Multiple sequence alignment - TraesCS4B01G324900

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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 TraesCS4B01G324900 chr4B 100.000 5549 0 0 1 5549 615778144 615772596 0.000000e+00 10248.0
1 TraesCS4B01G324900 chr4D 93.167 4566 212 43 781 5298 484272986 484268473 0.000000e+00 6612.0
2 TraesCS4B01G324900 chr4D 87.940 597 30 27 62 624 484273660 484273072 0.000000e+00 665.0
3 TraesCS4B01G324900 chr4D 95.437 263 6 4 5291 5549 484268314 484268054 1.110000e-111 414.0
4 TraesCS4B01G324900 chr5A 90.638 4593 240 90 781 5268 664536873 664532366 0.000000e+00 5925.0
5 TraesCS4B01G324900 chr5A 89.273 578 39 9 1177 1734 32012214 32012788 0.000000e+00 702.0
6 TraesCS4B01G324900 chr5A 88.360 567 37 19 78 624 664537514 664536957 0.000000e+00 654.0
7 TraesCS4B01G324900 chr4A 89.845 581 37 11 1173 1734 411855689 411855112 0.000000e+00 726.0
8 TraesCS4B01G324900 chr2A 89.863 582 35 10 1173 1734 164918350 164917773 0.000000e+00 726.0
9 TraesCS4B01G324900 chr2A 89.347 582 37 11 1173 1734 780183315 780182739 0.000000e+00 708.0
10 TraesCS4B01G324900 chr6A 89.573 585 37 10 1170 1734 439515419 439515999 0.000000e+00 721.0
11 TraesCS4B01G324900 chr5B 85.052 582 37 20 1173 1734 400140593 400140042 1.050000e-151 547.0
12 TraesCS4B01G324900 chr1B 84.682 581 41 15 1173 1734 4618532 4617981 2.270000e-148 536.0
13 TraesCS4B01G324900 chr3B 84.444 585 41 20 1170 1734 83159070 83159624 1.060000e-146 531.0
14 TraesCS4B01G324900 chr3A 84.509 581 41 22 1173 1734 749829509 749828959 3.810000e-146 529.0
15 TraesCS4B01G324900 chr3D 83.858 508 33 20 1173 1659 216614225 216613746 6.600000e-119 438.0
16 TraesCS4B01G324900 chr6B 100.000 28 0 0 1077 1104 1615172 1615145 1.000000e-02 52.8


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 TraesCS4B01G324900 chr4B 615772596 615778144 5548 True 10248.000000 10248 100.000000 1 5549 1 chr4B.!!$R1 5548
1 TraesCS4B01G324900 chr4D 484268054 484273660 5606 True 2563.666667 6612 92.181333 62 5549 3 chr4D.!!$R1 5487
2 TraesCS4B01G324900 chr5A 664532366 664537514 5148 True 3289.500000 5925 89.499000 78 5268 2 chr5A.!!$R1 5190
3 TraesCS4B01G324900 chr5A 32012214 32012788 574 False 702.000000 702 89.273000 1177 1734 1 chr5A.!!$F1 557
4 TraesCS4B01G324900 chr4A 411855112 411855689 577 True 726.000000 726 89.845000 1173 1734 1 chr4A.!!$R1 561
5 TraesCS4B01G324900 chr2A 164917773 164918350 577 True 726.000000 726 89.863000 1173 1734 1 chr2A.!!$R1 561
6 TraesCS4B01G324900 chr2A 780182739 780183315 576 True 708.000000 708 89.347000 1173 1734 1 chr2A.!!$R2 561
7 TraesCS4B01G324900 chr6A 439515419 439515999 580 False 721.000000 721 89.573000 1170 1734 1 chr6A.!!$F1 564
8 TraesCS4B01G324900 chr5B 400140042 400140593 551 True 547.000000 547 85.052000 1173 1734 1 chr5B.!!$R1 561
9 TraesCS4B01G324900 chr1B 4617981 4618532 551 True 536.000000 536 84.682000 1173 1734 1 chr1B.!!$R1 561
10 TraesCS4B01G324900 chr3B 83159070 83159624 554 False 531.000000 531 84.444000 1170 1734 1 chr3B.!!$F1 564
11 TraesCS4B01G324900 chr3A 749828959 749829509 550 True 529.000000 529 84.509000 1173 1734 1 chr3A.!!$R1 561

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
32 33 0.040692 GCGAGTGGGAAACGGAAAAC 60.041 55.000 0.00 0.00 0.00 2.43 F
946 1002 0.254747 TCCCAACCGGCCTTGATAAG 59.745 55.000 0.00 0.00 0.00 1.73 F
1734 1855 0.170561 GAGCTGCTGGCATTGTTCTG 59.829 55.000 7.01 0.00 44.79 3.02 F
2049 2200 0.800012 GCATACGGCGAAACAGGAAA 59.200 50.000 16.62 0.00 0.00 3.13 F
3638 3801 1.520342 AGAATTCAGAGCGAGCGCC 60.520 57.895 11.66 3.34 43.17 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1201 0.039527 AACCAAGACGAAAATGGCGC 60.040 50.0 0.00 0.0 37.77 6.53 R
2335 2495 0.179936 CCTGTTGCCATCTCTCCCTC 59.820 60.0 0.00 0.0 0.00 4.30 R
3631 3794 0.807275 TGTCAGATTGATGGCGCTCG 60.807 55.0 7.64 0.0 0.00 5.03 R
4012 4175 0.521735 GCTTTTGTCGGGTGATCCAC 59.478 55.0 0.00 0.0 34.36 4.02 R
5135 5317 0.036952 ACGTGATGTTCCTCCTGCTG 60.037 55.0 0.00 0.0 0.00 4.41 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
20 21 2.218603 ACTGGTTTTTACAGCGAGTGG 58.781 47.619 0.00 0.00 39.55 4.00
21 22 1.535462 CTGGTTTTTACAGCGAGTGGG 59.465 52.381 0.00 0.00 0.00 4.61
22 23 1.141254 TGGTTTTTACAGCGAGTGGGA 59.859 47.619 0.00 0.00 0.00 4.37
23 24 2.223745 GGTTTTTACAGCGAGTGGGAA 58.776 47.619 0.00 0.00 0.00 3.97
24 25 2.619646 GGTTTTTACAGCGAGTGGGAAA 59.380 45.455 0.00 0.00 0.00 3.13
25 26 3.549423 GGTTTTTACAGCGAGTGGGAAAC 60.549 47.826 0.00 4.17 32.04 2.78
26 27 1.504359 TTTACAGCGAGTGGGAAACG 58.496 50.000 0.00 0.00 0.00 3.60
27 28 0.320073 TTACAGCGAGTGGGAAACGG 60.320 55.000 0.00 0.00 0.00 4.44
28 29 1.180456 TACAGCGAGTGGGAAACGGA 61.180 55.000 0.00 0.00 0.00 4.69
29 30 1.301401 CAGCGAGTGGGAAACGGAA 60.301 57.895 0.00 0.00 0.00 4.30
30 31 0.882927 CAGCGAGTGGGAAACGGAAA 60.883 55.000 0.00 0.00 0.00 3.13
31 32 0.179040 AGCGAGTGGGAAACGGAAAA 60.179 50.000 0.00 0.00 0.00 2.29
32 33 0.040692 GCGAGTGGGAAACGGAAAAC 60.041 55.000 0.00 0.00 0.00 2.43
33 34 0.589708 CGAGTGGGAAACGGAAAACC 59.410 55.000 0.00 0.00 0.00 3.27
34 35 1.682740 GAGTGGGAAACGGAAAACCA 58.317 50.000 0.00 0.00 0.00 3.67
35 36 2.025898 GAGTGGGAAACGGAAAACCAA 58.974 47.619 0.00 0.00 32.19 3.67
36 37 2.626266 GAGTGGGAAACGGAAAACCAAT 59.374 45.455 0.00 0.00 32.19 3.16
37 38 3.822167 GAGTGGGAAACGGAAAACCAATA 59.178 43.478 0.00 0.00 32.19 1.90
38 39 3.824443 AGTGGGAAACGGAAAACCAATAG 59.176 43.478 0.00 0.00 32.19 1.73
39 40 2.559231 TGGGAAACGGAAAACCAATAGC 59.441 45.455 0.00 0.00 0.00 2.97
40 41 2.559231 GGGAAACGGAAAACCAATAGCA 59.441 45.455 0.00 0.00 0.00 3.49
41 42 3.366985 GGGAAACGGAAAACCAATAGCAG 60.367 47.826 0.00 0.00 0.00 4.24
42 43 3.366985 GGAAACGGAAAACCAATAGCAGG 60.367 47.826 0.00 0.00 0.00 4.85
43 44 1.834188 ACGGAAAACCAATAGCAGGG 58.166 50.000 0.00 0.00 0.00 4.45
44 45 1.074889 ACGGAAAACCAATAGCAGGGT 59.925 47.619 0.00 0.00 39.65 4.34
45 46 1.472480 CGGAAAACCAATAGCAGGGTG 59.528 52.381 0.00 0.00 37.50 4.61
46 47 1.824852 GGAAAACCAATAGCAGGGTGG 59.175 52.381 0.00 0.00 37.50 4.61
47 48 1.824852 GAAAACCAATAGCAGGGTGGG 59.175 52.381 0.00 0.00 37.50 4.61
48 49 1.080638 AAACCAATAGCAGGGTGGGA 58.919 50.000 0.00 0.00 37.50 4.37
49 50 1.080638 AACCAATAGCAGGGTGGGAA 58.919 50.000 0.00 0.00 37.50 3.97
50 51 1.080638 ACCAATAGCAGGGTGGGAAA 58.919 50.000 0.00 0.00 36.69 3.13
51 52 1.005924 ACCAATAGCAGGGTGGGAAAG 59.994 52.381 0.00 0.00 36.69 2.62
52 53 1.106285 CAATAGCAGGGTGGGAAAGC 58.894 55.000 0.00 0.00 0.00 3.51
53 54 0.394352 AATAGCAGGGTGGGAAAGCG 60.394 55.000 0.00 0.00 0.00 4.68
54 55 2.270874 ATAGCAGGGTGGGAAAGCGG 62.271 60.000 0.00 0.00 0.00 5.52
143 144 2.108976 CCCGTCCGTGCATATGCT 59.891 61.111 27.13 0.00 42.66 3.79
193 214 3.541632 ACAACTACCGCCATTCATAAGG 58.458 45.455 0.00 0.00 0.00 2.69
426 457 2.044555 TCGTCGACGATGCCTCCTT 61.045 57.895 34.97 0.00 44.22 3.36
452 483 9.354673 TCTTCTTGGTTGATTCTTCTTGTTTAT 57.645 29.630 0.00 0.00 0.00 1.40
453 484 9.971922 CTTCTTGGTTGATTCTTCTTGTTTATT 57.028 29.630 0.00 0.00 0.00 1.40
459 490 9.989869 GGTTGATTCTTCTTGTTTATTACTAGC 57.010 33.333 0.00 0.00 30.81 3.42
489 529 3.118555 TCTGGTTCGTTCCTTGTTCTTGA 60.119 43.478 1.16 0.00 0.00 3.02
561 602 3.645975 CACCACCCACGTTGACGC 61.646 66.667 3.05 0.00 44.43 5.19
584 625 2.143419 GGACCATCGCCCATCCTCT 61.143 63.158 0.00 0.00 0.00 3.69
586 627 1.383109 ACCATCGCCCATCCTCTCA 60.383 57.895 0.00 0.00 0.00 3.27
619 660 2.499289 TCCTCTGCTTCCTCTCATGAAC 59.501 50.000 0.00 0.00 0.00 3.18
624 665 2.842496 TGCTTCCTCTCATGAACCTGAT 59.158 45.455 0.00 0.00 0.00 2.90
626 667 4.263639 TGCTTCCTCTCATGAACCTGATTT 60.264 41.667 0.00 0.00 0.00 2.17
627 668 5.045651 TGCTTCCTCTCATGAACCTGATTTA 60.046 40.000 0.00 0.00 0.00 1.40
630 671 7.633772 GCTTCCTCTCATGAACCTGATTTACTA 60.634 40.741 0.00 0.00 0.00 1.82
631 672 7.353414 TCCTCTCATGAACCTGATTTACTAG 57.647 40.000 0.00 0.00 0.00 2.57
632 673 5.988561 CCTCTCATGAACCTGATTTACTAGC 59.011 44.000 0.00 0.00 0.00 3.42
634 675 7.014711 CCTCTCATGAACCTGATTTACTAGCTA 59.985 40.741 0.00 0.00 0.00 3.32
636 677 7.342026 TCTCATGAACCTGATTTACTAGCTACA 59.658 37.037 0.00 0.00 0.00 2.74
638 679 7.928167 TCATGAACCTGATTTACTAGCTACATG 59.072 37.037 0.00 0.00 0.00 3.21
640 681 6.156256 TGAACCTGATTTACTAGCTACATGGT 59.844 38.462 0.00 0.00 0.00 3.55
642 683 5.661312 ACCTGATTTACTAGCTACATGGTGA 59.339 40.000 0.00 0.00 0.00 4.02
643 684 6.327626 ACCTGATTTACTAGCTACATGGTGAT 59.672 38.462 0.00 0.00 0.00 3.06
644 685 6.870965 CCTGATTTACTAGCTACATGGTGATC 59.129 42.308 0.00 0.00 0.00 2.92
645 686 7.360113 TGATTTACTAGCTACATGGTGATCA 57.640 36.000 0.00 0.00 0.00 2.92
646 687 7.436933 TGATTTACTAGCTACATGGTGATCAG 58.563 38.462 0.00 0.00 0.00 2.90
647 688 5.791336 TTACTAGCTACATGGTGATCAGG 57.209 43.478 0.00 0.00 0.00 3.86
648 689 3.916035 ACTAGCTACATGGTGATCAGGA 58.084 45.455 0.00 0.00 0.00 3.86
649 690 4.290093 ACTAGCTACATGGTGATCAGGAA 58.710 43.478 0.00 0.00 0.00 3.36
650 691 3.550437 AGCTACATGGTGATCAGGAAC 57.450 47.619 0.00 0.00 0.00 3.62
651 692 3.110705 AGCTACATGGTGATCAGGAACT 58.889 45.455 0.00 0.00 43.88 3.01
652 693 3.521126 AGCTACATGGTGATCAGGAACTT 59.479 43.478 0.00 0.00 34.60 2.66
653 694 3.624861 GCTACATGGTGATCAGGAACTTG 59.375 47.826 0.00 0.00 34.60 3.16
654 695 3.077484 ACATGGTGATCAGGAACTTGG 57.923 47.619 0.00 0.00 34.60 3.61
655 696 2.376518 ACATGGTGATCAGGAACTTGGT 59.623 45.455 0.00 0.00 34.60 3.67
656 697 3.181429 ACATGGTGATCAGGAACTTGGTT 60.181 43.478 0.00 0.00 34.60 3.67
657 698 3.140325 TGGTGATCAGGAACTTGGTTC 57.860 47.619 0.00 2.19 41.32 3.62
669 710 5.899120 GAACTTGGTTCCTTATTTCCTCC 57.101 43.478 0.00 0.00 36.65 4.30
670 711 3.951663 ACTTGGTTCCTTATTTCCTCCG 58.048 45.455 0.00 0.00 0.00 4.63
671 712 3.279434 CTTGGTTCCTTATTTCCTCCGG 58.721 50.000 0.00 0.00 0.00 5.14
672 713 1.064979 TGGTTCCTTATTTCCTCCGGC 60.065 52.381 0.00 0.00 0.00 6.13
673 714 1.296727 GTTCCTTATTTCCTCCGGCG 58.703 55.000 0.00 0.00 0.00 6.46
674 715 0.906775 TTCCTTATTTCCTCCGGCGT 59.093 50.000 6.01 0.00 0.00 5.68
675 716 0.462789 TCCTTATTTCCTCCGGCGTC 59.537 55.000 6.01 0.00 0.00 5.19
676 717 0.464452 CCTTATTTCCTCCGGCGTCT 59.536 55.000 6.01 0.00 0.00 4.18
677 718 1.538419 CCTTATTTCCTCCGGCGTCTC 60.538 57.143 6.01 0.00 0.00 3.36
678 719 0.462789 TTATTTCCTCCGGCGTCTCC 59.537 55.000 6.01 0.00 0.00 3.71
679 720 0.396695 TATTTCCTCCGGCGTCTCCT 60.397 55.000 6.01 0.00 0.00 3.69
680 721 1.677637 ATTTCCTCCGGCGTCTCCTC 61.678 60.000 6.01 0.00 0.00 3.71
681 722 2.783122 TTTCCTCCGGCGTCTCCTCT 62.783 60.000 6.01 0.00 0.00 3.69
682 723 2.756283 CCTCCGGCGTCTCCTCTT 60.756 66.667 6.01 0.00 0.00 2.85
683 724 2.352032 CCTCCGGCGTCTCCTCTTT 61.352 63.158 6.01 0.00 0.00 2.52
684 725 1.153745 CTCCGGCGTCTCCTCTTTG 60.154 63.158 6.01 0.00 0.00 2.77
685 726 2.125512 CCGGCGTCTCCTCTTTGG 60.126 66.667 6.01 0.00 37.10 3.28
686 727 2.646175 CCGGCGTCTCCTCTTTGGA 61.646 63.158 6.01 0.00 43.86 3.53
712 753 6.693113 GGATAGATTCCGTTGAATTTTGCTTC 59.307 38.462 0.00 0.00 41.30 3.86
714 755 3.378911 TTCCGTTGAATTTTGCTTCCC 57.621 42.857 0.00 0.00 0.00 3.97
715 756 2.593026 TCCGTTGAATTTTGCTTCCCT 58.407 42.857 0.00 0.00 0.00 4.20
716 757 2.556622 TCCGTTGAATTTTGCTTCCCTC 59.443 45.455 0.00 0.00 0.00 4.30
718 759 2.352715 CGTTGAATTTTGCTTCCCTCCC 60.353 50.000 0.00 0.00 0.00 4.30
719 760 2.632512 GTTGAATTTTGCTTCCCTCCCA 59.367 45.455 0.00 0.00 0.00 4.37
720 761 2.969628 TGAATTTTGCTTCCCTCCCAA 58.030 42.857 0.00 0.00 0.00 4.12
721 762 3.312890 TGAATTTTGCTTCCCTCCCAAA 58.687 40.909 0.00 0.00 0.00 3.28
722 763 3.909364 TGAATTTTGCTTCCCTCCCAAAT 59.091 39.130 0.00 0.00 0.00 2.32
723 764 4.350520 TGAATTTTGCTTCCCTCCCAAATT 59.649 37.500 0.00 0.00 0.00 1.82
724 765 4.558226 ATTTTGCTTCCCTCCCAAATTC 57.442 40.909 0.00 0.00 0.00 2.17
725 766 2.999185 TTGCTTCCCTCCCAAATTCT 57.001 45.000 0.00 0.00 0.00 2.40
726 767 2.999185 TGCTTCCCTCCCAAATTCTT 57.001 45.000 0.00 0.00 0.00 2.52
728 769 3.586429 TGCTTCCCTCCCAAATTCTTTT 58.414 40.909 0.00 0.00 0.00 2.27
731 772 5.604650 TGCTTCCCTCCCAAATTCTTTTAAA 59.395 36.000 0.00 0.00 0.00 1.52
733 774 6.426937 GCTTCCCTCCCAAATTCTTTTAAAAC 59.573 38.462 0.00 0.00 0.00 2.43
734 775 7.684317 TTCCCTCCCAAATTCTTTTAAAACT 57.316 32.000 0.00 0.00 0.00 2.66
736 777 8.185506 TCCCTCCCAAATTCTTTTAAAACTAC 57.814 34.615 0.00 0.00 0.00 2.73
738 779 8.593679 CCCTCCCAAATTCTTTTAAAACTACAT 58.406 33.333 0.00 0.00 0.00 2.29
756 797 9.804758 AAACTACATACTAGATTACTCTGCAAC 57.195 33.333 0.00 0.00 32.66 4.17
757 798 8.754991 ACTACATACTAGATTACTCTGCAACT 57.245 34.615 0.00 0.00 32.66 3.16
758 799 9.191479 ACTACATACTAGATTACTCTGCAACTT 57.809 33.333 0.00 0.00 32.66 2.66
759 800 9.672086 CTACATACTAGATTACTCTGCAACTTC 57.328 37.037 0.00 0.00 32.66 3.01
760 801 8.299990 ACATACTAGATTACTCTGCAACTTCT 57.700 34.615 0.00 0.00 32.66 2.85
761 802 8.754080 ACATACTAGATTACTCTGCAACTTCTT 58.246 33.333 0.00 0.00 32.66 2.52
762 803 9.593134 CATACTAGATTACTCTGCAACTTCTTT 57.407 33.333 0.00 0.00 32.66 2.52
764 805 8.910351 ACTAGATTACTCTGCAACTTCTTTTT 57.090 30.769 0.00 0.00 32.66 1.94
791 832 8.109705 TCTTTTTGAGTAAATGCTCTGCAATA 57.890 30.769 0.00 0.00 43.62 1.90
795 836 6.856135 TGAGTAAATGCTCTGCAATATCTG 57.144 37.500 0.00 0.00 43.62 2.90
819 860 9.534565 CTGCTAGATTACTCTGTAATTTTGCTA 57.465 33.333 19.11 10.21 32.66 3.49
856 897 9.111613 TCTACTAGATTACTCTGTAGTTTCTGC 57.888 37.037 0.00 0.00 36.09 4.26
857 898 7.102847 ACTAGATTACTCTGTAGTTTCTGCC 57.897 40.000 0.00 0.00 37.15 4.85
858 899 6.663953 ACTAGATTACTCTGTAGTTTCTGCCA 59.336 38.462 0.00 0.00 37.15 4.92
859 900 5.971763 AGATTACTCTGTAGTTTCTGCCAG 58.028 41.667 0.00 0.00 37.15 4.85
872 913 5.530543 AGTTTCTGCCAGAGAAGAAGAAAAG 59.469 40.000 0.00 0.00 41.86 2.27
932 988 1.416401 GGATAGCGAGGTCAATCCCAA 59.584 52.381 0.00 0.00 36.75 4.12
939 995 2.355115 GTCAATCCCAACCGGCCT 59.645 61.111 0.00 0.00 0.00 5.19
941 997 1.304052 TCAATCCCAACCGGCCTTG 60.304 57.895 0.00 0.00 0.00 3.61
942 998 1.304052 CAATCCCAACCGGCCTTGA 60.304 57.895 0.00 0.00 0.00 3.02
943 999 0.684153 CAATCCCAACCGGCCTTGAT 60.684 55.000 0.00 0.00 0.00 2.57
945 1001 0.923358 ATCCCAACCGGCCTTGATAA 59.077 50.000 0.00 0.00 0.00 1.75
946 1002 0.254747 TCCCAACCGGCCTTGATAAG 59.745 55.000 0.00 0.00 0.00 1.73
947 1003 0.254747 CCCAACCGGCCTTGATAAGA 59.745 55.000 0.00 0.00 0.00 2.10
948 1004 1.133792 CCCAACCGGCCTTGATAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
950 1006 2.222027 CAACCGGCCTTGATAAGATCC 58.778 52.381 0.00 0.00 0.00 3.36
988 1046 1.409790 CAGACTGCAGGATCTCTCTGG 59.590 57.143 19.93 2.37 33.16 3.86
1099 1157 6.472887 GGCCAAGGTACATACATACATACAT 58.527 40.000 0.00 0.00 0.00 2.29
1100 1158 7.310796 GGGCCAAGGTACATACATACATACATA 60.311 40.741 4.39 0.00 0.00 2.29
1101 1159 7.548075 GGCCAAGGTACATACATACATACATAC 59.452 40.741 0.00 0.00 0.00 2.39
1102 1160 8.092068 GCCAAGGTACATACATACATACATACA 58.908 37.037 0.00 0.00 0.00 2.29
1113 1171 8.327941 ACATACATACATACATGCTGAATTCC 57.672 34.615 2.27 0.00 0.00 3.01
1133 1191 2.205074 CGAAATTCGACCATCTCCAGG 58.795 52.381 10.18 0.00 43.74 4.45
1134 1192 2.159099 CGAAATTCGACCATCTCCAGGA 60.159 50.000 10.18 0.00 43.74 3.86
1139 1197 0.461961 CGACCATCTCCAGGAACCTC 59.538 60.000 0.00 0.00 0.00 3.85
1143 1201 0.179089 CATCTCCAGGAACCTCTGCG 60.179 60.000 0.00 0.00 33.64 5.18
1157 1228 3.027170 CTGCGCGCCATTTTCGTCT 62.027 57.895 30.77 0.00 0.00 4.18
1190 1261 3.413327 TGGGTTCGCAGCAAGTTTAATA 58.587 40.909 0.00 0.00 0.00 0.98
1198 1269 4.318121 CGCAGCAAGTTTAATAGATCGTCC 60.318 45.833 0.00 0.00 0.00 4.79
1216 1287 1.077005 TCCTTGGGCTTAATTGCAGGT 59.923 47.619 0.00 0.00 34.04 4.00
1247 1318 1.066573 CGAGGAACAGCATGGAGTTCT 60.067 52.381 0.00 0.00 43.62 3.01
1266 1337 4.738998 CATGGAGGCGCCCCACAA 62.739 66.667 31.15 15.64 36.36 3.33
1327 1399 3.659183 ATCCCTTCCCTGTTCATTCTG 57.341 47.619 0.00 0.00 0.00 3.02
1336 1409 5.272402 TCCCTGTTCATTCTGTCTATCTGA 58.728 41.667 0.00 0.00 0.00 3.27
1356 1429 4.507710 TGACAGAGTAATTCACTGCATCC 58.492 43.478 0.00 0.00 37.72 3.51
1361 1434 7.168219 ACAGAGTAATTCACTGCATCCTTTTA 58.832 34.615 0.00 0.00 37.72 1.52
1363 1436 8.127327 CAGAGTAATTCACTGCATCCTTTTATG 58.873 37.037 0.00 0.00 37.72 1.90
1382 1472 6.539649 TTATGCTATGCGTCTGGTAAATTC 57.460 37.500 0.00 0.00 0.00 2.17
1437 1529 7.685398 GCCTTTTTCTTTCTTTCATTCCAGTCT 60.685 37.037 0.00 0.00 0.00 3.24
1610 1727 3.303132 GCTGTCAAACAAACAGTAGACCG 60.303 47.826 5.29 0.00 44.79 4.79
1734 1855 0.170561 GAGCTGCTGGCATTGTTCTG 59.829 55.000 7.01 0.00 44.79 3.02
1802 1953 1.098050 GCATGAGGCAGTACCCAAAG 58.902 55.000 0.00 0.00 43.97 2.77
1859 2010 2.686816 CGCGTCCTTCCGGCAAAAT 61.687 57.895 0.00 0.00 0.00 1.82
1935 2086 1.298713 CCGATGAACTCCGAGCTCG 60.299 63.158 29.06 29.06 39.44 5.03
2049 2200 0.800012 GCATACGGCGAAACAGGAAA 59.200 50.000 16.62 0.00 0.00 3.13
2118 2269 3.196469 TCAGCTGACCAAGAGGAGTAATG 59.804 47.826 13.74 0.00 38.69 1.90
2119 2270 2.503356 AGCTGACCAAGAGGAGTAATGG 59.497 50.000 0.00 0.00 38.69 3.16
2120 2271 2.911484 CTGACCAAGAGGAGTAATGGC 58.089 52.381 0.00 0.00 38.69 4.40
2137 2294 2.747022 CGGTGGTGGTGGTGATGA 59.253 61.111 0.00 0.00 0.00 2.92
2335 2495 1.960040 TACCACCAGCAGGATCGCAG 61.960 60.000 0.35 0.00 38.69 5.18
2377 2537 2.260154 TGCACGACAATGGCAGTGG 61.260 57.895 19.96 4.75 35.35 4.00
2930 3093 4.200283 CAGCTCTCCGACCGGCTC 62.200 72.222 0.00 0.00 32.30 4.70
3356 3519 2.124151 GGGGACTACTACGGCGGA 60.124 66.667 13.24 0.00 0.00 5.54
3383 3546 2.364317 CCGGAAGAGGAGAGGGCA 60.364 66.667 0.00 0.00 0.00 5.36
3419 3582 2.355115 GGGTTCGGCATCAAGGGT 59.645 61.111 0.00 0.00 0.00 4.34
3631 3794 4.225208 GCTGTTGTTTCAGAATTCAGAGC 58.775 43.478 8.44 0.74 37.61 4.09
3635 3798 2.738846 TGTTTCAGAATTCAGAGCGAGC 59.261 45.455 8.44 0.00 0.00 5.03
3638 3801 1.520342 AGAATTCAGAGCGAGCGCC 60.520 57.895 11.66 3.34 43.17 6.53
3684 3847 2.847234 AACTCCACCGAGGTGCCA 60.847 61.111 16.39 4.58 44.16 4.92
3735 3898 2.095364 GCCTGATGAAATGATGATCCGC 60.095 50.000 0.00 0.00 0.00 5.54
3833 3996 3.578716 AGCTCAAGTGCTTCTGGTAAGTA 59.421 43.478 0.00 0.00 40.93 2.24
3834 3997 3.929610 GCTCAAGTGCTTCTGGTAAGTAG 59.070 47.826 0.00 0.00 0.00 2.57
3835 3998 4.322049 GCTCAAGTGCTTCTGGTAAGTAGA 60.322 45.833 0.00 0.00 0.00 2.59
3836 3999 5.392767 TCAAGTGCTTCTGGTAAGTAGAG 57.607 43.478 0.00 0.00 0.00 2.43
3837 4000 3.878160 AGTGCTTCTGGTAAGTAGAGC 57.122 47.619 0.00 0.00 0.00 4.09
3873 4036 6.250344 TGCTCATGTCTGAATTTTCTTCAG 57.750 37.500 8.35 8.35 45.38 3.02
3924 4087 4.389374 GAAATGTTGTCTCAGAACCAGGA 58.611 43.478 0.00 0.00 0.00 3.86
3926 4089 4.647564 ATGTTGTCTCAGAACCAGGAAT 57.352 40.909 0.00 0.00 0.00 3.01
4056 4219 2.672307 AGAGCCGTCCTCGTCGTT 60.672 61.111 0.00 0.00 45.54 3.85
4095 4258 3.187699 CTCCGGCGATCACCTCTCG 62.188 68.421 9.30 0.00 39.11 4.04
4179 4342 2.345991 CCTCCGGAAGCCGTTTCA 59.654 61.111 5.23 0.00 46.80 2.69
4181 4344 1.292223 CTCCGGAAGCCGTTTCAGA 59.708 57.895 5.23 0.00 46.80 3.27
4182 4345 1.005394 TCCGGAAGCCGTTTCAGAC 60.005 57.895 0.00 0.00 46.80 3.51
4347 4510 2.990479 GGGCTGTGGAGATCCGTT 59.010 61.111 0.00 0.00 39.43 4.44
4362 4525 1.300620 CGTTCAGACGTGGCTGGAA 60.301 57.895 2.28 0.00 44.08 3.53
4624 4787 4.468153 ACAGTACATTTTGGGGTGTGTTTT 59.532 37.500 0.00 0.00 0.00 2.43
4644 4808 7.271438 GTGTTTTTCTCTGTTCTTCTTGTGTTC 59.729 37.037 0.00 0.00 0.00 3.18
4695 4859 3.387699 TGAGATGTTGGTGAGTGAGTGAA 59.612 43.478 0.00 0.00 0.00 3.18
4696 4860 3.733337 AGATGTTGGTGAGTGAGTGAAC 58.267 45.455 0.00 0.00 0.00 3.18
4820 4988 6.939163 AGGATTCTTATTCATGCCATGAGTAC 59.061 38.462 9.19 0.00 40.94 2.73
4825 4993 2.696989 TCATGCCATGAGTACACTGG 57.303 50.000 2.53 0.00 33.59 4.00
4826 4994 1.019673 CATGCCATGAGTACACTGGC 58.980 55.000 20.41 20.41 43.76 4.85
4827 4995 0.914644 ATGCCATGAGTACACTGGCT 59.085 50.000 24.73 13.42 43.80 4.75
4828 4996 0.036105 TGCCATGAGTACACTGGCTG 60.036 55.000 24.73 5.70 43.80 4.85
4829 4997 0.250234 GCCATGAGTACACTGGCTGA 59.750 55.000 20.11 0.00 42.10 4.26
4830 4998 2.009042 GCCATGAGTACACTGGCTGAC 61.009 57.143 20.11 0.00 42.10 3.51
4831 4999 1.276138 CCATGAGTACACTGGCTGACA 59.724 52.381 0.00 0.00 0.00 3.58
4859 5032 3.213206 ACAGTCCATCTGAAGCAACAA 57.787 42.857 1.79 0.00 46.27 2.83
4885 5058 1.281899 GGTACGCTACGACGACTAGT 58.718 55.000 0.00 0.00 36.70 2.57
4886 5059 1.256635 GGTACGCTACGACGACTAGTC 59.743 57.143 13.18 13.18 46.16 2.59
5093 5269 2.665000 CTCTGCTTCTTCCCGGCA 59.335 61.111 0.00 0.00 34.66 5.69
5110 5291 1.239968 GCACACCTGCCCAAAGAGAG 61.240 60.000 0.00 0.00 37.45 3.20
5115 5296 2.048222 TGCCCAAAGAGAGACGCG 60.048 61.111 3.53 3.53 0.00 6.01
5118 5299 1.448540 CCCAAAGAGAGACGCGCAT 60.449 57.895 5.73 0.00 0.00 4.73
5119 5300 1.699656 CCCAAAGAGAGACGCGCATG 61.700 60.000 5.73 0.00 0.00 4.06
5135 5317 2.028045 CGCATGTACACACGTCAGATTC 59.972 50.000 0.00 0.00 0.00 2.52
5140 5322 1.788258 ACACACGTCAGATTCAGCAG 58.212 50.000 0.00 0.00 0.00 4.24
5141 5323 1.073964 CACACGTCAGATTCAGCAGG 58.926 55.000 0.00 0.00 0.00 4.85
5149 5331 2.842496 TCAGATTCAGCAGGAGGAACAT 59.158 45.455 0.00 0.00 0.00 2.71
5155 5337 1.204704 CAGCAGGAGGAACATCACGTA 59.795 52.381 0.00 0.00 0.00 3.57
5188 5370 1.477295 CGAGTAAGAACTGGGGAGGAC 59.523 57.143 0.00 0.00 35.56 3.85
5189 5371 1.477295 GAGTAAGAACTGGGGAGGACG 59.523 57.143 0.00 0.00 35.56 4.79
5190 5372 1.076677 AGTAAGAACTGGGGAGGACGA 59.923 52.381 0.00 0.00 33.57 4.20
5278 5470 4.802051 GGCATGGCTCGCTGGGAA 62.802 66.667 12.86 0.00 0.00 3.97
5283 5475 4.400961 GGCTCGCTGGGAAGCTGT 62.401 66.667 12.94 0.00 0.00 4.40
5284 5476 3.123620 GCTCGCTGGGAAGCTGTG 61.124 66.667 0.00 0.00 0.00 3.66
5285 5477 3.123620 CTCGCTGGGAAGCTGTGC 61.124 66.667 0.00 0.00 0.00 4.57
5286 5478 3.602513 CTCGCTGGGAAGCTGTGCT 62.603 63.158 0.00 0.00 42.56 4.40
5288 5480 3.060615 GCTGGGAAGCTGTGCTGG 61.061 66.667 0.00 0.00 39.62 4.85
5289 5481 2.752358 CTGGGAAGCTGTGCTGGA 59.248 61.111 0.00 0.00 39.62 3.86
5358 5711 2.359107 CCTTGCAGAGCGGCAGAA 60.359 61.111 1.45 0.00 45.88 3.02
5359 5712 2.396955 CCTTGCAGAGCGGCAGAAG 61.397 63.158 1.45 0.00 45.88 2.85
5360 5713 3.036783 CTTGCAGAGCGGCAGAAGC 62.037 63.158 1.45 1.04 45.88 3.86
5361 5714 3.830464 TTGCAGAGCGGCAGAAGCA 62.830 57.895 1.45 3.96 45.88 3.91
5362 5715 3.497932 GCAGAGCGGCAGAAGCAG 61.498 66.667 1.45 0.00 44.61 4.24
5392 5748 0.525761 GCCGTTTAAGCTTGGCATGA 59.474 50.000 18.11 0.00 46.76 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.218603 CCACTCGCTGTAAAAACCAGT 58.781 47.619 0.00 0.00 32.41 4.00
1 2 1.535462 CCCACTCGCTGTAAAAACCAG 59.465 52.381 0.00 0.00 0.00 4.00
4 5 3.624900 GTTTCCCACTCGCTGTAAAAAC 58.375 45.455 0.00 0.00 0.00 2.43
6 7 1.868498 CGTTTCCCACTCGCTGTAAAA 59.132 47.619 0.00 0.00 0.00 1.52
7 8 1.504359 CGTTTCCCACTCGCTGTAAA 58.496 50.000 0.00 0.00 0.00 2.01
8 9 0.320073 CCGTTTCCCACTCGCTGTAA 60.320 55.000 0.00 0.00 0.00 2.41
9 10 1.180456 TCCGTTTCCCACTCGCTGTA 61.180 55.000 0.00 0.00 0.00 2.74
10 11 2.030562 CCGTTTCCCACTCGCTGT 59.969 61.111 0.00 0.00 0.00 4.40
11 12 0.882927 TTTCCGTTTCCCACTCGCTG 60.883 55.000 0.00 0.00 0.00 5.18
12 13 0.179040 TTTTCCGTTTCCCACTCGCT 60.179 50.000 0.00 0.00 0.00 4.93
13 14 0.040692 GTTTTCCGTTTCCCACTCGC 60.041 55.000 0.00 0.00 0.00 5.03
14 15 0.589708 GGTTTTCCGTTTCCCACTCG 59.410 55.000 0.00 0.00 0.00 4.18
15 16 1.682740 TGGTTTTCCGTTTCCCACTC 58.317 50.000 0.00 0.00 44.36 3.51
16 17 2.146920 TTGGTTTTCCGTTTCCCACT 57.853 45.000 0.00 0.00 44.36 4.00
17 18 3.613193 GCTATTGGTTTTCCGTTTCCCAC 60.613 47.826 0.00 0.00 44.36 4.61
18 19 2.559231 GCTATTGGTTTTCCGTTTCCCA 59.441 45.455 0.00 0.00 44.36 4.37
19 20 2.559231 TGCTATTGGTTTTCCGTTTCCC 59.441 45.455 0.00 0.00 44.36 3.97
20 21 3.366985 CCTGCTATTGGTTTTCCGTTTCC 60.367 47.826 0.00 0.00 44.36 3.13
21 22 3.366985 CCCTGCTATTGGTTTTCCGTTTC 60.367 47.826 0.00 0.00 44.36 2.78
22 23 2.560981 CCCTGCTATTGGTTTTCCGTTT 59.439 45.455 0.00 0.00 44.36 3.60
23 24 2.167662 CCCTGCTATTGGTTTTCCGTT 58.832 47.619 0.00 0.00 44.36 4.44
24 25 1.074889 ACCCTGCTATTGGTTTTCCGT 59.925 47.619 0.00 0.00 44.36 4.69
25 26 1.472480 CACCCTGCTATTGGTTTTCCG 59.528 52.381 0.00 0.00 44.36 4.30
26 27 1.824852 CCACCCTGCTATTGGTTTTCC 59.175 52.381 0.00 0.00 41.14 3.13
27 28 1.824852 CCCACCCTGCTATTGGTTTTC 59.175 52.381 0.00 0.00 30.70 2.29
28 29 1.431243 TCCCACCCTGCTATTGGTTTT 59.569 47.619 0.00 0.00 30.70 2.43
29 30 1.080638 TCCCACCCTGCTATTGGTTT 58.919 50.000 0.00 0.00 30.70 3.27
30 31 1.080638 TTCCCACCCTGCTATTGGTT 58.919 50.000 0.00 0.00 30.70 3.67
31 32 1.005924 CTTTCCCACCCTGCTATTGGT 59.994 52.381 0.00 0.00 34.40 3.67
32 33 1.767759 CTTTCCCACCCTGCTATTGG 58.232 55.000 0.00 0.00 0.00 3.16
33 34 1.106285 GCTTTCCCACCCTGCTATTG 58.894 55.000 0.00 0.00 0.00 1.90
34 35 0.394352 CGCTTTCCCACCCTGCTATT 60.394 55.000 0.00 0.00 0.00 1.73
35 36 1.224592 CGCTTTCCCACCCTGCTAT 59.775 57.895 0.00 0.00 0.00 2.97
36 37 2.668632 CGCTTTCCCACCCTGCTA 59.331 61.111 0.00 0.00 0.00 3.49
37 38 4.351054 CCGCTTTCCCACCCTGCT 62.351 66.667 0.00 0.00 0.00 4.24
55 56 0.323451 AAAAGCTAAGCCTTCCCCGG 60.323 55.000 0.00 0.00 0.00 5.73
56 57 0.811281 CAAAAGCTAAGCCTTCCCCG 59.189 55.000 0.00 0.00 0.00 5.73
57 58 1.186200 CCAAAAGCTAAGCCTTCCCC 58.814 55.000 0.00 0.00 0.00 4.81
58 59 0.532573 GCCAAAAGCTAAGCCTTCCC 59.467 55.000 0.00 0.00 38.99 3.97
59 60 0.171231 CGCCAAAAGCTAAGCCTTCC 59.829 55.000 0.00 0.00 40.39 3.46
60 61 1.131315 CTCGCCAAAAGCTAAGCCTTC 59.869 52.381 0.00 0.00 40.39 3.46
143 144 4.344865 GCGGGACAGGAGCCCAAA 62.345 66.667 0.00 0.00 46.36 3.28
251 282 1.406887 GGGTCAGCGAAGAATGCCTTA 60.407 52.381 0.00 0.00 34.68 2.69
252 283 0.678048 GGGTCAGCGAAGAATGCCTT 60.678 55.000 0.00 0.00 37.93 4.35
253 284 1.078143 GGGTCAGCGAAGAATGCCT 60.078 57.895 0.00 0.00 0.00 4.75
254 285 2.464459 CGGGTCAGCGAAGAATGCC 61.464 63.158 0.00 0.00 0.00 4.40
426 457 7.645058 AAACAAGAAGAATCAACCAAGAAGA 57.355 32.000 0.00 0.00 0.00 2.87
452 483 3.328382 ACCAGACGCAAATGCTAGTAA 57.672 42.857 3.63 0.00 39.32 2.24
453 484 3.259064 GAACCAGACGCAAATGCTAGTA 58.741 45.455 3.63 0.00 39.32 1.82
454 485 2.076863 GAACCAGACGCAAATGCTAGT 58.923 47.619 3.63 0.00 39.32 2.57
455 486 1.061131 CGAACCAGACGCAAATGCTAG 59.939 52.381 3.63 0.00 39.32 3.42
456 487 1.075542 CGAACCAGACGCAAATGCTA 58.924 50.000 3.63 0.00 39.32 3.49
457 488 0.884704 ACGAACCAGACGCAAATGCT 60.885 50.000 3.63 0.00 39.32 3.79
458 489 0.040425 AACGAACCAGACGCAAATGC 60.040 50.000 0.00 0.00 37.78 3.56
459 490 1.399727 GGAACGAACCAGACGCAAATG 60.400 52.381 0.00 0.00 0.00 2.32
460 491 0.872388 GGAACGAACCAGACGCAAAT 59.128 50.000 0.00 0.00 0.00 2.32
469 509 3.269538 TCAAGAACAAGGAACGAACCA 57.730 42.857 0.00 0.00 0.00 3.67
489 529 0.729116 CAGATCGCACGCATTTCCTT 59.271 50.000 0.00 0.00 0.00 3.36
577 618 4.262549 GGAGGAGATGAACATGAGAGGATG 60.263 50.000 0.00 0.00 0.00 3.51
578 619 3.903090 GGAGGAGATGAACATGAGAGGAT 59.097 47.826 0.00 0.00 0.00 3.24
584 625 2.433604 GCAGAGGAGGAGATGAACATGA 59.566 50.000 0.00 0.00 0.00 3.07
586 627 2.761809 AGCAGAGGAGGAGATGAACAT 58.238 47.619 0.00 0.00 0.00 2.71
619 660 6.161855 TCACCATGTAGCTAGTAAATCAGG 57.838 41.667 0.00 0.00 0.00 3.86
624 665 5.897250 TCCTGATCACCATGTAGCTAGTAAA 59.103 40.000 0.00 0.00 0.00 2.01
626 667 5.061721 TCCTGATCACCATGTAGCTAGTA 57.938 43.478 0.00 0.00 0.00 1.82
627 668 3.916035 TCCTGATCACCATGTAGCTAGT 58.084 45.455 0.00 0.00 0.00 2.57
630 671 3.110705 AGTTCCTGATCACCATGTAGCT 58.889 45.455 0.00 0.00 0.00 3.32
631 672 3.550437 AGTTCCTGATCACCATGTAGC 57.450 47.619 0.00 0.00 0.00 3.58
632 673 4.194640 CCAAGTTCCTGATCACCATGTAG 58.805 47.826 0.00 0.00 0.00 2.74
634 675 2.376518 ACCAAGTTCCTGATCACCATGT 59.623 45.455 0.00 0.00 0.00 3.21
636 677 3.690460 GAACCAAGTTCCTGATCACCAT 58.310 45.455 0.00 0.00 36.65 3.55
647 688 4.395231 CGGAGGAAATAAGGAACCAAGTTC 59.605 45.833 0.00 0.00 41.32 3.01
648 689 4.332828 CGGAGGAAATAAGGAACCAAGTT 58.667 43.478 0.00 0.00 0.00 2.66
649 690 3.951663 CGGAGGAAATAAGGAACCAAGT 58.048 45.455 0.00 0.00 0.00 3.16
666 707 1.153745 CAAAGAGGAGACGCCGGAG 60.154 63.158 5.05 3.72 43.43 4.63
667 708 2.646175 CCAAAGAGGAGACGCCGGA 61.646 63.158 5.05 0.00 43.43 5.14
668 709 2.125512 CCAAAGAGGAGACGCCGG 60.126 66.667 0.00 0.00 43.43 6.13
669 710 2.970639 TCCAAAGAGGAGACGCCG 59.029 61.111 0.00 0.00 43.07 6.46
678 719 4.946478 ACGGAATCTATCCTCCAAAGAG 57.054 45.455 0.00 0.00 46.98 2.85
679 720 4.714802 TCAACGGAATCTATCCTCCAAAGA 59.285 41.667 0.00 0.00 46.98 2.52
680 721 5.023533 TCAACGGAATCTATCCTCCAAAG 57.976 43.478 0.00 0.00 46.98 2.77
681 722 5.429681 TTCAACGGAATCTATCCTCCAAA 57.570 39.130 0.00 0.00 46.98 3.28
682 723 5.630415 ATTCAACGGAATCTATCCTCCAA 57.370 39.130 0.00 0.00 46.98 3.53
683 724 5.630415 AATTCAACGGAATCTATCCTCCA 57.370 39.130 0.00 0.00 46.98 3.86
684 725 6.729187 CAAAATTCAACGGAATCTATCCTCC 58.271 40.000 0.00 0.00 46.98 4.30
685 726 6.038714 AGCAAAATTCAACGGAATCTATCCTC 59.961 38.462 0.00 0.00 46.98 3.71
686 727 5.888161 AGCAAAATTCAACGGAATCTATCCT 59.112 36.000 0.00 0.00 46.98 3.24
687 728 6.136541 AGCAAAATTCAACGGAATCTATCC 57.863 37.500 0.00 0.00 42.87 2.59
688 729 6.693113 GGAAGCAAAATTCAACGGAATCTATC 59.307 38.462 0.00 0.00 42.87 2.08
689 730 6.405842 GGGAAGCAAAATTCAACGGAATCTAT 60.406 38.462 0.00 0.00 42.87 1.98
690 731 5.105917 GGGAAGCAAAATTCAACGGAATCTA 60.106 40.000 0.00 0.00 42.87 1.98
691 732 4.321974 GGGAAGCAAAATTCAACGGAATCT 60.322 41.667 0.00 0.00 42.87 2.40
692 733 3.926527 GGGAAGCAAAATTCAACGGAATC 59.073 43.478 0.00 0.00 42.87 2.52
693 734 3.578282 AGGGAAGCAAAATTCAACGGAAT 59.422 39.130 0.00 0.00 45.57 3.01
694 735 2.962421 AGGGAAGCAAAATTCAACGGAA 59.038 40.909 0.00 0.00 37.45 4.30
695 736 2.556622 GAGGGAAGCAAAATTCAACGGA 59.443 45.455 0.00 0.00 0.00 4.69
696 737 2.352715 GGAGGGAAGCAAAATTCAACGG 60.353 50.000 0.00 0.00 0.00 4.44
697 738 2.352715 GGGAGGGAAGCAAAATTCAACG 60.353 50.000 0.00 0.00 0.00 4.10
712 753 7.958088 TGTAGTTTTAAAAGAATTTGGGAGGG 58.042 34.615 0.00 0.00 39.02 4.30
731 772 9.191479 AGTTGCAGAGTAATCTAGTATGTAGTT 57.809 33.333 0.00 0.00 0.00 2.24
733 774 9.672086 GAAGTTGCAGAGTAATCTAGTATGTAG 57.328 37.037 0.00 0.00 0.00 2.74
734 775 9.409918 AGAAGTTGCAGAGTAATCTAGTATGTA 57.590 33.333 0.00 0.00 0.00 2.29
736 777 9.593134 AAAGAAGTTGCAGAGTAATCTAGTATG 57.407 33.333 0.00 0.00 0.00 2.39
738 779 9.998106 AAAAAGAAGTTGCAGAGTAATCTAGTA 57.002 29.630 0.00 0.00 0.00 1.82
762 803 7.763528 TGCAGAGCATTTACTCAAAAAGAAAAA 59.236 29.630 0.00 0.00 39.26 1.94
763 804 7.264221 TGCAGAGCATTTACTCAAAAAGAAAA 58.736 30.769 0.00 0.00 39.26 2.29
764 805 6.804677 TGCAGAGCATTTACTCAAAAAGAAA 58.195 32.000 0.00 0.00 39.26 2.52
765 806 6.389830 TGCAGAGCATTTACTCAAAAAGAA 57.610 33.333 0.00 0.00 39.26 2.52
766 807 6.389830 TTGCAGAGCATTTACTCAAAAAGA 57.610 33.333 0.00 0.00 38.76 2.52
767 808 8.922058 ATATTGCAGAGCATTTACTCAAAAAG 57.078 30.769 0.00 0.00 38.76 2.27
768 809 8.742777 AGATATTGCAGAGCATTTACTCAAAAA 58.257 29.630 0.00 0.00 38.76 1.94
769 810 8.186163 CAGATATTGCAGAGCATTTACTCAAAA 58.814 33.333 0.00 0.00 38.76 2.44
770 811 7.700505 CAGATATTGCAGAGCATTTACTCAAA 58.299 34.615 0.00 0.00 38.76 2.69
771 812 7.255491 CAGATATTGCAGAGCATTTACTCAA 57.745 36.000 0.00 0.00 38.76 3.02
772 813 6.856135 CAGATATTGCAGAGCATTTACTCA 57.144 37.500 0.00 0.00 38.76 3.41
791 832 9.050601 GCAAAATTACAGAGTAATCTAGCAGAT 57.949 33.333 3.16 0.00 36.28 2.90
848 889 4.696479 TTCTTCTTCTCTGGCAGAAACT 57.304 40.909 19.29 0.00 40.83 2.66
849 890 5.529060 TCTTTTCTTCTTCTCTGGCAGAAAC 59.471 40.000 19.29 0.00 40.83 2.78
850 891 5.684704 TCTTTTCTTCTTCTCTGGCAGAAA 58.315 37.500 19.29 13.89 40.83 2.52
851 892 5.296151 TCTTTTCTTCTTCTCTGGCAGAA 57.704 39.130 19.29 3.47 38.95 3.02
852 893 4.963318 TCTTTTCTTCTTCTCTGGCAGA 57.037 40.909 17.68 17.68 0.00 4.26
853 894 4.455190 CCTTCTTTTCTTCTTCTCTGGCAG 59.545 45.833 8.58 8.58 0.00 4.85
854 895 4.141390 ACCTTCTTTTCTTCTTCTCTGGCA 60.141 41.667 0.00 0.00 0.00 4.92
855 896 4.393834 ACCTTCTTTTCTTCTTCTCTGGC 58.606 43.478 0.00 0.00 0.00 4.85
856 897 5.615289 TGACCTTCTTTTCTTCTTCTCTGG 58.385 41.667 0.00 0.00 0.00 3.86
857 898 6.520272 TCTGACCTTCTTTTCTTCTTCTCTG 58.480 40.000 0.00 0.00 0.00 3.35
858 899 6.326323 ACTCTGACCTTCTTTTCTTCTTCTCT 59.674 38.462 0.00 0.00 0.00 3.10
859 900 6.521162 ACTCTGACCTTCTTTTCTTCTTCTC 58.479 40.000 0.00 0.00 0.00 2.87
932 988 1.807814 AGGATCTTATCAAGGCCGGT 58.192 50.000 1.90 0.00 0.00 5.28
939 995 2.563179 GGCGAGGCTAGGATCTTATCAA 59.437 50.000 0.00 0.00 0.00 2.57
941 997 2.171840 TGGCGAGGCTAGGATCTTATC 58.828 52.381 0.00 0.00 0.00 1.75
942 998 2.310779 TGGCGAGGCTAGGATCTTAT 57.689 50.000 0.00 0.00 0.00 1.73
943 999 2.171840 GATGGCGAGGCTAGGATCTTA 58.828 52.381 0.00 0.00 0.00 2.10
945 1001 1.247419 CGATGGCGAGGCTAGGATCT 61.247 60.000 0.00 0.00 40.82 2.75
946 1002 1.214062 CGATGGCGAGGCTAGGATC 59.786 63.158 0.00 0.00 40.82 3.36
947 1003 1.228583 TCGATGGCGAGGCTAGGAT 60.229 57.895 0.00 0.00 42.51 3.24
948 1004 2.194868 TCGATGGCGAGGCTAGGA 59.805 61.111 0.00 0.00 42.51 2.94
976 1034 1.554160 CACAACTGCCAGAGAGATCCT 59.446 52.381 0.00 0.00 0.00 3.24
988 1046 0.883153 TGCATCATGGTCACAACTGC 59.117 50.000 0.00 0.00 32.94 4.40
1055 1113 2.257676 GCTGCCTCTTGCTGTTGC 59.742 61.111 0.00 0.00 42.00 4.17
1058 1116 4.711949 CCGGCTGCCTCTTGCTGT 62.712 66.667 17.92 0.00 42.00 4.40
1113 1171 2.159099 TCCTGGAGATGGTCGAATTTCG 60.159 50.000 12.54 12.54 42.10 3.46
1123 1181 0.179936 GCAGAGGTTCCTGGAGATGG 59.820 60.000 0.00 0.00 34.82 3.51
1133 1191 2.200170 AAAATGGCGCGCAGAGGTTC 62.200 55.000 34.42 14.17 0.00 3.62
1134 1192 2.200170 GAAAATGGCGCGCAGAGGTT 62.200 55.000 34.42 19.01 0.00 3.50
1139 1197 2.513065 AAGACGAAAATGGCGCGCAG 62.513 55.000 34.42 15.88 0.00 5.18
1143 1201 0.039527 AACCAAGACGAAAATGGCGC 60.040 50.000 0.00 0.00 37.77 6.53
1157 1228 1.323412 CGAACCCAATCACCAACCAA 58.677 50.000 0.00 0.00 0.00 3.67
1190 1261 3.545703 CAATTAAGCCCAAGGACGATCT 58.454 45.455 0.00 0.00 0.00 2.75
1198 1269 3.588955 GAAACCTGCAATTAAGCCCAAG 58.411 45.455 0.00 0.00 0.00 3.61
1216 1287 0.606096 TGTTCCTCGGAGCATCGAAA 59.394 50.000 0.00 0.00 38.77 3.46
1266 1337 0.526662 CTCTTGGAAGACGCCGTAGT 59.473 55.000 0.00 0.00 0.00 2.73
1327 1399 6.695278 GCAGTGAATTACTCTGTCAGATAGAC 59.305 42.308 2.22 0.00 42.04 2.59
1336 1409 4.833478 AGGATGCAGTGAATTACTCTGT 57.167 40.909 0.00 0.00 40.77 3.41
1356 1429 5.984233 TTACCAGACGCATAGCATAAAAG 57.016 39.130 0.00 0.00 0.00 2.27
1361 1434 4.708177 AGAATTTACCAGACGCATAGCAT 58.292 39.130 0.00 0.00 0.00 3.79
1363 1436 5.485662 AAAGAATTTACCAGACGCATAGC 57.514 39.130 0.00 0.00 35.86 2.97
1365 1438 6.811253 ACAAAAGAATTTACCAGACGCATA 57.189 33.333 0.00 0.00 37.28 3.14
1382 1472 5.812127 CAGGTCCTTTTTCTGGAAACAAAAG 59.188 40.000 0.00 0.00 42.06 2.27
1437 1529 9.653287 CTAACTGAAAATTGGACAGTAGTATGA 57.347 33.333 11.09 0.00 42.81 2.15
1734 1855 3.744660 ACATGAAACTTGGTCAGGACTC 58.255 45.455 0.00 0.00 31.41 3.36
1817 1968 3.815962 CCTCATGGATCAGCTTCTTGATG 59.184 47.826 0.00 0.00 37.90 3.07
1855 2006 3.571401 CACTCTCTTGTGCCCTTCATTTT 59.429 43.478 0.00 0.00 0.00 1.82
1856 2007 3.152341 CACTCTCTTGTGCCCTTCATTT 58.848 45.455 0.00 0.00 0.00 2.32
1935 2086 2.124570 ATCATCAGCGTGGGTGGC 60.125 61.111 0.00 0.00 0.00 5.01
1944 2095 2.194212 CCTGCCTGGCATCATCAGC 61.194 63.158 23.64 0.00 38.13 4.26
1945 2096 4.159266 CCTGCCTGGCATCATCAG 57.841 61.111 23.64 9.18 38.13 2.90
1963 2114 3.094058 GCCTCGCGACGATCATCG 61.094 66.667 3.71 6.86 46.93 3.84
2049 2200 1.343506 GCGTCGTCGAAGGTGTAAAT 58.656 50.000 6.17 0.00 39.71 1.40
2118 2269 4.344865 ATCACCACCACCACCGCC 62.345 66.667 0.00 0.00 0.00 6.13
2119 2270 3.055719 CATCACCACCACCACCGC 61.056 66.667 0.00 0.00 0.00 5.68
2120 2271 1.375908 CTCATCACCACCACCACCG 60.376 63.158 0.00 0.00 0.00 4.94
2285 2445 1.420514 ACGATCTCCGAGGACCTATCA 59.579 52.381 0.00 0.00 41.76 2.15
2335 2495 0.179936 CCTGTTGCCATCTCTCCCTC 59.820 60.000 0.00 0.00 0.00 4.30
2606 2769 1.068753 CTTCATCAGCTCCGGCGAT 59.931 57.895 9.30 0.00 44.37 4.58
2861 3024 3.177920 CTCTGCACGTCGCTGCTC 61.178 66.667 16.80 0.00 43.06 4.26
2930 3093 1.079543 CCTCCTGAGCACGTTCCTG 60.080 63.158 0.00 0.00 0.00 3.86
3158 3321 1.218316 GGAGCTCTTGTACCACCCG 59.782 63.158 14.64 0.00 0.00 5.28
3278 3441 3.009115 TTTGGCTCCCCCTCCGAG 61.009 66.667 0.00 0.00 0.00 4.63
3326 3489 4.608774 TCCCCGTGTCCCTCGTGT 62.609 66.667 0.00 0.00 0.00 4.49
3365 3528 2.364448 GCCCTCTCCTCTTCCGGT 60.364 66.667 0.00 0.00 0.00 5.28
3371 3534 1.229209 TTTCGGTGCCCTCTCCTCT 60.229 57.895 0.00 0.00 0.00 3.69
3383 3546 1.542187 CGTCCTTCCTCCCTTTCGGT 61.542 60.000 0.00 0.00 0.00 4.69
3631 3794 0.807275 TGTCAGATTGATGGCGCTCG 60.807 55.000 7.64 0.00 0.00 5.03
3635 3798 0.949397 CCCATGTCAGATTGATGGCG 59.051 55.000 0.00 0.00 27.76 5.69
3638 3801 5.358725 TGAACATTCCCATGTCAGATTGATG 59.641 40.000 0.00 0.00 43.34 3.07
3717 3880 2.145536 CCGCGGATCATCATTTCATCA 58.854 47.619 24.07 0.00 0.00 3.07
3873 4036 8.190784 CAGAAACATAACCCCTGAACATTATTC 58.809 37.037 0.00 0.00 0.00 1.75
3876 4039 6.657541 GTCAGAAACATAACCCCTGAACATTA 59.342 38.462 0.00 0.00 35.89 1.90
3924 4087 5.205821 TGATCTTGCTCCATCCATGAAATT 58.794 37.500 0.00 0.00 0.00 1.82
3926 4089 4.239428 TGATCTTGCTCCATCCATGAAA 57.761 40.909 0.00 0.00 0.00 2.69
3933 4096 2.915349 TCAGCTTGATCTTGCTCCATC 58.085 47.619 9.48 0.00 37.44 3.51
3934 4097 3.054582 TCTTCAGCTTGATCTTGCTCCAT 60.055 43.478 9.48 0.00 37.44 3.41
4012 4175 0.521735 GCTTTTGTCGGGTGATCCAC 59.478 55.000 0.00 0.00 34.36 4.02
4095 4258 1.816074 TGATCGGTTGGCAGGTTAAC 58.184 50.000 0.00 0.00 0.00 2.01
4175 4338 1.369692 ACGTCATGGCCGTCTGAAA 59.630 52.632 0.00 0.00 31.97 2.69
4181 4344 4.430765 GGTCGACGTCATGGCCGT 62.431 66.667 17.16 10.46 42.06 5.68
4182 4345 4.429212 TGGTCGACGTCATGGCCG 62.429 66.667 17.16 0.39 0.00 6.13
4183 4346 2.813908 GTGGTCGACGTCATGGCC 60.814 66.667 17.16 11.74 0.00 5.36
4184 4347 2.813908 GGTGGTCGACGTCATGGC 60.814 66.667 17.16 0.89 0.00 4.40
4347 4510 2.741092 GGTTCCAGCCACGTCTGA 59.259 61.111 5.86 0.00 36.19 3.27
4624 4787 6.036083 CGAAAGAACACAAGAAGAACAGAGAA 59.964 38.462 0.00 0.00 0.00 2.87
4644 4808 0.385974 CGGCAAAAGCACTCCGAAAG 60.386 55.000 0.00 0.00 44.23 2.62
4695 4859 4.944930 AGCTTAGTTACATCTCTCACTCGT 59.055 41.667 0.00 0.00 0.00 4.18
4696 4860 5.493133 AGCTTAGTTACATCTCTCACTCG 57.507 43.478 0.00 0.00 0.00 4.18
4820 4988 0.969149 TACCACTCTGTCAGCCAGTG 59.031 55.000 12.64 12.64 42.19 3.66
4825 4993 1.067495 GGACTGTACCACTCTGTCAGC 60.067 57.143 0.00 0.00 36.14 4.26
4826 4994 2.239400 TGGACTGTACCACTCTGTCAG 58.761 52.381 0.00 0.00 36.14 3.51
4827 4995 2.375014 TGGACTGTACCACTCTGTCA 57.625 50.000 0.00 0.00 36.14 3.58
4828 4996 3.093057 AGATGGACTGTACCACTCTGTC 58.907 50.000 0.00 0.00 43.03 3.51
4829 4997 2.828520 CAGATGGACTGTACCACTCTGT 59.171 50.000 17.70 0.00 43.03 3.41
4830 4998 3.092301 TCAGATGGACTGTACCACTCTG 58.908 50.000 18.65 18.65 45.86 3.35
4831 4999 3.458044 TCAGATGGACTGTACCACTCT 57.542 47.619 0.00 0.00 45.86 3.24
4832 5000 3.677424 GCTTCAGATGGACTGTACCACTC 60.677 52.174 0.00 0.00 45.86 3.51
4844 5017 3.374745 GTGTGTTTGTTGCTTCAGATGG 58.625 45.455 0.00 0.00 0.00 3.51
4859 5032 0.385974 GTCGTAGCGTACCGTGTGTT 60.386 55.000 0.00 0.00 0.00 3.32
4879 5052 2.693591 TGATCAACCCATCCGACTAGTC 59.306 50.000 13.18 13.18 0.00 2.59
4882 5055 2.039418 CCTGATCAACCCATCCGACTA 58.961 52.381 0.00 0.00 0.00 2.59
4884 5057 0.815615 GCCTGATCAACCCATCCGAC 60.816 60.000 0.00 0.00 0.00 4.79
4885 5058 1.526887 GCCTGATCAACCCATCCGA 59.473 57.895 0.00 0.00 0.00 4.55
4886 5059 1.889105 CGCCTGATCAACCCATCCG 60.889 63.158 0.00 0.00 0.00 4.18
5093 5269 0.398318 GTCTCTCTTTGGGCAGGTGT 59.602 55.000 0.00 0.00 0.00 4.16
5106 5287 0.456142 TGTGTACATGCGCGTCTCTC 60.456 55.000 8.43 0.00 0.00 3.20
5110 5291 2.369629 ACGTGTGTACATGCGCGTC 61.370 57.895 16.55 0.00 46.82 5.19
5115 5296 2.993220 TGAATCTGACGTGTGTACATGC 59.007 45.455 0.00 0.00 36.36 4.06
5118 5299 2.035321 TGCTGAATCTGACGTGTGTACA 59.965 45.455 0.00 0.00 0.00 2.90
5119 5300 2.663602 CTGCTGAATCTGACGTGTGTAC 59.336 50.000 0.00 0.00 0.00 2.90
5135 5317 0.036952 ACGTGATGTTCCTCCTGCTG 60.037 55.000 0.00 0.00 0.00 4.41
5140 5322 0.454600 TCGCTACGTGATGTTCCTCC 59.545 55.000 0.00 0.00 0.00 4.30
5141 5323 1.546834 GTCGCTACGTGATGTTCCTC 58.453 55.000 0.00 0.00 0.00 3.71
5155 5337 1.374343 TTACTCGATCCAGCGTCGCT 61.374 55.000 15.47 15.47 40.77 4.93
5275 5467 2.045536 CCCTCCAGCACAGCTTCC 60.046 66.667 0.00 0.00 36.40 3.46
5276 5468 1.376553 GTCCCTCCAGCACAGCTTC 60.377 63.158 0.00 0.00 36.40 3.86
5277 5469 2.753029 GTCCCTCCAGCACAGCTT 59.247 61.111 0.00 0.00 36.40 3.74
5278 5470 3.699894 CGTCCCTCCAGCACAGCT 61.700 66.667 0.00 0.00 40.77 4.24
5285 5477 3.465403 CAGGCCTCGTCCCTCCAG 61.465 72.222 0.00 0.00 0.00 3.86
5306 5659 3.442273 GCTAGAGATCCTCCTGATAACCG 59.558 52.174 0.00 0.00 32.41 4.44
5308 5661 5.183140 GTCTGCTAGAGATCCTCCTGATAAC 59.817 48.000 0.00 0.00 32.41 1.89
5358 5711 4.101448 GGCCATCGACCACCTGCT 62.101 66.667 0.00 0.00 0.00 4.24
5360 5713 3.605749 AACGGCCATCGACCACCTG 62.606 63.158 2.24 0.00 42.43 4.00
5361 5714 1.546589 TAAACGGCCATCGACCACCT 61.547 55.000 2.24 0.00 42.43 4.00
5362 5715 0.674269 TTAAACGGCCATCGACCACC 60.674 55.000 2.24 0.00 42.43 4.61
5513 5869 4.095185 GTGCTATCGGGACTGCTACTATAG 59.905 50.000 0.00 0.00 33.31 1.31
5517 5873 1.033574 GTGCTATCGGGACTGCTACT 58.966 55.000 0.00 0.00 33.31 2.57


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

AutoCloner maintained by Alex Coulton.