Multiple sequence alignment - TraesCS5D01G445300

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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 TraesCS5D01G445300 chr5D 100.000 3550 0 0 1 3550 495744106 495747655 0.000000e+00 6556.0
1 TraesCS5D01G445300 chr5D 81.633 98 18 0 1003 1100 532278915 532278818 8.170000e-12 82.4
2 TraesCS5D01G445300 chr5A 95.243 2670 104 15 890 3550 619714583 619717238 0.000000e+00 4205.0
3 TraesCS5D01G445300 chr5A 91.833 502 38 3 13 512 428252131 428251631 0.000000e+00 697.0
4 TraesCS5D01G445300 chr5A 90.698 129 8 3 3346 3473 619726247 619726372 6.090000e-38 169.0
5 TraesCS5D01G445300 chr5B 93.850 2699 115 19 860 3550 612978361 612981016 0.000000e+00 4017.0
6 TraesCS5D01G445300 chr5B 85.265 1303 147 23 2269 3550 613081542 613082820 0.000000e+00 1301.0
7 TraesCS5D01G445300 chr5B 85.852 728 78 14 2269 2990 613097040 613097748 0.000000e+00 750.0
8 TraesCS5D01G445300 chr5B 82.854 834 107 20 2737 3550 613098122 613098939 0.000000e+00 715.0
9 TraesCS5D01G445300 chr5B 76.824 850 135 31 1144 1963 613044958 613045775 4.240000e-114 422.0
10 TraesCS5D01G445300 chr5B 82.653 98 17 0 1003 1100 671487093 671487190 1.760000e-13 87.9
11 TraesCS5D01G445300 chr5B 76.398 161 34 4 1003 1161 671714313 671714155 2.270000e-12 84.2
12 TraesCS5D01G445300 chr7D 93.130 524 34 2 1 523 510344527 510345049 0.000000e+00 767.0
13 TraesCS5D01G445300 chr7D 92.802 514 30 5 1 513 55490031 55490538 0.000000e+00 737.0
14 TraesCS5D01G445300 chr7D 92.398 513 38 1 1 512 556784172 556784684 0.000000e+00 730.0
15 TraesCS5D01G445300 chr7D 92.063 504 35 5 13 513 436882198 436881697 0.000000e+00 704.0
16 TraesCS5D01G445300 chr4B 93.555 512 30 3 1 510 399292652 399293162 0.000000e+00 760.0
17 TraesCS5D01G445300 chr3D 92.982 513 35 1 1 512 180446900 180447412 0.000000e+00 747.0
18 TraesCS5D01G445300 chr1B 92.731 509 35 2 1 507 569436312 569435804 0.000000e+00 734.0
19 TraesCS5D01G445300 chr4A 90.684 526 41 7 1 523 614137477 614137997 0.000000e+00 693.0
20 TraesCS5D01G445300 chr4A 76.596 141 29 4 1023 1161 639962094 639962232 1.370000e-09 75.0
21 TraesCS5D01G445300 chr1D 71.642 1005 228 47 1036 2009 81002229 81001251 1.280000e-54 224.0
22 TraesCS5D01G445300 chr2A 83.920 199 27 4 1003 1197 602796839 602796642 6.050000e-43 185.0
23 TraesCS5D01G445300 chr2B 83.929 112 16 2 1023 1133 541085991 541085881 4.850000e-19 106.0


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 TraesCS5D01G445300 chr5D 495744106 495747655 3549 False 6556.0 6556 100.000 1 3550 1 chr5D.!!$F1 3549
1 TraesCS5D01G445300 chr5A 619714583 619717238 2655 False 4205.0 4205 95.243 890 3550 1 chr5A.!!$F1 2660
2 TraesCS5D01G445300 chr5A 428251631 428252131 500 True 697.0 697 91.833 13 512 1 chr5A.!!$R1 499
3 TraesCS5D01G445300 chr5B 612978361 612981016 2655 False 4017.0 4017 93.850 860 3550 1 chr5B.!!$F1 2690
4 TraesCS5D01G445300 chr5B 613081542 613082820 1278 False 1301.0 1301 85.265 2269 3550 1 chr5B.!!$F3 1281
5 TraesCS5D01G445300 chr5B 613097040 613098939 1899 False 732.5 750 84.353 2269 3550 2 chr5B.!!$F5 1281
6 TraesCS5D01G445300 chr5B 613044958 613045775 817 False 422.0 422 76.824 1144 1963 1 chr5B.!!$F2 819
7 TraesCS5D01G445300 chr7D 510344527 510345049 522 False 767.0 767 93.130 1 523 1 chr7D.!!$F2 522
8 TraesCS5D01G445300 chr7D 55490031 55490538 507 False 737.0 737 92.802 1 513 1 chr7D.!!$F1 512
9 TraesCS5D01G445300 chr7D 556784172 556784684 512 False 730.0 730 92.398 1 512 1 chr7D.!!$F3 511
10 TraesCS5D01G445300 chr7D 436881697 436882198 501 True 704.0 704 92.063 13 513 1 chr7D.!!$R1 500
11 TraesCS5D01G445300 chr4B 399292652 399293162 510 False 760.0 760 93.555 1 510 1 chr4B.!!$F1 509
12 TraesCS5D01G445300 chr3D 180446900 180447412 512 False 747.0 747 92.982 1 512 1 chr3D.!!$F1 511
13 TraesCS5D01G445300 chr1B 569435804 569436312 508 True 734.0 734 92.731 1 507 1 chr1B.!!$R1 506
14 TraesCS5D01G445300 chr4A 614137477 614137997 520 False 693.0 693 90.684 1 523 1 chr4A.!!$F1 522
15 TraesCS5D01G445300 chr1D 81001251 81002229 978 True 224.0 224 71.642 1036 2009 1 chr1D.!!$R1 973

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
751 756 0.108520 TCAAACGGATAGGGTGCGAC 60.109 55.0 0.0 0.0 45.38 5.19 F
798 803 0.693049 CGCCTATCAGCCCCCTATTT 59.307 55.0 0.0 0.0 0.00 1.40 F
1975 2023 0.240145 GACGACAGACGATGGTGTCA 59.760 55.0 0.0 0.0 42.79 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1627 0.187117 TGGCCTCTCAGGATCTCGAT 59.813 55.000 3.32 0.00 37.67 3.59 R
2411 2474 0.390472 GTTTGCAGTCTAGAGCGCCT 60.390 55.000 2.29 3.28 0.00 5.52 R
2876 3569 3.839323 TCCAGGGAGAAGGTACTAACA 57.161 47.619 0.00 0.00 38.49 2.41 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
25 26 1.136891 CACGTGATCTAGGATGTGGCA 59.863 52.381 10.90 0.00 0.00 4.92
127 130 0.462225 TCTAGGGTGAGCGTCTCTCG 60.462 60.000 8.07 0.00 44.86 4.04
183 187 2.683933 GGAAGGGTCCCTCTGCGA 60.684 66.667 12.07 0.00 38.08 5.10
196 200 3.102107 CTGCGACGAGAGAGACGGG 62.102 68.421 0.00 0.00 34.93 5.28
220 224 5.279809 GGGATGTGTGTTGTCTTTCTACCTA 60.280 44.000 0.00 0.00 0.00 3.08
400 405 5.188988 TGAGTTGTAAGCCTCCTAGAGTA 57.811 43.478 0.00 0.00 0.00 2.59
412 417 5.656420 CCTCCTAGAGTATCCCCTTGTATT 58.344 45.833 0.00 0.00 33.66 1.89
458 463 3.083293 GTTTGTATTTCCTGGCCGGTTA 58.917 45.455 11.58 0.00 0.00 2.85
551 556 4.383602 CGGCGGGCAACAACGAAG 62.384 66.667 0.00 0.00 39.74 3.79
553 558 2.051345 GCGGGCAACAACGAAGTG 60.051 61.111 0.00 0.00 45.00 3.16
554 559 2.637025 CGGGCAACAACGAAGTGG 59.363 61.111 0.00 0.00 45.00 4.00
561 566 2.103410 ACAACGAAGTGGTGTTGCC 58.897 52.632 5.10 0.00 46.92 4.52
562 567 1.010125 CAACGAAGTGGTGTTGCCG 60.010 57.895 0.00 0.00 45.00 5.69
563 568 2.184167 AACGAAGTGGTGTTGCCGG 61.184 57.895 0.00 0.00 45.00 6.13
564 569 3.353836 CGAAGTGGTGTTGCCGGG 61.354 66.667 2.18 0.00 41.21 5.73
565 570 2.983592 GAAGTGGTGTTGCCGGGG 60.984 66.667 2.18 0.00 41.21 5.73
585 590 4.925576 GGCGACGCCGATGATCGT 62.926 66.667 25.24 0.00 39.62 3.73
586 591 3.682315 GCGACGCCGATGATCGTG 61.682 66.667 14.27 8.33 38.40 4.35
587 592 3.024609 CGACGCCGATGATCGTGG 61.025 66.667 14.27 7.41 38.40 4.94
588 593 3.330853 GACGCCGATGATCGTGGC 61.331 66.667 14.27 9.84 45.39 5.01
589 594 4.891727 ACGCCGATGATCGTGGCC 62.892 66.667 14.27 0.00 46.12 5.36
591 596 4.891727 GCCGATGATCGTGGCCGT 62.892 66.667 14.27 0.00 43.06 5.68
592 597 2.658593 CCGATGATCGTGGCCGTC 60.659 66.667 14.27 0.00 38.40 4.79
593 598 3.024609 CGATGATCGTGGCCGTCG 61.025 66.667 6.68 12.91 34.72 5.12
594 599 3.330853 GATGATCGTGGCCGTCGC 61.331 66.667 14.04 3.66 35.01 5.19
595 600 4.141965 ATGATCGTGGCCGTCGCA 62.142 61.111 14.04 8.59 36.38 5.10
596 601 3.445518 ATGATCGTGGCCGTCGCAT 62.446 57.895 14.04 10.23 36.38 4.73
597 602 3.330853 GATCGTGGCCGTCGCATC 61.331 66.667 14.04 13.14 36.38 3.91
598 603 3.774959 GATCGTGGCCGTCGCATCT 62.775 63.158 14.04 1.01 36.38 2.90
599 604 3.774959 ATCGTGGCCGTCGCATCTC 62.775 63.158 14.04 0.00 36.38 2.75
601 606 4.796231 GTGGCCGTCGCATCTCGT 62.796 66.667 0.00 0.00 39.67 4.18
602 607 4.794439 TGGCCGTCGCATCTCGTG 62.794 66.667 0.00 0.00 39.67 4.35
603 608 4.492160 GGCCGTCGCATCTCGTGA 62.492 66.667 0.00 0.00 39.67 4.35
604 609 2.506217 GCCGTCGCATCTCGTGAA 60.506 61.111 0.00 0.00 39.67 3.18
605 610 2.508891 GCCGTCGCATCTCGTGAAG 61.509 63.158 0.00 0.00 39.67 3.02
606 611 1.874019 CCGTCGCATCTCGTGAAGG 60.874 63.158 0.00 0.00 45.41 3.46
607 612 1.136774 CGTCGCATCTCGTGAAGGA 59.863 57.895 0.00 0.00 39.67 3.36
608 613 0.863538 CGTCGCATCTCGTGAAGGAG 60.864 60.000 0.00 0.00 39.67 3.69
609 614 1.139734 TCGCATCTCGTGAAGGAGC 59.860 57.895 0.00 0.00 39.67 4.70
610 615 1.153765 CGCATCTCGTGAAGGAGCA 60.154 57.895 0.00 0.00 33.98 4.26
611 616 1.144565 CGCATCTCGTGAAGGAGCAG 61.145 60.000 0.00 0.00 33.98 4.24
612 617 1.427592 GCATCTCGTGAAGGAGCAGC 61.428 60.000 0.00 0.00 33.98 5.25
613 618 0.809241 CATCTCGTGAAGGAGCAGCC 60.809 60.000 0.00 0.00 33.98 4.85
614 619 1.965754 ATCTCGTGAAGGAGCAGCCC 61.966 60.000 0.00 0.00 37.37 5.19
615 620 2.922503 TCGTGAAGGAGCAGCCCA 60.923 61.111 3.08 0.00 37.37 5.36
616 621 2.435586 CGTGAAGGAGCAGCCCAG 60.436 66.667 3.08 0.00 37.37 4.45
617 622 2.749441 GTGAAGGAGCAGCCCAGC 60.749 66.667 3.08 0.00 37.37 4.85
618 623 4.399395 TGAAGGAGCAGCCCAGCG 62.399 66.667 3.08 0.00 40.15 5.18
626 631 3.160047 CAGCCCAGCGGAGGAGAT 61.160 66.667 0.00 0.00 0.00 2.75
627 632 3.160047 AGCCCAGCGGAGGAGATG 61.160 66.667 0.00 0.00 0.00 2.90
628 633 4.925861 GCCCAGCGGAGGAGATGC 62.926 72.222 0.00 0.00 0.00 3.91
629 634 4.598894 CCCAGCGGAGGAGATGCG 62.599 72.222 0.00 0.00 46.94 4.73
635 640 4.593864 GGAGGAGATGCGACGGGC 62.594 72.222 0.00 0.00 43.96 6.13
660 665 3.031784 CGATTGCGCTCTCTTCTTTTC 57.968 47.619 9.73 0.00 0.00 2.29
661 666 2.670414 CGATTGCGCTCTCTTCTTTTCT 59.330 45.455 9.73 0.00 0.00 2.52
662 667 3.483248 CGATTGCGCTCTCTTCTTTTCTG 60.483 47.826 9.73 0.00 0.00 3.02
663 668 1.800805 TGCGCTCTCTTCTTTTCTGG 58.199 50.000 9.73 0.00 0.00 3.86
664 669 1.344438 TGCGCTCTCTTCTTTTCTGGA 59.656 47.619 9.73 0.00 0.00 3.86
665 670 2.027745 TGCGCTCTCTTCTTTTCTGGAT 60.028 45.455 9.73 0.00 0.00 3.41
666 671 2.351111 GCGCTCTCTTCTTTTCTGGATG 59.649 50.000 0.00 0.00 0.00 3.51
667 672 2.351111 CGCTCTCTTCTTTTCTGGATGC 59.649 50.000 0.00 0.00 0.00 3.91
668 673 2.351111 GCTCTCTTCTTTTCTGGATGCG 59.649 50.000 0.00 0.00 0.00 4.73
669 674 2.350522 TCTCTTCTTTTCTGGATGCGC 58.649 47.619 0.00 0.00 0.00 6.09
670 675 2.027745 TCTCTTCTTTTCTGGATGCGCT 60.028 45.455 9.73 0.00 0.00 5.92
671 676 3.195610 TCTCTTCTTTTCTGGATGCGCTA 59.804 43.478 9.73 0.00 0.00 4.26
672 677 3.262420 TCTTCTTTTCTGGATGCGCTAC 58.738 45.455 9.73 1.91 0.00 3.58
673 678 1.640428 TCTTTTCTGGATGCGCTACG 58.360 50.000 9.73 0.00 0.00 3.51
674 679 0.652592 CTTTTCTGGATGCGCTACGG 59.347 55.000 9.73 3.84 0.00 4.02
675 680 0.742990 TTTTCTGGATGCGCTACGGG 60.743 55.000 9.73 0.00 0.00 5.28
676 681 2.587322 TTTCTGGATGCGCTACGGGG 62.587 60.000 9.73 0.00 0.00 5.73
677 682 3.849951 CTGGATGCGCTACGGGGT 61.850 66.667 9.73 0.00 0.00 4.95
678 683 4.155733 TGGATGCGCTACGGGGTG 62.156 66.667 9.73 0.00 0.00 4.61
679 684 4.910585 GGATGCGCTACGGGGTGG 62.911 72.222 9.73 0.00 0.00 4.61
680 685 4.910585 GATGCGCTACGGGGTGGG 62.911 72.222 9.73 0.00 0.00 4.61
684 689 4.157120 CGCTACGGGGTGGGGAAG 62.157 72.222 0.00 0.00 0.00 3.46
685 690 3.793888 GCTACGGGGTGGGGAAGG 61.794 72.222 0.00 0.00 0.00 3.46
686 691 2.285144 CTACGGGGTGGGGAAGGT 60.285 66.667 0.00 0.00 0.00 3.50
687 692 1.921857 CTACGGGGTGGGGAAGGTT 60.922 63.158 0.00 0.00 0.00 3.50
688 693 2.193087 CTACGGGGTGGGGAAGGTTG 62.193 65.000 0.00 0.00 0.00 3.77
689 694 4.360405 CGGGGTGGGGAAGGTTGG 62.360 72.222 0.00 0.00 0.00 3.77
690 695 2.861974 GGGGTGGGGAAGGTTGGA 60.862 66.667 0.00 0.00 0.00 3.53
691 696 2.475172 GGGGTGGGGAAGGTTGGAA 61.475 63.158 0.00 0.00 0.00 3.53
692 697 1.228769 GGGTGGGGAAGGTTGGAAC 60.229 63.158 0.00 0.00 0.00 3.62
693 698 1.602605 GGTGGGGAAGGTTGGAACG 60.603 63.158 0.00 0.00 0.00 3.95
694 699 1.452801 GTGGGGAAGGTTGGAACGA 59.547 57.895 0.00 0.00 0.00 3.85
695 700 0.179012 GTGGGGAAGGTTGGAACGAA 60.179 55.000 0.00 0.00 0.00 3.85
696 701 0.109723 TGGGGAAGGTTGGAACGAAG 59.890 55.000 0.00 0.00 0.00 3.79
697 702 0.608308 GGGGAAGGTTGGAACGAAGG 60.608 60.000 0.00 0.00 0.00 3.46
698 703 0.399075 GGGAAGGTTGGAACGAAGGA 59.601 55.000 0.00 0.00 0.00 3.36
699 704 1.610886 GGGAAGGTTGGAACGAAGGAG 60.611 57.143 0.00 0.00 0.00 3.69
700 705 1.610886 GGAAGGTTGGAACGAAGGAGG 60.611 57.143 0.00 0.00 0.00 4.30
701 706 1.346722 GAAGGTTGGAACGAAGGAGGA 59.653 52.381 0.00 0.00 0.00 3.71
702 707 0.977395 AGGTTGGAACGAAGGAGGAG 59.023 55.000 0.00 0.00 0.00 3.69
703 708 0.974383 GGTTGGAACGAAGGAGGAGA 59.026 55.000 0.00 0.00 0.00 3.71
704 709 1.555533 GGTTGGAACGAAGGAGGAGAT 59.444 52.381 0.00 0.00 0.00 2.75
705 710 2.764572 GGTTGGAACGAAGGAGGAGATA 59.235 50.000 0.00 0.00 0.00 1.98
706 711 3.430513 GGTTGGAACGAAGGAGGAGATAC 60.431 52.174 0.00 0.00 0.00 2.24
707 712 2.022195 TGGAACGAAGGAGGAGATACG 58.978 52.381 0.00 0.00 0.00 3.06
708 713 2.295885 GGAACGAAGGAGGAGATACGA 58.704 52.381 0.00 0.00 0.00 3.43
709 714 2.885894 GGAACGAAGGAGGAGATACGAT 59.114 50.000 0.00 0.00 0.00 3.73
710 715 3.058085 GGAACGAAGGAGGAGATACGATC 60.058 52.174 0.00 0.00 0.00 3.69
711 716 3.495434 ACGAAGGAGGAGATACGATCT 57.505 47.619 0.00 0.00 43.70 2.75
712 717 3.142951 ACGAAGGAGGAGATACGATCTG 58.857 50.000 0.00 0.00 40.38 2.90
713 718 3.181453 ACGAAGGAGGAGATACGATCTGA 60.181 47.826 0.00 0.00 40.38 3.27
714 719 3.815962 CGAAGGAGGAGATACGATCTGAA 59.184 47.826 0.00 0.00 40.38 3.02
715 720 4.319911 CGAAGGAGGAGATACGATCTGAAC 60.320 50.000 0.00 0.00 40.38 3.18
716 721 4.171878 AGGAGGAGATACGATCTGAACA 57.828 45.455 0.00 0.00 40.38 3.18
717 722 4.141287 AGGAGGAGATACGATCTGAACAG 58.859 47.826 0.00 0.00 40.38 3.16
718 723 3.886505 GGAGGAGATACGATCTGAACAGT 59.113 47.826 0.00 0.00 40.38 3.55
719 724 4.339814 GGAGGAGATACGATCTGAACAGTT 59.660 45.833 0.00 0.00 40.38 3.16
720 725 5.531659 GGAGGAGATACGATCTGAACAGTTA 59.468 44.000 0.00 0.00 40.38 2.24
721 726 6.293735 GGAGGAGATACGATCTGAACAGTTAG 60.294 46.154 0.00 0.00 40.38 2.34
722 727 6.358178 AGGAGATACGATCTGAACAGTTAGA 58.642 40.000 0.00 0.00 40.38 2.10
723 728 6.485313 AGGAGATACGATCTGAACAGTTAGAG 59.515 42.308 0.00 0.00 40.38 2.43
724 729 6.261381 GGAGATACGATCTGAACAGTTAGAGT 59.739 42.308 0.00 0.75 40.38 3.24
725 730 7.022055 AGATACGATCTGAACAGTTAGAGTG 57.978 40.000 0.00 0.00 38.44 3.51
726 731 4.442375 ACGATCTGAACAGTTAGAGTGG 57.558 45.455 0.00 0.00 0.00 4.00
727 732 4.079970 ACGATCTGAACAGTTAGAGTGGA 58.920 43.478 0.00 0.00 0.00 4.02
728 733 4.523173 ACGATCTGAACAGTTAGAGTGGAA 59.477 41.667 0.00 0.00 0.00 3.53
729 734 4.859798 CGATCTGAACAGTTAGAGTGGAAC 59.140 45.833 1.73 0.00 0.00 3.62
730 735 4.602340 TCTGAACAGTTAGAGTGGAACC 57.398 45.455 1.73 0.00 37.80 3.62
731 736 3.964688 TCTGAACAGTTAGAGTGGAACCA 59.035 43.478 1.73 0.00 37.80 3.67
732 737 4.593206 TCTGAACAGTTAGAGTGGAACCAT 59.407 41.667 0.00 0.00 37.80 3.55
733 738 4.894784 TGAACAGTTAGAGTGGAACCATC 58.105 43.478 0.00 0.00 37.80 3.51
734 739 4.346709 TGAACAGTTAGAGTGGAACCATCA 59.653 41.667 0.00 0.00 37.80 3.07
735 740 4.974645 ACAGTTAGAGTGGAACCATCAA 57.025 40.909 0.00 0.00 37.80 2.57
736 741 5.304686 ACAGTTAGAGTGGAACCATCAAA 57.695 39.130 0.00 0.00 37.80 2.69
737 742 5.063880 ACAGTTAGAGTGGAACCATCAAAC 58.936 41.667 0.00 1.00 37.80 2.93
738 743 4.152402 CAGTTAGAGTGGAACCATCAAACG 59.848 45.833 0.00 0.00 37.80 3.60
739 744 2.185004 AGAGTGGAACCATCAAACGG 57.815 50.000 0.00 0.00 37.80 4.44
740 745 1.697432 AGAGTGGAACCATCAAACGGA 59.303 47.619 0.00 0.00 37.80 4.69
741 746 2.305927 AGAGTGGAACCATCAAACGGAT 59.694 45.455 0.00 0.00 37.80 4.18
742 747 3.517901 AGAGTGGAACCATCAAACGGATA 59.482 43.478 0.00 0.00 37.80 2.59
743 748 3.871594 GAGTGGAACCATCAAACGGATAG 59.128 47.826 0.00 0.00 37.80 2.08
744 749 2.943033 GTGGAACCATCAAACGGATAGG 59.057 50.000 0.00 0.00 33.95 2.57
745 750 2.092646 TGGAACCATCAAACGGATAGGG 60.093 50.000 0.00 0.00 33.95 3.53
746 751 2.092592 GGAACCATCAAACGGATAGGGT 60.093 50.000 0.00 0.00 34.61 4.34
747 752 2.710096 ACCATCAAACGGATAGGGTG 57.290 50.000 0.00 0.00 32.56 4.61
748 753 1.308998 CCATCAAACGGATAGGGTGC 58.691 55.000 0.00 0.00 33.95 5.01
750 755 0.828022 ATCAAACGGATAGGGTGCGA 59.172 50.000 0.00 0.00 45.38 5.10
751 756 0.108520 TCAAACGGATAGGGTGCGAC 60.109 55.000 0.00 0.00 45.38 5.19
752 757 1.087771 CAAACGGATAGGGTGCGACC 61.088 60.000 0.00 0.00 45.38 4.79
753 758 2.567564 AAACGGATAGGGTGCGACCG 62.568 60.000 0.00 0.00 45.38 4.79
754 759 4.280494 CGGATAGGGTGCGACCGG 62.280 72.222 0.00 0.00 45.38 5.28
755 760 4.603946 GGATAGGGTGCGACCGGC 62.604 72.222 0.00 0.00 39.83 6.13
756 761 4.603946 GATAGGGTGCGACCGGCC 62.604 72.222 0.00 0.00 39.83 6.13
762 767 3.370231 GTGCGACCGGCCCAATTT 61.370 61.111 0.00 0.00 42.61 1.82
763 768 2.598985 TGCGACCGGCCCAATTTT 60.599 55.556 0.00 0.00 42.61 1.82
764 769 1.303398 TGCGACCGGCCCAATTTTA 60.303 52.632 0.00 0.00 42.61 1.52
765 770 1.309499 TGCGACCGGCCCAATTTTAG 61.309 55.000 0.00 0.00 42.61 1.85
766 771 2.000215 GCGACCGGCCCAATTTTAGG 62.000 60.000 0.00 0.00 34.80 2.69
771 776 2.499205 GCCCAATTTTAGGCCCGC 59.501 61.111 0.00 0.00 43.76 6.13
772 777 2.804856 CCCAATTTTAGGCCCGCG 59.195 61.111 0.00 0.00 0.00 6.46
773 778 2.104132 CCAATTTTAGGCCCGCGC 59.896 61.111 0.00 0.00 0.00 6.86
774 779 2.705821 CCAATTTTAGGCCCGCGCA 61.706 57.895 8.75 0.00 36.38 6.09
775 780 1.516169 CAATTTTAGGCCCGCGCAC 60.516 57.895 8.75 0.00 36.38 5.34
776 781 2.706834 AATTTTAGGCCCGCGCACC 61.707 57.895 8.75 5.46 36.38 5.01
795 800 2.923035 GCGCCTATCAGCCCCCTA 60.923 66.667 0.00 0.00 0.00 3.53
796 801 2.294078 GCGCCTATCAGCCCCCTAT 61.294 63.158 0.00 0.00 0.00 2.57
797 802 1.842381 GCGCCTATCAGCCCCCTATT 61.842 60.000 0.00 0.00 0.00 1.73
798 803 0.693049 CGCCTATCAGCCCCCTATTT 59.307 55.000 0.00 0.00 0.00 1.40
799 804 1.906574 CGCCTATCAGCCCCCTATTTA 59.093 52.381 0.00 0.00 0.00 1.40
800 805 2.093447 CGCCTATCAGCCCCCTATTTAG 60.093 54.545 0.00 0.00 0.00 1.85
801 806 3.182152 GCCTATCAGCCCCCTATTTAGA 58.818 50.000 0.00 0.00 0.00 2.10
802 807 3.587506 GCCTATCAGCCCCCTATTTAGAA 59.412 47.826 0.00 0.00 0.00 2.10
803 808 4.042934 GCCTATCAGCCCCCTATTTAGAAA 59.957 45.833 0.00 0.00 0.00 2.52
804 809 5.561679 CCTATCAGCCCCCTATTTAGAAAC 58.438 45.833 0.00 0.00 0.00 2.78
805 810 3.553828 TCAGCCCCCTATTTAGAAACG 57.446 47.619 0.00 0.00 0.00 3.60
806 811 2.171870 TCAGCCCCCTATTTAGAAACGG 59.828 50.000 0.00 0.00 0.00 4.44
807 812 2.171870 CAGCCCCCTATTTAGAAACGGA 59.828 50.000 0.00 0.00 0.00 4.69
808 813 2.438392 AGCCCCCTATTTAGAAACGGAG 59.562 50.000 0.00 0.00 0.00 4.63
809 814 2.486727 GCCCCCTATTTAGAAACGGAGG 60.487 54.545 0.00 0.00 0.00 4.30
810 815 3.043418 CCCCCTATTTAGAAACGGAGGA 58.957 50.000 0.00 0.00 0.00 3.71
811 816 3.071167 CCCCCTATTTAGAAACGGAGGAG 59.929 52.174 0.00 0.00 0.00 3.69
825 830 9.144298 AGAAACGGAGGAGTAATAATTATGAGA 57.856 33.333 0.00 0.00 0.00 3.27
826 831 9.413048 GAAACGGAGGAGTAATAATTATGAGAG 57.587 37.037 0.00 0.00 0.00 3.20
827 832 8.480133 AACGGAGGAGTAATAATTATGAGAGT 57.520 34.615 0.00 0.00 0.00 3.24
828 833 8.480133 ACGGAGGAGTAATAATTATGAGAGTT 57.520 34.615 0.00 0.00 0.00 3.01
829 834 8.361139 ACGGAGGAGTAATAATTATGAGAGTTG 58.639 37.037 0.00 0.00 0.00 3.16
830 835 7.329717 CGGAGGAGTAATAATTATGAGAGTTGC 59.670 40.741 0.00 0.00 0.00 4.17
831 836 8.371699 GGAGGAGTAATAATTATGAGAGTTGCT 58.628 37.037 0.00 0.00 0.00 3.91
832 837 9.771534 GAGGAGTAATAATTATGAGAGTTGCTT 57.228 33.333 0.00 0.00 0.00 3.91
836 841 9.905713 AGTAATAATTATGAGAGTTGCTTTGGA 57.094 29.630 0.00 0.00 0.00 3.53
881 886 3.249080 CGTGGTGGACGTCTTGTTTTATT 59.751 43.478 16.46 0.00 43.50 1.40
938 943 3.088532 TGTCTCTCTCTCCTCTTTCAGC 58.911 50.000 0.00 0.00 0.00 4.26
995 1000 2.571231 CAAAATTCCACCGGCGGG 59.429 61.111 31.78 18.68 40.11 6.13
1336 1347 1.068741 ACCCTATTCGAATCACCGAGC 59.931 52.381 15.25 0.00 39.90 5.03
1600 1627 0.988145 CTCTTGCCCCCACCCTGATA 60.988 60.000 0.00 0.00 0.00 2.15
1678 1717 0.815734 CGAGTACCACCCGAATGAGT 59.184 55.000 0.00 0.00 0.00 3.41
1679 1718 2.019249 CGAGTACCACCCGAATGAGTA 58.981 52.381 0.00 0.00 0.00 2.59
1816 1858 0.681733 TATGCAGGGATCTCGGCTTC 59.318 55.000 18.79 0.00 0.00 3.86
1831 1873 2.954753 CTTCGCCTGTGGTTGACGC 61.955 63.158 0.00 0.00 0.00 5.19
1840 1882 1.227527 TGGTTGACGCAGACTGGTG 60.228 57.895 4.26 0.00 0.00 4.17
1855 1897 4.357947 GTGCCGACGGAGCTGTGA 62.358 66.667 20.50 0.00 0.00 3.58
1865 1907 1.434622 GGAGCTGTGACATGGATGCG 61.435 60.000 0.00 0.00 0.00 4.73
1866 1908 1.434622 GAGCTGTGACATGGATGCGG 61.435 60.000 0.00 0.00 0.00 5.69
1916 1964 4.688021 CTCCCTTCTAACTCATTCTTCCG 58.312 47.826 0.00 0.00 0.00 4.30
1946 1994 2.680339 GCTTTGAGGATAGAGTTGGTGC 59.320 50.000 0.00 0.00 0.00 5.01
1975 2023 0.240145 GACGACAGACGATGGTGTCA 59.760 55.000 0.00 0.00 42.79 3.58
1977 2025 1.065572 CGACAGACGATGGTGTCACG 61.066 60.000 0.00 0.00 42.79 4.35
2038 2092 4.243270 CGATTCCAATATCGTTCCCTACC 58.757 47.826 0.00 0.00 41.79 3.18
2039 2093 4.262292 CGATTCCAATATCGTTCCCTACCA 60.262 45.833 0.00 0.00 41.79 3.25
2040 2094 5.617252 GATTCCAATATCGTTCCCTACCAA 58.383 41.667 0.00 0.00 0.00 3.67
2041 2095 5.640158 TTCCAATATCGTTCCCTACCAAT 57.360 39.130 0.00 0.00 0.00 3.16
2042 2096 5.223449 TCCAATATCGTTCCCTACCAATC 57.777 43.478 0.00 0.00 0.00 2.67
2043 2097 4.905456 TCCAATATCGTTCCCTACCAATCT 59.095 41.667 0.00 0.00 0.00 2.40
2044 2098 4.997395 CCAATATCGTTCCCTACCAATCTG 59.003 45.833 0.00 0.00 0.00 2.90
2045 2099 5.454755 CCAATATCGTTCCCTACCAATCTGT 60.455 44.000 0.00 0.00 0.00 3.41
2046 2100 5.888982 ATATCGTTCCCTACCAATCTGTT 57.111 39.130 0.00 0.00 0.00 3.16
2047 2101 3.604875 TCGTTCCCTACCAATCTGTTC 57.395 47.619 0.00 0.00 0.00 3.18
2048 2102 2.235402 TCGTTCCCTACCAATCTGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
2049 2103 2.679930 CGTTCCCTACCAATCTGTTCCC 60.680 54.545 0.00 0.00 0.00 3.97
2050 2104 2.576648 GTTCCCTACCAATCTGTTCCCT 59.423 50.000 0.00 0.00 0.00 4.20
2051 2105 3.778629 GTTCCCTACCAATCTGTTCCCTA 59.221 47.826 0.00 0.00 0.00 3.53
2052 2106 3.381335 TCCCTACCAATCTGTTCCCTAC 58.619 50.000 0.00 0.00 0.00 3.18
2053 2107 3.112263 CCCTACCAATCTGTTCCCTACA 58.888 50.000 0.00 0.00 34.95 2.74
2054 2108 3.716872 CCCTACCAATCTGTTCCCTACAT 59.283 47.826 0.00 0.00 35.85 2.29
2194 2254 1.246649 TGTGAATGTGTGGGTGATGC 58.753 50.000 0.00 0.00 0.00 3.91
2219 2279 4.916249 GCATTTTCTCAAGAAAGAGCTGTG 59.084 41.667 17.07 8.54 43.90 3.66
2265 2325 8.632679 AGCATACACTTTTCTTTTCAGATCAAA 58.367 29.630 0.00 0.00 0.00 2.69
2363 2426 0.905357 AGGTAGAGAAAGCCGTGCAT 59.095 50.000 0.00 0.00 0.00 3.96
2411 2474 3.958798 CCCTTAAGGATGAGGACTTCGTA 59.041 47.826 23.74 0.00 38.24 3.43
2418 2481 1.064458 GAGGACTTCGTAGGCGCTC 59.936 63.158 7.64 0.00 38.14 5.03
2474 2537 2.026729 AGGCTTCTTCCTTTCTACCTGC 60.027 50.000 0.00 0.00 30.82 4.85
2475 2538 2.026729 GGCTTCTTCCTTTCTACCTGCT 60.027 50.000 0.00 0.00 0.00 4.24
2605 2668 3.570926 ATGTGATTTGTTGCTCTGCAG 57.429 42.857 7.63 7.63 40.61 4.41
2705 2769 2.300152 CTGTACTTGGGAGCTGACTTGA 59.700 50.000 0.00 0.00 0.00 3.02
2706 2770 2.906389 TGTACTTGGGAGCTGACTTGAT 59.094 45.455 0.00 0.00 0.00 2.57
2735 2799 9.230122 TCTTATGTTATGATGTGTGAATTGTGT 57.770 29.630 0.00 0.00 0.00 3.72
2781 3470 9.904198 TCTCTGGATGTAAATATTTCATCACAA 57.096 29.630 25.33 16.59 39.47 3.33
2876 3569 6.539464 ACAAAATGCAATCAACATTGAACACT 59.461 30.769 0.00 0.00 41.97 3.55
3055 3748 6.071447 ACAATTATGGATGTGCTTTGCTACAA 60.071 34.615 0.00 0.00 0.00 2.41
3101 3794 3.139077 GTGAAGAGTACAACCACCCAAG 58.861 50.000 0.00 0.00 0.00 3.61
3146 3839 2.241176 GAGGGTATGTCACATTCCCCAA 59.759 50.000 25.17 0.00 38.97 4.12
3155 3849 6.381498 TGTCACATTCCCCAATTAGTCTTA 57.619 37.500 0.00 0.00 0.00 2.10
3540 4248 1.002430 TGATCTCGATGCTTATGGCCC 59.998 52.381 0.00 0.00 40.92 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.602257 TTGCCACATCCTAGATCACG 57.398 50.000 0.00 0.00 0.00 4.35
11 12 1.544093 CCGCATTGCCACATCCTAGAT 60.544 52.381 2.41 0.00 0.00 1.98
183 187 1.454111 CATCCCCCGTCTCTCTCGT 60.454 63.158 0.00 0.00 0.00 4.18
196 200 3.751698 GGTAGAAAGACAACACACATCCC 59.248 47.826 0.00 0.00 0.00 3.85
400 405 2.466846 GGCCAAACAATACAAGGGGAT 58.533 47.619 0.00 0.00 0.00 3.85
412 417 1.076632 AAACCACCTCGGCCAAACA 60.077 52.632 2.24 0.00 39.03 2.83
458 463 4.578871 GGCTTTGAATTAACCAAGCCATT 58.421 39.130 15.37 0.00 37.55 3.16
534 539 4.383602 CTTCGTTGTTGCCCGCCG 62.384 66.667 0.00 0.00 0.00 6.46
535 540 3.284449 ACTTCGTTGTTGCCCGCC 61.284 61.111 0.00 0.00 0.00 6.13
536 541 2.051345 CACTTCGTTGTTGCCCGC 60.051 61.111 0.00 0.00 0.00 6.13
537 542 2.184167 ACCACTTCGTTGTTGCCCG 61.184 57.895 0.00 0.00 0.00 6.13
538 543 1.358759 CACCACTTCGTTGTTGCCC 59.641 57.895 0.00 0.00 0.00 5.36
539 544 0.454196 AACACCACTTCGTTGTTGCC 59.546 50.000 0.00 0.00 0.00 4.52
540 545 1.544686 CAACACCACTTCGTTGTTGC 58.455 50.000 1.08 0.00 38.14 4.17
541 546 1.544686 GCAACACCACTTCGTTGTTG 58.455 50.000 8.91 8.91 43.52 3.33
542 547 0.454196 GGCAACACCACTTCGTTGTT 59.546 50.000 0.00 0.00 43.52 2.83
543 548 1.711060 CGGCAACACCACTTCGTTGT 61.711 55.000 0.00 0.00 43.52 3.32
544 549 1.010125 CGGCAACACCACTTCGTTG 60.010 57.895 0.00 0.00 44.26 4.10
545 550 2.184167 CCGGCAACACCACTTCGTT 61.184 57.895 0.00 0.00 39.03 3.85
546 551 2.590575 CCGGCAACACCACTTCGT 60.591 61.111 0.00 0.00 39.03 3.85
547 552 3.353836 CCCGGCAACACCACTTCG 61.354 66.667 0.00 0.00 39.03 3.79
548 553 2.983592 CCCCGGCAACACCACTTC 60.984 66.667 0.00 0.00 39.03 3.01
568 573 4.925576 ACGATCATCGGCGTCGCC 62.926 66.667 26.69 26.69 45.59 5.54
569 574 3.682315 CACGATCATCGGCGTCGC 61.682 66.667 12.67 9.22 45.59 5.19
570 575 3.024609 CCACGATCATCGGCGTCG 61.025 66.667 12.67 14.78 45.59 5.12
571 576 3.330853 GCCACGATCATCGGCGTC 61.331 66.667 12.67 0.00 45.59 5.19
574 579 4.891727 ACGGCCACGATCATCGGC 62.892 66.667 12.67 5.84 45.59 5.54
575 580 2.658593 GACGGCCACGATCATCGG 60.659 66.667 12.67 0.04 45.59 4.18
576 581 3.024609 CGACGGCCACGATCATCG 61.025 66.667 5.22 5.22 46.93 3.84
577 582 3.330853 GCGACGGCCACGATCATC 61.331 66.667 20.85 1.62 44.60 2.92
578 583 3.445518 ATGCGACGGCCACGATCAT 62.446 57.895 20.85 13.05 44.60 2.45
579 584 4.141965 ATGCGACGGCCACGATCA 62.142 61.111 20.85 11.54 44.60 2.92
580 585 3.330853 GATGCGACGGCCACGATC 61.331 66.667 20.85 15.69 44.60 3.69
581 586 3.774959 GAGATGCGACGGCCACGAT 62.775 63.158 20.85 11.97 44.60 3.73
582 587 4.492160 GAGATGCGACGGCCACGA 62.492 66.667 20.85 8.28 44.60 4.35
584 589 4.796231 ACGAGATGCGACGGCCAC 62.796 66.667 2.24 0.00 44.57 5.01
585 590 4.794439 CACGAGATGCGACGGCCA 62.794 66.667 2.24 0.00 44.57 5.36
586 591 3.982372 TTCACGAGATGCGACGGCC 62.982 63.158 0.00 0.00 44.57 6.13
587 592 2.506217 TTCACGAGATGCGACGGC 60.506 61.111 0.00 0.00 44.57 5.68
588 593 1.874019 CCTTCACGAGATGCGACGG 60.874 63.158 0.00 0.00 44.57 4.79
589 594 0.863538 CTCCTTCACGAGATGCGACG 60.864 60.000 0.00 0.00 44.57 5.12
590 595 1.142778 GCTCCTTCACGAGATGCGAC 61.143 60.000 0.00 0.00 44.57 5.19
591 596 1.139734 GCTCCTTCACGAGATGCGA 59.860 57.895 0.00 0.00 44.57 5.10
593 598 1.427592 GCTGCTCCTTCACGAGATGC 61.428 60.000 0.00 0.00 30.97 3.91
594 599 0.809241 GGCTGCTCCTTCACGAGATG 60.809 60.000 0.00 0.00 30.97 2.90
595 600 1.519719 GGCTGCTCCTTCACGAGAT 59.480 57.895 0.00 0.00 30.97 2.75
596 601 2.650116 GGGCTGCTCCTTCACGAGA 61.650 63.158 0.00 0.00 34.39 4.04
597 602 2.125350 GGGCTGCTCCTTCACGAG 60.125 66.667 0.00 0.00 34.39 4.18
598 603 2.922503 TGGGCTGCTCCTTCACGA 60.923 61.111 0.00 0.00 34.39 4.35
599 604 2.435586 CTGGGCTGCTCCTTCACG 60.436 66.667 0.00 0.00 34.39 4.35
600 605 2.749441 GCTGGGCTGCTCCTTCAC 60.749 66.667 0.00 0.00 34.39 3.18
601 606 4.399395 CGCTGGGCTGCTCCTTCA 62.399 66.667 0.00 0.00 34.39 3.02
609 614 3.160047 ATCTCCTCCGCTGGGCTG 61.160 66.667 0.00 0.00 0.00 4.85
610 615 3.160047 CATCTCCTCCGCTGGGCT 61.160 66.667 0.00 0.00 0.00 5.19
611 616 4.925861 GCATCTCCTCCGCTGGGC 62.926 72.222 0.00 0.00 0.00 5.36
612 617 4.598894 CGCATCTCCTCCGCTGGG 62.599 72.222 0.00 0.00 0.00 4.45
613 618 3.531207 TCGCATCTCCTCCGCTGG 61.531 66.667 0.00 0.00 0.00 4.85
614 619 2.279120 GTCGCATCTCCTCCGCTG 60.279 66.667 0.00 0.00 0.00 5.18
615 620 3.893763 CGTCGCATCTCCTCCGCT 61.894 66.667 0.00 0.00 0.00 5.52
616 621 4.933064 CCGTCGCATCTCCTCCGC 62.933 72.222 0.00 0.00 0.00 5.54
617 622 4.271816 CCCGTCGCATCTCCTCCG 62.272 72.222 0.00 0.00 0.00 4.63
618 623 4.593864 GCCCGTCGCATCTCCTCC 62.594 72.222 0.00 0.00 37.47 4.30
619 624 4.933064 CGCCCGTCGCATCTCCTC 62.933 72.222 0.00 0.00 37.30 3.71
640 645 2.670414 AGAAAAGAAGAGAGCGCAATCG 59.330 45.455 11.47 0.00 39.07 3.34
641 646 3.181512 CCAGAAAAGAAGAGAGCGCAATC 60.182 47.826 11.47 7.02 0.00 2.67
642 647 2.746362 CCAGAAAAGAAGAGAGCGCAAT 59.254 45.455 11.47 0.00 0.00 3.56
643 648 2.146342 CCAGAAAAGAAGAGAGCGCAA 58.854 47.619 11.47 0.00 0.00 4.85
644 649 1.344438 TCCAGAAAAGAAGAGAGCGCA 59.656 47.619 11.47 0.00 0.00 6.09
645 650 2.086054 TCCAGAAAAGAAGAGAGCGC 57.914 50.000 0.00 0.00 0.00 5.92
646 651 2.351111 GCATCCAGAAAAGAAGAGAGCG 59.649 50.000 0.00 0.00 0.00 5.03
647 652 2.351111 CGCATCCAGAAAAGAAGAGAGC 59.649 50.000 0.00 0.00 0.00 4.09
648 653 2.351111 GCGCATCCAGAAAAGAAGAGAG 59.649 50.000 0.30 0.00 0.00 3.20
649 654 2.027745 AGCGCATCCAGAAAAGAAGAGA 60.028 45.455 11.47 0.00 0.00 3.10
650 655 2.354259 AGCGCATCCAGAAAAGAAGAG 58.646 47.619 11.47 0.00 0.00 2.85
651 656 2.479566 AGCGCATCCAGAAAAGAAGA 57.520 45.000 11.47 0.00 0.00 2.87
652 657 2.029728 CGTAGCGCATCCAGAAAAGAAG 59.970 50.000 11.47 0.00 0.00 2.85
653 658 1.999735 CGTAGCGCATCCAGAAAAGAA 59.000 47.619 11.47 0.00 0.00 2.52
654 659 1.640428 CGTAGCGCATCCAGAAAAGA 58.360 50.000 11.47 0.00 0.00 2.52
655 660 0.652592 CCGTAGCGCATCCAGAAAAG 59.347 55.000 11.47 0.00 0.00 2.27
656 661 0.742990 CCCGTAGCGCATCCAGAAAA 60.743 55.000 11.47 0.00 0.00 2.29
657 662 1.153449 CCCGTAGCGCATCCAGAAA 60.153 57.895 11.47 0.00 0.00 2.52
658 663 2.499205 CCCGTAGCGCATCCAGAA 59.501 61.111 11.47 0.00 0.00 3.02
659 664 3.536917 CCCCGTAGCGCATCCAGA 61.537 66.667 11.47 0.00 0.00 3.86
660 665 3.849951 ACCCCGTAGCGCATCCAG 61.850 66.667 11.47 0.00 0.00 3.86
661 666 4.155733 CACCCCGTAGCGCATCCA 62.156 66.667 11.47 0.00 0.00 3.41
662 667 4.910585 CCACCCCGTAGCGCATCC 62.911 72.222 11.47 0.00 0.00 3.51
663 668 4.910585 CCCACCCCGTAGCGCATC 62.911 72.222 11.47 0.04 0.00 3.91
667 672 4.157120 CTTCCCCACCCCGTAGCG 62.157 72.222 0.00 0.00 0.00 4.26
668 673 3.793888 CCTTCCCCACCCCGTAGC 61.794 72.222 0.00 0.00 0.00 3.58
669 674 1.921857 AACCTTCCCCACCCCGTAG 60.922 63.158 0.00 0.00 0.00 3.51
670 675 2.207768 AACCTTCCCCACCCCGTA 59.792 61.111 0.00 0.00 0.00 4.02
671 676 3.576259 CAACCTTCCCCACCCCGT 61.576 66.667 0.00 0.00 0.00 5.28
672 677 4.360405 CCAACCTTCCCCACCCCG 62.360 72.222 0.00 0.00 0.00 5.73
673 678 2.475172 TTCCAACCTTCCCCACCCC 61.475 63.158 0.00 0.00 0.00 4.95
674 679 1.228769 GTTCCAACCTTCCCCACCC 60.229 63.158 0.00 0.00 0.00 4.61
675 680 1.602605 CGTTCCAACCTTCCCCACC 60.603 63.158 0.00 0.00 0.00 4.61
676 681 0.179012 TTCGTTCCAACCTTCCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
677 682 0.109723 CTTCGTTCCAACCTTCCCCA 59.890 55.000 0.00 0.00 0.00 4.96
678 683 0.608308 CCTTCGTTCCAACCTTCCCC 60.608 60.000 0.00 0.00 0.00 4.81
679 684 0.399075 TCCTTCGTTCCAACCTTCCC 59.601 55.000 0.00 0.00 0.00 3.97
680 685 1.610886 CCTCCTTCGTTCCAACCTTCC 60.611 57.143 0.00 0.00 0.00 3.46
681 686 1.346722 TCCTCCTTCGTTCCAACCTTC 59.653 52.381 0.00 0.00 0.00 3.46
682 687 1.348036 CTCCTCCTTCGTTCCAACCTT 59.652 52.381 0.00 0.00 0.00 3.50
683 688 0.977395 CTCCTCCTTCGTTCCAACCT 59.023 55.000 0.00 0.00 0.00 3.50
684 689 0.974383 TCTCCTCCTTCGTTCCAACC 59.026 55.000 0.00 0.00 0.00 3.77
685 690 3.734293 CGTATCTCCTCCTTCGTTCCAAC 60.734 52.174 0.00 0.00 0.00 3.77
686 691 2.426024 CGTATCTCCTCCTTCGTTCCAA 59.574 50.000 0.00 0.00 0.00 3.53
687 692 2.022195 CGTATCTCCTCCTTCGTTCCA 58.978 52.381 0.00 0.00 0.00 3.53
688 693 2.295885 TCGTATCTCCTCCTTCGTTCC 58.704 52.381 0.00 0.00 0.00 3.62
689 694 3.816523 AGATCGTATCTCCTCCTTCGTTC 59.183 47.826 0.00 0.00 33.42 3.95
690 695 3.566322 CAGATCGTATCTCCTCCTTCGTT 59.434 47.826 0.00 0.00 37.58 3.85
691 696 3.142951 CAGATCGTATCTCCTCCTTCGT 58.857 50.000 0.00 0.00 37.58 3.85
692 697 3.403968 TCAGATCGTATCTCCTCCTTCG 58.596 50.000 0.00 0.00 37.58 3.79
693 698 4.580995 TGTTCAGATCGTATCTCCTCCTTC 59.419 45.833 0.00 0.00 37.58 3.46
694 699 4.537751 TGTTCAGATCGTATCTCCTCCTT 58.462 43.478 0.00 0.00 37.58 3.36
695 700 4.141287 CTGTTCAGATCGTATCTCCTCCT 58.859 47.826 0.00 0.00 37.58 3.69
696 701 3.886505 ACTGTTCAGATCGTATCTCCTCC 59.113 47.826 6.83 0.00 37.58 4.30
697 702 5.508200 AACTGTTCAGATCGTATCTCCTC 57.492 43.478 6.83 0.00 37.58 3.71
698 703 6.358178 TCTAACTGTTCAGATCGTATCTCCT 58.642 40.000 6.83 0.00 37.58 3.69
699 704 6.261381 ACTCTAACTGTTCAGATCGTATCTCC 59.739 42.308 6.83 0.00 37.58 3.71
700 705 7.129622 CACTCTAACTGTTCAGATCGTATCTC 58.870 42.308 6.83 0.00 37.58 2.75
701 706 6.038825 CCACTCTAACTGTTCAGATCGTATCT 59.961 42.308 6.83 0.00 41.15 1.98
702 707 6.038382 TCCACTCTAACTGTTCAGATCGTATC 59.962 42.308 6.83 0.00 0.00 2.24
703 708 5.886474 TCCACTCTAACTGTTCAGATCGTAT 59.114 40.000 6.83 0.00 0.00 3.06
704 709 5.250982 TCCACTCTAACTGTTCAGATCGTA 58.749 41.667 6.83 0.00 0.00 3.43
705 710 4.079970 TCCACTCTAACTGTTCAGATCGT 58.920 43.478 6.83 0.00 0.00 3.73
706 711 4.703645 TCCACTCTAACTGTTCAGATCG 57.296 45.455 6.83 0.00 0.00 3.69
707 712 5.172205 GGTTCCACTCTAACTGTTCAGATC 58.828 45.833 6.83 0.00 0.00 2.75
708 713 4.593206 TGGTTCCACTCTAACTGTTCAGAT 59.407 41.667 6.83 0.00 0.00 2.90
709 714 3.964688 TGGTTCCACTCTAACTGTTCAGA 59.035 43.478 6.83 0.00 0.00 3.27
710 715 4.336889 TGGTTCCACTCTAACTGTTCAG 57.663 45.455 0.00 0.00 0.00 3.02
711 716 4.346709 TGATGGTTCCACTCTAACTGTTCA 59.653 41.667 0.00 0.00 0.00 3.18
712 717 4.894784 TGATGGTTCCACTCTAACTGTTC 58.105 43.478 0.00 0.00 0.00 3.18
713 718 4.974645 TGATGGTTCCACTCTAACTGTT 57.025 40.909 0.00 0.00 0.00 3.16
714 719 4.974645 TTGATGGTTCCACTCTAACTGT 57.025 40.909 0.00 0.00 0.00 3.55
715 720 4.152402 CGTTTGATGGTTCCACTCTAACTG 59.848 45.833 16.66 11.36 0.00 3.16
716 721 4.315803 CGTTTGATGGTTCCACTCTAACT 58.684 43.478 16.66 0.00 0.00 2.24
717 722 3.435671 CCGTTTGATGGTTCCACTCTAAC 59.564 47.826 0.00 6.23 0.00 2.34
718 723 3.325425 TCCGTTTGATGGTTCCACTCTAA 59.675 43.478 0.00 0.00 0.00 2.10
719 724 2.901192 TCCGTTTGATGGTTCCACTCTA 59.099 45.455 0.00 0.00 0.00 2.43
720 725 1.697432 TCCGTTTGATGGTTCCACTCT 59.303 47.619 0.00 0.00 0.00 3.24
721 726 2.178912 TCCGTTTGATGGTTCCACTC 57.821 50.000 0.00 0.00 0.00 3.51
722 727 2.879103 ATCCGTTTGATGGTTCCACT 57.121 45.000 0.00 0.00 30.54 4.00
723 728 2.943033 CCTATCCGTTTGATGGTTCCAC 59.057 50.000 0.00 0.00 34.76 4.02
724 729 2.092646 CCCTATCCGTTTGATGGTTCCA 60.093 50.000 0.00 0.00 34.76 3.53
725 730 2.092592 ACCCTATCCGTTTGATGGTTCC 60.093 50.000 0.00 0.00 34.76 3.62
726 731 2.943033 CACCCTATCCGTTTGATGGTTC 59.057 50.000 0.00 0.00 34.76 3.62
727 732 2.944094 GCACCCTATCCGTTTGATGGTT 60.944 50.000 0.00 0.00 34.76 3.67
728 733 1.408266 GCACCCTATCCGTTTGATGGT 60.408 52.381 0.00 0.00 34.76 3.55
729 734 1.308998 GCACCCTATCCGTTTGATGG 58.691 55.000 0.00 0.00 34.76 3.51
730 735 0.937304 CGCACCCTATCCGTTTGATG 59.063 55.000 0.00 0.00 34.76 3.07
731 736 0.828022 TCGCACCCTATCCGTTTGAT 59.172 50.000 0.00 0.00 37.49 2.57
732 737 0.108520 GTCGCACCCTATCCGTTTGA 60.109 55.000 0.00 0.00 0.00 2.69
733 738 1.087771 GGTCGCACCCTATCCGTTTG 61.088 60.000 0.00 0.00 30.04 2.93
734 739 1.219935 GGTCGCACCCTATCCGTTT 59.780 57.895 0.00 0.00 30.04 3.60
735 740 2.897972 GGTCGCACCCTATCCGTT 59.102 61.111 0.00 0.00 30.04 4.44
736 741 3.524606 CGGTCGCACCCTATCCGT 61.525 66.667 0.00 0.00 33.75 4.69
737 742 4.280494 CCGGTCGCACCCTATCCG 62.280 72.222 0.00 0.00 40.72 4.18
738 743 4.603946 GCCGGTCGCACCCTATCC 62.604 72.222 1.90 0.00 33.75 2.59
739 744 4.603946 GGCCGGTCGCACCCTATC 62.604 72.222 1.90 0.00 40.31 2.08
745 750 1.587933 TAAAATTGGGCCGGTCGCAC 61.588 55.000 13.63 0.00 43.39 5.34
746 751 1.303398 TAAAATTGGGCCGGTCGCA 60.303 52.632 1.90 7.47 40.31 5.10
747 752 1.431845 CTAAAATTGGGCCGGTCGC 59.568 57.895 1.90 4.53 0.00 5.19
748 753 2.103410 CCTAAAATTGGGCCGGTCG 58.897 57.895 1.90 0.00 0.00 4.79
755 760 2.804856 CGCGGGCCTAAAATTGGG 59.195 61.111 0.84 0.00 0.00 4.12
756 761 2.104132 GCGCGGGCCTAAAATTGG 59.896 61.111 14.45 0.00 0.00 3.16
757 762 1.516169 GTGCGCGGGCCTAAAATTG 60.516 57.895 22.70 0.00 38.85 2.32
758 763 2.706834 GGTGCGCGGGCCTAAAATT 61.707 57.895 22.70 0.00 38.85 1.82
759 764 3.138128 GGTGCGCGGGCCTAAAAT 61.138 61.111 22.70 0.00 38.85 1.82
779 784 0.693049 AAATAGGGGGCTGATAGGCG 59.307 55.000 0.00 0.00 42.43 5.52
780 785 3.182152 TCTAAATAGGGGGCTGATAGGC 58.818 50.000 0.00 0.00 40.51 3.93
781 786 5.561679 GTTTCTAAATAGGGGGCTGATAGG 58.438 45.833 0.00 0.00 0.00 2.57
782 787 5.238583 CGTTTCTAAATAGGGGGCTGATAG 58.761 45.833 0.00 0.00 0.00 2.08
783 788 4.041198 CCGTTTCTAAATAGGGGGCTGATA 59.959 45.833 0.00 0.00 0.00 2.15
784 789 3.181443 CCGTTTCTAAATAGGGGGCTGAT 60.181 47.826 0.00 0.00 0.00 2.90
785 790 2.171870 CCGTTTCTAAATAGGGGGCTGA 59.828 50.000 0.00 0.00 0.00 4.26
786 791 2.171870 TCCGTTTCTAAATAGGGGGCTG 59.828 50.000 0.00 0.00 0.00 4.85
787 792 2.438392 CTCCGTTTCTAAATAGGGGGCT 59.562 50.000 0.00 0.00 0.00 5.19
788 793 2.486727 CCTCCGTTTCTAAATAGGGGGC 60.487 54.545 6.07 0.00 34.14 5.80
789 794 3.043418 TCCTCCGTTTCTAAATAGGGGG 58.957 50.000 10.79 10.79 39.26 5.40
790 795 3.710165 ACTCCTCCGTTTCTAAATAGGGG 59.290 47.826 0.00 0.00 0.00 4.79
791 796 6.475596 TTACTCCTCCGTTTCTAAATAGGG 57.524 41.667 0.00 0.00 0.00 3.53
799 804 9.144298 TCTCATAATTATTACTCCTCCGTTTCT 57.856 33.333 0.00 0.00 0.00 2.52
800 805 9.413048 CTCTCATAATTATTACTCCTCCGTTTC 57.587 37.037 0.00 0.00 0.00 2.78
801 806 8.925338 ACTCTCATAATTATTACTCCTCCGTTT 58.075 33.333 0.00 0.00 0.00 3.60
802 807 8.480133 ACTCTCATAATTATTACTCCTCCGTT 57.520 34.615 0.00 0.00 0.00 4.44
803 808 8.361139 CAACTCTCATAATTATTACTCCTCCGT 58.639 37.037 0.00 0.00 0.00 4.69
804 809 7.329717 GCAACTCTCATAATTATTACTCCTCCG 59.670 40.741 0.00 0.00 0.00 4.63
805 810 8.371699 AGCAACTCTCATAATTATTACTCCTCC 58.628 37.037 0.00 0.00 0.00 4.30
806 811 9.771534 AAGCAACTCTCATAATTATTACTCCTC 57.228 33.333 0.00 0.00 0.00 3.71
810 815 9.905713 TCCAAAGCAACTCTCATAATTATTACT 57.094 29.630 0.00 0.00 0.00 2.24
846 851 2.230508 TCCACCACGCTAGTACTGAAAG 59.769 50.000 5.39 0.00 42.29 2.62
847 852 2.029649 GTCCACCACGCTAGTACTGAAA 60.030 50.000 5.39 0.00 0.00 2.69
848 853 1.542915 GTCCACCACGCTAGTACTGAA 59.457 52.381 5.39 0.00 0.00 3.02
849 854 1.171308 GTCCACCACGCTAGTACTGA 58.829 55.000 5.39 0.00 0.00 3.41
850 855 0.179171 CGTCCACCACGCTAGTACTG 60.179 60.000 5.39 0.00 42.87 2.74
851 856 2.177950 CGTCCACCACGCTAGTACT 58.822 57.895 0.00 0.00 42.87 2.73
852 857 4.779819 CGTCCACCACGCTAGTAC 57.220 61.111 0.00 0.00 42.87 2.73
869 874 4.675114 CGTGAGCCAACAATAAAACAAGAC 59.325 41.667 0.00 0.00 0.00 3.01
871 876 4.440758 CACGTGAGCCAACAATAAAACAAG 59.559 41.667 10.90 0.00 0.00 3.16
881 886 0.602638 GATGGTCACGTGAGCCAACA 60.603 55.000 36.78 23.12 41.53 3.33
1336 1347 3.490759 GCTCACGGCGTGGTCATG 61.491 66.667 36.30 22.01 33.87 3.07
1600 1627 0.187117 TGGCCTCTCAGGATCTCGAT 59.813 55.000 3.32 0.00 37.67 3.59
1678 1717 4.832248 AGGTCGAAGCACAGAATGAAATA 58.168 39.130 0.00 0.00 39.69 1.40
1679 1718 3.679389 AGGTCGAAGCACAGAATGAAAT 58.321 40.909 0.00 0.00 39.69 2.17
1794 1833 0.394565 GCCGAGATCCCTGCATACTT 59.605 55.000 0.00 0.00 0.00 2.24
1816 1858 3.716006 CTGCGTCAACCACAGGCG 61.716 66.667 0.00 0.00 0.00 5.52
1826 1868 4.662961 CGGCACCAGTCTGCGTCA 62.663 66.667 0.00 0.00 38.12 4.35
1831 1873 3.633094 CTCCGTCGGCACCAGTCTG 62.633 68.421 6.34 0.00 0.00 3.51
1840 1882 3.649277 ATGTCACAGCTCCGTCGGC 62.649 63.158 6.34 0.00 0.00 5.54
1889 1931 0.905357 TGAGTTAGAAGGGAGCAGCC 59.095 55.000 0.00 0.00 0.00 4.85
1916 1964 4.517285 TCTATCCTCAAAGCCAATCACAC 58.483 43.478 0.00 0.00 0.00 3.82
1975 2023 3.367087 CCTGACTTAAGATCAACCGTCGT 60.367 47.826 10.09 0.00 0.00 4.34
1977 2025 2.930682 GCCTGACTTAAGATCAACCGTC 59.069 50.000 10.09 0.00 0.00 4.79
2038 2092 6.352516 AGAAGCTTATGTAGGGAACAGATTG 58.647 40.000 0.00 0.00 42.70 2.67
2039 2093 6.567602 AGAAGCTTATGTAGGGAACAGATT 57.432 37.500 0.00 0.00 42.70 2.40
2040 2094 6.611642 TGTAGAAGCTTATGTAGGGAACAGAT 59.388 38.462 3.25 0.00 42.70 2.90
2041 2095 5.955959 TGTAGAAGCTTATGTAGGGAACAGA 59.044 40.000 3.25 0.00 42.70 3.41
2042 2096 6.043411 GTGTAGAAGCTTATGTAGGGAACAG 58.957 44.000 3.25 0.00 42.70 3.16
2043 2097 5.720041 AGTGTAGAAGCTTATGTAGGGAACA 59.280 40.000 3.25 0.00 43.86 3.18
2044 2098 6.223351 AGTGTAGAAGCTTATGTAGGGAAC 57.777 41.667 3.25 0.00 0.00 3.62
2045 2099 5.363005 GGAGTGTAGAAGCTTATGTAGGGAA 59.637 44.000 3.25 0.00 0.00 3.97
2046 2100 4.894114 GGAGTGTAGAAGCTTATGTAGGGA 59.106 45.833 3.25 0.00 0.00 4.20
2047 2101 4.649674 TGGAGTGTAGAAGCTTATGTAGGG 59.350 45.833 3.25 0.00 0.00 3.53
2048 2102 5.221342 CCTGGAGTGTAGAAGCTTATGTAGG 60.221 48.000 3.25 0.00 0.00 3.18
2049 2103 5.361285 ACCTGGAGTGTAGAAGCTTATGTAG 59.639 44.000 3.25 0.00 0.00 2.74
2050 2104 5.127194 CACCTGGAGTGTAGAAGCTTATGTA 59.873 44.000 3.25 0.00 41.93 2.29
2051 2105 4.081420 CACCTGGAGTGTAGAAGCTTATGT 60.081 45.833 3.25 0.00 41.93 2.29
2052 2106 4.437239 CACCTGGAGTGTAGAAGCTTATG 58.563 47.826 3.25 0.00 41.93 1.90
2053 2107 4.744795 CACCTGGAGTGTAGAAGCTTAT 57.255 45.455 0.00 0.00 41.93 1.73
2117 2176 8.201554 TGATCAACAATTACAGCAGAGATAAC 57.798 34.615 0.00 0.00 0.00 1.89
2130 2189 9.647797 ACACTCGTACTAAATGATCAACAATTA 57.352 29.630 0.00 0.00 0.00 1.40
2170 2230 2.106338 TCACCCACACATTCACATCACT 59.894 45.455 0.00 0.00 0.00 3.41
2181 2241 0.540133 AATGCAGCATCACCCACACA 60.540 50.000 8.77 0.00 0.00 3.72
2194 2254 5.154932 CAGCTCTTTCTTGAGAAAATGCAG 58.845 41.667 21.39 14.83 42.72 4.41
2219 2279 5.918608 TGCTGGATTACTATCTCCAACTTC 58.081 41.667 0.00 0.00 40.92 3.01
2363 2426 0.555769 ACCCCTTGGTGAAAAGCTCA 59.444 50.000 0.00 0.00 45.58 4.26
2411 2474 0.390472 GTTTGCAGTCTAGAGCGCCT 60.390 55.000 2.29 3.28 0.00 5.52
2474 2537 2.457598 TGGAGTAAGAGTGGCAGGTAG 58.542 52.381 0.00 0.00 0.00 3.18
2475 2538 2.615986 TGGAGTAAGAGTGGCAGGTA 57.384 50.000 0.00 0.00 0.00 3.08
2735 2799 7.378966 CAGAGATACTCCAGTTTGACACTAAA 58.621 38.462 0.00 0.00 32.76 1.85
2781 3470 4.060038 AGTAGCGTACAATAAGCTGCAT 57.940 40.909 12.60 0.00 45.14 3.96
2876 3569 3.839323 TCCAGGGAGAAGGTACTAACA 57.161 47.619 0.00 0.00 38.49 2.41
3025 3718 6.418819 GCAAAGCACATCCATAATTGTGATAC 59.581 38.462 3.41 0.00 44.74 2.24
3055 3748 8.800332 ACTGAATCTTGATTTGATAGTGCTTTT 58.200 29.630 0.00 0.00 0.00 2.27
3061 3754 9.381033 CTCTTCACTGAATCTTGATTTGATAGT 57.619 33.333 0.00 0.00 0.00 2.12
3101 3794 7.280356 TCTGCTATTTCCCTTTCAGTATTACC 58.720 38.462 0.00 0.00 0.00 2.85
3180 3876 8.900511 TCAGTAACGTTATCAACTACATGTAC 57.099 34.615 11.86 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.