Multiple sequence alignment - TraesCS4A01G409500

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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 TraesCS4A01G409500 chr4A 100.000 2717 0 0 1 2717 681935744 681933028 0.000000e+00 5018.0
1 TraesCS4A01G409500 chr4A 87.097 93 9 3 2110 2200 704171912 704171821 4.790000e-18 102.0
2 TraesCS4A01G409500 chr4D 89.926 2035 115 49 744 2717 475202278 475200273 0.000000e+00 2540.0
3 TraesCS4A01G409500 chr4B 93.438 1463 54 23 783 2208 599957915 599956458 0.000000e+00 2132.0
4 TraesCS4A01G409500 chr4B 83.737 578 59 14 1 545 599958566 599957991 5.190000e-142 514.0
5 TraesCS4A01G409500 chr7A 84.000 925 56 32 1016 1871 496085939 496085038 0.000000e+00 804.0
6 TraesCS4A01G409500 chr7A 83.019 106 15 3 2114 2217 18120563 18120459 2.880000e-15 93.5
7 TraesCS4A01G409500 chr7A 82.653 98 16 1 221 317 581032759 581032856 4.820000e-13 86.1
8 TraesCS4A01G409500 chr7A 94.444 54 3 0 1869 1922 496084886 496084833 1.730000e-12 84.2
9 TraesCS4A01G409500 chr7D 83.843 916 62 37 1016 1868 445459926 445460818 0.000000e+00 793.0
10 TraesCS4A01G409500 chr7D 85.315 143 15 6 542 680 545351653 545351513 2.820000e-30 143.0
11 TraesCS4A01G409500 chr7D 91.228 57 5 0 1866 1922 445460963 445461019 8.070000e-11 78.7
12 TraesCS4A01G409500 chr7B 82.972 922 68 35 1016 1868 462060805 462061706 0.000000e+00 750.0
13 TraesCS4A01G409500 chr7B 86.667 135 13 5 541 672 540065244 540065376 7.840000e-31 145.0
14 TraesCS4A01G409500 chr7B 83.607 122 17 3 2098 2217 27814853 27814973 7.950000e-21 111.0
15 TraesCS4A01G409500 chr7B 92.982 57 4 0 1866 1922 462061841 462061897 1.730000e-12 84.2
16 TraesCS4A01G409500 chr1A 88.148 135 12 4 541 672 2161885 2162018 1.010000e-34 158.0
17 TraesCS4A01G409500 chr1A 84.466 103 13 3 2110 2210 578929465 578929364 6.190000e-17 99.0
18 TraesCS4A01G409500 chr6A 86.567 134 16 2 557 689 542709362 542709494 2.180000e-31 147.0
19 TraesCS4A01G409500 chr6A 84.138 145 19 3 537 678 381084353 381084210 1.310000e-28 137.0
20 TraesCS4A01G409500 chr6A 81.000 100 13 5 451 546 501886435 501886338 1.040000e-09 75.0
21 TraesCS4A01G409500 chr5A 86.232 138 15 4 542 676 675668164 675668300 2.180000e-31 147.0
22 TraesCS4A01G409500 chr2D 86.232 138 14 5 539 672 632057854 632057990 7.840000e-31 145.0
23 TraesCS4A01G409500 chr3B 85.926 135 16 3 556 689 545011360 545011228 1.010000e-29 141.0
24 TraesCS4A01G409500 chr3B 83.784 111 13 5 2110 2217 662419336 662419228 1.720000e-17 100.0
25 TraesCS4A01G409500 chr3B 84.615 104 11 5 2110 2210 365501979 365501878 6.190000e-17 99.0
26 TraesCS4A01G409500 chrUn 84.106 151 17 7 524 671 254470595 254470449 3.650000e-29 139.0
27 TraesCS4A01G409500 chr5B 84.545 110 13 4 2110 2217 649452855 649452962 3.700000e-19 106.0
28 TraesCS4A01G409500 chr5B 82.727 110 16 3 2110 2217 470054891 470054783 8.010000e-16 95.3
29 TraesCS4A01G409500 chr5D 83.962 106 14 3 2114 2217 488833202 488833098 6.190000e-17 99.0


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 TraesCS4A01G409500 chr4A 681933028 681935744 2716 True 5018.00 5018 100.0000 1 2717 1 chr4A.!!$R1 2716
1 TraesCS4A01G409500 chr4D 475200273 475202278 2005 True 2540.00 2540 89.9260 744 2717 1 chr4D.!!$R1 1973
2 TraesCS4A01G409500 chr4B 599956458 599958566 2108 True 1323.00 2132 88.5875 1 2208 2 chr4B.!!$R1 2207
3 TraesCS4A01G409500 chr7A 496084833 496085939 1106 True 444.10 804 89.2220 1016 1922 2 chr7A.!!$R2 906
4 TraesCS4A01G409500 chr7D 445459926 445461019 1093 False 435.85 793 87.5355 1016 1922 2 chr7D.!!$F1 906
5 TraesCS4A01G409500 chr7B 462060805 462061897 1092 False 417.10 750 87.9770 1016 1922 2 chr7B.!!$F3 906

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
155 161 0.105593 AGACATGCCAGACATAGCCG 59.894 55.0 0.0 0.0 36.64 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2235 0.586319 GCACTAAGCGCAAGACAACA 59.414 50.0 11.47 0.0 43.02 3.33 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
24 25 3.190439 ACTAAGCCCCATAAGAAGGTGT 58.810 45.455 0.00 0.00 0.00 4.16
36 37 7.106239 CCATAAGAAGGTGTCATACTTGTTCT 58.894 38.462 6.08 0.00 33.11 3.01
44 45 6.042781 AGGTGTCATACTTGTTCTAAAGGTGA 59.957 38.462 0.00 0.00 0.00 4.02
80 83 2.010817 CCTTTGAAACAGCGCACGC 61.011 57.895 11.47 6.99 42.33 5.34
97 103 2.670905 CACGCGTACATCAAGAATGGAA 59.329 45.455 13.44 0.00 39.90 3.53
118 124 4.015872 AGCCAAGTAAAATTCCACTCGA 57.984 40.909 0.00 0.00 0.00 4.04
119 125 4.589908 AGCCAAGTAAAATTCCACTCGAT 58.410 39.130 0.00 0.00 0.00 3.59
121 127 4.494199 GCCAAGTAAAATTCCACTCGATCG 60.494 45.833 9.36 9.36 0.00 3.69
126 132 3.543680 AAATTCCACTCGATCGTCCAT 57.456 42.857 15.94 0.00 0.00 3.41
134 140 1.270826 CTCGATCGTCCATATGCAGGT 59.729 52.381 15.94 0.00 0.00 4.00
140 146 3.028130 TCGTCCATATGCAGGTAAGACA 58.972 45.455 0.00 0.00 0.00 3.41
151 157 4.406648 CAGGTAAGACATGCCAGACATA 57.593 45.455 0.00 0.00 36.64 2.29
153 159 3.134458 GGTAAGACATGCCAGACATAGC 58.866 50.000 0.00 0.00 36.64 2.97
155 161 0.105593 AGACATGCCAGACATAGCCG 59.894 55.000 0.00 0.00 36.64 5.52
156 162 0.882042 GACATGCCAGACATAGCCGG 60.882 60.000 0.00 0.00 36.64 6.13
157 163 1.337384 ACATGCCAGACATAGCCGGA 61.337 55.000 5.05 0.00 36.64 5.14
170 176 0.400213 AGCCGGAACCACATGAAAGA 59.600 50.000 5.05 0.00 0.00 2.52
172 178 1.133025 GCCGGAACCACATGAAAGATG 59.867 52.381 5.05 0.00 0.00 2.90
173 179 1.745087 CCGGAACCACATGAAAGATGG 59.255 52.381 0.00 0.00 39.57 3.51
178 184 4.878397 GGAACCACATGAAAGATGGTCTAG 59.122 45.833 0.00 0.00 46.18 2.43
190 196 7.180229 TGAAAGATGGTCTAGGACATGTTTCTA 59.820 37.037 28.66 20.46 36.15 2.10
219 225 4.862574 CACGTCTAGTGGATTTCGAAATGA 59.137 41.667 27.27 14.15 46.77 2.57
229 235 5.154222 GGATTTCGAAATGACCACAAAGTC 58.846 41.667 27.27 9.35 37.28 3.01
236 242 6.015504 CGAAATGACCACAAAGTCTAAATCG 58.984 40.000 0.00 0.00 37.66 3.34
256 262 2.795329 GTGACCCCTCACACAATTGAT 58.205 47.619 13.59 0.00 45.57 2.57
284 290 5.070001 TGTTTATGCTTAGCCAAGTCACTT 58.930 37.500 0.29 0.00 34.00 3.16
288 294 4.079980 TGCTTAGCCAAGTCACTTAACA 57.920 40.909 0.29 0.00 34.00 2.41
291 297 4.938226 GCTTAGCCAAGTCACTTAACATCT 59.062 41.667 0.00 0.00 34.00 2.90
298 304 6.127897 GCCAAGTCACTTAACATCTGCTATTT 60.128 38.462 0.00 0.00 0.00 1.40
311 317 7.533426 ACATCTGCTATTTCAAAACATGTCTC 58.467 34.615 0.00 0.00 0.00 3.36
357 365 2.186125 GCCTAACTTACGCGGGCT 59.814 61.111 12.47 0.00 39.68 5.19
364 372 1.396653 ACTTACGCGGGCTGTAGTAT 58.603 50.000 12.47 0.00 0.00 2.12
375 383 5.238650 GCGGGCTGTAGTATGATTTAAATGT 59.761 40.000 5.17 0.00 0.00 2.71
377 385 7.132213 CGGGCTGTAGTATGATTTAAATGTTG 58.868 38.462 5.17 0.00 0.00 3.33
417 445 9.448438 TTTGTACTCTTAATCACATATTGCACT 57.552 29.630 0.00 0.00 0.00 4.40
436 464 8.655651 TTGCACTTTAATACCTTTTCCTTTTG 57.344 30.769 0.00 0.00 0.00 2.44
479 510 5.424252 TCCCTCCGTTCACTATAAGATGTTT 59.576 40.000 0.00 0.00 0.00 2.83
567 600 8.519799 TGTACTTCCTCTTTCAAAATTCTTGT 57.480 30.769 0.00 0.00 0.00 3.16
568 601 8.621286 TGTACTTCCTCTTTCAAAATTCTTGTC 58.379 33.333 0.00 0.00 0.00 3.18
569 602 7.888250 ACTTCCTCTTTCAAAATTCTTGTCT 57.112 32.000 0.00 0.00 0.00 3.41
570 603 8.298729 ACTTCCTCTTTCAAAATTCTTGTCTT 57.701 30.769 0.00 0.00 0.00 3.01
571 604 9.408648 ACTTCCTCTTTCAAAATTCTTGTCTTA 57.591 29.630 0.00 0.00 0.00 2.10
572 605 9.890352 CTTCCTCTTTCAAAATTCTTGTCTTAG 57.110 33.333 0.00 0.00 0.00 2.18
574 607 9.799106 TCCTCTTTCAAAATTCTTGTCTTAGAT 57.201 29.630 0.00 0.00 0.00 1.98
588 621 7.339721 TCTTGTCTTAGATTTGTCTAGATCCGT 59.660 37.037 0.00 0.00 0.00 4.69
589 622 8.515695 TTGTCTTAGATTTGTCTAGATCCGTA 57.484 34.615 0.00 0.00 0.00 4.02
591 624 8.784994 TGTCTTAGATTTGTCTAGATCCGTATC 58.215 37.037 0.00 0.00 0.00 2.24
607 640 9.005777 AGATCCGTATCTAGACAAATCTAAGAC 57.994 37.037 0.00 0.00 40.82 3.01
611 644 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
656 689 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
657 690 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
658 691 8.923270 ACAAATCTAAGACAAGAATTTTGGGAA 58.077 29.630 0.00 0.00 33.04 3.97
659 692 9.415544 CAAATCTAAGACAAGAATTTTGGGAAG 57.584 33.333 5.68 0.00 28.49 3.46
660 693 7.709149 ATCTAAGACAAGAATTTTGGGAAGG 57.291 36.000 5.68 0.00 0.00 3.46
661 694 6.848069 TCTAAGACAAGAATTTTGGGAAGGA 58.152 36.000 5.68 0.00 0.00 3.36
662 695 6.942576 TCTAAGACAAGAATTTTGGGAAGGAG 59.057 38.462 5.68 0.00 0.00 3.69
663 696 4.411013 AGACAAGAATTTTGGGAAGGAGG 58.589 43.478 5.68 0.00 0.00 4.30
664 697 3.510459 ACAAGAATTTTGGGAAGGAGGG 58.490 45.455 5.68 0.00 0.00 4.30
665 698 3.142028 ACAAGAATTTTGGGAAGGAGGGA 59.858 43.478 5.68 0.00 0.00 4.20
666 699 3.746792 AGAATTTTGGGAAGGAGGGAG 57.253 47.619 0.00 0.00 0.00 4.30
667 700 2.996742 AGAATTTTGGGAAGGAGGGAGT 59.003 45.455 0.00 0.00 0.00 3.85
668 701 4.183916 AGAATTTTGGGAAGGAGGGAGTA 58.816 43.478 0.00 0.00 0.00 2.59
669 702 4.018324 AGAATTTTGGGAAGGAGGGAGTAC 60.018 45.833 0.00 0.00 0.00 2.73
670 703 2.735259 TTTGGGAAGGAGGGAGTACT 57.265 50.000 0.00 0.00 0.00 2.73
671 704 3.858696 TTTGGGAAGGAGGGAGTACTA 57.141 47.619 0.00 0.00 0.00 1.82
672 705 4.363546 TTTGGGAAGGAGGGAGTACTAT 57.636 45.455 0.00 0.00 0.00 2.12
673 706 3.330126 TGGGAAGGAGGGAGTACTATG 57.670 52.381 0.00 0.00 0.00 2.23
674 707 2.590611 TGGGAAGGAGGGAGTACTATGT 59.409 50.000 0.00 0.00 0.00 2.29
675 708 3.795545 TGGGAAGGAGGGAGTACTATGTA 59.204 47.826 0.00 0.00 0.00 2.29
676 709 4.140994 TGGGAAGGAGGGAGTACTATGTAG 60.141 50.000 0.00 0.00 0.00 2.74
677 710 4.140971 GGGAAGGAGGGAGTACTATGTAGT 60.141 50.000 0.00 0.00 40.24 2.73
678 711 5.456779 GGAAGGAGGGAGTACTATGTAGTT 58.543 45.833 0.00 0.00 37.73 2.24
679 712 5.898397 GGAAGGAGGGAGTACTATGTAGTTT 59.102 44.000 0.00 0.00 37.73 2.66
680 713 7.065504 GGAAGGAGGGAGTACTATGTAGTTTA 58.934 42.308 0.00 0.00 37.73 2.01
681 714 7.729431 GGAAGGAGGGAGTACTATGTAGTTTAT 59.271 40.741 0.00 0.00 37.73 1.40
682 715 9.804977 GAAGGAGGGAGTACTATGTAGTTTATA 57.195 37.037 0.00 0.00 37.73 0.98
719 752 8.193250 TCCAAAACGTATTCTAATAGTGAAGC 57.807 34.615 0.00 0.00 0.00 3.86
720 753 7.009815 TCCAAAACGTATTCTAATAGTGAAGCG 59.990 37.037 0.00 0.00 34.46 4.68
721 754 6.823678 AAACGTATTCTAATAGTGAAGCGG 57.176 37.500 0.00 0.00 33.45 5.52
722 755 5.762825 ACGTATTCTAATAGTGAAGCGGA 57.237 39.130 0.00 0.00 33.45 5.54
723 756 5.759963 ACGTATTCTAATAGTGAAGCGGAG 58.240 41.667 0.00 0.00 33.45 4.63
724 757 5.154932 CGTATTCTAATAGTGAAGCGGAGG 58.845 45.833 0.00 0.00 0.00 4.30
725 758 4.608948 ATTCTAATAGTGAAGCGGAGGG 57.391 45.455 0.00 0.00 0.00 4.30
726 759 2.317040 TCTAATAGTGAAGCGGAGGGG 58.683 52.381 0.00 0.00 0.00 4.79
727 760 1.344763 CTAATAGTGAAGCGGAGGGGG 59.655 57.143 0.00 0.00 0.00 5.40
728 761 1.984288 AATAGTGAAGCGGAGGGGGC 61.984 60.000 0.00 0.00 0.00 5.80
729 762 3.916438 TAGTGAAGCGGAGGGGGCA 62.916 63.158 0.00 0.00 0.00 5.36
730 763 4.785453 GTGAAGCGGAGGGGGCAG 62.785 72.222 0.00 0.00 0.00 4.85
732 765 3.081409 GAAGCGGAGGGGGCAGTA 61.081 66.667 0.00 0.00 0.00 2.74
733 766 3.083997 AAGCGGAGGGGGCAGTAG 61.084 66.667 0.00 0.00 0.00 2.57
734 767 3.925914 AAGCGGAGGGGGCAGTAGT 62.926 63.158 0.00 0.00 0.00 2.73
735 768 4.162690 GCGGAGGGGGCAGTAGTG 62.163 72.222 0.00 0.00 0.00 2.74
736 769 2.683933 CGGAGGGGGCAGTAGTGT 60.684 66.667 0.00 0.00 0.00 3.55
737 770 1.380785 CGGAGGGGGCAGTAGTGTA 60.381 63.158 0.00 0.00 0.00 2.90
738 771 1.673808 CGGAGGGGGCAGTAGTGTAC 61.674 65.000 0.00 0.00 0.00 2.90
739 772 0.325390 GGAGGGGGCAGTAGTGTACT 60.325 60.000 0.00 0.00 40.28 2.73
740 773 1.112950 GAGGGGGCAGTAGTGTACTC 58.887 60.000 0.00 0.00 36.76 2.59
741 774 0.412244 AGGGGGCAGTAGTGTACTCA 59.588 55.000 0.00 0.00 36.76 3.41
742 775 1.008449 AGGGGGCAGTAGTGTACTCAT 59.992 52.381 0.00 0.00 36.76 2.90
743 776 1.139058 GGGGGCAGTAGTGTACTCATG 59.861 57.143 0.00 0.00 36.76 3.07
744 777 1.831736 GGGGCAGTAGTGTACTCATGT 59.168 52.381 0.00 0.00 36.76 3.21
745 778 2.159085 GGGGCAGTAGTGTACTCATGTC 60.159 54.545 0.00 0.00 36.76 3.06
746 779 2.159085 GGGCAGTAGTGTACTCATGTCC 60.159 54.545 0.00 4.81 36.76 4.02
781 815 1.072331 TGCACTTCCTTTCCAGTCCTC 59.928 52.381 0.00 0.00 0.00 3.71
806 845 1.403914 CGCTCTGCTCTCACACTTGAT 60.404 52.381 0.00 0.00 0.00 2.57
837 879 6.213677 TCATAGTACATCGCAGTTCCATTAC 58.786 40.000 0.00 0.00 0.00 1.89
851 893 2.749076 TCCATTACACTGATGCTTGCAC 59.251 45.455 0.00 0.00 0.00 4.57
855 897 2.267174 ACACTGATGCTTGCACTTCT 57.733 45.000 0.00 0.00 0.00 2.85
859 901 3.979495 CACTGATGCTTGCACTTCTTTTC 59.021 43.478 0.00 0.00 0.00 2.29
886 930 6.414408 AACTTCTATCTGATTGTTTGCTCG 57.586 37.500 0.00 0.00 0.00 5.03
1230 1283 0.673644 CCTGCCCCAAGAACTACGTG 60.674 60.000 0.00 0.00 0.00 4.49
1332 1388 3.582120 CAGCACGGCAACAACGGT 61.582 61.111 0.00 0.00 35.23 4.83
1351 1416 1.883084 GGCTACGATCACGGCAAGG 60.883 63.158 0.00 0.00 44.46 3.61
1403 1480 2.125350 GCAGAAGGAGGACAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
1471 1557 3.691342 CGGGTCGCACTTCAGGGA 61.691 66.667 0.00 0.00 0.00 4.20
1475 1561 2.922503 TCGCACTTCAGGGAGCCA 60.923 61.111 0.00 0.00 0.00 4.75
1677 1778 1.629043 ACCTCAAGTCGCTCAAGGTA 58.371 50.000 9.71 0.00 38.56 3.08
1767 1874 3.552875 ACTCAATGAGCTCAATGATGGG 58.447 45.455 29.78 21.72 35.47 4.00
1957 2235 3.490761 GCACAGTTGCTTACCATGTTGTT 60.491 43.478 0.00 0.00 46.17 2.83
1963 2241 4.300189 TGCTTACCATGTTGTTGTTGTC 57.700 40.909 0.00 0.00 0.00 3.18
2015 2293 6.350906 TGTGTTTACCTAGGCACATATTACC 58.649 40.000 9.30 0.00 37.00 2.85
2017 2295 6.996282 GTGTTTACCTAGGCACATATTACCAT 59.004 38.462 9.30 0.00 32.62 3.55
2018 2296 7.501225 GTGTTTACCTAGGCACATATTACCATT 59.499 37.037 9.30 0.00 32.62 3.16
2075 2353 0.185901 ACCTTGGGTTGAGCATGTGT 59.814 50.000 0.00 0.00 27.29 3.72
2081 2359 2.039613 TGGGTTGAGCATGTGTGTCATA 59.960 45.455 0.00 0.00 34.67 2.15
2082 2360 2.679837 GGGTTGAGCATGTGTGTCATAG 59.320 50.000 0.00 0.00 34.67 2.23
2083 2361 2.096496 GGTTGAGCATGTGTGTCATAGC 59.904 50.000 0.00 0.00 34.67 2.97
2084 2362 2.743664 GTTGAGCATGTGTGTCATAGCA 59.256 45.455 0.00 0.00 35.02 3.49
2085 2363 3.056588 TGAGCATGTGTGTCATAGCAA 57.943 42.857 0.00 0.00 35.02 3.91
2086 2364 2.743664 TGAGCATGTGTGTCATAGCAAC 59.256 45.455 0.00 0.00 35.02 4.17
2088 2366 2.086869 GCATGTGTGTCATAGCAACCT 58.913 47.619 0.00 0.00 34.67 3.50
2089 2367 2.159476 GCATGTGTGTCATAGCAACCTG 60.159 50.000 0.00 0.00 34.67 4.00
2090 2368 2.183478 TGTGTGTCATAGCAACCTGG 57.817 50.000 0.00 0.00 0.00 4.45
2091 2369 1.271325 TGTGTGTCATAGCAACCTGGG 60.271 52.381 0.00 0.00 0.00 4.45
2092 2370 1.003118 GTGTGTCATAGCAACCTGGGA 59.997 52.381 0.00 0.00 0.00 4.37
2100 2383 4.534500 TCATAGCAACCTGGGAGTTTTCTA 59.466 41.667 0.00 0.00 0.00 2.10
2155 2451 3.827722 TCCAAATCCTGAACCGTTTTCT 58.172 40.909 0.00 0.00 0.00 2.52
2219 2517 7.919690 TCATGTCAATAGATTTCAACGAATCC 58.080 34.615 0.00 0.00 36.84 3.01
2223 2521 9.443323 TGTCAATAGATTTCAACGAATCCTTTA 57.557 29.630 0.00 0.00 36.84 1.85
2228 2526 9.892130 ATAGATTTCAACGAATCCTTTAGTTCT 57.108 29.630 0.00 0.00 36.84 3.01
2230 2528 9.372369 AGATTTCAACGAATCCTTTAGTTCTAG 57.628 33.333 0.00 0.00 36.84 2.43
2233 2531 9.720769 TTTCAACGAATCCTTTAGTTCTAGAAT 57.279 29.630 8.75 0.85 29.50 2.40
2294 2594 5.984695 ACTTTCTTTCTTTATTGGGAGGC 57.015 39.130 0.00 0.00 0.00 4.70
2295 2595 5.393866 ACTTTCTTTCTTTATTGGGAGGCA 58.606 37.500 0.00 0.00 0.00 4.75
2296 2596 5.243954 ACTTTCTTTCTTTATTGGGAGGCAC 59.756 40.000 0.00 0.00 0.00 5.01
2297 2597 4.380843 TCTTTCTTTATTGGGAGGCACA 57.619 40.909 0.00 0.00 0.00 4.57
2298 2598 4.335416 TCTTTCTTTATTGGGAGGCACAG 58.665 43.478 0.00 0.00 0.00 3.66
2299 2599 3.806949 TTCTTTATTGGGAGGCACAGT 57.193 42.857 0.00 0.00 0.00 3.55
2300 2600 3.806949 TCTTTATTGGGAGGCACAGTT 57.193 42.857 0.00 0.00 0.00 3.16
2301 2601 4.919774 TCTTTATTGGGAGGCACAGTTA 57.080 40.909 0.00 0.00 0.00 2.24
2302 2602 5.450818 TCTTTATTGGGAGGCACAGTTAT 57.549 39.130 0.00 0.00 0.00 1.89
2303 2603 5.192927 TCTTTATTGGGAGGCACAGTTATG 58.807 41.667 0.00 0.00 0.00 1.90
2304 2604 4.584638 TTATTGGGAGGCACAGTTATGT 57.415 40.909 0.00 0.00 41.57 2.29
2306 2606 1.656587 TGGGAGGCACAGTTATGTCT 58.343 50.000 0.00 0.00 37.65 3.41
2313 2613 5.016051 AGGCACAGTTATGTCTCACATAG 57.984 43.478 0.00 0.00 41.56 2.23
2314 2614 4.711846 AGGCACAGTTATGTCTCACATAGA 59.288 41.667 0.00 0.00 41.56 1.98
2315 2615 5.187772 AGGCACAGTTATGTCTCACATAGAA 59.812 40.000 0.00 0.00 41.56 2.10
2316 2616 5.874810 GGCACAGTTATGTCTCACATAGAAA 59.125 40.000 0.00 0.00 41.56 2.52
2318 2618 7.710907 GGCACAGTTATGTCTCACATAGAAATA 59.289 37.037 0.00 0.00 41.56 1.40
2319 2619 9.098355 GCACAGTTATGTCTCACATAGAAATAA 57.902 33.333 0.00 0.00 41.56 1.40
2406 2708 2.548057 TGTTTCGAGAGACAATTGTGCC 59.452 45.455 17.58 7.25 41.84 5.01
2418 2720 2.172483 ATTGTGCCTCTCGCGGAAGT 62.172 55.000 6.13 0.00 42.08 3.01
2432 2734 3.489785 CGCGGAAGTAAATATGTGACTCC 59.510 47.826 0.00 0.00 0.00 3.85
2476 2778 6.350110 CCTCCTGTGTGAAAGAGAAACAAAAA 60.350 38.462 0.00 0.00 0.00 1.94
2477 2779 6.386654 TCCTGTGTGAAAGAGAAACAAAAAC 58.613 36.000 0.00 0.00 0.00 2.43
2478 2780 6.015856 TCCTGTGTGAAAGAGAAACAAAAACA 60.016 34.615 0.00 0.00 0.00 2.83
2479 2781 6.089417 CCTGTGTGAAAGAGAAACAAAAACAC 59.911 38.462 0.00 0.00 36.73 3.32
2480 2782 6.507900 TGTGTGAAAGAGAAACAAAAACACA 58.492 32.000 0.00 0.00 42.05 3.72
2483 2785 8.495148 GTGTGAAAGAGAAACAAAAACACATTT 58.505 29.630 0.00 0.00 37.87 2.32
2485 2787 8.925700 GTGAAAGAGAAACAAAAACACATTTCT 58.074 29.630 0.00 0.00 42.61 2.52
2490 2793 6.573434 AGAAACAAAAACACATTTCTCCCTC 58.427 36.000 0.00 0.00 36.86 4.30
2508 2811 3.374220 CTCTTCTGAGAGGCATAGCAG 57.626 52.381 0.00 0.00 44.69 4.24
2509 2812 1.411977 TCTTCTGAGAGGCATAGCAGC 59.588 52.381 0.00 0.00 0.00 5.25
2510 2813 0.103755 TTCTGAGAGGCATAGCAGCG 59.896 55.000 0.00 0.00 34.64 5.18
2511 2814 1.955157 CTGAGAGGCATAGCAGCGC 60.955 63.158 0.00 0.00 34.64 5.92
2516 2819 2.664518 GGCATAGCAGCGCCTCTC 60.665 66.667 2.29 0.00 45.29 3.20
2517 2820 2.107750 GCATAGCAGCGCCTCTCA 59.892 61.111 2.29 0.00 0.00 3.27
2518 2821 1.955157 GCATAGCAGCGCCTCTCAG 60.955 63.158 2.29 0.00 0.00 3.35
2539 2842 4.578105 CAGAGAAGAAAATATGTGCCTCCC 59.422 45.833 0.00 0.00 0.00 4.30
2540 2843 4.228210 AGAGAAGAAAATATGTGCCTCCCA 59.772 41.667 0.00 0.00 0.00 4.37
2541 2844 5.103771 AGAGAAGAAAATATGTGCCTCCCAT 60.104 40.000 0.00 0.00 0.00 4.00
2543 2846 6.302269 AGAAGAAAATATGTGCCTCCCATAG 58.698 40.000 0.00 0.00 0.00 2.23
2546 2849 6.302269 AGAAAATATGTGCCTCCCATAGAAG 58.698 40.000 0.00 0.00 0.00 2.85
2550 2853 1.354031 TGTGCCTCCCATAGAAGCAAA 59.646 47.619 0.00 0.00 43.53 3.68
2551 2854 2.224992 TGTGCCTCCCATAGAAGCAAAA 60.225 45.455 0.00 0.00 43.53 2.44
2553 2856 3.091545 TGCCTCCCATAGAAGCAAAAAG 58.908 45.455 0.00 0.00 39.02 2.27
2554 2857 3.245229 TGCCTCCCATAGAAGCAAAAAGA 60.245 43.478 0.00 0.00 39.02 2.52
2555 2858 3.763897 GCCTCCCATAGAAGCAAAAAGAA 59.236 43.478 0.00 0.00 31.72 2.52
2556 2859 4.380973 GCCTCCCATAGAAGCAAAAAGAAC 60.381 45.833 0.00 0.00 31.72 3.01
2557 2860 4.766891 CCTCCCATAGAAGCAAAAAGAACA 59.233 41.667 0.00 0.00 0.00 3.18
2558 2861 5.420104 CCTCCCATAGAAGCAAAAAGAACAT 59.580 40.000 0.00 0.00 0.00 2.71
2559 2862 6.271488 TCCCATAGAAGCAAAAAGAACATG 57.729 37.500 0.00 0.00 0.00 3.21
2595 2914 1.871080 AGAGGCACAACTTTGTCTCG 58.129 50.000 0.00 0.00 39.91 4.04
2636 2955 5.712917 TGCCTCCCGTGTAAGAAAATAAAAT 59.287 36.000 0.00 0.00 0.00 1.82
2639 2958 7.066645 GCCTCCCGTGTAAGAAAATAAAATACT 59.933 37.037 0.00 0.00 0.00 2.12
2640 2959 8.953313 CCTCCCGTGTAAGAAAATAAAATACTT 58.047 33.333 0.00 0.00 0.00 2.24
2679 2998 1.457346 CGGAAGCAAATCTCTGCCTT 58.543 50.000 0.00 0.00 43.73 4.35
2694 3013 5.360714 TCTCTGCCTTCACAAGAAACAAATT 59.639 36.000 0.00 0.00 32.35 1.82
2702 3021 7.361116 CCTTCACAAGAAACAAATTTGTGCTTT 60.361 33.333 23.93 14.68 46.88 3.51
2705 3024 7.333921 TCACAAGAAACAAATTTGTGCTTTCAT 59.666 29.630 23.93 13.86 46.88 2.57
2713 3032 6.822676 ACAAATTTGTGCTTTCATGGAAGAAA 59.177 30.769 22.71 9.47 40.49 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.745227 ACAAGTATGACACCTTCTTATGGG 58.255 41.667 0.00 0.00 0.00 4.00
15 16 7.661847 CCTTTAGAACAAGTATGACACCTTCTT 59.338 37.037 0.00 0.00 0.00 2.52
36 37 8.956426 GGAGTATCACATCAAATTTCACCTTTA 58.044 33.333 0.00 0.00 36.25 1.85
44 45 8.421249 TTCAAAGGGAGTATCACATCAAATTT 57.579 30.769 0.00 0.00 45.06 1.82
49 50 5.875224 TGTTTCAAAGGGAGTATCACATCA 58.125 37.500 0.00 0.00 45.06 3.07
59 60 0.040067 GTGCGCTGTTTCAAAGGGAG 60.040 55.000 9.73 0.00 0.00 4.30
80 83 3.270027 TGGCTTCCATTCTTGATGTACG 58.730 45.455 0.00 0.00 33.71 3.67
81 84 4.702131 ACTTGGCTTCCATTCTTGATGTAC 59.298 41.667 0.00 0.00 33.71 2.90
82 85 4.922206 ACTTGGCTTCCATTCTTGATGTA 58.078 39.130 0.00 0.00 33.71 2.29
83 86 3.771216 ACTTGGCTTCCATTCTTGATGT 58.229 40.909 0.00 0.00 33.71 3.06
84 87 5.902613 TTACTTGGCTTCCATTCTTGATG 57.097 39.130 0.00 0.00 31.53 3.07
85 88 6.916360 TTTTACTTGGCTTCCATTCTTGAT 57.084 33.333 0.00 0.00 31.53 2.57
86 89 6.916360 ATTTTACTTGGCTTCCATTCTTGA 57.084 33.333 0.00 0.00 31.53 3.02
87 90 6.591448 GGAATTTTACTTGGCTTCCATTCTTG 59.409 38.462 0.00 0.00 36.28 3.02
89 92 5.779771 TGGAATTTTACTTGGCTTCCATTCT 59.220 36.000 0.00 0.00 40.21 2.40
97 103 4.015872 TCGAGTGGAATTTTACTTGGCT 57.984 40.909 9.24 0.00 0.00 4.75
118 124 3.641436 TGTCTTACCTGCATATGGACGAT 59.359 43.478 4.56 0.00 0.00 3.73
119 125 3.028130 TGTCTTACCTGCATATGGACGA 58.972 45.455 4.56 0.00 0.00 4.20
121 127 3.499918 GCATGTCTTACCTGCATATGGAC 59.500 47.826 4.56 2.22 39.16 4.02
126 132 2.771372 TCTGGCATGTCTTACCTGCATA 59.229 45.455 0.00 0.00 40.76 3.14
134 140 2.224042 CGGCTATGTCTGGCATGTCTTA 60.224 50.000 4.74 0.00 38.47 2.10
140 146 0.179045 GTTCCGGCTATGTCTGGCAT 60.179 55.000 0.00 0.00 41.42 4.40
151 157 0.400213 TCTTTCATGTGGTTCCGGCT 59.600 50.000 0.00 0.00 0.00 5.52
153 159 1.745087 CCATCTTTCATGTGGTTCCGG 59.255 52.381 0.00 0.00 0.00 5.14
155 161 3.690460 AGACCATCTTTCATGTGGTTCC 58.310 45.455 6.41 0.00 45.79 3.62
156 162 4.878397 CCTAGACCATCTTTCATGTGGTTC 59.122 45.833 6.41 1.49 45.79 3.62
157 163 4.536090 TCCTAGACCATCTTTCATGTGGTT 59.464 41.667 6.41 0.99 45.79 3.67
195 201 3.928727 TTCGAAATCCACTAGACGTGT 57.071 42.857 0.00 0.00 42.20 4.49
196 202 4.862574 TCATTTCGAAATCCACTAGACGTG 59.137 41.667 20.31 6.87 43.41 4.49
219 225 4.062991 GGTCACGATTTAGACTTTGTGGT 58.937 43.478 0.00 0.00 35.18 4.16
229 235 2.028476 TGTGTGAGGGGTCACGATTTAG 60.028 50.000 0.00 0.00 43.12 1.85
236 242 2.270352 TCAATTGTGTGAGGGGTCAC 57.730 50.000 5.13 0.00 40.78 3.67
256 262 8.836413 GTGACTTGGCTAAGCATAAACATATTA 58.164 33.333 10.10 0.00 37.43 0.98
284 290 9.013229 AGACATGTTTTGAAATAGCAGATGTTA 57.987 29.630 0.00 0.00 0.00 2.41
288 294 7.609146 TGAGAGACATGTTTTGAAATAGCAGAT 59.391 33.333 0.00 0.00 0.00 2.90
291 297 7.692460 ATGAGAGACATGTTTTGAAATAGCA 57.308 32.000 0.00 0.00 37.87 3.49
345 352 1.066605 CATACTACAGCCCGCGTAAGT 59.933 52.381 4.92 0.21 41.68 2.24
348 355 1.612676 ATCATACTACAGCCCGCGTA 58.387 50.000 4.92 0.00 0.00 4.42
351 359 5.238650 ACATTTAAATCATACTACAGCCCGC 59.761 40.000 0.00 0.00 0.00 6.13
390 418 9.708222 GTGCAATATGTGATTAAGAGTACAAAG 57.292 33.333 0.00 0.00 0.00 2.77
417 445 7.040271 CCCTCGTCAAAAGGAAAAGGTATTAAA 60.040 37.037 0.00 0.00 35.83 1.52
425 453 5.959618 ATAACCCTCGTCAAAAGGAAAAG 57.040 39.130 0.00 0.00 35.83 2.27
430 458 4.451900 AGCATATAACCCTCGTCAAAAGG 58.548 43.478 0.00 0.00 0.00 3.11
436 464 3.193056 GGGAGTAGCATATAACCCTCGTC 59.807 52.174 0.00 0.00 35.03 4.20
505 537 9.228636 AGTGAATAAACACATTAAAAACACGTC 57.771 29.630 0.00 0.00 42.45 4.34
506 538 9.575783 AAGTGAATAAACACATTAAAAACACGT 57.424 25.926 0.00 0.00 42.45 4.49
541 574 9.136323 ACAAGAATTTTGAAAGAGGAAGTACAT 57.864 29.630 0.00 0.00 0.00 2.29
545 578 7.888250 AGACAAGAATTTTGAAAGAGGAAGT 57.112 32.000 7.18 0.00 0.00 3.01
546 579 9.890352 CTAAGACAAGAATTTTGAAAGAGGAAG 57.110 33.333 7.18 0.00 0.00 3.46
547 580 9.627123 TCTAAGACAAGAATTTTGAAAGAGGAA 57.373 29.630 7.18 0.00 0.00 3.36
561 594 8.191446 CGGATCTAGACAAATCTAAGACAAGAA 58.809 37.037 0.00 0.00 36.98 2.52
562 595 7.339721 ACGGATCTAGACAAATCTAAGACAAGA 59.660 37.037 0.00 0.00 36.98 3.02
563 596 7.484975 ACGGATCTAGACAAATCTAAGACAAG 58.515 38.462 0.00 0.00 36.98 3.16
564 597 7.406031 ACGGATCTAGACAAATCTAAGACAA 57.594 36.000 0.00 0.00 36.98 3.18
565 598 8.693120 ATACGGATCTAGACAAATCTAAGACA 57.307 34.615 0.00 0.00 36.98 3.41
566 599 9.005777 AGATACGGATCTAGACAAATCTAAGAC 57.994 37.037 8.88 0.00 40.85 3.01
581 614 9.005777 GTCTTAGATTTGTCTAGATACGGATCT 57.994 37.037 15.99 15.99 44.90 2.75
582 615 8.784994 TGTCTTAGATTTGTCTAGATACGGATC 58.215 37.037 0.00 0.00 0.00 3.36
630 663 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
631 664 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
632 665 8.477419 TCCCAAAATTCTTGTCTTAGATTTGT 57.523 30.769 0.00 0.00 28.79 2.83
633 666 9.415544 CTTCCCAAAATTCTTGTCTTAGATTTG 57.584 33.333 0.00 0.00 29.84 2.32
634 667 8.588472 CCTTCCCAAAATTCTTGTCTTAGATTT 58.412 33.333 0.00 0.00 0.00 2.17
635 668 7.950124 TCCTTCCCAAAATTCTTGTCTTAGATT 59.050 33.333 0.00 0.00 0.00 2.40
636 669 7.470192 TCCTTCCCAAAATTCTTGTCTTAGAT 58.530 34.615 0.00 0.00 0.00 1.98
637 670 6.848069 TCCTTCCCAAAATTCTTGTCTTAGA 58.152 36.000 0.00 0.00 0.00 2.10
638 671 6.151817 CCTCCTTCCCAAAATTCTTGTCTTAG 59.848 42.308 0.00 0.00 0.00 2.18
639 672 6.010219 CCTCCTTCCCAAAATTCTTGTCTTA 58.990 40.000 0.00 0.00 0.00 2.10
640 673 4.835056 CCTCCTTCCCAAAATTCTTGTCTT 59.165 41.667 0.00 0.00 0.00 3.01
641 674 4.411013 CCTCCTTCCCAAAATTCTTGTCT 58.589 43.478 0.00 0.00 0.00 3.41
642 675 3.511540 CCCTCCTTCCCAAAATTCTTGTC 59.488 47.826 0.00 0.00 0.00 3.18
643 676 3.142028 TCCCTCCTTCCCAAAATTCTTGT 59.858 43.478 0.00 0.00 0.00 3.16
644 677 3.766051 CTCCCTCCTTCCCAAAATTCTTG 59.234 47.826 0.00 0.00 0.00 3.02
645 678 3.402708 ACTCCCTCCTTCCCAAAATTCTT 59.597 43.478 0.00 0.00 0.00 2.52
646 679 2.996742 ACTCCCTCCTTCCCAAAATTCT 59.003 45.455 0.00 0.00 0.00 2.40
647 680 3.458044 ACTCCCTCCTTCCCAAAATTC 57.542 47.619 0.00 0.00 0.00 2.17
648 681 3.923425 AGTACTCCCTCCTTCCCAAAATT 59.077 43.478 0.00 0.00 0.00 1.82
649 682 3.542604 AGTACTCCCTCCTTCCCAAAAT 58.457 45.455 0.00 0.00 0.00 1.82
650 683 2.999928 AGTACTCCCTCCTTCCCAAAA 58.000 47.619 0.00 0.00 0.00 2.44
651 684 2.735259 AGTACTCCCTCCTTCCCAAA 57.265 50.000 0.00 0.00 0.00 3.28
652 685 3.013648 ACATAGTACTCCCTCCTTCCCAA 59.986 47.826 0.00 0.00 0.00 4.12
653 686 2.590611 ACATAGTACTCCCTCCTTCCCA 59.409 50.000 0.00 0.00 0.00 4.37
654 687 3.331718 ACATAGTACTCCCTCCTTCCC 57.668 52.381 0.00 0.00 0.00 3.97
655 688 5.064314 ACTACATAGTACTCCCTCCTTCC 57.936 47.826 0.00 0.00 34.13 3.46
656 689 8.709272 ATAAACTACATAGTACTCCCTCCTTC 57.291 38.462 0.00 0.00 34.99 3.46
693 726 8.827677 GCTTCACTATTAGAATACGTTTTGGAT 58.172 33.333 0.00 0.00 0.00 3.41
694 727 7.009815 CGCTTCACTATTAGAATACGTTTTGGA 59.990 37.037 0.00 0.00 0.00 3.53
695 728 7.117454 CGCTTCACTATTAGAATACGTTTTGG 58.883 38.462 0.00 0.00 0.00 3.28
696 729 7.009815 TCCGCTTCACTATTAGAATACGTTTTG 59.990 37.037 0.00 0.00 0.00 2.44
697 730 7.037438 TCCGCTTCACTATTAGAATACGTTTT 58.963 34.615 0.00 0.00 0.00 2.43
698 731 6.567050 TCCGCTTCACTATTAGAATACGTTT 58.433 36.000 0.00 0.00 0.00 3.60
699 732 6.140303 TCCGCTTCACTATTAGAATACGTT 57.860 37.500 0.00 0.00 0.00 3.99
700 733 5.278364 CCTCCGCTTCACTATTAGAATACGT 60.278 44.000 0.00 0.00 0.00 3.57
701 734 5.154932 CCTCCGCTTCACTATTAGAATACG 58.845 45.833 0.00 0.00 0.00 3.06
702 735 5.471257 CCCTCCGCTTCACTATTAGAATAC 58.529 45.833 0.00 0.00 0.00 1.89
703 736 4.527038 CCCCTCCGCTTCACTATTAGAATA 59.473 45.833 0.00 0.00 0.00 1.75
704 737 3.325135 CCCCTCCGCTTCACTATTAGAAT 59.675 47.826 0.00 0.00 0.00 2.40
705 738 2.698797 CCCCTCCGCTTCACTATTAGAA 59.301 50.000 0.00 0.00 0.00 2.10
706 739 2.317040 CCCCTCCGCTTCACTATTAGA 58.683 52.381 0.00 0.00 0.00 2.10
707 740 1.344763 CCCCCTCCGCTTCACTATTAG 59.655 57.143 0.00 0.00 0.00 1.73
708 741 1.420430 CCCCCTCCGCTTCACTATTA 58.580 55.000 0.00 0.00 0.00 0.98
709 742 1.984288 GCCCCCTCCGCTTCACTATT 61.984 60.000 0.00 0.00 0.00 1.73
710 743 2.444256 GCCCCCTCCGCTTCACTAT 61.444 63.158 0.00 0.00 0.00 2.12
711 744 3.081409 GCCCCCTCCGCTTCACTA 61.081 66.667 0.00 0.00 0.00 2.74
713 746 4.785453 CTGCCCCCTCCGCTTCAC 62.785 72.222 0.00 0.00 0.00 3.18
714 747 3.916438 TACTGCCCCCTCCGCTTCA 62.916 63.158 0.00 0.00 0.00 3.02
715 748 3.081409 TACTGCCCCCTCCGCTTC 61.081 66.667 0.00 0.00 0.00 3.86
716 749 3.083997 CTACTGCCCCCTCCGCTT 61.084 66.667 0.00 0.00 0.00 4.68
717 750 4.400251 ACTACTGCCCCCTCCGCT 62.400 66.667 0.00 0.00 0.00 5.52
718 751 4.162690 CACTACTGCCCCCTCCGC 62.163 72.222 0.00 0.00 0.00 5.54
719 752 1.380785 TACACTACTGCCCCCTCCG 60.381 63.158 0.00 0.00 0.00 4.63
720 753 0.325390 AGTACACTACTGCCCCCTCC 60.325 60.000 0.00 0.00 37.69 4.30
721 754 1.112950 GAGTACACTACTGCCCCCTC 58.887 60.000 0.00 0.00 39.59 4.30
722 755 0.412244 TGAGTACACTACTGCCCCCT 59.588 55.000 0.00 0.00 39.59 4.79
723 756 1.139058 CATGAGTACACTACTGCCCCC 59.861 57.143 0.00 0.00 39.59 5.40
724 757 1.831736 ACATGAGTACACTACTGCCCC 59.168 52.381 0.00 0.00 39.59 5.80
725 758 2.159085 GGACATGAGTACACTACTGCCC 60.159 54.545 0.00 0.00 39.59 5.36
726 759 2.761208 AGGACATGAGTACACTACTGCC 59.239 50.000 0.00 0.00 39.59 4.85
727 760 3.193691 ACAGGACATGAGTACACTACTGC 59.806 47.826 0.00 0.00 39.59 4.40
728 761 5.184096 AGAACAGGACATGAGTACACTACTG 59.816 44.000 0.00 0.00 39.59 2.74
729 762 5.184096 CAGAACAGGACATGAGTACACTACT 59.816 44.000 0.00 0.00 42.86 2.57
730 763 5.403246 CAGAACAGGACATGAGTACACTAC 58.597 45.833 0.00 0.00 0.00 2.73
731 764 4.462834 CCAGAACAGGACATGAGTACACTA 59.537 45.833 0.00 0.00 0.00 2.74
732 765 3.259374 CCAGAACAGGACATGAGTACACT 59.741 47.826 0.00 0.00 0.00 3.55
733 766 3.589988 CCAGAACAGGACATGAGTACAC 58.410 50.000 0.00 0.00 0.00 2.90
734 767 2.028112 GCCAGAACAGGACATGAGTACA 60.028 50.000 0.00 0.00 0.00 2.90
735 768 2.028112 TGCCAGAACAGGACATGAGTAC 60.028 50.000 0.00 0.00 0.00 2.73
736 769 2.256306 TGCCAGAACAGGACATGAGTA 58.744 47.619 0.00 0.00 0.00 2.59
737 770 1.059098 TGCCAGAACAGGACATGAGT 58.941 50.000 0.00 0.00 0.00 3.41
738 771 2.014857 CATGCCAGAACAGGACATGAG 58.985 52.381 0.00 0.00 41.53 2.90
739 772 1.352017 ACATGCCAGAACAGGACATGA 59.648 47.619 18.67 0.00 41.53 3.07
740 773 1.830279 ACATGCCAGAACAGGACATG 58.170 50.000 13.91 13.91 43.06 3.21
741 774 3.548770 CATACATGCCAGAACAGGACAT 58.451 45.455 0.00 0.00 0.00 3.06
742 775 2.989909 CATACATGCCAGAACAGGACA 58.010 47.619 0.00 0.00 0.00 4.02
773 807 0.734253 CAGAGCGAAACGAGGACTGG 60.734 60.000 0.00 0.00 0.00 4.00
781 815 0.664466 TGTGAGAGCAGAGCGAAACG 60.664 55.000 0.00 0.00 0.00 3.60
806 845 8.027189 GGAACTGCGATGTACTATGATACATTA 58.973 37.037 5.45 0.00 44.14 1.90
837 879 3.637998 AAAGAAGTGCAAGCATCAGTG 57.362 42.857 0.00 0.00 0.00 3.66
859 901 9.766277 GAGCAAACAATCAGATAGAAGTTAAAG 57.234 33.333 0.00 0.00 31.07 1.85
886 930 3.987404 CCTGCAAGTGGTAGGCAC 58.013 61.111 0.00 0.00 42.76 5.01
1230 1283 4.612943 GGTCGTAGGTCTGATCAAAGATC 58.387 47.826 0.00 0.15 0.00 2.75
1332 1388 1.153647 CTTGCCGTGATCGTAGCCA 60.154 57.895 0.00 0.00 35.01 4.75
1351 1416 4.886121 GCCGCCGTAGTAGGTGCC 62.886 72.222 0.00 0.00 40.31 5.01
1677 1778 2.348998 CCGTGCTTCTTGGCCTCT 59.651 61.111 3.32 0.00 0.00 3.69
1957 2235 0.586319 GCACTAAGCGCAAGACAACA 59.414 50.000 11.47 0.00 43.02 3.33
2075 2353 1.656587 ACTCCCAGGTTGCTATGACA 58.343 50.000 0.00 0.00 0.00 3.58
2081 2359 4.388577 AATAGAAAACTCCCAGGTTGCT 57.611 40.909 0.00 0.00 0.00 3.91
2082 2360 5.468540 AAAATAGAAAACTCCCAGGTTGC 57.531 39.130 0.00 0.00 0.00 4.17
2136 2432 6.743575 ATAGAGAAAACGGTTCAGGATTTG 57.256 37.500 0.00 0.00 0.00 2.32
2205 2503 9.367444 TCTAGAACTAAAGGATTCGTTGAAATC 57.633 33.333 0.00 0.00 35.35 2.17
2213 2511 9.672086 CTGTCTATTCTAGAACTAAAGGATTCG 57.328 37.037 7.48 0.00 36.40 3.34
2269 2569 7.507616 TGCCTCCCAATAAAGAAAGAAAGTAAA 59.492 33.333 0.00 0.00 0.00 2.01
2270 2570 7.007723 TGCCTCCCAATAAAGAAAGAAAGTAA 58.992 34.615 0.00 0.00 0.00 2.24
2271 2571 6.433093 GTGCCTCCCAATAAAGAAAGAAAGTA 59.567 38.462 0.00 0.00 0.00 2.24
2272 2572 5.243954 GTGCCTCCCAATAAAGAAAGAAAGT 59.756 40.000 0.00 0.00 0.00 2.66
2273 2573 5.243730 TGTGCCTCCCAATAAAGAAAGAAAG 59.756 40.000 0.00 0.00 0.00 2.62
2278 2578 4.112634 ACTGTGCCTCCCAATAAAGAAA 57.887 40.909 0.00 0.00 0.00 2.52
2279 2579 3.806949 ACTGTGCCTCCCAATAAAGAA 57.193 42.857 0.00 0.00 0.00 2.52
2280 2580 3.806949 AACTGTGCCTCCCAATAAAGA 57.193 42.857 0.00 0.00 0.00 2.52
2281 2581 4.949856 ACATAACTGTGCCTCCCAATAAAG 59.050 41.667 0.00 0.00 33.22 1.85
2283 2583 4.227300 AGACATAACTGTGCCTCCCAATAA 59.773 41.667 0.00 0.00 35.14 1.40
2286 2586 1.985159 AGACATAACTGTGCCTCCCAA 59.015 47.619 0.00 0.00 35.14 4.12
2288 2588 1.555075 TGAGACATAACTGTGCCTCCC 59.445 52.381 0.00 0.00 35.14 4.30
2290 2590 3.319137 TGTGAGACATAACTGTGCCTC 57.681 47.619 0.00 0.00 35.14 4.70
2291 2591 3.988976 ATGTGAGACATAACTGTGCCT 57.011 42.857 0.00 0.00 36.99 4.75
2292 2592 5.011090 TCTATGTGAGACATAACTGTGCC 57.989 43.478 0.00 0.00 40.23 5.01
2293 2593 6.968131 TTTCTATGTGAGACATAACTGTGC 57.032 37.500 0.00 0.00 40.23 4.57
2385 2685 2.548057 GGCACAATTGTCTCTCGAAACA 59.452 45.455 8.48 0.00 0.00 2.83
2386 2686 2.808543 AGGCACAATTGTCTCTCGAAAC 59.191 45.455 8.48 0.00 28.58 2.78
2402 2704 0.389426 TTTACTTCCGCGAGAGGCAC 60.389 55.000 8.23 0.00 43.84 5.01
2406 2708 4.441415 GTCACATATTTACTTCCGCGAGAG 59.559 45.833 8.23 7.50 0.00 3.20
2418 2720 8.603898 TTACTTCTCCTGGAGTCACATATTTA 57.396 34.615 22.50 0.00 0.00 1.40
2432 2734 4.156739 GGAGGCACAAATTTACTTCTCCTG 59.843 45.833 16.26 0.00 37.25 3.86
2476 2778 4.163427 TCTCAGAAGAGGGAGAAATGTGT 58.837 43.478 0.00 0.00 42.34 3.72
2477 2779 4.757594 CTCTCAGAAGAGGGAGAAATGTG 58.242 47.826 0.00 0.00 45.73 3.21
2490 2793 1.868469 GCTGCTATGCCTCTCAGAAG 58.132 55.000 0.00 0.00 0.00 2.85
2504 2807 1.947597 CTTCTCTGAGAGGCGCTGCT 61.948 60.000 9.97 4.53 0.00 4.24
2505 2808 1.519013 CTTCTCTGAGAGGCGCTGC 60.519 63.158 9.97 0.00 0.00 5.25
2506 2809 0.529833 TTCTTCTCTGAGAGGCGCTG 59.470 55.000 9.97 0.00 0.00 5.18
2507 2810 1.261480 TTTCTTCTCTGAGAGGCGCT 58.739 50.000 9.97 0.00 0.00 5.92
2508 2811 2.086054 TTTTCTTCTCTGAGAGGCGC 57.914 50.000 9.97 0.00 0.00 6.53
2509 2812 5.233902 CACATATTTTCTTCTCTGAGAGGCG 59.766 44.000 9.97 1.19 0.00 5.52
2510 2813 5.007528 GCACATATTTTCTTCTCTGAGAGGC 59.992 44.000 9.97 0.00 0.00 4.70
2511 2814 5.526846 GGCACATATTTTCTTCTCTGAGAGG 59.473 44.000 9.97 10.30 0.00 3.69
2512 2815 6.347696 AGGCACATATTTTCTTCTCTGAGAG 58.652 40.000 7.52 2.28 0.00 3.20
2513 2816 6.305272 AGGCACATATTTTCTTCTCTGAGA 57.695 37.500 2.58 2.58 0.00 3.27
2514 2817 5.526846 GGAGGCACATATTTTCTTCTCTGAG 59.473 44.000 0.00 0.00 0.00 3.35
2515 2818 5.431765 GGAGGCACATATTTTCTTCTCTGA 58.568 41.667 0.00 0.00 0.00 3.27
2516 2819 4.578105 GGGAGGCACATATTTTCTTCTCTG 59.422 45.833 0.00 0.00 0.00 3.35
2517 2820 4.228210 TGGGAGGCACATATTTTCTTCTCT 59.772 41.667 0.00 0.00 0.00 3.10
2518 2821 4.526970 TGGGAGGCACATATTTTCTTCTC 58.473 43.478 0.00 0.00 0.00 2.87
2567 2886 4.391405 AAGTTGTGCCTCTTGAAAAAGG 57.609 40.909 0.00 0.00 35.65 3.11
2569 2888 5.047377 AGACAAAGTTGTGCCTCTTGAAAAA 60.047 36.000 0.42 0.00 42.43 1.94
2595 2914 0.587768 GCACACATTTGCTTTTGGGC 59.412 50.000 0.00 0.00 39.59 5.36
2660 2979 1.399791 GAAGGCAGAGATTTGCTTCCG 59.600 52.381 0.00 0.00 43.57 4.30
2661 2980 2.163211 GTGAAGGCAGAGATTTGCTTCC 59.837 50.000 0.00 0.00 43.57 3.46


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

AutoCloner maintained by Alex Coulton.