Multiple sequence alignment - TraesCS6D01G021000

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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 TraesCS6D01G021000 chr6D 100.000 3545 0 0 1 3545 8317726 8314182 0.000000e+00 6547
1 TraesCS6D01G021000 chr6D 86.910 1482 179 11 1095 2566 8348933 8347457 0.000000e+00 1648
2 TraesCS6D01G021000 chr6D 85.257 1594 212 13 985 2561 8386717 8385130 0.000000e+00 1620
3 TraesCS6D01G021000 chr6D 81.109 487 85 6 1123 1604 420569130 420568646 2.000000e-102 383
4 TraesCS6D01G021000 chr6D 80.498 482 85 7 1139 1614 408157042 408156564 9.360000e-96 361
5 TraesCS6D01G021000 chr6A 91.214 2743 174 28 764 3471 8755408 8752698 0.000000e+00 3668
6 TraesCS6D01G021000 chr6A 85.650 1561 205 12 982 2525 8792860 8791302 0.000000e+00 1624
7 TraesCS6D01G021000 chr6A 84.760 1601 212 23 950 2525 8869224 8867631 0.000000e+00 1576
8 TraesCS6D01G021000 chr6B 89.029 1668 156 16 1529 3174 16246898 16248560 0.000000e+00 2041
9 TraesCS6D01G021000 chr6B 82.191 1561 227 33 977 2525 16240775 16242296 0.000000e+00 1295
10 TraesCS6D01G021000 chr6B 80.493 487 88 6 1123 1604 633730705 633731189 2.010000e-97 366
11 TraesCS6D01G021000 chr4B 84.296 1420 194 18 1120 2523 604139333 604140739 0.000000e+00 1360
12 TraesCS6D01G021000 chr4B 81.625 1317 207 21 1224 2523 604130914 604132212 0.000000e+00 1059
13 TraesCS6D01G021000 chr4B 85.558 547 57 12 10 549 546838204 546838735 1.440000e-153 553
14 TraesCS6D01G021000 chr4B 80.153 393 55 10 3 380 635048397 635048013 4.510000e-69 272
15 TraesCS6D01G021000 chr4D 83.795 1444 202 19 1096 2520 477911940 477913370 0.000000e+00 1341
16 TraesCS6D01G021000 chr5A 83.811 803 123 5 1724 2524 680709640 680710437 0.000000e+00 756
17 TraesCS6D01G021000 chr5A 91.486 552 42 4 3 550 623218244 623217694 0.000000e+00 754
18 TraesCS6D01G021000 chr5A 85.233 623 88 4 1096 1716 680708645 680709265 3.860000e-179 638
19 TraesCS6D01G021000 chr5A 84.314 306 34 11 9 302 664630906 664630603 1.610000e-73 287
20 TraesCS6D01G021000 chr7D 90.659 546 47 3 10 551 164851545 164852090 0.000000e+00 723
21 TraesCS6D01G021000 chr2A 90.146 548 48 5 10 552 171634863 171635409 0.000000e+00 708
22 TraesCS6D01G021000 chr7A 91.205 523 39 5 8 526 725192568 725192049 0.000000e+00 704
23 TraesCS6D01G021000 chr4A 83.226 775 109 8 1401 2163 684610552 684611317 0.000000e+00 691
24 TraesCS6D01G021000 chr1A 90.650 492 41 4 62 549 561134771 561134281 0.000000e+00 649
25 TraesCS6D01G021000 chr1A 94.595 111 4 2 3 113 561134878 561134770 1.690000e-38 171
26 TraesCS6D01G021000 chr1B 89.412 340 30 2 212 548 390700322 390700658 1.180000e-114 424
27 TraesCS6D01G021000 chr3A 79.359 562 86 23 9 549 245462518 245463070 5.590000e-98 368
28 TraesCS6D01G021000 chr3B 83.077 390 49 11 3 380 826367958 826367574 4.380000e-89 339
29 TraesCS6D01G021000 chr3B 84.795 171 19 3 384 554 50419540 50419377 7.870000e-37 165
30 TraesCS6D01G021000 chr2D 93.038 158 11 0 377 534 638440233 638440076 7.650000e-57 231


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 TraesCS6D01G021000 chr6D 8314182 8317726 3544 True 6547 6547 100.0000 1 3545 1 chr6D.!!$R1 3544
1 TraesCS6D01G021000 chr6D 8347457 8348933 1476 True 1648 1648 86.9100 1095 2566 1 chr6D.!!$R2 1471
2 TraesCS6D01G021000 chr6D 8385130 8386717 1587 True 1620 1620 85.2570 985 2561 1 chr6D.!!$R3 1576
3 TraesCS6D01G021000 chr6A 8752698 8755408 2710 True 3668 3668 91.2140 764 3471 1 chr6A.!!$R1 2707
4 TraesCS6D01G021000 chr6A 8791302 8792860 1558 True 1624 1624 85.6500 982 2525 1 chr6A.!!$R2 1543
5 TraesCS6D01G021000 chr6A 8867631 8869224 1593 True 1576 1576 84.7600 950 2525 1 chr6A.!!$R3 1575
6 TraesCS6D01G021000 chr6B 16246898 16248560 1662 False 2041 2041 89.0290 1529 3174 1 chr6B.!!$F2 1645
7 TraesCS6D01G021000 chr6B 16240775 16242296 1521 False 1295 1295 82.1910 977 2525 1 chr6B.!!$F1 1548
8 TraesCS6D01G021000 chr4B 604139333 604140739 1406 False 1360 1360 84.2960 1120 2523 1 chr4B.!!$F3 1403
9 TraesCS6D01G021000 chr4B 604130914 604132212 1298 False 1059 1059 81.6250 1224 2523 1 chr4B.!!$F2 1299
10 TraesCS6D01G021000 chr4B 546838204 546838735 531 False 553 553 85.5580 10 549 1 chr4B.!!$F1 539
11 TraesCS6D01G021000 chr4D 477911940 477913370 1430 False 1341 1341 83.7950 1096 2520 1 chr4D.!!$F1 1424
12 TraesCS6D01G021000 chr5A 623217694 623218244 550 True 754 754 91.4860 3 550 1 chr5A.!!$R1 547
13 TraesCS6D01G021000 chr5A 680708645 680710437 1792 False 697 756 84.5220 1096 2524 2 chr5A.!!$F1 1428
14 TraesCS6D01G021000 chr7D 164851545 164852090 545 False 723 723 90.6590 10 551 1 chr7D.!!$F1 541
15 TraesCS6D01G021000 chr2A 171634863 171635409 546 False 708 708 90.1460 10 552 1 chr2A.!!$F1 542
16 TraesCS6D01G021000 chr7A 725192049 725192568 519 True 704 704 91.2050 8 526 1 chr7A.!!$R1 518
17 TraesCS6D01G021000 chr4A 684610552 684611317 765 False 691 691 83.2260 1401 2163 1 chr4A.!!$F1 762
18 TraesCS6D01G021000 chr1A 561134281 561134878 597 True 410 649 92.6225 3 549 2 chr1A.!!$R1 546
19 TraesCS6D01G021000 chr3A 245462518 245463070 552 False 368 368 79.3590 9 549 1 chr3A.!!$F1 540

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
710 789 0.106268 TGTGGACAAACATGGTGGCT 60.106 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2596 3156 0.034089 AGAAGGGATTTTCCGGCCTG 60.034 55.0 0.0 0.0 37.43 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
147 201 1.480212 TTGCTCGTCCTGTGGTCCAT 61.480 55.000 0.00 0.00 0.00 3.41
168 222 8.137437 GTCCATGTCCAAAATCAAGGTTATATG 58.863 37.037 0.00 0.00 0.00 1.78
292 360 9.810545 ATGCATTCTAGTTCTAGAAGAAAGTAC 57.189 33.333 21.49 10.18 39.19 2.73
375 450 4.463891 AGGGGTGCTCTTGATAAATTTGTG 59.536 41.667 0.00 0.00 0.00 3.33
536 615 4.296351 TGGGGCCCCAAATTCCTA 57.704 55.556 42.66 16.25 44.12 2.94
542 621 1.564348 GGCCCCAAATTCCTAGAGACA 59.436 52.381 0.00 0.00 0.00 3.41
552 631 0.177604 CCTAGAGACAGCCCTGCTTG 59.822 60.000 0.00 0.00 36.40 4.01
553 632 0.901124 CTAGAGACAGCCCTGCTTGT 59.099 55.000 0.00 0.00 36.40 3.16
554 633 2.103373 CTAGAGACAGCCCTGCTTGTA 58.897 52.381 0.00 0.00 36.40 2.41
555 634 1.577736 AGAGACAGCCCTGCTTGTAT 58.422 50.000 0.00 0.00 36.40 2.29
556 635 1.484240 AGAGACAGCCCTGCTTGTATC 59.516 52.381 0.00 0.00 36.40 2.24
557 636 1.208052 GAGACAGCCCTGCTTGTATCA 59.792 52.381 0.00 0.00 36.40 2.15
558 637 1.630369 AGACAGCCCTGCTTGTATCAA 59.370 47.619 0.00 0.00 36.40 2.57
559 638 1.740025 GACAGCCCTGCTTGTATCAAC 59.260 52.381 0.00 0.00 36.40 3.18
560 639 1.073763 ACAGCCCTGCTTGTATCAACA 59.926 47.619 0.00 0.00 36.40 3.33
561 640 1.470098 CAGCCCTGCTTGTATCAACAC 59.530 52.381 0.00 0.00 36.40 3.32
562 641 1.073763 AGCCCTGCTTGTATCAACACA 59.926 47.619 0.00 0.00 33.89 3.72
563 642 1.885887 GCCCTGCTTGTATCAACACAA 59.114 47.619 0.00 0.00 34.61 3.33
564 643 2.295909 GCCCTGCTTGTATCAACACAAA 59.704 45.455 0.00 0.00 37.93 2.83
565 644 3.612479 GCCCTGCTTGTATCAACACAAAG 60.612 47.826 0.00 0.00 37.93 2.77
566 645 3.569701 CCCTGCTTGTATCAACACAAAGT 59.430 43.478 0.00 0.00 37.93 2.66
567 646 4.759693 CCCTGCTTGTATCAACACAAAGTA 59.240 41.667 0.00 0.00 37.93 2.24
568 647 5.415701 CCCTGCTTGTATCAACACAAAGTAT 59.584 40.000 0.00 0.00 37.93 2.12
569 648 6.317088 CCTGCTTGTATCAACACAAAGTATG 58.683 40.000 0.00 0.00 37.93 2.39
570 649 6.072508 CCTGCTTGTATCAACACAAAGTATGT 60.073 38.462 0.00 0.00 45.34 2.29
571 650 7.270757 TGCTTGTATCAACACAAAGTATGTT 57.729 32.000 0.00 0.00 41.46 2.71
572 651 7.138081 TGCTTGTATCAACACAAAGTATGTTG 58.862 34.615 10.83 10.83 41.46 3.33
573 652 7.138736 GCTTGTATCAACACAAAGTATGTTGT 58.861 34.615 15.35 7.59 41.46 3.32
574 653 8.286800 GCTTGTATCAACACAAAGTATGTTGTA 58.713 33.333 15.35 6.83 41.46 2.41
575 654 9.594038 CTTGTATCAACACAAAGTATGTTGTAC 57.406 33.333 15.35 15.56 41.46 2.90
576 655 8.664211 TGTATCAACACAAAGTATGTTGTACA 57.336 30.769 15.35 17.25 41.46 2.90
577 656 8.552865 TGTATCAACACAAAGTATGTTGTACAC 58.447 33.333 15.35 12.20 41.46 2.90
578 657 7.801716 ATCAACACAAAGTATGTTGTACACT 57.198 32.000 15.35 0.00 41.46 3.55
579 658 7.618502 TCAACACAAAGTATGTTGTACACTT 57.381 32.000 15.35 0.00 41.46 3.16
580 659 8.046294 TCAACACAAAGTATGTTGTACACTTT 57.954 30.769 15.35 0.00 41.46 2.66
581 660 8.516234 TCAACACAAAGTATGTTGTACACTTTT 58.484 29.630 15.35 0.00 41.46 2.27
582 661 9.776158 CAACACAAAGTATGTTGTACACTTTTA 57.224 29.630 9.22 0.00 41.46 1.52
584 663 9.777575 ACACAAAGTATGTTGTACACTTTTAAC 57.222 29.630 0.00 0.00 41.46 2.01
585 664 8.939926 CACAAAGTATGTTGTACACTTTTAACG 58.060 33.333 0.00 0.00 41.46 3.18
586 665 8.667463 ACAAAGTATGTTGTACACTTTTAACGT 58.333 29.630 0.00 0.00 40.06 3.99
587 666 8.939926 CAAAGTATGTTGTACACTTTTAACGTG 58.060 33.333 0.00 0.00 39.78 4.49
588 667 8.422973 AAGTATGTTGTACACTTTTAACGTGA 57.577 30.769 8.56 0.00 36.29 4.35
589 668 7.844482 AGTATGTTGTACACTTTTAACGTGAC 58.156 34.615 8.56 3.60 36.29 3.67
590 669 6.665474 ATGTTGTACACTTTTAACGTGACA 57.335 33.333 8.56 5.86 36.29 3.58
591 670 6.477669 TGTTGTACACTTTTAACGTGACAA 57.522 33.333 8.56 10.66 36.29 3.18
592 671 7.074507 TGTTGTACACTTTTAACGTGACAAT 57.925 32.000 8.56 0.00 36.19 2.71
593 672 8.194433 TGTTGTACACTTTTAACGTGACAATA 57.806 30.769 8.56 9.36 36.19 1.90
594 673 8.115520 TGTTGTACACTTTTAACGTGACAATAC 58.884 33.333 8.56 1.78 36.19 1.89
595 674 7.176285 TGTACACTTTTAACGTGACAATACC 57.824 36.000 8.56 0.00 36.29 2.73
596 675 6.985645 TGTACACTTTTAACGTGACAATACCT 59.014 34.615 8.56 0.00 36.29 3.08
597 676 6.930667 ACACTTTTAACGTGACAATACCTT 57.069 33.333 8.56 0.00 36.29 3.50
598 677 7.324354 ACACTTTTAACGTGACAATACCTTT 57.676 32.000 8.56 0.00 36.29 3.11
599 678 8.436046 ACACTTTTAACGTGACAATACCTTTA 57.564 30.769 8.56 0.00 36.29 1.85
600 679 9.059260 ACACTTTTAACGTGACAATACCTTTAT 57.941 29.630 8.56 0.00 36.29 1.40
601 680 9.537848 CACTTTTAACGTGACAATACCTTTATC 57.462 33.333 0.00 0.00 34.35 1.75
602 681 9.498176 ACTTTTAACGTGACAATACCTTTATCT 57.502 29.630 0.00 0.00 0.00 1.98
603 682 9.755064 CTTTTAACGTGACAATACCTTTATCTG 57.245 33.333 0.00 0.00 0.00 2.90
604 683 8.836268 TTTAACGTGACAATACCTTTATCTGT 57.164 30.769 0.00 0.00 0.00 3.41
605 684 6.721571 AACGTGACAATACCTTTATCTGTG 57.278 37.500 0.00 0.00 0.00 3.66
606 685 4.630069 ACGTGACAATACCTTTATCTGTGC 59.370 41.667 0.00 0.00 0.00 4.57
607 686 4.629634 CGTGACAATACCTTTATCTGTGCA 59.370 41.667 0.00 0.00 0.00 4.57
608 687 5.445939 CGTGACAATACCTTTATCTGTGCAC 60.446 44.000 10.75 10.75 0.00 4.57
609 688 5.411361 GTGACAATACCTTTATCTGTGCACA 59.589 40.000 20.37 20.37 0.00 4.57
610 689 6.000840 TGACAATACCTTTATCTGTGCACAA 58.999 36.000 21.98 12.25 0.00 3.33
611 690 6.658816 TGACAATACCTTTATCTGTGCACAAT 59.341 34.615 21.98 18.06 0.00 2.71
612 691 7.826744 TGACAATACCTTTATCTGTGCACAATA 59.173 33.333 21.98 17.11 0.00 1.90
613 692 8.574251 ACAATACCTTTATCTGTGCACAATAA 57.426 30.769 21.98 21.20 0.00 1.40
614 693 9.189156 ACAATACCTTTATCTGTGCACAATAAT 57.811 29.630 21.98 16.13 0.00 1.28
617 696 7.466746 ACCTTTATCTGTGCACAATAATTGT 57.533 32.000 21.98 19.34 46.75 2.71
618 697 7.895759 ACCTTTATCTGTGCACAATAATTGTT 58.104 30.769 21.98 5.72 43.23 2.83
619 698 7.814107 ACCTTTATCTGTGCACAATAATTGTTG 59.186 33.333 21.98 12.84 43.23 3.33
620 699 7.201461 CCTTTATCTGTGCACAATAATTGTTGC 60.201 37.037 21.98 3.58 43.23 4.17
621 700 3.563508 TCTGTGCACAATAATTGTTGCG 58.436 40.909 21.98 6.70 43.23 4.85
622 701 2.057316 TGTGCACAATAATTGTTGCGC 58.943 42.857 19.28 17.85 43.23 6.09
623 702 1.057566 GTGCACAATAATTGTTGCGCG 59.942 47.619 18.93 0.00 43.23 6.86
624 703 1.335415 TGCACAATAATTGTTGCGCGT 60.335 42.857 18.93 0.00 43.23 6.01
625 704 2.095718 TGCACAATAATTGTTGCGCGTA 60.096 40.909 18.93 0.00 43.23 4.42
626 705 2.911723 GCACAATAATTGTTGCGCGTAA 59.088 40.909 14.17 5.23 43.23 3.18
627 706 3.241208 GCACAATAATTGTTGCGCGTAAC 60.241 43.478 29.66 29.66 43.23 2.50
628 707 4.155449 CACAATAATTGTTGCGCGTAACT 58.845 39.130 34.03 20.45 43.23 2.24
629 708 4.259734 CACAATAATTGTTGCGCGTAACTC 59.740 41.667 34.03 15.03 43.23 3.01
630 709 4.153475 ACAATAATTGTTGCGCGTAACTCT 59.847 37.500 34.03 22.33 42.22 3.24
631 710 4.939509 ATAATTGTTGCGCGTAACTCTT 57.060 36.364 34.03 27.65 0.00 2.85
632 711 3.619233 AATTGTTGCGCGTAACTCTTT 57.381 38.095 34.03 22.98 0.00 2.52
633 712 4.735662 AATTGTTGCGCGTAACTCTTTA 57.264 36.364 34.03 15.94 0.00 1.85
634 713 4.939509 ATTGTTGCGCGTAACTCTTTAT 57.060 36.364 34.03 19.00 0.00 1.40
635 714 6.411630 AATTGTTGCGCGTAACTCTTTATA 57.588 33.333 34.03 14.58 0.00 0.98
636 715 6.598753 ATTGTTGCGCGTAACTCTTTATAT 57.401 33.333 34.03 16.19 0.00 0.86
637 716 5.630896 TGTTGCGCGTAACTCTTTATATC 57.369 39.130 34.03 10.23 0.00 1.63
638 717 5.345702 TGTTGCGCGTAACTCTTTATATCT 58.654 37.500 34.03 0.00 0.00 1.98
639 718 5.808540 TGTTGCGCGTAACTCTTTATATCTT 59.191 36.000 34.03 0.00 0.00 2.40
640 719 6.311935 TGTTGCGCGTAACTCTTTATATCTTT 59.688 34.615 34.03 0.00 0.00 2.52
641 720 6.897259 TGCGCGTAACTCTTTATATCTTTT 57.103 33.333 8.43 0.00 0.00 2.27
642 721 7.990541 TGCGCGTAACTCTTTATATCTTTTA 57.009 32.000 8.43 0.00 0.00 1.52
643 722 8.410030 TGCGCGTAACTCTTTATATCTTTTAA 57.590 30.769 8.43 0.00 0.00 1.52
644 723 9.037737 TGCGCGTAACTCTTTATATCTTTTAAT 57.962 29.630 8.43 0.00 0.00 1.40
645 724 9.513554 GCGCGTAACTCTTTATATCTTTTAATC 57.486 33.333 8.43 0.00 0.00 1.75
652 731 9.905713 ACTCTTTATATCTTTTAATCACAGGCA 57.094 29.630 0.00 0.00 0.00 4.75
660 739 7.759489 TCTTTTAATCACAGGCATTACAACT 57.241 32.000 0.00 0.00 0.00 3.16
661 740 8.856153 TCTTTTAATCACAGGCATTACAACTA 57.144 30.769 0.00 0.00 0.00 2.24
662 741 8.946085 TCTTTTAATCACAGGCATTACAACTAG 58.054 33.333 0.00 0.00 0.00 2.57
663 742 7.624360 TTTAATCACAGGCATTACAACTAGG 57.376 36.000 0.00 0.00 0.00 3.02
664 743 5.435686 AATCACAGGCATTACAACTAGGA 57.564 39.130 0.00 0.00 0.00 2.94
665 744 5.636903 ATCACAGGCATTACAACTAGGAT 57.363 39.130 0.00 0.00 0.00 3.24
666 745 5.023533 TCACAGGCATTACAACTAGGATC 57.976 43.478 0.00 0.00 0.00 3.36
667 746 3.804325 CACAGGCATTACAACTAGGATCG 59.196 47.826 0.00 0.00 0.00 3.69
668 747 3.704566 ACAGGCATTACAACTAGGATCGA 59.295 43.478 0.00 0.00 0.00 3.59
669 748 4.345257 ACAGGCATTACAACTAGGATCGAT 59.655 41.667 0.00 0.00 0.00 3.59
670 749 4.687948 CAGGCATTACAACTAGGATCGATG 59.312 45.833 0.54 0.00 0.00 3.84
671 750 4.588951 AGGCATTACAACTAGGATCGATGA 59.411 41.667 0.54 0.00 0.00 2.92
672 751 5.070446 AGGCATTACAACTAGGATCGATGAA 59.930 40.000 0.54 0.00 0.00 2.57
673 752 5.406780 GGCATTACAACTAGGATCGATGAAG 59.593 44.000 0.54 0.00 0.00 3.02
674 753 5.107298 GCATTACAACTAGGATCGATGAAGC 60.107 44.000 0.54 0.00 0.00 3.86
675 754 5.592104 TTACAACTAGGATCGATGAAGCA 57.408 39.130 0.54 0.00 0.00 3.91
676 755 4.679373 ACAACTAGGATCGATGAAGCAT 57.321 40.909 0.54 0.00 0.00 3.79
677 756 5.791336 ACAACTAGGATCGATGAAGCATA 57.209 39.130 0.54 0.00 0.00 3.14
678 757 6.352016 ACAACTAGGATCGATGAAGCATAT 57.648 37.500 0.54 0.00 0.00 1.78
679 758 7.468141 ACAACTAGGATCGATGAAGCATATA 57.532 36.000 0.54 0.00 0.00 0.86
680 759 8.072321 ACAACTAGGATCGATGAAGCATATAT 57.928 34.615 0.54 0.00 0.00 0.86
681 760 8.535335 ACAACTAGGATCGATGAAGCATATATT 58.465 33.333 0.54 0.00 0.00 1.28
682 761 9.376075 CAACTAGGATCGATGAAGCATATATTT 57.624 33.333 0.54 0.00 0.00 1.40
683 762 9.950496 AACTAGGATCGATGAAGCATATATTTT 57.050 29.630 0.54 0.00 0.00 1.82
684 763 9.950496 ACTAGGATCGATGAAGCATATATTTTT 57.050 29.630 0.54 0.00 0.00 1.94
708 787 6.713762 ATAATATGTGGACAAACATGGTGG 57.286 37.500 0.00 0.00 40.93 4.61
709 788 0.968405 ATGTGGACAAACATGGTGGC 59.032 50.000 0.00 0.00 39.32 5.01
710 789 0.106268 TGTGGACAAACATGGTGGCT 60.106 50.000 0.00 0.00 0.00 4.75
711 790 0.598065 GTGGACAAACATGGTGGCTC 59.402 55.000 0.00 0.00 0.00 4.70
712 791 0.478072 TGGACAAACATGGTGGCTCT 59.522 50.000 0.00 0.00 0.00 4.09
713 792 1.702401 TGGACAAACATGGTGGCTCTA 59.298 47.619 0.00 0.00 0.00 2.43
714 793 2.308570 TGGACAAACATGGTGGCTCTAT 59.691 45.455 0.00 0.00 0.00 1.98
715 794 3.245229 TGGACAAACATGGTGGCTCTATT 60.245 43.478 0.00 0.00 0.00 1.73
716 795 3.763897 GGACAAACATGGTGGCTCTATTT 59.236 43.478 0.00 0.00 0.00 1.40
717 796 4.220602 GGACAAACATGGTGGCTCTATTTT 59.779 41.667 0.00 0.00 0.00 1.82
718 797 5.279456 GGACAAACATGGTGGCTCTATTTTT 60.279 40.000 0.00 0.00 0.00 1.94
906 1020 1.671979 ACATGTCCATGCCTCAATCG 58.328 50.000 7.18 0.00 42.39 3.34
912 1026 7.208724 CATGTCCATGCCTCAATCGAAAGAG 62.209 48.000 9.77 9.77 36.20 2.85
948 1062 7.954788 AAGAAATCTCAGTTCAGTCTACAAC 57.045 36.000 0.00 0.00 0.00 3.32
975 1089 3.908081 CATCGCCATTGCTGCCCC 61.908 66.667 0.00 0.00 34.43 5.80
1022 1144 0.674895 GCAAGGTCGACAGAGCCATT 60.675 55.000 18.91 0.00 45.43 3.16
1089 1224 0.948678 ACAAAACCCCATTGTCGTCG 59.051 50.000 0.00 0.00 36.28 5.12
1121 1271 2.041485 TGGGTTCATCTTCAGCATTGGA 59.959 45.455 0.00 0.00 0.00 3.53
1365 1518 1.447663 CGTCACGCATGATGTCCCA 60.448 57.895 0.00 0.00 37.12 4.37
1379 1532 1.355381 TGTCCCATCAATCTGCAAGGT 59.645 47.619 0.00 0.00 0.00 3.50
1468 1627 4.758251 CGCCCGTGACCTGCATCA 62.758 66.667 0.00 0.00 0.00 3.07
1530 1689 2.194056 CTCGGCCTCCCCTACGTA 59.806 66.667 0.00 0.00 0.00 3.57
1627 1787 2.613977 CCGATCAAGGACTTCAAGCAGT 60.614 50.000 0.00 0.00 0.00 4.40
1717 1877 1.138859 TCCCATCCTTCATACGCAGTG 59.861 52.381 0.00 0.00 45.73 3.66
1718 1878 1.134401 CCCATCCTTCATACGCAGTGT 60.134 52.381 0.00 0.00 45.73 3.55
1756 2283 2.331893 TTGCATTTCACGCTCGGGG 61.332 57.895 0.00 0.00 0.00 5.73
1800 2327 3.690475 TCAGCACTGATCATCAACACT 57.310 42.857 0.00 0.00 34.14 3.55
2011 2563 1.078214 AGCACCACCATCATGACCG 60.078 57.895 0.00 0.00 0.00 4.79
2015 2567 1.521457 CCACCATCATGACCGACGG 60.521 63.158 13.61 13.61 0.00 4.79
2236 2789 1.320344 TAGCGGCTGGAACTCGACAT 61.320 55.000 13.86 0.00 0.00 3.06
2256 2809 1.153168 GGATAGCATGTGTGGCGGT 60.153 57.895 0.00 0.00 36.08 5.68
2283 2836 2.097825 GTCATCAGCTGGCCATTCTTT 58.902 47.619 15.13 0.00 0.00 2.52
2447 3000 2.422231 CGCAGGAGTGGAGGGAGAG 61.422 68.421 0.00 0.00 0.00 3.20
2631 3191 3.416156 CCTTCTTTTGGAGGAGGTCTTG 58.584 50.000 0.00 0.00 45.12 3.02
2664 3233 9.543783 GGTTTTGAGAATATCTCGGTAATTACT 57.456 33.333 15.05 0.00 46.25 2.24
2678 3247 6.829298 TCGGTAATTACTGCCCAATAAAATGA 59.171 34.615 18.08 0.00 32.63 2.57
2734 3303 5.923733 AAATAAATGTAATTGCCCCGTGA 57.076 34.783 0.00 0.00 36.10 4.35
2740 3309 2.267426 GTAATTGCCCCGTGATTTTGC 58.733 47.619 0.00 0.00 0.00 3.68
2756 3325 6.466097 GTGATTTTGCGATTAGTAGTTCTTGC 59.534 38.462 0.00 0.00 0.00 4.01
2790 3359 2.290071 CCCACTTCGTTACTTCCCACAT 60.290 50.000 0.00 0.00 0.00 3.21
2803 3372 4.289672 ACTTCCCACATGTCCATTCTAACT 59.710 41.667 0.00 0.00 0.00 2.24
2804 3373 4.487714 TCCCACATGTCCATTCTAACTC 57.512 45.455 0.00 0.00 0.00 3.01
2805 3374 4.104086 TCCCACATGTCCATTCTAACTCT 58.896 43.478 0.00 0.00 0.00 3.24
2822 3391 1.195442 TCTTGGTACCGGGTGCATGA 61.195 55.000 17.21 8.49 0.00 3.07
2832 3401 1.442017 GGTGCATGAACGAAACGGC 60.442 57.895 0.00 0.00 0.00 5.68
2845 3414 0.111639 AAACGGCCACTAACCACCAT 59.888 50.000 2.24 0.00 0.00 3.55
2869 3438 0.764890 AGGCCTGTGAAGTAGCAACA 59.235 50.000 3.11 0.00 0.00 3.33
2903 3474 6.430925 CACACCTGATTTGAACCTATTCAGAA 59.569 38.462 0.00 0.00 45.54 3.02
2970 3542 1.602377 CTCGAAAGGGAACGCAAAAGT 59.398 47.619 0.00 0.00 0.00 2.66
2973 3545 1.332686 GAAAGGGAACGCAAAAGTCGT 59.667 47.619 0.00 0.00 42.54 4.34
2979 3551 2.288729 GGAACGCAAAAGTCGTAAACCT 59.711 45.455 0.00 0.00 39.48 3.50
2984 3556 3.242478 CGCAAAAGTCGTAAACCTGTCAA 60.242 43.478 0.00 0.00 0.00 3.18
3033 3607 2.924757 TGGACATGCTCCATGAGATC 57.075 50.000 11.78 0.00 44.99 2.75
3039 3613 5.411977 GGACATGCTCCATGAGATCATTTAG 59.588 44.000 11.78 0.00 43.81 1.85
3097 3671 2.451490 GAGAGATGTGTGAGTGGGAGA 58.549 52.381 0.00 0.00 0.00 3.71
3124 3699 1.333619 CCGGTTTCAACAAGGTGTCAG 59.666 52.381 0.00 0.00 0.00 3.51
3175 3750 0.238289 GCATGTACATATGCCGCACC 59.762 55.000 8.32 0.00 45.93 5.01
3184 3759 2.997952 TATGCCGCACCGTGTTGTGT 62.998 55.000 0.00 0.00 38.52 3.72
3185 3760 3.883180 GCCGCACCGTGTTGTGTT 61.883 61.111 0.00 0.00 38.52 3.32
3186 3761 2.326550 CCGCACCGTGTTGTGTTC 59.673 61.111 0.00 0.00 38.52 3.18
3187 3762 2.465299 CCGCACCGTGTTGTGTTCA 61.465 57.895 0.00 0.00 38.52 3.18
3188 3763 1.646540 CGCACCGTGTTGTGTTCAT 59.353 52.632 0.00 0.00 38.52 2.57
3189 3764 0.657077 CGCACCGTGTTGTGTTCATG 60.657 55.000 0.00 0.00 38.52 3.07
3190 3765 0.317770 GCACCGTGTTGTGTTCATGG 60.318 55.000 0.00 0.00 44.72 3.66
3191 3766 1.304254 CACCGTGTTGTGTTCATGGA 58.696 50.000 10.55 0.00 42.63 3.41
3192 3767 1.264020 CACCGTGTTGTGTTCATGGAG 59.736 52.381 10.55 0.06 42.63 3.86
3193 3768 1.140052 ACCGTGTTGTGTTCATGGAGA 59.860 47.619 10.55 0.00 42.63 3.71
3194 3769 1.531149 CCGTGTTGTGTTCATGGAGAC 59.469 52.381 0.00 0.00 42.63 3.36
3195 3770 1.192312 CGTGTTGTGTTCATGGAGACG 59.808 52.381 0.00 0.00 0.00 4.18
3196 3771 2.479837 GTGTTGTGTTCATGGAGACGA 58.520 47.619 0.00 0.00 0.00 4.20
3197 3772 3.067106 GTGTTGTGTTCATGGAGACGAT 58.933 45.455 0.00 0.00 0.00 3.73
3198 3773 3.066380 TGTTGTGTTCATGGAGACGATG 58.934 45.455 0.00 0.00 0.00 3.84
3199 3774 3.244044 TGTTGTGTTCATGGAGACGATGA 60.244 43.478 0.00 0.00 0.00 2.92
3200 3775 3.893326 TGTGTTCATGGAGACGATGAT 57.107 42.857 0.00 0.00 31.22 2.45
3201 3776 5.109210 GTTGTGTTCATGGAGACGATGATA 58.891 41.667 0.00 0.00 31.22 2.15
3202 3777 4.682787 TGTGTTCATGGAGACGATGATAC 58.317 43.478 0.00 0.00 31.22 2.24
3203 3778 4.051922 GTGTTCATGGAGACGATGATACC 58.948 47.826 0.00 0.00 31.22 2.73
3204 3779 3.069586 TGTTCATGGAGACGATGATACCC 59.930 47.826 0.00 0.00 31.22 3.69
3205 3780 2.248248 TCATGGAGACGATGATACCCC 58.752 52.381 0.00 0.00 0.00 4.95
3206 3781 1.276421 CATGGAGACGATGATACCCCC 59.724 57.143 0.00 0.00 0.00 5.40
3207 3782 0.561184 TGGAGACGATGATACCCCCT 59.439 55.000 0.00 0.00 0.00 4.79
3226 3801 3.339093 CCCCCAACCTCCCCAGTC 61.339 72.222 0.00 0.00 0.00 3.51
3227 3802 2.531685 CCCCAACCTCCCCAGTCA 60.532 66.667 0.00 0.00 0.00 3.41
3247 3822 7.256439 CCAGTCAGATTGGATATCATGACCTTA 60.256 40.741 6.05 0.00 38.20 2.69
3267 3842 6.092259 ACCTTATGTAATGAGAAGCGTTTGAC 59.908 38.462 0.00 0.00 30.21 3.18
3277 3852 0.738389 AGCGTTTGACCTGTGTTTGG 59.262 50.000 0.00 0.00 0.00 3.28
3280 3855 2.792749 CGTTTGACCTGTGTTTGGAAC 58.207 47.619 0.00 0.00 0.00 3.62
3286 3861 2.282407 ACCTGTGTTTGGAACGTGTAC 58.718 47.619 0.00 0.00 0.00 2.90
3310 3885 5.624344 AGACTTGCTCAACATCTGATTTG 57.376 39.130 0.00 0.00 32.14 2.32
3313 3888 4.823442 ACTTGCTCAACATCTGATTTGTGA 59.177 37.500 13.61 6.64 32.14 3.58
3325 3900 5.139727 TCTGATTTGTGATTGAAAGGTGGT 58.860 37.500 0.00 0.00 0.00 4.16
3379 3954 0.459759 GGTAACACGGCTAGAGGCAC 60.460 60.000 3.81 0.00 44.01 5.01
3432 4007 4.222886 GACACGAATCAGATAGATGACGG 58.777 47.826 0.00 0.00 39.74 4.79
3442 4017 6.971602 TCAGATAGATGACGGATGACTTAAC 58.028 40.000 0.00 0.00 0.00 2.01
3452 4027 5.120399 ACGGATGACTTAACACAGACAAAA 58.880 37.500 0.00 0.00 0.00 2.44
3471 4046 6.784176 ACAAAATTTTGCTGGAACAAATGAC 58.216 32.000 26.94 0.00 41.79 3.06
3472 4047 6.373774 ACAAAATTTTGCTGGAACAAATGACA 59.626 30.769 26.94 0.00 41.79 3.58
3473 4048 5.989551 AATTTTGCTGGAACAAATGACAC 57.010 34.783 0.00 0.00 39.18 3.67
3474 4049 4.462508 TTTTGCTGGAACAAATGACACA 57.537 36.364 0.00 0.00 39.18 3.72
3475 4050 3.435105 TTGCTGGAACAAATGACACAC 57.565 42.857 0.00 0.00 38.70 3.82
3476 4051 2.653726 TGCTGGAACAAATGACACACT 58.346 42.857 0.00 0.00 38.70 3.55
3477 4052 2.618241 TGCTGGAACAAATGACACACTC 59.382 45.455 0.00 0.00 38.70 3.51
3478 4053 2.618241 GCTGGAACAAATGACACACTCA 59.382 45.455 0.00 0.00 38.70 3.41
3479 4054 3.066621 GCTGGAACAAATGACACACTCAA 59.933 43.478 0.00 0.00 38.70 3.02
3480 4055 4.261741 GCTGGAACAAATGACACACTCAAT 60.262 41.667 0.00 0.00 38.70 2.57
3481 4056 5.737063 GCTGGAACAAATGACACACTCAATT 60.737 40.000 0.00 0.00 38.70 2.32
3482 4057 6.514870 GCTGGAACAAATGACACACTCAATTA 60.515 38.462 0.00 0.00 38.70 1.40
3483 4058 6.734137 TGGAACAAATGACACACTCAATTAC 58.266 36.000 0.00 0.00 31.92 1.89
3484 4059 5.851177 GGAACAAATGACACACTCAATTACG 59.149 40.000 0.00 0.00 30.60 3.18
3485 4060 6.371809 AACAAATGACACACTCAATTACGT 57.628 33.333 0.00 0.00 30.60 3.57
3486 4061 6.371809 ACAAATGACACACTCAATTACGTT 57.628 33.333 0.00 0.00 30.60 3.99
3487 4062 7.485418 ACAAATGACACACTCAATTACGTTA 57.515 32.000 0.00 0.00 30.60 3.18
3488 4063 8.094798 ACAAATGACACACTCAATTACGTTAT 57.905 30.769 0.00 0.00 30.60 1.89
3489 4064 8.564574 ACAAATGACACACTCAATTACGTTATT 58.435 29.630 0.00 0.00 30.60 1.40
3490 4065 9.393249 CAAATGACACACTCAATTACGTTATTT 57.607 29.630 0.00 0.00 30.60 1.40
3491 4066 9.959749 AAATGACACACTCAATTACGTTATTTT 57.040 25.926 0.00 0.00 30.60 1.82
3508 4083 9.362539 ACGTTATTTTATCAATGAGTTAGACGT 57.637 29.630 0.00 0.00 0.00 4.34
3512 4087 7.972832 TTTTATCAATGAGTTAGACGTTGGT 57.027 32.000 0.00 0.00 35.68 3.67
3513 4088 6.961359 TTATCAATGAGTTAGACGTTGGTG 57.039 37.500 0.00 0.00 35.68 4.17
3514 4089 3.064207 TCAATGAGTTAGACGTTGGTGC 58.936 45.455 0.00 0.00 35.68 5.01
3515 4090 2.094762 ATGAGTTAGACGTTGGTGCC 57.905 50.000 0.00 0.00 0.00 5.01
3516 4091 0.753867 TGAGTTAGACGTTGGTGCCA 59.246 50.000 0.00 0.00 0.00 4.92
3517 4092 1.346395 TGAGTTAGACGTTGGTGCCAT 59.654 47.619 0.00 0.00 0.00 4.40
3518 4093 2.224426 TGAGTTAGACGTTGGTGCCATT 60.224 45.455 0.00 0.00 0.00 3.16
3519 4094 2.151202 AGTTAGACGTTGGTGCCATTG 58.849 47.619 0.00 0.00 0.00 2.82
3520 4095 2.147958 GTTAGACGTTGGTGCCATTGA 58.852 47.619 0.00 0.00 0.00 2.57
3521 4096 1.803334 TAGACGTTGGTGCCATTGAC 58.197 50.000 0.00 0.00 0.00 3.18
3522 4097 0.179032 AGACGTTGGTGCCATTGACA 60.179 50.000 0.00 0.00 0.00 3.58
3523 4098 0.040425 GACGTTGGTGCCATTGACAC 60.040 55.000 0.00 0.00 37.31 3.67
3524 4099 0.749818 ACGTTGGTGCCATTGACACA 60.750 50.000 5.45 0.00 39.87 3.72
3525 4100 0.383590 CGTTGGTGCCATTGACACAA 59.616 50.000 5.45 0.00 39.87 3.33
3526 4101 1.202348 CGTTGGTGCCATTGACACAAA 60.202 47.619 5.45 0.00 39.87 2.83
3527 4102 2.472816 GTTGGTGCCATTGACACAAAG 58.527 47.619 5.45 0.00 39.87 2.77
3528 4103 2.064434 TGGTGCCATTGACACAAAGA 57.936 45.000 5.45 0.00 39.87 2.52
3529 4104 2.382882 TGGTGCCATTGACACAAAGAA 58.617 42.857 5.45 0.00 39.87 2.52
3530 4105 2.361757 TGGTGCCATTGACACAAAGAAG 59.638 45.455 5.45 0.00 39.87 2.85
3531 4106 2.362077 GGTGCCATTGACACAAAGAAGT 59.638 45.455 5.45 0.00 39.87 3.01
3532 4107 3.550842 GGTGCCATTGACACAAAGAAGTC 60.551 47.826 5.45 0.00 39.87 3.01
3533 4108 2.622942 TGCCATTGACACAAAGAAGTCC 59.377 45.455 0.00 0.00 33.89 3.85
3534 4109 2.887152 GCCATTGACACAAAGAAGTCCT 59.113 45.455 0.00 0.00 33.89 3.85
3535 4110 4.072131 GCCATTGACACAAAGAAGTCCTA 58.928 43.478 0.00 0.00 33.89 2.94
3536 4111 4.518970 GCCATTGACACAAAGAAGTCCTAA 59.481 41.667 0.00 0.00 33.89 2.69
3537 4112 5.009610 GCCATTGACACAAAGAAGTCCTAAA 59.990 40.000 0.00 0.00 33.89 1.85
3538 4113 6.672147 CCATTGACACAAAGAAGTCCTAAAG 58.328 40.000 0.00 0.00 33.89 1.85
3539 4114 5.751243 TTGACACAAAGAAGTCCTAAAGC 57.249 39.130 0.00 0.00 33.89 3.51
3540 4115 5.036117 TGACACAAAGAAGTCCTAAAGCT 57.964 39.130 0.00 0.00 33.89 3.74
3541 4116 6.169557 TGACACAAAGAAGTCCTAAAGCTA 57.830 37.500 0.00 0.00 33.89 3.32
3542 4117 6.223852 TGACACAAAGAAGTCCTAAAGCTAG 58.776 40.000 0.00 0.00 33.89 3.42
3543 4118 6.041637 TGACACAAAGAAGTCCTAAAGCTAGA 59.958 38.462 0.00 0.00 33.89 2.43
3544 4119 7.010339 ACACAAAGAAGTCCTAAAGCTAGAT 57.990 36.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 201 8.821686 ATCACATATAACCTTGATTTTGGACA 57.178 30.769 0.00 0.00 0.00 4.02
168 222 7.148722 GCTTGTGACTTGAGTAGTAAGAATCAC 60.149 40.741 0.00 0.00 37.17 3.06
292 360 6.664515 TCTTACACTTTAAGGCACAAAATCG 58.335 36.000 0.00 0.00 0.00 3.34
375 450 4.708726 AGTAGCAATGCAAATTCTCACC 57.291 40.909 8.35 0.00 0.00 4.02
536 615 1.484240 GATACAAGCAGGGCTGTCTCT 59.516 52.381 0.00 0.00 39.62 3.10
542 621 1.073763 TGTGTTGATACAAGCAGGGCT 59.926 47.619 0.00 0.00 42.56 5.19
558 637 9.777575 GTTAAAAGTGTACAACATACTTTGTGT 57.222 29.630 8.64 0.00 44.92 3.72
559 638 8.939926 CGTTAAAAGTGTACAACATACTTTGTG 58.060 33.333 8.64 0.00 44.92 3.33
560 639 8.667463 ACGTTAAAAGTGTACAACATACTTTGT 58.333 29.630 8.64 1.71 44.92 2.83
561 640 8.939926 CACGTTAAAAGTGTACAACATACTTTG 58.060 33.333 8.64 1.22 44.92 2.77
562 641 8.881743 TCACGTTAAAAGTGTACAACATACTTT 58.118 29.630 0.00 0.00 46.88 2.66
563 642 8.330302 GTCACGTTAAAAGTGTACAACATACTT 58.670 33.333 0.00 0.00 40.02 2.24
564 643 7.492020 TGTCACGTTAAAAGTGTACAACATACT 59.508 33.333 0.00 0.00 40.28 2.12
565 644 7.620215 TGTCACGTTAAAAGTGTACAACATAC 58.380 34.615 0.00 0.00 40.28 2.39
566 645 7.767745 TGTCACGTTAAAAGTGTACAACATA 57.232 32.000 0.00 0.00 40.28 2.29
567 646 6.665474 TGTCACGTTAAAAGTGTACAACAT 57.335 33.333 0.00 0.00 40.28 2.71
568 647 6.477669 TTGTCACGTTAAAAGTGTACAACA 57.522 33.333 0.00 10.52 40.28 3.33
569 648 7.583762 GGTATTGTCACGTTAAAAGTGTACAAC 59.416 37.037 19.61 14.09 39.66 3.32
570 649 7.495279 AGGTATTGTCACGTTAAAAGTGTACAA 59.505 33.333 19.56 19.56 40.32 2.41
571 650 6.985645 AGGTATTGTCACGTTAAAAGTGTACA 59.014 34.615 10.83 0.00 40.28 2.90
572 651 7.412137 AGGTATTGTCACGTTAAAAGTGTAC 57.588 36.000 10.83 8.88 40.28 2.90
573 652 8.436046 AAAGGTATTGTCACGTTAAAAGTGTA 57.564 30.769 10.83 1.90 40.28 2.90
574 653 6.930667 AAGGTATTGTCACGTTAAAAGTGT 57.069 33.333 10.83 0.00 40.28 3.55
575 654 9.537848 GATAAAGGTATTGTCACGTTAAAAGTG 57.462 33.333 6.11 6.11 40.71 3.16
576 655 9.498176 AGATAAAGGTATTGTCACGTTAAAAGT 57.502 29.630 0.00 0.00 0.00 2.66
577 656 9.755064 CAGATAAAGGTATTGTCACGTTAAAAG 57.245 33.333 0.00 0.00 0.00 2.27
578 657 9.275398 ACAGATAAAGGTATTGTCACGTTAAAA 57.725 29.630 0.00 0.00 0.00 1.52
579 658 8.714179 CACAGATAAAGGTATTGTCACGTTAAA 58.286 33.333 0.00 0.00 0.00 1.52
580 659 7.148540 GCACAGATAAAGGTATTGTCACGTTAA 60.149 37.037 0.00 0.00 0.00 2.01
581 660 6.311935 GCACAGATAAAGGTATTGTCACGTTA 59.688 38.462 0.00 0.00 0.00 3.18
582 661 5.121768 GCACAGATAAAGGTATTGTCACGTT 59.878 40.000 0.00 0.00 0.00 3.99
583 662 4.630069 GCACAGATAAAGGTATTGTCACGT 59.370 41.667 0.00 0.00 0.00 4.49
584 663 4.629634 TGCACAGATAAAGGTATTGTCACG 59.370 41.667 0.00 0.00 0.00 4.35
585 664 5.411361 TGTGCACAGATAAAGGTATTGTCAC 59.589 40.000 17.42 0.00 0.00 3.67
586 665 5.555966 TGTGCACAGATAAAGGTATTGTCA 58.444 37.500 17.42 0.00 0.00 3.58
587 666 6.494893 TTGTGCACAGATAAAGGTATTGTC 57.505 37.500 20.59 0.00 0.00 3.18
588 667 8.574251 TTATTGTGCACAGATAAAGGTATTGT 57.426 30.769 20.59 0.00 0.00 2.71
591 670 9.189156 ACAATTATTGTGCACAGATAAAGGTAT 57.811 29.630 24.85 15.33 43.48 2.73
592 671 8.574251 ACAATTATTGTGCACAGATAAAGGTA 57.426 30.769 24.85 10.36 43.48 3.08
593 672 7.466746 ACAATTATTGTGCACAGATAAAGGT 57.533 32.000 24.85 22.40 43.48 3.50
594 673 7.201461 GCAACAATTATTGTGCACAGATAAAGG 60.201 37.037 24.85 22.01 44.59 3.11
595 674 7.461807 CGCAACAATTATTGTGCACAGATAAAG 60.462 37.037 24.85 22.38 44.59 1.85
596 675 6.307558 CGCAACAATTATTGTGCACAGATAAA 59.692 34.615 24.85 17.28 44.59 1.40
597 676 5.799435 CGCAACAATTATTGTGCACAGATAA 59.201 36.000 20.59 22.82 44.59 1.75
598 677 5.331098 CGCAACAATTATTGTGCACAGATA 58.669 37.500 20.59 16.56 44.59 1.98
599 678 4.168014 CGCAACAATTATTGTGCACAGAT 58.832 39.130 20.59 17.52 44.59 2.90
600 679 3.563508 CGCAACAATTATTGTGCACAGA 58.436 40.909 20.59 11.62 44.59 3.41
601 680 3.957747 CGCAACAATTATTGTGCACAG 57.042 42.857 20.59 9.81 44.59 3.66
606 685 4.155449 AGTTACGCGCAACAATTATTGTG 58.845 39.130 23.26 5.64 44.59 3.33
608 687 4.647964 AGAGTTACGCGCAACAATTATTG 58.352 39.130 23.26 3.07 0.00 1.90
609 688 4.939509 AGAGTTACGCGCAACAATTATT 57.060 36.364 23.26 1.99 0.00 1.40
610 689 4.939509 AAGAGTTACGCGCAACAATTAT 57.060 36.364 23.26 2.75 0.00 1.28
611 690 4.735662 AAAGAGTTACGCGCAACAATTA 57.264 36.364 23.26 0.00 0.00 1.40
612 691 3.619233 AAAGAGTTACGCGCAACAATT 57.381 38.095 23.26 14.17 0.00 2.32
613 692 4.939509 ATAAAGAGTTACGCGCAACAAT 57.060 36.364 23.26 8.97 0.00 2.71
614 693 5.808540 AGATATAAAGAGTTACGCGCAACAA 59.191 36.000 23.26 1.98 0.00 2.83
615 694 5.345702 AGATATAAAGAGTTACGCGCAACA 58.654 37.500 23.26 3.35 0.00 3.33
616 695 5.885020 AGATATAAAGAGTTACGCGCAAC 57.115 39.130 14.38 14.38 0.00 4.17
617 696 6.897259 AAAGATATAAAGAGTTACGCGCAA 57.103 33.333 5.73 0.00 0.00 4.85
618 697 6.897259 AAAAGATATAAAGAGTTACGCGCA 57.103 33.333 5.73 0.00 0.00 6.09
619 698 9.513554 GATTAAAAGATATAAAGAGTTACGCGC 57.486 33.333 5.73 0.00 0.00 6.86
626 705 9.905713 TGCCTGTGATTAAAAGATATAAAGAGT 57.094 29.630 0.00 0.00 0.00 3.24
634 713 9.461312 AGTTGTAATGCCTGTGATTAAAAGATA 57.539 29.630 0.00 0.00 0.00 1.98
635 714 8.353423 AGTTGTAATGCCTGTGATTAAAAGAT 57.647 30.769 0.00 0.00 0.00 2.40
636 715 7.759489 AGTTGTAATGCCTGTGATTAAAAGA 57.241 32.000 0.00 0.00 0.00 2.52
637 716 8.184192 CCTAGTTGTAATGCCTGTGATTAAAAG 58.816 37.037 0.00 0.00 0.00 2.27
638 717 7.885922 TCCTAGTTGTAATGCCTGTGATTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
639 718 7.398829 TCCTAGTTGTAATGCCTGTGATTAAA 58.601 34.615 0.00 0.00 0.00 1.52
640 719 6.953101 TCCTAGTTGTAATGCCTGTGATTAA 58.047 36.000 0.00 0.00 0.00 1.40
641 720 6.553953 TCCTAGTTGTAATGCCTGTGATTA 57.446 37.500 0.00 0.00 0.00 1.75
642 721 5.435686 TCCTAGTTGTAATGCCTGTGATT 57.564 39.130 0.00 0.00 0.00 2.57
643 722 5.615289 GATCCTAGTTGTAATGCCTGTGAT 58.385 41.667 0.00 0.00 0.00 3.06
644 723 4.441495 CGATCCTAGTTGTAATGCCTGTGA 60.441 45.833 0.00 0.00 0.00 3.58
645 724 3.804325 CGATCCTAGTTGTAATGCCTGTG 59.196 47.826 0.00 0.00 0.00 3.66
646 725 3.704566 TCGATCCTAGTTGTAATGCCTGT 59.295 43.478 0.00 0.00 0.00 4.00
647 726 4.322080 TCGATCCTAGTTGTAATGCCTG 57.678 45.455 0.00 0.00 0.00 4.85
648 727 4.588951 TCATCGATCCTAGTTGTAATGCCT 59.411 41.667 0.00 0.00 0.00 4.75
649 728 4.883083 TCATCGATCCTAGTTGTAATGCC 58.117 43.478 0.00 0.00 0.00 4.40
650 729 5.107298 GCTTCATCGATCCTAGTTGTAATGC 60.107 44.000 0.00 0.00 0.00 3.56
651 730 5.985530 TGCTTCATCGATCCTAGTTGTAATG 59.014 40.000 0.00 0.00 0.00 1.90
652 731 6.161855 TGCTTCATCGATCCTAGTTGTAAT 57.838 37.500 0.00 0.00 0.00 1.89
653 732 5.592104 TGCTTCATCGATCCTAGTTGTAA 57.408 39.130 0.00 0.00 0.00 2.41
654 733 5.791336 ATGCTTCATCGATCCTAGTTGTA 57.209 39.130 0.00 0.00 0.00 2.41
655 734 4.679373 ATGCTTCATCGATCCTAGTTGT 57.321 40.909 0.00 0.00 0.00 3.32
656 735 8.939201 AATATATGCTTCATCGATCCTAGTTG 57.061 34.615 0.00 0.00 0.00 3.16
657 736 9.950496 AAAATATATGCTTCATCGATCCTAGTT 57.050 29.630 0.00 0.00 0.00 2.24
658 737 9.950496 AAAAATATATGCTTCATCGATCCTAGT 57.050 29.630 0.00 0.00 0.00 2.57
682 761 8.690884 CCACCATGTTTGTCCACATATTATAAA 58.309 33.333 0.00 0.00 35.51 1.40
683 762 7.201866 GCCACCATGTTTGTCCACATATTATAA 60.202 37.037 0.00 0.00 35.51 0.98
684 763 6.264292 GCCACCATGTTTGTCCACATATTATA 59.736 38.462 0.00 0.00 35.51 0.98
685 764 5.068987 GCCACCATGTTTGTCCACATATTAT 59.931 40.000 0.00 0.00 35.51 1.28
686 765 4.400884 GCCACCATGTTTGTCCACATATTA 59.599 41.667 0.00 0.00 35.51 0.98
687 766 3.195396 GCCACCATGTTTGTCCACATATT 59.805 43.478 0.00 0.00 35.51 1.28
688 767 2.760092 GCCACCATGTTTGTCCACATAT 59.240 45.455 0.00 0.00 35.51 1.78
689 768 2.166829 GCCACCATGTTTGTCCACATA 58.833 47.619 0.00 0.00 35.51 2.29
690 769 0.968405 GCCACCATGTTTGTCCACAT 59.032 50.000 0.00 0.00 37.93 3.21
691 770 0.106268 AGCCACCATGTTTGTCCACA 60.106 50.000 0.00 0.00 0.00 4.17
692 771 0.598065 GAGCCACCATGTTTGTCCAC 59.402 55.000 0.00 0.00 0.00 4.02
693 772 0.478072 AGAGCCACCATGTTTGTCCA 59.522 50.000 0.00 0.00 0.00 4.02
694 773 2.489938 TAGAGCCACCATGTTTGTCC 57.510 50.000 0.00 0.00 0.00 4.02
695 774 5.391312 AAAATAGAGCCACCATGTTTGTC 57.609 39.130 0.00 0.00 0.00 3.18
696 775 5.806654 AAAAATAGAGCCACCATGTTTGT 57.193 34.783 0.00 0.00 0.00 2.83
843 929 9.469807 CTTTCGCTCAAAAGTCTATGTATCTAT 57.530 33.333 0.00 0.00 32.67 1.98
844 930 7.921214 CCTTTCGCTCAAAAGTCTATGTATCTA 59.079 37.037 0.00 0.00 34.99 1.98
845 931 6.758886 CCTTTCGCTCAAAAGTCTATGTATCT 59.241 38.462 0.00 0.00 34.99 1.98
846 932 6.535508 ACCTTTCGCTCAAAAGTCTATGTATC 59.464 38.462 0.00 0.00 34.99 2.24
886 975 2.019249 CGATTGAGGCATGGACATGTT 58.981 47.619 13.29 3.17 40.80 2.71
946 1060 1.184322 TGGCGATGGGCAAACATGTT 61.184 50.000 4.92 4.92 46.91 2.71
947 1061 1.606025 TGGCGATGGGCAAACATGT 60.606 52.632 0.18 0.00 46.91 3.21
948 1062 3.286407 TGGCGATGGGCAAACATG 58.714 55.556 0.18 0.00 46.91 3.21
1089 1224 1.322538 ATGAACCCATTTCCAGCGGC 61.323 55.000 0.00 0.00 32.58 6.53
1121 1271 1.065273 ACGACGTGTGCTTTCTCGT 59.935 52.632 0.00 0.00 39.59 4.18
1365 1518 2.941064 CGTGATGACCTTGCAGATTGAT 59.059 45.455 0.00 0.00 0.00 2.57
1379 1532 1.305297 AGGCAGACCTCCGTGATGA 60.305 57.895 0.00 0.00 46.34 2.92
1468 1627 0.746923 TCCATCACGACGTCGGAGAT 60.747 55.000 37.89 33.45 44.95 2.75
1530 1689 2.353958 CTGGATGCCCACAGCTGT 59.646 61.111 15.25 15.25 44.23 4.40
1627 1787 2.358582 TGTCAAGGTACTCGTTCGTCAA 59.641 45.455 0.00 0.00 38.49 3.18
1717 1877 2.126189 GTAGTCGTCCGGTGCCAC 60.126 66.667 0.00 0.00 0.00 5.01
1718 1878 1.980232 ATGTAGTCGTCCGGTGCCA 60.980 57.895 0.00 0.00 0.00 4.92
1800 2327 0.601558 CTCCCTCAAGGTCGTCGAAA 59.398 55.000 0.00 0.00 36.75 3.46
1884 2412 2.032528 TTTGAGCTCGGTGCCAGG 59.967 61.111 9.64 0.00 44.23 4.45
1950 2502 3.059982 CCAGGCTCCTTGTCGTCA 58.940 61.111 0.00 0.00 0.00 4.35
2015 2567 3.123620 CGAACTCCAGCAGCTGCC 61.124 66.667 34.39 16.40 43.38 4.85
2175 2728 1.604604 CCGGGTGATTCAACACTTGT 58.395 50.000 3.73 0.00 40.22 3.16
2236 2789 0.747644 CCGCCACACATGCTATCCAA 60.748 55.000 0.00 0.00 0.00 3.53
2256 2809 2.046988 CAGCTGATGACGGGCACA 60.047 61.111 8.42 0.00 0.00 4.57
2283 2836 2.927856 ATGGTCTGGTGGTCCGCA 60.928 61.111 4.48 0.00 36.30 5.69
2567 3121 4.586306 AAACCGGGATTGAGAAACCTAT 57.414 40.909 6.32 0.00 0.00 2.57
2568 3122 4.376225 AAAACCGGGATTGAGAAACCTA 57.624 40.909 6.32 0.00 0.00 3.08
2596 3156 0.034089 AGAAGGGATTTTCCGGCCTG 60.034 55.000 0.00 0.00 37.43 4.85
2629 3189 6.472887 AGATATTCTCAAAACCGGTTCTCAA 58.527 36.000 22.53 9.73 0.00 3.02
2631 3191 5.232414 CGAGATATTCTCAAAACCGGTTCTC 59.768 44.000 22.53 16.87 43.55 2.87
2664 3233 9.730705 TCACAATTTATTTCATTTTATTGGGCA 57.269 25.926 0.00 0.00 0.00 5.36
2705 3274 6.320926 GGGGCAATTACATTTATTTTTGGCAT 59.679 34.615 8.86 0.00 40.26 4.40
2734 3303 5.163652 GGGCAAGAACTACTAATCGCAAAAT 60.164 40.000 0.00 0.00 0.00 1.82
2740 3309 2.470821 CGGGGCAAGAACTACTAATCG 58.529 52.381 0.00 0.00 0.00 3.34
2768 3337 1.071228 GTGGGAAGTAACGAAGTGGGT 59.929 52.381 0.00 0.00 45.00 4.51
2790 3359 4.081862 CGGTACCAAGAGTTAGAATGGACA 60.082 45.833 13.54 0.00 36.75 4.02
2803 3372 1.195442 TCATGCACCCGGTACCAAGA 61.195 55.000 13.54 0.00 0.00 3.02
2804 3373 0.322098 TTCATGCACCCGGTACCAAG 60.322 55.000 13.54 4.53 0.00 3.61
2805 3374 0.606944 GTTCATGCACCCGGTACCAA 60.607 55.000 13.54 0.00 0.00 3.67
2822 3391 0.179051 TGGTTAGTGGCCGTTTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
2832 3401 1.176527 CTTGGCATGGTGGTTAGTGG 58.823 55.000 0.00 0.00 0.00 4.00
2845 3414 0.036732 CTACTTCACAGGCCTTGGCA 59.963 55.000 0.00 0.00 0.00 4.92
2869 3438 5.981088 TCAAATCAGGTGTGTATGCAATT 57.019 34.783 0.00 0.00 0.00 2.32
2885 3454 9.780413 GATTTGAGTTCTGAATAGGTTCAAATC 57.220 33.333 22.74 22.74 43.39 2.17
2919 3490 5.048224 TGTTACCGTCCAAAAAGTTTCAACA 60.048 36.000 0.00 0.00 0.00 3.33
2927 3498 7.198306 AGAATTACTGTTACCGTCCAAAAAG 57.802 36.000 0.00 0.00 0.00 2.27
3033 3607 4.003648 GTGGTGTGTCCTCCTTCTAAATG 58.996 47.826 0.00 0.00 37.07 2.32
3039 3613 1.004918 CGGTGGTGTGTCCTCCTTC 60.005 63.158 3.98 0.00 45.01 3.46
3097 3671 3.181437 ACCTTGTTGAAACCGGGATAACT 60.181 43.478 6.32 0.00 0.00 2.24
3124 3699 4.981806 TGGGATTGCTAAGCATAAACAC 57.018 40.909 0.00 0.00 38.76 3.32
3158 3733 0.105964 ACGGTGCGGCATATGTACAT 59.894 50.000 13.93 13.93 0.00 2.29
3162 3737 1.376683 AACACGGTGCGGCATATGT 60.377 52.632 5.72 8.40 0.00 2.29
3175 3750 1.192312 CGTCTCCATGAACACAACACG 59.808 52.381 0.00 0.00 0.00 4.49
3184 3759 2.632996 GGGGTATCATCGTCTCCATGAA 59.367 50.000 0.00 0.00 33.94 2.57
3185 3760 2.248248 GGGGTATCATCGTCTCCATGA 58.752 52.381 0.00 0.00 34.74 3.07
3186 3761 1.276421 GGGGGTATCATCGTCTCCATG 59.724 57.143 0.00 0.00 0.00 3.66
3187 3762 1.150135 AGGGGGTATCATCGTCTCCAT 59.850 52.381 0.00 0.00 0.00 3.41
3188 3763 0.561184 AGGGGGTATCATCGTCTCCA 59.439 55.000 0.00 0.00 0.00 3.86
3189 3764 1.258676 GAGGGGGTATCATCGTCTCC 58.741 60.000 0.00 0.00 0.00 3.71
3190 3765 1.258676 GGAGGGGGTATCATCGTCTC 58.741 60.000 0.00 0.00 0.00 3.36
3191 3766 0.178929 GGGAGGGGGTATCATCGTCT 60.179 60.000 0.00 0.00 0.00 4.18
3192 3767 1.192803 GGGGAGGGGGTATCATCGTC 61.193 65.000 0.00 0.00 0.00 4.20
3193 3768 1.152096 GGGGAGGGGGTATCATCGT 60.152 63.158 0.00 0.00 0.00 3.73
3194 3769 1.918800 GGGGGAGGGGGTATCATCG 60.919 68.421 0.00 0.00 0.00 3.84
3195 3770 4.252493 GGGGGAGGGGGTATCATC 57.748 66.667 0.00 0.00 0.00 2.92
3224 3799 8.099537 ACATAAGGTCATGATATCCAATCTGAC 58.900 37.037 0.00 5.77 33.86 3.51
3226 3801 9.948964 TTACATAAGGTCATGATATCCAATCTG 57.051 33.333 0.00 0.00 0.00 2.90
3247 3822 4.393062 CAGGTCAAACGCTTCTCATTACAT 59.607 41.667 0.00 0.00 0.00 2.29
3267 3842 2.281517 TGTACACGTTCCAAACACAGG 58.718 47.619 0.00 0.00 0.00 4.00
3277 3852 3.120792 TGAGCAAGTCTTGTACACGTTC 58.879 45.455 14.03 0.00 0.00 3.95
3280 3855 2.863740 TGTTGAGCAAGTCTTGTACACG 59.136 45.455 14.03 0.00 0.00 4.49
3286 3861 5.624344 AATCAGATGTTGAGCAAGTCTTG 57.376 39.130 8.31 8.31 39.68 3.02
3310 3885 3.068024 TCTTGCAACCACCTTTCAATCAC 59.932 43.478 0.00 0.00 0.00 3.06
3313 3888 2.629617 CCTCTTGCAACCACCTTTCAAT 59.370 45.455 0.00 0.00 0.00 2.57
3325 3900 1.151810 AGGGACCCTCCTCTTGCAA 60.152 57.895 7.44 0.00 36.57 4.08
3370 3945 4.162320 TCAACTCCCTTATTGTGCCTCTAG 59.838 45.833 0.00 0.00 0.00 2.43
3432 4007 8.268738 GCAAAATTTTGTCTGTGTTAAGTCATC 58.731 33.333 27.13 5.40 40.24 2.92
3442 4017 4.869297 TGTTCCAGCAAAATTTTGTCTGTG 59.131 37.500 31.01 25.89 38.97 3.66
3452 4027 4.810491 GTGTGTCATTTGTTCCAGCAAAAT 59.190 37.500 0.00 0.00 41.03 1.82
3482 4057 9.362539 ACGTCTAACTCATTGATAAAATAACGT 57.637 29.630 0.00 0.00 0.00 3.99
3486 4061 9.661563 ACCAACGTCTAACTCATTGATAAAATA 57.338 29.630 0.00 0.00 0.00 1.40
3487 4062 8.450964 CACCAACGTCTAACTCATTGATAAAAT 58.549 33.333 0.00 0.00 0.00 1.82
3488 4063 7.572353 GCACCAACGTCTAACTCATTGATAAAA 60.572 37.037 0.00 0.00 0.00 1.52
3489 4064 6.128391 GCACCAACGTCTAACTCATTGATAAA 60.128 38.462 0.00 0.00 0.00 1.40
3490 4065 5.350365 GCACCAACGTCTAACTCATTGATAA 59.650 40.000 0.00 0.00 0.00 1.75
3491 4066 4.868171 GCACCAACGTCTAACTCATTGATA 59.132 41.667 0.00 0.00 0.00 2.15
3492 4067 3.684788 GCACCAACGTCTAACTCATTGAT 59.315 43.478 0.00 0.00 0.00 2.57
3493 4068 3.064207 GCACCAACGTCTAACTCATTGA 58.936 45.455 0.00 0.00 0.00 2.57
3494 4069 2.159627 GGCACCAACGTCTAACTCATTG 59.840 50.000 0.00 0.00 0.00 2.82
3495 4070 2.224426 TGGCACCAACGTCTAACTCATT 60.224 45.455 0.00 0.00 0.00 2.57
3496 4071 1.346395 TGGCACCAACGTCTAACTCAT 59.654 47.619 0.00 0.00 0.00 2.90
3497 4072 0.753867 TGGCACCAACGTCTAACTCA 59.246 50.000 0.00 0.00 0.00 3.41
3498 4073 2.094762 ATGGCACCAACGTCTAACTC 57.905 50.000 0.00 0.00 0.00 3.01
3499 4074 2.151202 CAATGGCACCAACGTCTAACT 58.849 47.619 0.00 0.00 0.00 2.24
3500 4075 2.095919 GTCAATGGCACCAACGTCTAAC 60.096 50.000 0.00 0.00 0.00 2.34
3501 4076 2.147958 GTCAATGGCACCAACGTCTAA 58.852 47.619 0.00 0.00 0.00 2.10
3502 4077 1.070914 TGTCAATGGCACCAACGTCTA 59.929 47.619 0.00 0.00 0.00 2.59
3503 4078 0.179032 TGTCAATGGCACCAACGTCT 60.179 50.000 0.00 0.00 0.00 4.18
3504 4079 0.040425 GTGTCAATGGCACCAACGTC 60.040 55.000 6.73 0.00 0.00 4.34
3505 4080 0.749818 TGTGTCAATGGCACCAACGT 60.750 50.000 15.91 0.00 36.11 3.99
3506 4081 0.383590 TTGTGTCAATGGCACCAACG 59.616 50.000 15.91 0.00 36.11 4.10
3507 4082 2.100584 TCTTTGTGTCAATGGCACCAAC 59.899 45.455 15.91 0.00 36.11 3.77
3508 4083 2.382882 TCTTTGTGTCAATGGCACCAA 58.617 42.857 15.91 9.89 36.11 3.67
3509 4084 2.064434 TCTTTGTGTCAATGGCACCA 57.936 45.000 15.91 0.76 36.11 4.17
3510 4085 2.362077 ACTTCTTTGTGTCAATGGCACC 59.638 45.455 15.91 0.00 36.11 5.01
3511 4086 3.550842 GGACTTCTTTGTGTCAATGGCAC 60.551 47.826 11.55 11.55 35.11 5.01
3512 4087 2.622942 GGACTTCTTTGTGTCAATGGCA 59.377 45.455 0.00 0.00 35.11 4.92
3513 4088 2.887152 AGGACTTCTTTGTGTCAATGGC 59.113 45.455 0.00 0.00 35.11 4.40
3514 4089 6.633500 TTTAGGACTTCTTTGTGTCAATGG 57.367 37.500 0.00 0.00 35.11 3.16
3515 4090 6.016777 AGCTTTAGGACTTCTTTGTGTCAATG 60.017 38.462 0.00 0.00 35.11 2.82
3516 4091 6.064717 AGCTTTAGGACTTCTTTGTGTCAAT 58.935 36.000 0.00 0.00 35.11 2.57
3517 4092 5.437060 AGCTTTAGGACTTCTTTGTGTCAA 58.563 37.500 0.00 0.00 35.11 3.18
3518 4093 5.036117 AGCTTTAGGACTTCTTTGTGTCA 57.964 39.130 0.00 0.00 35.11 3.58
3519 4094 6.456501 TCTAGCTTTAGGACTTCTTTGTGTC 58.543 40.000 0.00 0.00 0.00 3.67
3520 4095 6.420913 TCTAGCTTTAGGACTTCTTTGTGT 57.579 37.500 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.