423892 GCAGAATCGAGGACTCACACTA 59.576 50.000 0.00 0.00 0.00 2.74
680 709 3.067461 GCAGAATCGAGGACTCACACTAT 59.933 47.826 0.00 0.00 0.00 2.12
681 710 4.440802 GCAGAATCGAGGACTCACACTATT 60.441 45.833 0.00 0.00 0.00 1.73
682 711 5.655488 CAGAATCGAGGACTCACACTATTT 58.345 41.667 0.00 0.00 0.00 1.40
683 712 6.102663 CAGAATCGAGGACTCACACTATTTT 58.897 40.000 0.00 0.00 0.00 1.82
684 713 7.258441 CAGAATCGAGGACTCACACTATTTTA 58.742 38.462 0.00 0.00 0.00 1.52
685 714 7.759886 CAGAATCGAGGACTCACACTATTTTAA 59.240 37.037 0.00 0.00 0.00 1.52
686 715 7.976734 AGAATCGAGGACTCACACTATTTTAAG 59.023 37.037 0.00 0.00 0.00 1.85
687 716 5.962433 TCGAGGACTCACACTATTTTAAGG 58.038 41.667 0.00 0.00 0.00 2.69
688 717 5.479375 TCGAGGACTCACACTATTTTAAGGT 59.521 40.000 0.00 0.00 0.00 3.50
689 718 5.577164 CGAGGACTCACACTATTTTAAGGTG 59.423 44.000 0.00 0.00 37.05 4.00
690 719 6.571731 CGAGGACTCACACTATTTTAAGGTGA 60.572 42.308 0.00 0.00 37.02 4.02
691 720 7.074653 AGGACTCACACTATTTTAAGGTGAA 57.925 36.000 0.00 0.00 37.96 3.18
692 721 7.162082 AGGACTCACACTATTTTAAGGTGAAG 58.838 38.462 0.00 0.00 37.96 3.02
693 722 6.935208 GGACTCACACTATTTTAAGGTGAAGT 59.065 38.462 0.00 0.00 37.96 3.01
694 723 7.444487 GGACTCACACTATTTTAAGGTGAAGTT 59.556 37.037 0.00 0.00 37.96 2.66
695 724 8.747538 ACTCACACTATTTTAAGGTGAAGTTT 57.252 30.769 0.00 0.00 37.96 2.66
696 725 8.621286 ACTCACACTATTTTAAGGTGAAGTTTG 58.379 33.333 0.00 0.00 37.96 2.93
697 726 7.936584 TCACACTATTTTAAGGTGAAGTTTGG 58.063 34.615 0.00 0.00 35.72 3.28
698 727 6.640907 CACACTATTTTAAGGTGAAGTTTGGC 59.359 38.462 0.00 0.00 35.28 4.52
699 728 5.856455 CACTATTTTAAGGTGAAGTTTGGCG 59.144 40.000 0.00 0.00 33.32 5.69
700 729 3.719173 TTTTAAGGTGAAGTTTGGCGG 57.281 42.857 0.00 0.00 0.00 6.13
701 730 1.611519 TTAAGGTGAAGTTTGGCGGG 58.388 50.000 0.00 0.00 0.00 6.13
702 731 0.766131 TAAGGTGAAGTTTGGCGGGA 59.234 50.000 0.00 0.00 0.00 5.14
703 732 0.106419 AAGGTGAAGTTTGGCGGGAA 60.106 50.000 0.00 0.00 0.00 3.97
704 733 0.822121 AGGTGAAGTTTGGCGGGAAC 60.822 55.000 0.00 0.00 0.00 3.62
705 734 1.104577 GGTGAAGTTTGGCGGGAACA 61.105 55.000 1.95 0.00 0.00 3.18
706 735 0.030235 GTGAAGTTTGGCGGGAACAC 59.970 55.000 0.00 0.00 0.00 3.32
707 736 0.106918 TGAAGTTTGGCGGGAACACT 60.107 50.000 1.95 0.00 0.00 3.55
708 737 0.310854 GAAGTTTGGCGGGAACACTG 59.689 55.000 1.95 0.00 0.00 3.66
709 738 0.395173 AAGTTTGGCGGGAACACTGT 60.395 50.000 1.95 0.00 0.00 3.55
710 739 0.470766 AGTTTGGCGGGAACACTGTA 59.529 50.000 1.95 0.00 0.00 2.74
711 740 0.589708 GTTTGGCGGGAACACTGTAC 59.410 55.000 0.00 0.00 0.00 2.90
712 741 0.180642 TTTGGCGGGAACACTGTACA 59.819 50.000 0.00 0.00 0.00 2.90
713 742 0.398696 TTGGCGGGAACACTGTACAT 59.601 50.000 0.00 0.00 0.00 2.29
714 743 0.321210 TGGCGGGAACACTGTACATG 60.321 55.000 0.00 0.00 0.00 3.21
715 744 0.321298 GGCGGGAACACTGTACATGT 60.321 55.000 2.69 2.69 0.00 3.21
716 745 0.796312 GCGGGAACACTGTACATGTG 59.204 55.000 9.11 18.18 40.87 3.21
717 746 1.438651 CGGGAACACTGTACATGTGG 58.561 55.000 21.58 1.11 39.52 4.17
718 747 1.270625 CGGGAACACTGTACATGTGGT 60.271 52.381 21.58 17.98 39.52 4.16
719 748 2.151202 GGGAACACTGTACATGTGGTG 58.849 52.381 21.58 19.56 39.52 4.17
720 749 2.151202 GGAACACTGTACATGTGGTGG 58.849 52.381 22.73 9.61 39.52 4.61
721 750 2.486548 GGAACACTGTACATGTGGTGGT 60.487 50.000 22.73 19.41 39.52 4.16
722 751 3.244284 GGAACACTGTACATGTGGTGGTA 60.244 47.826 22.73 0.00 39.52 3.25
723 752 4.382291 GAACACTGTACATGTGGTGGTAA 58.618 43.478 22.73 0.00 39.52 2.85
724 753 4.425180 ACACTGTACATGTGGTGGTAAA 57.575 40.909 22.73 0.00 39.52 2.01
725 754 4.980573 ACACTGTACATGTGGTGGTAAAT 58.019 39.130 22.73 7.53 39.52 1.40
726 755 5.001232 ACACTGTACATGTGGTGGTAAATC 58.999 41.667 22.73 1.01 39.52 2.17
727 756 4.092821 CACTGTACATGTGGTGGTAAATCG 59.907 45.833 9.11 0.00 0.00 3.34
728 757 3.601435 TGTACATGTGGTGGTAAATCGG 58.399 45.455 9.11 0.00 0.00 4.18
729 758 3.261137 TGTACATGTGGTGGTAAATCGGA 59.739 43.478 9.11 0.00 0.00 4.55
730 759 3.426787 ACATGTGGTGGTAAATCGGAA 57.573 42.857 0.00 0.00 0.00 4.30
731 760 3.343617 ACATGTGGTGGTAAATCGGAAG 58.656 45.455 0.00 0.00 0.00 3.46
732 761 3.244770 ACATGTGGTGGTAAATCGGAAGT 60.245 43.478 0.00 0.00 0.00 3.01
733 762 3.495434 TGTGGTGGTAAATCGGAAGTT 57.505 42.857 0.00 0.00 0.00 2.66
734 763 3.404899 TGTGGTGGTAAATCGGAAGTTC 58.595 45.455 0.00 0.00 0.00 3.01
735 764 3.181453 TGTGGTGGTAAATCGGAAGTTCA 60.181 43.478 5.01 0.00 0.00 3.18
736 765 3.816523 GTGGTGGTAAATCGGAAGTTCAA 59.183 43.478 5.01 0.00 0.00 2.69
737 766 4.276431 GTGGTGGTAAATCGGAAGTTCAAA 59.724 41.667 5.01 0.00 0.00 2.69
738 767 4.888239 TGGTGGTAAATCGGAAGTTCAAAA 59.112 37.500 5.01 0.00 0.00 2.44
739 768 5.360144 TGGTGGTAAATCGGAAGTTCAAAAA 59.640 36.000 5.01 0.00 0.00 1.94
740 769 5.688621 GGTGGTAAATCGGAAGTTCAAAAAC 59.311 40.000 5.01 0.00 35.50 2.43
742 771 6.416750 GTGGTAAATCGGAAGTTCAAAAACTG 59.583 38.462 5.01 0.00 45.07 3.16
743 772 6.095720 TGGTAAATCGGAAGTTCAAAAACTGT 59.904 34.615 5.01 0.00 45.07 3.55
744 773 6.976349 GGTAAATCGGAAGTTCAAAAACTGTT 59.024 34.615 5.01 0.00 45.07 3.16
745 774 6.885735 AAATCGGAAGTTCAAAAACTGTTG 57.114 33.333 5.01 0.00 45.07 3.33
746 775 5.576447 ATCGGAAGTTCAAAAACTGTTGT 57.424 34.783 5.01 0.00 45.07 3.32
747 776 6.687081 ATCGGAAGTTCAAAAACTGTTGTA 57.313 33.333 5.01 0.00 45.07 2.41
748 777 6.687081 TCGGAAGTTCAAAAACTGTTGTAT 57.313 33.333 5.01 0.00 45.07 2.29
749 778 7.090953 TCGGAAGTTCAAAAACTGTTGTATT 57.909 32.000 5.01 0.00 45.07 1.89
750 779 8.211116 TCGGAAGTTCAAAAACTGTTGTATTA 57.789 30.769 5.01 0.00 45.07 0.98
751 780 8.842280 TCGGAAGTTCAAAAACTGTTGTATTAT 58.158 29.630 5.01 0.00 45.07 1.28
793 822 7.900782 AAGTGTAAACTAGATAATTGCGTGT 57.099 32.000 0.00 0.00 0.00 4.49
794 823 7.900782 AGTGTAAACTAGATAATTGCGTGTT 57.099 32.000 0.00 0.00 0.00 3.32
795 824 7.739295 AGTGTAAACTAGATAATTGCGTGTTG 58.261 34.615 0.00 0.00 0.00 3.33
796 825 6.464834 GTGTAAACTAGATAATTGCGTGTTGC 59.535 38.462 0.00 0.00 46.70 4.17
805 834 3.023950 GCGTGTTGCAACGGGTTA 58.976 55.556 23.79 3.67 45.45 2.85
806 835 1.082366 GCGTGTTGCAACGGGTTAG 60.082 57.895 23.79 12.04 45.45 2.34
807 836 1.500512 GCGTGTTGCAACGGGTTAGA 61.501 55.000 23.79 2.11 45.45 2.10
808 837 0.938713 CGTGTTGCAACGGGTTAGAA 59.061 50.000 23.79 1.33 39.89 2.10
809 838 1.533731 CGTGTTGCAACGGGTTAGAAT 59.466 47.619 23.79 0.00 39.89 2.40
810 839 2.737783 CGTGTTGCAACGGGTTAGAATA 59.262 45.455 23.79 0.00 39.89 1.75
811 840 3.372822 CGTGTTGCAACGGGTTAGAATAT 59.627 43.478 23.79 0.00 39.89 1.28
812 841 4.142773 CGTGTTGCAACGGGTTAGAATATT 60.143 41.667 23.79 0.00 39.89 1.28
813 842 5.329493 GTGTTGCAACGGGTTAGAATATTC 58.671 41.667 23.79 7.41 0.00 1.75
814 843 5.123344 GTGTTGCAACGGGTTAGAATATTCT 59.877 40.000 23.79 21.28 41.24 2.40
815 844 6.314400 GTGTTGCAACGGGTTAGAATATTCTA 59.686 38.462 23.79 19.23 38.70 2.10
816 845 6.879993 TGTTGCAACGGGTTAGAATATTCTAA 59.120 34.615 26.90 26.90 44.93 2.10
841 870 9.631257 AATATGTTCATGTGATTTATCTGGTCA 57.369 29.630 0.00 0.00 0.00 4.02
842 871 9.803507 ATATGTTCATGTGATTTATCTGGTCAT 57.196 29.630 0.00 0.00 0.00 3.06
843 872 7.324354 TGTTCATGTGATTTATCTGGTCATG 57.676 36.000 0.00 0.00 34.46 3.07
844 873 6.885918 TGTTCATGTGATTTATCTGGTCATGT 59.114 34.615 0.00 0.00 34.67 3.21
845 874 7.394077 TGTTCATGTGATTTATCTGGTCATGTT 59.606 33.333 0.00 0.00 34.67 2.71
846 875 8.892723 GTTCATGTGATTTATCTGGTCATGTTA 58.107 33.333 0.00 0.00 34.67 2.41
847 876 9.460019 TTCATGTGATTTATCTGGTCATGTTAA 57.540 29.630 0.00 0.00 34.67 2.01
848 877 9.631257 TCATGTGATTTATCTGGTCATGTTAAT 57.369 29.630 0.00 0.00 34.67 1.40
851 880 9.898152 TGTGATTTATCTGGTCATGTTAATACA 57.102 29.630 0.00 0.00 38.95 2.29
862 891 8.769891 TGGTCATGTTAATACAATTATGTAGCG 58.230 33.333 0.00 0.00 44.85 4.26
863 892 8.984764 GGTCATGTTAATACAATTATGTAGCGA 58.015 33.333 0.00 0.00 44.85 4.93
865 894 9.974980 TCATGTTAATACAATTATGTAGCGAGA 57.025 29.630 0.00 0.00 44.85 4.04
868 897 9.124807 TGTTAATACAATTATGTAGCGAGATCG 57.875 33.333 0.00 0.00 44.85 3.69
869 898 9.338291 GTTAATACAATTATGTAGCGAGATCGA 57.662 33.333 6.39 0.00 44.85 3.59
870 899 9.556030 TTAATACAATTATGTAGCGAGATCGAG 57.444 33.333 6.39 0.00 44.85 4.04
871 900 5.690997 ACAATTATGTAGCGAGATCGAGA 57.309 39.130 6.39 0.00 38.87 4.04
872 901 6.073327 ACAATTATGTAGCGAGATCGAGAA 57.927 37.500 6.39 0.00 38.87 2.87
873 902 6.146216 ACAATTATGTAGCGAGATCGAGAAG 58.854 40.000 6.39 0.00 38.87 2.85
951 981 3.459969 AGAGTCTCCCCATCCAATTTACC 59.540 47.826 0.00 0.00 0.00 2.85
981 1013 1.084370 CCTCCGTCGATCCTTGCAAC 61.084 60.000 0.00 0.00 0.00 4.17
991 1024 2.452600 TCCTTGCAACCTTTCCTGTT 57.547 45.000 0.00 0.00 0.00 3.16
998 1031 1.106944 AACCTTTCCTGTTGTGCCCG 61.107 55.000 0.00 0.00 0.00 6.13
1324 1360 1.224592 GGTGATTGGGAGCGGATGT 59.775 57.895 0.00 0.00 0.00 3.06
1417 1453 6.054295 GCTGATGAGGTAGTCTTTGATCATT 58.946 40.000 0.00 0.00 0.00 2.57
1491 1527 3.642848 AGATTGTGGGCAAACTGTTGAAT 59.357 39.130 0.00 0.00 36.55 2.57
1521 1557 3.434167 GCAAAATCCTGGAGATGAGGCTA 60.434 47.826 1.52 0.00 34.56 3.93
1638 1675 4.618460 GCAAGACAAGTCTATCTGGTTCGA 60.618 45.833 2.72 0.00 39.39 3.71
1666 1703 0.108945 GTTGGCCAGATTCTGCAAGC 60.109 55.000 5.11 6.51 0.00 4.01
1754 1791 0.742505 TTCGGTGACTGGCTATACGG 59.257 55.000 0.00 0.00 0.00 4.02
1798 1835 0.323629 CGAACCAAACCCTAGCAGGA 59.676 55.000 4.00 0.00 37.67 3.86
1859 1896 2.365105 TCCGGTGGATCCTGGGAC 60.365 66.667 14.23 1.97 33.11 4.46
1914 1951 0.175073 CCAGCCCGACTAAGGTACAC 59.825 60.000 0.00 0.00 0.00 2.90
1923 1960 3.730061 CGACTAAGGTACACCGTGATCAC 60.730 52.174 16.21 16.21 42.08 3.06
1979 2016 3.535239 ACATGGATATAGCTGGGGATGT 58.465 45.455 0.00 0.00 0.00 3.06
2091 2128 3.425359 GCAGTACGTCTAGTAGCAAACGA 60.425 47.826 14.69 0.00 38.44 3.85
2117 2154 7.611467 AGCCAAATTGTCACAAGATCATACTAA 59.389 33.333 0.00 0.00 0.00 2.24
2477 2585 2.054799 AGAAGTGGTGGTTTGGCTCTA 58.945 47.619 0.00 0.00 0.00 2.43
2501 2609 1.069513 TGGGATGAGTCGTTGAACGTT 59.930 47.619 17.86 0.00 43.14 3.99
2504 2612 3.311106 GGATGAGTCGTTGAACGTTACA 58.689 45.455 17.86 14.90 43.14 2.41
2752 2860 1.271108 TGAAGCTCAAATGGTGGCGTA 60.271 47.619 0.00 0.00 0.00 4.42
2801 2909 2.273179 GGACCTGGGTTTTTCGGGC 61.273 63.158 0.00 0.00 34.06 6.13
2804 2912 0.826256 ACCTGGGTTTTTCGGGCTTC 60.826 55.000 0.00 0.00 34.06 3.86
2828 2936 4.515944 CCGTTTACCTACAACAATGGACAA 59.484 41.667 0.00 0.00 0.00 3.18
2839 2947 0.327924 AATGGACAACAGGCGGATCA 59.672 50.000 0.00 0.00 0.00 2.92
2855 2963 2.431057 GGATCAGAATGTACAGGTCCGT 59.569 50.000 0.33 0.00 37.40 4.69
2856 2964 3.118738 GGATCAGAATGTACAGGTCCGTT 60.119 47.826 0.33 0.00 37.40 4.44
2861 2969 7.032242 TCAGAATGTACAGGTCCGTTTGGAT 62.032 44.000 0.33 0.00 41.99 3.41
2981 3090 1.075659 GGAGGGCCAGCAAGAAGTT 59.924 57.895 6.18 0.00 0.00 2.66
2987 3096 1.202188 GGCCAGCAAGAAGTTAATCGC 60.202 52.381 0.00 0.00 0.00 4.58
3025 3134 4.036262 GCGCTATGAAATTATGTGGGAACA 59.964 41.667 0.00 0.00 38.70 3.18
3029 3138 6.491403 GCTATGAAATTATGTGGGAACAGGAT 59.509 38.462 0.00 0.00 44.46 3.24
3045 3154 1.787676 AGGATCATACCCTACCCGAGT 59.212 52.381 0.00 0.00 30.92 4.18
3085 3194 0.764890 AGACACAAACAGCCTGGCTA 59.235 50.000 22.90 0.00 36.40 3.93
3090 3199 1.142870 ACAAACAGCCTGGCTACTTGA 59.857 47.619 32.39 0.00 36.40 3.02
3107 3216 0.036732 TGAGCTCGGTGGCAAATTCT 59.963 50.000 9.64 0.00 34.17 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.582998 ATCAATTAAGCTGCCAGCCTA 57.417 42.857 14.25 1.00 43.77 3.93
285 286 4.445452 AGTTGGCAGCTTAATTGATGTG 57.555 40.909 0.00 0.00 0.00 3.21
575 604 0.672342 ACGGCTCAGACTGTTTACGT 59.328 50.000 1.59 6.85 0.00 3.57
576 605 1.335597 TGACGGCTCAGACTGTTTACG 60.336 52.381 1.59 6.25 0.00 3.18
577 606 2.030185 TCTGACGGCTCAGACTGTTTAC 60.030 50.000 11.13 0.00 46.79 2.01
578 607 2.235891 TCTGACGGCTCAGACTGTTTA 58.764 47.619 11.13 0.00 46.79 2.01
579 608 1.040646 TCTGACGGCTCAGACTGTTT 58.959 50.000 11.13 0.00 46.79 2.83
580 609 2.733590 TCTGACGGCTCAGACTGTT 58.266 52.632 11.13 0.00 46.79 3.16
581 610 4.502187 TCTGACGGCTCAGACTGT 57.498 55.556 11.13 0.00 46.79 3.55
586 615 0.671251 GGGTAGATCTGACGGCTCAG 59.329 60.000 5.18 7.40 44.94 3.35
587 616 0.033503 TGGGTAGATCTGACGGCTCA 60.034 55.000 5.18 0.00 0.00 4.26
588 617 1.333177 ATGGGTAGATCTGACGGCTC 58.667 55.000 5.18 0.00 0.00 4.70
589 618 2.677542 TATGGGTAGATCTGACGGCT 57.322 50.000 5.18 0.00 0.00 5.52
590 619 2.159366 CGATATGGGTAGATCTGACGGC 60.159 54.545 5.18 0.00 0.00 5.68
591 620 3.127203 GTCGATATGGGTAGATCTGACGG 59.873 52.174 5.18 0.00 0.00 4.79
592 621 3.181519 CGTCGATATGGGTAGATCTGACG 60.182 52.174 5.18 8.66 40.82 4.35
593 622 3.127203 CCGTCGATATGGGTAGATCTGAC 59.873 52.174 5.18 0.00 31.25 3.51
594 623 3.344515 CCGTCGATATGGGTAGATCTGA 58.655 50.000 5.18 0.00 0.00 3.27
595 624 2.159366 GCCGTCGATATGGGTAGATCTG 60.159 54.545 5.18 0.00 31.75 2.90
596 625 2.093106 GCCGTCGATATGGGTAGATCT 58.907 52.381 0.00 0.00 31.75 2.75
597 626 1.134560 GGCCGTCGATATGGGTAGATC 59.865 57.143 0.00 0.00 31.75 2.75
598 627 1.183549 GGCCGTCGATATGGGTAGAT 58.816 55.000 0.00 0.00 31.75 1.98
599 628 0.178984 TGGCCGTCGATATGGGTAGA 60.179 55.000 0.00 0.00 31.75 2.59
600 629 0.038526 GTGGCCGTCGATATGGGTAG 60.039 60.000 0.00 0.00 31.75 3.18
601 630 1.466025 GGTGGCCGTCGATATGGGTA 61.466 60.000 0.00 0.00 31.75 3.69
602 631 2.803817 GGTGGCCGTCGATATGGGT 61.804 63.158 0.00 0.00 31.75 4.51
603 632 2.030562 GGTGGCCGTCGATATGGG 59.969 66.667 0.00 0.00 31.75 4.00
604 633 0.179056 AAAGGTGGCCGTCGATATGG 60.179 55.000 0.00 0.00 34.56 2.74
605 634 1.202533 AGAAAGGTGGCCGTCGATATG 60.203 52.381 0.00 0.00 0.00 1.78
606 635 1.120530 AGAAAGGTGGCCGTCGATAT 58.879 50.000 0.00 0.00 0.00 1.63
607 636 0.899720 AAGAAAGGTGGCCGTCGATA 59.100 50.000 0.00 0.00 0.00 2.92
608 637 0.036306 AAAGAAAGGTGGCCGTCGAT 59.964 50.000 0.00 0.00 0.00 3.59
609 638 0.179040 AAAAGAAAGGTGGCCGTCGA 60.179 50.000 0.00 0.00 0.00 4.20
610 639 0.040425 CAAAAGAAAGGTGGCCGTCG 60.040 55.000 0.00 0.00 0.00 5.12
611 640 1.314730 TCAAAAGAAAGGTGGCCGTC 58.685 50.000 0.00 0.00 0.00 4.79
612 641 1.995376 ATCAAAAGAAAGGTGGCCGT 58.005 45.000 0.00 0.00 0.00 5.68
613 642 2.295909 TGAATCAAAAGAAAGGTGGCCG 59.704 45.455 0.00 0.00 0.00 6.13
614 643 3.321968 AGTGAATCAAAAGAAAGGTGGCC 59.678 43.478 0.00 0.00 0.00 5.36
615 644 4.550422 GAGTGAATCAAAAGAAAGGTGGC 58.450 43.478 0.00 0.00 0.00 5.01
616 645 4.829492 AGGAGTGAATCAAAAGAAAGGTGG 59.171 41.667 0.00 0.00 0.00 4.61
617 646 6.264067 AGAAGGAGTGAATCAAAAGAAAGGTG 59.736 38.462 0.00 0.00 0.00 4.00
618 647 6.368805 AGAAGGAGTGAATCAAAAGAAAGGT 58.631 36.000 0.00 0.00 0.00 3.50
619 648 6.890979 AGAAGGAGTGAATCAAAAGAAAGG 57.109 37.500 0.00 0.00 0.00 3.11
620 649 9.061435 ACTAAGAAGGAGTGAATCAAAAGAAAG 57.939 33.333 0.00 0.00 0.00 2.62
621 650 8.980481 ACTAAGAAGGAGTGAATCAAAAGAAA 57.020 30.769 0.00 0.00 0.00 2.52
622 651 7.661847 GGACTAAGAAGGAGTGAATCAAAAGAA 59.338 37.037 0.00 0.00 0.00 2.52
623 652 7.162082 GGACTAAGAAGGAGTGAATCAAAAGA 58.838 38.462 0.00 0.00 0.00 2.52
624 653 6.091441 CGGACTAAGAAGGAGTGAATCAAAAG 59.909 42.308 0.00 0.00 0.00 2.27
625 654 5.932303 CGGACTAAGAAGGAGTGAATCAAAA 59.068 40.000 0.00 0.00 0.00 2.44
626 655 5.011738 ACGGACTAAGAAGGAGTGAATCAAA 59.988 40.000 0.00 0.00 0.00 2.69
627 656 4.527038 ACGGACTAAGAAGGAGTGAATCAA 59.473 41.667 0.00 0.00 0.00 2.57
628 657 4.087182 ACGGACTAAGAAGGAGTGAATCA 58.913 43.478 0.00 0.00 0.00 2.57
629 658 4.722361 ACGGACTAAGAAGGAGTGAATC 57.278 45.455 0.00 0.00 0.00 2.52
630 659 4.322801 CCAACGGACTAAGAAGGAGTGAAT 60.323 45.833 0.00 0.00 0.00 2.57
631 660 3.006537 CCAACGGACTAAGAAGGAGTGAA 59.993 47.826 0.00 0.00 0.00 3.18
632 661 2.561419 CCAACGGACTAAGAAGGAGTGA 59.439 50.000 0.00 0.00 0.00 3.41
633 662 2.561419 TCCAACGGACTAAGAAGGAGTG 59.439 50.000 0.00 0.00 0.00 3.51
634 663 2.885616 TCCAACGGACTAAGAAGGAGT 58.114 47.619 0.00 0.00 0.00 3.85
635 664 3.702045 AGATCCAACGGACTAAGAAGGAG 59.298 47.826 0.00 0.00 32.98 3.69
636 665 3.447586 CAGATCCAACGGACTAAGAAGGA 59.552 47.826 0.00 0.00 32.98 3.36
637 666 3.786635 CAGATCCAACGGACTAAGAAGG 58.213 50.000 0.00 0.00 32.98 3.46
638 667 3.190874 GCAGATCCAACGGACTAAGAAG 58.809 50.000 0.00 0.00 32.98 2.85
639 668 2.565391 TGCAGATCCAACGGACTAAGAA 59.435 45.455 0.00 0.00 32.98 2.52
640 669 2.166459 CTGCAGATCCAACGGACTAAGA 59.834 50.000 8.42 0.00 32.98 2.10
641 670 2.166459 TCTGCAGATCCAACGGACTAAG 59.834 50.000 13.74 0.00 32.98 2.18
642 671 2.176045 TCTGCAGATCCAACGGACTAA 58.824 47.619 13.74 0.00 32.98 2.24
643 672 1.847328 TCTGCAGATCCAACGGACTA 58.153 50.000 13.74 0.00 32.98 2.59
644 673 0.976641 TTCTGCAGATCCAACGGACT 59.023 50.000 19.04 0.00 32.98 3.85
645 674 1.936547 GATTCTGCAGATCCAACGGAC 59.063 52.381 19.04 0.00 32.98 4.79
646 675 1.471501 CGATTCTGCAGATCCAACGGA 60.472 52.381 19.04 0.00 35.55 4.69
647 676 0.933097 CGATTCTGCAGATCCAACGG 59.067 55.000 19.04 0.00 0.00 4.44
648 677 1.857217 CTCGATTCTGCAGATCCAACG 59.143 52.381 19.04 13.42 0.00 4.10
649 678 2.159043 TCCTCGATTCTGCAGATCCAAC 60.159 50.000 19.04 0.23 0.00 3.77
650 679 2.110578 TCCTCGATTCTGCAGATCCAA 58.889 47.619 19.04 2.08 0.00 3.53
651 680 1.410517 GTCCTCGATTCTGCAGATCCA 59.589 52.381 19.04 2.52 0.00 3.41
652 681 1.686052 AGTCCTCGATTCTGCAGATCC 59.314 52.381 19.04 11.31 0.00 3.36
653 682 2.360483 TGAGTCCTCGATTCTGCAGATC 59.640 50.000 19.04 15.37 0.00 2.75
654 683 2.100584 GTGAGTCCTCGATTCTGCAGAT 59.899 50.000 19.04 7.83 0.00 2.90
655 684 1.474478 GTGAGTCCTCGATTCTGCAGA 59.526 52.381 13.74 13.74 0.00 4.26
656 685 1.203287 TGTGAGTCCTCGATTCTGCAG 59.797 52.381 7.63 7.63 0.00 4.41
657 686 1.067565 GTGTGAGTCCTCGATTCTGCA 60.068 52.381 0.00 0.00 0.00 4.41
658 687 1.203523 AGTGTGAGTCCTCGATTCTGC 59.796 52.381 0.00 0.00 0.00 4.26
659 688 4.909696 ATAGTGTGAGTCCTCGATTCTG 57.090 45.455 0.00 0.00 0.00 3.02
660 689 5.923733 AAATAGTGTGAGTCCTCGATTCT 57.076 39.130 0.00 0.00 0.00 2.40
661 690 7.222999 CCTTAAAATAGTGTGAGTCCTCGATTC 59.777 40.741 0.00 0.00 0.00 2.52
662 691 7.042335 CCTTAAAATAGTGTGAGTCCTCGATT 58.958 38.462 0.00 0.00 0.00 3.34
663 692 6.154706 ACCTTAAAATAGTGTGAGTCCTCGAT 59.845 38.462 0.00 0.00 0.00 3.59
664 693 5.479375 ACCTTAAAATAGTGTGAGTCCTCGA 59.521 40.000 0.00 0.00 0.00 4.04
665 694 5.577164 CACCTTAAAATAGTGTGAGTCCTCG 59.423 44.000 0.00 0.00 0.00 4.63
666 695 6.698380 TCACCTTAAAATAGTGTGAGTCCTC 58.302 40.000 0.00 0.00 32.56 3.71
667 696 6.681729 TCACCTTAAAATAGTGTGAGTCCT 57.318 37.500 0.00 0.00 32.56 3.85
668 697 6.935208 ACTTCACCTTAAAATAGTGTGAGTCC 59.065 38.462 0.00 0.00 37.27 3.85
669 698 7.964604 ACTTCACCTTAAAATAGTGTGAGTC 57.035 36.000 0.00 0.00 37.27 3.36
670 699 8.621286 CAAACTTCACCTTAAAATAGTGTGAGT 58.379 33.333 0.00 0.00 37.27 3.41
671 700 8.076178 CCAAACTTCACCTTAAAATAGTGTGAG 58.924 37.037 0.00 0.00 37.27 3.51
672 701 7.469456 GCCAAACTTCACCTTAAAATAGTGTGA 60.469 37.037 0.00 0.00 34.38 3.58
673 702 6.640907 GCCAAACTTCACCTTAAAATAGTGTG 59.359 38.462 0.00 0.00 33.21 3.82
674 703 6.514376 CGCCAAACTTCACCTTAAAATAGTGT 60.514 38.462 0.00 0.00 33.21 3.55
675 704 5.856455 CGCCAAACTTCACCTTAAAATAGTG 59.144 40.000 0.00 0.00 0.00 2.74
676 705 5.048294 CCGCCAAACTTCACCTTAAAATAGT 60.048 40.000 0.00 0.00 0.00 2.12
677 706 5.399013 CCGCCAAACTTCACCTTAAAATAG 58.601 41.667 0.00 0.00 0.00 1.73
678 707 4.218852 CCCGCCAAACTTCACCTTAAAATA 59.781 41.667 0.00 0.00 0.00 1.40
679 708 3.006430 CCCGCCAAACTTCACCTTAAAAT 59.994 43.478 0.00 0.00 0.00 1.82
680 709 2.362717 CCCGCCAAACTTCACCTTAAAA 59.637 45.455 0.00 0.00 0.00 1.52
681 710 1.957877 CCCGCCAAACTTCACCTTAAA 59.042 47.619 0.00 0.00 0.00 1.52
682 711 1.143277 TCCCGCCAAACTTCACCTTAA 59.857 47.619 0.00 0.00 0.00 1.85
683 712 0.766131 TCCCGCCAAACTTCACCTTA 59.234 50.000 0.00 0.00 0.00 2.69
684 713 0.106419 TTCCCGCCAAACTTCACCTT 60.106 50.000 0.00 0.00 0.00 3.50
685 714 0.822121 GTTCCCGCCAAACTTCACCT 60.822 55.000 0.00 0.00 0.00 4.00
686 715 1.104577 TGTTCCCGCCAAACTTCACC 61.105 55.000 0.00 0.00 0.00 4.02
687 716 0.030235 GTGTTCCCGCCAAACTTCAC 59.970 55.000 0.00 0.00 0.00 3.18
688 717 0.106918 AGTGTTCCCGCCAAACTTCA 60.107 50.000 0.00 0.00 0.00 3.02
689 718 0.310854 CAGTGTTCCCGCCAAACTTC 59.689 55.000 0.00 0.00 0.00 3.01
690 719 0.395173 ACAGTGTTCCCGCCAAACTT 60.395 50.000 0.00 0.00 0.00 2.66
691 720 0.470766 TACAGTGTTCCCGCCAAACT 59.529 50.000 0.00 0.00 0.00 2.66
692 721 0.589708 GTACAGTGTTCCCGCCAAAC 59.410 55.000 0.00 0.00 0.00 2.93
693 722 0.180642 TGTACAGTGTTCCCGCCAAA 59.819 50.000 0.00 0.00 0.00 3.28
694 723 0.398696 ATGTACAGTGTTCCCGCCAA 59.601 50.000 0.00 0.00 0.00 4.52
695 724 0.321210 CATGTACAGTGTTCCCGCCA 60.321 55.000 0.00 0.00 0.00 5.69
696 725 0.321298 ACATGTACAGTGTTCCCGCC 60.321 55.000 0.00 0.00 0.00 6.13
697 726 0.796312 CACATGTACAGTGTTCCCGC 59.204 55.000 0.00 0.00 32.44 6.13
698 727 1.270625 ACCACATGTACAGTGTTCCCG 60.271 52.381 18.15 9.33 35.24 5.14
699 728 2.151202 CACCACATGTACAGTGTTCCC 58.849 52.381 18.15 0.00 35.24 3.97
700 729 2.151202 CCACCACATGTACAGTGTTCC 58.849 52.381 18.15 0.00 35.24 3.62
701 730 2.846193 ACCACCACATGTACAGTGTTC 58.154 47.619 18.15 0.00 35.24 3.18
702 731 4.425180 TTACCACCACATGTACAGTGTT 57.575 40.909 18.15 9.14 35.24 3.32
703 732 4.425180 TTTACCACCACATGTACAGTGT 57.575 40.909 18.15 0.00 35.24 3.55
704 733 4.092821 CGATTTACCACCACATGTACAGTG 59.907 45.833 14.75 14.75 36.76 3.66
705 734 4.250464 CGATTTACCACCACATGTACAGT 58.750 43.478 0.00 0.00 0.00 3.55
706 735 3.621268 CCGATTTACCACCACATGTACAG 59.379 47.826 0.00 0.00 0.00 2.74
707 736 3.261137 TCCGATTTACCACCACATGTACA 59.739 43.478 0.00 0.00 0.00 2.90
708 737 3.864243 TCCGATTTACCACCACATGTAC 58.136 45.455 0.00 0.00 0.00 2.90
709 738 4.020039 ACTTCCGATTTACCACCACATGTA 60.020 41.667 0.00 0.00 0.00 2.29
710 739 3.244770 ACTTCCGATTTACCACCACATGT 60.245 43.478 0.00 0.00 0.00 3.21
711 740 3.343617 ACTTCCGATTTACCACCACATG 58.656 45.455 0.00 0.00 0.00 3.21
712 741 3.713826 ACTTCCGATTTACCACCACAT 57.286 42.857 0.00 0.00 0.00 3.21
713 742 3.181453 TGAACTTCCGATTTACCACCACA 60.181 43.478 0.00 0.00 0.00 4.17
714 743 3.404899 TGAACTTCCGATTTACCACCAC 58.595 45.455 0.00 0.00 0.00 4.16
715 744 3.773418 TGAACTTCCGATTTACCACCA 57.227 42.857 0.00 0.00 0.00 4.17
716 745 5.441709 TTTTGAACTTCCGATTTACCACC 57.558 39.130 0.00 0.00 0.00 4.61
717 746 6.416750 CAGTTTTTGAACTTCCGATTTACCAC 59.583 38.462 0.00 0.00 0.00 4.16
718 747 6.095720 ACAGTTTTTGAACTTCCGATTTACCA 59.904 34.615 0.00 0.00 0.00 3.25
719 748 6.500910 ACAGTTTTTGAACTTCCGATTTACC 58.499 36.000 0.00 0.00 0.00 2.85
720 749 7.486870 ACAACAGTTTTTGAACTTCCGATTTAC 59.513 33.333 0.00 0.00 0.00 2.01
721 750 7.540299 ACAACAGTTTTTGAACTTCCGATTTA 58.460 30.769 0.00 0.00 0.00 1.40
722 751 6.394809 ACAACAGTTTTTGAACTTCCGATTT 58.605 32.000 0.00 0.00 0.00 2.17
723 752 5.961272 ACAACAGTTTTTGAACTTCCGATT 58.039 33.333 0.00 0.00 0.00 3.34
724 753 5.576447 ACAACAGTTTTTGAACTTCCGAT 57.424 34.783 0.00 0.00 0.00 4.18
725 754 6.687081 ATACAACAGTTTTTGAACTTCCGA 57.313 33.333 0.00 0.00 0.00 4.55
767 796 9.426837 ACACGCAATTATCTAGTTTACACTTAA 57.573 29.630 0.00 0.00 34.06 1.85
768 797 8.991243 ACACGCAATTATCTAGTTTACACTTA 57.009 30.769 0.00 0.00 34.06 2.24
769 798 7.900782 ACACGCAATTATCTAGTTTACACTT 57.099 32.000 0.00 0.00 34.06 3.16
770 799 7.623506 GCAACACGCAATTATCTAGTTTACACT 60.624 37.037 0.00 0.00 41.79 3.55
771 800 6.464834 GCAACACGCAATTATCTAGTTTACAC 59.535 38.462 0.00 0.00 41.79 2.90
772 801 6.539324 GCAACACGCAATTATCTAGTTTACA 58.461 36.000 0.00 0.00 41.79 2.41
788 817 1.082366 CTAACCCGTTGCAACACGC 60.082 57.895 28.01 2.38 38.93 5.34
789 818 0.938713 TTCTAACCCGTTGCAACACG 59.061 50.000 28.01 18.88 40.02 4.49
790 819 4.957759 ATATTCTAACCCGTTGCAACAC 57.042 40.909 28.01 4.26 0.00 3.32
791 820 5.250200 AGAATATTCTAACCCGTTGCAACA 58.750 37.500 28.01 8.32 35.34 3.33
792 821 5.813080 AGAATATTCTAACCCGTTGCAAC 57.187 39.130 19.89 19.89 35.34 4.17
815 844 9.631257 TGACCAGATAAATCACATGAACATATT 57.369 29.630 0.00 0.00 0.00 1.28
816 845 9.803507 ATGACCAGATAAATCACATGAACATAT 57.196 29.630 0.00 0.00 0.00 1.78
817 846 9.059260 CATGACCAGATAAATCACATGAACATA 57.941 33.333 0.00 0.00 36.70 2.29
818 847 7.558807 ACATGACCAGATAAATCACATGAACAT 59.441 33.333 0.00 0.00 37.59 2.71
819 848 6.885918 ACATGACCAGATAAATCACATGAACA 59.114 34.615 0.00 0.00 37.59 3.18
820 849 7.325660 ACATGACCAGATAAATCACATGAAC 57.674 36.000 0.00 0.00 37.59 3.18
821 850 7.943079 AACATGACCAGATAAATCACATGAA 57.057 32.000 0.00 0.00 37.59 2.57
822 851 9.631257 ATTAACATGACCAGATAAATCACATGA 57.369 29.630 0.00 0.00 37.59 3.07
825 854 9.898152 TGTATTAACATGACCAGATAAATCACA 57.102 29.630 0.00 0.00 0.00 3.58
836 865 8.769891 CGCTACATAATTGTATTAACATGACCA 58.230 33.333 0.00 0.00 37.68 4.02
837 866 8.984764 TCGCTACATAATTGTATTAACATGACC 58.015 33.333 0.00 0.00 37.68 4.02
839 868 9.974980 TCTCGCTACATAATTGTATTAACATGA 57.025 29.630 0.00 0.00 37.68 3.07
842 871 9.124807 CGATCTCGCTACATAATTGTATTAACA 57.875 33.333 0.00 0.00 37.68 2.41
843 872 9.338291 TCGATCTCGCTACATAATTGTATTAAC 57.662 33.333 0.00 0.00 36.59 2.01
844 873 9.556030 CTCGATCTCGCTACATAATTGTATTAA 57.444 33.333 0.00 0.00 36.59 1.40
845 874 8.943002 TCTCGATCTCGCTACATAATTGTATTA 58.057 33.333 0.00 0.00 36.59 0.98
846 875 7.817641 TCTCGATCTCGCTACATAATTGTATT 58.182 34.615 0.00 0.00 36.59 1.89
847 876 7.379098 TCTCGATCTCGCTACATAATTGTAT 57.621 36.000 0.00 0.00 36.59 2.29
848 877 6.796705 TCTCGATCTCGCTACATAATTGTA 57.203 37.500 0.00 0.00 36.96 2.41
849 878 5.690997 TCTCGATCTCGCTACATAATTGT 57.309 39.130 0.00 0.00 38.37 2.71
850 879 6.304445 GTCTTCTCGATCTCGCTACATAATTG 59.696 42.308 0.00 0.00 39.60 2.32
851 880 6.205853 AGTCTTCTCGATCTCGCTACATAATT 59.794 38.462 0.00 0.00 39.60 1.40
852 881 5.703592 AGTCTTCTCGATCTCGCTACATAAT 59.296 40.000 0.00 0.00 39.60 1.28
853 882 5.057819 AGTCTTCTCGATCTCGCTACATAA 58.942 41.667 0.00 0.00 39.60 1.90
854 883 4.633175 AGTCTTCTCGATCTCGCTACATA 58.367 43.478 0.00 0.00 39.60 2.29
855 884 3.472652 AGTCTTCTCGATCTCGCTACAT 58.527 45.455 0.00 0.00 39.60 2.29
856 885 2.867368 GAGTCTTCTCGATCTCGCTACA 59.133 50.000 0.00 0.00 39.60 2.74
857 886 2.222445 GGAGTCTTCTCGATCTCGCTAC 59.778 54.545 0.00 0.00 41.26 3.58
858 887 2.485903 GGAGTCTTCTCGATCTCGCTA 58.514 52.381 0.00 0.00 41.26 4.26
859 888 1.305201 GGAGTCTTCTCGATCTCGCT 58.695 55.000 0.00 0.00 41.26 4.93
860 889 0.309612 GGGAGTCTTCTCGATCTCGC 59.690 60.000 0.00 0.00 41.26 5.03
861 890 0.948678 GGGGAGTCTTCTCGATCTCG 59.051 60.000 0.00 0.00 41.26 4.04
862 891 2.358322 AGGGGAGTCTTCTCGATCTC 57.642 55.000 0.00 0.00 41.26 2.75
863 892 2.485835 CGTAGGGGAGTCTTCTCGATCT 60.486 54.545 0.00 0.00 41.26 2.75
864 893 1.874872 CGTAGGGGAGTCTTCTCGATC 59.125 57.143 0.00 0.00 41.26 3.69
865 894 1.970092 CGTAGGGGAGTCTTCTCGAT 58.030 55.000 0.00 0.00 41.26 3.59
866 895 0.747283 GCGTAGGGGAGTCTTCTCGA 60.747 60.000 0.00 0.00 41.26 4.04
867 896 0.748729 AGCGTAGGGGAGTCTTCTCG 60.749 60.000 0.00 0.00 41.26 4.04
868 897 1.026584 GAGCGTAGGGGAGTCTTCTC 58.973 60.000 0.00 0.00 39.76 2.87
869 898 0.396001 GGAGCGTAGGGGAGTCTTCT 60.396 60.000 0.00 0.00 0.00 2.85
870 899 0.396001 AGGAGCGTAGGGGAGTCTTC 60.396 60.000 0.00 0.00 0.00 2.87
871 900 0.396001 GAGGAGCGTAGGGGAGTCTT 60.396 60.000 0.00 0.00 0.00 3.01
872 901 1.227946 GAGGAGCGTAGGGGAGTCT 59.772 63.158 0.00 0.00 0.00 3.24
873 902 2.188161 CGAGGAGCGTAGGGGAGTC 61.188 68.421 0.00 0.00 34.64 3.36
964 996 1.079405 GGTTGCAAGGATCGACGGA 60.079 57.895 0.00 0.00 0.00 4.69
981 1013 2.268076 CCGGGCACAACAGGAAAGG 61.268 63.158 0.00 0.00 0.00 3.11
1324 1360 2.436544 GCCATGGCCCATGCATCAA 61.437 57.895 27.24 0.00 40.20 2.57
1381 1417 3.074538 ACCTCATCAGCTTTGGTAAACCT 59.925 43.478 0.02 0.00 36.82 3.50
1417 1453 6.894682 TGTGAATCTGTAACCATATAGGCAA 58.105 36.000 0.00 0.00 43.14 4.52
1491 1527 1.215912 CAGGATTTTGCATGCGCCA 59.784 52.632 14.09 0.00 37.32 5.69
1521 1557 3.128845 CCGCGGGTATTGCCGTTT 61.129 61.111 20.10 0.00 38.44 3.60
1638 1675 5.374921 CAGAATCTGGCCAACTTCTCATAT 58.625 41.667 21.12 3.94 0.00 1.78
1666 1703 0.325933 TGTCCAATGAGGCCACAGAG 59.674 55.000 9.30 3.39 37.29 3.35
1914 1951 0.812811 CCAGCTCCATGTGATCACGG 60.813 60.000 20.54 16.14 0.00 4.94
1923 1960 0.742281 CCTCACGTTCCAGCTCCATG 60.742 60.000 0.00 0.00 0.00 3.66
2035 2072 0.466124 GTCTCCCCTTCATCCTTCCG 59.534 60.000 0.00 0.00 0.00 4.30
2091 2128 5.948162 AGTATGATCTTGTGACAATTTGGCT 59.052 36.000 3.47 0.00 0.00 4.75
2117 2154 0.320771 GGCCGCCGATATCTCATTGT 60.321 55.000 0.34 0.00 0.00 2.71
2477 2585 3.188460 CGTTCAACGACTCATCCCAAAAT 59.812 43.478 3.01 0.00 46.05 1.82
2501 2609 3.525537 GCTGCAAGAATCTAGCACTGTA 58.474 45.455 0.00 0.00 34.07 2.74
2504 2612 1.741732 CGGCTGCAAGAATCTAGCACT 60.742 52.381 0.50 0.00 37.89 4.40
2752 2860 3.635591 CACCTTTCCAAGCAATCCCTAT 58.364 45.455 0.00 0.00 0.00 2.57
2801 2909 4.155280 CCATTGTTGTAGGTAAACGGGAAG 59.845 45.833 0.00 0.00 0.00 3.46
2804 2912 3.437741 GTCCATTGTTGTAGGTAAACGGG 59.562 47.826 0.00 0.00 0.00 5.28
2807 2915 6.380095 TGTTGTCCATTGTTGTAGGTAAAC 57.620 37.500 0.00 0.00 0.00 2.01
2828 2936 1.831106 TGTACATTCTGATCCGCCTGT 59.169 47.619 0.00 0.00 0.00 4.00
2839 2947 2.635915 TCCAAACGGACCTGTACATTCT 59.364 45.455 0.00 0.00 0.00 2.40
2855 2963 1.102809 CAGCGCATGCCCTATCCAAA 61.103 55.000 13.15 0.00 44.31 3.28
2856 2964 1.526686 CAGCGCATGCCCTATCCAA 60.527 57.895 13.15 0.00 44.31 3.53
2861 2969 0.109153 ATTCATCAGCGCATGCCCTA 59.891 50.000 13.15 0.00 44.31 3.53
2996 3105 5.682862 CCACATAATTTCATAGCGCAAAGTC 59.317 40.000 11.47 0.00 0.00 3.01
3002 3111 4.036262 TGTTCCCACATAATTTCATAGCGC 59.964 41.667 0.00 0.00 0.00 5.92
3025 3134 1.787676 ACTCGGGTAGGGTATGATCCT 59.212 52.381 0.00 0.00 38.36 3.24
3029 3138 1.117150 GCAACTCGGGTAGGGTATGA 58.883 55.000 0.00 0.00 29.81 2.15
3085 3194 0.250901 ATTTGCCACCGAGCTCAAGT 60.251 50.000 15.40 7.60 0.00 3.16
3090 3199 0.326264 AGAGAATTTGCCACCGAGCT 59.674 50.000 0.00 0.00 0.00 4.09
3107 3216 2.902608 TCCTTCAGCACCTCCTTTAGA 58.097 47.619 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.