Multiple sequence alignment - TraesCS3D01G055100

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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 TraesCS3D01G055100 chr3D 100.000 1491 0 0 1524 3014 22929568 22931058 0.000000e+00 2754
1 TraesCS3D01G055100 chr3D 100.000 1327 0 0 1 1327 22928045 22929371 0.000000e+00 2451
2 TraesCS3D01G055100 chr3D 84.236 609 65 20 2140 2720 22726406 22725801 5.640000e-157 564
3 TraesCS3D01G055100 chr3D 82.114 369 48 13 2330 2689 22384421 22384780 1.760000e-77 300
4 TraesCS3D01G055100 chr3D 86.345 249 33 1 972 1219 22727417 22727169 1.380000e-68 270
5 TraesCS3D01G055100 chr3B 94.807 1502 39 10 1524 3014 40192791 40194264 0.000000e+00 2305
6 TraesCS3D01G055100 chr3B 93.502 554 21 2 42 584 40191146 40191695 0.000000e+00 809
7 TraesCS3D01G055100 chr3B 92.586 526 17 13 821 1327 40192160 40192682 0.000000e+00 736
8 TraesCS3D01G055100 chr3B 83.013 624 59 28 2140 2720 40164859 40165478 3.440000e-144 521
9 TraesCS3D01G055100 chr3B 82.294 401 56 13 2330 2720 40232058 40232453 1.730000e-87 333
10 TraesCS3D01G055100 chr3B 86.585 246 32 1 972 1216 40163810 40164055 1.380000e-68 270
11 TraesCS3D01G055100 chr3B 97.973 148 2 1 645 791 606376207 606376354 3.860000e-64 255
12 TraesCS3D01G055100 chr3B 82.642 265 27 7 302 562 40145529 40145778 1.820000e-52 217
13 TraesCS3D01G055100 chr3B 81.498 227 28 4 302 525 40147040 40147255 1.110000e-39 174
14 TraesCS3D01G055100 chr3B 81.498 227 28 4 302 525 40156021 40156236 1.110000e-39 174
15 TraesCS3D01G055100 chr3B 81.498 227 28 4 302 525 40158162 40158377 1.110000e-39 174
16 TraesCS3D01G055100 chr7D 99.320 147 1 0 645 791 32648245 32648391 1.780000e-67 267
17 TraesCS3D01G055100 chr7D 97.973 148 2 1 645 791 548022532 548022385 3.860000e-64 255
18 TraesCS3D01G055100 chr1B 96.835 158 5 0 645 802 94937468 94937625 6.410000e-67 265
19 TraesCS3D01G055100 chr2B 98.000 150 2 1 645 793 757357660 757357511 2.980000e-65 259
20 TraesCS3D01G055100 chr7B 97.973 148 3 0 645 792 652145289 652145142 1.070000e-64 257
21 TraesCS3D01G055100 chr7B 88.144 194 18 3 2821 3014 725510058 725510246 3.020000e-55 226
22 TraesCS3D01G055100 chr6A 97.959 147 3 0 645 791 181909995 181909849 3.860000e-64 255
23 TraesCS3D01G055100 chr4D 96.154 156 4 2 645 799 208562465 208562311 1.390000e-63 254
24 TraesCS3D01G055100 chr5B 97.279 147 4 0 645 791 703506439 703506585 1.790000e-62 250


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 TraesCS3D01G055100 chr3D 22928045 22931058 3013 False 2602.500000 2754 100.000000 1 3014 2 chr3D.!!$F2 3013
1 TraesCS3D01G055100 chr3D 22725801 22727417 1616 True 417.000000 564 85.290500 972 2720 2 chr3D.!!$R1 1748
2 TraesCS3D01G055100 chr3B 40191146 40194264 3118 False 1283.333333 2305 93.631667 42 3014 3 chr3B.!!$F6 2972
3 TraesCS3D01G055100 chr3B 40163810 40165478 1668 False 395.500000 521 84.799000 972 2720 2 chr3B.!!$F5 1748

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
739 819 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 2808 0.896019 CTCGTGGTGAGTGACTCCCT 60.896 60.0 10.52 0.0 40.03 4.2 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
18 19 4.379174 GTGAGAGGCCTCGCAAAA 57.621 55.556 36.62 15.51 46.41 2.44
19 20 2.166270 GTGAGAGGCCTCGCAAAAG 58.834 57.895 36.62 0.00 46.41 2.27
20 21 1.003355 TGAGAGGCCTCGCAAAAGG 60.003 57.895 33.74 0.00 42.33 3.11
21 22 1.003233 GAGAGGCCTCGCAAAAGGT 60.003 57.895 29.33 9.17 38.79 3.50
22 23 0.606673 GAGAGGCCTCGCAAAAGGTT 60.607 55.000 29.33 8.39 38.79 3.50
23 24 0.606673 AGAGGCCTCGCAAAAGGTTC 60.607 55.000 26.95 0.00 38.79 3.62
24 25 0.889186 GAGGCCTCGCAAAAGGTTCA 60.889 55.000 19.06 0.00 38.79 3.18
25 26 0.890996 AGGCCTCGCAAAAGGTTCAG 60.891 55.000 0.00 0.00 38.79 3.02
26 27 1.172812 GGCCTCGCAAAAGGTTCAGT 61.173 55.000 0.00 0.00 38.79 3.41
27 28 0.668535 GCCTCGCAAAAGGTTCAGTT 59.331 50.000 0.00 0.00 38.79 3.16
28 29 1.067060 GCCTCGCAAAAGGTTCAGTTT 59.933 47.619 0.00 0.00 38.79 2.66
29 30 2.481276 GCCTCGCAAAAGGTTCAGTTTT 60.481 45.455 0.00 0.00 38.79 2.43
30 31 3.243267 GCCTCGCAAAAGGTTCAGTTTTA 60.243 43.478 0.00 0.00 38.79 1.52
31 32 4.287720 CCTCGCAAAAGGTTCAGTTTTAC 58.712 43.478 0.00 0.00 0.00 2.01
32 33 4.036380 CCTCGCAAAAGGTTCAGTTTTACT 59.964 41.667 0.00 0.00 0.00 2.24
34 35 4.396790 TCGCAAAAGGTTCAGTTTTACTGT 59.603 37.500 6.71 0.00 46.03 3.55
35 36 5.099575 CGCAAAAGGTTCAGTTTTACTGTT 58.900 37.500 6.71 0.00 46.03 3.16
36 37 5.229260 CGCAAAAGGTTCAGTTTTACTGTTC 59.771 40.000 6.71 2.27 46.03 3.18
37 38 6.330278 GCAAAAGGTTCAGTTTTACTGTTCT 58.670 36.000 6.71 1.52 46.03 3.01
38 39 6.811665 GCAAAAGGTTCAGTTTTACTGTTCTT 59.188 34.615 6.71 6.52 46.03 2.52
39 40 7.971722 GCAAAAGGTTCAGTTTTACTGTTCTTA 59.028 33.333 6.71 0.00 46.03 2.10
40 41 9.849166 CAAAAGGTTCAGTTTTACTGTTCTTAA 57.151 29.630 6.71 0.00 46.03 1.85
67 68 8.902040 AATGAATAAGAAAAGCGAAAGATCAC 57.098 30.769 0.00 0.00 0.00 3.06
166 167 1.276989 GGGTGTGGTAATCGAGTCCAA 59.723 52.381 7.42 0.00 32.82 3.53
206 207 4.929479 AGAAGCTCCAGAAGAGAAGACTA 58.071 43.478 0.00 0.00 46.50 2.59
244 245 1.337387 GTAGACTCATACCGGTGCTCC 59.663 57.143 19.93 1.17 0.00 4.70
245 246 0.324368 AGACTCATACCGGTGCTCCA 60.324 55.000 19.93 0.00 0.00 3.86
246 247 0.179108 GACTCATACCGGTGCTCCAC 60.179 60.000 19.93 0.82 0.00 4.02
247 248 0.614979 ACTCATACCGGTGCTCCACT 60.615 55.000 19.93 0.00 34.40 4.00
257 269 2.124403 GCTCCACTGCCTCCATGG 60.124 66.667 4.97 4.97 39.35 3.66
288 300 3.002791 TGACATCTTTCGTGAAGGCATC 58.997 45.455 0.00 0.00 35.98 3.91
289 301 3.265791 GACATCTTTCGTGAAGGCATCT 58.734 45.455 0.00 0.00 35.98 2.90
290 302 4.081697 TGACATCTTTCGTGAAGGCATCTA 60.082 41.667 0.00 0.00 35.98 1.98
291 303 5.028549 ACATCTTTCGTGAAGGCATCTAT 57.971 39.130 0.00 0.00 35.98 1.98
340 352 0.725117 GAAACCCTATTCCGTGCACG 59.275 55.000 31.77 31.77 39.44 5.34
356 368 1.207329 GCACGAGGTCCATAGAAAGGT 59.793 52.381 0.00 0.00 0.00 3.50
418 430 2.653953 TATCCCTTTGTAGCCGCCGC 62.654 60.000 0.00 0.00 0.00 6.53
430 442 4.996434 CGCCGCCATCCCCATCTC 62.996 72.222 0.00 0.00 0.00 2.75
431 443 4.650377 GCCGCCATCCCCATCTCC 62.650 72.222 0.00 0.00 0.00 3.71
435 447 1.674057 GCCATCCCCATCTCCGTAG 59.326 63.158 0.00 0.00 0.00 3.51
438 450 0.319728 CATCCCCATCTCCGTAGCTG 59.680 60.000 0.00 0.00 0.00 4.24
486 498 1.812571 GGTTGTGGCTTGTAGTGGATG 59.187 52.381 0.00 0.00 0.00 3.51
567 579 8.345565 GCTCAAATATGATTTTACATTCCTCGT 58.654 33.333 0.00 0.00 34.37 4.18
568 580 9.655769 CTCAAATATGATTTTACATTCCTCGTG 57.344 33.333 0.00 0.00 34.37 4.35
574 590 8.742554 ATGATTTTACATTCCTCGTGAAAAAC 57.257 30.769 0.00 0.00 36.33 2.43
612 692 9.896263 ATTTTACATTGAATTGCAATTTTCCAC 57.104 25.926 24.81 12.66 44.68 4.02
616 696 5.649602 TTGAATTGCAATTTTCCACGAAC 57.350 34.783 24.81 9.95 0.00 3.95
623 703 2.270352 ATTTTCCACGAACTGAGCCA 57.730 45.000 0.00 0.00 0.00 4.75
631 711 3.490761 CCACGAACTGAGCCAAAATTGTT 60.491 43.478 0.00 0.00 0.00 2.83
632 712 4.261405 CCACGAACTGAGCCAAAATTGTTA 60.261 41.667 0.00 0.00 0.00 2.41
633 713 5.460646 CACGAACTGAGCCAAAATTGTTAT 58.539 37.500 0.00 0.00 0.00 1.89
634 714 5.343058 CACGAACTGAGCCAAAATTGTTATG 59.657 40.000 0.00 0.00 0.00 1.90
635 715 5.009610 ACGAACTGAGCCAAAATTGTTATGT 59.990 36.000 0.00 0.00 0.00 2.29
636 716 5.920273 CGAACTGAGCCAAAATTGTTATGTT 59.080 36.000 0.00 0.00 0.00 2.71
637 717 7.081349 CGAACTGAGCCAAAATTGTTATGTTA 58.919 34.615 0.00 0.00 0.00 2.41
638 718 7.754924 CGAACTGAGCCAAAATTGTTATGTTAT 59.245 33.333 0.00 0.00 0.00 1.89
639 719 8.761575 AACTGAGCCAAAATTGTTATGTTATG 57.238 30.769 0.00 0.00 0.00 1.90
640 720 8.121305 ACTGAGCCAAAATTGTTATGTTATGA 57.879 30.769 0.00 0.00 0.00 2.15
641 721 8.752187 ACTGAGCCAAAATTGTTATGTTATGAT 58.248 29.630 0.00 0.00 0.00 2.45
642 722 9.590451 CTGAGCCAAAATTGTTATGTTATGATT 57.410 29.630 0.00 0.00 0.00 2.57
643 723 9.941325 TGAGCCAAAATTGTTATGTTATGATTT 57.059 25.926 0.00 0.00 0.00 2.17
652 732 9.997482 ATTGTTATGTTATGATTTTACGGTGAC 57.003 29.630 0.00 0.00 0.00 3.67
653 733 8.780846 TGTTATGTTATGATTTTACGGTGACT 57.219 30.769 0.00 0.00 0.00 3.41
654 734 9.221933 TGTTATGTTATGATTTTACGGTGACTT 57.778 29.630 0.00 0.00 0.00 3.01
655 735 9.698617 GTTATGTTATGATTTTACGGTGACTTC 57.301 33.333 0.00 0.00 0.00 3.01
656 736 6.397831 TGTTATGATTTTACGGTGACTTCG 57.602 37.500 0.00 0.00 0.00 3.79
657 737 5.927689 TGTTATGATTTTACGGTGACTTCGT 59.072 36.000 0.00 0.00 43.64 3.85
658 738 7.089538 TGTTATGATTTTACGGTGACTTCGTA 58.910 34.615 0.00 0.00 41.38 3.43
659 739 7.598118 TGTTATGATTTTACGGTGACTTCGTAA 59.402 33.333 3.34 3.34 46.82 3.18
665 745 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
666 746 4.247267 ACGGTGACTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.22 3.02
667 747 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
668 748 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
669 749 5.103000 CGGTGACTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 36.07 2.40
670 750 5.004821 CGGTGACTTCGTAAATCTCAAGATG 59.995 44.000 0.00 0.00 34.49 2.90
671 751 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
672 752 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
673 753 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
674 754 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
675 755 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
676 756 8.304202 ACTTCGTAAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
677 757 7.386299 ACTTCGTAAATCTCAAGATGATATGCC 59.614 37.037 0.00 0.00 34.49 4.40
678 758 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
679 759 5.062683 CGTAAATCTCAAGATGATATGCCGG 59.937 44.000 0.00 0.00 34.49 6.13
680 760 2.462456 TCTCAAGATGATATGCCGGC 57.538 50.000 22.73 22.73 0.00 6.13
681 761 1.973515 TCTCAAGATGATATGCCGGCT 59.026 47.619 29.70 15.76 0.00 5.52
682 762 2.369860 TCTCAAGATGATATGCCGGCTT 59.630 45.455 29.70 24.47 0.00 4.35
683 763 3.578282 TCTCAAGATGATATGCCGGCTTA 59.422 43.478 29.70 25.95 0.00 3.09
684 764 3.930336 TCAAGATGATATGCCGGCTTAG 58.070 45.455 29.70 11.66 0.00 2.18
685 765 3.324846 TCAAGATGATATGCCGGCTTAGT 59.675 43.478 29.70 15.20 0.00 2.24
686 766 3.601443 AGATGATATGCCGGCTTAGTC 57.399 47.619 29.70 21.82 0.00 2.59
687 767 3.169099 AGATGATATGCCGGCTTAGTCT 58.831 45.455 29.70 23.43 0.00 3.24
688 768 3.580458 AGATGATATGCCGGCTTAGTCTT 59.420 43.478 29.70 19.48 0.00 3.01
689 769 3.838244 TGATATGCCGGCTTAGTCTTT 57.162 42.857 29.70 10.12 0.00 2.52
690 770 3.728845 TGATATGCCGGCTTAGTCTTTC 58.271 45.455 29.70 18.59 0.00 2.62
691 771 2.218953 TATGCCGGCTTAGTCTTTCG 57.781 50.000 29.70 0.00 0.00 3.46
692 772 0.462047 ATGCCGGCTTAGTCTTTCGG 60.462 55.000 29.70 0.00 43.13 4.30
693 773 1.217244 GCCGGCTTAGTCTTTCGGA 59.783 57.895 22.15 0.00 42.94 4.55
694 774 0.806492 GCCGGCTTAGTCTTTCGGAG 60.806 60.000 22.15 0.00 42.94 4.63
695 775 0.179108 CCGGCTTAGTCTTTCGGAGG 60.179 60.000 0.00 0.00 42.94 4.30
696 776 0.531200 CGGCTTAGTCTTTCGGAGGT 59.469 55.000 0.00 0.00 0.00 3.85
697 777 1.736032 CGGCTTAGTCTTTCGGAGGTG 60.736 57.143 0.00 0.00 0.00 4.00
698 778 1.360820 GCTTAGTCTTTCGGAGGTGC 58.639 55.000 0.00 0.00 0.00 5.01
699 779 1.066787 GCTTAGTCTTTCGGAGGTGCT 60.067 52.381 0.00 0.00 0.00 4.40
700 780 2.882324 CTTAGTCTTTCGGAGGTGCTC 58.118 52.381 0.00 0.00 0.00 4.26
701 781 1.919240 TAGTCTTTCGGAGGTGCTCA 58.081 50.000 0.00 0.00 31.08 4.26
702 782 1.270907 AGTCTTTCGGAGGTGCTCAT 58.729 50.000 0.00 0.00 31.08 2.90
703 783 2.457598 AGTCTTTCGGAGGTGCTCATA 58.542 47.619 0.00 0.00 31.08 2.15
704 784 2.428890 AGTCTTTCGGAGGTGCTCATAG 59.571 50.000 0.00 0.00 31.08 2.23
705 785 1.757118 TCTTTCGGAGGTGCTCATAGG 59.243 52.381 0.00 0.00 31.08 2.57
706 786 0.830648 TTTCGGAGGTGCTCATAGGG 59.169 55.000 0.00 0.00 31.08 3.53
707 787 1.048724 TTCGGAGGTGCTCATAGGGG 61.049 60.000 0.00 0.00 31.08 4.79
708 788 1.762460 CGGAGGTGCTCATAGGGGT 60.762 63.158 0.00 0.00 31.08 4.95
709 789 0.469331 CGGAGGTGCTCATAGGGGTA 60.469 60.000 0.00 0.00 31.08 3.69
710 790 1.343069 GGAGGTGCTCATAGGGGTAG 58.657 60.000 0.00 0.00 31.08 3.18
711 791 1.343069 GAGGTGCTCATAGGGGTAGG 58.657 60.000 0.00 0.00 0.00 3.18
712 792 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
713 793 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
714 794 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
715 795 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
716 796 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
717 797 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
718 798 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
719 799 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
720 800 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
721 801 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
722 802 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
723 803 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
724 804 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
725 805 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
728 808 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
729 809 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
730 810 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
731 811 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
732 812 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
733 813 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
734 814 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
735 815 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
736 816 1.358725 CGTGTGTGCGTTCATAGGGG 61.359 60.000 0.00 0.00 0.00 4.79
737 817 0.321298 GTGTGTGCGTTCATAGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
738 818 0.321210 TGTGTGCGTTCATAGGGGTG 60.321 55.000 0.00 0.00 0.00 4.61
739 819 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.000 0.00 0.00 0.00 4.02
740 820 0.249120 TGTGCGTTCATAGGGGTGAG 59.751 55.000 0.00 0.00 0.00 3.51
741 821 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
742 822 0.249120 TGCGTTCATAGGGGTGAGTG 59.751 55.000 0.00 0.00 0.00 3.51
743 823 0.249398 GCGTTCATAGGGGTGAGTGT 59.751 55.000 0.00 0.00 0.00 3.55
744 824 1.479323 GCGTTCATAGGGGTGAGTGTA 59.521 52.381 0.00 0.00 0.00 2.90
745 825 2.102588 GCGTTCATAGGGGTGAGTGTAT 59.897 50.000 0.00 0.00 0.00 2.29
746 826 3.717707 CGTTCATAGGGGTGAGTGTATG 58.282 50.000 0.00 0.00 0.00 2.39
747 827 3.467803 GTTCATAGGGGTGAGTGTATGC 58.532 50.000 0.00 0.00 0.00 3.14
748 828 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
749 829 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
750 830 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
751 831 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
752 832 2.452813 GGGTGAGTGTATGCGCGTG 61.453 63.158 13.61 0.00 0.00 5.34
753 833 1.736645 GGTGAGTGTATGCGCGTGT 60.737 57.895 13.61 0.00 0.00 4.49
754 834 0.457166 GGTGAGTGTATGCGCGTGTA 60.457 55.000 13.61 0.00 0.00 2.90
755 835 1.556564 GTGAGTGTATGCGCGTGTAT 58.443 50.000 13.61 4.63 0.00 2.29
756 836 2.542205 GGTGAGTGTATGCGCGTGTATA 60.542 50.000 13.61 2.40 0.00 1.47
757 837 3.305964 GTGAGTGTATGCGCGTGTATAT 58.694 45.455 13.61 0.00 0.00 0.86
758 838 3.119628 GTGAGTGTATGCGCGTGTATATG 59.880 47.826 13.61 0.00 0.00 1.78
759 839 3.003897 TGAGTGTATGCGCGTGTATATGA 59.996 43.478 13.61 0.00 0.00 2.15
760 840 3.565516 AGTGTATGCGCGTGTATATGAG 58.434 45.455 13.61 0.00 0.00 2.90
761 841 2.090658 GTGTATGCGCGTGTATATGAGC 59.909 50.000 13.61 0.41 38.85 4.26
764 844 4.228451 CGCGTGTATATGAGCGCT 57.772 55.556 11.27 11.27 46.56 5.92
765 845 2.506544 CGCGTGTATATGAGCGCTT 58.493 52.632 13.26 0.00 46.56 4.68
766 846 0.159554 CGCGTGTATATGAGCGCTTG 59.840 55.000 13.26 0.00 46.56 4.01
767 847 1.209128 GCGTGTATATGAGCGCTTGT 58.791 50.000 13.26 5.98 45.48 3.16
768 848 1.071239 GCGTGTATATGAGCGCTTGTG 60.071 52.381 13.26 0.00 45.48 3.33
769 849 2.193447 CGTGTATATGAGCGCTTGTGT 58.807 47.619 13.26 4.27 0.00 3.72
770 850 2.216488 CGTGTATATGAGCGCTTGTGTC 59.784 50.000 13.26 0.00 0.00 3.67
771 851 3.448686 GTGTATATGAGCGCTTGTGTCT 58.551 45.455 13.26 0.00 0.00 3.41
772 852 3.243877 GTGTATATGAGCGCTTGTGTCTG 59.756 47.826 13.26 0.00 0.00 3.51
773 853 2.680312 ATATGAGCGCTTGTGTCTGT 57.320 45.000 13.26 0.00 0.00 3.41
774 854 3.801114 ATATGAGCGCTTGTGTCTGTA 57.199 42.857 13.26 0.00 0.00 2.74
775 855 1.714794 ATGAGCGCTTGTGTCTGTAC 58.285 50.000 13.26 0.00 0.00 2.90
776 856 0.673985 TGAGCGCTTGTGTCTGTACT 59.326 50.000 13.26 0.00 0.00 2.73
777 857 1.063806 GAGCGCTTGTGTCTGTACTG 58.936 55.000 13.26 0.00 0.00 2.74
778 858 0.673985 AGCGCTTGTGTCTGTACTGA 59.326 50.000 2.64 0.00 0.00 3.41
779 859 1.273606 AGCGCTTGTGTCTGTACTGAT 59.726 47.619 2.64 0.00 0.00 2.90
780 860 1.391485 GCGCTTGTGTCTGTACTGATG 59.609 52.381 0.00 0.00 0.00 3.07
781 861 2.677199 CGCTTGTGTCTGTACTGATGT 58.323 47.619 5.69 0.00 0.00 3.06
782 862 3.059884 CGCTTGTGTCTGTACTGATGTT 58.940 45.455 5.69 0.00 0.00 2.71
783 863 4.234574 CGCTTGTGTCTGTACTGATGTTA 58.765 43.478 5.69 0.00 0.00 2.41
784 864 4.684242 CGCTTGTGTCTGTACTGATGTTAA 59.316 41.667 5.69 0.07 0.00 2.01
785 865 5.176774 CGCTTGTGTCTGTACTGATGTTAAA 59.823 40.000 5.69 0.00 0.00 1.52
786 866 6.292649 CGCTTGTGTCTGTACTGATGTTAAAA 60.293 38.462 5.69 0.00 0.00 1.52
787 867 7.414436 GCTTGTGTCTGTACTGATGTTAAAAA 58.586 34.615 5.69 0.00 0.00 1.94
933 1174 0.600255 ACTTGTCTAAAGCGCGCACT 60.600 50.000 35.10 21.81 0.00 4.40
937 1178 1.736645 TCTAAAGCGCGCACTCCAC 60.737 57.895 35.10 0.72 0.00 4.02
949 1190 1.878102 GCACTCCACATTGGTTCGTCT 60.878 52.381 0.00 0.00 39.03 4.18
951 1192 1.691976 ACTCCACATTGGTTCGTCTCA 59.308 47.619 0.00 0.00 39.03 3.27
953 1194 1.414550 TCCACATTGGTTCGTCTCACA 59.585 47.619 0.00 0.00 39.03 3.58
954 1195 1.531149 CCACATTGGTTCGTCTCACAC 59.469 52.381 0.00 0.00 31.35 3.82
956 1197 1.156736 CATTGGTTCGTCTCACACCC 58.843 55.000 0.00 0.00 0.00 4.61
959 1200 2.214920 GGTTCGTCTCACACCCCCT 61.215 63.158 0.00 0.00 0.00 4.79
960 1201 1.752833 GTTCGTCTCACACCCCCTT 59.247 57.895 0.00 0.00 0.00 3.95
962 1203 1.477685 TTCGTCTCACACCCCCTTCC 61.478 60.000 0.00 0.00 0.00 3.46
965 1206 2.531685 CTCACACCCCCTTCCCCA 60.532 66.667 0.00 0.00 0.00 4.96
966 1207 2.856988 TCACACCCCCTTCCCCAC 60.857 66.667 0.00 0.00 0.00 4.61
967 1208 3.182263 CACACCCCCTTCCCCACA 61.182 66.667 0.00 0.00 0.00 4.17
968 1209 2.121042 ACACCCCCTTCCCCACAT 60.121 61.111 0.00 0.00 0.00 3.21
969 1210 1.782608 ACACCCCCTTCCCCACATT 60.783 57.895 0.00 0.00 0.00 2.71
970 1211 1.305213 CACCCCCTTCCCCACATTG 60.305 63.158 0.00 0.00 0.00 2.82
974 1233 1.214305 CCCCTTCCCCACATTGGAGA 61.214 60.000 0.00 0.00 40.96 3.71
1073 1332 4.400961 GCTCGGCTCCAAGCAGGT 62.401 66.667 0.86 0.00 44.75 4.00
1161 1420 2.808321 GCCGTCCGTCGTTTCTCC 60.808 66.667 0.00 0.00 37.94 3.71
1246 1526 0.036164 CCGTGACATCACCAAGGGAA 59.964 55.000 6.44 0.00 43.66 3.97
1254 1534 0.546747 TCACCAAGGGAATCGAGGGT 60.547 55.000 0.00 0.00 0.00 4.34
1668 1986 2.003301 GAAGAAGCTAGCCAAGTTCCG 58.997 52.381 12.13 0.00 0.00 4.30
1710 2028 2.419574 GGCCTTGGCGTTTCTATCTGTA 60.420 50.000 5.49 0.00 0.00 2.74
1731 2049 1.304713 AGGGGTTCTCGCTTACGGA 60.305 57.895 0.00 0.00 40.63 4.69
1915 2233 3.713826 ATAGCCTTTTCTTTGGACGGA 57.286 42.857 0.00 0.00 0.00 4.69
1934 2252 0.912006 AAGGTGGAGGGAGAGAAGGC 60.912 60.000 0.00 0.00 0.00 4.35
1944 2262 1.625818 GGAGAGAAGGCCAAGAAGACA 59.374 52.381 5.01 0.00 0.00 3.41
2076 2415 8.056407 AGGCTGATATTTTTGGTCTAAAACTC 57.944 34.615 0.00 0.00 37.96 3.01
2077 2416 7.669722 AGGCTGATATTTTTGGTCTAAAACTCA 59.330 33.333 0.00 0.00 37.96 3.41
2133 2529 2.439519 GGTGGCCACCGGGTTATG 60.440 66.667 38.35 0.00 42.29 1.90
2315 2722 1.840630 CGCTTTGTGTCGCATGACCA 61.841 55.000 0.00 0.00 44.86 4.02
2317 2724 1.268999 GCTTTGTGTCGCATGACCAAA 60.269 47.619 0.00 9.85 44.86 3.28
2345 2757 1.084289 GTAAATGTCAGGTGCCGGAC 58.916 55.000 5.05 13.33 40.62 4.79
2403 2816 2.656002 CTATCCAAGTCGAGGGAGTCA 58.344 52.381 6.56 0.00 36.45 3.41
2406 2819 0.528470 CCAAGTCGAGGGAGTCACTC 59.472 60.000 12.76 12.76 0.00 3.51
2407 2820 1.248486 CAAGTCGAGGGAGTCACTCA 58.752 55.000 22.12 6.81 34.66 3.41
2470 2886 3.411446 TCAAAGCATGTGGGTTACTCTG 58.589 45.455 0.00 0.00 35.85 3.35
2560 2997 0.949397 ATGATGGCATTGTGCTAGCG 59.051 50.000 10.77 0.00 43.36 4.26
2588 3029 2.417243 GGTGACAGCTTGCTTGTTTTGT 60.417 45.455 0.00 0.00 0.00 2.83
2623 3066 3.665675 GACCCTGAAGCGATGCGGT 62.666 63.158 0.00 0.00 40.00 5.68
2656 3099 2.279921 CACGCAATATATCCTCATCGCG 59.720 50.000 0.00 0.00 46.35 5.87
2774 3218 4.058731 TGGGAATTAGTGGGTGGGATTAT 58.941 43.478 0.00 0.00 0.00 1.28
2800 3244 1.518903 GCTGCAAGGAAGGTGTGGAC 61.519 60.000 0.00 0.00 0.00 4.02
2819 3263 4.081862 TGGACAGTAAACTAATCTGGTCCG 60.082 45.833 0.00 0.00 34.92 4.79
2924 3368 5.614308 TGAAGTGATATACCCTGCTGAATG 58.386 41.667 0.00 0.00 0.00 2.67
2925 3369 4.630644 AGTGATATACCCTGCTGAATGG 57.369 45.455 0.00 0.00 0.00 3.16
2960 3404 6.146184 CCTGGATTATAGTTGTATTGTCAGCG 59.854 42.308 0.00 0.00 0.00 5.18
2985 3429 4.574013 GGTGCTTGTCTAGATCCTGAATTG 59.426 45.833 0.00 0.00 0.00 2.32
2988 3432 6.372659 GTGCTTGTCTAGATCCTGAATTGAAA 59.627 38.462 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.630244 CTTTTGCGAGGCCTCTCACG 61.630 60.000 29.73 18.64 39.95 4.35
1 2 1.301677 CCTTTTGCGAGGCCTCTCAC 61.302 60.000 29.73 19.00 39.95 3.51
2 3 1.003355 CCTTTTGCGAGGCCTCTCA 60.003 57.895 29.73 25.79 39.95 3.27
3 4 0.606673 AACCTTTTGCGAGGCCTCTC 60.607 55.000 29.73 23.27 40.65 3.20
4 5 0.606673 GAACCTTTTGCGAGGCCTCT 60.607 55.000 29.73 8.20 40.65 3.69
5 6 0.889186 TGAACCTTTTGCGAGGCCTC 60.889 55.000 23.79 23.79 40.65 4.70
6 7 0.890996 CTGAACCTTTTGCGAGGCCT 60.891 55.000 3.86 3.86 40.65 5.19
7 8 1.172812 ACTGAACCTTTTGCGAGGCC 61.173 55.000 0.00 0.00 40.65 5.19
8 9 0.668535 AACTGAACCTTTTGCGAGGC 59.331 50.000 0.89 0.00 40.65 4.70
9 10 3.436700 AAAACTGAACCTTTTGCGAGG 57.563 42.857 0.00 0.00 42.75 4.63
10 11 5.169836 AGTAAAACTGAACCTTTTGCGAG 57.830 39.130 0.00 0.00 30.92 5.03
41 42 9.988350 GTGATCTTTCGCTTTTCTTATTCATTA 57.012 29.630 0.00 0.00 0.00 1.90
42 43 7.693951 CGTGATCTTTCGCTTTTCTTATTCATT 59.306 33.333 0.00 0.00 0.00 2.57
43 44 7.064609 TCGTGATCTTTCGCTTTTCTTATTCAT 59.935 33.333 0.00 0.00 0.00 2.57
44 45 6.367695 TCGTGATCTTTCGCTTTTCTTATTCA 59.632 34.615 0.00 0.00 0.00 2.57
45 46 6.762108 TCGTGATCTTTCGCTTTTCTTATTC 58.238 36.000 0.00 0.00 0.00 1.75
46 47 6.721571 TCGTGATCTTTCGCTTTTCTTATT 57.278 33.333 0.00 0.00 0.00 1.40
47 48 6.721571 TTCGTGATCTTTCGCTTTTCTTAT 57.278 33.333 0.00 0.00 0.00 1.73
106 107 6.980593 TGACTTGATTTGTCACCTAAAATGG 58.019 36.000 0.00 0.00 39.23 3.16
166 167 1.003118 TCTTGTGCGCCTCCAGTTAAT 59.997 47.619 4.18 0.00 0.00 1.40
206 207 3.011513 CGCGCTCGTAACTAAGTGT 57.988 52.632 5.56 0.00 0.00 3.55
288 300 0.976641 TGCGATTGGGCCCTAGATAG 59.023 55.000 25.70 15.11 0.00 2.08
289 301 1.429930 TTGCGATTGGGCCCTAGATA 58.570 50.000 25.70 0.00 0.00 1.98
290 302 0.773644 ATTGCGATTGGGCCCTAGAT 59.226 50.000 25.70 14.50 0.00 1.98
291 303 0.179020 CATTGCGATTGGGCCCTAGA 60.179 55.000 25.70 9.65 0.00 2.43
340 352 5.422214 TTCTTCACCTTTCTATGGACCTC 57.578 43.478 0.00 0.00 0.00 3.85
356 368 4.588528 CCTTCCATCAAAGGGTTTTCTTCA 59.411 41.667 0.00 0.00 41.86 3.02
418 430 0.833834 AGCTACGGAGATGGGGATGG 60.834 60.000 0.00 0.00 0.00 3.51
430 442 6.791887 ATCATGTTCATATTTCAGCTACGG 57.208 37.500 0.00 0.00 0.00 4.02
431 443 7.854534 TCAATCATGTTCATATTTCAGCTACG 58.145 34.615 0.00 0.00 0.00 3.51
461 473 3.627577 CCACTACAAGCCACAACCATATC 59.372 47.826 0.00 0.00 0.00 1.63
586 602 9.896263 GTGGAAAATTGCAATTCAATGTAAAAT 57.104 25.926 24.28 2.58 44.23 1.82
587 603 8.066595 CGTGGAAAATTGCAATTCAATGTAAAA 58.933 29.630 24.28 2.31 44.23 1.52
593 673 5.990996 AGTTCGTGGAAAATTGCAATTCAAT 59.009 32.000 24.28 13.88 46.82 2.57
604 684 2.270352 TGGCTCAGTTCGTGGAAAAT 57.730 45.000 0.00 0.00 0.00 1.82
612 692 5.460646 ACATAACAATTTTGGCTCAGTTCG 58.539 37.500 0.00 0.00 0.00 3.95
616 696 9.590451 AATCATAACATAACAATTTTGGCTCAG 57.410 29.630 0.00 0.00 0.00 3.35
631 711 7.760794 ACGAAGTCACCGTAAAATCATAACATA 59.239 33.333 0.00 0.00 29.74 2.29
632 712 6.592607 ACGAAGTCACCGTAAAATCATAACAT 59.407 34.615 0.00 0.00 29.74 2.71
633 713 5.927689 ACGAAGTCACCGTAAAATCATAACA 59.072 36.000 0.00 0.00 29.74 2.41
634 714 6.399204 ACGAAGTCACCGTAAAATCATAAC 57.601 37.500 0.00 0.00 29.74 1.89
643 723 5.375417 TGAGATTTACGAAGTCACCGTAA 57.625 39.130 0.00 0.00 46.58 3.18
644 724 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
645 725 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
646 726 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
647 727 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
648 728 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
649 729 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
650 730 8.431593 GCATATCATCTTGAGATTTACGAAGTC 58.568 37.037 0.00 0.00 35.39 3.01
651 731 7.386299 GGCATATCATCTTGAGATTTACGAAGT 59.614 37.037 0.00 0.00 37.29 3.01
652 732 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
653 733 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
654 734 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
655 735 5.062683 CCGGCATATCATCTTGAGATTTACG 59.937 44.000 0.00 0.00 31.21 3.18
656 736 5.163814 GCCGGCATATCATCTTGAGATTTAC 60.164 44.000 24.80 0.00 31.21 2.01
657 737 4.937620 GCCGGCATATCATCTTGAGATTTA 59.062 41.667 24.80 0.00 31.21 1.40
658 738 3.755378 GCCGGCATATCATCTTGAGATTT 59.245 43.478 24.80 0.00 31.21 2.17
659 739 3.008813 AGCCGGCATATCATCTTGAGATT 59.991 43.478 31.54 0.00 31.21 2.40
660 740 2.570752 AGCCGGCATATCATCTTGAGAT 59.429 45.455 31.54 0.00 34.56 2.75
661 741 1.973515 AGCCGGCATATCATCTTGAGA 59.026 47.619 31.54 0.00 0.00 3.27
662 742 2.469274 AGCCGGCATATCATCTTGAG 57.531 50.000 31.54 0.00 0.00 3.02
663 743 2.936919 AAGCCGGCATATCATCTTGA 57.063 45.000 31.54 0.00 0.00 3.02
664 744 3.668447 ACTAAGCCGGCATATCATCTTG 58.332 45.455 31.54 9.76 0.00 3.02
665 745 3.580458 AGACTAAGCCGGCATATCATCTT 59.420 43.478 31.54 14.07 0.00 2.40
666 746 3.169099 AGACTAAGCCGGCATATCATCT 58.831 45.455 31.54 19.69 0.00 2.90
667 747 3.601443 AGACTAAGCCGGCATATCATC 57.399 47.619 31.54 17.82 0.00 2.92
668 748 4.319177 GAAAGACTAAGCCGGCATATCAT 58.681 43.478 31.54 10.54 0.00 2.45
669 749 3.728845 GAAAGACTAAGCCGGCATATCA 58.271 45.455 31.54 7.27 0.00 2.15
670 750 2.731976 CGAAAGACTAAGCCGGCATATC 59.268 50.000 31.54 19.70 0.00 1.63
671 751 2.548067 CCGAAAGACTAAGCCGGCATAT 60.548 50.000 31.54 17.05 33.47 1.78
672 752 1.202486 CCGAAAGACTAAGCCGGCATA 60.202 52.381 31.54 21.29 33.47 3.14
673 753 0.462047 CCGAAAGACTAAGCCGGCAT 60.462 55.000 31.54 21.32 33.47 4.40
674 754 1.079405 CCGAAAGACTAAGCCGGCA 60.079 57.895 31.54 7.98 33.47 5.69
675 755 0.806492 CTCCGAAAGACTAAGCCGGC 60.806 60.000 21.89 21.89 39.96 6.13
676 756 0.179108 CCTCCGAAAGACTAAGCCGG 60.179 60.000 0.00 0.00 41.36 6.13
677 757 0.531200 ACCTCCGAAAGACTAAGCCG 59.469 55.000 0.00 0.00 0.00 5.52
678 758 2.007547 GCACCTCCGAAAGACTAAGCC 61.008 57.143 0.00 0.00 0.00 4.35
679 759 1.066787 AGCACCTCCGAAAGACTAAGC 60.067 52.381 0.00 0.00 0.00 3.09
680 760 2.231478 TGAGCACCTCCGAAAGACTAAG 59.769 50.000 0.00 0.00 0.00 2.18
681 761 2.244695 TGAGCACCTCCGAAAGACTAA 58.755 47.619 0.00 0.00 0.00 2.24
682 762 1.919240 TGAGCACCTCCGAAAGACTA 58.081 50.000 0.00 0.00 0.00 2.59
683 763 1.270907 ATGAGCACCTCCGAAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
684 764 2.482142 CCTATGAGCACCTCCGAAAGAC 60.482 54.545 0.00 0.00 0.00 3.01
685 765 1.757118 CCTATGAGCACCTCCGAAAGA 59.243 52.381 0.00 0.00 0.00 2.52
686 766 1.202580 CCCTATGAGCACCTCCGAAAG 60.203 57.143 0.00 0.00 0.00 2.62
687 767 0.830648 CCCTATGAGCACCTCCGAAA 59.169 55.000 0.00 0.00 0.00 3.46
688 768 1.048724 CCCCTATGAGCACCTCCGAA 61.049 60.000 0.00 0.00 0.00 4.30
689 769 1.457643 CCCCTATGAGCACCTCCGA 60.458 63.158 0.00 0.00 0.00 4.55
690 770 0.469331 TACCCCTATGAGCACCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
691 771 1.343069 CTACCCCTATGAGCACCTCC 58.657 60.000 0.00 0.00 0.00 4.30
692 772 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
693 773 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
694 774 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
695 775 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
696 776 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
697 777 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
698 778 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
699 779 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
700 780 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
701 781 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
702 782 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
703 783 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
704 784 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
705 785 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
706 786 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
707 787 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
708 788 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
711 791 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
712 792 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
713 793 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
714 794 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
715 795 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
716 796 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
717 797 1.358725 CCCCTATGAACGCACACACG 61.359 60.000 0.00 0.00 39.50 4.49
718 798 0.321298 ACCCCTATGAACGCACACAC 60.321 55.000 0.00 0.00 0.00 3.82
719 799 0.321210 CACCCCTATGAACGCACACA 60.321 55.000 0.00 0.00 0.00 3.72
720 800 0.036765 TCACCCCTATGAACGCACAC 60.037 55.000 0.00 0.00 0.00 3.82
721 801 0.249120 CTCACCCCTATGAACGCACA 59.751 55.000 0.00 0.00 0.00 4.57
722 802 0.249398 ACTCACCCCTATGAACGCAC 59.751 55.000 0.00 0.00 0.00 5.34
723 803 0.249120 CACTCACCCCTATGAACGCA 59.751 55.000 0.00 0.00 0.00 5.24
724 804 0.249398 ACACTCACCCCTATGAACGC 59.751 55.000 0.00 0.00 0.00 4.84
725 805 3.717707 CATACACTCACCCCTATGAACG 58.282 50.000 0.00 0.00 0.00 3.95
726 806 3.467803 GCATACACTCACCCCTATGAAC 58.532 50.000 0.00 0.00 0.00 3.18
727 807 2.102420 CGCATACACTCACCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
728 808 1.686587 CGCATACACTCACCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
729 809 1.873903 GCGCATACACTCACCCCTATG 60.874 57.143 0.30 0.00 0.00 2.23
730 810 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
731 811 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
732 812 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
733 813 2.890474 CGCGCATACACTCACCCC 60.890 66.667 8.75 0.00 0.00 4.95
734 814 2.125673 ACGCGCATACACTCACCC 60.126 61.111 5.73 0.00 0.00 4.61
735 815 0.457166 TACACGCGCATACACTCACC 60.457 55.000 5.73 0.00 0.00 4.02
736 816 1.556564 ATACACGCGCATACACTCAC 58.443 50.000 5.73 0.00 0.00 3.51
737 817 3.003897 TCATATACACGCGCATACACTCA 59.996 43.478 5.73 0.00 0.00 3.41
738 818 3.561503 TCATATACACGCGCATACACTC 58.438 45.455 5.73 0.00 0.00 3.51
739 819 3.565516 CTCATATACACGCGCATACACT 58.434 45.455 5.73 0.00 0.00 3.55
740 820 2.090658 GCTCATATACACGCGCATACAC 59.909 50.000 5.73 0.00 0.00 2.90
741 821 2.324860 GCTCATATACACGCGCATACA 58.675 47.619 5.73 0.00 0.00 2.29
742 822 1.317611 CGCTCATATACACGCGCATAC 59.682 52.381 5.73 0.00 39.11 2.39
743 823 1.613270 CGCTCATATACACGCGCATA 58.387 50.000 5.73 1.53 39.11 3.14
744 824 2.434688 CGCTCATATACACGCGCAT 58.565 52.632 5.73 0.00 39.11 4.73
745 825 3.916439 CGCTCATATACACGCGCA 58.084 55.556 5.73 0.00 39.11 6.09
749 829 2.193447 ACACAAGCGCTCATATACACG 58.807 47.619 12.06 0.00 0.00 4.49
750 830 3.243877 CAGACACAAGCGCTCATATACAC 59.756 47.826 12.06 0.00 0.00 2.90
751 831 3.119137 ACAGACACAAGCGCTCATATACA 60.119 43.478 12.06 0.00 0.00 2.29
752 832 3.448686 ACAGACACAAGCGCTCATATAC 58.551 45.455 12.06 1.00 0.00 1.47
753 833 3.801114 ACAGACACAAGCGCTCATATA 57.199 42.857 12.06 0.00 0.00 0.86
754 834 2.680312 ACAGACACAAGCGCTCATAT 57.320 45.000 12.06 0.00 0.00 1.78
755 835 2.492088 AGTACAGACACAAGCGCTCATA 59.508 45.455 12.06 0.00 0.00 2.15
756 836 1.273606 AGTACAGACACAAGCGCTCAT 59.726 47.619 12.06 0.00 0.00 2.90
757 837 0.673985 AGTACAGACACAAGCGCTCA 59.326 50.000 12.06 0.00 0.00 4.26
758 838 1.063806 CAGTACAGACACAAGCGCTC 58.936 55.000 12.06 0.00 0.00 5.03
759 839 0.673985 TCAGTACAGACACAAGCGCT 59.326 50.000 2.64 2.64 0.00 5.92
760 840 1.391485 CATCAGTACAGACACAAGCGC 59.609 52.381 0.00 0.00 0.00 5.92
761 841 2.677199 ACATCAGTACAGACACAAGCG 58.323 47.619 0.00 0.00 0.00 4.68
762 842 6.539649 TTTAACATCAGTACAGACACAAGC 57.460 37.500 0.00 0.00 0.00 4.01
827 1032 2.516448 GATGTCGACATCCCCTCCA 58.484 57.895 37.48 8.10 45.24 3.86
933 1174 1.414550 TGTGAGACGAACCAATGTGGA 59.585 47.619 0.18 0.00 40.96 4.02
937 1178 1.156736 GGGTGTGAGACGAACCAATG 58.843 55.000 0.00 0.00 35.56 2.82
949 1190 2.856988 GTGGGGAAGGGGGTGTGA 60.857 66.667 0.00 0.00 0.00 3.58
951 1192 1.782608 AATGTGGGGAAGGGGGTGT 60.783 57.895 0.00 0.00 0.00 4.16
953 1194 2.557181 CCAATGTGGGGAAGGGGGT 61.557 63.158 0.00 0.00 32.67 4.95
954 1195 2.228841 CTCCAATGTGGGGAAGGGGG 62.229 65.000 0.00 0.00 41.85 5.40
956 1197 2.397815 TCTCCAATGTGGGGAAGGG 58.602 57.895 0.00 0.00 45.82 3.95
960 1201 2.342406 TTCTCTCTCCAATGTGGGGA 57.658 50.000 0.00 0.00 46.84 4.81
962 1203 3.084786 GGTTTTCTCTCTCCAATGTGGG 58.915 50.000 0.00 0.00 38.32 4.61
965 1206 4.323868 GCTAGGGTTTTCTCTCTCCAATGT 60.324 45.833 0.00 0.00 0.00 2.71
966 1207 4.195416 GCTAGGGTTTTCTCTCTCCAATG 58.805 47.826 0.00 0.00 0.00 2.82
967 1208 3.201045 GGCTAGGGTTTTCTCTCTCCAAT 59.799 47.826 0.00 0.00 0.00 3.16
968 1209 2.572104 GGCTAGGGTTTTCTCTCTCCAA 59.428 50.000 0.00 0.00 0.00 3.53
969 1210 2.188817 GGCTAGGGTTTTCTCTCTCCA 58.811 52.381 0.00 0.00 0.00 3.86
970 1211 1.137282 CGGCTAGGGTTTTCTCTCTCC 59.863 57.143 0.00 0.00 0.00 3.71
974 1233 0.531200 CGACGGCTAGGGTTTTCTCT 59.469 55.000 0.00 0.00 0.00 3.10
1161 1420 0.462759 GATCCCCCTTGCTCTTGTCG 60.463 60.000 0.00 0.00 0.00 4.35
1246 1526 5.048364 CGATAAGATCTTCAAGACCCTCGAT 60.048 44.000 12.24 0.00 0.00 3.59
1254 1534 3.243434 GCCGTCCGATAAGATCTTCAAGA 60.243 47.826 12.24 2.35 0.00 3.02
1568 1886 9.958180 AAAAATCCAAAGAAGAAAGGAAGAAAA 57.042 25.926 0.00 0.00 33.17 2.29
1575 1893 8.421002 TCCAGTTAAAAATCCAAAGAAGAAAGG 58.579 33.333 0.00 0.00 0.00 3.11
1597 1915 5.649782 ACAAGGCAGACAATAAAATCCAG 57.350 39.130 0.00 0.00 0.00 3.86
1668 1986 1.456287 GATACCCAGATGCCCCCAC 59.544 63.158 0.00 0.00 0.00 4.61
1710 2028 1.321074 CGTAAGCGAGAACCCCTCCT 61.321 60.000 0.00 0.00 41.33 3.69
1731 2049 2.450502 AAGAGGTGTGTGCCCCCT 60.451 61.111 0.00 0.00 0.00 4.79
1858 2176 9.073475 GCTCTTCATACCCTGGTCTATATATAG 57.927 40.741 12.84 12.84 0.00 1.31
1915 2233 0.912006 GCCTTCTCTCCCTCCACCTT 60.912 60.000 0.00 0.00 0.00 3.50
1944 2262 3.056821 GCCCAAAGAAACGGCTAAAGAAT 60.057 43.478 0.00 0.00 39.70 2.40
2133 2529 6.128526 CCAAAAGAAGAGACCTTGAATCGTAC 60.129 42.308 0.00 0.00 31.62 3.67
2315 2722 7.362920 GGCACCTGACATTTACATGAACTATTT 60.363 37.037 0.00 0.00 34.11 1.40
2317 2724 5.590259 GGCACCTGACATTTACATGAACTAT 59.410 40.000 0.00 0.00 34.11 2.12
2345 2757 0.944386 CCACAAGAACCTGGAACACG 59.056 55.000 0.00 0.00 0.00 4.49
2380 2793 1.757118 CTCCCTCGACTTGGATAGCAA 59.243 52.381 0.00 0.00 0.00 3.91
2395 2808 0.896019 CTCGTGGTGAGTGACTCCCT 60.896 60.000 10.52 0.00 40.03 4.20
2403 2816 1.908793 CAGGGTCCTCGTGGTGAGT 60.909 63.158 2.99 0.00 43.64 3.41
2406 2819 3.625897 TGCAGGGTCCTCGTGGTG 61.626 66.667 2.99 0.00 34.23 4.17
2407 2820 3.626924 GTGCAGGGTCCTCGTGGT 61.627 66.667 2.99 0.00 34.23 4.16
2470 2886 6.392625 AAAGAGGAAGAAAAAGTAACAGCC 57.607 37.500 0.00 0.00 0.00 4.85
2560 2997 1.008538 CAAGCTGTCACCAAACCGC 60.009 57.895 0.00 0.00 0.00 5.68
2588 3029 6.312529 TCAGGGTCTCTGTTACTAGAAAAGA 58.687 40.000 0.00 0.00 43.76 2.52
2623 3066 2.223537 ATTGCGTGTCATCAGCGATA 57.776 45.000 0.00 0.00 33.59 2.92
2627 3070 4.248859 AGGATATATTGCGTGTCATCAGC 58.751 43.478 0.00 0.00 0.00 4.26
2656 3099 3.562505 CTTGTCTGAAGCATCAAACTGC 58.437 45.455 0.00 0.00 42.62 4.40
2774 3218 3.009033 ACACCTTCCTTGCAGCATACTTA 59.991 43.478 0.00 0.00 0.00 2.24
2800 3244 4.124851 AGCGGACCAGATTAGTTTACTG 57.875 45.455 0.00 0.00 0.00 2.74
2819 3263 3.013219 GGATCCAGACAAGGAAGAAAGC 58.987 50.000 6.95 0.00 41.92 3.51
2912 3356 1.077663 ACCAATTCCATTCAGCAGGGT 59.922 47.619 0.00 0.00 0.00 4.34
2924 3368 2.452600 TAATCCAGGCCACCAATTCC 57.547 50.000 5.01 0.00 0.00 3.01
2925 3369 4.729868 ACTATAATCCAGGCCACCAATTC 58.270 43.478 5.01 0.00 0.00 2.17
2960 3404 3.027412 TCAGGATCTAGACAAGCACCTC 58.973 50.000 0.00 0.00 31.30 3.85
2985 3429 4.154942 ACCATAATCCAGGCCATCATTTC 58.845 43.478 5.01 0.00 0.00 2.17
2988 3432 3.117016 ACAACCATAATCCAGGCCATCAT 60.117 43.478 5.01 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.