Multiple sequence alignment - TraesCS1A01G299100

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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 TraesCS1A01G299100 chr1A 100.000 5283 0 0 1 5283 493924295 493919013 0.000000e+00 9756.0
1 TraesCS1A01G299100 chr1A 81.951 820 117 20 3 807 15588169 15587366 0.000000e+00 665.0
2 TraesCS1A01G299100 chr1D 91.737 4272 204 64 853 5020 391308440 391312666 0.000000e+00 5795.0
3 TraesCS1A01G299100 chr1D 85.448 804 82 11 3 805 25218651 25219420 0.000000e+00 804.0
4 TraesCS1A01G299100 chr1D 88.390 267 13 4 5023 5283 391312791 391313045 6.650000e-79 305.0
5 TraesCS1A01G299100 chr1D 91.111 45 4 0 2534 2578 437336768 437336812 1.590000e-05 62.1
6 TraesCS1A01G299100 chr1B 96.368 1762 54 6 2915 4669 531213052 531211294 0.000000e+00 2891.0
7 TraesCS1A01G299100 chr1B 89.620 2129 118 48 853 2916 531215246 531213156 0.000000e+00 2612.0
8 TraesCS1A01G299100 chr1B 90.152 264 11 2 5023 5283 531210723 531210472 3.940000e-86 329.0
9 TraesCS1A01G299100 chr1B 89.773 176 8 8 4708 4877 531211125 531210954 3.200000e-52 217.0
10 TraesCS1A01G299100 chr1B 87.500 120 4 4 4902 5021 531210954 531210846 1.540000e-25 128.0
11 TraesCS1A01G299100 chr2B 92.317 807 61 1 1 807 705695308 705694503 0.000000e+00 1146.0
12 TraesCS1A01G299100 chr2D 92.019 827 40 3 1 807 36580544 36579724 0.000000e+00 1138.0
13 TraesCS1A01G299100 chr2D 90.850 765 45 7 1 746 573907120 573907878 0.000000e+00 1002.0
14 TraesCS1A01G299100 chr6D 91.019 824 49 7 1 805 270581500 270582317 0.000000e+00 1088.0
15 TraesCS1A01G299100 chr6D 83.802 747 94 14 3 736 24879000 24878268 0.000000e+00 684.0
16 TraesCS1A01G299100 chr7D 90.326 827 56 10 1 807 133689033 133689855 0.000000e+00 1062.0
17 TraesCS1A01G299100 chr6B 90.303 825 55 13 1 805 4465970 4466789 0.000000e+00 1057.0
18 TraesCS1A01G299100 chr4D 90.944 773 47 9 1 753 426869235 426870004 0.000000e+00 1018.0
19 TraesCS1A01G299100 chr3D 93.653 646 35 4 1 646 293814082 293813443 0.000000e+00 961.0
20 TraesCS1A01G299100 chr5B 87.500 816 86 8 3 811 657724364 657723558 0.000000e+00 928.0
21 TraesCS1A01G299100 chr3B 83.661 814 111 15 3 805 720856736 720857538 0.000000e+00 747.0
22 TraesCS1A01G299100 chr7A 82.903 813 102 22 3 805 457571736 457572521 0.000000e+00 697.0
23 TraesCS1A01G299100 chr6A 81.907 818 116 18 3 805 54371251 54370451 0.000000e+00 662.0
24 TraesCS1A01G299100 chr3A 81.104 815 132 17 6 807 350458368 350457563 2.680000e-177 632.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G299100 chr1A 493919013 493924295 5282 True 9756.0 9756 100.0000 1 5283 1 chr1A.!!$R2 5282
1 TraesCS1A01G299100 chr1A 15587366 15588169 803 True 665.0 665 81.9510 3 807 1 chr1A.!!$R1 804
2 TraesCS1A01G299100 chr1D 391308440 391313045 4605 False 3050.0 5795 90.0635 853 5283 2 chr1D.!!$F3 4430
3 TraesCS1A01G299100 chr1D 25218651 25219420 769 False 804.0 804 85.4480 3 805 1 chr1D.!!$F1 802
4 TraesCS1A01G299100 chr1B 531210472 531215246 4774 True 1235.4 2891 90.6826 853 5283 5 chr1B.!!$R1 4430
5 TraesCS1A01G299100 chr2B 705694503 705695308 805 True 1146.0 1146 92.3170 1 807 1 chr2B.!!$R1 806
6 TraesCS1A01G299100 chr2D 36579724 36580544 820 True 1138.0 1138 92.0190 1 807 1 chr2D.!!$R1 806
7 TraesCS1A01G299100 chr2D 573907120 573907878 758 False 1002.0 1002 90.8500 1 746 1 chr2D.!!$F1 745
8 TraesCS1A01G299100 chr6D 270581500 270582317 817 False 1088.0 1088 91.0190 1 805 1 chr6D.!!$F1 804
9 TraesCS1A01G299100 chr6D 24878268 24879000 732 True 684.0 684 83.8020 3 736 1 chr6D.!!$R1 733
10 TraesCS1A01G299100 chr7D 133689033 133689855 822 False 1062.0 1062 90.3260 1 807 1 chr7D.!!$F1 806
11 TraesCS1A01G299100 chr6B 4465970 4466789 819 False 1057.0 1057 90.3030 1 805 1 chr6B.!!$F1 804
12 TraesCS1A01G299100 chr4D 426869235 426870004 769 False 1018.0 1018 90.9440 1 753 1 chr4D.!!$F1 752
13 TraesCS1A01G299100 chr3D 293813443 293814082 639 True 961.0 961 93.6530 1 646 1 chr3D.!!$R1 645
14 TraesCS1A01G299100 chr5B 657723558 657724364 806 True 928.0 928 87.5000 3 811 1 chr5B.!!$R1 808
15 TraesCS1A01G299100 chr3B 720856736 720857538 802 False 747.0 747 83.6610 3 805 1 chr3B.!!$F1 802
16 TraesCS1A01G299100 chr7A 457571736 457572521 785 False 697.0 697 82.9030 3 805 1 chr7A.!!$F1 802
17 TraesCS1A01G299100 chr6A 54370451 54371251 800 True 662.0 662 81.9070 3 805 1 chr6A.!!$R1 802
18 TraesCS1A01G299100 chr3A 350457563 350458368 805 True 632.0 632 81.1040 6 807 1 chr3A.!!$R1 801

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
835 894 0.031857 TGTTGCAAGGGAAATGCGTG 59.968 50.000 0.00 0.0 46.76 5.34 F
1581 1665 0.106519 GGTGATTGGTGGGATCTGGG 60.107 60.000 0.00 0.0 0.00 4.45 F
2599 2723 1.001068 TCATCCTCGTAAAACGGTGCA 59.999 47.619 0.00 0.0 42.81 4.57 F
2721 2853 1.143684 TGAAGCTGCTCTTGTTCCCTT 59.856 47.619 1.00 0.0 34.56 3.95 F
2859 2991 1.532316 AGCTGCAACAATGGGTGCT 60.532 52.632 12.35 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2582 2706 0.104487 TGTGCACCGTTTTACGAGGA 59.896 50.000 15.69 0.00 46.05 3.71 R
3334 3574 0.462759 CGAATCCCCAGAAGTGGCTC 60.463 60.000 0.00 0.00 43.44 4.70 R
3584 3828 0.671163 TGCGGGTTAACACCTTAGCG 60.671 55.000 8.10 0.00 43.65 4.26 R
3979 4224 0.797542 GTACAGAGACGCGACAGAGT 59.202 55.000 15.93 9.08 0.00 3.24 R
4826 5217 1.379843 ACCCAAAATGCCTAGCCCG 60.380 57.895 0.00 0.00 0.00 6.13 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
116 117 1.226491 CGTTCTTCGTACGCCGGAT 60.226 57.895 11.24 0.00 37.11 4.18
117 118 1.198608 CGTTCTTCGTACGCCGGATC 61.199 60.000 11.24 6.66 37.11 3.36
118 119 0.869028 GTTCTTCGTACGCCGGATCC 60.869 60.000 11.24 0.00 37.11 3.36
119 120 1.033746 TTCTTCGTACGCCGGATCCT 61.034 55.000 11.24 0.00 37.11 3.24
120 121 1.008767 CTTCGTACGCCGGATCCTC 60.009 63.158 11.24 0.18 37.11 3.71
121 122 2.403671 CTTCGTACGCCGGATCCTCC 62.404 65.000 11.24 0.00 37.11 4.30
437 454 2.600769 AGAAGGCGGACGAGTGGT 60.601 61.111 0.00 0.00 0.00 4.16
503 521 0.175760 CTTCGGCGAGGAGGATTGAA 59.824 55.000 14.40 0.00 0.00 2.69
585 611 5.886474 ACCCCCTAGTACTAGTTTAACGTAC 59.114 44.000 24.84 5.54 35.05 3.67
589 615 9.998106 CCCCTAGTACTAGTTTAACGTACTATA 57.002 37.037 24.84 5.25 42.50 1.31
633 689 8.425577 AGTTTGTGATGAACTATGTAGTATGC 57.574 34.615 0.00 0.00 35.68 3.14
700 759 8.725405 TTCAAATTATGCAGGTTTAGATACGA 57.275 30.769 0.00 0.00 0.00 3.43
701 760 8.725405 TCAAATTATGCAGGTTTAGATACGAA 57.275 30.769 0.00 0.00 0.00 3.85
753 812 3.628017 CAAAAGCGATTTTCGTGAACCT 58.372 40.909 8.70 0.00 42.81 3.50
778 837 1.336702 ACGTGTTTTGCGGGTCGTATA 60.337 47.619 0.00 0.00 0.00 1.47
785 844 0.102663 TGCGGGTCGTATATTTGCGA 59.897 50.000 0.00 0.00 37.65 5.10
790 849 2.401351 GGTCGTATATTTGCGAGGTCC 58.599 52.381 0.00 0.00 40.72 4.46
807 866 2.165845 GGTCCGCTAGAGTTGCTCTAAA 59.834 50.000 7.22 0.00 41.74 1.85
811 870 4.888239 TCCGCTAGAGTTGCTCTAAATACT 59.112 41.667 7.22 0.00 41.74 2.12
812 871 5.008811 TCCGCTAGAGTTGCTCTAAATACTC 59.991 44.000 7.22 0.00 41.74 2.59
813 872 5.221067 CCGCTAGAGTTGCTCTAAATACTCA 60.221 44.000 7.22 0.00 41.74 3.41
814 873 6.442952 CGCTAGAGTTGCTCTAAATACTCAT 58.557 40.000 7.22 0.00 41.74 2.90
815 874 7.308649 CCGCTAGAGTTGCTCTAAATACTCATA 60.309 40.741 7.22 0.00 41.74 2.15
816 875 8.240682 CGCTAGAGTTGCTCTAAATACTCATAT 58.759 37.037 7.22 0.00 41.74 1.78
817 876 9.352784 GCTAGAGTTGCTCTAAATACTCATATG 57.647 37.037 7.22 0.00 41.74 1.78
820 879 9.539825 AGAGTTGCTCTAAATACTCATATGTTG 57.460 33.333 1.90 0.00 39.28 3.33
821 880 8.147642 AGTTGCTCTAAATACTCATATGTTGC 57.852 34.615 1.90 0.00 0.00 4.17
822 881 7.770433 AGTTGCTCTAAATACTCATATGTTGCA 59.230 33.333 1.90 0.00 0.00 4.08
823 882 8.397906 GTTGCTCTAAATACTCATATGTTGCAA 58.602 33.333 1.90 0.00 32.86 4.08
824 883 8.146479 TGCTCTAAATACTCATATGTTGCAAG 57.854 34.615 0.00 0.00 0.00 4.01
825 884 7.227314 TGCTCTAAATACTCATATGTTGCAAGG 59.773 37.037 0.00 0.00 0.00 3.61
826 885 7.308229 GCTCTAAATACTCATATGTTGCAAGGG 60.308 40.741 0.00 0.00 0.00 3.95
827 886 7.801104 TCTAAATACTCATATGTTGCAAGGGA 58.199 34.615 0.00 0.00 0.00 4.20
828 887 8.271458 TCTAAATACTCATATGTTGCAAGGGAA 58.729 33.333 0.00 0.00 0.00 3.97
829 888 7.716799 AAATACTCATATGTTGCAAGGGAAA 57.283 32.000 0.00 0.00 0.00 3.13
830 889 7.902920 AATACTCATATGTTGCAAGGGAAAT 57.097 32.000 0.00 0.00 0.00 2.17
831 890 5.587388 ACTCATATGTTGCAAGGGAAATG 57.413 39.130 0.00 0.12 0.00 2.32
832 891 4.142093 ACTCATATGTTGCAAGGGAAATGC 60.142 41.667 0.00 0.00 44.08 3.56
833 892 2.937469 TATGTTGCAAGGGAAATGCG 57.063 45.000 0.00 0.00 46.76 4.73
834 893 0.968405 ATGTTGCAAGGGAAATGCGT 59.032 45.000 0.00 0.00 46.76 5.24
835 894 0.031857 TGTTGCAAGGGAAATGCGTG 59.968 50.000 0.00 0.00 46.76 5.34
836 895 1.006337 TTGCAAGGGAAATGCGTGC 60.006 52.632 0.00 0.00 46.76 5.34
837 896 1.462731 TTGCAAGGGAAATGCGTGCT 61.463 50.000 0.00 0.00 46.76 4.40
838 897 1.153958 GCAAGGGAAATGCGTGCTC 60.154 57.895 0.00 0.00 33.57 4.26
839 898 1.135315 CAAGGGAAATGCGTGCTCG 59.865 57.895 3.31 3.31 40.37 5.03
840 899 1.302511 AAGGGAAATGCGTGCTCGT 60.303 52.632 10.18 0.00 39.49 4.18
841 900 0.889186 AAGGGAAATGCGTGCTCGTT 60.889 50.000 10.18 0.00 39.49 3.85
842 901 1.134694 GGGAAATGCGTGCTCGTTC 59.865 57.895 10.18 5.83 39.49 3.95
843 902 1.134694 GGAAATGCGTGCTCGTTCC 59.865 57.895 10.18 11.03 39.49 3.62
844 903 1.134694 GAAATGCGTGCTCGTTCCC 59.865 57.895 10.18 0.00 39.49 3.97
845 904 1.298859 GAAATGCGTGCTCGTTCCCT 61.299 55.000 10.18 0.00 39.49 4.20
846 905 1.298859 AAATGCGTGCTCGTTCCCTC 61.299 55.000 10.18 0.00 39.49 4.30
847 906 3.989698 ATGCGTGCTCGTTCCCTCG 62.990 63.158 10.18 0.00 39.49 4.63
848 907 4.415332 GCGTGCTCGTTCCCTCGA 62.415 66.667 10.18 0.00 39.49 4.04
849 908 2.257371 CGTGCTCGTTCCCTCGAA 59.743 61.111 0.00 0.00 39.34 3.71
850 909 1.372499 CGTGCTCGTTCCCTCGAAA 60.372 57.895 0.00 0.00 39.34 3.46
851 910 0.942410 CGTGCTCGTTCCCTCGAAAA 60.942 55.000 0.00 0.00 39.34 2.29
1236 1299 2.183555 CACTTCTACGACCGCCCC 59.816 66.667 0.00 0.00 0.00 5.80
1274 1337 1.380380 CCCTTGCCACCCTCCATTC 60.380 63.158 0.00 0.00 0.00 2.67
1364 1435 4.130118 CCTCCTCGAGGGAAATTGTTATG 58.870 47.826 30.80 1.85 45.43 1.90
1365 1436 4.141711 CCTCCTCGAGGGAAATTGTTATGA 60.142 45.833 30.80 6.05 45.43 2.15
1368 1439 6.423182 TCCTCGAGGGAAATTGTTATGAATT 58.577 36.000 30.80 0.00 41.91 2.17
1370 1441 7.497909 TCCTCGAGGGAAATTGTTATGAATTAC 59.502 37.037 30.80 0.00 41.91 1.89
1371 1442 7.499232 CCTCGAGGGAAATTGTTATGAATTACT 59.501 37.037 24.62 0.00 37.23 2.24
1372 1443 8.433421 TCGAGGGAAATTGTTATGAATTACTC 57.567 34.615 0.00 0.00 0.00 2.59
1373 1444 8.265055 TCGAGGGAAATTGTTATGAATTACTCT 58.735 33.333 0.00 0.00 0.00 3.24
1374 1445 9.542462 CGAGGGAAATTGTTATGAATTACTCTA 57.458 33.333 0.00 0.00 0.00 2.43
1406 1477 3.096852 CCTGGTTTTAATTCCCCACTCC 58.903 50.000 0.00 0.00 0.00 3.85
1411 1483 5.428783 TGGTTTTAATTCCCCACTCCAAAAA 59.571 36.000 0.00 0.00 0.00 1.94
1416 1488 2.570284 CCCCACTCCAAAAACGCCC 61.570 63.158 0.00 0.00 0.00 6.13
1445 1517 3.838120 ACAGTACATGTGACATGTCTCG 58.162 45.455 31.95 22.40 41.91 4.04
1446 1518 3.506067 ACAGTACATGTGACATGTCTCGA 59.494 43.478 31.95 14.14 41.91 4.04
1457 1529 8.267620 TGTGACATGTCTCGATTAAAATGATT 57.732 30.769 25.55 0.00 0.00 2.57
1462 1534 8.335356 ACATGTCTCGATTAAAATGATTAACGG 58.665 33.333 0.00 0.00 0.00 4.44
1463 1535 6.711579 TGTCTCGATTAAAATGATTAACGGC 58.288 36.000 0.00 0.00 0.00 5.68
1467 1539 6.186785 TCGATTAAAATGATTAACGGCGTTC 58.813 36.000 30.35 16.12 0.00 3.95
1475 1547 3.310227 TGATTAACGGCGTTCGCATAATT 59.690 39.130 30.35 6.81 43.89 1.40
1477 1549 5.177881 TGATTAACGGCGTTCGCATAATTAT 59.822 36.000 30.35 9.31 43.89 1.28
1479 1551 2.206750 ACGGCGTTCGCATAATTATGT 58.793 42.857 23.14 1.21 43.89 2.29
1480 1552 2.033236 ACGGCGTTCGCATAATTATGTG 60.033 45.455 26.29 26.29 43.61 3.21
1481 1553 2.661709 CGGCGTTCGCATAATTATGTGG 60.662 50.000 29.55 20.02 42.75 4.17
1482 1554 2.350388 GGCGTTCGCATAATTATGTGGG 60.350 50.000 29.55 21.81 42.75 4.61
1487 1571 5.179368 CGTTCGCATAATTATGTGGGATCTT 59.821 40.000 29.55 0.00 42.75 2.40
1495 1579 8.571336 CATAATTATGTGGGATCTTCTTGTTCC 58.429 37.037 16.03 0.00 34.55 3.62
1497 1581 1.974957 TGTGGGATCTTCTTGTTCCGA 59.025 47.619 0.00 0.00 35.81 4.55
1501 1585 1.861575 GGATCTTCTTGTTCCGATCGC 59.138 52.381 10.32 0.00 34.54 4.58
1503 1587 2.279582 TCTTCTTGTTCCGATCGCTC 57.720 50.000 10.32 2.55 0.00 5.03
1514 1598 2.159282 TCCGATCGCTCTTGGTAGTTTC 60.159 50.000 10.32 0.00 0.00 2.78
1581 1665 0.106519 GGTGATTGGTGGGATCTGGG 60.107 60.000 0.00 0.00 0.00 4.45
1590 1674 1.561542 GTGGGATCTGGGAATCACAGT 59.438 52.381 12.75 0.00 39.68 3.55
1596 1680 4.517285 GATCTGGGAATCACAGTGCTAAA 58.483 43.478 12.75 0.00 37.25 1.85
1597 1681 3.942829 TCTGGGAATCACAGTGCTAAAG 58.057 45.455 12.75 0.00 37.25 1.85
1598 1682 3.582647 TCTGGGAATCACAGTGCTAAAGA 59.417 43.478 12.75 0.00 37.25 2.52
1600 1684 4.922206 TGGGAATCACAGTGCTAAAGATT 58.078 39.130 0.00 0.00 0.00 2.40
1601 1685 4.943705 TGGGAATCACAGTGCTAAAGATTC 59.056 41.667 0.00 0.00 42.21 2.52
1602 1686 5.189180 GGGAATCACAGTGCTAAAGATTCT 58.811 41.667 15.88 0.00 42.44 2.40
1603 1687 5.295540 GGGAATCACAGTGCTAAAGATTCTC 59.704 44.000 15.88 11.69 42.44 2.87
1678 1767 4.142609 TCTGCACTTCATTGGATCTACC 57.857 45.455 0.00 0.00 39.54 3.18
1688 1780 7.839705 ACTTCATTGGATCTACCTCTGTACTAA 59.160 37.037 0.00 0.00 39.86 2.24
1709 1801 6.942576 ACTAATGTAGCTATGCTTTATTGGGG 59.057 38.462 0.00 0.00 40.44 4.96
1749 1841 5.802956 ACAAAAACGTTGTGGTTGTATCTTG 59.197 36.000 14.57 0.00 30.88 3.02
1771 1863 1.665679 CACTGACAAGTTCGCACAACT 59.334 47.619 0.00 0.00 32.98 3.16
1774 1866 3.308866 ACTGACAAGTTCGCACAACTAAC 59.691 43.478 0.00 0.00 30.14 2.34
1775 1867 3.527533 TGACAAGTTCGCACAACTAACT 58.472 40.909 0.00 0.00 35.91 2.24
1776 1868 4.684877 TGACAAGTTCGCACAACTAACTA 58.315 39.130 0.00 0.00 33.41 2.24
1777 1869 4.505191 TGACAAGTTCGCACAACTAACTAC 59.495 41.667 0.00 0.00 33.41 2.73
1797 1889 1.202687 CCTCCTGTGCAAGTCTGTGAA 60.203 52.381 0.00 0.00 0.00 3.18
1798 1890 2.564771 CTCCTGTGCAAGTCTGTGAAA 58.435 47.619 0.00 0.00 0.00 2.69
1799 1891 3.144506 CTCCTGTGCAAGTCTGTGAAAT 58.855 45.455 0.00 0.00 0.00 2.17
1800 1892 3.141398 TCCTGTGCAAGTCTGTGAAATC 58.859 45.455 0.00 0.00 0.00 2.17
1801 1893 3.144506 CCTGTGCAAGTCTGTGAAATCT 58.855 45.455 0.00 0.00 0.00 2.40
1802 1894 3.567164 CCTGTGCAAGTCTGTGAAATCTT 59.433 43.478 0.00 0.00 0.00 2.40
1803 1895 4.756642 CCTGTGCAAGTCTGTGAAATCTTA 59.243 41.667 0.00 0.00 0.00 2.10
1804 1896 5.334414 CCTGTGCAAGTCTGTGAAATCTTAC 60.334 44.000 0.00 0.00 0.00 2.34
1805 1897 5.122519 TGTGCAAGTCTGTGAAATCTTACA 58.877 37.500 0.00 0.00 0.00 2.41
1806 1898 5.237127 TGTGCAAGTCTGTGAAATCTTACAG 59.763 40.000 0.00 0.00 44.31 2.74
1807 1899 5.237344 GTGCAAGTCTGTGAAATCTTACAGT 59.763 40.000 0.00 0.00 43.59 3.55
1808 1900 6.423905 GTGCAAGTCTGTGAAATCTTACAGTA 59.576 38.462 0.00 0.00 43.59 2.74
1809 1901 6.423905 TGCAAGTCTGTGAAATCTTACAGTAC 59.576 38.462 0.00 0.00 43.59 2.73
1810 1902 6.647067 GCAAGTCTGTGAAATCTTACAGTACT 59.353 38.462 0.00 0.00 43.59 2.73
1826 1918 5.881447 ACAGTACTTCTTACATCTGTAGCG 58.119 41.667 0.00 0.00 34.95 4.26
1829 1921 3.362706 ACTTCTTACATCTGTAGCGGGA 58.637 45.455 0.00 0.00 0.00 5.14
1830 1922 3.381908 ACTTCTTACATCTGTAGCGGGAG 59.618 47.826 0.00 0.00 0.00 4.30
1875 1967 3.057174 AGAGAGTGATCACGGACAACTTC 60.057 47.826 19.85 9.48 36.20 3.01
1878 1970 2.028930 AGTGATCACGGACAACTTCCTC 60.029 50.000 19.85 0.00 43.25 3.71
1915 2008 6.539464 CACATGCATGGCCAAAGTTAATAAAT 59.461 34.615 29.41 0.09 0.00 1.40
1931 2024 9.408648 AGTTAATAAATTACTGTCAAGATGGGG 57.591 33.333 0.00 0.00 0.00 4.96
1932 2025 9.185680 GTTAATAAATTACTGTCAAGATGGGGT 57.814 33.333 0.00 0.00 0.00 4.95
2090 2183 6.627395 ATCCAATTTACACGACACAAAGAA 57.373 33.333 0.00 0.00 0.00 2.52
2177 2270 5.592104 AAATTCTTTCGTGAAAACAGGGT 57.408 34.783 0.00 0.00 0.00 4.34
2178 2271 5.592104 AATTCTTTCGTGAAAACAGGGTT 57.408 34.783 0.00 0.00 0.00 4.11
2190 2292 7.036829 GTGAAAACAGGGTTAAAAAGTTAGCA 58.963 34.615 0.00 0.00 0.00 3.49
2238 2342 8.298854 TCAGTAATTTCTGTTGGATTCAATGTG 58.701 33.333 11.33 0.00 36.85 3.21
2261 2365 1.346068 AGTCTGACCAGGACAAAGAGC 59.654 52.381 3.76 0.00 36.29 4.09
2276 2380 6.348540 GGACAAAGAGCGTAGTTTGATGATTT 60.349 38.462 11.02 0.00 37.16 2.17
2277 2381 6.603095 ACAAAGAGCGTAGTTTGATGATTTC 58.397 36.000 11.02 0.00 37.16 2.17
2278 2382 6.204688 ACAAAGAGCGTAGTTTGATGATTTCA 59.795 34.615 11.02 0.00 37.16 2.69
2443 2567 2.804856 GTTTGTTGCGGGCACTGT 59.195 55.556 0.00 0.00 36.83 3.55
2515 2639 5.728471 CACTCCACAGTTCTGTATCTGAAT 58.272 41.667 5.11 0.00 35.84 2.57
2594 2718 5.166398 AGGTACTTTCATCCTCGTAAAACG 58.834 41.667 0.00 0.00 38.37 3.60
2595 2719 4.328169 GGTACTTTCATCCTCGTAAAACGG 59.672 45.833 0.00 0.00 42.81 4.44
2597 2721 3.744426 ACTTTCATCCTCGTAAAACGGTG 59.256 43.478 0.00 0.00 42.81 4.94
2599 2723 1.001068 TCATCCTCGTAAAACGGTGCA 59.999 47.619 0.00 0.00 42.81 4.57
2677 2809 7.062371 GGCACGTCTGATACACATAGATTATTC 59.938 40.741 0.00 0.00 0.00 1.75
2690 2822 9.559958 CACATAGATTATTCTGTTTGTTTGACC 57.440 33.333 0.00 0.00 33.17 4.02
2694 2826 6.934645 AGATTATTCTGTTTGTTTGACCGAGA 59.065 34.615 0.00 0.00 0.00 4.04
2695 2827 6.928979 TTATTCTGTTTGTTTGACCGAGAA 57.071 33.333 0.00 0.00 0.00 2.87
2718 2850 1.597742 TGTGAAGCTGCTCTTGTTCC 58.402 50.000 1.00 0.00 34.56 3.62
2721 2853 1.143684 TGAAGCTGCTCTTGTTCCCTT 59.856 47.619 1.00 0.00 34.56 3.95
2817 2949 5.418524 TGGTTCCCATGACATTATTTCACTG 59.581 40.000 0.00 0.00 0.00 3.66
2859 2991 1.532316 AGCTGCAACAATGGGTGCT 60.532 52.632 12.35 0.00 0.00 4.40
2869 3001 1.741706 CAATGGGTGCTACTGCTCAAG 59.258 52.381 0.00 0.00 40.48 3.02
2964 3204 7.801716 TCATGGCTTATTAGTGACATTTACC 57.198 36.000 0.00 0.00 0.00 2.85
3322 3562 2.652095 CGAAGTTCAGGCGGGGGTA 61.652 63.158 3.32 0.00 0.00 3.69
3385 3625 4.021016 GGTGTCATCCCTGATATAGTCACC 60.021 50.000 0.00 0.00 35.61 4.02
3434 3674 7.439157 TTCTCCACAGTTTTCATCATACTTG 57.561 36.000 0.00 0.00 0.00 3.16
3480 3723 4.183865 TGTCATTAGGTTCAGCTTCATCG 58.816 43.478 0.00 0.00 0.00 3.84
3584 3828 3.335579 GGTTGTTACCACACCTGAGATC 58.664 50.000 0.00 0.00 44.36 2.75
3769 4013 2.899900 AGAAGCATGACAGTGAGTACCA 59.100 45.455 0.00 0.00 0.00 3.25
3851 4096 2.205074 CTTCTTGCAGTTATCGGCGAT 58.795 47.619 26.95 26.95 37.57 4.58
3979 4224 6.089820 GGTAATTGATTACACGAACTGACGAA 59.910 38.462 14.01 0.00 43.33 3.85
4045 4290 3.181456 GCAGAGCTTTGGACCTGATATCT 60.181 47.826 6.36 0.00 0.00 1.98
4059 4304 4.569966 CCTGATATCTGAGTGTGTTCTTGC 59.430 45.833 10.93 0.00 0.00 4.01
4210 4458 6.656693 AGCATGTATATGTTATCTTGGCTTCC 59.343 38.462 1.14 0.00 36.65 3.46
4223 4471 4.404394 TCTTGGCTTCCGATACATAACTGA 59.596 41.667 0.00 0.00 0.00 3.41
4233 4481 4.723862 CGATACATAACTGAAACTTTGCGC 59.276 41.667 0.00 0.00 0.00 6.09
4360 4608 3.248602 GTCTCGTGTTCTGTCTTGCAAAT 59.751 43.478 0.00 0.00 0.00 2.32
4556 4804 5.183904 ACATTTACTTGTCAGAATTCCAGGC 59.816 40.000 0.65 0.00 0.00 4.85
4589 4842 9.824534 AAAAATTGAATTGACCATTAAAATCGC 57.175 25.926 0.00 0.00 0.00 4.58
4601 4854 5.508922 CCATTAAAATCGCAAGCAAAAATGC 59.491 36.000 0.00 0.00 39.17 3.56
4675 4928 3.289407 AGGCCTTTTCAGGAAGATAGC 57.711 47.619 0.00 0.00 44.19 2.97
4787 5177 6.133356 TCCCACTGAAAAGAAATACCACTTT 58.867 36.000 0.00 0.00 37.85 2.66
4796 5186 6.463995 AAGAAATACCACTTTGTTGCTTGA 57.536 33.333 0.00 0.00 0.00 3.02
4826 5217 0.673985 GTGTCCCAAAAGACCAAGGC 59.326 55.000 0.00 0.00 35.83 4.35
4935 5326 7.310485 CCCTGTCCAGAAAGTTATTACTAGTGT 60.310 40.741 5.39 0.00 33.17 3.55
4938 5329 9.485206 TGTCCAGAAAGTTATTACTAGTGTTTC 57.515 33.333 5.39 5.34 33.17 2.78
4974 5366 3.353342 GGGAGGATCATTGCATCCC 57.647 57.895 3.58 3.58 43.31 3.85
4999 5391 3.776656 CGTTGTGCTACGTAGGGC 58.223 61.111 23.47 12.00 36.80 5.19
5005 5397 1.325355 GTGCTACGTAGGGCAGGATA 58.675 55.000 23.47 0.00 40.40 2.59
5016 5408 5.299279 CGTAGGGCAGGATATTGTTTCAAAT 59.701 40.000 0.00 0.00 0.00 2.32
5017 5409 6.485313 CGTAGGGCAGGATATTGTTTCAAATA 59.515 38.462 0.00 0.00 0.00 1.40
5018 5410 6.715347 AGGGCAGGATATTGTTTCAAATAC 57.285 37.500 0.00 0.00 0.00 1.89
5020 5412 6.547510 AGGGCAGGATATTGTTTCAAATACTC 59.452 38.462 0.00 0.00 0.00 2.59
5033 5546 6.928348 TTCAAATACTCCTACTTGGACTGA 57.072 37.500 0.00 0.00 40.56 3.41
5041 5554 2.105821 CCTACTTGGACTGAACCAACCA 59.894 50.000 0.00 0.00 43.79 3.67
5131 5644 7.665561 TTTTATGCCAAACAATTAGAAAGGC 57.334 32.000 0.00 0.00 40.93 4.35
5133 5646 4.679373 TGCCAAACAATTAGAAAGGCAA 57.321 36.364 0.00 0.00 46.55 4.52
5134 5647 4.630111 TGCCAAACAATTAGAAAGGCAAG 58.370 39.130 0.00 0.00 46.55 4.01
5135 5648 3.996363 GCCAAACAATTAGAAAGGCAAGG 59.004 43.478 0.00 0.00 40.29 3.61
5136 5649 3.996363 CCAAACAATTAGAAAGGCAAGGC 59.004 43.478 0.00 0.00 0.00 4.35
5137 5650 4.502950 CCAAACAATTAGAAAGGCAAGGCA 60.503 41.667 0.00 0.00 0.00 4.75
5142 5655 7.516198 ACAATTAGAAAGGCAAGGCATATAG 57.484 36.000 0.00 0.00 0.00 1.31
5199 5712 7.556844 TGGGAACAGAGAATGAACTCTATTAC 58.443 38.462 0.00 0.00 44.18 1.89
5254 5773 0.753262 AGCATCCTAGTTAGGTGGCG 59.247 55.000 5.16 0.00 43.35 5.69
5256 5775 0.464036 CATCCTAGTTAGGTGGCGCA 59.536 55.000 10.83 0.00 44.02 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
117 118 2.197324 CGGAGGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
118 119 1.152839 GACGGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
119 120 3.008408 GACGGAGGAGGAGGAGGA 58.992 66.667 0.00 0.00 0.00 3.71
120 121 2.517402 CGACGGAGGAGGAGGAGG 60.517 72.222 0.00 0.00 0.00 4.30
121 122 3.213402 GCGACGGAGGAGGAGGAG 61.213 72.222 0.00 0.00 0.00 3.69
335 352 1.606889 ACCGACGCTCCTCCTTCTT 60.607 57.895 0.00 0.00 0.00 2.52
414 431 2.196382 CTCGTCCGCCTTCTCGTTGA 62.196 60.000 0.00 0.00 0.00 3.18
459 476 2.937149 CAGAGATCGACGTACTTCTCCA 59.063 50.000 14.22 0.00 36.16 3.86
503 521 2.049433 CGTGGAGAAGCCGAACGT 60.049 61.111 0.00 0.00 40.66 3.99
529 548 2.740826 GCGAGGTTGCGGCAACTA 60.741 61.111 36.11 7.29 43.14 2.24
633 689 6.803320 AGAAATTGCACAAACATAGTTCATCG 59.197 34.615 0.00 0.00 0.00 3.84
700 759 2.644555 ATACGCGGCCGAGCAGAATT 62.645 55.000 33.48 11.43 38.29 2.17
701 760 3.151958 ATACGCGGCCGAGCAGAAT 62.152 57.895 33.48 14.90 38.29 2.40
785 844 0.323908 AGAGCAACTCTAGCGGACCT 60.324 55.000 0.00 0.00 39.28 3.85
790 849 5.822278 TGAGTATTTAGAGCAACTCTAGCG 58.178 41.667 4.64 0.00 42.92 4.26
807 866 6.239120 GCATTTCCCTTGCAACATATGAGTAT 60.239 38.462 10.38 0.00 39.90 2.12
811 870 3.181488 CGCATTTCCCTTGCAACATATGA 60.181 43.478 10.38 0.00 40.14 2.15
812 871 3.117794 CGCATTTCCCTTGCAACATATG 58.882 45.455 0.00 0.00 40.14 1.78
813 872 2.760092 ACGCATTTCCCTTGCAACATAT 59.240 40.909 0.00 0.00 40.14 1.78
814 873 2.094803 CACGCATTTCCCTTGCAACATA 60.095 45.455 0.00 0.00 40.14 2.29
815 874 0.968405 ACGCATTTCCCTTGCAACAT 59.032 45.000 0.00 0.00 40.14 2.71
816 875 0.031857 CACGCATTTCCCTTGCAACA 59.968 50.000 0.00 0.00 40.14 3.33
817 876 1.284297 GCACGCATTTCCCTTGCAAC 61.284 55.000 0.00 0.00 40.14 4.17
818 877 1.006337 GCACGCATTTCCCTTGCAA 60.006 52.632 0.00 0.00 40.14 4.08
819 878 1.865788 GAGCACGCATTTCCCTTGCA 61.866 55.000 0.00 0.00 40.14 4.08
820 879 1.153958 GAGCACGCATTTCCCTTGC 60.154 57.895 0.00 0.00 36.74 4.01
821 880 1.135315 CGAGCACGCATTTCCCTTG 59.865 57.895 0.00 0.00 0.00 3.61
822 881 0.889186 AACGAGCACGCATTTCCCTT 60.889 50.000 2.62 0.00 43.96 3.95
823 882 1.298859 GAACGAGCACGCATTTCCCT 61.299 55.000 2.62 0.00 43.96 4.20
824 883 1.134694 GAACGAGCACGCATTTCCC 59.865 57.895 2.62 0.00 43.96 3.97
825 884 1.134694 GGAACGAGCACGCATTTCC 59.865 57.895 2.62 6.06 43.96 3.13
826 885 1.134694 GGGAACGAGCACGCATTTC 59.865 57.895 2.62 0.00 43.96 2.17
827 886 1.298859 GAGGGAACGAGCACGCATTT 61.299 55.000 2.62 0.00 43.96 2.32
828 887 1.741770 GAGGGAACGAGCACGCATT 60.742 57.895 2.62 0.00 43.96 3.56
829 888 2.125512 GAGGGAACGAGCACGCAT 60.126 61.111 2.62 0.00 43.96 4.73
830 889 4.717629 CGAGGGAACGAGCACGCA 62.718 66.667 2.62 0.00 43.96 5.24
831 890 3.909258 TTCGAGGGAACGAGCACGC 62.909 63.158 2.62 0.00 43.04 5.34
832 891 0.942410 TTTTCGAGGGAACGAGCACG 60.942 55.000 0.76 0.76 43.04 5.34
833 892 1.223187 TTTTTCGAGGGAACGAGCAC 58.777 50.000 0.00 0.00 43.04 4.40
834 893 3.690487 TTTTTCGAGGGAACGAGCA 57.310 47.368 0.00 0.00 43.04 4.26
851 910 0.951558 AATGACGAGCACGCCTTTTT 59.048 45.000 2.62 0.00 43.96 1.94
855 914 1.076332 GTAAAATGACGAGCACGCCT 58.924 50.000 2.62 0.00 43.96 5.52
1260 1323 1.617018 CGAGAGAATGGAGGGTGGCA 61.617 60.000 0.00 0.00 0.00 4.92
1274 1337 1.080025 GGTGGTTCGTTCCCGAGAG 60.080 63.158 0.00 0.00 45.24 3.20
1309 1380 8.648698 TGGAGATGGAAATCAAACTTCATTTA 57.351 30.769 0.00 0.00 0.00 1.40
1313 1384 7.452501 AGAAATGGAGATGGAAATCAAACTTCA 59.547 33.333 0.00 0.00 0.00 3.02
1374 1445 8.712103 GGGAATTAAAACCAGGTAGTAGTATCT 58.288 37.037 0.00 0.00 0.00 1.98
1375 1446 7.935755 GGGGAATTAAAACCAGGTAGTAGTATC 59.064 40.741 0.00 0.00 0.00 2.24
1377 1448 6.734755 TGGGGAATTAAAACCAGGTAGTAGTA 59.265 38.462 0.00 0.00 0.00 1.82
1378 1449 5.552766 TGGGGAATTAAAACCAGGTAGTAGT 59.447 40.000 0.00 0.00 0.00 2.73
1379 1450 5.884232 GTGGGGAATTAAAACCAGGTAGTAG 59.116 44.000 0.00 0.00 32.84 2.57
1380 1451 5.552766 AGTGGGGAATTAAAACCAGGTAGTA 59.447 40.000 0.00 0.00 32.84 1.82
1382 1453 4.930696 AGTGGGGAATTAAAACCAGGTAG 58.069 43.478 0.00 0.00 32.84 3.18
1384 1455 3.501568 GGAGTGGGGAATTAAAACCAGGT 60.502 47.826 0.00 0.00 32.84 4.00
1386 1457 3.773560 TGGAGTGGGGAATTAAAACCAG 58.226 45.455 0.00 0.00 32.84 4.00
1393 1464 2.559231 GCGTTTTTGGAGTGGGGAATTA 59.441 45.455 0.00 0.00 0.00 1.40
1406 1477 0.917939 GTTCGTGTTGGGCGTTTTTG 59.082 50.000 0.00 0.00 0.00 2.44
1411 1483 0.877213 GTACTGTTCGTGTTGGGCGT 60.877 55.000 0.00 0.00 0.00 5.68
1416 1488 3.553917 TGTCACATGTACTGTTCGTGTTG 59.446 43.478 9.23 6.31 35.29 3.33
1445 1517 5.108891 GCGAACGCCGTTAATCATTTTAATC 60.109 40.000 0.79 0.00 41.15 1.75
1446 1518 4.731480 GCGAACGCCGTTAATCATTTTAAT 59.269 37.500 0.79 0.00 41.15 1.40
1457 1529 3.803231 ACATAATTATGCGAACGCCGTTA 59.197 39.130 22.66 9.95 41.09 3.18
1459 1531 2.033236 CACATAATTATGCGAACGCCGT 60.033 45.455 22.66 7.90 41.09 5.68
1462 1534 2.546368 TCCCACATAATTATGCGAACGC 59.454 45.455 22.66 12.33 37.19 4.84
1463 1535 4.690748 AGATCCCACATAATTATGCGAACG 59.309 41.667 22.66 8.35 37.19 3.95
1467 1539 6.205464 ACAAGAAGATCCCACATAATTATGCG 59.795 38.462 22.66 14.70 37.19 4.73
1475 1547 3.772572 TCGGAACAAGAAGATCCCACATA 59.227 43.478 0.00 0.00 35.86 2.29
1477 1549 1.974957 TCGGAACAAGAAGATCCCACA 59.025 47.619 0.00 0.00 35.86 4.17
1479 1551 2.159099 CGATCGGAACAAGAAGATCCCA 60.159 50.000 7.38 0.00 35.86 4.37
1480 1552 2.474816 CGATCGGAACAAGAAGATCCC 58.525 52.381 7.38 0.00 35.86 3.85
1481 1553 1.861575 GCGATCGGAACAAGAAGATCC 59.138 52.381 18.30 0.00 35.92 3.36
1482 1554 2.792116 GAGCGATCGGAACAAGAAGATC 59.208 50.000 18.30 0.00 0.00 2.75
1487 1571 1.404181 CCAAGAGCGATCGGAACAAGA 60.404 52.381 18.30 0.00 0.00 3.02
1495 1579 1.846782 CGAAACTACCAAGAGCGATCG 59.153 52.381 11.69 11.69 0.00 3.69
1497 1581 2.607187 CACGAAACTACCAAGAGCGAT 58.393 47.619 0.00 0.00 0.00 4.58
1501 1585 3.005472 TCTCACCACGAAACTACCAAGAG 59.995 47.826 0.00 0.00 0.00 2.85
1503 1587 3.380479 TCTCACCACGAAACTACCAAG 57.620 47.619 0.00 0.00 0.00 3.61
1514 1598 3.045601 AGACCATCTTTTCTCACCACG 57.954 47.619 0.00 0.00 0.00 4.94
1545 1629 0.609131 ACCACAATTCGGGCAAGGAG 60.609 55.000 0.00 0.00 0.00 3.69
1581 1665 6.974932 TGAGAATCTTTAGCACTGTGATTC 57.025 37.500 12.86 10.28 41.67 2.52
1618 1702 6.626302 ACTAACAATCTTAGCTCTGTGAGAC 58.374 40.000 0.00 0.00 0.00 3.36
1619 1703 6.842437 ACTAACAATCTTAGCTCTGTGAGA 57.158 37.500 0.00 0.00 0.00 3.27
1620 1704 7.767261 ACTACTAACAATCTTAGCTCTGTGAG 58.233 38.462 0.00 0.00 0.00 3.51
1621 1705 7.704578 ACTACTAACAATCTTAGCTCTGTGA 57.295 36.000 0.00 0.00 0.00 3.58
1622 1706 7.646130 GCTACTACTAACAATCTTAGCTCTGTG 59.354 40.741 0.00 0.00 0.00 3.66
1623 1707 7.339721 TGCTACTACTAACAATCTTAGCTCTGT 59.660 37.037 0.00 0.00 33.22 3.41
1624 1708 7.708051 TGCTACTACTAACAATCTTAGCTCTG 58.292 38.462 0.00 0.00 33.22 3.35
1688 1780 4.082125 GCCCCAATAAAGCATAGCTACAT 58.918 43.478 0.00 0.00 38.25 2.29
1709 1801 1.527034 TTGTGCTTGACTCATCTGGC 58.473 50.000 0.00 0.00 0.00 4.85
1749 1841 1.286501 TGTGCGAACTTGTCAGTGAC 58.713 50.000 16.68 16.68 31.60 3.67
1759 1851 3.305881 GGAGGTAGTTAGTTGTGCGAACT 60.306 47.826 0.00 6.23 43.68 3.01
1760 1852 2.991866 GGAGGTAGTTAGTTGTGCGAAC 59.008 50.000 0.00 0.00 33.67 3.95
1771 1863 3.258372 CAGACTTGCACAGGAGGTAGTTA 59.742 47.826 0.00 0.00 0.00 2.24
1774 1866 1.620819 ACAGACTTGCACAGGAGGTAG 59.379 52.381 0.00 0.00 0.00 3.18
1775 1867 1.344438 CACAGACTTGCACAGGAGGTA 59.656 52.381 0.00 0.00 0.00 3.08
1776 1868 0.107456 CACAGACTTGCACAGGAGGT 59.893 55.000 0.00 0.00 0.00 3.85
1777 1869 0.394192 TCACAGACTTGCACAGGAGG 59.606 55.000 0.00 0.00 0.00 4.30
1799 1891 8.675504 GCTACAGATGTAAGAAGTACTGTAAGA 58.324 37.037 0.00 0.00 39.29 2.10
1800 1892 7.640630 CGCTACAGATGTAAGAAGTACTGTAAG 59.359 40.741 0.00 0.00 39.29 2.34
1801 1893 7.414873 CCGCTACAGATGTAAGAAGTACTGTAA 60.415 40.741 0.00 0.00 39.29 2.41
1802 1894 6.037940 CCGCTACAGATGTAAGAAGTACTGTA 59.962 42.308 0.00 0.00 38.99 2.74
1803 1895 5.163642 CCGCTACAGATGTAAGAAGTACTGT 60.164 44.000 0.00 0.00 40.74 3.55
1804 1896 5.274718 CCGCTACAGATGTAAGAAGTACTG 58.725 45.833 0.00 0.00 33.46 2.74
1805 1897 4.338682 CCCGCTACAGATGTAAGAAGTACT 59.661 45.833 0.00 0.00 33.46 2.73
1806 1898 4.337555 TCCCGCTACAGATGTAAGAAGTAC 59.662 45.833 0.00 0.00 0.00 2.73
1807 1899 4.529897 TCCCGCTACAGATGTAAGAAGTA 58.470 43.478 0.00 0.00 0.00 2.24
1808 1900 3.362706 TCCCGCTACAGATGTAAGAAGT 58.637 45.455 0.00 0.00 0.00 3.01
1809 1901 3.797184 GCTCCCGCTACAGATGTAAGAAG 60.797 52.174 0.00 0.00 0.00 2.85
1810 1902 2.100916 GCTCCCGCTACAGATGTAAGAA 59.899 50.000 0.00 0.00 0.00 2.52
1829 1921 1.001974 TGAAATACTGGTGCTCGTGCT 59.998 47.619 11.19 0.00 40.48 4.40
1830 1922 1.438651 TGAAATACTGGTGCTCGTGC 58.561 50.000 1.71 1.71 40.20 5.34
1831 1923 5.580691 TCTTTATGAAATACTGGTGCTCGTG 59.419 40.000 0.00 0.00 0.00 4.35
1832 1924 5.730550 TCTTTATGAAATACTGGTGCTCGT 58.269 37.500 0.00 0.00 0.00 4.18
1833 1925 6.042777 TCTCTTTATGAAATACTGGTGCTCG 58.957 40.000 0.00 0.00 0.00 5.03
1834 1926 7.010923 CACTCTCTTTATGAAATACTGGTGCTC 59.989 40.741 0.00 0.00 0.00 4.26
1875 1967 3.054878 GCATGTGCAGTTGAAAAAGAGG 58.945 45.455 0.00 0.00 41.59 3.69
1899 1992 9.353999 CTTGACAGTAATTTATTAACTTTGGCC 57.646 33.333 0.00 0.00 0.00 5.36
1915 2008 2.041081 CCCAACCCCATCTTGACAGTAA 59.959 50.000 0.00 0.00 0.00 2.24
1927 2020 2.200092 GCAGAAACCCCAACCCCA 59.800 61.111 0.00 0.00 0.00 4.96
1928 2021 1.908299 CTGCAGAAACCCCAACCCC 60.908 63.158 8.42 0.00 0.00 4.95
1929 2022 0.251787 ATCTGCAGAAACCCCAACCC 60.252 55.000 22.50 0.00 0.00 4.11
1930 2023 2.290960 ACTATCTGCAGAAACCCCAACC 60.291 50.000 22.50 0.00 0.00 3.77
1931 2024 2.749621 CACTATCTGCAGAAACCCCAAC 59.250 50.000 22.50 0.00 0.00 3.77
1932 2025 2.375174 ACACTATCTGCAGAAACCCCAA 59.625 45.455 22.50 0.00 0.00 4.12
2108 2201 1.134175 AGAGCTAGCTGACGAAAGAGC 59.866 52.381 24.99 3.00 35.28 4.09
2158 2251 6.512342 TTTAACCCTGTTTTCACGAAAGAA 57.488 33.333 0.00 0.00 0.00 2.52
2159 2252 6.512342 TTTTAACCCTGTTTTCACGAAAGA 57.488 33.333 0.00 0.00 0.00 2.52
2169 2262 6.785337 ACTGCTAACTTTTTAACCCTGTTT 57.215 33.333 0.00 0.00 0.00 2.83
2175 2268 9.229784 GAAGTAACAACTGCTAACTTTTTAACC 57.770 33.333 0.00 0.00 30.83 2.85
2190 2292 9.030452 ACTGAGAGAGATATTGAAGTAACAACT 57.970 33.333 0.00 0.00 32.50 3.16
2206 2310 6.918067 TCCAACAGAAATTACTGAGAGAGA 57.082 37.500 0.00 0.00 40.63 3.10
2218 2322 5.733620 AGCACATTGAATCCAACAGAAAT 57.266 34.783 0.00 0.00 34.72 2.17
2238 2342 2.563179 TCTTTGTCCTGGTCAGACTAGC 59.437 50.000 8.44 0.00 0.00 3.42
2261 2365 6.017933 GTCTTGCTGAAATCATCAAACTACG 58.982 40.000 1.87 0.00 37.67 3.51
2276 2380 4.639755 TGAAATCACACTTTGTCTTGCTGA 59.360 37.500 0.00 0.00 0.00 4.26
2277 2381 4.923893 TGAAATCACACTTTGTCTTGCTG 58.076 39.130 0.00 0.00 0.00 4.41
2278 2382 4.498682 GCTGAAATCACACTTTGTCTTGCT 60.499 41.667 0.00 0.00 0.00 3.91
2515 2639 1.669502 GCAAAGTCGGCAATTGCATGA 60.670 47.619 30.32 23.53 46.57 3.07
2578 2702 2.070783 GCACCGTTTTACGAGGATGAA 58.929 47.619 0.05 0.00 46.05 2.57
2582 2706 0.104487 TGTGCACCGTTTTACGAGGA 59.896 50.000 15.69 0.00 46.05 3.71
2586 2710 2.970609 CTGAAATGTGCACCGTTTTACG 59.029 45.455 15.69 4.87 42.11 3.18
2647 2779 2.384828 TGTGTATCAGACGTGCCCTAT 58.615 47.619 0.00 0.00 0.00 2.57
2653 2785 9.122613 CAGAATAATCTATGTGTATCAGACGTG 57.877 37.037 0.00 0.00 33.50 4.49
2655 2787 9.684448 AACAGAATAATCTATGTGTATCAGACG 57.316 33.333 0.00 0.00 33.50 4.18
2677 2809 4.811555 TGATTCTCGGTCAAACAAACAG 57.188 40.909 0.00 0.00 0.00 3.16
2687 2819 2.606725 CAGCTTCACATGATTCTCGGTC 59.393 50.000 0.00 0.00 0.00 4.79
2689 2821 1.329906 GCAGCTTCACATGATTCTCGG 59.670 52.381 0.00 0.00 0.00 4.63
2690 2822 2.277969 AGCAGCTTCACATGATTCTCG 58.722 47.619 0.00 0.00 0.00 4.04
2694 2826 3.418995 ACAAGAGCAGCTTCACATGATT 58.581 40.909 0.00 0.00 33.60 2.57
2695 2827 3.069079 ACAAGAGCAGCTTCACATGAT 57.931 42.857 0.00 0.00 33.60 2.45
2718 2850 4.981806 TGTGAAGAAAACAACCTGAAGG 57.018 40.909 0.00 0.00 42.17 3.46
2721 2853 7.035004 CAGAATTTGTGAAGAAAACAACCTGA 58.965 34.615 0.00 0.00 37.26 3.86
2817 2949 4.338879 CATTCCCATGGTATCCATTCCTC 58.661 47.826 11.73 0.00 42.23 3.71
2859 2991 1.055849 TCCAGTTGGCTTGAGCAGTA 58.944 50.000 5.24 0.00 44.36 2.74
2869 3001 5.408299 GGACAACATTAAATTTCCAGTTGGC 59.592 40.000 22.54 21.01 42.64 4.52
2964 3204 2.353011 GGTCTGGACACATTGCAAATGG 60.353 50.000 16.06 6.77 0.00 3.16
3334 3574 0.462759 CGAATCCCCAGAAGTGGCTC 60.463 60.000 0.00 0.00 43.44 4.70
3385 3625 3.057969 TCAGTACTCACCTTTGCCATG 57.942 47.619 0.00 0.00 0.00 3.66
3401 3641 6.591935 TGAAAACTGTGGAGAAACTATCAGT 58.408 36.000 0.00 0.00 37.68 3.41
3434 3674 8.790718 ACATATAATGGAATGCATGAACTCTTC 58.209 33.333 0.00 0.00 33.60 2.87
3480 3723 7.931948 AGCCTATAGTTTGATACATTGTACACC 59.068 37.037 0.00 0.00 0.00 4.16
3584 3828 0.671163 TGCGGGTTAACACCTTAGCG 60.671 55.000 8.10 0.00 43.65 4.26
3656 3900 2.300152 CTCCAGTACCTTGAGAACAGCA 59.700 50.000 0.00 0.00 0.00 4.41
3731 3975 3.181525 GCTTCTCTTTCAGAGCGTTAAGC 60.182 47.826 8.39 8.39 42.04 3.09
3769 4013 5.048782 TGTTTGCGATGTGATTTTTCTAGCT 60.049 36.000 0.00 0.00 0.00 3.32
3851 4096 1.212250 GGAGGCCTTTCCCCCTAACA 61.212 60.000 6.77 0.00 34.51 2.41
3957 4202 5.694910 AGTTCGTCAGTTCGTGTAATCAATT 59.305 36.000 0.00 0.00 0.00 2.32
3979 4224 0.797542 GTACAGAGACGCGACAGAGT 59.202 55.000 15.93 9.08 0.00 3.24
4045 4290 2.288666 GTTCAGGCAAGAACACACTCA 58.711 47.619 15.22 0.00 45.53 3.41
4059 4304 1.586422 CACGCCCATATCTGTTCAGG 58.414 55.000 0.00 0.00 0.00 3.86
4210 4458 4.723862 GCGCAAAGTTTCAGTTATGTATCG 59.276 41.667 0.30 0.00 0.00 2.92
4223 4471 1.724582 AAGTCTGCGGCGCAAAGTTT 61.725 50.000 35.41 22.50 38.41 2.66
4233 4481 1.485397 CTCGATCATGAAGTCTGCGG 58.515 55.000 0.00 0.00 0.00 5.69
4360 4608 3.112842 GCATGTGCGCATCATGGA 58.887 55.556 33.57 12.54 41.77 3.41
4464 4712 9.784531 ACATGTATCATAAAAGCTGCTATAACT 57.215 29.630 0.90 0.00 0.00 2.24
4470 4718 7.389884 CAGGATACATGTATCATAAAAGCTGCT 59.610 37.037 35.28 21.38 42.76 4.24
4567 4820 7.201548 GCTTGCGATTTTAATGGTCAATTCAAT 60.202 33.333 0.00 0.00 0.00 2.57
4601 4854 6.710295 TGTTCCATATCCGGTTGATTATCAAG 59.290 38.462 8.00 0.00 37.00 3.02
4642 4895 2.717639 AAGGCCTAGCTATGGTTGTG 57.282 50.000 5.16 0.00 0.00 3.33
4770 5160 7.491048 TCAAGCAACAAAGTGGTATTTCTTTTC 59.509 33.333 0.00 0.00 32.52 2.29
4772 5162 6.872920 TCAAGCAACAAAGTGGTATTTCTTT 58.127 32.000 0.00 0.00 34.74 2.52
4787 5177 3.081061 ACACACTTTGTCTCAAGCAACA 58.919 40.909 0.00 0.00 29.79 3.33
4796 5186 2.799126 TTGGGACACACACTTTGTCT 57.201 45.000 2.73 0.00 42.63 3.41
4826 5217 1.379843 ACCCAAAATGCCTAGCCCG 60.380 57.895 0.00 0.00 0.00 6.13
4935 5326 5.370289 TCCCAGAACCTAGTAAAACTGGAAA 59.630 40.000 0.00 0.00 45.02 3.13
4938 5329 4.323562 CCTCCCAGAACCTAGTAAAACTGG 60.324 50.000 0.00 0.00 42.82 4.00
4974 5366 2.738730 CGTAGCACAACGTTTAGTCG 57.261 50.000 0.00 0.00 38.07 4.18
4999 5391 9.838339 AGTAGGAGTATTTGAAACAATATCCTG 57.162 33.333 0.00 0.00 36.17 3.86
5020 5412 2.105821 TGGTTGGTTCAGTCCAAGTAGG 59.894 50.000 0.00 0.00 46.35 3.18
5033 5546 1.140652 CAAATGCCTTGGTGGTTGGTT 59.859 47.619 0.00 0.00 38.35 3.67
5041 5554 5.481473 ACATCTTTATGTCAAATGCCTTGGT 59.519 36.000 0.00 0.00 42.92 3.67
5136 5649 8.873830 CCTATTTACCGAATCTTGCACTATATG 58.126 37.037 0.00 0.00 0.00 1.78
5137 5650 8.594550 ACCTATTTACCGAATCTTGCACTATAT 58.405 33.333 0.00 0.00 0.00 0.86
5142 5655 7.492352 AATACCTATTTACCGAATCTTGCAC 57.508 36.000 0.00 0.00 0.00 4.57
5156 5669 9.408648 CTGTTCCCATGTCTTAAATACCTATTT 57.591 33.333 0.00 0.00 39.14 1.40
5199 5712 7.436673 GCTTAAGACAAGAGGTACTGATGTATG 59.563 40.741 6.67 0.00 41.55 2.39
5254 5773 1.230635 TTCTCGTGGAAGCAAGCTGC 61.231 55.000 0.00 0.00 45.46 5.25
5256 5775 3.223661 CTTCTCGTGGAAGCAAGCT 57.776 52.632 7.65 0.00 43.88 3.74


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

AutoCloner maintained by Alex Coulton.