Multiple sequence alignment - TraesCS7D01G086000

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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 TraesCS7D01G086000 chr7D 100.000 4341 0 0 1 4341 52840404 52836064 0.000000e+00 8017
1 TraesCS7D01G086000 chr7D 91.743 109 6 2 4236 4341 53410444 53410552 9.730000e-32 148
2 TraesCS7D01G086000 chr4A 92.456 2439 108 27 1930 4341 667853774 667856163 0.000000e+00 3415
3 TraesCS7D01G086000 chr4A 89.453 1005 47 26 704 1669 667852631 667853615 0.000000e+00 1214
4 TraesCS7D01G086000 chr4A 89.502 562 41 14 1 553 667852087 667852639 0.000000e+00 695
5 TraesCS7D01G086000 chr4A 94.615 130 7 0 1796 1925 667853609 667853738 7.360000e-48 202
6 TraesCS7D01G086000 chr7A 91.193 1635 96 20 2724 4341 55363765 55365368 0.000000e+00 2178
7 TraesCS7D01G086000 chr7A 91.727 834 31 17 704 1519 55361719 55362532 0.000000e+00 1123
8 TraesCS7D01G086000 chr7A 91.529 543 24 12 19 553 55361199 55361727 0.000000e+00 728
9 TraesCS7D01G086000 chr7A 80.698 860 111 36 1524 2366 55362572 55363393 6.170000e-173 617
10 TraesCS7D01G086000 chr7A 98.246 114 2 0 2541 2654 55363651 55363764 2.650000e-47 200
11 TraesCS7D01G086000 chr7A 84.058 138 6 2 2408 2545 55363392 55363513 7.630000e-23 119
12 TraesCS7D01G086000 chr6D 83.333 198 31 2 3146 3342 9868364 9868560 9.590000e-42 182
13 TraesCS7D01G086000 chrUn 87.742 155 17 2 3146 3299 479644566 479644719 3.450000e-41 180
14 TraesCS7D01G086000 chr3A 87.742 155 17 2 3146 3299 748197588 748197741 3.450000e-41 180
15 TraesCS7D01G086000 chr3A 87.742 155 17 2 3146 3299 748630642 748630795 3.450000e-41 180
16 TraesCS7D01G086000 chr6B 85.321 109 16 0 3234 3342 17989924 17989816 3.550000e-21 113


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 TraesCS7D01G086000 chr7D 52836064 52840404 4340 True 8017.0 8017 100.000000 1 4341 1 chr7D.!!$R1 4340
1 TraesCS7D01G086000 chr4A 667852087 667856163 4076 False 1381.5 3415 91.506500 1 4341 4 chr4A.!!$F1 4340
2 TraesCS7D01G086000 chr7A 55361199 55365368 4169 False 827.5 2178 89.575167 19 4341 6 chr7A.!!$F1 4322

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
669 689 0.101219 CTGAATTTGCTTAGCCGGGC 59.899 55.0 12.11 12.11 0.0 6.13 F
1535 1625 0.043310 GCGCGATTGGATTGTACGTC 60.043 55.0 12.10 0.00 0.0 4.34 F
1991 2129 0.179179 GTGCGCTTTCATCTTCTGGC 60.179 55.0 9.73 0.00 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1821 0.301687 CGATTGCGACGATTTCCCAG 59.698 55.000 0.00 0.0 40.82 4.45 R
3105 3387 0.251922 ACTGGGCATTCATGTGGCTT 60.252 50.000 9.33 0.0 43.55 4.35 R
3754 4038 2.478894 ACACGATCGATGACAAACAACC 59.521 45.455 24.34 0.0 0.00 3.77 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
72 73 1.070758 CCCGGAGTATGTGATTCCCAG 59.929 57.143 0.73 0.00 29.89 4.45
123 124 2.234414 GGCATGTTTGGTCCATGAACAT 59.766 45.455 13.92 13.92 42.85 2.71
142 143 0.321564 TGCAAATGTCCAGGACTCGG 60.322 55.000 20.82 8.66 33.15 4.63
285 289 1.741706 CAAATGCCGCACTCAGAGAAT 59.258 47.619 3.79 0.00 0.00 2.40
286 290 1.376543 AATGCCGCACTCAGAGAATG 58.623 50.000 3.79 0.00 0.00 2.67
348 352 9.339850 AGTAAACTTGTCTCGAGCTATAAGATA 57.660 33.333 14.80 7.01 0.00 1.98
374 379 8.523915 AACACCATATTTAAGCATCTGAATGA 57.476 30.769 0.00 0.00 34.61 2.57
546 566 9.851686 AACTCTTAATCATATCCAGTTTATGCA 57.148 29.630 0.00 0.00 0.00 3.96
547 567 9.851686 ACTCTTAATCATATCCAGTTTATGCAA 57.148 29.630 0.00 0.00 0.00 4.08
556 576 9.630098 CATATCCAGTTTATGCAATCAAATACC 57.370 33.333 0.00 0.00 0.00 2.73
557 577 6.130298 TCCAGTTTATGCAATCAAATACCG 57.870 37.500 0.00 0.00 0.00 4.02
558 578 5.650266 TCCAGTTTATGCAATCAAATACCGT 59.350 36.000 0.00 0.00 0.00 4.83
559 579 5.743398 CCAGTTTATGCAATCAAATACCGTG 59.257 40.000 0.00 0.00 0.00 4.94
560 580 5.229887 CAGTTTATGCAATCAAATACCGTGC 59.770 40.000 0.00 0.00 35.75 5.34
561 581 2.869233 ATGCAATCAAATACCGTGCC 57.131 45.000 0.00 0.00 34.25 5.01
562 582 0.449786 TGCAATCAAATACCGTGCCG 59.550 50.000 0.00 0.00 34.25 5.69
563 583 0.450184 GCAATCAAATACCGTGCCGT 59.550 50.000 0.00 0.00 0.00 5.68
564 584 1.793714 GCAATCAAATACCGTGCCGTG 60.794 52.381 0.00 0.00 0.00 4.94
565 585 0.450184 AATCAAATACCGTGCCGTGC 59.550 50.000 0.00 0.00 0.00 5.34
566 586 0.675208 ATCAAATACCGTGCCGTGCA 60.675 50.000 0.00 0.00 35.60 4.57
567 587 0.675208 TCAAATACCGTGCCGTGCAT 60.675 50.000 1.90 0.00 41.91 3.96
568 588 0.248054 CAAATACCGTGCCGTGCATC 60.248 55.000 1.90 0.00 41.91 3.91
569 589 1.701545 AAATACCGTGCCGTGCATCG 61.702 55.000 1.90 7.56 41.91 3.84
587 607 4.096003 GCCTAGCCAACCGCCAGA 62.096 66.667 0.00 0.00 38.78 3.86
588 608 2.187946 CCTAGCCAACCGCCAGAG 59.812 66.667 0.00 0.00 38.78 3.35
589 609 2.359169 CCTAGCCAACCGCCAGAGA 61.359 63.158 0.00 0.00 38.78 3.10
590 610 1.142748 CTAGCCAACCGCCAGAGAG 59.857 63.158 0.00 0.00 38.78 3.20
591 611 1.304962 TAGCCAACCGCCAGAGAGA 60.305 57.895 0.00 0.00 38.78 3.10
592 612 0.902984 TAGCCAACCGCCAGAGAGAA 60.903 55.000 0.00 0.00 38.78 2.87
593 613 1.302511 GCCAACCGCCAGAGAGAAA 60.303 57.895 0.00 0.00 0.00 2.52
594 614 0.678048 GCCAACCGCCAGAGAGAAAT 60.678 55.000 0.00 0.00 0.00 2.17
595 615 1.373570 CCAACCGCCAGAGAGAAATC 58.626 55.000 0.00 0.00 0.00 2.17
596 616 1.002366 CAACCGCCAGAGAGAAATCG 58.998 55.000 0.00 0.00 0.00 3.34
597 617 0.741221 AACCGCCAGAGAGAAATCGC 60.741 55.000 0.00 0.00 0.00 4.58
598 618 1.153568 CCGCCAGAGAGAAATCGCA 60.154 57.895 0.00 0.00 0.00 5.10
599 619 0.531532 CCGCCAGAGAGAAATCGCAT 60.532 55.000 0.00 0.00 0.00 4.73
600 620 0.857935 CGCCAGAGAGAAATCGCATC 59.142 55.000 0.00 0.00 0.00 3.91
601 621 1.224965 GCCAGAGAGAAATCGCATCC 58.775 55.000 0.00 0.00 0.00 3.51
602 622 1.876322 CCAGAGAGAAATCGCATCCC 58.124 55.000 0.00 0.00 0.00 3.85
603 623 1.415659 CCAGAGAGAAATCGCATCCCT 59.584 52.381 0.00 0.00 0.00 4.20
604 624 2.630098 CCAGAGAGAAATCGCATCCCTA 59.370 50.000 0.00 0.00 0.00 3.53
605 625 3.070159 CCAGAGAGAAATCGCATCCCTAA 59.930 47.826 0.00 0.00 0.00 2.69
606 626 4.262808 CCAGAGAGAAATCGCATCCCTAAT 60.263 45.833 0.00 0.00 0.00 1.73
607 627 4.689812 CAGAGAGAAATCGCATCCCTAATG 59.310 45.833 0.00 0.00 38.50 1.90
616 636 1.636148 CATCCCTAATGCAATGGGGG 58.364 55.000 22.09 14.53 39.67 5.40
617 637 1.133072 CATCCCTAATGCAATGGGGGT 60.133 52.381 22.09 13.58 39.67 4.95
618 638 1.914272 TCCCTAATGCAATGGGGGTA 58.086 50.000 22.09 1.80 39.67 3.69
619 639 2.218673 TCCCTAATGCAATGGGGGTAA 58.781 47.619 22.09 1.03 39.67 2.85
620 640 2.587777 TCCCTAATGCAATGGGGGTAAA 59.412 45.455 22.09 0.65 39.67 2.01
621 641 2.965147 CCCTAATGCAATGGGGGTAAAG 59.035 50.000 15.40 0.00 36.78 1.85
622 642 3.373658 CCCTAATGCAATGGGGGTAAAGA 60.374 47.826 15.40 0.00 36.78 2.52
623 643 4.285863 CCTAATGCAATGGGGGTAAAGAA 58.714 43.478 0.00 0.00 0.00 2.52
624 644 4.714308 CCTAATGCAATGGGGGTAAAGAAA 59.286 41.667 0.00 0.00 0.00 2.52
625 645 5.188751 CCTAATGCAATGGGGGTAAAGAAAA 59.811 40.000 0.00 0.00 0.00 2.29
626 646 5.777526 AATGCAATGGGGGTAAAGAAAAT 57.222 34.783 0.00 0.00 0.00 1.82
627 647 6.882768 AATGCAATGGGGGTAAAGAAAATA 57.117 33.333 0.00 0.00 0.00 1.40
628 648 7.450323 AATGCAATGGGGGTAAAGAAAATAT 57.550 32.000 0.00 0.00 0.00 1.28
629 649 6.232581 TGCAATGGGGGTAAAGAAAATATG 57.767 37.500 0.00 0.00 0.00 1.78
630 650 5.723887 TGCAATGGGGGTAAAGAAAATATGT 59.276 36.000 0.00 0.00 0.00 2.29
631 651 6.897966 TGCAATGGGGGTAAAGAAAATATGTA 59.102 34.615 0.00 0.00 0.00 2.29
632 652 7.147811 TGCAATGGGGGTAAAGAAAATATGTAC 60.148 37.037 0.00 0.00 0.00 2.90
633 653 7.422399 CAATGGGGGTAAAGAAAATATGTACG 58.578 38.462 0.00 0.00 0.00 3.67
634 654 5.438833 TGGGGGTAAAGAAAATATGTACGG 58.561 41.667 0.00 0.00 0.00 4.02
635 655 5.191323 TGGGGGTAAAGAAAATATGTACGGA 59.809 40.000 0.00 0.00 0.00 4.69
636 656 6.121590 GGGGGTAAAGAAAATATGTACGGAA 58.878 40.000 0.00 0.00 0.00 4.30
637 657 6.038603 GGGGGTAAAGAAAATATGTACGGAAC 59.961 42.308 0.00 0.00 0.00 3.62
638 658 6.598850 GGGGTAAAGAAAATATGTACGGAACA 59.401 38.462 0.00 0.00 43.86 3.18
650 670 5.927954 TGTACGGAACATGGTTTTTACTC 57.072 39.130 0.00 0.00 31.43 2.59
651 671 5.613329 TGTACGGAACATGGTTTTTACTCT 58.387 37.500 0.00 0.00 31.43 3.24
652 672 5.467399 TGTACGGAACATGGTTTTTACTCTG 59.533 40.000 0.00 0.00 31.43 3.35
653 673 4.710324 ACGGAACATGGTTTTTACTCTGA 58.290 39.130 0.00 0.00 0.00 3.27
654 674 5.127491 ACGGAACATGGTTTTTACTCTGAA 58.873 37.500 0.00 0.00 0.00 3.02
655 675 5.768164 ACGGAACATGGTTTTTACTCTGAAT 59.232 36.000 0.00 0.00 0.00 2.57
656 676 6.264518 ACGGAACATGGTTTTTACTCTGAATT 59.735 34.615 0.00 0.00 0.00 2.17
657 677 7.145323 CGGAACATGGTTTTTACTCTGAATTT 58.855 34.615 0.00 0.00 0.00 1.82
658 678 7.114811 CGGAACATGGTTTTTACTCTGAATTTG 59.885 37.037 0.00 0.00 0.00 2.32
659 679 7.095649 GGAACATGGTTTTTACTCTGAATTTGC 60.096 37.037 0.00 0.00 0.00 3.68
660 680 7.054491 ACATGGTTTTTACTCTGAATTTGCT 57.946 32.000 0.00 0.00 0.00 3.91
661 681 7.500141 ACATGGTTTTTACTCTGAATTTGCTT 58.500 30.769 0.00 0.00 0.00 3.91
662 682 8.637986 ACATGGTTTTTACTCTGAATTTGCTTA 58.362 29.630 0.00 0.00 0.00 3.09
663 683 9.132521 CATGGTTTTTACTCTGAATTTGCTTAG 57.867 33.333 0.00 0.00 0.00 2.18
664 684 7.145323 TGGTTTTTACTCTGAATTTGCTTAGC 58.855 34.615 0.00 0.00 0.00 3.09
665 685 6.586463 GGTTTTTACTCTGAATTTGCTTAGCC 59.414 38.462 0.29 0.00 0.00 3.93
666 686 5.545658 TTTACTCTGAATTTGCTTAGCCG 57.454 39.130 0.29 0.00 0.00 5.52
667 687 2.359900 ACTCTGAATTTGCTTAGCCGG 58.640 47.619 0.29 0.00 0.00 6.13
668 688 1.672881 CTCTGAATTTGCTTAGCCGGG 59.327 52.381 2.18 0.00 0.00 5.73
669 689 0.101219 CTGAATTTGCTTAGCCGGGC 59.899 55.000 12.11 12.11 0.00 6.13
670 690 1.319614 TGAATTTGCTTAGCCGGGCC 61.320 55.000 17.02 0.00 0.00 5.80
671 691 2.016393 GAATTTGCTTAGCCGGGCCC 62.016 60.000 17.02 13.57 0.00 5.80
683 703 4.222847 GGGCCCGACCGAGTCATC 62.223 72.222 5.69 0.00 40.62 2.92
684 704 3.458163 GGCCCGACCGAGTCATCA 61.458 66.667 0.00 0.00 32.09 3.07
685 705 2.202756 GCCCGACCGAGTCATCAC 60.203 66.667 5.15 0.00 32.09 3.06
686 706 3.001902 GCCCGACCGAGTCATCACA 62.002 63.158 5.15 0.00 32.09 3.58
687 707 1.816537 CCCGACCGAGTCATCACAT 59.183 57.895 5.15 0.00 32.09 3.21
688 708 0.528466 CCCGACCGAGTCATCACATG 60.528 60.000 0.00 0.00 32.09 3.21
689 709 0.173481 CCGACCGAGTCATCACATGT 59.827 55.000 0.00 0.00 32.09 3.21
690 710 1.404035 CCGACCGAGTCATCACATGTA 59.596 52.381 0.00 0.00 32.09 2.29
691 711 2.451132 CGACCGAGTCATCACATGTAC 58.549 52.381 0.00 0.00 32.09 2.90
692 712 2.159435 CGACCGAGTCATCACATGTACA 60.159 50.000 0.00 0.00 32.09 2.90
693 713 3.672241 CGACCGAGTCATCACATGTACAA 60.672 47.826 0.00 0.00 32.09 2.41
694 714 3.585862 ACCGAGTCATCACATGTACAAC 58.414 45.455 0.00 0.00 0.00 3.32
695 715 3.006430 ACCGAGTCATCACATGTACAACA 59.994 43.478 0.00 0.00 0.00 3.33
696 716 3.993736 CCGAGTCATCACATGTACAACAA 59.006 43.478 0.00 0.00 0.00 2.83
697 717 4.450757 CCGAGTCATCACATGTACAACAAA 59.549 41.667 0.00 0.00 0.00 2.83
698 718 5.122239 CCGAGTCATCACATGTACAACAAAT 59.878 40.000 0.00 0.00 0.00 2.32
699 719 6.348458 CCGAGTCATCACATGTACAACAAATT 60.348 38.462 0.00 0.00 0.00 1.82
700 720 6.738200 CGAGTCATCACATGTACAACAAATTC 59.262 38.462 0.00 0.00 0.00 2.17
701 721 7.509141 AGTCATCACATGTACAACAAATTCA 57.491 32.000 0.00 0.00 0.00 2.57
702 722 7.587629 AGTCATCACATGTACAACAAATTCAG 58.412 34.615 0.00 0.00 0.00 3.02
736 756 1.526455 CTAGGAGGAGGGACGGACG 60.526 68.421 0.00 0.00 0.00 4.79
737 757 2.962142 CTAGGAGGAGGGACGGACGG 62.962 70.000 0.00 0.00 0.00 4.79
738 758 4.437587 GGAGGAGGGACGGACGGA 62.438 72.222 0.00 0.00 0.00 4.69
739 759 3.139469 GAGGAGGGACGGACGGAC 61.139 72.222 0.00 0.00 0.00 4.79
763 783 1.369091 CGTGGAAAATCAGCCGAGGG 61.369 60.000 0.00 0.00 0.00 4.30
766 786 1.284785 TGGAAAATCAGCCGAGGGAAT 59.715 47.619 0.00 0.00 0.00 3.01
779 799 2.645192 GGGAATGGGGTTGCCAACG 61.645 63.158 0.74 0.00 46.77 4.10
794 814 3.171277 GCCAACGAAAATCGAAATGGAG 58.829 45.455 19.79 4.01 43.74 3.86
801 822 4.505922 CGAAAATCGAAATGGAGAGAGAGG 59.494 45.833 0.00 0.00 43.74 3.69
828 849 5.357878 TGAGATTTTTCATCATTTCGAGGGG 59.642 40.000 0.00 0.00 0.00 4.79
911 932 0.692756 TTCCATAGGACCCATCGGCA 60.693 55.000 0.00 0.00 0.00 5.69
912 933 1.121407 TCCATAGGACCCATCGGCAG 61.121 60.000 0.00 0.00 0.00 4.85
913 934 1.121407 CCATAGGACCCATCGGCAGA 61.121 60.000 0.00 0.00 0.00 4.26
914 935 0.319728 CATAGGACCCATCGGCAGAG 59.680 60.000 0.00 0.00 0.00 3.35
915 936 0.188587 ATAGGACCCATCGGCAGAGA 59.811 55.000 0.00 0.00 0.00 3.10
916 937 0.468214 TAGGACCCATCGGCAGAGAG 60.468 60.000 0.00 0.00 0.00 3.20
917 938 1.758514 GGACCCATCGGCAGAGAGA 60.759 63.158 0.00 0.00 0.00 3.10
918 939 1.739049 GACCCATCGGCAGAGAGAG 59.261 63.158 0.00 0.00 0.00 3.20
969 997 2.352032 CGACCTGTCTCCTCCCCAC 61.352 68.421 0.00 0.00 0.00 4.61
971 999 2.689034 CCTGTCTCCTCCCCACCC 60.689 72.222 0.00 0.00 0.00 4.61
972 1000 2.452114 CTGTCTCCTCCCCACCCT 59.548 66.667 0.00 0.00 0.00 4.34
974 1002 2.174876 CTGTCTCCTCCCCACCCTCT 62.175 65.000 0.00 0.00 0.00 3.69
977 1005 2.874245 TCCTCCCCACCCTCTCCA 60.874 66.667 0.00 0.00 0.00 3.86
978 1006 2.263099 CTCCTCCCCACCCTCTCCAT 62.263 65.000 0.00 0.00 0.00 3.41
1136 1167 1.218316 CCACCCTCGGTAAGCAGTC 59.782 63.158 0.00 0.00 32.11 3.51
1137 1168 1.153823 CACCCTCGGTAAGCAGTCG 60.154 63.158 0.00 0.00 32.11 4.18
1193 1234 2.813474 CCGATTTGACAGCGGCGA 60.813 61.111 12.98 0.00 38.46 5.54
1531 1596 1.425267 CCGTGCGCGATTGGATTGTA 61.425 55.000 23.45 0.00 41.33 2.41
1532 1597 0.315059 CGTGCGCGATTGGATTGTAC 60.315 55.000 16.08 0.00 41.33 2.90
1535 1625 0.043310 GCGCGATTGGATTGTACGTC 60.043 55.000 12.10 0.00 0.00 4.34
1574 1664 1.003839 TGTGGTCCTTAGGCTTGCG 60.004 57.895 0.00 0.00 0.00 4.85
1591 1681 1.472082 TGCGGTTATTGCCTTGATGTG 59.528 47.619 0.00 0.00 0.00 3.21
1672 1776 5.048782 TGCCATTGCTCTAGTTGTAAGTTTG 60.049 40.000 0.00 0.00 38.71 2.93
1673 1777 5.619981 GCCATTGCTCTAGTTGTAAGTTTGG 60.620 44.000 0.00 0.00 33.53 3.28
1674 1778 5.106157 CCATTGCTCTAGTTGTAAGTTTGGG 60.106 44.000 0.00 0.00 0.00 4.12
1675 1779 4.015872 TGCTCTAGTTGTAAGTTTGGGG 57.984 45.455 0.00 0.00 0.00 4.96
1676 1780 3.244770 TGCTCTAGTTGTAAGTTTGGGGG 60.245 47.826 0.00 0.00 0.00 5.40
1724 1828 7.889873 TTTGTTTATTGAGAGAACTGGGAAA 57.110 32.000 0.00 0.00 0.00 3.13
1725 1829 8.477419 TTTGTTTATTGAGAGAACTGGGAAAT 57.523 30.769 0.00 0.00 0.00 2.17
1726 1830 7.687941 TGTTTATTGAGAGAACTGGGAAATC 57.312 36.000 0.00 0.00 0.00 2.17
1727 1831 6.371548 TGTTTATTGAGAGAACTGGGAAATCG 59.628 38.462 0.00 0.00 0.00 3.34
1729 1833 3.594603 TGAGAGAACTGGGAAATCGTC 57.405 47.619 0.00 0.00 0.00 4.20
1730 1834 2.094700 TGAGAGAACTGGGAAATCGTCG 60.095 50.000 0.00 0.00 0.00 5.12
1736 1840 2.379054 TGGGAAATCGTCGCAATCG 58.621 52.632 0.00 0.00 45.52 3.34
1740 1844 3.243468 TGGGAAATCGTCGCAATCGTATA 60.243 43.478 0.00 0.00 45.52 1.47
1741 1845 3.924686 GGGAAATCGTCGCAATCGTATAT 59.075 43.478 0.00 0.00 39.02 0.86
1743 1847 3.972706 AATCGTCGCAATCGTATATGC 57.027 42.857 0.00 0.00 39.17 3.14
1753 1857 6.422400 TCGCAATCGTATATGCAATTGAGTTA 59.578 34.615 10.34 0.00 42.68 2.24
1755 1859 8.379902 CGCAATCGTATATGCAATTGAGTTATA 58.620 33.333 10.34 4.26 42.68 0.98
1759 1863 8.628882 TCGTATATGCAATTGAGTTATATCCG 57.371 34.615 10.34 9.55 0.00 4.18
1774 1878 6.652062 AGTTATATCCGTTGGTTCTTTTCGTT 59.348 34.615 0.00 0.00 0.00 3.85
1778 1882 2.372350 CGTTGGTTCTTTTCGTTGAGC 58.628 47.619 0.00 0.00 0.00 4.26
1783 1887 4.307432 TGGTTCTTTTCGTTGAGCTAGAG 58.693 43.478 0.00 0.00 0.00 2.43
1787 1891 4.307432 TCTTTTCGTTGAGCTAGAGGTTG 58.693 43.478 0.00 0.00 0.00 3.77
1793 1897 1.632589 TGAGCTAGAGGTTGCACAGA 58.367 50.000 0.00 0.00 0.00 3.41
1808 1912 2.030007 GCACAGAATTGTAAGGCAGCAA 60.030 45.455 0.00 0.00 35.25 3.91
1930 2036 6.255020 GCATCCAAATTTGTCTTCTTGCTATG 59.745 38.462 16.73 5.94 0.00 2.23
1931 2037 7.541162 CATCCAAATTTGTCTTCTTGCTATGA 58.459 34.615 16.73 2.88 0.00 2.15
1932 2038 6.913170 TCCAAATTTGTCTTCTTGCTATGAC 58.087 36.000 16.73 0.00 0.00 3.06
1934 2040 7.231317 TCCAAATTTGTCTTCTTGCTATGACTT 59.769 33.333 16.73 0.00 0.00 3.01
1935 2041 7.540055 CCAAATTTGTCTTCTTGCTATGACTTC 59.460 37.037 16.73 0.00 0.00 3.01
1936 2042 7.750229 AATTTGTCTTCTTGCTATGACTTCA 57.250 32.000 0.00 0.00 0.00 3.02
1937 2043 6.791887 TTTGTCTTCTTGCTATGACTTCAG 57.208 37.500 0.00 0.00 0.00 3.02
1976 2113 3.490155 TCATTGCTTGAACATTTTGTGCG 59.510 39.130 0.00 0.00 0.00 5.34
1991 2129 0.179179 GTGCGCTTTCATCTTCTGGC 60.179 55.000 9.73 0.00 0.00 4.85
2076 2214 6.184068 TGTCTTGGGCTTTTAGCATGTTATA 58.816 36.000 0.67 0.00 44.75 0.98
2118 2257 4.911514 TGCAAGGGTTAACTTTCTGAAC 57.088 40.909 5.42 0.00 0.00 3.18
2141 2280 2.503765 TCCAACCACTTGTTCTGACTCA 59.496 45.455 0.00 0.00 34.00 3.41
2277 2417 8.846943 AATATCATGTGAACACTGAACACTTA 57.153 30.769 6.51 0.00 35.83 2.24
2320 2460 6.660887 TTGTTTGAAAAATCCTGCTTGTTC 57.339 33.333 0.00 0.00 0.00 3.18
2457 2597 8.410141 TGGTTGTAACTCTTATTTTGAAGTTGG 58.590 33.333 0.00 0.00 0.00 3.77
2479 2619 9.190317 GTTGGATTTATGGTTTCTTATCTTCCT 57.810 33.333 0.00 0.00 0.00 3.36
2671 2953 4.488126 TTGACTTGCAACAGCTGTTATC 57.512 40.909 30.67 23.78 36.32 1.75
2673 2955 3.499537 TGACTTGCAACAGCTGTTATCTG 59.500 43.478 30.67 20.46 36.32 2.90
2850 3132 5.757320 GTGTCCACATCTTCATTCATAGGAG 59.243 44.000 0.00 0.00 0.00 3.69
2934 3216 9.847224 GAAGGAGGTATATTAACTTGAATCCAA 57.153 33.333 0.00 0.00 0.00 3.53
3030 3312 7.969536 ACCCATCATGAATCTAATTAACTCG 57.030 36.000 0.00 0.00 0.00 4.18
3103 3385 4.524714 TGTGTGGTTTTGGTTGAAGAAAGA 59.475 37.500 0.00 0.00 0.00 2.52
3105 3387 4.524714 TGTGGTTTTGGTTGAAGAAAGACA 59.475 37.500 0.00 0.00 0.00 3.41
3164 3446 4.718961 AGGTATGTTGCTGTCTTCTGTTT 58.281 39.130 0.00 0.00 0.00 2.83
3240 3522 3.068024 GTGTTGCCTCCATGTTTTCTGAA 59.932 43.478 0.00 0.00 0.00 3.02
3249 3531 6.421801 CCTCCATGTTTTCTGAACATTGAAAC 59.578 38.462 1.88 0.00 38.69 2.78
3255 3537 7.555087 TGTTTTCTGAACATTGAAACTCCAAT 58.445 30.769 0.00 0.00 37.24 3.16
3274 3556 4.928615 CCAATTTTATTTCCGCAGCTTGAA 59.071 37.500 0.00 0.00 0.00 2.69
3313 3595 0.537188 ACCCTGACGGACATGATGAC 59.463 55.000 0.00 0.00 34.64 3.06
3351 3635 4.141937 CCACCACCATTAAGATCGAAGAGA 60.142 45.833 0.00 0.00 43.63 3.10
3352 3636 5.419542 CACCACCATTAAGATCGAAGAGAA 58.580 41.667 0.00 0.00 43.63 2.87
3391 3675 1.152830 AGTGGACCGGTGCCAATTT 59.847 52.632 24.47 10.90 37.12 1.82
3556 3840 9.599866 ACATAGTTTTTCTTTTCTTTTTGGAGG 57.400 29.630 0.00 0.00 0.00 4.30
3568 3852 1.523154 TTTGGAGGATTGCCGCACAC 61.523 55.000 0.00 0.00 39.96 3.82
3569 3853 3.499737 GGAGGATTGCCGCACACG 61.500 66.667 0.00 0.00 39.96 4.49
3608 3892 3.547054 AAACAAACAGTGACGTCCCTA 57.453 42.857 14.12 0.00 0.00 3.53
3656 3940 9.733556 TCTAGTCAATAAGGTTTTAATTGCTGA 57.266 29.630 0.00 0.00 0.00 4.26
3711 3995 2.015227 AACTGTTTTGCTGGTGGGCG 62.015 55.000 0.00 0.00 34.52 6.13
3744 4028 4.209452 GAGCATCGTTTTCACTTTGACA 57.791 40.909 0.00 0.00 0.00 3.58
3754 4038 6.085458 CGTTTTCACTTTGACAATCTTGATCG 59.915 38.462 0.00 0.00 0.00 3.69
3765 4049 4.578516 ACAATCTTGATCGGTTGTTTGTCA 59.421 37.500 0.00 0.00 31.20 3.58
3767 4051 5.551760 ATCTTGATCGGTTGTTTGTCATC 57.448 39.130 0.00 0.00 0.00 2.92
3768 4052 3.431912 TCTTGATCGGTTGTTTGTCATCG 59.568 43.478 0.00 0.00 0.00 3.84
3769 4053 3.033368 TGATCGGTTGTTTGTCATCGA 57.967 42.857 0.00 0.00 36.87 3.59
3773 4057 1.724623 CGGTTGTTTGTCATCGATCGT 59.275 47.619 15.94 0.00 0.00 3.73
3814 4098 4.070716 AGAGCTTGAGGAAACTGTCAATG 58.929 43.478 0.00 0.00 44.43 2.82
3908 4195 1.588674 TCACCAACCACGAATGACAC 58.411 50.000 0.00 0.00 0.00 3.67
3986 4274 8.534333 TGCTCATCTACTTAACAACTTAACAG 57.466 34.615 0.00 0.00 0.00 3.16
4021 4309 2.927477 TGGAATTCTCGACGAAATTCCG 59.073 45.455 31.64 13.36 39.52 4.30
4079 4374 5.163457 GGTTCTTGGTTTGAACATTTCCTCA 60.163 40.000 8.54 0.00 43.84 3.86
4089 4384 0.890683 CATTTCCTCACCTGTTGCCC 59.109 55.000 0.00 0.00 0.00 5.36
4111 4406 5.107607 CCCATCCTATTCGAAATTTACGACG 60.108 44.000 0.00 0.00 39.46 5.12
4112 4407 5.363517 CATCCTATTCGAAATTTACGACGC 58.636 41.667 0.00 0.00 39.46 5.19
4113 4408 4.422840 TCCTATTCGAAATTTACGACGCA 58.577 39.130 0.00 0.84 39.46 5.24
4114 4409 4.863689 TCCTATTCGAAATTTACGACGCAA 59.136 37.500 0.00 0.00 39.46 4.85
4115 4410 5.005012 TCCTATTCGAAATTTACGACGCAAG 59.995 40.000 0.00 7.27 39.46 4.01
4116 4411 4.914312 ATTCGAAATTTACGACGCAAGA 57.086 36.364 0.00 0.00 39.46 3.02
4129 4424 1.620819 ACGCAAGACAAGAGAGACCAT 59.379 47.619 0.00 0.00 43.62 3.55
4131 4426 3.182967 CGCAAGACAAGAGAGACCATAC 58.817 50.000 0.00 0.00 43.02 2.39
4140 4435 3.626930 AGAGAGACCATACGAAAGCTCT 58.373 45.455 0.00 0.00 35.59 4.09
4141 4436 3.630312 AGAGAGACCATACGAAAGCTCTC 59.370 47.826 0.00 0.00 45.28 3.20
4145 4441 4.894784 AGACCATACGAAAGCTCTCAAAA 58.105 39.130 0.00 0.00 0.00 2.44
4146 4442 5.305585 AGACCATACGAAAGCTCTCAAAAA 58.694 37.500 0.00 0.00 0.00 1.94
4177 4473 3.364889 AGTTGAGAATGTCGTTGTCGA 57.635 42.857 0.00 0.00 44.12 4.20
4233 4529 3.056035 GTCAAAACTGGGAGTAGGACGAT 60.056 47.826 0.00 0.00 0.00 3.73
4235 4531 1.486211 AACTGGGAGTAGGACGATGG 58.514 55.000 0.00 0.00 0.00 3.51
4236 4532 0.335361 ACTGGGAGTAGGACGATGGT 59.665 55.000 0.00 0.00 0.00 3.55
4237 4533 1.033574 CTGGGAGTAGGACGATGGTC 58.966 60.000 0.00 0.00 42.66 4.02
4241 4537 1.033574 GAGTAGGACGATGGTCAGGG 58.966 60.000 10.22 0.00 45.28 4.45
4242 4538 0.629596 AGTAGGACGATGGTCAGGGA 59.370 55.000 10.22 0.00 45.28 4.20
4243 4539 1.218196 AGTAGGACGATGGTCAGGGAT 59.782 52.381 10.22 0.00 45.28 3.85
4244 4540 1.614413 GTAGGACGATGGTCAGGGATC 59.386 57.143 10.22 0.00 45.28 3.36
4245 4541 0.032117 AGGACGATGGTCAGGGATCA 60.032 55.000 10.22 0.00 45.28 2.92
4246 4542 0.105039 GGACGATGGTCAGGGATCAC 59.895 60.000 10.22 0.00 45.28 3.06
4249 4559 0.528466 CGATGGTCAGGGATCACACG 60.528 60.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.420687 GGAGAAGCTCAAGTATGGGGTG 60.421 54.545 0.00 0.00 37.93 4.61
72 73 5.505173 TTCTCTGCAGCCTAATAAATTGC 57.495 39.130 9.47 0.00 35.42 3.56
123 124 0.321564 CCGAGTCCTGGACATTTGCA 60.322 55.000 27.48 0.00 34.60 4.08
142 143 3.347958 TGAATTATTCGCCCGCAAATC 57.652 42.857 0.23 0.00 0.00 2.17
234 236 6.041409 TGTGCTTTCTGTTTAAATTCCCATGA 59.959 34.615 0.00 0.00 0.00 3.07
285 289 3.304911 TTCAAAATCACCCACCTGACA 57.695 42.857 0.00 0.00 0.00 3.58
286 290 3.383185 TGTTTCAAAATCACCCACCTGAC 59.617 43.478 0.00 0.00 0.00 3.51
348 352 8.970020 TCATTCAGATGCTTAAATATGGTGTTT 58.030 29.630 0.00 0.00 33.14 2.83
466 474 0.179124 GTGTCTCAGAGATGGACGGC 60.179 60.000 2.64 0.00 33.21 5.68
573 593 0.902984 TTCTCTCTGGCGGTTGGCTA 60.903 55.000 0.00 0.00 42.94 3.93
574 594 1.768684 TTTCTCTCTGGCGGTTGGCT 61.769 55.000 0.00 0.00 42.94 4.75
575 595 0.678048 ATTTCTCTCTGGCGGTTGGC 60.678 55.000 0.00 0.00 42.51 4.52
576 596 1.373570 GATTTCTCTCTGGCGGTTGG 58.626 55.000 0.00 0.00 0.00 3.77
577 597 1.002366 CGATTTCTCTCTGGCGGTTG 58.998 55.000 0.00 0.00 0.00 3.77
578 598 0.741221 GCGATTTCTCTCTGGCGGTT 60.741 55.000 0.00 0.00 0.00 4.44
579 599 1.153549 GCGATTTCTCTCTGGCGGT 60.154 57.895 0.00 0.00 0.00 5.68
580 600 0.531532 ATGCGATTTCTCTCTGGCGG 60.532 55.000 0.00 0.00 0.00 6.13
581 601 0.857935 GATGCGATTTCTCTCTGGCG 59.142 55.000 0.00 0.00 0.00 5.69
582 602 1.224965 GGATGCGATTTCTCTCTGGC 58.775 55.000 0.00 0.00 0.00 4.85
583 603 1.415659 AGGGATGCGATTTCTCTCTGG 59.584 52.381 0.00 0.00 0.00 3.86
584 604 2.906691 AGGGATGCGATTTCTCTCTG 57.093 50.000 0.00 0.00 0.00 3.35
585 605 4.892433 CATTAGGGATGCGATTTCTCTCT 58.108 43.478 0.00 0.00 0.00 3.10
597 617 1.133072 ACCCCCATTGCATTAGGGATG 60.133 52.381 17.58 11.51 45.80 3.51
598 618 1.244366 ACCCCCATTGCATTAGGGAT 58.756 50.000 17.58 0.00 45.80 3.85
599 619 1.914272 TACCCCCATTGCATTAGGGA 58.086 50.000 17.58 0.00 45.80 4.20
600 620 2.765689 TTACCCCCATTGCATTAGGG 57.234 50.000 10.79 10.79 43.88 3.53
601 621 3.909732 TCTTTACCCCCATTGCATTAGG 58.090 45.455 0.00 0.00 0.00 2.69
602 622 5.930837 TTTCTTTACCCCCATTGCATTAG 57.069 39.130 0.00 0.00 0.00 1.73
603 623 6.882768 ATTTTCTTTACCCCCATTGCATTA 57.117 33.333 0.00 0.00 0.00 1.90
604 624 5.777526 ATTTTCTTTACCCCCATTGCATT 57.222 34.783 0.00 0.00 0.00 3.56
605 625 6.386635 ACATATTTTCTTTACCCCCATTGCAT 59.613 34.615 0.00 0.00 0.00 3.96
606 626 5.723887 ACATATTTTCTTTACCCCCATTGCA 59.276 36.000 0.00 0.00 0.00 4.08
607 627 6.233905 ACATATTTTCTTTACCCCCATTGC 57.766 37.500 0.00 0.00 0.00 3.56
608 628 7.422399 CGTACATATTTTCTTTACCCCCATTG 58.578 38.462 0.00 0.00 0.00 2.82
609 629 6.548251 CCGTACATATTTTCTTTACCCCCATT 59.452 38.462 0.00 0.00 0.00 3.16
610 630 6.066032 CCGTACATATTTTCTTTACCCCCAT 58.934 40.000 0.00 0.00 0.00 4.00
611 631 5.191323 TCCGTACATATTTTCTTTACCCCCA 59.809 40.000 0.00 0.00 0.00 4.96
612 632 5.683681 TCCGTACATATTTTCTTTACCCCC 58.316 41.667 0.00 0.00 0.00 5.40
613 633 6.598850 TGTTCCGTACATATTTTCTTTACCCC 59.401 38.462 0.00 0.00 0.00 4.95
614 634 7.614124 TGTTCCGTACATATTTTCTTTACCC 57.386 36.000 0.00 0.00 0.00 3.69
615 635 8.126700 CCATGTTCCGTACATATTTTCTTTACC 58.873 37.037 0.00 0.00 45.71 2.85
616 636 8.671028 ACCATGTTCCGTACATATTTTCTTTAC 58.329 33.333 0.00 0.00 45.71 2.01
617 637 8.795842 ACCATGTTCCGTACATATTTTCTTTA 57.204 30.769 0.00 0.00 45.71 1.85
618 638 7.696992 ACCATGTTCCGTACATATTTTCTTT 57.303 32.000 0.00 0.00 45.71 2.52
619 639 7.696992 AACCATGTTCCGTACATATTTTCTT 57.303 32.000 0.00 0.00 45.71 2.52
620 640 7.696992 AAACCATGTTCCGTACATATTTTCT 57.303 32.000 0.00 0.00 45.71 2.52
621 641 8.751302 AAAAACCATGTTCCGTACATATTTTC 57.249 30.769 15.09 0.00 45.71 2.29
622 642 9.628746 GTAAAAACCATGTTCCGTACATATTTT 57.371 29.630 14.88 14.88 45.71 1.82
623 643 9.016438 AGTAAAAACCATGTTCCGTACATATTT 57.984 29.630 0.00 3.07 45.71 1.40
624 644 8.570068 AGTAAAAACCATGTTCCGTACATATT 57.430 30.769 0.00 0.00 45.71 1.28
625 645 8.044908 AGAGTAAAAACCATGTTCCGTACATAT 58.955 33.333 0.00 0.00 45.71 1.78
626 646 7.332430 CAGAGTAAAAACCATGTTCCGTACATA 59.668 37.037 0.00 0.00 45.71 2.29
628 648 5.467399 CAGAGTAAAAACCATGTTCCGTACA 59.533 40.000 0.00 0.00 41.97 2.90
629 649 5.697633 TCAGAGTAAAAACCATGTTCCGTAC 59.302 40.000 0.00 0.00 0.00 3.67
630 650 5.856156 TCAGAGTAAAAACCATGTTCCGTA 58.144 37.500 0.00 0.00 0.00 4.02
631 651 4.710324 TCAGAGTAAAAACCATGTTCCGT 58.290 39.130 0.00 0.00 0.00 4.69
632 652 5.682943 TTCAGAGTAAAAACCATGTTCCG 57.317 39.130 0.00 0.00 0.00 4.30
633 653 7.095649 GCAAATTCAGAGTAAAAACCATGTTCC 60.096 37.037 0.00 0.00 0.00 3.62
634 654 7.653311 AGCAAATTCAGAGTAAAAACCATGTTC 59.347 33.333 0.00 0.00 0.00 3.18
635 655 7.500141 AGCAAATTCAGAGTAAAAACCATGTT 58.500 30.769 0.00 0.00 0.00 2.71
636 656 7.054491 AGCAAATTCAGAGTAAAAACCATGT 57.946 32.000 0.00 0.00 0.00 3.21
637 657 7.951530 AAGCAAATTCAGAGTAAAAACCATG 57.048 32.000 0.00 0.00 0.00 3.66
638 658 7.814587 GCTAAGCAAATTCAGAGTAAAAACCAT 59.185 33.333 0.00 0.00 0.00 3.55
639 659 7.145323 GCTAAGCAAATTCAGAGTAAAAACCA 58.855 34.615 0.00 0.00 0.00 3.67
640 660 6.586463 GGCTAAGCAAATTCAGAGTAAAAACC 59.414 38.462 0.00 0.00 0.00 3.27
641 661 6.305638 CGGCTAAGCAAATTCAGAGTAAAAAC 59.694 38.462 0.00 0.00 0.00 2.43
642 662 6.378582 CGGCTAAGCAAATTCAGAGTAAAAA 58.621 36.000 0.00 0.00 0.00 1.94
643 663 5.106317 CCGGCTAAGCAAATTCAGAGTAAAA 60.106 40.000 0.00 0.00 0.00 1.52
644 664 4.394920 CCGGCTAAGCAAATTCAGAGTAAA 59.605 41.667 0.00 0.00 0.00 2.01
645 665 3.938963 CCGGCTAAGCAAATTCAGAGTAA 59.061 43.478 0.00 0.00 0.00 2.24
646 666 3.531538 CCGGCTAAGCAAATTCAGAGTA 58.468 45.455 0.00 0.00 0.00 2.59
647 667 2.359900 CCGGCTAAGCAAATTCAGAGT 58.640 47.619 0.00 0.00 0.00 3.24
648 668 1.672881 CCCGGCTAAGCAAATTCAGAG 59.327 52.381 0.00 0.00 0.00 3.35
649 669 1.750193 CCCGGCTAAGCAAATTCAGA 58.250 50.000 0.00 0.00 0.00 3.27
650 670 0.101219 GCCCGGCTAAGCAAATTCAG 59.899 55.000 0.71 0.00 0.00 3.02
651 671 1.319614 GGCCCGGCTAAGCAAATTCA 61.320 55.000 9.86 0.00 0.00 2.57
652 672 1.437573 GGCCCGGCTAAGCAAATTC 59.562 57.895 9.86 0.00 0.00 2.17
653 673 2.058001 GGGCCCGGCTAAGCAAATT 61.058 57.895 5.69 0.00 0.00 1.82
654 674 2.442087 GGGCCCGGCTAAGCAAAT 60.442 61.111 5.69 0.00 0.00 2.32
666 686 4.222847 GATGACTCGGTCGGGCCC 62.223 72.222 13.57 13.57 34.95 5.80
667 687 3.458163 TGATGACTCGGTCGGGCC 61.458 66.667 0.00 0.00 34.95 5.80
668 688 2.202756 GTGATGACTCGGTCGGGC 60.203 66.667 0.00 0.00 34.95 6.13
669 689 0.528466 CATGTGATGACTCGGTCGGG 60.528 60.000 0.00 0.00 34.95 5.14
670 690 0.173481 ACATGTGATGACTCGGTCGG 59.827 55.000 0.00 0.00 34.95 4.79
671 691 2.159435 TGTACATGTGATGACTCGGTCG 60.159 50.000 9.11 0.00 34.95 4.79
672 692 3.503827 TGTACATGTGATGACTCGGTC 57.496 47.619 9.11 0.00 0.00 4.79
673 693 3.006430 TGTTGTACATGTGATGACTCGGT 59.994 43.478 9.11 0.00 0.00 4.69
674 694 3.584834 TGTTGTACATGTGATGACTCGG 58.415 45.455 9.11 0.00 0.00 4.63
675 695 5.590104 TTTGTTGTACATGTGATGACTCG 57.410 39.130 9.11 0.00 0.00 4.18
676 696 7.584108 TGAATTTGTTGTACATGTGATGACTC 58.416 34.615 9.11 0.00 0.00 3.36
677 697 7.308770 CCTGAATTTGTTGTACATGTGATGACT 60.309 37.037 9.11 0.00 0.00 3.41
678 698 6.803320 CCTGAATTTGTTGTACATGTGATGAC 59.197 38.462 9.11 0.00 0.00 3.06
679 699 6.570186 GCCTGAATTTGTTGTACATGTGATGA 60.570 38.462 9.11 0.00 0.00 2.92
680 700 5.574055 GCCTGAATTTGTTGTACATGTGATG 59.426 40.000 9.11 0.00 0.00 3.07
681 701 5.243507 TGCCTGAATTTGTTGTACATGTGAT 59.756 36.000 9.11 0.00 0.00 3.06
682 702 4.582240 TGCCTGAATTTGTTGTACATGTGA 59.418 37.500 9.11 0.00 0.00 3.58
683 703 4.869215 TGCCTGAATTTGTTGTACATGTG 58.131 39.130 9.11 0.00 0.00 3.21
684 704 5.288804 GTTGCCTGAATTTGTTGTACATGT 58.711 37.500 2.69 2.69 0.00 3.21
685 705 4.685628 GGTTGCCTGAATTTGTTGTACATG 59.314 41.667 0.00 0.00 0.00 3.21
686 706 4.343526 TGGTTGCCTGAATTTGTTGTACAT 59.656 37.500 0.00 0.00 0.00 2.29
687 707 3.701542 TGGTTGCCTGAATTTGTTGTACA 59.298 39.130 0.00 0.00 0.00 2.90
688 708 4.314740 TGGTTGCCTGAATTTGTTGTAC 57.685 40.909 0.00 0.00 0.00 2.90
689 709 5.112686 GTTTGGTTGCCTGAATTTGTTGTA 58.887 37.500 0.00 0.00 0.00 2.41
690 710 3.902881 TTGGTTGCCTGAATTTGTTGT 57.097 38.095 0.00 0.00 0.00 3.32
691 711 3.937706 TGTTTGGTTGCCTGAATTTGTTG 59.062 39.130 0.00 0.00 0.00 3.33
692 712 3.938334 GTGTTTGGTTGCCTGAATTTGTT 59.062 39.130 0.00 0.00 0.00 2.83
693 713 3.530535 GTGTTTGGTTGCCTGAATTTGT 58.469 40.909 0.00 0.00 0.00 2.83
694 714 2.539274 CGTGTTTGGTTGCCTGAATTTG 59.461 45.455 0.00 0.00 0.00 2.32
695 715 2.820330 CGTGTTTGGTTGCCTGAATTT 58.180 42.857 0.00 0.00 0.00 1.82
696 716 1.537990 GCGTGTTTGGTTGCCTGAATT 60.538 47.619 0.00 0.00 0.00 2.17
697 717 0.031994 GCGTGTTTGGTTGCCTGAAT 59.968 50.000 0.00 0.00 0.00 2.57
698 718 1.034838 AGCGTGTTTGGTTGCCTGAA 61.035 50.000 0.00 0.00 0.00 3.02
699 719 1.444119 GAGCGTGTTTGGTTGCCTGA 61.444 55.000 0.00 0.00 0.00 3.86
700 720 1.008538 GAGCGTGTTTGGTTGCCTG 60.009 57.895 0.00 0.00 0.00 4.85
701 721 0.107831 TAGAGCGTGTTTGGTTGCCT 59.892 50.000 0.00 0.00 0.00 4.75
702 722 0.517316 CTAGAGCGTGTTTGGTTGCC 59.483 55.000 0.00 0.00 0.00 4.52
736 756 0.320946 TGATTTTCCACGTCCGGTCC 60.321 55.000 0.00 0.00 0.00 4.46
737 757 1.076332 CTGATTTTCCACGTCCGGTC 58.924 55.000 0.00 0.00 0.00 4.79
738 758 0.953960 GCTGATTTTCCACGTCCGGT 60.954 55.000 0.00 0.00 0.00 5.28
739 759 1.644786 GGCTGATTTTCCACGTCCGG 61.645 60.000 0.00 0.00 0.00 5.14
742 762 0.721718 CTCGGCTGATTTTCCACGTC 59.278 55.000 0.00 0.00 0.00 4.34
743 763 0.673644 CCTCGGCTGATTTTCCACGT 60.674 55.000 0.00 0.00 0.00 4.49
744 764 1.369091 CCCTCGGCTGATTTTCCACG 61.369 60.000 0.00 0.00 0.00 4.94
745 765 0.035439 TCCCTCGGCTGATTTTCCAC 60.035 55.000 0.00 0.00 0.00 4.02
746 766 0.695924 TTCCCTCGGCTGATTTTCCA 59.304 50.000 0.00 0.00 0.00 3.53
747 767 1.678101 CATTCCCTCGGCTGATTTTCC 59.322 52.381 0.00 0.00 0.00 3.13
763 783 0.676736 TTTCGTTGGCAACCCCATTC 59.323 50.000 23.68 0.00 44.89 2.67
766 786 0.676736 GATTTTCGTTGGCAACCCCA 59.323 50.000 23.68 6.03 43.51 4.96
779 799 4.813697 CCCTCTCTCTCCATTTCGATTTTC 59.186 45.833 0.00 0.00 0.00 2.29
794 814 4.559862 TGAAAAATCTCACCCCTCTCTC 57.440 45.455 0.00 0.00 0.00 3.20
801 822 6.194796 TCGAAATGATGAAAAATCTCACCC 57.805 37.500 0.00 0.00 0.00 4.61
854 875 4.580580 ACTTGGTGTTTCTTTTCTAGGCAG 59.419 41.667 0.00 0.00 0.00 4.85
911 932 0.179045 GGCTCGCTCTCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
912 933 0.463654 TGGCTCGCTCTCTCTCTCTC 60.464 60.000 0.00 0.00 0.00 3.20
913 934 0.183492 ATGGCTCGCTCTCTCTCTCT 59.817 55.000 0.00 0.00 0.00 3.10
914 935 1.001378 GAATGGCTCGCTCTCTCTCTC 60.001 57.143 0.00 0.00 0.00 3.20
915 936 1.032014 GAATGGCTCGCTCTCTCTCT 58.968 55.000 0.00 0.00 0.00 3.10
916 937 0.317770 CGAATGGCTCGCTCTCTCTC 60.318 60.000 0.00 0.00 41.49 3.20
917 938 1.732917 CGAATGGCTCGCTCTCTCT 59.267 57.895 0.00 0.00 41.49 3.10
918 939 4.317529 CGAATGGCTCGCTCTCTC 57.682 61.111 0.00 0.00 41.49 3.20
956 977 2.169590 GAGAGGGTGGGGAGGAGACA 62.170 65.000 0.00 0.00 0.00 3.41
1531 1596 1.070758 ACCATTTCAGTGCAGAGACGT 59.929 47.619 0.00 0.00 0.00 4.34
1532 1597 1.462283 CACCATTTCAGTGCAGAGACG 59.538 52.381 0.00 0.00 0.00 4.18
1535 1625 3.079578 ACATCACCATTTCAGTGCAGAG 58.920 45.455 0.00 0.00 35.14 3.35
1574 1664 3.947834 ACTAGCACATCAAGGCAATAACC 59.052 43.478 0.00 0.00 0.00 2.85
1591 1681 6.702716 AACCAGTCTCTGACTATTACTAGC 57.297 41.667 0.00 0.00 41.37 3.42
1650 1754 5.106157 CCCAAACTTACAACTAGAGCAATGG 60.106 44.000 0.00 0.00 0.00 3.16
1712 1816 1.000145 GCGACGATTTCCCAGTTCTC 59.000 55.000 0.00 0.00 0.00 2.87
1713 1817 0.320374 TGCGACGATTTCCCAGTTCT 59.680 50.000 0.00 0.00 0.00 3.01
1714 1818 1.153353 TTGCGACGATTTCCCAGTTC 58.847 50.000 0.00 0.00 0.00 3.01
1715 1819 1.737793 GATTGCGACGATTTCCCAGTT 59.262 47.619 0.00 0.00 0.00 3.16
1717 1821 0.301687 CGATTGCGACGATTTCCCAG 59.698 55.000 0.00 0.00 40.82 4.45
1720 1824 4.721226 GCATATACGATTGCGACGATTTCC 60.721 45.833 0.00 0.00 41.64 3.13
1724 1828 2.941428 TGCATATACGATTGCGACGAT 58.059 42.857 0.00 0.00 41.80 3.73
1725 1829 2.409152 TGCATATACGATTGCGACGA 57.591 45.000 0.00 0.00 41.80 4.20
1726 1830 3.705275 ATTGCATATACGATTGCGACG 57.295 42.857 0.00 0.00 41.80 5.12
1727 1831 5.017484 TCAATTGCATATACGATTGCGAC 57.983 39.130 10.13 0.00 41.80 5.19
1729 1833 5.022335 ACTCAATTGCATATACGATTGCG 57.978 39.130 10.13 7.45 41.80 4.85
1733 1837 9.249457 CGGATATAACTCAATTGCATATACGAT 57.751 33.333 18.83 4.46 37.87 3.73
1736 1840 9.973246 CAACGGATATAACTCAATTGCATATAC 57.027 33.333 0.00 1.79 0.00 1.47
1740 1844 5.827797 ACCAACGGATATAACTCAATTGCAT 59.172 36.000 0.00 0.00 0.00 3.96
1741 1845 5.189928 ACCAACGGATATAACTCAATTGCA 58.810 37.500 0.00 0.00 0.00 4.08
1743 1847 7.553881 AGAACCAACGGATATAACTCAATTG 57.446 36.000 0.00 0.00 0.00 2.32
1753 1857 4.998672 TCAACGAAAAGAACCAACGGATAT 59.001 37.500 0.00 0.00 0.00 1.63
1755 1859 3.207778 TCAACGAAAAGAACCAACGGAT 58.792 40.909 0.00 0.00 0.00 4.18
1756 1860 2.610374 CTCAACGAAAAGAACCAACGGA 59.390 45.455 0.00 0.00 0.00 4.69
1757 1861 2.853281 GCTCAACGAAAAGAACCAACGG 60.853 50.000 0.00 0.00 0.00 4.44
1758 1862 2.031683 AGCTCAACGAAAAGAACCAACG 59.968 45.455 0.00 0.00 0.00 4.10
1759 1863 3.692791 AGCTCAACGAAAAGAACCAAC 57.307 42.857 0.00 0.00 0.00 3.77
1774 1878 1.632589 TCTGTGCAACCTCTAGCTCA 58.367 50.000 0.00 0.00 34.36 4.26
1778 1882 5.352569 CCTTACAATTCTGTGCAACCTCTAG 59.647 44.000 0.00 0.00 36.96 2.43
1783 1887 2.295909 TGCCTTACAATTCTGTGCAACC 59.704 45.455 0.00 0.00 36.96 3.77
1787 1891 1.541147 TGCTGCCTTACAATTCTGTGC 59.459 47.619 0.00 0.00 36.96 4.57
1793 1897 6.780457 AATGTATCTTGCTGCCTTACAATT 57.220 33.333 0.00 0.00 0.00 2.32
1930 2036 6.578023 ACTAGGTCATAAGAATGCTGAAGTC 58.422 40.000 0.00 0.00 32.76 3.01
1931 2037 6.155221 TGACTAGGTCATAAGAATGCTGAAGT 59.845 38.462 0.00 0.00 37.67 3.01
1932 2038 6.577103 TGACTAGGTCATAAGAATGCTGAAG 58.423 40.000 0.00 0.00 37.67 3.02
1976 2113 2.816087 TCACAAGCCAGAAGATGAAAGC 59.184 45.455 0.00 0.00 0.00 3.51
1991 2129 6.057533 TGCCAAGGTCTGATATTATCACAAG 58.942 40.000 2.14 0.00 35.06 3.16
2076 2214 4.683129 GCAACAACCCCTGAATTGTCTTTT 60.683 41.667 0.00 0.00 38.08 2.27
2118 2257 3.545703 AGTCAGAACAAGTGGTTGGAAG 58.454 45.455 0.00 0.00 40.63 3.46
2141 2280 5.342866 AGTATAAGTTCAAGAGGTGGGTCT 58.657 41.667 0.00 0.00 0.00 3.85
2320 2460 7.776107 TGATAAGGAACAGACTCACAGAATAG 58.224 38.462 0.00 0.00 0.00 1.73
2457 2597 7.503902 AGGCAGGAAGATAAGAAACCATAAATC 59.496 37.037 0.00 0.00 0.00 2.17
2464 2604 5.009110 GCATTAGGCAGGAAGATAAGAAACC 59.991 44.000 0.00 0.00 43.97 3.27
2698 2980 8.256605 TCAAAAGAACAAAACAGAATGGAATGA 58.743 29.630 0.00 0.00 43.62 2.57
2702 2984 6.929625 TGTCAAAAGAACAAAACAGAATGGA 58.070 32.000 0.00 0.00 43.62 3.41
2703 2985 7.593875 TTGTCAAAAGAACAAAACAGAATGG 57.406 32.000 0.00 0.00 35.29 3.16
2812 3094 4.242475 TGTGGACACATATTCGTTCAGTC 58.758 43.478 0.13 0.00 36.21 3.51
2837 3119 4.237843 AGCTGGATCCTCCTATGAATGAA 58.762 43.478 14.23 0.00 37.46 2.57
2850 3132 4.613925 TGACTGAATGATAGCTGGATCC 57.386 45.455 4.20 4.20 0.00 3.36
2934 3216 4.437682 TCTGTTGGTGGAGACAGAATTT 57.562 40.909 3.89 0.00 46.64 1.82
3030 3312 8.659491 GGAGCAAAATAGTGAAATTTGGAATTC 58.341 33.333 0.00 0.00 35.21 2.17
3103 3385 0.542467 TGGGCATTCATGTGGCTTGT 60.542 50.000 9.33 0.00 43.55 3.16
3105 3387 0.251922 ACTGGGCATTCATGTGGCTT 60.252 50.000 9.33 0.00 43.55 4.35
3164 3446 7.946207 TCACACAAGGAAAAGCAAATTATGTA 58.054 30.769 0.00 0.00 0.00 2.29
3240 3522 7.117667 GCGGAAATAAAATTGGAGTTTCAATGT 59.882 33.333 0.00 0.00 37.42 2.71
3249 3531 4.376340 AGCTGCGGAAATAAAATTGGAG 57.624 40.909 0.00 0.00 0.00 3.86
3255 3537 4.846779 ACTTCAAGCTGCGGAAATAAAA 57.153 36.364 0.00 0.00 0.00 1.52
3274 3556 3.560668 GGTTTCCTCCGTTCCCAATAACT 60.561 47.826 0.00 0.00 0.00 2.24
3313 3595 4.016629 TGGTGGTCGTCGTCGTCG 62.017 66.667 5.50 5.50 38.33 5.12
3351 3635 4.910195 TGTTTCATCAGTAGACATGCCTT 58.090 39.130 0.00 0.00 0.00 4.35
3352 3636 4.019860 ACTGTTTCATCAGTAGACATGCCT 60.020 41.667 0.00 0.00 45.31 4.75
3569 3853 6.968004 TGTTTAATGAATCGCATTATTCGC 57.032 33.333 0.00 0.00 46.01 4.70
3579 3863 6.133392 ACGTCACTGTTTGTTTAATGAATCG 58.867 36.000 0.00 0.00 0.00 3.34
3608 3892 3.334691 TGAAAGGCGAGTCGAAAATGAT 58.665 40.909 18.61 0.00 0.00 2.45
3655 3939 2.750888 GGAGCCGTCCACGCAAATC 61.751 63.158 0.00 0.00 43.31 2.17
3656 3940 2.746277 GGAGCCGTCCACGCAAAT 60.746 61.111 0.00 0.00 43.31 2.32
3711 3995 4.795970 AACGATGCTCGGATAACAAATC 57.204 40.909 9.75 0.00 45.59 2.17
3736 4020 4.821805 ACAACCGATCAAGATTGTCAAAGT 59.178 37.500 0.00 0.00 29.30 2.66
3744 4028 5.390885 CGATGACAAACAACCGATCAAGATT 60.391 40.000 0.00 0.00 0.00 2.40
3754 4038 2.478894 ACACGATCGATGACAAACAACC 59.521 45.455 24.34 0.00 0.00 3.77
3765 4049 3.507786 TCGTCATCAAAACACGATCGAT 58.492 40.909 24.34 6.46 37.62 3.59
3773 4057 5.700832 AGCTCTGTTTATCGTCATCAAAACA 59.299 36.000 0.00 0.00 38.97 2.83
3814 4098 4.310769 TGTTGCAGAGAAACTAGAGCTTC 58.689 43.478 0.00 0.00 0.00 3.86
3986 4274 4.798574 AGAATTCCATTCGCACTTTCAAC 58.201 39.130 0.65 0.00 43.92 3.18
4079 4374 1.134098 CGAATAGGATGGGCAACAGGT 60.134 52.381 0.00 0.00 39.74 4.00
4089 4384 5.051307 TGCGTCGTAAATTTCGAATAGGATG 60.051 40.000 12.24 6.73 39.01 3.51
4111 4406 3.119459 TCGTATGGTCTCTCTTGTCTTGC 60.119 47.826 0.00 0.00 0.00 4.01
4112 4407 4.703645 TCGTATGGTCTCTCTTGTCTTG 57.296 45.455 0.00 0.00 0.00 3.02
4113 4408 5.715070 CTTTCGTATGGTCTCTCTTGTCTT 58.285 41.667 0.00 0.00 0.00 3.01
4114 4409 4.381079 GCTTTCGTATGGTCTCTCTTGTCT 60.381 45.833 0.00 0.00 0.00 3.41
4115 4410 3.860536 GCTTTCGTATGGTCTCTCTTGTC 59.139 47.826 0.00 0.00 0.00 3.18
4116 4411 3.511934 AGCTTTCGTATGGTCTCTCTTGT 59.488 43.478 0.00 0.00 0.00 3.16
4150 4446 7.359264 CGACAACGACATTCTCAACTAGAATTT 60.359 37.037 0.00 0.00 45.68 1.82
4151 4447 6.089551 CGACAACGACATTCTCAACTAGAATT 59.910 38.462 0.00 0.00 45.68 2.17
4156 4452 4.492791 TCGACAACGACATTCTCAACTA 57.507 40.909 0.00 0.00 43.81 2.24
4177 4473 8.070034 TGTTGATCCTTGCAAATCATAAAGAT 57.930 30.769 13.25 1.00 39.09 2.40
4233 4529 1.873270 CGTCGTGTGATCCCTGACCA 61.873 60.000 0.00 0.00 0.00 4.02
4235 4531 1.153823 CCGTCGTGTGATCCCTGAC 60.154 63.158 0.00 0.00 0.00 3.51
4236 4532 0.683179 ATCCGTCGTGTGATCCCTGA 60.683 55.000 0.00 0.00 0.00 3.86
4237 4533 0.528466 CATCCGTCGTGTGATCCCTG 60.528 60.000 0.00 0.00 0.00 4.45
4241 4537 2.230940 CGCCATCCGTCGTGTGATC 61.231 63.158 0.00 0.00 0.00 2.92
4242 4538 2.202743 CGCCATCCGTCGTGTGAT 60.203 61.111 0.00 0.00 0.00 3.06
4243 4539 3.336715 CTCGCCATCCGTCGTGTGA 62.337 63.158 0.00 0.00 38.35 3.58
4244 4540 2.880879 CTCGCCATCCGTCGTGTG 60.881 66.667 0.00 0.00 38.35 3.82
4245 4541 4.796231 GCTCGCCATCCGTCGTGT 62.796 66.667 0.00 0.00 38.35 4.49
4246 4542 4.794439 TGCTCGCCATCCGTCGTG 62.794 66.667 0.00 0.00 38.35 4.35
4249 4559 1.424493 CTTTCTGCTCGCCATCCGTC 61.424 60.000 0.00 0.00 38.35 4.79


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

AutoCloner maintained by Alex Coulton.