Multiple sequence alignment - TraesCS2D01G191200

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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 TraesCS2D01G191200 chr2D 100.000 3409 0 0 1 3409 135379598 135383006 0.000000e+00 6296.0
1 TraesCS2D01G191200 chr2B 90.291 1133 69 21 1742 2853 192437707 192438819 0.000000e+00 1445.0
2 TraesCS2D01G191200 chr2B 94.899 843 33 3 901 1742 192436840 192437673 0.000000e+00 1310.0
3 TraesCS2D01G191200 chr2B 82.456 912 82 29 2532 3409 192438972 192439839 0.000000e+00 726.0
4 TraesCS2D01G191200 chr2A 96.690 846 22 4 903 1742 143240939 143241784 0.000000e+00 1402.0
5 TraesCS2D01G191200 chr2A 90.678 826 48 14 1737 2538 143241813 143242633 0.000000e+00 1072.0
6 TraesCS2D01G191200 chr2A 85.685 489 61 7 2532 3014 143243345 143243830 1.090000e-139 507.0
7 TraesCS2D01G191200 chr2A 92.199 282 20 2 3127 3407 143243830 143244110 6.850000e-107 398.0
8 TraesCS2D01G191200 chr2A 82.682 179 27 4 697 872 768055611 768055788 4.550000e-34 156.0
9 TraesCS2D01G191200 chr3D 90.813 566 39 7 1 558 48175359 48174799 0.000000e+00 745.0
10 TraesCS2D01G191200 chr3D 80.672 238 40 5 605 838 157175824 157175589 2.700000e-41 180.0
11 TraesCS2D01G191200 chr3B 85.455 275 34 6 601 871 439676761 439677033 7.200000e-72 281.0
12 TraesCS2D01G191200 chr3B 79.592 196 27 12 682 870 16626479 16626290 9.930000e-26 128.0
13 TraesCS2D01G191200 chr3B 75.556 270 44 12 556 811 440411919 440412180 2.780000e-21 113.0
14 TraesCS2D01G191200 chr3B 100.000 32 0 0 527 558 523155543 523155574 3.670000e-05 60.2
15 TraesCS2D01G191200 chr3B 96.970 33 0 1 527 558 18138109 18138141 2.000000e-03 54.7
16 TraesCS2D01G191200 chr3A 82.534 292 36 7 559 847 20155930 20155651 3.400000e-60 243.0
17 TraesCS2D01G191200 chr1A 78.157 293 51 10 557 838 404487247 404486957 1.260000e-39 174.0
18 TraesCS2D01G191200 chr1A 79.026 267 36 15 620 877 516590430 516590175 7.570000e-37 165.0
19 TraesCS2D01G191200 chr6A 79.798 198 34 6 601 794 613346041 613345846 4.590000e-29 139.0
20 TraesCS2D01G191200 chr6A 90.411 73 5 2 601 672 15925448 15925519 1.010000e-15 95.3
21 TraesCS2D01G191200 chr6B 82.581 155 14 13 722 871 707419906 707419760 1.280000e-24 124.0
22 TraesCS2D01G191200 chr7B 80.745 161 28 3 713 871 489132907 489133066 4.620000e-24 122.0
23 TraesCS2D01G191200 chr7B 100.000 33 0 0 526 558 549349026 549349058 1.020000e-05 62.1
24 TraesCS2D01G191200 chr1B 78.610 187 32 8 693 873 657184686 657184870 2.150000e-22 117.0
25 TraesCS2D01G191200 chr1D 81.890 127 22 1 745 870 464639357 464639483 4.650000e-19 106.0
26 TraesCS2D01G191200 chr6D 90.411 73 5 2 601 672 14941380 14941451 1.010000e-15 95.3


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 TraesCS2D01G191200 chr2D 135379598 135383006 3408 False 6296.000000 6296 100.000000 1 3409 1 chr2D.!!$F1 3408
1 TraesCS2D01G191200 chr2B 192436840 192439839 2999 False 1160.333333 1445 89.215333 901 3409 3 chr2B.!!$F1 2508
2 TraesCS2D01G191200 chr2A 143240939 143244110 3171 False 844.750000 1402 91.313000 903 3407 4 chr2A.!!$F2 2504
3 TraesCS2D01G191200 chr3D 48174799 48175359 560 True 745.000000 745 90.813000 1 558 1 chr3D.!!$R1 557

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
707 716 0.038599 GTTTTAAGGAAGGGGCCCGA 59.961 55.0 18.95 0.0 0.0 5.14 F
815 824 0.039165 CCGGCTTGGTTTTCTGCTTC 60.039 55.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1689 0.033601 AGAGCATGACGAGGAGGTCT 60.034 55.0 0.0 0.0 37.81 3.85 R
2488 2569 0.034059 CACGGTCTTGGAGCACTTCT 59.966 55.0 0.0 0.0 0.00 2.85 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
35 36 0.387202 AGCGCTGCACCACTAGATAG 59.613 55.000 10.39 0.00 0.00 2.08
93 94 6.689178 ATTTTCACAACACGAATATGCAAC 57.311 33.333 0.00 0.00 0.00 4.17
96 97 4.532276 TCACAACACGAATATGCAACAAC 58.468 39.130 0.00 0.00 0.00 3.32
363 370 5.193679 ACCCTTTCATATGTTCAGCCTAAC 58.806 41.667 1.90 0.00 0.00 2.34
369 376 5.242434 TCATATGTTCAGCCTAACGTGTTT 58.758 37.500 1.90 0.00 31.24 2.83
398 406 4.853924 ATTGGAAAACACGAGCAAGAAT 57.146 36.364 0.00 0.00 0.00 2.40
406 414 1.469703 CACGAGCAAGAATGGAATGCA 59.530 47.619 0.00 0.00 42.45 3.96
413 421 3.792401 CAAGAATGGAATGCATGCACAT 58.208 40.909 25.37 19.03 29.34 3.21
415 423 4.848562 AGAATGGAATGCATGCACATAG 57.151 40.909 25.37 0.00 29.34 2.23
430 438 4.012374 GCACATAGCCCAGCATATACAAT 58.988 43.478 0.00 0.00 37.23 2.71
492 501 3.093814 ACCAAAGTTTCGGACAAAAGGT 58.906 40.909 10.03 0.00 0.00 3.50
494 503 3.380320 CCAAAGTTTCGGACAAAAGGTCT 59.620 43.478 0.00 0.00 46.16 3.85
505 514 2.093711 ACAAAAGGTCTGTTGGCAAACC 60.094 45.455 10.89 10.89 35.25 3.27
508 517 0.106918 AGGTCTGTTGGCAAACCGAA 60.107 50.000 12.60 0.00 39.70 4.30
509 518 0.958822 GGTCTGTTGGCAAACCGAAT 59.041 50.000 0.00 0.00 39.70 3.34
513 522 3.003897 GTCTGTTGGCAAACCGAATAACA 59.996 43.478 0.00 0.00 39.70 2.41
514 523 3.823873 TCTGTTGGCAAACCGAATAACAT 59.176 39.130 0.00 0.00 39.70 2.71
537 546 5.184479 ATGATGGGACAACAAAGTGAATGAG 59.816 40.000 0.00 0.00 46.01 2.90
539 548 3.882888 TGGGACAACAAAGTGAATGAGAC 59.117 43.478 0.00 0.00 31.92 3.36
561 570 8.184304 AGACCAAACTATGTCTCATCTATACC 57.816 38.462 0.00 0.00 37.24 2.73
562 571 8.007742 AGACCAAACTATGTCTCATCTATACCT 58.992 37.037 0.00 0.00 37.24 3.08
563 572 7.957002 ACCAAACTATGTCTCATCTATACCTG 58.043 38.462 0.00 0.00 0.00 4.00
564 573 7.015682 ACCAAACTATGTCTCATCTATACCTGG 59.984 40.741 0.00 0.00 0.00 4.45
565 574 6.597832 AACTATGTCTCATCTATACCTGGC 57.402 41.667 0.00 0.00 0.00 4.85
566 575 5.020132 ACTATGTCTCATCTATACCTGGCC 58.980 45.833 0.00 0.00 0.00 5.36
567 576 3.328535 TGTCTCATCTATACCTGGCCA 57.671 47.619 4.71 4.71 0.00 5.36
568 577 3.861846 TGTCTCATCTATACCTGGCCAT 58.138 45.455 5.51 0.00 0.00 4.40
569 578 3.580022 TGTCTCATCTATACCTGGCCATG 59.420 47.826 5.51 6.06 0.00 3.66
570 579 3.055530 GTCTCATCTATACCTGGCCATGG 60.056 52.174 5.51 13.05 0.00 3.66
571 580 2.238144 CTCATCTATACCTGGCCATGGG 59.762 54.545 20.97 16.10 0.00 4.00
572 581 1.988107 CATCTATACCTGGCCATGGGT 59.012 52.381 19.76 19.76 39.40 4.51
573 582 2.206322 TCTATACCTGGCCATGGGTT 57.794 50.000 20.92 11.67 37.07 4.11
574 583 3.354233 TCTATACCTGGCCATGGGTTA 57.646 47.619 20.92 12.11 37.07 2.85
575 584 2.976882 TCTATACCTGGCCATGGGTTAC 59.023 50.000 20.92 0.00 37.07 2.50
576 585 0.850784 ATACCTGGCCATGGGTTACC 59.149 55.000 20.92 6.52 37.07 2.85
577 586 1.283381 TACCTGGCCATGGGTTACCC 61.283 60.000 20.92 14.66 45.71 3.69
586 595 4.105553 GGGTTACCCGGCCTGGTC 62.106 72.222 23.70 9.37 39.91 4.02
587 596 4.462280 GGTTACCCGGCCTGGTCG 62.462 72.222 23.70 14.95 39.91 4.79
597 606 2.281900 CCTGGTCGGCCCGAAAAA 60.282 61.111 7.77 0.00 37.72 1.94
598 607 2.332654 CCTGGTCGGCCCGAAAAAG 61.333 63.158 7.77 5.66 37.72 2.27
599 608 1.599797 CTGGTCGGCCCGAAAAAGT 60.600 57.895 7.77 0.00 37.72 2.66
600 609 1.574702 CTGGTCGGCCCGAAAAAGTC 61.575 60.000 7.77 0.00 37.72 3.01
601 610 2.330372 GGTCGGCCCGAAAAAGTCC 61.330 63.158 7.77 0.00 37.72 3.85
602 611 2.357760 TCGGCCCGAAAAAGTCCG 60.358 61.111 1.70 0.00 41.30 4.79
603 612 2.357760 CGGCCCGAAAAAGTCCGA 60.358 61.111 0.00 0.00 42.43 4.55
604 613 2.674084 CGGCCCGAAAAAGTCCGAC 61.674 63.158 0.00 0.00 42.43 4.79
605 614 2.330372 GGCCCGAAAAAGTCCGACC 61.330 63.158 0.00 0.00 0.00 4.79
606 615 2.330372 GCCCGAAAAAGTCCGACCC 61.330 63.158 0.00 0.00 0.00 4.46
607 616 2.030958 CCCGAAAAAGTCCGACCCG 61.031 63.158 0.00 0.00 0.00 5.28
618 627 4.715523 CGACCCGGTGTTGCCCAT 62.716 66.667 0.00 0.00 0.00 4.00
619 628 3.061848 GACCCGGTGTTGCCCATG 61.062 66.667 0.00 0.00 0.00 3.66
620 629 4.676951 ACCCGGTGTTGCCCATGG 62.677 66.667 4.14 4.14 0.00 3.66
643 652 3.369921 GCCTGGGCCTGAGTTTTG 58.630 61.111 12.58 0.00 34.56 2.44
644 653 1.228552 GCCTGGGCCTGAGTTTTGA 60.229 57.895 12.58 0.00 34.56 2.69
645 654 1.246737 GCCTGGGCCTGAGTTTTGAG 61.247 60.000 12.58 0.00 34.56 3.02
646 655 1.246737 CCTGGGCCTGAGTTTTGAGC 61.247 60.000 12.58 0.00 0.00 4.26
647 656 1.228552 TGGGCCTGAGTTTTGAGCC 60.229 57.895 4.53 0.00 43.09 4.70
648 657 3.686760 GGCCTGAGTTTTGAGCCC 58.313 61.111 0.00 0.00 37.66 5.19
649 658 2.335712 GGCCTGAGTTTTGAGCCCG 61.336 63.158 0.00 0.00 37.66 6.13
650 659 1.302511 GCCTGAGTTTTGAGCCCGA 60.303 57.895 0.00 0.00 0.00 5.14
651 660 0.889186 GCCTGAGTTTTGAGCCCGAA 60.889 55.000 0.00 0.00 0.00 4.30
652 661 1.160137 CCTGAGTTTTGAGCCCGAAG 58.840 55.000 0.00 0.00 0.00 3.79
653 662 0.519077 CTGAGTTTTGAGCCCGAAGC 59.481 55.000 0.00 0.00 44.25 3.86
662 671 3.414700 GCCCGAAGCACACGTCAG 61.415 66.667 0.00 0.00 42.97 3.51
663 672 2.738521 CCCGAAGCACACGTCAGG 60.739 66.667 0.00 0.00 0.00 3.86
664 673 3.414700 CCGAAGCACACGTCAGGC 61.415 66.667 0.00 0.00 0.00 4.85
665 674 3.414700 CGAAGCACACGTCAGGCC 61.415 66.667 0.00 0.00 0.00 5.19
666 675 3.414700 GAAGCACACGTCAGGCCG 61.415 66.667 0.00 0.00 0.00 6.13
667 676 4.988598 AAGCACACGTCAGGCCGG 62.989 66.667 0.00 0.00 0.00 6.13
678 687 3.801997 AGGCCGGCCTGAGATTGG 61.802 66.667 46.71 0.00 46.22 3.16
689 698 4.730949 CCTGAGATTGGCATTTTCATGT 57.269 40.909 3.48 0.00 32.28 3.21
690 699 5.080969 CCTGAGATTGGCATTTTCATGTT 57.919 39.130 3.48 0.00 32.28 2.71
691 700 5.484715 CCTGAGATTGGCATTTTCATGTTT 58.515 37.500 3.48 0.00 32.28 2.83
692 701 5.935789 CCTGAGATTGGCATTTTCATGTTTT 59.064 36.000 3.48 0.00 32.28 2.43
693 702 7.098477 CCTGAGATTGGCATTTTCATGTTTTA 58.902 34.615 3.48 0.00 32.28 1.52
694 703 7.603404 CCTGAGATTGGCATTTTCATGTTTTAA 59.397 33.333 3.48 0.00 32.28 1.52
695 704 8.537049 TGAGATTGGCATTTTCATGTTTTAAG 57.463 30.769 0.00 0.00 32.28 1.85
696 705 7.603404 TGAGATTGGCATTTTCATGTTTTAAGG 59.397 33.333 0.00 0.00 32.28 2.69
697 706 7.678837 AGATTGGCATTTTCATGTTTTAAGGA 58.321 30.769 0.00 0.00 32.28 3.36
698 707 8.156165 AGATTGGCATTTTCATGTTTTAAGGAA 58.844 29.630 0.00 0.00 32.28 3.36
699 708 7.727331 TTGGCATTTTCATGTTTTAAGGAAG 57.273 32.000 0.00 0.00 32.28 3.46
700 709 6.229733 TGGCATTTTCATGTTTTAAGGAAGG 58.770 36.000 0.00 0.00 32.28 3.46
701 710 5.643348 GGCATTTTCATGTTTTAAGGAAGGG 59.357 40.000 0.00 0.00 32.28 3.95
702 711 5.643348 GCATTTTCATGTTTTAAGGAAGGGG 59.357 40.000 0.00 0.00 32.28 4.79
703 712 4.882842 TTTCATGTTTTAAGGAAGGGGC 57.117 40.909 0.00 0.00 0.00 5.80
704 713 2.815158 TCATGTTTTAAGGAAGGGGCC 58.185 47.619 0.00 0.00 0.00 5.80
705 714 1.831106 CATGTTTTAAGGAAGGGGCCC 59.169 52.381 17.12 17.12 0.00 5.80
706 715 0.251430 TGTTTTAAGGAAGGGGCCCG 60.251 55.000 18.95 0.00 0.00 6.13
707 716 0.038599 GTTTTAAGGAAGGGGCCCGA 59.961 55.000 18.95 0.00 0.00 5.14
708 717 0.038599 TTTTAAGGAAGGGGCCCGAC 59.961 55.000 18.95 15.14 0.00 4.79
709 718 1.855441 TTTAAGGAAGGGGCCCGACC 61.855 60.000 26.17 26.17 37.93 4.79
741 750 2.403252 CCCGTCAGGCTTTATCACTT 57.597 50.000 0.00 0.00 35.76 3.16
742 751 2.711542 CCCGTCAGGCTTTATCACTTT 58.288 47.619 0.00 0.00 35.76 2.66
743 752 2.678336 CCCGTCAGGCTTTATCACTTTC 59.322 50.000 0.00 0.00 35.76 2.62
744 753 2.348666 CCGTCAGGCTTTATCACTTTCG 59.651 50.000 0.00 0.00 0.00 3.46
745 754 2.348666 CGTCAGGCTTTATCACTTTCGG 59.651 50.000 0.00 0.00 0.00 4.30
746 755 2.678336 GTCAGGCTTTATCACTTTCGGG 59.322 50.000 0.00 0.00 0.00 5.14
747 756 1.401905 CAGGCTTTATCACTTTCGGGC 59.598 52.381 0.00 0.00 0.00 6.13
748 757 0.738975 GGCTTTATCACTTTCGGGCC 59.261 55.000 0.00 0.00 0.00 5.80
749 758 0.377203 GCTTTATCACTTTCGGGCCG 59.623 55.000 22.51 22.51 0.00 6.13
750 759 1.014352 CTTTATCACTTTCGGGCCGG 58.986 55.000 27.98 13.02 0.00 6.13
751 760 0.393267 TTTATCACTTTCGGGCCGGG 60.393 55.000 27.98 18.37 0.00 5.73
752 761 1.266160 TTATCACTTTCGGGCCGGGA 61.266 55.000 27.98 15.88 0.00 5.14
753 762 1.052124 TATCACTTTCGGGCCGGGAT 61.052 55.000 27.98 21.07 0.00 3.85
754 763 1.921869 ATCACTTTCGGGCCGGGATT 61.922 55.000 27.98 6.29 0.00 3.01
755 764 2.045340 ACTTTCGGGCCGGGATTG 60.045 61.111 27.98 14.14 0.00 2.67
756 765 2.828549 CTTTCGGGCCGGGATTGG 60.829 66.667 27.98 6.96 0.00 3.16
757 766 4.434354 TTTCGGGCCGGGATTGGG 62.434 66.667 27.98 0.00 0.00 4.12
807 816 2.282462 CAGGCTCCGGCTTGGTTT 60.282 61.111 0.00 0.00 41.09 3.27
808 817 1.903404 CAGGCTCCGGCTTGGTTTT 60.903 57.895 0.00 0.00 41.09 2.43
809 818 1.603739 AGGCTCCGGCTTGGTTTTC 60.604 57.895 0.00 0.00 39.52 2.29
810 819 1.603739 GGCTCCGGCTTGGTTTTCT 60.604 57.895 0.00 0.00 39.52 2.52
811 820 1.581447 GCTCCGGCTTGGTTTTCTG 59.419 57.895 0.00 0.00 39.52 3.02
812 821 1.581447 CTCCGGCTTGGTTTTCTGC 59.419 57.895 0.00 0.00 39.52 4.26
813 822 0.890996 CTCCGGCTTGGTTTTCTGCT 60.891 55.000 0.00 0.00 39.52 4.24
814 823 0.467290 TCCGGCTTGGTTTTCTGCTT 60.467 50.000 0.00 0.00 39.52 3.91
815 824 0.039165 CCGGCTTGGTTTTCTGCTTC 60.039 55.000 0.00 0.00 0.00 3.86
816 825 0.667993 CGGCTTGGTTTTCTGCTTCA 59.332 50.000 0.00 0.00 0.00 3.02
817 826 1.335324 CGGCTTGGTTTTCTGCTTCAG 60.335 52.381 0.00 0.00 0.00 3.02
818 827 1.603931 GGCTTGGTTTTCTGCTTCAGC 60.604 52.381 0.00 0.00 42.50 4.26
819 828 1.339291 GCTTGGTTTTCTGCTTCAGCT 59.661 47.619 0.00 0.00 42.66 4.24
820 829 2.223900 GCTTGGTTTTCTGCTTCAGCTT 60.224 45.455 0.00 0.00 42.66 3.74
821 830 3.739209 GCTTGGTTTTCTGCTTCAGCTTT 60.739 43.478 0.00 0.00 42.66 3.51
822 831 3.441496 TGGTTTTCTGCTTCAGCTTTG 57.559 42.857 0.00 0.00 42.66 2.77
823 832 2.101249 TGGTTTTCTGCTTCAGCTTTGG 59.899 45.455 0.00 0.00 42.66 3.28
824 833 2.101415 GGTTTTCTGCTTCAGCTTTGGT 59.899 45.455 0.00 0.00 42.66 3.67
825 834 3.317993 GGTTTTCTGCTTCAGCTTTGGTA 59.682 43.478 0.00 0.00 42.66 3.25
826 835 4.540824 GTTTTCTGCTTCAGCTTTGGTAG 58.459 43.478 0.00 0.00 42.66 3.18
827 836 2.479566 TCTGCTTCAGCTTTGGTAGG 57.520 50.000 0.00 0.00 42.66 3.18
828 837 0.807496 CTGCTTCAGCTTTGGTAGGC 59.193 55.000 0.00 0.00 42.66 3.93
829 838 0.609131 TGCTTCAGCTTTGGTAGGCC 60.609 55.000 0.00 0.00 42.66 5.19
830 839 1.315981 GCTTCAGCTTTGGTAGGCCC 61.316 60.000 0.00 0.00 38.21 5.80
831 840 1.002624 TTCAGCTTTGGTAGGCCCG 60.003 57.895 0.00 0.00 35.15 6.13
832 841 2.438434 CAGCTTTGGTAGGCCCGG 60.438 66.667 0.00 0.00 35.15 5.73
833 842 4.426313 AGCTTTGGTAGGCCCGGC 62.426 66.667 0.00 0.00 35.15 6.13
868 877 3.323622 CCAGCAGATGGCCAGGTA 58.676 61.111 13.05 0.00 43.83 3.08
869 878 1.842007 CCAGCAGATGGCCAGGTAT 59.158 57.895 13.05 0.00 43.83 2.73
870 879 1.059098 CCAGCAGATGGCCAGGTATA 58.941 55.000 13.05 0.00 43.83 1.47
871 880 1.002888 CCAGCAGATGGCCAGGTATAG 59.997 57.143 13.05 0.00 43.83 1.31
872 881 1.973515 CAGCAGATGGCCAGGTATAGA 59.026 52.381 13.05 0.00 46.50 1.98
873 882 1.974236 AGCAGATGGCCAGGTATAGAC 59.026 52.381 13.05 0.00 46.50 2.59
874 883 1.974236 GCAGATGGCCAGGTATAGACT 59.026 52.381 13.05 0.00 36.11 3.24
875 884 2.028567 GCAGATGGCCAGGTATAGACTC 60.029 54.545 13.05 0.00 36.11 3.36
876 885 3.234353 CAGATGGCCAGGTATAGACTCA 58.766 50.000 13.05 0.00 0.00 3.41
877 886 3.837146 CAGATGGCCAGGTATAGACTCAT 59.163 47.826 13.05 0.00 0.00 2.90
878 887 4.081752 CAGATGGCCAGGTATAGACTCATC 60.082 50.000 13.05 0.00 0.00 2.92
879 888 3.619900 TGGCCAGGTATAGACTCATCT 57.380 47.619 0.00 0.00 39.15 2.90
880 889 4.741928 TGGCCAGGTATAGACTCATCTA 57.258 45.455 0.00 0.00 41.76 1.98
881 890 5.074746 TGGCCAGGTATAGACTCATCTAA 57.925 43.478 0.00 0.00 40.88 2.10
882 891 5.464069 TGGCCAGGTATAGACTCATCTAAA 58.536 41.667 0.00 0.00 40.88 1.85
883 892 6.084738 TGGCCAGGTATAGACTCATCTAAAT 58.915 40.000 0.00 0.00 40.88 1.40
884 893 6.014242 TGGCCAGGTATAGACTCATCTAAATG 60.014 42.308 0.00 0.00 40.88 2.32
885 894 6.211584 GGCCAGGTATAGACTCATCTAAATGA 59.788 42.308 0.00 0.00 40.88 2.57
897 906 6.798427 TCATCTAAATGAGTTCTAGCCACT 57.202 37.500 0.00 0.00 36.98 4.00
898 907 6.810911 TCATCTAAATGAGTTCTAGCCACTC 58.189 40.000 12.71 12.71 41.08 3.51
899 908 5.599999 TCTAAATGAGTTCTAGCCACTCC 57.400 43.478 15.57 3.39 40.12 3.85
919 928 8.585018 CCACTCCTTTATTTTTCAAACACCTAT 58.415 33.333 0.00 0.00 0.00 2.57
1019 1034 4.962751 CCACATGAAAACGCACAATTTTTG 59.037 37.500 0.00 0.00 29.44 2.44
1026 1041 2.318578 ACGCACAATTTTTGCTCGATG 58.681 42.857 6.02 0.00 37.87 3.84
1476 1491 2.025321 AGAGAAGGAGGAGGAGACTGAC 60.025 54.545 0.00 0.00 44.43 3.51
1602 1617 3.172825 GGGGTTAGGCCGGCCATA 61.173 66.667 45.13 30.18 38.92 2.74
1674 1689 1.077357 GCGAGACAGGAGGGAGAGA 60.077 63.158 0.00 0.00 0.00 3.10
1774 1823 7.408756 TGAATTGATTAATTGGACCCAAGAG 57.591 36.000 7.60 0.00 39.47 2.85
1779 1828 6.595682 TGATTAATTGGACCCAAGAGATCTC 58.404 40.000 15.29 15.29 39.47 2.75
1920 1998 1.055040 GGGGATGACTGGGAGATGAG 58.945 60.000 0.00 0.00 0.00 2.90
1990 2068 5.658190 TGTGTCAGTCATGGATGATTAGAGA 59.342 40.000 4.41 0.00 39.30 3.10
2139 2218 6.854496 TCTTGTTATAATTGATGCGTACCC 57.146 37.500 0.00 0.00 0.00 3.69
2164 2243 6.299805 TGTCATAGCCTTCTGTCTAAACAT 57.700 37.500 0.00 0.00 34.13 2.71
2215 2294 3.377485 TCTCATCTACGGTTGCTACTGTC 59.623 47.826 16.19 0.00 42.85 3.51
2221 2300 0.456312 CGGTTGCTACTGTCGAGTCC 60.456 60.000 0.00 0.00 33.21 3.85
2233 2312 3.162666 TGTCGAGTCCTGTGAATAAGGT 58.837 45.455 0.00 0.00 36.14 3.50
2234 2313 3.576982 TGTCGAGTCCTGTGAATAAGGTT 59.423 43.478 0.00 0.00 36.14 3.50
2276 2355 7.280876 CAGTTTGGCACTACTACACATATGATT 59.719 37.037 10.38 0.00 32.76 2.57
2427 2508 2.902705 ACCGTTGCTTCACTGTAGAA 57.097 45.000 0.00 0.00 0.00 2.10
2437 2518 4.503296 GCTTCACTGTAGAAGAGGTTTGGA 60.503 45.833 18.02 0.00 46.18 3.53
2488 2569 5.048083 GGTAGTTGCAGAATGTTTTCATCCA 60.048 40.000 0.00 0.00 39.94 3.41
2500 2581 3.507162 TTTCATCCAGAAGTGCTCCAA 57.493 42.857 0.00 0.00 37.57 3.53
2518 2599 2.353704 CCAAGACCGTGTAGCTTGATCA 60.354 50.000 0.00 0.00 41.03 2.92
2692 3526 3.072330 TCAAATTGTGCTGGACTCAGGTA 59.928 43.478 0.00 0.00 41.19 3.08
2696 3530 3.101643 TGTGCTGGACTCAGGTACTAT 57.898 47.619 0.00 0.00 41.19 2.12
2735 3570 5.499139 TTTTCGGCTATGAATTGATGGAC 57.501 39.130 0.00 0.00 0.00 4.02
2742 3577 2.133281 TGAATTGATGGACCTGCTGG 57.867 50.000 8.29 8.29 39.83 4.85
2748 3583 0.393537 GATGGACCTGCTGGACCTTG 60.394 60.000 26.35 0.00 46.17 3.61
2758 3593 4.156739 CCTGCTGGACCTTGAATTTAACTC 59.843 45.833 2.92 0.00 34.57 3.01
2759 3594 4.724399 TGCTGGACCTTGAATTTAACTCA 58.276 39.130 0.00 0.00 0.00 3.41
2765 3600 7.514721 TGGACCTTGAATTTAACTCAAGTACT 58.485 34.615 13.84 0.00 45.53 2.73
2831 3666 3.126001 TGAACCTGACCAGTGATTCAC 57.874 47.619 8.82 8.82 34.10 3.18
2836 3671 3.265221 ACCTGACCAGTGATTCACATGAT 59.735 43.478 18.57 1.57 36.74 2.45
2839 3674 5.106876 TGACCAGTGATTCACATGATCAT 57.893 39.130 18.57 1.18 36.74 2.45
2843 3678 3.630312 CAGTGATTCACATGATCATGCCA 59.370 43.478 31.17 17.53 42.39 4.92
2858 3693 0.881118 TGCCACTCATTTTCGAAGCC 59.119 50.000 0.00 0.00 0.00 4.35
2859 3694 0.179189 GCCACTCATTTTCGAAGCCG 60.179 55.000 0.00 0.00 37.07 5.52
2863 3698 2.092838 CACTCATTTTCGAAGCCGAGAC 59.907 50.000 20.18 0.00 46.39 3.36
2877 3712 1.271926 CCGAGACCCCCAGTTTTCATT 60.272 52.381 0.00 0.00 0.00 2.57
2900 3738 5.607477 TGGAACGGATTGATACTGGTTATC 58.393 41.667 0.00 0.00 37.67 1.75
2917 3755 9.268282 ACTGGTTATCTACTGGAGAAGAAAATA 57.732 33.333 0.00 0.00 37.85 1.40
2942 3780 3.446516 AGTAAAGAACGGATAGACGCCTT 59.553 43.478 0.00 0.00 37.37 4.35
2951 3789 0.539051 ATAGACGCCTTGCTGCTTCT 59.461 50.000 0.00 7.40 41.96 2.85
2955 3793 1.103398 ACGCCTTGCTGCTTCTTTGT 61.103 50.000 0.00 0.00 0.00 2.83
2981 3819 6.721318 TCATTTCCTTATAAACAGCAGGACT 58.279 36.000 0.00 0.00 35.04 3.85
2992 3830 5.596836 AACAGCAGGACTTTCAAATTTGA 57.403 34.783 16.91 16.91 34.92 2.69
3045 3883 4.359706 GCAGAAAAACAATGGTCGAAGTT 58.640 39.130 0.00 0.00 0.00 2.66
3046 3884 4.803613 GCAGAAAAACAATGGTCGAAGTTT 59.196 37.500 0.00 0.00 35.87 2.66
3047 3885 5.276348 GCAGAAAAACAATGGTCGAAGTTTG 60.276 40.000 0.00 0.00 34.70 2.93
3048 3886 5.231991 CAGAAAAACAATGGTCGAAGTTTGG 59.768 40.000 0.00 0.00 34.70 3.28
3049 3887 3.726291 AAACAATGGTCGAAGTTTGGG 57.274 42.857 0.00 0.00 33.35 4.12
3051 3889 3.495434 ACAATGGTCGAAGTTTGGGTA 57.505 42.857 0.00 0.00 0.00 3.69
3052 3890 3.408634 ACAATGGTCGAAGTTTGGGTAG 58.591 45.455 0.00 0.00 0.00 3.18
3055 3919 1.141254 TGGTCGAAGTTTGGGTAGCAA 59.859 47.619 0.00 0.00 0.00 3.91
3060 3924 4.156008 GTCGAAGTTTGGGTAGCAATCAAT 59.844 41.667 0.00 0.00 0.00 2.57
3070 3934 5.133221 GGGTAGCAATCAATTATCACCTGT 58.867 41.667 0.00 0.00 0.00 4.00
3110 3974 2.554032 GCAGTTGTGTGGTAAGCAGAAT 59.446 45.455 0.00 0.00 0.00 2.40
3141 4005 2.693069 ACACTAAGATGCTGTGCACTC 58.307 47.619 19.41 10.42 43.04 3.51
3198 4062 7.695618 GCTGTTCATAAGCAAGAAATGTCTAAG 59.304 37.037 0.00 0.00 40.52 2.18
3235 4099 2.094338 CCAAGCAAGAAATGGCTTCCTC 60.094 50.000 0.00 0.00 46.82 3.71
3240 4104 1.573108 AGAAATGGCTTCCTCGAGGA 58.427 50.000 30.49 30.49 43.73 3.71
3244 4108 0.324738 ATGGCTTCCTCGAGGACTCA 60.325 55.000 33.75 27.89 45.39 3.41
3245 4109 0.967887 TGGCTTCCTCGAGGACTCAG 60.968 60.000 33.75 27.24 45.39 3.35
3246 4110 1.671901 GGCTTCCTCGAGGACTCAGG 61.672 65.000 33.75 20.14 45.39 3.86
3259 4123 2.616510 GGACTCAGGTCAGTGGGAAATG 60.617 54.545 0.00 0.00 43.77 2.32
3311 4175 7.550551 TCTCAGACATACCATCATTCAGAAAAC 59.449 37.037 0.00 0.00 0.00 2.43
3324 4188 3.136763 TCAGAAAACAGCTCAGCTCTTG 58.863 45.455 0.00 0.00 36.40 3.02
3326 4190 2.158696 AGAAAACAGCTCAGCTCTTGGT 60.159 45.455 0.00 0.00 36.40 3.67
3337 4201 3.646162 TCAGCTCTTGGTCTCCTTAACAA 59.354 43.478 0.00 0.00 0.00 2.83
3349 4213 5.860716 GTCTCCTTAACAAGTGGTACTAACG 59.139 44.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.326283 AGTAGATCCTATCTAGTGGTGCA 57.674 43.478 3.94 0.00 42.44 4.57
69 70 7.363431 TGTTGCATATTCGTGTTGTGAAAATA 58.637 30.769 0.00 0.00 0.00 1.40
70 71 6.212235 TGTTGCATATTCGTGTTGTGAAAAT 58.788 32.000 0.00 0.00 0.00 1.82
219 226 9.753669 AAACGACAAAAGAAACATTGAATTTTC 57.246 25.926 0.00 5.34 32.76 2.29
224 231 6.146184 TGCAAAACGACAAAAGAAACATTGAA 59.854 30.769 0.00 0.00 0.00 2.69
324 331 0.538977 GGGTCAGCTGCCATGCATAT 60.539 55.000 23.05 0.00 38.13 1.78
325 332 1.152902 GGGTCAGCTGCCATGCATA 60.153 57.895 23.05 0.00 38.13 3.14
326 333 2.441532 GGGTCAGCTGCCATGCAT 60.442 61.111 23.05 0.00 38.13 3.96
327 334 2.718487 AAAGGGTCAGCTGCCATGCA 62.718 55.000 23.05 0.00 36.92 3.96
328 335 1.941999 GAAAGGGTCAGCTGCCATGC 61.942 60.000 23.05 12.06 0.00 4.06
329 336 0.609957 TGAAAGGGTCAGCTGCCATG 60.610 55.000 23.05 0.00 0.00 3.66
330 337 0.333993 ATGAAAGGGTCAGCTGCCAT 59.666 50.000 23.05 16.38 40.43 4.40
363 370 0.958091 TCCAATTCTGGCCAAACACG 59.042 50.000 7.01 0.00 43.17 4.49
369 376 1.339610 CGTGTTTTCCAATTCTGGCCA 59.660 47.619 4.71 4.71 43.17 5.36
375 382 4.223320 TCTTGCTCGTGTTTTCCAATTC 57.777 40.909 0.00 0.00 0.00 2.17
387 394 1.825090 TGCATTCCATTCTTGCTCGT 58.175 45.000 0.00 0.00 37.28 4.18
398 406 1.034356 GGCTATGTGCATGCATTCCA 58.966 50.000 25.64 17.76 45.15 3.53
406 414 2.893215 ATATGCTGGGCTATGTGCAT 57.107 45.000 0.00 0.00 46.22 3.96
413 421 3.181446 TGTGCATTGTATATGCTGGGCTA 60.181 43.478 10.67 0.00 44.79 3.93
415 423 1.955778 TGTGCATTGTATATGCTGGGC 59.044 47.619 10.67 0.00 44.79 5.36
481 490 0.310854 GCCAACAGACCTTTTGTCCG 59.689 55.000 0.00 0.00 45.68 4.79
492 501 3.215151 TGTTATTCGGTTTGCCAACAGA 58.785 40.909 2.78 0.99 35.56 3.41
494 503 3.570125 TCATGTTATTCGGTTTGCCAACA 59.430 39.130 2.78 0.00 34.15 3.33
505 514 5.559427 TTGTTGTCCCATCATGTTATTCG 57.441 39.130 0.00 0.00 0.00 3.34
508 517 6.009589 TCACTTTGTTGTCCCATCATGTTAT 58.990 36.000 0.00 0.00 0.00 1.89
509 518 5.380900 TCACTTTGTTGTCCCATCATGTTA 58.619 37.500 0.00 0.00 0.00 2.41
513 522 5.078949 TCATTCACTTTGTTGTCCCATCAT 58.921 37.500 0.00 0.00 0.00 2.45
514 523 4.468713 TCATTCACTTTGTTGTCCCATCA 58.531 39.130 0.00 0.00 0.00 3.07
537 546 8.085296 CAGGTATAGATGAGACATAGTTTGGTC 58.915 40.741 0.00 0.00 0.00 4.02
539 548 7.382110 CCAGGTATAGATGAGACATAGTTTGG 58.618 42.308 0.00 0.00 0.00 3.28
558 567 2.313362 GGTAACCCATGGCCAGGTA 58.687 57.895 16.63 0.17 34.45 3.08
559 568 3.096357 GGTAACCCATGGCCAGGT 58.904 61.111 17.55 14.08 38.27 4.00
571 580 4.462280 CCGACCAGGCCGGGTAAC 62.462 72.222 28.75 15.45 42.53 2.50
580 589 2.281900 TTTTTCGGGCCGACCAGG 60.282 61.111 31.23 0.00 44.97 4.45
581 590 1.574702 GACTTTTTCGGGCCGACCAG 61.575 60.000 31.23 24.93 40.22 4.00
582 591 1.598685 GACTTTTTCGGGCCGACCA 60.599 57.895 31.23 16.19 40.22 4.02
583 592 2.330372 GGACTTTTTCGGGCCGACC 61.330 63.158 31.23 21.62 34.89 4.79
584 593 2.674084 CGGACTTTTTCGGGCCGAC 61.674 63.158 31.23 16.12 44.43 4.79
585 594 2.357760 CGGACTTTTTCGGGCCGA 60.358 61.111 27.46 27.46 44.43 5.54
586 595 2.357760 TCGGACTTTTTCGGGCCG 60.358 61.111 22.51 22.51 43.11 6.13
587 596 2.330372 GGTCGGACTTTTTCGGGCC 61.330 63.158 8.23 0.00 41.68 5.80
588 597 2.330372 GGGTCGGACTTTTTCGGGC 61.330 63.158 8.23 0.00 0.00 6.13
589 598 2.030958 CGGGTCGGACTTTTTCGGG 61.031 63.158 8.23 0.00 0.00 5.14
590 599 3.557824 CGGGTCGGACTTTTTCGG 58.442 61.111 8.23 0.00 0.00 4.30
601 610 4.715523 ATGGGCAACACCGGGTCG 62.716 66.667 6.32 0.00 40.62 4.79
602 611 3.061848 CATGGGCAACACCGGGTC 61.062 66.667 6.32 0.00 40.62 4.46
603 612 4.676951 CCATGGGCAACACCGGGT 62.677 66.667 6.32 0.00 40.62 5.28
626 635 1.228552 TCAAAACTCAGGCCCAGGC 60.229 57.895 0.00 0.00 41.06 4.85
627 636 1.246737 GCTCAAAACTCAGGCCCAGG 61.247 60.000 0.00 0.00 0.00 4.45
628 637 1.246737 GGCTCAAAACTCAGGCCCAG 61.247 60.000 0.00 0.00 37.12 4.45
629 638 1.228552 GGCTCAAAACTCAGGCCCA 60.229 57.895 0.00 0.00 37.12 5.36
630 639 3.686760 GGCTCAAAACTCAGGCCC 58.313 61.111 0.00 0.00 37.12 5.80
632 641 0.889186 TTCGGGCTCAAAACTCAGGC 60.889 55.000 0.00 0.00 34.44 4.85
633 642 1.160137 CTTCGGGCTCAAAACTCAGG 58.840 55.000 0.00 0.00 0.00 3.86
634 643 0.519077 GCTTCGGGCTCAAAACTCAG 59.481 55.000 0.00 0.00 38.06 3.35
635 644 0.179032 TGCTTCGGGCTCAAAACTCA 60.179 50.000 3.33 0.00 42.39 3.41
636 645 0.238553 GTGCTTCGGGCTCAAAACTC 59.761 55.000 3.33 0.00 42.39 3.01
637 646 0.465460 TGTGCTTCGGGCTCAAAACT 60.465 50.000 4.21 0.00 40.78 2.66
638 647 0.317854 GTGTGCTTCGGGCTCAAAAC 60.318 55.000 7.39 0.00 44.42 2.43
639 648 1.781025 CGTGTGCTTCGGGCTCAAAA 61.781 55.000 7.39 0.00 44.42 2.44
640 649 2.250939 CGTGTGCTTCGGGCTCAAA 61.251 57.895 7.39 0.00 44.42 2.69
641 650 2.664851 CGTGTGCTTCGGGCTCAA 60.665 61.111 7.39 0.00 44.42 3.02
642 651 3.858868 GACGTGTGCTTCGGGCTCA 62.859 63.158 0.00 3.10 41.35 4.26
643 652 3.112709 GACGTGTGCTTCGGGCTC 61.113 66.667 0.00 0.73 42.39 4.70
644 653 3.865929 CTGACGTGTGCTTCGGGCT 62.866 63.158 0.00 0.00 42.39 5.19
645 654 3.414700 CTGACGTGTGCTTCGGGC 61.415 66.667 0.00 0.00 42.22 6.13
646 655 2.738521 CCTGACGTGTGCTTCGGG 60.739 66.667 0.00 0.00 33.82 5.14
647 656 3.414700 GCCTGACGTGTGCTTCGG 61.415 66.667 0.00 0.00 0.00 4.30
648 657 3.414700 GGCCTGACGTGTGCTTCG 61.415 66.667 0.00 0.00 0.00 3.79
649 658 3.414700 CGGCCTGACGTGTGCTTC 61.415 66.667 0.00 0.00 0.00 3.86
650 659 4.988598 CCGGCCTGACGTGTGCTT 62.989 66.667 0.00 0.00 0.00 3.91
668 677 4.730949 ACATGAAAATGCCAATCTCAGG 57.269 40.909 0.00 0.00 0.00 3.86
669 678 8.537049 TTAAAACATGAAAATGCCAATCTCAG 57.463 30.769 0.00 0.00 0.00 3.35
670 679 7.603404 CCTTAAAACATGAAAATGCCAATCTCA 59.397 33.333 0.00 0.00 0.00 3.27
671 680 7.818930 TCCTTAAAACATGAAAATGCCAATCTC 59.181 33.333 0.00 0.00 0.00 2.75
672 681 7.678837 TCCTTAAAACATGAAAATGCCAATCT 58.321 30.769 0.00 0.00 0.00 2.40
673 682 7.903995 TCCTTAAAACATGAAAATGCCAATC 57.096 32.000 0.00 0.00 0.00 2.67
674 683 7.391275 CCTTCCTTAAAACATGAAAATGCCAAT 59.609 33.333 0.00 0.00 0.00 3.16
675 684 6.709846 CCTTCCTTAAAACATGAAAATGCCAA 59.290 34.615 0.00 0.00 0.00 4.52
676 685 6.229733 CCTTCCTTAAAACATGAAAATGCCA 58.770 36.000 0.00 0.00 0.00 4.92
677 686 5.643348 CCCTTCCTTAAAACATGAAAATGCC 59.357 40.000 0.00 0.00 0.00 4.40
678 687 5.643348 CCCCTTCCTTAAAACATGAAAATGC 59.357 40.000 0.00 0.00 0.00 3.56
679 688 5.643348 GCCCCTTCCTTAAAACATGAAAATG 59.357 40.000 0.00 0.00 0.00 2.32
680 689 5.280470 GGCCCCTTCCTTAAAACATGAAAAT 60.280 40.000 0.00 0.00 0.00 1.82
681 690 4.041075 GGCCCCTTCCTTAAAACATGAAAA 59.959 41.667 0.00 0.00 0.00 2.29
682 691 3.580895 GGCCCCTTCCTTAAAACATGAAA 59.419 43.478 0.00 0.00 0.00 2.69
683 692 3.169908 GGCCCCTTCCTTAAAACATGAA 58.830 45.455 0.00 0.00 0.00 2.57
684 693 2.558800 GGGCCCCTTCCTTAAAACATGA 60.559 50.000 12.23 0.00 0.00 3.07
685 694 1.831106 GGGCCCCTTCCTTAAAACATG 59.169 52.381 12.23 0.00 0.00 3.21
686 695 1.618616 CGGGCCCCTTCCTTAAAACAT 60.619 52.381 18.66 0.00 0.00 2.71
687 696 0.251430 CGGGCCCCTTCCTTAAAACA 60.251 55.000 18.66 0.00 0.00 2.83
688 697 0.038599 TCGGGCCCCTTCCTTAAAAC 59.961 55.000 18.66 0.00 0.00 2.43
689 698 0.038599 GTCGGGCCCCTTCCTTAAAA 59.961 55.000 18.66 0.00 0.00 1.52
690 699 1.687014 GTCGGGCCCCTTCCTTAAA 59.313 57.895 18.66 0.00 0.00 1.52
691 700 2.303282 GGTCGGGCCCCTTCCTTAA 61.303 63.158 18.66 0.00 0.00 1.85
692 701 2.689771 GGTCGGGCCCCTTCCTTA 60.690 66.667 18.66 0.00 0.00 2.69
722 731 2.403252 AAGTGATAAAGCCTGACGGG 57.597 50.000 0.00 0.00 38.36 5.28
723 732 2.348666 CGAAAGTGATAAAGCCTGACGG 59.651 50.000 0.00 0.00 0.00 4.79
724 733 2.348666 CCGAAAGTGATAAAGCCTGACG 59.651 50.000 0.00 0.00 0.00 4.35
725 734 2.678336 CCCGAAAGTGATAAAGCCTGAC 59.322 50.000 0.00 0.00 0.00 3.51
726 735 2.939640 GCCCGAAAGTGATAAAGCCTGA 60.940 50.000 0.00 0.00 0.00 3.86
727 736 1.401905 GCCCGAAAGTGATAAAGCCTG 59.598 52.381 0.00 0.00 0.00 4.85
728 737 1.682087 GGCCCGAAAGTGATAAAGCCT 60.682 52.381 0.00 0.00 36.22 4.58
729 738 0.738975 GGCCCGAAAGTGATAAAGCC 59.261 55.000 0.00 0.00 0.00 4.35
730 739 0.377203 CGGCCCGAAAGTGATAAAGC 59.623 55.000 0.00 0.00 0.00 3.51
731 740 1.014352 CCGGCCCGAAAGTGATAAAG 58.986 55.000 3.71 0.00 0.00 1.85
732 741 0.393267 CCCGGCCCGAAAGTGATAAA 60.393 55.000 3.71 0.00 0.00 1.40
733 742 1.222387 CCCGGCCCGAAAGTGATAA 59.778 57.895 3.71 0.00 0.00 1.75
734 743 1.052124 ATCCCGGCCCGAAAGTGATA 61.052 55.000 3.71 0.00 0.00 2.15
735 744 1.921869 AATCCCGGCCCGAAAGTGAT 61.922 55.000 3.71 0.00 0.00 3.06
736 745 2.598787 AATCCCGGCCCGAAAGTGA 61.599 57.895 3.71 0.00 0.00 3.41
737 746 2.045340 AATCCCGGCCCGAAAGTG 60.045 61.111 3.71 0.00 0.00 3.16
738 747 2.045340 CAATCCCGGCCCGAAAGT 60.045 61.111 3.71 0.00 0.00 2.66
739 748 2.828549 CCAATCCCGGCCCGAAAG 60.829 66.667 3.71 0.00 0.00 2.62
740 749 4.434354 CCCAATCCCGGCCCGAAA 62.434 66.667 3.71 0.00 0.00 3.46
790 799 1.866853 GAAAACCAAGCCGGAGCCTG 61.867 60.000 5.05 0.00 41.25 4.85
791 800 1.603739 GAAAACCAAGCCGGAGCCT 60.604 57.895 5.05 0.00 41.25 4.58
792 801 1.603739 AGAAAACCAAGCCGGAGCC 60.604 57.895 5.05 0.00 41.25 4.70
793 802 1.581447 CAGAAAACCAAGCCGGAGC 59.419 57.895 5.05 0.00 38.63 4.70
794 803 0.890996 AGCAGAAAACCAAGCCGGAG 60.891 55.000 5.05 0.00 38.63 4.63
795 804 0.467290 AAGCAGAAAACCAAGCCGGA 60.467 50.000 5.05 0.00 38.63 5.14
796 805 0.039165 GAAGCAGAAAACCAAGCCGG 60.039 55.000 0.00 0.00 42.50 6.13
797 806 0.667993 TGAAGCAGAAAACCAAGCCG 59.332 50.000 0.00 0.00 0.00 5.52
798 807 1.603931 GCTGAAGCAGAAAACCAAGCC 60.604 52.381 0.00 0.00 41.59 4.35
799 808 1.339291 AGCTGAAGCAGAAAACCAAGC 59.661 47.619 4.90 0.00 45.16 4.01
800 809 3.722728 AAGCTGAAGCAGAAAACCAAG 57.277 42.857 4.90 0.00 45.16 3.61
801 810 3.430651 CCAAAGCTGAAGCAGAAAACCAA 60.431 43.478 4.90 0.00 45.16 3.67
802 811 2.101249 CCAAAGCTGAAGCAGAAAACCA 59.899 45.455 4.90 0.00 45.16 3.67
803 812 2.101415 ACCAAAGCTGAAGCAGAAAACC 59.899 45.455 4.90 0.00 45.16 3.27
804 813 3.443099 ACCAAAGCTGAAGCAGAAAAC 57.557 42.857 4.90 0.00 45.16 2.43
805 814 3.569701 CCTACCAAAGCTGAAGCAGAAAA 59.430 43.478 4.90 0.00 45.16 2.29
806 815 3.149196 CCTACCAAAGCTGAAGCAGAAA 58.851 45.455 4.90 0.00 45.16 2.52
807 816 2.783135 CCTACCAAAGCTGAAGCAGAA 58.217 47.619 4.90 0.00 45.16 3.02
808 817 1.611673 GCCTACCAAAGCTGAAGCAGA 60.612 52.381 4.90 0.00 45.16 4.26
809 818 0.807496 GCCTACCAAAGCTGAAGCAG 59.193 55.000 4.90 0.00 45.16 4.24
810 819 0.609131 GGCCTACCAAAGCTGAAGCA 60.609 55.000 4.90 0.00 38.78 3.91
811 820 1.315981 GGGCCTACCAAAGCTGAAGC 61.316 60.000 0.84 0.00 39.85 3.86
812 821 1.026718 CGGGCCTACCAAAGCTGAAG 61.027 60.000 0.84 0.00 40.22 3.02
813 822 1.002624 CGGGCCTACCAAAGCTGAA 60.003 57.895 0.84 0.00 40.22 3.02
814 823 2.668632 CGGGCCTACCAAAGCTGA 59.331 61.111 0.84 0.00 40.22 4.26
815 824 2.438434 CCGGGCCTACCAAAGCTG 60.438 66.667 0.84 0.00 40.22 4.24
816 825 4.426313 GCCGGGCCTACCAAAGCT 62.426 66.667 8.12 0.00 40.22 3.74
850 859 1.713005 ATACCTGGCCATCTGCTGGG 61.713 60.000 5.51 4.26 46.06 4.45
852 861 1.973515 TCTATACCTGGCCATCTGCTG 59.026 52.381 5.51 0.00 40.92 4.41
853 862 1.974236 GTCTATACCTGGCCATCTGCT 59.026 52.381 5.51 0.00 40.92 4.24
854 863 1.974236 AGTCTATACCTGGCCATCTGC 59.026 52.381 5.51 0.00 40.16 4.26
855 864 3.234353 TGAGTCTATACCTGGCCATCTG 58.766 50.000 5.51 0.00 0.00 2.90
856 865 3.619900 TGAGTCTATACCTGGCCATCT 57.380 47.619 5.51 0.00 0.00 2.90
857 866 4.093011 AGATGAGTCTATACCTGGCCATC 58.907 47.826 5.51 0.00 31.36 3.51
858 867 4.139162 AGATGAGTCTATACCTGGCCAT 57.861 45.455 5.51 0.00 31.36 4.40
859 868 3.619900 AGATGAGTCTATACCTGGCCA 57.380 47.619 4.71 4.71 31.36 5.36
860 869 6.211584 TCATTTAGATGAGTCTATACCTGGCC 59.788 42.308 0.00 0.00 37.37 5.36
861 870 7.233389 TCATTTAGATGAGTCTATACCTGGC 57.767 40.000 0.00 0.00 37.37 4.85
874 883 6.183360 GGAGTGGCTAGAACTCATTTAGATGA 60.183 42.308 21.07 0.00 44.86 2.92
875 884 5.988561 GGAGTGGCTAGAACTCATTTAGATG 59.011 44.000 21.07 0.00 44.86 2.90
876 885 5.902431 AGGAGTGGCTAGAACTCATTTAGAT 59.098 40.000 21.07 2.84 44.86 1.98
877 886 5.273208 AGGAGTGGCTAGAACTCATTTAGA 58.727 41.667 21.07 0.00 44.86 2.10
878 887 5.606348 AGGAGTGGCTAGAACTCATTTAG 57.394 43.478 21.07 0.00 44.86 1.85
880 889 4.917906 AAGGAGTGGCTAGAACTCATTT 57.082 40.909 21.07 14.29 43.93 2.32
882 891 6.567602 AATAAAGGAGTGGCTAGAACTCAT 57.432 37.500 21.07 14.75 44.86 2.90
883 892 6.374417 AAATAAAGGAGTGGCTAGAACTCA 57.626 37.500 21.07 7.09 44.86 3.41
884 893 7.390718 TGAAAAATAAAGGAGTGGCTAGAACTC 59.609 37.037 14.57 14.57 42.79 3.01
885 894 7.231467 TGAAAAATAAAGGAGTGGCTAGAACT 58.769 34.615 0.00 0.00 0.00 3.01
886 895 7.448748 TGAAAAATAAAGGAGTGGCTAGAAC 57.551 36.000 0.00 0.00 0.00 3.01
887 896 8.357402 GTTTGAAAAATAAAGGAGTGGCTAGAA 58.643 33.333 0.00 0.00 0.00 2.10
888 897 7.504238 TGTTTGAAAAATAAAGGAGTGGCTAGA 59.496 33.333 0.00 0.00 0.00 2.43
889 898 7.595130 GTGTTTGAAAAATAAAGGAGTGGCTAG 59.405 37.037 0.00 0.00 0.00 3.42
890 899 7.430441 GTGTTTGAAAAATAAAGGAGTGGCTA 58.570 34.615 0.00 0.00 0.00 3.93
891 900 6.280643 GTGTTTGAAAAATAAAGGAGTGGCT 58.719 36.000 0.00 0.00 0.00 4.75
892 901 5.465390 GGTGTTTGAAAAATAAAGGAGTGGC 59.535 40.000 0.00 0.00 0.00 5.01
893 902 6.816136 AGGTGTTTGAAAAATAAAGGAGTGG 58.184 36.000 0.00 0.00 0.00 4.00
894 903 9.981114 AATAGGTGTTTGAAAAATAAAGGAGTG 57.019 29.630 0.00 0.00 0.00 3.51
919 928 4.701765 ACAATGCAATGCAAGGTGTTTAA 58.298 34.783 13.45 0.00 43.62 1.52
921 930 3.196939 ACAATGCAATGCAAGGTGTTT 57.803 38.095 13.45 0.00 43.62 2.83
924 933 3.581024 ACTACAATGCAATGCAAGGTG 57.419 42.857 13.45 13.26 43.62 4.00
925 934 4.335416 ACTACTACAATGCAATGCAAGGT 58.665 39.130 13.45 15.64 43.62 3.50
926 935 4.970662 ACTACTACAATGCAATGCAAGG 57.029 40.909 13.45 10.05 43.62 3.61
1026 1041 7.795431 TTCAATTTGCGTTTGAGATGTTATC 57.205 32.000 0.00 0.00 34.76 1.75
1476 1491 2.752238 AGCCACTCCTCCTCGTCG 60.752 66.667 0.00 0.00 0.00 5.12
1545 1560 3.303135 ACGAGCACGGCCTCTGAA 61.303 61.111 8.74 0.00 44.46 3.02
1590 1605 2.579657 CGACCATATGGCCGGCCTA 61.580 63.158 43.34 31.56 37.42 3.93
1674 1689 0.033601 AGAGCATGACGAGGAGGTCT 60.034 55.000 0.00 0.00 37.81 3.85
1760 1809 5.198965 CAATGAGATCTCTTGGGTCCAATT 58.801 41.667 22.95 8.52 35.20 2.32
1774 1823 7.867305 AATGATGATAGATGCCAATGAGATC 57.133 36.000 0.00 0.00 0.00 2.75
1808 1859 9.012161 CCCCAATTATCAATTGTTTTGAATGTT 57.988 29.630 5.13 0.00 45.28 2.71
1818 1869 9.833179 ATATCATCTTCCCCAATTATCAATTGT 57.167 29.630 5.13 0.00 45.28 2.71
1820 1871 9.833179 ACATATCATCTTCCCCAATTATCAATT 57.167 29.630 0.00 0.00 0.00 2.32
1823 1874 9.910267 CATACATATCATCTTCCCCAATTATCA 57.090 33.333 0.00 0.00 0.00 2.15
1920 1998 7.992754 AATGGAGTGAATAAAGGATATCTGC 57.007 36.000 2.05 0.00 0.00 4.26
1990 2068 0.545071 CCCAGCCCCAAAACCAAGAT 60.545 55.000 0.00 0.00 0.00 2.40
2133 2212 2.431057 AGAAGGCTATGACAAGGGTACG 59.569 50.000 0.00 0.00 0.00 3.67
2139 2218 6.166279 TGTTTAGACAGAAGGCTATGACAAG 58.834 40.000 6.64 0.00 0.00 3.16
2215 2294 5.962433 TCTAAACCTTATTCACAGGACTCG 58.038 41.667 0.00 0.00 35.14 4.18
2221 2300 9.643693 AAATGCATTTCTAAACCTTATTCACAG 57.356 29.630 18.99 0.00 0.00 3.66
2253 2332 9.845740 AATAATCATATGTGTAGTAGTGCCAAA 57.154 29.630 1.90 0.00 0.00 3.28
2393 2474 3.125316 GCAACGGTTAAGAGTTCCTCATG 59.875 47.826 0.00 0.00 32.06 3.07
2427 2508 6.374417 ACACAGTATTACATCCAAACCTCT 57.626 37.500 0.00 0.00 0.00 3.69
2437 2518 6.472887 ACCAAAGTGCTACACAGTATTACAT 58.527 36.000 0.00 0.00 36.74 2.29
2488 2569 0.034059 CACGGTCTTGGAGCACTTCT 59.966 55.000 0.00 0.00 0.00 2.85
2500 2581 2.563179 ACTTGATCAAGCTACACGGTCT 59.437 45.455 30.95 8.50 41.99 3.85
2518 2599 7.052873 AGATCATGCAACTGAGCTAATTACTT 58.947 34.615 6.29 0.00 39.97 2.24
2553 2636 8.078596 GCAGTTCTTCAATTACAGAAACATCTT 58.921 33.333 1.04 0.00 30.76 2.40
2554 2637 7.229306 TGCAGTTCTTCAATTACAGAAACATCT 59.771 33.333 1.04 0.00 30.76 2.90
2562 3395 7.140705 TGATGTTTGCAGTTCTTCAATTACAG 58.859 34.615 0.00 0.00 0.00 2.74
2568 3401 3.633525 AGCTGATGTTTGCAGTTCTTCAA 59.366 39.130 0.00 0.00 35.81 2.69
2571 3404 3.911661 GAGCTGATGTTTGCAGTTCTT 57.088 42.857 0.00 0.00 39.55 2.52
2660 3493 6.311200 GTCCAGCACAATTTGAACATATTTCC 59.689 38.462 2.79 0.00 0.00 3.13
2665 3498 5.069318 TGAGTCCAGCACAATTTGAACATA 58.931 37.500 2.79 0.00 0.00 2.29
2668 3501 3.304928 CCTGAGTCCAGCACAATTTGAAC 60.305 47.826 2.79 0.00 39.07 3.18
2669 3502 2.886523 CCTGAGTCCAGCACAATTTGAA 59.113 45.455 2.79 0.00 39.07 2.69
2671 3504 2.233271 ACCTGAGTCCAGCACAATTTG 58.767 47.619 0.00 0.00 39.07 2.32
2677 3510 6.659668 TCATATATAGTACCTGAGTCCAGCAC 59.340 42.308 0.00 0.00 39.07 4.40
2718 3552 2.555757 GCAGGTCCATCAATTCATAGCC 59.444 50.000 0.00 0.00 0.00 3.93
2719 3553 3.252701 CAGCAGGTCCATCAATTCATAGC 59.747 47.826 0.00 0.00 0.00 2.97
2720 3554 3.819337 CCAGCAGGTCCATCAATTCATAG 59.181 47.826 0.00 0.00 0.00 2.23
2735 3570 4.082125 AGTTAAATTCAAGGTCCAGCAGG 58.918 43.478 0.00 0.00 0.00 4.85
2800 3635 5.104941 ACTGGTCAGGTTCATTCATAATCGA 60.105 40.000 2.87 0.00 0.00 3.59
2805 3640 5.698741 ATCACTGGTCAGGTTCATTCATA 57.301 39.130 2.87 0.00 0.00 2.15
2808 3643 4.154918 GTGAATCACTGGTCAGGTTCATTC 59.845 45.833 6.07 10.30 33.96 2.67
2814 3649 2.639347 TCATGTGAATCACTGGTCAGGT 59.361 45.455 14.97 0.00 35.11 4.00
2815 3650 3.339253 TCATGTGAATCACTGGTCAGG 57.661 47.619 14.97 0.00 35.11 3.86
2831 3666 4.035909 TCGAAAATGAGTGGCATGATCATG 59.964 41.667 28.04 28.04 41.60 3.07
2836 3671 2.162208 GCTTCGAAAATGAGTGGCATGA 59.838 45.455 0.00 0.00 37.28 3.07
2839 3674 0.881118 GGCTTCGAAAATGAGTGGCA 59.119 50.000 0.00 0.00 0.00 4.92
2843 3678 2.338500 GTCTCGGCTTCGAAAATGAGT 58.662 47.619 15.60 0.00 42.80 3.41
2858 3693 1.812571 CAATGAAAACTGGGGGTCTCG 59.187 52.381 0.00 0.00 0.00 4.04
2859 3694 2.171003 CCAATGAAAACTGGGGGTCTC 58.829 52.381 0.00 0.00 0.00 3.36
2863 3698 1.272212 CGTTCCAATGAAAACTGGGGG 59.728 52.381 0.00 0.00 33.19 5.40
2877 3712 3.992943 AACCAGTATCAATCCGTTCCA 57.007 42.857 0.00 0.00 0.00 3.53
2917 3755 4.628766 GGCGTCTATCCGTTCTTTACTTTT 59.371 41.667 0.00 0.00 0.00 2.27
2921 3759 3.433513 AGGCGTCTATCCGTTCTTTAC 57.566 47.619 0.00 0.00 0.00 2.01
2930 3768 0.462759 AAGCAGCAAGGCGTCTATCC 60.463 55.000 0.00 0.00 39.27 2.59
2934 3772 2.746359 AGAAGCAGCAAGGCGTCT 59.254 55.556 7.45 7.45 45.66 4.18
2935 3773 0.386478 CAAAGAAGCAGCAAGGCGTC 60.386 55.000 0.00 3.49 41.69 5.19
2942 3780 4.099881 AGGAAATGAAACAAAGAAGCAGCA 59.900 37.500 0.00 0.00 0.00 4.41
2951 3789 9.474920 CTGCTGTTTATAAGGAAATGAAACAAA 57.525 29.630 0.00 0.00 38.97 2.83
2955 3793 7.669722 AGTCCTGCTGTTTATAAGGAAATGAAA 59.330 33.333 0.00 0.00 40.45 2.69
2992 3830 2.722094 TCCAAACTGTGTGCAGACTTT 58.278 42.857 15.76 5.51 45.28 2.66
2995 3833 1.334869 CCTTCCAAACTGTGTGCAGAC 59.665 52.381 7.12 7.12 45.28 3.51
2999 3837 1.065551 GACACCTTCCAAACTGTGTGC 59.934 52.381 0.00 0.00 41.69 4.57
3021 3859 1.611491 TCGACCATTGTTTTTCTGCCC 59.389 47.619 0.00 0.00 0.00 5.36
3022 3860 3.243401 ACTTCGACCATTGTTTTTCTGCC 60.243 43.478 0.00 0.00 0.00 4.85
3026 3864 4.506288 CCCAAACTTCGACCATTGTTTTTC 59.494 41.667 0.00 0.00 31.30 2.29
3045 3883 5.593909 CAGGTGATAATTGATTGCTACCCAA 59.406 40.000 0.00 0.00 37.94 4.12
3046 3884 5.132502 CAGGTGATAATTGATTGCTACCCA 58.867 41.667 0.00 0.00 0.00 4.51
3047 3885 5.133221 ACAGGTGATAATTGATTGCTACCC 58.867 41.667 0.00 0.00 0.00 3.69
3048 3886 6.498304 CAACAGGTGATAATTGATTGCTACC 58.502 40.000 0.00 0.00 0.00 3.18
3049 3887 5.973565 GCAACAGGTGATAATTGATTGCTAC 59.026 40.000 0.00 0.00 38.48 3.58
3051 3889 4.708421 AGCAACAGGTGATAATTGATTGCT 59.292 37.500 2.44 2.44 44.92 3.91
3052 3890 5.002464 AGCAACAGGTGATAATTGATTGC 57.998 39.130 0.00 0.00 41.11 3.56
3055 3919 5.263599 TGGAAGCAACAGGTGATAATTGAT 58.736 37.500 0.00 0.00 0.00 2.57
3060 3924 2.754552 GCATGGAAGCAACAGGTGATAA 59.245 45.455 0.00 0.00 0.00 1.75
3070 3934 3.025262 TGCATATTCAGCATGGAAGCAA 58.975 40.909 0.00 0.00 37.02 3.91
3110 3974 7.119116 CACAGCATCTTAGTGTAACACCATAAA 59.881 37.037 0.00 0.00 41.43 1.40
3198 4062 6.913673 TCTTGCTTGGTTTTTGTAATAACGAC 59.086 34.615 0.00 0.00 0.00 4.34
3235 4099 1.599606 CCCACTGACCTGAGTCCTCG 61.600 65.000 0.00 0.00 42.81 4.63
3240 4104 1.271597 GCATTTCCCACTGACCTGAGT 60.272 52.381 0.00 0.00 0.00 3.41
3244 4108 2.684927 GCATAGCATTTCCCACTGACCT 60.685 50.000 0.00 0.00 0.00 3.85
3245 4109 1.678101 GCATAGCATTTCCCACTGACC 59.322 52.381 0.00 0.00 0.00 4.02
3246 4110 2.098117 GTGCATAGCATTTCCCACTGAC 59.902 50.000 0.00 0.00 41.91 3.51
3259 4123 2.477863 GGTGAATTGGTTCGTGCATAGC 60.478 50.000 0.00 0.00 37.15 2.97
3311 4175 0.108233 GGAGACCAAGAGCTGAGCTG 60.108 60.000 13.71 0.00 39.88 4.24
3324 4188 4.886496 AGTACCACTTGTTAAGGAGACC 57.114 45.455 0.00 0.00 0.00 3.85
3326 4190 5.769662 TCGTTAGTACCACTTGTTAAGGAGA 59.230 40.000 0.00 0.00 0.00 3.71
3337 4201 4.638304 ACAAAGCATTCGTTAGTACCACT 58.362 39.130 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.