Multiple sequence alignment - TraesCS2A01G076400

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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 TraesCS2A01G076400 chr2A 100.000 2913 0 0 1 2913 34153184 34150272 0.000000e+00 5380
1 TraesCS2A01G076400 chr2A 84.615 1040 124 17 789 1807 34096281 34097305 0.000000e+00 1002
2 TraesCS2A01G076400 chr2D 91.738 1162 78 11 715 1863 32072043 32070887 0.000000e+00 1598
3 TraesCS2A01G076400 chr2D 86.167 1041 121 12 785 1807 32035257 32036292 0.000000e+00 1103
4 TraesCS2A01G076400 chr2D 88.046 527 28 11 2390 2913 32068945 32068451 2.500000e-165 592
5 TraesCS2A01G076400 chr2D 93.382 408 13 5 1980 2381 32070567 32070168 2.500000e-165 592
6 TraesCS2A01G076400 chr2B 85.043 1043 121 22 785 1807 52625002 52626029 0.000000e+00 1029
7 TraesCS2A01G076400 chr2B 85.238 989 117 13 831 1800 52340515 52339537 0.000000e+00 990
8 TraesCS2A01G076400 chr2B 92.133 572 36 6 716 1284 52683564 52682999 0.000000e+00 798
9 TraesCS2A01G076400 chr2B 88.209 670 55 7 1281 1932 52678046 52677383 0.000000e+00 778
10 TraesCS2A01G076400 chr2B 92.821 195 10 2 2390 2583 52674776 52674585 2.210000e-71 279
11 TraesCS2A01G076400 chr2B 86.397 272 10 11 1965 2229 52675268 52675017 3.700000e-69 272
12 TraesCS2A01G076400 chr3A 95.118 553 27 0 3 555 718014262 718014814 0.000000e+00 872
13 TraesCS2A01G076400 chr3A 93.440 564 32 3 3 565 718027906 718028465 0.000000e+00 832
14 TraesCS2A01G076400 chr1A 94.494 563 30 1 3 565 565320931 565321492 0.000000e+00 867
15 TraesCS2A01G076400 chr1A 93.606 563 35 1 3 565 491252916 491252355 0.000000e+00 839
16 TraesCS2A01G076400 chr1A 93.474 567 31 6 3 565 293724255 293723691 0.000000e+00 837
17 TraesCS2A01G076400 chr4A 94.170 566 29 2 3 568 465552376 465552937 0.000000e+00 859
18 TraesCS2A01G076400 chr4D 94.139 563 31 2 3 565 28419675 28420235 0.000000e+00 856
19 TraesCS2A01G076400 chr7D 93.606 563 35 1 3 565 16184920 16184359 0.000000e+00 839
20 TraesCS2A01G076400 chr7D 93.606 563 31 4 3 565 69045098 69044541 0.000000e+00 835


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 TraesCS2A01G076400 chr2A 34150272 34153184 2912 True 5380.000000 5380 100.000000 1 2913 1 chr2A.!!$R1 2912
1 TraesCS2A01G076400 chr2A 34096281 34097305 1024 False 1002.000000 1002 84.615000 789 1807 1 chr2A.!!$F1 1018
2 TraesCS2A01G076400 chr2D 32035257 32036292 1035 False 1103.000000 1103 86.167000 785 1807 1 chr2D.!!$F1 1022
3 TraesCS2A01G076400 chr2D 32068451 32072043 3592 True 927.333333 1598 91.055333 715 2913 3 chr2D.!!$R1 2198
4 TraesCS2A01G076400 chr2B 52625002 52626029 1027 False 1029.000000 1029 85.043000 785 1807 1 chr2B.!!$F1 1022
5 TraesCS2A01G076400 chr2B 52339537 52340515 978 True 990.000000 990 85.238000 831 1800 1 chr2B.!!$R1 969
6 TraesCS2A01G076400 chr2B 52682999 52683564 565 True 798.000000 798 92.133000 716 1284 1 chr2B.!!$R2 568
7 TraesCS2A01G076400 chr2B 52674585 52678046 3461 True 443.000000 778 89.142333 1281 2583 3 chr2B.!!$R3 1302
8 TraesCS2A01G076400 chr3A 718014262 718014814 552 False 872.000000 872 95.118000 3 555 1 chr3A.!!$F1 552
9 TraesCS2A01G076400 chr3A 718027906 718028465 559 False 832.000000 832 93.440000 3 565 1 chr3A.!!$F2 562
10 TraesCS2A01G076400 chr1A 565320931 565321492 561 False 867.000000 867 94.494000 3 565 1 chr1A.!!$F1 562
11 TraesCS2A01G076400 chr1A 491252355 491252916 561 True 839.000000 839 93.606000 3 565 1 chr1A.!!$R2 562
12 TraesCS2A01G076400 chr1A 293723691 293724255 564 True 837.000000 837 93.474000 3 565 1 chr1A.!!$R1 562
13 TraesCS2A01G076400 chr4A 465552376 465552937 561 False 859.000000 859 94.170000 3 568 1 chr4A.!!$F1 565
14 TraesCS2A01G076400 chr4D 28419675 28420235 560 False 856.000000 856 94.139000 3 565 1 chr4D.!!$F1 562
15 TraesCS2A01G076400 chr7D 16184359 16184920 561 True 839.000000 839 93.606000 3 565 1 chr7D.!!$R1 562
16 TraesCS2A01G076400 chr7D 69044541 69045098 557 True 835.000000 835 93.606000 3 565 1 chr7D.!!$R2 562

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
621 627 0.478072 AATGACCAGTGGTGAAGCCA 59.522 50.0 22.5 11.61 46.95 4.75 F
1100 1128 0.541998 TGCCTTCCTCTTCCTCACGA 60.542 55.0 0.0 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1913 0.036765 TCGGCCTACATGTTCCACAC 60.037 55.0 2.30 0.0 0.0 3.82 R
2673 6174 0.384309 CAGTGCGCGTTCCCTATAGA 59.616 55.0 8.43 0.0 0.0 1.98 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
44 45 9.406113 CTCCTCTTCCATATCAAATTCTTCTTT 57.594 33.333 0.00 0.00 0.00 2.52
223 224 2.599281 TTCGTCGGAGGACCAGCA 60.599 61.111 0.00 0.00 40.17 4.41
294 297 2.078665 GGGATAGGCAGGGGAAGCA 61.079 63.158 0.00 0.00 0.00 3.91
435 441 0.953471 CGATTGAGTTTCGGCCCACA 60.953 55.000 0.00 0.00 33.05 4.17
527 533 1.989864 CTAAAACGGGGAATTTTGCGC 59.010 47.619 0.00 0.00 31.79 6.09
568 574 2.430465 GCTGTTGGAGATGCTCTCAAA 58.570 47.619 13.06 7.06 45.12 2.69
569 575 2.419324 GCTGTTGGAGATGCTCTCAAAG 59.581 50.000 13.06 7.12 45.12 2.77
581 587 1.265095 CTCTCAAAGCACGTGCATTGT 59.735 47.619 40.61 23.01 46.25 2.71
582 588 1.264020 TCTCAAAGCACGTGCATTGTC 59.736 47.619 40.61 17.31 46.25 3.18
583 589 1.265095 CTCAAAGCACGTGCATTGTCT 59.735 47.619 40.61 22.00 46.25 3.41
584 590 1.675483 TCAAAGCACGTGCATTGTCTT 59.325 42.857 40.61 25.75 46.25 3.01
585 591 2.875317 TCAAAGCACGTGCATTGTCTTA 59.125 40.909 40.61 27.43 46.25 2.10
586 592 3.058983 TCAAAGCACGTGCATTGTCTTAG 60.059 43.478 40.61 24.63 46.25 2.18
587 593 2.169832 AGCACGTGCATTGTCTTAGT 57.830 45.000 39.21 14.41 45.16 2.24
588 594 3.313012 AGCACGTGCATTGTCTTAGTA 57.687 42.857 39.21 0.00 45.16 1.82
589 595 3.659786 AGCACGTGCATTGTCTTAGTAA 58.340 40.909 39.21 0.00 45.16 2.24
590 596 4.062293 AGCACGTGCATTGTCTTAGTAAA 58.938 39.130 39.21 0.00 45.16 2.01
591 597 4.152402 AGCACGTGCATTGTCTTAGTAAAG 59.848 41.667 39.21 0.00 45.16 1.85
592 598 4.084013 GCACGTGCATTGTCTTAGTAAAGT 60.084 41.667 34.52 0.00 41.59 2.66
593 599 5.119588 GCACGTGCATTGTCTTAGTAAAGTA 59.880 40.000 34.52 0.00 41.59 2.24
594 600 6.522761 CACGTGCATTGTCTTAGTAAAGTAC 58.477 40.000 0.82 0.00 34.13 2.73
595 601 6.144886 CACGTGCATTGTCTTAGTAAAGTACA 59.855 38.462 0.82 0.00 34.13 2.90
596 602 6.365247 ACGTGCATTGTCTTAGTAAAGTACAG 59.635 38.462 0.00 0.00 34.13 2.74
597 603 6.534934 GTGCATTGTCTTAGTAAAGTACAGC 58.465 40.000 0.00 0.00 34.13 4.40
598 604 6.369065 GTGCATTGTCTTAGTAAAGTACAGCT 59.631 38.462 0.00 0.00 34.13 4.24
599 605 6.590292 TGCATTGTCTTAGTAAAGTACAGCTC 59.410 38.462 0.00 0.00 34.13 4.09
600 606 6.590292 GCATTGTCTTAGTAAAGTACAGCTCA 59.410 38.462 0.00 0.00 34.13 4.26
601 607 7.412020 GCATTGTCTTAGTAAAGTACAGCTCAC 60.412 40.741 0.00 0.00 34.13 3.51
602 608 6.644248 TGTCTTAGTAAAGTACAGCTCACA 57.356 37.500 0.00 0.00 34.13 3.58
603 609 7.046292 TGTCTTAGTAAAGTACAGCTCACAA 57.954 36.000 0.00 0.00 34.13 3.33
604 610 7.667557 TGTCTTAGTAAAGTACAGCTCACAAT 58.332 34.615 0.00 0.00 34.13 2.71
605 611 7.598869 TGTCTTAGTAAAGTACAGCTCACAATG 59.401 37.037 0.00 0.00 34.13 2.82
606 612 7.813148 GTCTTAGTAAAGTACAGCTCACAATGA 59.187 37.037 0.00 0.00 34.13 2.57
607 613 7.813148 TCTTAGTAAAGTACAGCTCACAATGAC 59.187 37.037 0.00 0.00 34.13 3.06
608 614 5.238583 AGTAAAGTACAGCTCACAATGACC 58.761 41.667 0.00 0.00 0.00 4.02
609 615 3.769739 AAGTACAGCTCACAATGACCA 57.230 42.857 0.00 0.00 0.00 4.02
610 616 3.325293 AGTACAGCTCACAATGACCAG 57.675 47.619 0.00 0.00 0.00 4.00
611 617 2.634940 AGTACAGCTCACAATGACCAGT 59.365 45.455 0.00 0.00 0.00 4.00
612 618 1.888215 ACAGCTCACAATGACCAGTG 58.112 50.000 0.00 0.00 37.10 3.66
613 619 1.162698 CAGCTCACAATGACCAGTGG 58.837 55.000 7.91 7.91 36.43 4.00
614 620 0.767375 AGCTCACAATGACCAGTGGT 59.233 50.000 16.70 16.70 39.44 4.16
615 621 0.877071 GCTCACAATGACCAGTGGTG 59.123 55.000 22.50 7.86 35.25 4.17
616 622 1.543208 GCTCACAATGACCAGTGGTGA 60.543 52.381 22.50 13.04 35.25 4.02
617 623 2.849942 CTCACAATGACCAGTGGTGAA 58.150 47.619 22.50 8.29 35.25 3.18
618 624 2.810274 CTCACAATGACCAGTGGTGAAG 59.190 50.000 22.50 11.31 35.25 3.02
619 625 1.267806 CACAATGACCAGTGGTGAAGC 59.732 52.381 22.50 5.55 35.25 3.86
620 626 0.883833 CAATGACCAGTGGTGAAGCC 59.116 55.000 22.50 5.12 35.25 4.35
621 627 0.478072 AATGACCAGTGGTGAAGCCA 59.522 50.000 22.50 11.61 46.95 4.75
631 637 3.931907 TGGTGAAGCCACATATAAGCT 57.068 42.857 0.00 0.00 43.61 3.74
632 638 3.544684 TGGTGAAGCCACATATAAGCTG 58.455 45.455 0.00 0.00 43.61 4.24
633 639 3.054434 TGGTGAAGCCACATATAAGCTGT 60.054 43.478 0.00 0.00 43.61 4.40
634 640 3.313526 GGTGAAGCCACATATAAGCTGTG 59.686 47.826 0.00 0.00 44.93 3.66
635 641 3.941483 GTGAAGCCACATATAAGCTGTGT 59.059 43.478 4.66 0.00 41.93 3.72
636 642 5.116180 GTGAAGCCACATATAAGCTGTGTA 58.884 41.667 4.66 0.00 41.93 2.90
637 643 5.235186 GTGAAGCCACATATAAGCTGTGTAG 59.765 44.000 4.66 0.00 41.93 2.74
638 644 5.104941 TGAAGCCACATATAAGCTGTGTAGT 60.105 40.000 4.66 0.00 41.93 2.73
639 645 4.950050 AGCCACATATAAGCTGTGTAGTC 58.050 43.478 4.66 0.00 41.93 2.59
640 646 4.405680 AGCCACATATAAGCTGTGTAGTCA 59.594 41.667 4.66 0.00 41.93 3.41
641 647 5.104941 AGCCACATATAAGCTGTGTAGTCAA 60.105 40.000 4.66 0.00 41.93 3.18
642 648 5.760253 GCCACATATAAGCTGTGTAGTCAAT 59.240 40.000 4.66 0.00 41.93 2.57
643 649 6.260936 GCCACATATAAGCTGTGTAGTCAATT 59.739 38.462 4.66 0.00 41.93 2.32
644 650 7.633621 CCACATATAAGCTGTGTAGTCAATTG 58.366 38.462 0.00 0.00 41.93 2.32
645 651 7.495606 CCACATATAAGCTGTGTAGTCAATTGA 59.504 37.037 3.38 3.38 41.93 2.57
646 652 8.331022 CACATATAAGCTGTGTAGTCAATTGAC 58.669 37.037 27.69 27.69 40.75 3.18
661 667 7.755582 GTCAATTGACTTTTTAGCAACAACT 57.244 32.000 27.66 0.00 41.65 3.16
662 668 8.185003 GTCAATTGACTTTTTAGCAACAACTT 57.815 30.769 27.66 0.00 41.65 2.66
663 669 8.321005 GTCAATTGACTTTTTAGCAACAACTTC 58.679 33.333 27.66 0.00 41.65 3.01
664 670 8.031864 TCAATTGACTTTTTAGCAACAACTTCA 58.968 29.630 3.38 0.00 0.00 3.02
665 671 8.819974 CAATTGACTTTTTAGCAACAACTTCAT 58.180 29.630 0.00 0.00 0.00 2.57
666 672 8.947055 ATTGACTTTTTAGCAACAACTTCATT 57.053 26.923 0.00 0.00 0.00 2.57
667 673 8.770438 TTGACTTTTTAGCAACAACTTCATTT 57.230 26.923 0.00 0.00 0.00 2.32
668 674 9.862371 TTGACTTTTTAGCAACAACTTCATTTA 57.138 25.926 0.00 0.00 0.00 1.40
669 675 9.296400 TGACTTTTTAGCAACAACTTCATTTAC 57.704 29.630 0.00 0.00 0.00 2.01
670 676 9.296400 GACTTTTTAGCAACAACTTCATTTACA 57.704 29.630 0.00 0.00 0.00 2.41
671 677 9.083080 ACTTTTTAGCAACAACTTCATTTACAC 57.917 29.630 0.00 0.00 0.00 2.90
672 678 7.672351 TTTTAGCAACAACTTCATTTACACG 57.328 32.000 0.00 0.00 0.00 4.49
673 679 3.628017 AGCAACAACTTCATTTACACGC 58.372 40.909 0.00 0.00 0.00 5.34
674 680 3.066064 AGCAACAACTTCATTTACACGCA 59.934 39.130 0.00 0.00 0.00 5.24
675 681 3.179599 GCAACAACTTCATTTACACGCAC 59.820 43.478 0.00 0.00 0.00 5.34
676 682 4.346970 CAACAACTTCATTTACACGCACA 58.653 39.130 0.00 0.00 0.00 4.57
677 683 4.624336 ACAACTTCATTTACACGCACAA 57.376 36.364 0.00 0.00 0.00 3.33
678 684 4.987832 ACAACTTCATTTACACGCACAAA 58.012 34.783 0.00 0.00 0.00 2.83
679 685 5.587289 ACAACTTCATTTACACGCACAAAT 58.413 33.333 0.00 0.00 0.00 2.32
680 686 5.685511 ACAACTTCATTTACACGCACAAATC 59.314 36.000 0.00 0.00 0.00 2.17
681 687 5.431420 ACTTCATTTACACGCACAAATCA 57.569 34.783 0.00 0.00 0.00 2.57
682 688 6.012658 ACTTCATTTACACGCACAAATCAT 57.987 33.333 0.00 0.00 0.00 2.45
683 689 5.858049 ACTTCATTTACACGCACAAATCATG 59.142 36.000 0.00 0.00 0.00 3.07
684 690 4.165036 TCATTTACACGCACAAATCATGC 58.835 39.130 0.00 0.00 39.81 4.06
685 691 3.632855 TTTACACGCACAAATCATGCA 57.367 38.095 0.00 0.00 43.57 3.96
686 692 3.632855 TTACACGCACAAATCATGCAA 57.367 38.095 0.00 0.00 43.57 4.08
687 693 2.505628 ACACGCACAAATCATGCAAA 57.494 40.000 0.00 0.00 43.57 3.68
688 694 2.126467 ACACGCACAAATCATGCAAAC 58.874 42.857 0.00 0.00 43.57 2.93
689 695 2.223782 ACACGCACAAATCATGCAAACT 60.224 40.909 0.00 0.00 43.57 2.66
690 696 3.004210 ACACGCACAAATCATGCAAACTA 59.996 39.130 0.00 0.00 43.57 2.24
691 697 3.980134 CACGCACAAATCATGCAAACTAA 59.020 39.130 0.00 0.00 43.57 2.24
692 698 4.622313 CACGCACAAATCATGCAAACTAAT 59.378 37.500 0.00 0.00 43.57 1.73
693 699 4.622313 ACGCACAAATCATGCAAACTAATG 59.378 37.500 0.00 0.00 43.57 1.90
694 700 4.858140 CGCACAAATCATGCAAACTAATGA 59.142 37.500 0.00 0.00 43.57 2.57
695 701 5.517411 CGCACAAATCATGCAAACTAATGAT 59.483 36.000 0.00 0.00 43.69 2.45
696 702 6.692249 CGCACAAATCATGCAAACTAATGATA 59.308 34.615 0.00 0.00 41.56 2.15
697 703 7.380333 CGCACAAATCATGCAAACTAATGATAT 59.620 33.333 0.00 0.00 41.56 1.63
698 704 9.681692 GCACAAATCATGCAAACTAATGATATA 57.318 29.630 0.00 0.00 41.56 0.86
762 769 6.575162 ATGACTACACAAAATTGAAGTCCC 57.425 37.500 17.14 4.30 36.31 4.46
763 770 5.690865 TGACTACACAAAATTGAAGTCCCT 58.309 37.500 17.14 0.00 36.31 4.20
764 771 5.530915 TGACTACACAAAATTGAAGTCCCTG 59.469 40.000 17.14 2.62 36.31 4.45
765 772 4.827284 ACTACACAAAATTGAAGTCCCTGG 59.173 41.667 0.00 0.00 0.00 4.45
766 773 2.365293 ACACAAAATTGAAGTCCCTGGC 59.635 45.455 0.00 0.00 0.00 4.85
767 774 2.364970 CACAAAATTGAAGTCCCTGGCA 59.635 45.455 0.00 0.00 0.00 4.92
768 775 3.007182 CACAAAATTGAAGTCCCTGGCAT 59.993 43.478 0.00 0.00 0.00 4.40
787 794 1.664965 GCACCACCGTCACTGAGTC 60.665 63.158 0.00 0.00 0.00 3.36
803 814 3.797039 TGAGTCGGATTGCCATTTAGAG 58.203 45.455 0.00 0.00 0.00 2.43
834 847 8.737168 ACTAGAAATTCATATACTGCAAAGCA 57.263 30.769 0.00 0.00 36.92 3.91
915 932 3.963647 ATGCAACGCACGCAAGCA 61.964 55.556 7.02 7.02 43.04 3.91
973 992 7.201705 CCTCTAGATCCGGACCAAATTAAAAAC 60.202 40.741 6.12 0.00 0.00 2.43
984 1003 7.373617 ACCAAATTAAAAACATCAGGGTTCT 57.626 32.000 0.00 0.00 0.00 3.01
1100 1128 0.541998 TGCCTTCCTCTTCCTCACGA 60.542 55.000 0.00 0.00 0.00 4.35
1251 1291 4.424711 TGGCCATGGCTCCGGAAC 62.425 66.667 34.70 17.52 41.60 3.62
1662 1705 2.660064 AAGGTTCTGGGAGCGCGAT 61.660 57.895 12.10 1.23 0.00 4.58
1800 1853 5.200454 GTTCAGTTATGATGCATGTTAGCG 58.800 41.667 2.46 0.00 34.73 4.26
1813 1866 3.326836 TGTTAGCGAATCCATGTGTGA 57.673 42.857 0.00 0.00 0.00 3.58
1819 1872 3.136763 GCGAATCCATGTGTGATCAGAT 58.863 45.455 0.00 0.00 0.00 2.90
1820 1873 3.562973 GCGAATCCATGTGTGATCAGATT 59.437 43.478 0.00 0.00 0.00 2.40
1835 1897 9.061435 TGTGATCAGATTATCTCTAGTGTGTAG 57.939 37.037 0.00 0.00 31.13 2.74
1857 1919 2.519377 CTGTAAGGTTGACGTGTGGA 57.481 50.000 0.00 0.00 0.00 4.02
1858 1920 2.828877 CTGTAAGGTTGACGTGTGGAA 58.171 47.619 0.00 0.00 0.00 3.53
1859 1921 2.542595 CTGTAAGGTTGACGTGTGGAAC 59.457 50.000 0.00 0.00 37.35 3.62
1924 2009 6.142798 GCAAGTGTTGATGAATAATATTGGCG 59.857 38.462 0.00 0.00 0.00 5.69
1932 2017 6.656270 TGATGAATAATATTGGCGCTTGATCT 59.344 34.615 7.64 0.00 0.00 2.75
1933 2018 6.245115 TGAATAATATTGGCGCTTGATCTG 57.755 37.500 7.64 0.00 0.00 2.90
1940 2250 1.303309 GGCGCTTGATCTGCACTATT 58.697 50.000 7.64 0.00 0.00 1.73
1942 2252 2.098117 GGCGCTTGATCTGCACTATTTT 59.902 45.455 7.64 0.00 0.00 1.82
2087 4309 3.667087 GATGCCTTGCAACGACCA 58.333 55.556 0.00 0.00 43.62 4.02
2163 4385 1.814586 GCTGATTCTGCTGAGCGCT 60.815 57.895 11.27 11.27 40.11 5.92
2209 4435 2.202566 GCATAACCTACGCCTTCTGAC 58.797 52.381 0.00 0.00 0.00 3.51
2233 4459 2.096980 AGATCATTGCACGCATTCACTG 59.903 45.455 0.00 0.00 0.00 3.66
2311 4537 0.873054 CATGGGAGCGATGCTGAATC 59.127 55.000 0.00 0.00 39.88 2.52
2352 4578 1.203364 AGTCCTGGACTCCTGGTCATT 60.203 52.381 23.49 0.00 46.16 2.57
2353 4579 1.065854 GTCCTGGACTCCTGGTCATTG 60.066 57.143 19.53 0.00 46.16 2.82
2354 4580 1.203300 TCCTGGACTCCTGGTCATTGA 60.203 52.381 18.16 0.00 46.16 2.57
2355 4581 1.065854 CCTGGACTCCTGGTCATTGAC 60.066 57.143 12.05 8.34 46.16 3.18
2356 4582 1.905215 CTGGACTCCTGGTCATTGACT 59.095 52.381 16.02 0.00 46.16 3.41
2357 4583 2.304180 CTGGACTCCTGGTCATTGACTT 59.696 50.000 16.02 0.00 46.16 3.01
2358 4584 3.515502 CTGGACTCCTGGTCATTGACTTA 59.484 47.826 16.02 5.61 46.16 2.24
2376 4662 7.288810 TGACTTAACTTACTCCGACCTTTTA 57.711 36.000 0.00 0.00 0.00 1.52
2381 4667 8.937634 TTAACTTACTCCGACCTTTTATCATC 57.062 34.615 0.00 0.00 0.00 2.92
2382 4668 5.915175 ACTTACTCCGACCTTTTATCATCC 58.085 41.667 0.00 0.00 0.00 3.51
2383 4669 5.424252 ACTTACTCCGACCTTTTATCATCCA 59.576 40.000 0.00 0.00 0.00 3.41
2384 4670 4.138487 ACTCCGACCTTTTATCATCCAC 57.862 45.455 0.00 0.00 0.00 4.02
2385 4671 3.118371 ACTCCGACCTTTTATCATCCACC 60.118 47.826 0.00 0.00 0.00 4.61
2386 4672 2.159014 TCCGACCTTTTATCATCCACCG 60.159 50.000 0.00 0.00 0.00 4.94
2387 4673 2.210116 CGACCTTTTATCATCCACCGG 58.790 52.381 0.00 0.00 0.00 5.28
2388 4674 1.947456 GACCTTTTATCATCCACCGGC 59.053 52.381 0.00 0.00 0.00 6.13
2444 5945 2.279517 GACCTGCCGTCGCCATAG 60.280 66.667 0.00 0.00 0.00 2.23
2445 5946 4.530857 ACCTGCCGTCGCCATAGC 62.531 66.667 0.00 0.00 0.00 2.97
2481 5982 1.394917 CGCGAAGGAAGAATCAACTGG 59.605 52.381 0.00 0.00 0.00 4.00
2482 5983 2.699954 GCGAAGGAAGAATCAACTGGA 58.300 47.619 0.00 0.00 0.00 3.86
2530 6031 4.494350 ACAGACAATGTTGATGTGCTTC 57.506 40.909 0.00 0.00 39.96 3.86
2583 6084 5.532032 AGATTCCTCCTAGTTAGTTACTCGC 59.468 44.000 0.00 0.00 38.33 5.03
2598 6099 2.928334 ACTCGCCGTAGATTCCTCTAA 58.072 47.619 0.00 0.00 35.76 2.10
2604 6105 5.533903 TCGCCGTAGATTCCTCTAATTAGTT 59.466 40.000 12.19 0.00 35.76 2.24
2605 6106 6.712095 TCGCCGTAGATTCCTCTAATTAGTTA 59.288 38.462 12.19 0.00 35.76 2.24
2606 6107 7.022384 CGCCGTAGATTCCTCTAATTAGTTAG 58.978 42.308 12.19 3.57 35.76 2.34
2607 6108 7.308469 CGCCGTAGATTCCTCTAATTAGTTAGT 60.308 40.741 12.19 0.00 38.72 2.24
2608 6109 8.358895 GCCGTAGATTCCTCTAATTAGTTAGTT 58.641 37.037 12.19 0.00 38.72 2.24
2691 6192 0.669077 CTCTATAGGGAACGCGCACT 59.331 55.000 5.73 0.00 0.00 4.40
2726 6227 9.919348 TGTGTTTAACTTATTTAACGTGAGAAC 57.081 29.630 0.00 0.00 28.84 3.01
2786 6288 1.589716 GCAATCTTTGGAGCTGGCGT 61.590 55.000 0.00 0.00 0.00 5.68
2787 6289 0.449388 CAATCTTTGGAGCTGGCGTC 59.551 55.000 0.00 0.00 0.00 5.19
2796 6298 3.461773 GCTGGCGTCCTGGCTAGA 61.462 66.667 0.00 0.00 43.45 2.43
2804 6306 2.548920 GCGTCCTGGCTAGATTGCTATT 60.549 50.000 0.00 0.00 0.00 1.73
2885 6388 5.070001 TCAGTTCCTTTTTATGTGGAGTGG 58.930 41.667 0.00 0.00 0.00 4.00
2892 6395 1.072266 TTATGTGGAGTGGGCAAGGT 58.928 50.000 0.00 0.00 0.00 3.50
2897 6400 2.359975 GAGTGGGCAAGGTTCGGG 60.360 66.667 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.948315 GGAGGAGGATCTTGCAATGAAC 59.052 50.000 0.00 0.00 31.31 3.18
1 2 2.848694 AGGAGGAGGATCTTGCAATGAA 59.151 45.455 0.00 0.00 34.14 2.57
44 45 4.157105 TGAGTTCGTCGTATGATTCTTCCA 59.843 41.667 0.00 0.00 0.00 3.53
285 288 4.016706 CGTTCCGGTGCTTCCCCT 62.017 66.667 0.00 0.00 0.00 4.79
435 441 1.852942 CGGCATATGTAGTTCAGCGT 58.147 50.000 4.29 0.00 0.00 5.07
568 574 2.169832 ACTAAGACAATGCACGTGCT 57.830 45.000 37.59 20.65 42.66 4.40
569 575 4.084013 ACTTTACTAAGACAATGCACGTGC 60.084 41.667 33.11 33.11 37.03 5.34
570 576 5.591643 ACTTTACTAAGACAATGCACGTG 57.408 39.130 12.28 12.28 35.30 4.49
571 577 6.218019 TGTACTTTACTAAGACAATGCACGT 58.782 36.000 0.00 0.00 35.30 4.49
572 578 6.669977 GCTGTACTTTACTAAGACAATGCACG 60.670 42.308 0.00 0.00 35.30 5.34
573 579 6.369065 AGCTGTACTTTACTAAGACAATGCAC 59.631 38.462 0.00 0.00 35.30 4.57
574 580 6.464222 AGCTGTACTTTACTAAGACAATGCA 58.536 36.000 0.00 0.00 35.30 3.96
575 581 6.590292 TGAGCTGTACTTTACTAAGACAATGC 59.410 38.462 0.00 0.00 35.30 3.56
576 582 7.598869 TGTGAGCTGTACTTTACTAAGACAATG 59.401 37.037 0.00 0.00 35.30 2.82
577 583 7.667557 TGTGAGCTGTACTTTACTAAGACAAT 58.332 34.615 0.00 0.00 35.30 2.71
578 584 7.046292 TGTGAGCTGTACTTTACTAAGACAA 57.954 36.000 0.00 0.00 35.30 3.18
579 585 6.644248 TGTGAGCTGTACTTTACTAAGACA 57.356 37.500 0.00 0.00 35.30 3.41
580 586 7.813148 TCATTGTGAGCTGTACTTTACTAAGAC 59.187 37.037 0.00 0.00 35.30 3.01
581 587 7.813148 GTCATTGTGAGCTGTACTTTACTAAGA 59.187 37.037 0.00 0.00 35.30 2.10
582 588 7.063544 GGTCATTGTGAGCTGTACTTTACTAAG 59.936 40.741 0.00 0.00 41.34 2.18
583 589 6.872020 GGTCATTGTGAGCTGTACTTTACTAA 59.128 38.462 0.00 0.00 41.34 2.24
584 590 6.014925 TGGTCATTGTGAGCTGTACTTTACTA 60.015 38.462 10.09 0.00 44.58 1.82
585 591 5.221641 TGGTCATTGTGAGCTGTACTTTACT 60.222 40.000 10.09 0.00 44.58 2.24
586 592 4.994852 TGGTCATTGTGAGCTGTACTTTAC 59.005 41.667 10.09 0.00 44.58 2.01
587 593 5.222079 TGGTCATTGTGAGCTGTACTTTA 57.778 39.130 10.09 0.00 44.58 1.85
588 594 4.067896 CTGGTCATTGTGAGCTGTACTTT 58.932 43.478 10.09 0.00 44.58 2.66
589 595 3.668447 CTGGTCATTGTGAGCTGTACTT 58.332 45.455 10.09 0.00 44.58 2.24
590 596 3.325293 CTGGTCATTGTGAGCTGTACT 57.675 47.619 10.09 0.00 44.58 2.73
594 600 1.162698 CCACTGGTCATTGTGAGCTG 58.837 55.000 12.44 12.44 44.58 4.24
595 601 0.767375 ACCACTGGTCATTGTGAGCT 59.233 50.000 10.09 0.00 44.58 4.09
596 602 0.877071 CACCACTGGTCATTGTGAGC 59.123 55.000 0.00 2.40 44.54 4.26
597 603 2.549064 TCACCACTGGTCATTGTGAG 57.451 50.000 0.00 0.00 36.38 3.51
598 604 2.849942 CTTCACCACTGGTCATTGTGA 58.150 47.619 0.00 0.00 36.38 3.58
599 605 1.267806 GCTTCACCACTGGTCATTGTG 59.732 52.381 0.00 0.00 31.02 3.33
600 606 1.609208 GCTTCACCACTGGTCATTGT 58.391 50.000 0.00 0.00 31.02 2.71
601 607 0.883833 GGCTTCACCACTGGTCATTG 59.116 55.000 0.00 0.00 38.86 2.82
602 608 0.478072 TGGCTTCACCACTGGTCATT 59.522 50.000 0.00 0.00 46.36 2.57
603 609 2.154139 TGGCTTCACCACTGGTCAT 58.846 52.632 0.00 0.00 46.36 3.06
604 610 3.654021 TGGCTTCACCACTGGTCA 58.346 55.556 0.00 0.00 46.36 4.02
612 618 3.313526 CACAGCTTATATGTGGCTTCACC 59.686 47.826 0.00 0.00 43.47 4.02
613 619 4.542662 CACAGCTTATATGTGGCTTCAC 57.457 45.455 0.00 0.00 43.47 3.18
620 626 8.331022 GTCAATTGACTACACAGCTTATATGTG 58.669 37.037 27.66 4.61 45.37 3.21
621 627 8.425577 GTCAATTGACTACACAGCTTATATGT 57.574 34.615 27.66 0.00 41.65 2.29
637 643 7.755582 AGTTGTTGCTAAAAAGTCAATTGAC 57.244 32.000 27.69 27.69 45.08 3.18
638 644 8.031864 TGAAGTTGTTGCTAAAAAGTCAATTGA 58.968 29.630 3.38 3.38 0.00 2.57
639 645 8.183830 TGAAGTTGTTGCTAAAAAGTCAATTG 57.816 30.769 0.00 0.00 0.00 2.32
640 646 8.947055 ATGAAGTTGTTGCTAAAAAGTCAATT 57.053 26.923 0.00 0.00 0.00 2.32
641 647 8.947055 AATGAAGTTGTTGCTAAAAAGTCAAT 57.053 26.923 0.00 0.00 0.00 2.57
642 648 8.770438 AAATGAAGTTGTTGCTAAAAAGTCAA 57.230 26.923 0.00 0.00 0.00 3.18
643 649 9.296400 GTAAATGAAGTTGTTGCTAAAAAGTCA 57.704 29.630 0.00 0.00 0.00 3.41
644 650 9.296400 TGTAAATGAAGTTGTTGCTAAAAAGTC 57.704 29.630 0.00 0.00 0.00 3.01
645 651 9.083080 GTGTAAATGAAGTTGTTGCTAAAAAGT 57.917 29.630 0.00 0.00 0.00 2.66
646 652 8.259194 CGTGTAAATGAAGTTGTTGCTAAAAAG 58.741 33.333 0.00 0.00 0.00 2.27
647 653 7.253817 GCGTGTAAATGAAGTTGTTGCTAAAAA 60.254 33.333 0.00 0.00 0.00 1.94
648 654 6.197468 GCGTGTAAATGAAGTTGTTGCTAAAA 59.803 34.615 0.00 0.00 0.00 1.52
649 655 5.683743 GCGTGTAAATGAAGTTGTTGCTAAA 59.316 36.000 0.00 0.00 0.00 1.85
650 656 5.209240 GCGTGTAAATGAAGTTGTTGCTAA 58.791 37.500 0.00 0.00 0.00 3.09
651 657 4.273724 TGCGTGTAAATGAAGTTGTTGCTA 59.726 37.500 0.00 0.00 0.00 3.49
652 658 3.066064 TGCGTGTAAATGAAGTTGTTGCT 59.934 39.130 0.00 0.00 0.00 3.91
653 659 3.179599 GTGCGTGTAAATGAAGTTGTTGC 59.820 43.478 0.00 0.00 0.00 4.17
654 660 4.346970 TGTGCGTGTAAATGAAGTTGTTG 58.653 39.130 0.00 0.00 0.00 3.33
655 661 4.624336 TGTGCGTGTAAATGAAGTTGTT 57.376 36.364 0.00 0.00 0.00 2.83
656 662 4.624336 TTGTGCGTGTAAATGAAGTTGT 57.376 36.364 0.00 0.00 0.00 3.32
657 663 5.685068 TGATTTGTGCGTGTAAATGAAGTTG 59.315 36.000 0.00 0.00 0.00 3.16
658 664 5.826586 TGATTTGTGCGTGTAAATGAAGTT 58.173 33.333 0.00 0.00 0.00 2.66
659 665 5.431420 TGATTTGTGCGTGTAAATGAAGT 57.569 34.783 0.00 0.00 0.00 3.01
660 666 5.220080 GCATGATTTGTGCGTGTAAATGAAG 60.220 40.000 0.00 0.00 32.29 3.02
661 667 4.620609 GCATGATTTGTGCGTGTAAATGAA 59.379 37.500 0.00 0.00 32.29 2.57
662 668 4.165036 GCATGATTTGTGCGTGTAAATGA 58.835 39.130 0.00 0.00 32.29 2.57
663 669 3.919197 TGCATGATTTGTGCGTGTAAATG 59.081 39.130 0.00 0.00 45.37 2.32
664 670 4.171663 TGCATGATTTGTGCGTGTAAAT 57.828 36.364 0.00 0.00 45.37 1.40
665 671 3.632855 TGCATGATTTGTGCGTGTAAA 57.367 38.095 0.00 0.00 45.37 2.01
666 672 3.632855 TTGCATGATTTGTGCGTGTAA 57.367 38.095 0.00 0.00 45.37 2.41
667 673 3.004210 AGTTTGCATGATTTGTGCGTGTA 59.996 39.130 0.00 0.00 45.37 2.90
668 674 2.126467 GTTTGCATGATTTGTGCGTGT 58.874 42.857 0.00 0.00 45.37 4.49
669 675 2.396601 AGTTTGCATGATTTGTGCGTG 58.603 42.857 0.00 0.00 45.37 5.34
670 676 2.798976 AGTTTGCATGATTTGTGCGT 57.201 40.000 0.00 0.00 45.37 5.24
671 677 4.858140 TCATTAGTTTGCATGATTTGTGCG 59.142 37.500 0.00 0.00 45.37 5.34
672 678 6.897259 ATCATTAGTTTGCATGATTTGTGC 57.103 33.333 0.00 0.00 36.87 4.57
746 753 2.364970 TGCCAGGGACTTCAATTTTGTG 59.635 45.455 0.00 0.00 34.60 3.33
762 769 3.434319 GACGGTGGTGCATGCCAG 61.434 66.667 16.68 2.57 39.53 4.85
763 770 4.262089 TGACGGTGGTGCATGCCA 62.262 61.111 16.68 3.51 35.93 4.92
764 771 3.737172 GTGACGGTGGTGCATGCC 61.737 66.667 16.68 6.42 0.00 4.40
765 772 2.669569 AGTGACGGTGGTGCATGC 60.670 61.111 11.82 11.82 0.00 4.06
766 773 1.293963 CTCAGTGACGGTGGTGCATG 61.294 60.000 0.00 0.00 0.00 4.06
767 774 1.004560 CTCAGTGACGGTGGTGCAT 60.005 57.895 0.00 0.00 0.00 3.96
768 775 2.363711 GACTCAGTGACGGTGGTGCA 62.364 60.000 0.00 0.00 0.00 4.57
787 794 6.226787 AGTCTTATCTCTAAATGGCAATCCG 58.773 40.000 0.00 0.00 34.14 4.18
826 839 1.138464 TCATTTGGCTGTTGCTTTGCA 59.862 42.857 0.00 0.00 39.59 4.08
827 840 1.868469 TCATTTGGCTGTTGCTTTGC 58.132 45.000 0.00 0.00 39.59 3.68
834 847 3.387374 TGTTGACCATTCATTTGGCTGTT 59.613 39.130 0.00 0.00 40.68 3.16
915 932 0.608640 AGTCGGCTTTGGATCGAACT 59.391 50.000 0.00 0.00 34.62 3.01
973 992 1.064166 AGCCATGGAAGAACCCTGATG 60.064 52.381 18.40 0.00 36.59 3.07
984 1003 8.154856 GGTTTATATAGTGAGTTAGCCATGGAA 58.845 37.037 18.40 0.00 0.00 3.53
1042 1061 5.221263 GGTAGAGATAGCCATTCTCGTTTGA 60.221 44.000 3.35 0.00 43.55 2.69
1251 1291 4.733542 AACCGAACCCATGGCCGG 62.734 66.667 26.53 26.53 44.09 6.13
1473 1516 2.338620 CGCCAAGACCGACACTGA 59.661 61.111 0.00 0.00 0.00 3.41
1785 1832 3.479489 TGGATTCGCTAACATGCATCAT 58.521 40.909 0.00 0.00 0.00 2.45
1787 1834 3.251729 ACATGGATTCGCTAACATGCATC 59.748 43.478 0.00 0.00 43.28 3.91
1800 1853 8.095792 AGAGATAATCTGATCACACATGGATTC 58.904 37.037 8.43 0.00 36.69 2.52
1813 1866 6.435904 GGCCTACACACTAGAGATAATCTGAT 59.564 42.308 0.00 0.00 39.20 2.90
1819 1872 4.868268 ACAGGCCTACACACTAGAGATAA 58.132 43.478 3.98 0.00 0.00 1.75
1820 1873 4.521536 ACAGGCCTACACACTAGAGATA 57.478 45.455 3.98 0.00 0.00 1.98
1835 1897 0.250166 ACACGTCAACCTTACAGGCC 60.250 55.000 0.00 0.00 39.63 5.19
1846 1908 2.761559 CCTACATGTTCCACACGTCAA 58.238 47.619 2.30 0.00 0.00 3.18
1848 1910 1.076332 GCCTACATGTTCCACACGTC 58.924 55.000 2.30 0.00 0.00 4.34
1849 1911 0.321298 GGCCTACATGTTCCACACGT 60.321 55.000 2.30 0.00 0.00 4.49
1850 1912 1.358725 CGGCCTACATGTTCCACACG 61.359 60.000 2.30 0.00 0.00 4.49
1851 1913 0.036765 TCGGCCTACATGTTCCACAC 60.037 55.000 2.30 0.00 0.00 3.82
1852 1914 0.036765 GTCGGCCTACATGTTCCACA 60.037 55.000 2.30 0.00 0.00 4.17
1853 1915 1.082117 CGTCGGCCTACATGTTCCAC 61.082 60.000 2.30 4.32 0.00 4.02
1854 1916 1.216977 CGTCGGCCTACATGTTCCA 59.783 57.895 2.30 0.00 0.00 3.53
1855 1917 1.082117 CACGTCGGCCTACATGTTCC 61.082 60.000 2.30 2.39 0.00 3.62
1856 1918 0.108992 TCACGTCGGCCTACATGTTC 60.109 55.000 2.30 0.00 0.00 3.18
1857 1919 0.108804 CTCACGTCGGCCTACATGTT 60.109 55.000 2.30 0.00 0.00 2.71
1858 1920 1.511305 CTCACGTCGGCCTACATGT 59.489 57.895 8.31 2.69 0.00 3.21
1859 1921 1.226974 CCTCACGTCGGCCTACATG 60.227 63.158 8.31 2.22 0.00 3.21
1860 1922 0.968901 TTCCTCACGTCGGCCTACAT 60.969 55.000 8.31 0.00 0.00 2.29
1861 1923 0.968901 ATTCCTCACGTCGGCCTACA 60.969 55.000 8.31 0.00 0.00 2.74
1862 1924 1.027357 TATTCCTCACGTCGGCCTAC 58.973 55.000 0.00 0.00 0.00 3.18
1863 1925 1.611977 CATATTCCTCACGTCGGCCTA 59.388 52.381 0.00 0.00 0.00 3.93
1864 1926 0.389391 CATATTCCTCACGTCGGCCT 59.611 55.000 0.00 0.00 0.00 5.19
1865 1927 0.387929 TCATATTCCTCACGTCGGCC 59.612 55.000 0.00 0.00 0.00 6.13
1866 1928 1.859080 GTTCATATTCCTCACGTCGGC 59.141 52.381 0.00 0.00 0.00 5.54
1867 1929 3.438297 AGTTCATATTCCTCACGTCGG 57.562 47.619 0.00 0.00 0.00 4.79
1868 1930 4.441415 GCTTAGTTCATATTCCTCACGTCG 59.559 45.833 0.00 0.00 0.00 5.12
1932 2017 6.919115 CATGCAATGTATAGCAAAATAGTGCA 59.081 34.615 7.61 7.61 44.88 4.57
1933 2018 7.140705 TCATGCAATGTATAGCAAAATAGTGC 58.859 34.615 0.00 0.00 46.80 4.40
2084 4306 1.056700 AGCAGAGGGTTGAGTGTGGT 61.057 55.000 0.00 0.00 0.00 4.16
2086 4308 1.233285 GCAGCAGAGGGTTGAGTGTG 61.233 60.000 0.00 0.00 0.00 3.82
2087 4309 1.072159 GCAGCAGAGGGTTGAGTGT 59.928 57.895 0.00 0.00 0.00 3.55
2121 4343 6.432936 CAATTCAGCATGTCATATGTGTACC 58.567 40.000 1.90 0.00 37.40 3.34
2193 4419 2.367567 TCTTTGTCAGAAGGCGTAGGTT 59.632 45.455 0.00 0.00 0.00 3.50
2209 4435 3.302434 GTGAATGCGTGCAATGATCTTTG 59.698 43.478 15.23 15.23 0.00 2.77
2268 4494 2.416260 CCGGAGTAACCTAGCCGC 59.584 66.667 0.00 0.00 42.29 6.53
2271 4497 0.459078 GTGACCCGGAGTAACCTAGC 59.541 60.000 0.73 0.00 36.31 3.42
2311 4537 1.627864 ATGTTGGAGGGGAAAAACGG 58.372 50.000 0.00 0.00 0.00 4.44
2352 4578 5.796424 AAAGGTCGGAGTAAGTTAAGTCA 57.204 39.130 0.00 0.00 0.00 3.41
2353 4579 8.031277 TGATAAAAGGTCGGAGTAAGTTAAGTC 58.969 37.037 0.00 0.00 0.00 3.01
2354 4580 7.899973 TGATAAAAGGTCGGAGTAAGTTAAGT 58.100 34.615 0.00 0.00 0.00 2.24
2355 4581 8.943909 ATGATAAAAGGTCGGAGTAAGTTAAG 57.056 34.615 0.00 0.00 0.00 1.85
2356 4582 7.983484 GGATGATAAAAGGTCGGAGTAAGTTAA 59.017 37.037 0.00 0.00 0.00 2.01
2357 4583 7.124599 TGGATGATAAAAGGTCGGAGTAAGTTA 59.875 37.037 0.00 0.00 0.00 2.24
2358 4584 6.070424 TGGATGATAAAAGGTCGGAGTAAGTT 60.070 38.462 0.00 0.00 0.00 2.66
2376 4662 2.757124 GGAAGGGCCGGTGGATGAT 61.757 63.158 1.90 0.00 0.00 2.45
2469 5970 3.882888 TGTTTTCGCTCCAGTTGATTCTT 59.117 39.130 0.00 0.00 0.00 2.52
2481 5982 1.123655 GCTGCAACTTGTTTTCGCTC 58.876 50.000 0.00 0.00 0.00 5.03
2482 5983 0.740737 AGCTGCAACTTGTTTTCGCT 59.259 45.000 1.02 0.00 0.00 4.93
2530 6031 2.073117 TGCATGAACAGCAAGCAATG 57.927 45.000 0.00 0.00 46.97 2.82
2604 6105 9.923143 TGTACTACAAGTAGTAACGAGTAACTA 57.077 33.333 18.70 0.00 46.55 2.24
2605 6106 8.833231 TGTACTACAAGTAGTAACGAGTAACT 57.167 34.615 18.70 0.00 46.55 2.24
2606 6107 9.695884 GATGTACTACAAGTAGTAACGAGTAAC 57.304 37.037 18.70 9.33 46.55 2.50
2607 6108 9.658799 AGATGTACTACAAGTAGTAACGAGTAA 57.341 33.333 18.70 0.00 46.55 2.24
2608 6109 9.091784 CAGATGTACTACAAGTAGTAACGAGTA 57.908 37.037 18.70 5.42 46.55 2.59
2609 6110 7.605691 ACAGATGTACTACAAGTAGTAACGAGT 59.394 37.037 18.70 12.21 46.55 4.18
2610 6111 7.972527 ACAGATGTACTACAAGTAGTAACGAG 58.027 38.462 18.70 11.73 46.55 4.18
2611 6112 7.912056 ACAGATGTACTACAAGTAGTAACGA 57.088 36.000 18.70 8.81 46.55 3.85
2615 6116 8.668353 CCGTTAACAGATGTACTACAAGTAGTA 58.332 37.037 14.38 14.38 43.98 1.82
2617 6118 7.533426 ACCGTTAACAGATGTACTACAAGTAG 58.467 38.462 6.39 5.72 39.04 2.57
2618 6119 7.452880 ACCGTTAACAGATGTACTACAAGTA 57.547 36.000 6.39 0.00 0.00 2.24
2619 6120 6.336842 ACCGTTAACAGATGTACTACAAGT 57.663 37.500 6.39 0.00 0.00 3.16
2622 6123 9.177608 ACTTATACCGTTAACAGATGTACTACA 57.822 33.333 6.39 0.00 0.00 2.74
2623 6124 9.443283 CACTTATACCGTTAACAGATGTACTAC 57.557 37.037 6.39 0.00 0.00 2.73
2624 6125 9.394767 TCACTTATACCGTTAACAGATGTACTA 57.605 33.333 6.39 0.00 0.00 1.82
2625 6126 8.284945 TCACTTATACCGTTAACAGATGTACT 57.715 34.615 6.39 0.00 0.00 2.73
2626 6127 8.915871 TTCACTTATACCGTTAACAGATGTAC 57.084 34.615 6.39 0.00 0.00 2.90
2663 6164 5.298347 GCGTTCCCTATAGAGTAGCAAATT 58.702 41.667 0.00 0.00 0.00 1.82
2669 6170 1.878088 TGCGCGTTCCCTATAGAGTAG 59.122 52.381 8.43 0.00 0.00 2.57
2670 6171 1.605710 GTGCGCGTTCCCTATAGAGTA 59.394 52.381 8.43 0.00 0.00 2.59
2671 6172 0.384669 GTGCGCGTTCCCTATAGAGT 59.615 55.000 8.43 0.00 0.00 3.24
2672 6173 0.669077 AGTGCGCGTTCCCTATAGAG 59.331 55.000 8.43 0.00 0.00 2.43
2673 6174 0.384309 CAGTGCGCGTTCCCTATAGA 59.616 55.000 8.43 0.00 0.00 1.98
2674 6175 0.597637 CCAGTGCGCGTTCCCTATAG 60.598 60.000 8.43 0.00 0.00 1.31
2691 6192 9.624373 TTAAATAAGTTAAACACACTGTACCCA 57.376 29.630 0.00 0.00 0.00 4.51
2711 6212 5.188163 TGGGGATCAGTTCTCACGTTAAATA 59.812 40.000 0.00 0.00 0.00 1.40
2726 6227 1.690219 CCGGACCTTCTGGGGATCAG 61.690 65.000 0.00 0.00 39.28 2.90
2769 6270 0.678048 GGACGCCAGCTCCAAAGATT 60.678 55.000 0.00 0.00 0.00 2.40
2772 6273 2.037136 CAGGACGCCAGCTCCAAAG 61.037 63.158 9.72 0.00 0.00 2.77
2774 6275 4.020617 CCAGGACGCCAGCTCCAA 62.021 66.667 9.72 0.00 0.00 3.53
2786 6288 5.247110 CCTAAGAATAGCAATCTAGCCAGGA 59.753 44.000 0.00 0.00 34.23 3.86
2787 6289 5.486526 CCTAAGAATAGCAATCTAGCCAGG 58.513 45.833 0.00 0.00 34.23 4.45
2796 6298 5.815581 TGTGTGTTCCCTAAGAATAGCAAT 58.184 37.500 0.00 0.00 36.69 3.56
2804 6306 3.630312 GCAAGTTTGTGTGTTCCCTAAGA 59.370 43.478 0.00 0.00 0.00 2.10
2892 6395 1.304052 CAATGTCCCAAGGCCCGAA 60.304 57.895 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.