Multiple sequence alignment - TraesCS1D01G296400

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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 TraesCS1D01G296400 chr1D 100.000 2579 0 0 1 2579 394453186 394450608 0.000000e+00 4763.0
1 TraesCS1D01G296400 chr1D 92.426 1175 50 12 593 1741 394409868 394408707 0.000000e+00 1640.0
2 TraesCS1D01G296400 chr1D 83.092 692 71 32 1758 2424 469060821 469060151 2.860000e-164 588.0
3 TraesCS1D01G296400 chr1D 85.571 499 32 20 117 588 394410393 394409908 1.070000e-133 486.0
4 TraesCS1D01G296400 chr1D 97.143 35 1 0 1761 1795 228798519 228798553 2.770000e-05 60.2
5 TraesCS1D01G296400 chr1A 92.888 1167 49 15 603 1739 490893469 490894631 0.000000e+00 1664.0
6 TraesCS1D01G296400 chr1A 87.391 230 17 6 188 409 490893008 490893233 1.180000e-63 254.0
7 TraesCS1D01G296400 chr1A 87.500 104 8 4 442 542 490893234 490893335 5.830000e-22 115.0
8 TraesCS1D01G296400 chr1A 89.091 55 1 3 111 165 490892953 490893002 2.140000e-06 63.9
9 TraesCS1D01G296400 chr4B 90.180 1222 52 26 593 1757 326093801 326095011 0.000000e+00 1530.0
10 TraesCS1D01G296400 chr4B 90.123 405 26 7 146 542 326093285 326093683 4.920000e-142 514.0
11 TraesCS1D01G296400 chr2B 83.310 713 71 26 1758 2458 207849285 207848609 4.720000e-172 614.0
12 TraesCS1D01G296400 chr1B 82.754 690 77 28 1758 2424 194965475 194966145 6.190000e-161 577.0
13 TraesCS1D01G296400 chr1B 81.727 695 78 27 1758 2424 666238183 666237510 3.780000e-148 534.0
14 TraesCS1D01G296400 chrUn 82.232 681 71 31 1758 2424 105324375 105325019 2.260000e-150 542.0
15 TraesCS1D01G296400 chrUn 81.727 695 78 27 1758 2424 227012231 227012904 3.780000e-148 534.0
16 TraesCS1D01G296400 chr6B 80.444 675 84 27 1764 2424 128739863 128739223 3.000000e-129 472.0
17 TraesCS1D01G296400 chr6A 81.351 370 43 16 1957 2310 540041250 540040891 7.030000e-71 278.0
18 TraesCS1D01G296400 chr7B 100.000 32 0 0 1764 1795 440351183 440351152 2.770000e-05 60.2
19 TraesCS1D01G296400 chr7B 100.000 30 0 0 1766 1795 8444564 8444535 3.590000e-04 56.5


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 TraesCS1D01G296400 chr1D 394450608 394453186 2578 True 4763.000 4763 100.0000 1 2579 1 chr1D.!!$R1 2578
1 TraesCS1D01G296400 chr1D 394408707 394410393 1686 True 1063.000 1640 88.9985 117 1741 2 chr1D.!!$R3 1624
2 TraesCS1D01G296400 chr1D 469060151 469060821 670 True 588.000 588 83.0920 1758 2424 1 chr1D.!!$R2 666
3 TraesCS1D01G296400 chr1A 490892953 490894631 1678 False 524.225 1664 89.2175 111 1739 4 chr1A.!!$F1 1628
4 TraesCS1D01G296400 chr4B 326093285 326095011 1726 False 1022.000 1530 90.1515 146 1757 2 chr4B.!!$F1 1611
5 TraesCS1D01G296400 chr2B 207848609 207849285 676 True 614.000 614 83.3100 1758 2458 1 chr2B.!!$R1 700
6 TraesCS1D01G296400 chr1B 194965475 194966145 670 False 577.000 577 82.7540 1758 2424 1 chr1B.!!$F1 666
7 TraesCS1D01G296400 chr1B 666237510 666238183 673 True 534.000 534 81.7270 1758 2424 1 chr1B.!!$R1 666
8 TraesCS1D01G296400 chrUn 105324375 105325019 644 False 542.000 542 82.2320 1758 2424 1 chrUn.!!$F1 666
9 TraesCS1D01G296400 chrUn 227012231 227012904 673 False 534.000 534 81.7270 1758 2424 1 chrUn.!!$F2 666
10 TraesCS1D01G296400 chr6B 128739223 128739863 640 True 472.000 472 80.4440 1764 2424 1 chr6B.!!$R1 660

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
223 226 0.040067 GCGGCAGAGAAAAGGTTGTG 60.04 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2420 0.609131 CCAAAGGTTCCAGCATCCGT 60.609 55.0 0.0 0.0 0.0 4.69 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
17 18 2.034066 CACACGGGAATGGCAGGT 59.966 61.111 0.00 0.00 0.00 4.00
18 19 1.603455 CACACGGGAATGGCAGGTT 60.603 57.895 0.00 0.00 0.00 3.50
19 20 1.152830 ACACGGGAATGGCAGGTTT 59.847 52.632 0.00 0.00 0.00 3.27
20 21 0.402504 ACACGGGAATGGCAGGTTTA 59.597 50.000 0.00 0.00 0.00 2.01
21 22 1.094785 CACGGGAATGGCAGGTTTAG 58.905 55.000 0.00 0.00 0.00 1.85
22 23 0.696501 ACGGGAATGGCAGGTTTAGT 59.303 50.000 0.00 0.00 0.00 2.24
23 24 1.074889 ACGGGAATGGCAGGTTTAGTT 59.925 47.619 0.00 0.00 0.00 2.24
24 25 1.472480 CGGGAATGGCAGGTTTAGTTG 59.528 52.381 0.00 0.00 0.00 3.16
25 26 2.802719 GGGAATGGCAGGTTTAGTTGA 58.197 47.619 0.00 0.00 0.00 3.18
26 27 3.365472 GGGAATGGCAGGTTTAGTTGAT 58.635 45.455 0.00 0.00 0.00 2.57
27 28 4.532834 GGGAATGGCAGGTTTAGTTGATA 58.467 43.478 0.00 0.00 0.00 2.15
28 29 4.953579 GGGAATGGCAGGTTTAGTTGATAA 59.046 41.667 0.00 0.00 0.00 1.75
29 30 5.067805 GGGAATGGCAGGTTTAGTTGATAAG 59.932 44.000 0.00 0.00 0.00 1.73
30 31 5.652452 GGAATGGCAGGTTTAGTTGATAAGT 59.348 40.000 0.00 0.00 0.00 2.24
31 32 6.826741 GGAATGGCAGGTTTAGTTGATAAGTA 59.173 38.462 0.00 0.00 0.00 2.24
32 33 7.502561 GGAATGGCAGGTTTAGTTGATAAGTAT 59.497 37.037 0.00 0.00 0.00 2.12
33 34 7.807977 ATGGCAGGTTTAGTTGATAAGTATG 57.192 36.000 0.00 0.00 0.00 2.39
34 35 6.119536 TGGCAGGTTTAGTTGATAAGTATGG 58.880 40.000 0.00 0.00 0.00 2.74
35 36 5.008712 GGCAGGTTTAGTTGATAAGTATGGC 59.991 44.000 0.00 0.00 0.00 4.40
36 37 5.588648 GCAGGTTTAGTTGATAAGTATGGCA 59.411 40.000 0.00 0.00 0.00 4.92
37 38 6.094881 GCAGGTTTAGTTGATAAGTATGGCAA 59.905 38.462 0.00 0.00 0.00 4.52
38 39 7.201821 GCAGGTTTAGTTGATAAGTATGGCAAT 60.202 37.037 0.00 0.00 0.00 3.56
39 40 8.686334 CAGGTTTAGTTGATAAGTATGGCAATT 58.314 33.333 0.00 0.00 0.00 2.32
40 41 8.903820 AGGTTTAGTTGATAAGTATGGCAATTC 58.096 33.333 0.00 0.00 0.00 2.17
41 42 8.135529 GGTTTAGTTGATAAGTATGGCAATTCC 58.864 37.037 0.00 0.00 0.00 3.01
42 43 7.817418 TTAGTTGATAAGTATGGCAATTCCC 57.183 36.000 0.00 0.00 0.00 3.97
43 44 5.765510 AGTTGATAAGTATGGCAATTCCCA 58.234 37.500 0.00 0.00 39.65 4.37
44 45 5.594317 AGTTGATAAGTATGGCAATTCCCAC 59.406 40.000 0.00 0.00 37.79 4.61
45 46 4.469657 TGATAAGTATGGCAATTCCCACC 58.530 43.478 0.00 0.00 37.79 4.61
46 47 4.167892 TGATAAGTATGGCAATTCCCACCT 59.832 41.667 0.00 0.00 37.79 4.00
47 48 2.736670 AGTATGGCAATTCCCACCTC 57.263 50.000 0.00 0.00 37.79 3.85
48 49 1.922447 AGTATGGCAATTCCCACCTCA 59.078 47.619 0.00 0.00 37.79 3.86
49 50 2.092212 AGTATGGCAATTCCCACCTCAG 60.092 50.000 0.00 0.00 37.79 3.35
50 51 0.706433 ATGGCAATTCCCACCTCAGT 59.294 50.000 0.00 0.00 37.79 3.41
51 52 0.482446 TGGCAATTCCCACCTCAGTT 59.518 50.000 0.00 0.00 0.00 3.16
52 53 1.133199 TGGCAATTCCCACCTCAGTTT 60.133 47.619 0.00 0.00 0.00 2.66
53 54 1.970640 GGCAATTCCCACCTCAGTTTT 59.029 47.619 0.00 0.00 0.00 2.43
54 55 2.289010 GGCAATTCCCACCTCAGTTTTG 60.289 50.000 0.00 0.00 0.00 2.44
55 56 2.627699 GCAATTCCCACCTCAGTTTTGA 59.372 45.455 0.00 0.00 0.00 2.69
56 57 3.259123 GCAATTCCCACCTCAGTTTTGAT 59.741 43.478 0.00 0.00 31.68 2.57
57 58 4.462483 GCAATTCCCACCTCAGTTTTGATA 59.538 41.667 0.00 0.00 31.68 2.15
58 59 5.127682 GCAATTCCCACCTCAGTTTTGATAT 59.872 40.000 0.00 0.00 31.68 1.63
59 60 6.351286 GCAATTCCCACCTCAGTTTTGATATT 60.351 38.462 0.00 0.00 31.68 1.28
60 61 7.260603 CAATTCCCACCTCAGTTTTGATATTC 58.739 38.462 0.00 0.00 31.68 1.75
61 62 5.512942 TCCCACCTCAGTTTTGATATTCA 57.487 39.130 0.00 0.00 31.68 2.57
62 63 6.078456 TCCCACCTCAGTTTTGATATTCAT 57.922 37.500 0.00 0.00 31.68 2.57
63 64 6.122277 TCCCACCTCAGTTTTGATATTCATC 58.878 40.000 0.00 0.00 31.68 2.92
64 65 5.008019 CCCACCTCAGTTTTGATATTCATCG 59.992 44.000 0.00 0.00 33.51 3.84
65 66 5.008019 CCACCTCAGTTTTGATATTCATCGG 59.992 44.000 0.00 0.00 33.51 4.18
66 67 4.576463 ACCTCAGTTTTGATATTCATCGGC 59.424 41.667 0.00 0.00 33.51 5.54
67 68 4.818546 CCTCAGTTTTGATATTCATCGGCT 59.181 41.667 0.00 0.00 33.51 5.52
68 69 5.277683 CCTCAGTTTTGATATTCATCGGCTG 60.278 44.000 0.00 0.00 33.51 4.85
69 70 4.576053 TCAGTTTTGATATTCATCGGCTGG 59.424 41.667 0.00 0.00 33.51 4.85
70 71 4.576053 CAGTTTTGATATTCATCGGCTGGA 59.424 41.667 0.00 0.00 33.51 3.86
71 72 5.240183 CAGTTTTGATATTCATCGGCTGGAT 59.760 40.000 0.00 0.00 33.51 3.41
72 73 5.829924 AGTTTTGATATTCATCGGCTGGATT 59.170 36.000 0.00 0.00 33.51 3.01
73 74 5.694231 TTTGATATTCATCGGCTGGATTG 57.306 39.130 0.00 0.00 33.51 2.67
74 75 4.622260 TGATATTCATCGGCTGGATTGA 57.378 40.909 0.00 0.00 33.51 2.57
75 76 4.572909 TGATATTCATCGGCTGGATTGAG 58.427 43.478 0.00 0.00 33.51 3.02
76 77 1.602311 ATTCATCGGCTGGATTGAGC 58.398 50.000 0.00 0.00 38.34 4.26
77 78 0.252761 TTCATCGGCTGGATTGAGCA 59.747 50.000 0.00 0.00 41.08 4.26
78 79 0.252761 TCATCGGCTGGATTGAGCAA 59.747 50.000 0.00 0.00 41.08 3.91
79 80 0.379669 CATCGGCTGGATTGAGCAAC 59.620 55.000 0.00 0.00 41.08 4.17
80 81 1.091771 ATCGGCTGGATTGAGCAACG 61.092 55.000 0.00 0.00 41.08 4.10
81 82 2.486966 GGCTGGATTGAGCAACGC 59.513 61.111 0.00 0.00 41.08 4.84
82 83 2.486966 GCTGGATTGAGCAACGCC 59.513 61.111 0.00 0.00 38.95 5.68
83 84 2.334946 GCTGGATTGAGCAACGCCA 61.335 57.895 6.51 6.51 38.95 5.69
84 85 1.865788 GCTGGATTGAGCAACGCCAA 61.866 55.000 7.69 0.00 38.95 4.52
85 86 0.109597 CTGGATTGAGCAACGCCAAC 60.110 55.000 7.69 0.00 30.78 3.77
86 87 1.212751 GGATTGAGCAACGCCAACC 59.787 57.895 0.00 0.00 0.00 3.77
87 88 1.212751 GATTGAGCAACGCCAACCC 59.787 57.895 0.00 0.00 0.00 4.11
88 89 1.228552 ATTGAGCAACGCCAACCCT 60.229 52.632 0.00 0.00 0.00 4.34
89 90 1.244019 ATTGAGCAACGCCAACCCTC 61.244 55.000 0.00 0.00 0.00 4.30
90 91 2.281484 GAGCAACGCCAACCCTCA 60.281 61.111 0.00 0.00 0.00 3.86
91 92 1.675641 GAGCAACGCCAACCCTCAT 60.676 57.895 0.00 0.00 0.00 2.90
92 93 1.926511 GAGCAACGCCAACCCTCATG 61.927 60.000 0.00 0.00 0.00 3.07
93 94 2.268076 GCAACGCCAACCCTCATGT 61.268 57.895 0.00 0.00 0.00 3.21
94 95 1.580942 CAACGCCAACCCTCATGTG 59.419 57.895 0.00 0.00 0.00 3.21
95 96 2.268076 AACGCCAACCCTCATGTGC 61.268 57.895 0.00 0.00 0.00 4.57
96 97 3.443045 CGCCAACCCTCATGTGCC 61.443 66.667 0.00 0.00 0.00 5.01
97 98 2.283101 GCCAACCCTCATGTGCCA 60.283 61.111 0.00 0.00 0.00 4.92
98 99 1.683365 GCCAACCCTCATGTGCCAT 60.683 57.895 0.00 0.00 0.00 4.40
99 100 1.669999 GCCAACCCTCATGTGCCATC 61.670 60.000 0.00 0.00 0.00 3.51
100 101 0.323633 CCAACCCTCATGTGCCATCA 60.324 55.000 0.00 0.00 0.00 3.07
101 102 0.813184 CAACCCTCATGTGCCATCAC 59.187 55.000 0.00 0.00 43.40 3.06
102 103 0.700564 AACCCTCATGTGCCATCACT 59.299 50.000 0.00 0.00 43.49 3.41
103 104 0.254178 ACCCTCATGTGCCATCACTC 59.746 55.000 0.00 0.00 43.49 3.51
104 105 0.545171 CCCTCATGTGCCATCACTCT 59.455 55.000 0.00 0.00 43.49 3.24
105 106 1.064906 CCCTCATGTGCCATCACTCTT 60.065 52.381 0.00 0.00 43.49 2.85
106 107 2.014857 CCTCATGTGCCATCACTCTTG 58.985 52.381 0.00 0.00 43.49 3.02
107 108 2.617276 CCTCATGTGCCATCACTCTTGT 60.617 50.000 0.00 0.00 43.49 3.16
108 109 3.079578 CTCATGTGCCATCACTCTTGTT 58.920 45.455 0.00 0.00 43.49 2.83
109 110 3.076621 TCATGTGCCATCACTCTTGTTC 58.923 45.455 0.00 0.00 43.49 3.18
115 116 2.887152 GCCATCACTCTTGTTCAAAGGT 59.113 45.455 0.00 0.00 0.00 3.50
141 142 3.077359 CAATGTGAGAGTGGAGAAACCC 58.923 50.000 0.00 0.00 38.00 4.11
142 143 2.103153 TGTGAGAGTGGAGAAACCCT 57.897 50.000 0.00 0.00 38.00 4.34
143 144 3.254093 TGTGAGAGTGGAGAAACCCTA 57.746 47.619 0.00 0.00 38.00 3.53
144 145 3.165875 TGTGAGAGTGGAGAAACCCTAG 58.834 50.000 0.00 0.00 38.00 3.02
185 187 0.734253 CCGCAACCACGAAGAGAGAG 60.734 60.000 0.00 0.00 34.06 3.20
203 205 2.178580 GAGGGAGAGGAGCATGGATAG 58.821 57.143 0.00 0.00 0.00 2.08
223 226 0.040067 GCGGCAGAGAAAAGGTTGTG 60.040 55.000 0.00 0.00 0.00 3.33
225 228 1.813862 CGGCAGAGAAAAGGTTGTGGA 60.814 52.381 0.00 0.00 0.00 4.02
226 229 2.519013 GGCAGAGAAAAGGTTGTGGAT 58.481 47.619 0.00 0.00 0.00 3.41
251 254 3.358111 AGATTCTCTCGAGTCACCTGA 57.642 47.619 13.13 0.19 0.00 3.86
321 332 1.678970 GGAGCAGGACGGCCAATTT 60.679 57.895 11.69 0.00 36.29 1.82
349 364 2.161410 TGGCGATGTAATTGTCACAAGC 59.839 45.455 0.00 0.00 37.43 4.01
477 492 2.023741 GTCTGAATGCATGCGCGG 59.976 61.111 14.09 10.15 42.97 6.46
494 523 1.062206 GGAGCTCCGTTAGTCGTCG 59.938 63.158 19.06 0.00 37.94 5.12
545 606 1.002250 CGGAACCGGAGAATATCGCG 61.002 60.000 9.46 0.00 35.56 5.87
547 608 0.318784 GAACCGGAGAATATCGCGCT 60.319 55.000 9.46 0.00 0.00 5.92
623 734 2.577059 CGGCTAGCTTCCGTTCCA 59.423 61.111 15.72 0.00 41.85 3.53
704 820 5.263968 TGAATTTTTAAAACCACGCTCCA 57.736 34.783 0.00 0.00 0.00 3.86
709 825 2.851263 TAAAACCACGCTCCACATCT 57.149 45.000 0.00 0.00 0.00 2.90
710 826 1.523758 AAAACCACGCTCCACATCTC 58.476 50.000 0.00 0.00 0.00 2.75
796 936 1.745320 TATTTCCTCGCCCGCTCCTC 61.745 60.000 0.00 0.00 0.00 3.71
852 1000 4.899239 CTCGGTCTCCCATGCGCC 62.899 72.222 4.18 0.00 0.00 6.53
910 1058 3.695606 ATGGCGTGAGAGCGTGGT 61.696 61.111 0.00 0.00 38.18 4.16
994 1165 1.681486 CGGAGGGAGAGGAAGGAAGC 61.681 65.000 0.00 0.00 0.00 3.86
995 1166 1.681486 GGAGGGAGAGGAAGGAAGCG 61.681 65.000 0.00 0.00 0.00 4.68
1594 1777 0.315568 GTGACTCGTGAGCCAGAAGT 59.684 55.000 0.00 0.00 0.00 3.01
1607 1790 2.016704 AGAAGTCAACGTGCTCGCG 61.017 57.895 8.29 0.00 41.18 5.87
1670 1861 2.860735 GCCACTTACTGCTATCTTGACG 59.139 50.000 0.00 0.00 0.00 4.35
1696 1887 0.604511 AAGCCTGTCCCGGTTTAACG 60.605 55.000 0.00 0.00 0.00 3.18
1702 1893 1.411977 TGTCCCGGTTTAACGACAGAA 59.588 47.619 0.00 0.00 35.47 3.02
1798 1989 2.207788 AAATTTGCTACCACCGGCGC 62.208 55.000 0.00 0.00 0.00 6.53
1818 2010 3.361917 CGCTTTTGATTTTGCTGAAACCG 60.362 43.478 0.00 0.00 0.00 4.44
1829 2021 1.198178 GCTGAAACCGACGCCAATTTA 59.802 47.619 0.00 0.00 0.00 1.40
1830 2022 2.727916 GCTGAAACCGACGCCAATTTAG 60.728 50.000 0.00 0.00 0.00 1.85
1831 2023 1.198178 TGAAACCGACGCCAATTTAGC 59.802 47.619 0.00 0.00 0.00 3.09
1832 2024 1.198178 GAAACCGACGCCAATTTAGCA 59.802 47.619 0.00 0.00 0.00 3.49
1833 2025 1.240256 AACCGACGCCAATTTAGCAA 58.760 45.000 0.00 0.00 0.00 3.91
1834 2026 1.240256 ACCGACGCCAATTTAGCAAA 58.760 45.000 0.00 0.00 0.00 3.68
1835 2027 1.609555 ACCGACGCCAATTTAGCAAAA 59.390 42.857 0.00 0.00 0.00 2.44
1836 2028 1.982913 CCGACGCCAATTTAGCAAAAC 59.017 47.619 0.00 0.00 0.00 2.43
1837 2029 2.351350 CCGACGCCAATTTAGCAAAACT 60.351 45.455 0.00 0.00 0.00 2.66
1838 2030 2.656422 CGACGCCAATTTAGCAAAACTG 59.344 45.455 0.00 0.00 0.00 3.16
1839 2031 3.638484 GACGCCAATTTAGCAAAACTGT 58.362 40.909 0.00 0.00 0.00 3.55
1840 2032 4.048504 GACGCCAATTTAGCAAAACTGTT 58.951 39.130 0.00 0.00 0.00 3.16
1841 2033 4.438148 ACGCCAATTTAGCAAAACTGTTT 58.562 34.783 0.00 0.00 0.00 2.83
1842 2034 4.506288 ACGCCAATTTAGCAAAACTGTTTC 59.494 37.500 6.20 0.00 0.00 2.78
1857 2049 3.255642 ACTGTTTCGCAATTTGCTACCAT 59.744 39.130 18.57 3.55 42.25 3.55
1858 2050 4.236935 CTGTTTCGCAATTTGCTACCATT 58.763 39.130 18.57 0.00 42.25 3.16
1868 2060 0.038709 TGCTACCATTGGCGTTTTGC 60.039 50.000 1.54 0.00 45.38 3.68
1873 2065 1.137872 ACCATTGGCGTTTTGCTTTGA 59.862 42.857 1.54 0.00 45.43 2.69
1881 2073 2.726241 GCGTTTTGCTTTGATGGAACTC 59.274 45.455 0.00 0.00 41.73 3.01
1885 2077 4.685169 TTTGCTTTGATGGAACTCGATC 57.315 40.909 0.00 0.00 0.00 3.69
1912 2105 3.372660 TTTGTTACAACCGGGCATTTC 57.627 42.857 6.32 0.00 0.00 2.17
1922 2117 0.170116 CGGGCATTTCGCTTTTGCTA 59.830 50.000 0.00 0.00 44.80 3.49
1930 2125 5.119125 GCATTTCGCTTTTGCTAGAACAAAT 59.881 36.000 0.00 0.00 44.80 2.32
1933 2128 5.181690 TCGCTTTTGCTAGAACAAATGTT 57.818 34.783 0.00 0.00 44.80 2.71
1970 2169 1.202580 TGTTTCCAATGGCGTTTTGGG 60.203 47.619 12.09 1.64 43.19 4.12
2052 2253 5.280164 CCCGATTTTTGCATTTTTGCTTTT 58.720 33.333 0.00 0.00 35.49 2.27
2088 2290 3.677963 CTGGGACCAGCCTCAAAAT 57.322 52.632 5.27 0.00 37.24 1.82
2134 2337 3.090952 TGCTGGAACCGACAATTTTTG 57.909 42.857 0.00 0.00 0.00 2.44
2216 2420 2.166050 TCGTTTGCTACAACCGGCTATA 59.834 45.455 0.00 0.00 0.00 1.31
2277 2491 1.673665 CTGGTGAAGGAGCTGCCAC 60.674 63.158 0.00 3.65 40.02 5.01
2291 2515 3.069980 GCCACGGTGTTGCAACCAA 62.070 57.895 26.14 6.30 40.53 3.67
2292 2516 1.739049 CCACGGTGTTGCAACCAAT 59.261 52.632 26.14 7.00 40.53 3.16
2349 2574 3.461061 TCAGGAATTTATCGAGCTGCAG 58.539 45.455 10.11 10.11 0.00 4.41
2354 2579 0.250234 TTTATCGAGCTGCAGCCTGT 59.750 50.000 34.39 17.46 43.38 4.00
2360 2587 3.054503 GCTGCAGCCTGTCCACAG 61.055 66.667 28.76 0.00 43.40 3.66
2364 2591 2.831770 CAGCCTGTCCACAGTGGT 59.168 61.111 19.65 0.00 42.27 4.16
2365 2592 1.149174 CAGCCTGTCCACAGTGGTT 59.851 57.895 19.65 0.00 42.27 3.67
2428 2657 3.717294 GGCACCGGTGGGACTCAT 61.717 66.667 34.58 0.00 36.97 2.90
2429 2658 2.436646 GCACCGGTGGGACTCATG 60.437 66.667 34.58 7.67 36.97 3.07
2430 2659 2.268920 CACCGGTGGGACTCATGG 59.731 66.667 27.57 0.00 36.97 3.66
2431 2660 3.009115 ACCGGTGGGACTCATGGG 61.009 66.667 6.12 0.00 36.97 4.00
2451 2680 0.916845 AGGGAAGGGGAGAGGAAAGC 60.917 60.000 0.00 0.00 0.00 3.51
2458 2687 0.390472 GGGAGAGGAAAGCTGTGACG 60.390 60.000 0.00 0.00 0.00 4.35
2459 2688 0.603569 GGAGAGGAAAGCTGTGACGA 59.396 55.000 0.00 0.00 0.00 4.20
2460 2689 1.205893 GGAGAGGAAAGCTGTGACGAT 59.794 52.381 0.00 0.00 0.00 3.73
2461 2690 2.266554 GAGAGGAAAGCTGTGACGATG 58.733 52.381 0.00 0.00 0.00 3.84
2462 2691 1.066573 AGAGGAAAGCTGTGACGATGG 60.067 52.381 0.00 0.00 0.00 3.51
2463 2692 0.674895 AGGAAAGCTGTGACGATGGC 60.675 55.000 0.00 0.00 0.00 4.40
2464 2693 1.648467 GGAAAGCTGTGACGATGGCC 61.648 60.000 0.00 0.00 0.00 5.36
2465 2694 0.955428 GAAAGCTGTGACGATGGCCA 60.955 55.000 8.56 8.56 0.00 5.36
2466 2695 0.322816 AAAGCTGTGACGATGGCCAT 60.323 50.000 20.96 20.96 0.00 4.40
2467 2696 0.541392 AAGCTGTGACGATGGCCATA 59.459 50.000 20.84 0.00 0.00 2.74
2468 2697 0.105593 AGCTGTGACGATGGCCATAG 59.894 55.000 20.84 21.98 0.00 2.23
2469 2698 0.179073 GCTGTGACGATGGCCATAGT 60.179 55.000 29.03 29.03 0.00 2.12
2470 2699 1.575244 CTGTGACGATGGCCATAGTG 58.425 55.000 32.88 20.93 0.00 2.74
2471 2700 1.136891 CTGTGACGATGGCCATAGTGA 59.863 52.381 32.88 23.80 0.00 3.41
2472 2701 1.762370 TGTGACGATGGCCATAGTGAT 59.238 47.619 32.88 11.54 0.00 3.06
2473 2702 2.170397 TGTGACGATGGCCATAGTGATT 59.830 45.455 32.88 11.16 0.00 2.57
2474 2703 2.802816 GTGACGATGGCCATAGTGATTC 59.197 50.000 32.88 19.61 0.00 2.52
2475 2704 2.433970 TGACGATGGCCATAGTGATTCA 59.566 45.455 32.88 21.76 0.00 2.57
2476 2705 2.802816 GACGATGGCCATAGTGATTCAC 59.197 50.000 32.88 15.41 34.10 3.18
2477 2706 2.170397 ACGATGGCCATAGTGATTCACA 59.830 45.455 28.24 5.61 36.74 3.58
2478 2707 2.804527 CGATGGCCATAGTGATTCACAG 59.195 50.000 20.84 8.01 36.74 3.66
2479 2708 3.742327 CGATGGCCATAGTGATTCACAGT 60.742 47.826 20.84 4.05 36.74 3.55
2480 2709 2.989909 TGGCCATAGTGATTCACAGTG 58.010 47.619 18.57 14.87 36.74 3.66
2481 2710 1.672881 GGCCATAGTGATTCACAGTGC 59.327 52.381 18.57 13.85 36.74 4.40
2482 2711 2.358957 GCCATAGTGATTCACAGTGCA 58.641 47.619 18.57 0.00 36.74 4.57
2483 2712 2.096496 GCCATAGTGATTCACAGTGCAC 59.904 50.000 18.57 9.40 36.74 4.57
2484 2713 3.337358 CCATAGTGATTCACAGTGCACA 58.663 45.455 21.04 0.00 36.74 4.57
2485 2714 3.943381 CCATAGTGATTCACAGTGCACAT 59.057 43.478 21.04 2.45 36.74 3.21
2486 2715 4.201881 CCATAGTGATTCACAGTGCACATG 60.202 45.833 21.04 16.73 36.74 3.21
2487 2716 1.538512 AGTGATTCACAGTGCACATGC 59.461 47.619 21.04 5.10 36.74 4.06
2488 2717 1.267533 GTGATTCACAGTGCACATGCA 59.732 47.619 21.04 7.79 40.57 3.96
2489 2718 2.094906 GTGATTCACAGTGCACATGCAT 60.095 45.455 21.04 12.53 42.80 3.96
2490 2719 3.127376 GTGATTCACAGTGCACATGCATA 59.873 43.478 21.04 6.29 42.80 3.14
2491 2720 4.379708 GTGATTCACAGTGCACATGCATAA 60.380 41.667 21.04 7.77 42.80 1.90
2492 2721 6.401868 GTGATTCACAGTGCACATGCATAAC 61.402 44.000 21.04 11.86 42.80 1.89
2501 2730 4.164822 GCACATGCATAACCCACATATC 57.835 45.455 0.00 0.00 41.59 1.63
2502 2731 3.822735 GCACATGCATAACCCACATATCT 59.177 43.478 0.00 0.00 41.59 1.98
2503 2732 4.279169 GCACATGCATAACCCACATATCTT 59.721 41.667 0.00 0.00 41.59 2.40
2504 2733 5.563475 GCACATGCATAACCCACATATCTTC 60.563 44.000 0.00 0.00 41.59 2.87
2505 2734 5.532032 CACATGCATAACCCACATATCTTCA 59.468 40.000 0.00 0.00 0.00 3.02
2506 2735 5.532406 ACATGCATAACCCACATATCTTCAC 59.468 40.000 0.00 0.00 0.00 3.18
2507 2736 5.109500 TGCATAACCCACATATCTTCACA 57.891 39.130 0.00 0.00 0.00 3.58
2508 2737 5.125356 TGCATAACCCACATATCTTCACAG 58.875 41.667 0.00 0.00 0.00 3.66
2509 2738 5.126067 GCATAACCCACATATCTTCACAGT 58.874 41.667 0.00 0.00 0.00 3.55
2510 2739 6.126911 TGCATAACCCACATATCTTCACAGTA 60.127 38.462 0.00 0.00 0.00 2.74
2511 2740 6.202954 GCATAACCCACATATCTTCACAGTAC 59.797 42.308 0.00 0.00 0.00 2.73
2512 2741 4.386867 ACCCACATATCTTCACAGTACG 57.613 45.455 0.00 0.00 0.00 3.67
2513 2742 3.767673 ACCCACATATCTTCACAGTACGT 59.232 43.478 0.00 0.00 0.00 3.57
2515 2744 4.381612 CCCACATATCTTCACAGTACGTGT 60.382 45.833 14.51 5.27 46.44 4.49
2516 2745 5.168569 CCACATATCTTCACAGTACGTGTT 58.831 41.667 14.51 0.00 46.44 3.32
2517 2746 6.327154 CCACATATCTTCACAGTACGTGTTA 58.673 40.000 14.51 6.53 46.44 2.41
2518 2747 6.809689 CCACATATCTTCACAGTACGTGTTAA 59.190 38.462 14.51 5.33 46.44 2.01
2519 2748 7.491372 CCACATATCTTCACAGTACGTGTTAAT 59.509 37.037 14.51 10.09 46.44 1.40
2520 2749 8.869897 CACATATCTTCACAGTACGTGTTAATT 58.130 33.333 14.51 0.00 46.44 1.40
2521 2750 9.431887 ACATATCTTCACAGTACGTGTTAATTT 57.568 29.630 14.51 3.73 46.44 1.82
2522 2751 9.901724 CATATCTTCACAGTACGTGTTAATTTC 57.098 33.333 14.51 0.00 46.44 2.17
2523 2752 6.442487 TCTTCACAGTACGTGTTAATTTCG 57.558 37.500 14.51 0.00 46.44 3.46
2524 2753 6.207928 TCTTCACAGTACGTGTTAATTTCGA 58.792 36.000 14.51 0.00 46.44 3.71
2525 2754 5.811018 TCACAGTACGTGTTAATTTCGAC 57.189 39.130 14.51 0.00 46.44 4.20
2526 2755 5.280164 TCACAGTACGTGTTAATTTCGACA 58.720 37.500 14.51 0.00 46.44 4.35
2527 2756 5.173673 TCACAGTACGTGTTAATTTCGACAC 59.826 40.000 14.51 8.54 46.44 3.67
2528 2757 5.042593 ACAGTACGTGTTAATTTCGACACA 58.957 37.500 15.30 0.00 44.85 3.72
2529 2758 5.519566 ACAGTACGTGTTAATTTCGACACAA 59.480 36.000 15.30 4.77 44.85 3.33
2530 2759 6.035866 ACAGTACGTGTTAATTTCGACACAAA 59.964 34.615 15.30 4.52 44.85 2.83
2531 2760 6.900828 CAGTACGTGTTAATTTCGACACAAAA 59.099 34.615 15.30 0.00 44.85 2.44
2532 2761 7.425882 CAGTACGTGTTAATTTCGACACAAAAA 59.574 33.333 15.30 0.00 44.85 1.94
2553 2782 5.991328 AAATGCTACTGATCATTACGGTG 57.009 39.130 0.00 0.00 33.05 4.94
2554 2783 4.672587 ATGCTACTGATCATTACGGTGT 57.327 40.909 0.00 0.00 0.00 4.16
2555 2784 4.465632 TGCTACTGATCATTACGGTGTT 57.534 40.909 0.00 0.00 0.00 3.32
2556 2785 4.180817 TGCTACTGATCATTACGGTGTTG 58.819 43.478 0.00 0.00 0.00 3.33
2557 2786 4.181578 GCTACTGATCATTACGGTGTTGT 58.818 43.478 0.00 0.00 0.00 3.32
2558 2787 5.105675 TGCTACTGATCATTACGGTGTTGTA 60.106 40.000 0.00 0.00 0.00 2.41
2559 2788 5.459107 GCTACTGATCATTACGGTGTTGTAG 59.541 44.000 0.00 1.62 0.00 2.74
2560 2789 5.654603 ACTGATCATTACGGTGTTGTAGA 57.345 39.130 0.00 0.00 0.00 2.59
2561 2790 5.408356 ACTGATCATTACGGTGTTGTAGAC 58.592 41.667 0.00 0.00 0.00 2.59
2562 2791 4.417506 TGATCATTACGGTGTTGTAGACG 58.582 43.478 0.00 0.00 0.00 4.18
2563 2792 3.220507 TCATTACGGTGTTGTAGACGG 57.779 47.619 0.00 0.00 0.00 4.79
2564 2793 1.657094 CATTACGGTGTTGTAGACGGC 59.343 52.381 0.00 0.00 0.00 5.68
2565 2794 0.672889 TTACGGTGTTGTAGACGGCA 59.327 50.000 0.00 0.00 0.00 5.69
2566 2795 0.241749 TACGGTGTTGTAGACGGCAG 59.758 55.000 0.00 0.00 0.00 4.85
2567 2796 1.736645 CGGTGTTGTAGACGGCAGG 60.737 63.158 0.00 0.00 0.00 4.85
2568 2797 2.033194 GGTGTTGTAGACGGCAGGC 61.033 63.158 0.00 0.00 0.00 4.85
2569 2798 2.033194 GTGTTGTAGACGGCAGGCC 61.033 63.158 0.00 0.00 0.00 5.19
2570 2799 2.436115 GTTGTAGACGGCAGGCCC 60.436 66.667 0.00 0.00 0.00 5.80
2571 2800 2.925706 TTGTAGACGGCAGGCCCA 60.926 61.111 0.00 0.00 0.00 5.36
2572 2801 2.521451 TTGTAGACGGCAGGCCCAA 61.521 57.895 0.00 0.00 0.00 4.12
2573 2802 1.847798 TTGTAGACGGCAGGCCCAAT 61.848 55.000 0.00 0.00 0.00 3.16
2574 2803 1.523938 GTAGACGGCAGGCCCAATC 60.524 63.158 0.00 0.35 0.00 2.67
2575 2804 2.742116 TAGACGGCAGGCCCAATCC 61.742 63.158 0.00 0.00 0.00 3.01
2576 2805 4.115199 GACGGCAGGCCCAATCCT 62.115 66.667 0.00 0.00 36.78 3.24
2577 2806 3.645268 GACGGCAGGCCCAATCCTT 62.645 63.158 0.00 0.00 33.25 3.36
2578 2807 3.142838 CGGCAGGCCCAATCCTTG 61.143 66.667 0.00 0.00 33.25 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.178534 AAACCTGCCATTCCCGTGTG 61.179 55.000 0.00 0.00 0.00 3.82
1 2 0.402504 TAAACCTGCCATTCCCGTGT 59.597 50.000 0.00 0.00 0.00 4.49
2 3 1.094785 CTAAACCTGCCATTCCCGTG 58.905 55.000 0.00 0.00 0.00 4.94
3 4 0.696501 ACTAAACCTGCCATTCCCGT 59.303 50.000 0.00 0.00 0.00 5.28
4 5 1.472480 CAACTAAACCTGCCATTCCCG 59.528 52.381 0.00 0.00 0.00 5.14
5 6 2.802719 TCAACTAAACCTGCCATTCCC 58.197 47.619 0.00 0.00 0.00 3.97
6 7 5.652452 ACTTATCAACTAAACCTGCCATTCC 59.348 40.000 0.00 0.00 0.00 3.01
7 8 6.759497 ACTTATCAACTAAACCTGCCATTC 57.241 37.500 0.00 0.00 0.00 2.67
8 9 7.285401 CCATACTTATCAACTAAACCTGCCATT 59.715 37.037 0.00 0.00 0.00 3.16
9 10 6.772716 CCATACTTATCAACTAAACCTGCCAT 59.227 38.462 0.00 0.00 0.00 4.40
10 11 6.119536 CCATACTTATCAACTAAACCTGCCA 58.880 40.000 0.00 0.00 0.00 4.92
11 12 5.008712 GCCATACTTATCAACTAAACCTGCC 59.991 44.000 0.00 0.00 0.00 4.85
12 13 5.588648 TGCCATACTTATCAACTAAACCTGC 59.411 40.000 0.00 0.00 0.00 4.85
13 14 7.624360 TTGCCATACTTATCAACTAAACCTG 57.376 36.000 0.00 0.00 0.00 4.00
14 15 8.823220 AATTGCCATACTTATCAACTAAACCT 57.177 30.769 0.00 0.00 0.00 3.50
15 16 8.135529 GGAATTGCCATACTTATCAACTAAACC 58.864 37.037 0.00 0.00 36.34 3.27
16 17 8.135529 GGGAATTGCCATACTTATCAACTAAAC 58.864 37.037 11.71 0.00 38.95 2.01
17 18 7.836685 TGGGAATTGCCATACTTATCAACTAAA 59.163 33.333 15.64 0.00 38.95 1.85
18 19 7.284489 GTGGGAATTGCCATACTTATCAACTAA 59.716 37.037 22.56 0.00 38.95 2.24
19 20 6.770785 GTGGGAATTGCCATACTTATCAACTA 59.229 38.462 22.56 0.00 38.95 2.24
20 21 5.594317 GTGGGAATTGCCATACTTATCAACT 59.406 40.000 22.56 0.00 38.95 3.16
21 22 5.221244 GGTGGGAATTGCCATACTTATCAAC 60.221 44.000 22.56 4.72 38.95 3.18
22 23 4.892934 GGTGGGAATTGCCATACTTATCAA 59.107 41.667 22.56 0.00 38.95 2.57
23 24 4.167892 AGGTGGGAATTGCCATACTTATCA 59.832 41.667 22.56 0.00 38.95 2.15
24 25 4.729868 AGGTGGGAATTGCCATACTTATC 58.270 43.478 22.56 6.95 38.95 1.75
25 26 4.167892 TGAGGTGGGAATTGCCATACTTAT 59.832 41.667 22.56 4.76 38.95 1.73
26 27 3.525609 TGAGGTGGGAATTGCCATACTTA 59.474 43.478 22.56 16.21 38.95 2.24
27 28 2.311542 TGAGGTGGGAATTGCCATACTT 59.688 45.455 22.56 6.44 38.95 2.24
28 29 1.922447 TGAGGTGGGAATTGCCATACT 59.078 47.619 22.56 21.52 38.95 2.12
29 30 2.301346 CTGAGGTGGGAATTGCCATAC 58.699 52.381 22.56 17.32 38.95 2.39
30 31 1.922447 ACTGAGGTGGGAATTGCCATA 59.078 47.619 22.56 8.28 38.95 2.74
31 32 0.706433 ACTGAGGTGGGAATTGCCAT 59.294 50.000 22.56 6.91 38.95 4.40
32 33 0.482446 AACTGAGGTGGGAATTGCCA 59.518 50.000 15.64 15.64 38.95 4.92
33 34 1.632589 AAACTGAGGTGGGAATTGCC 58.367 50.000 9.44 9.44 0.00 4.52
34 35 2.627699 TCAAAACTGAGGTGGGAATTGC 59.372 45.455 0.00 0.00 0.00 3.56
35 36 6.780457 ATATCAAAACTGAGGTGGGAATTG 57.220 37.500 0.00 0.00 0.00 2.32
36 37 6.953520 TGAATATCAAAACTGAGGTGGGAATT 59.046 34.615 0.00 0.00 0.00 2.17
37 38 6.493166 TGAATATCAAAACTGAGGTGGGAAT 58.507 36.000 0.00 0.00 0.00 3.01
38 39 5.886609 TGAATATCAAAACTGAGGTGGGAA 58.113 37.500 0.00 0.00 0.00 3.97
39 40 5.512942 TGAATATCAAAACTGAGGTGGGA 57.487 39.130 0.00 0.00 0.00 4.37
40 41 5.008019 CGATGAATATCAAAACTGAGGTGGG 59.992 44.000 0.00 0.00 32.67 4.61
41 42 5.008019 CCGATGAATATCAAAACTGAGGTGG 59.992 44.000 0.00 0.00 32.67 4.61
42 43 5.504665 GCCGATGAATATCAAAACTGAGGTG 60.505 44.000 0.00 0.00 32.67 4.00
43 44 4.576463 GCCGATGAATATCAAAACTGAGGT 59.424 41.667 0.00 0.00 32.67 3.85
44 45 4.818546 AGCCGATGAATATCAAAACTGAGG 59.181 41.667 0.00 0.00 32.67 3.86
45 46 5.277683 CCAGCCGATGAATATCAAAACTGAG 60.278 44.000 0.00 0.00 32.67 3.35
46 47 4.576053 CCAGCCGATGAATATCAAAACTGA 59.424 41.667 0.00 0.00 32.67 3.41
47 48 4.576053 TCCAGCCGATGAATATCAAAACTG 59.424 41.667 0.00 0.00 32.67 3.16
48 49 4.780815 TCCAGCCGATGAATATCAAAACT 58.219 39.130 0.00 0.00 32.67 2.66
49 50 5.695851 ATCCAGCCGATGAATATCAAAAC 57.304 39.130 0.00 0.00 32.67 2.43
50 51 5.827267 TCAATCCAGCCGATGAATATCAAAA 59.173 36.000 0.00 0.00 32.67 2.44
51 52 5.375773 TCAATCCAGCCGATGAATATCAAA 58.624 37.500 0.00 0.00 32.67 2.69
52 53 4.971939 TCAATCCAGCCGATGAATATCAA 58.028 39.130 0.00 0.00 32.67 2.57
53 54 4.572909 CTCAATCCAGCCGATGAATATCA 58.427 43.478 0.00 0.00 32.67 2.15
54 55 3.373439 GCTCAATCCAGCCGATGAATATC 59.627 47.826 0.00 0.00 32.76 1.63
55 56 3.244665 TGCTCAATCCAGCCGATGAATAT 60.245 43.478 0.00 0.00 38.80 1.28
56 57 2.104622 TGCTCAATCCAGCCGATGAATA 59.895 45.455 0.00 0.00 38.80 1.75
57 58 1.134007 TGCTCAATCCAGCCGATGAAT 60.134 47.619 0.00 0.00 38.80 2.57
58 59 0.252761 TGCTCAATCCAGCCGATGAA 59.747 50.000 0.00 0.00 38.80 2.57
59 60 0.252761 TTGCTCAATCCAGCCGATGA 59.747 50.000 0.00 0.00 38.80 2.92
60 61 0.379669 GTTGCTCAATCCAGCCGATG 59.620 55.000 0.00 0.00 38.80 3.84
61 62 1.091771 CGTTGCTCAATCCAGCCGAT 61.092 55.000 0.00 0.00 38.80 4.18
62 63 1.741401 CGTTGCTCAATCCAGCCGA 60.741 57.895 0.00 0.00 38.80 5.54
63 64 2.787249 CGTTGCTCAATCCAGCCG 59.213 61.111 0.00 0.00 38.80 5.52
64 65 2.486966 GCGTTGCTCAATCCAGCC 59.513 61.111 0.00 0.00 38.80 4.85
65 66 1.865788 TTGGCGTTGCTCAATCCAGC 61.866 55.000 6.64 0.00 40.13 4.85
66 67 0.109597 GTTGGCGTTGCTCAATCCAG 60.110 55.000 6.64 0.00 31.09 3.86
67 68 1.523154 GGTTGGCGTTGCTCAATCCA 61.523 55.000 3.53 3.53 0.00 3.41
68 69 1.212751 GGTTGGCGTTGCTCAATCC 59.787 57.895 0.00 0.00 0.00 3.01
69 70 1.212751 GGGTTGGCGTTGCTCAATC 59.787 57.895 0.00 0.00 0.00 2.67
70 71 1.228552 AGGGTTGGCGTTGCTCAAT 60.229 52.632 0.00 0.00 0.00 2.57
71 72 1.896660 GAGGGTTGGCGTTGCTCAA 60.897 57.895 0.00 0.00 0.00 3.02
72 73 2.281484 GAGGGTTGGCGTTGCTCA 60.281 61.111 0.00 0.00 0.00 4.26
73 74 1.675641 ATGAGGGTTGGCGTTGCTC 60.676 57.895 0.00 0.00 0.00 4.26
74 75 1.973281 CATGAGGGTTGGCGTTGCT 60.973 57.895 0.00 0.00 0.00 3.91
75 76 2.268076 ACATGAGGGTTGGCGTTGC 61.268 57.895 0.00 0.00 0.00 4.17
76 77 1.580942 CACATGAGGGTTGGCGTTG 59.419 57.895 0.00 0.00 0.00 4.10
77 78 2.268076 GCACATGAGGGTTGGCGTT 61.268 57.895 0.00 0.00 0.00 4.84
78 79 2.672996 GCACATGAGGGTTGGCGT 60.673 61.111 0.00 0.00 0.00 5.68
79 80 3.443045 GGCACATGAGGGTTGGCG 61.443 66.667 0.00 0.00 0.00 5.69
80 81 2.283101 TGGCACATGAGGGTTGGC 60.283 61.111 0.00 0.00 0.00 4.52
92 93 3.304928 CCTTTGAACAAGAGTGATGGCAC 60.305 47.826 0.00 0.00 45.49 5.01
93 94 2.886523 CCTTTGAACAAGAGTGATGGCA 59.113 45.455 0.00 0.00 0.00 4.92
94 95 2.887152 ACCTTTGAACAAGAGTGATGGC 59.113 45.455 0.00 0.00 0.00 4.40
95 96 5.551233 TCTACCTTTGAACAAGAGTGATGG 58.449 41.667 0.00 0.00 0.00 3.51
96 97 6.875726 TGATCTACCTTTGAACAAGAGTGATG 59.124 38.462 0.00 0.00 0.00 3.07
97 98 7.009179 TGATCTACCTTTGAACAAGAGTGAT 57.991 36.000 0.00 0.00 0.00 3.06
98 99 6.419484 TGATCTACCTTTGAACAAGAGTGA 57.581 37.500 0.00 0.00 0.00 3.41
99 100 7.173907 ACATTGATCTACCTTTGAACAAGAGTG 59.826 37.037 0.00 0.00 31.60 3.51
100 101 7.173907 CACATTGATCTACCTTTGAACAAGAGT 59.826 37.037 0.00 0.00 31.60 3.24
101 102 7.388776 TCACATTGATCTACCTTTGAACAAGAG 59.611 37.037 0.00 0.00 31.60 2.85
102 103 7.223584 TCACATTGATCTACCTTTGAACAAGA 58.776 34.615 0.00 0.00 31.60 3.02
103 104 7.388776 TCTCACATTGATCTACCTTTGAACAAG 59.611 37.037 0.00 0.00 31.60 3.16
104 105 7.223584 TCTCACATTGATCTACCTTTGAACAA 58.776 34.615 0.00 0.00 32.38 2.83
105 106 6.768483 TCTCACATTGATCTACCTTTGAACA 58.232 36.000 0.00 0.00 0.00 3.18
106 107 6.876257 ACTCTCACATTGATCTACCTTTGAAC 59.124 38.462 0.00 0.00 0.00 3.18
107 108 6.875726 CACTCTCACATTGATCTACCTTTGAA 59.124 38.462 0.00 0.00 0.00 2.69
108 109 6.401394 CACTCTCACATTGATCTACCTTTGA 58.599 40.000 0.00 0.00 0.00 2.69
109 110 5.583854 CCACTCTCACATTGATCTACCTTTG 59.416 44.000 0.00 0.00 0.00 2.77
115 116 6.351371 GGTTTCTCCACTCTCACATTGATCTA 60.351 42.308 0.00 0.00 35.97 1.98
141 142 1.773054 TTCGACGCGCTCCTAGCTAG 61.773 60.000 14.20 14.20 39.60 3.42
142 143 1.773054 CTTCGACGCGCTCCTAGCTA 61.773 60.000 5.73 0.00 39.60 3.32
143 144 3.114647 CTTCGACGCGCTCCTAGCT 62.115 63.158 5.73 0.00 39.60 3.32
144 145 2.652496 CTTCGACGCGCTCCTAGC 60.652 66.667 5.73 0.00 38.02 3.42
185 187 1.274712 CCTATCCATGCTCCTCTCCC 58.725 60.000 0.00 0.00 0.00 4.30
203 205 1.172812 ACAACCTTTTCTCTGCCGCC 61.173 55.000 0.00 0.00 0.00 6.13
223 226 9.027205 AGGTGACTCGAGAGAATCTACAAATCC 62.027 44.444 21.68 4.24 42.61 3.01
225 228 5.654650 AGGTGACTCGAGAGAATCTACAAAT 59.345 40.000 21.68 0.00 42.61 2.32
226 229 5.010933 AGGTGACTCGAGAGAATCTACAAA 58.989 41.667 21.68 0.00 42.61 2.83
307 318 1.595093 GGGTGAAATTGGCCGTCCTG 61.595 60.000 0.00 0.00 0.00 3.86
321 332 2.290641 ACAATTACATCGCCAAGGGTGA 60.291 45.455 0.38 0.38 46.70 4.02
349 364 1.243342 TGGCGAATTTGTGGCTGGAG 61.243 55.000 0.00 0.00 0.00 3.86
484 499 1.000496 GGGATGGGATCGACGACTAAC 60.000 57.143 0.00 0.00 0.00 2.34
494 523 2.447765 TCCACGGGGGATGGGATC 60.448 66.667 2.42 0.00 42.15 3.36
640 751 2.315720 AGCTTGGAAAAATGGCTCCT 57.684 45.000 0.00 0.00 32.51 3.69
704 820 1.138459 CGAGTGAGCTGCGAGATGT 59.862 57.895 0.00 0.00 0.00 3.06
772 888 1.663739 CGGGCGAGGAAATATCGGA 59.336 57.895 0.00 0.00 40.50 4.55
799 939 3.188786 GTGGTGCAGGCGATCGAC 61.189 66.667 21.57 18.32 0.00 4.20
800 940 3.233259 TTGTGGTGCAGGCGATCGA 62.233 57.895 21.57 0.00 0.00 3.59
852 1000 2.740714 GCTGCGGTAGTCAAAGGCG 61.741 63.158 0.00 0.00 0.00 5.52
910 1058 5.361285 GGACTTCTTGGACTTATCAGCTAGA 59.639 44.000 0.00 0.00 0.00 2.43
967 1138 2.754658 TCTCCCTCCGCGAACTCC 60.755 66.667 8.23 0.00 0.00 3.85
1405 1585 2.351276 CTTCACCTTGTCCCCGGG 59.649 66.667 15.80 15.80 0.00 5.73
1607 1790 1.709147 ATGCTTCGATGAGTTGGCGC 61.709 55.000 0.00 0.00 0.00 6.53
1682 1873 1.039068 TCTGTCGTTAAACCGGGACA 58.961 50.000 6.32 7.64 37.77 4.02
1696 1887 4.549458 CACATTGGTCATTTGGTTCTGTC 58.451 43.478 0.00 0.00 0.00 3.51
1702 1893 2.014010 AGCCACATTGGTCATTTGGT 57.986 45.000 0.00 0.00 40.46 3.67
1798 1989 4.085619 CGTCGGTTTCAGCAAAATCAAAAG 60.086 41.667 0.00 0.00 0.00 2.27
1818 2010 3.638484 ACAGTTTTGCTAAATTGGCGTC 58.362 40.909 17.50 0.00 35.84 5.19
1857 2049 1.410517 TCCATCAAAGCAAAACGCCAA 59.589 42.857 0.00 0.00 44.04 4.52
1858 2050 1.035923 TCCATCAAAGCAAAACGCCA 58.964 45.000 0.00 0.00 44.04 5.69
1896 2089 1.877367 GCGAAATGCCCGGTTGTAA 59.123 52.632 0.00 0.00 37.76 2.41
1970 2169 3.733443 AATTGAAGTGGTTCCAGCAAC 57.267 42.857 0.00 0.00 0.00 4.17
2009 2209 2.124122 GCAATGTTCCAACAAACCGAC 58.876 47.619 0.00 0.00 43.03 4.79
2074 2276 3.391506 AGCAAAATTTTGAGGCTGGTC 57.608 42.857 30.40 12.63 40.55 4.02
2088 2290 6.926630 AAAAGGAATATGGTGGTAGCAAAA 57.073 33.333 0.00 0.00 0.00 2.44
2114 2316 2.428890 ACAAAAATTGTCGGTTCCAGCA 59.571 40.909 0.00 0.00 40.56 4.41
2125 2327 4.111916 CTCGGTTGAAGCACAAAAATTGT 58.888 39.130 0.00 0.00 46.75 2.71
2134 2337 1.000506 TCCAGTACTCGGTTGAAGCAC 59.999 52.381 10.08 0.00 0.00 4.40
2216 2420 0.609131 CCAAAGGTTCCAGCATCCGT 60.609 55.000 0.00 0.00 0.00 4.69
2277 2491 0.597118 CACCATTGGTTGCAACACCG 60.597 55.000 29.55 14.79 40.09 4.94
2354 2579 0.393132 TGTCGCAAAACCACTGTGGA 60.393 50.000 32.30 5.91 40.96 4.02
2360 2587 0.657368 CGAAGCTGTCGCAAAACCAC 60.657 55.000 5.58 0.00 44.14 4.16
2424 2653 1.004758 TCCCCTTCCCTCCCATGAG 59.995 63.158 0.00 0.00 38.42 2.90
2425 2654 1.004758 CTCCCCTTCCCTCCCATGA 59.995 63.158 0.00 0.00 0.00 3.07
2426 2655 1.004758 TCTCCCCTTCCCTCCCATG 59.995 63.158 0.00 0.00 0.00 3.66
2427 2656 1.319799 CTCTCCCCTTCCCTCCCAT 59.680 63.158 0.00 0.00 0.00 4.00
2428 2657 2.787866 CTCTCCCCTTCCCTCCCA 59.212 66.667 0.00 0.00 0.00 4.37
2429 2658 2.040359 CCTCTCCCCTTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
2430 2659 0.253207 TTTCCTCTCCCCTTCCCTCC 60.253 60.000 0.00 0.00 0.00 4.30
2431 2660 1.208706 CTTTCCTCTCCCCTTCCCTC 58.791 60.000 0.00 0.00 0.00 4.30
2451 2680 1.136891 TCACTATGGCCATCGTCACAG 59.863 52.381 24.80 15.60 0.00 3.66
2458 2687 3.562973 CACTGTGAATCACTATGGCCATC 59.437 47.826 24.80 7.51 35.11 3.51
2459 2688 3.548770 CACTGTGAATCACTATGGCCAT 58.451 45.455 24.45 24.45 35.11 4.40
2460 2689 2.940971 GCACTGTGAATCACTATGGCCA 60.941 50.000 8.56 8.56 35.11 5.36
2461 2690 1.672881 GCACTGTGAATCACTATGGCC 59.327 52.381 14.97 0.00 35.11 5.36
2462 2691 2.096496 GTGCACTGTGAATCACTATGGC 59.904 50.000 14.97 12.61 35.11 4.40
2463 2692 3.337358 TGTGCACTGTGAATCACTATGG 58.663 45.455 19.41 5.07 35.11 2.74
2464 2693 4.729746 GCATGTGCACTGTGAATCACTATG 60.730 45.833 19.41 12.92 41.59 2.23
2465 2694 3.376234 GCATGTGCACTGTGAATCACTAT 59.624 43.478 19.41 0.00 41.59 2.12
2466 2695 2.743664 GCATGTGCACTGTGAATCACTA 59.256 45.455 19.41 0.48 41.59 2.74
2467 2696 1.538512 GCATGTGCACTGTGAATCACT 59.461 47.619 19.41 0.00 41.59 3.41
2468 2697 1.973138 GCATGTGCACTGTGAATCAC 58.027 50.000 19.41 6.41 41.59 3.06
2480 2709 3.822735 AGATATGTGGGTTATGCATGTGC 59.177 43.478 10.16 0.00 42.50 4.57
2481 2710 5.532032 TGAAGATATGTGGGTTATGCATGTG 59.468 40.000 10.16 0.00 0.00 3.21
2482 2711 5.532406 GTGAAGATATGTGGGTTATGCATGT 59.468 40.000 10.16 0.00 0.00 3.21
2483 2712 5.532032 TGTGAAGATATGTGGGTTATGCATG 59.468 40.000 10.16 0.00 0.00 4.06
2484 2713 5.693961 TGTGAAGATATGTGGGTTATGCAT 58.306 37.500 3.79 3.79 0.00 3.96
2485 2714 5.109500 TGTGAAGATATGTGGGTTATGCA 57.891 39.130 0.00 0.00 0.00 3.96
2486 2715 5.126067 ACTGTGAAGATATGTGGGTTATGC 58.874 41.667 0.00 0.00 0.00 3.14
2487 2716 6.420903 CGTACTGTGAAGATATGTGGGTTATG 59.579 42.308 0.00 0.00 0.00 1.90
2488 2717 6.097839 ACGTACTGTGAAGATATGTGGGTTAT 59.902 38.462 0.00 0.00 0.00 1.89
2489 2718 5.419788 ACGTACTGTGAAGATATGTGGGTTA 59.580 40.000 0.00 0.00 0.00 2.85
2490 2719 4.222145 ACGTACTGTGAAGATATGTGGGTT 59.778 41.667 0.00 0.00 0.00 4.11
2491 2720 3.767673 ACGTACTGTGAAGATATGTGGGT 59.232 43.478 0.00 0.00 0.00 4.51
2492 2721 4.386867 ACGTACTGTGAAGATATGTGGG 57.613 45.455 0.00 0.00 0.00 4.61
2505 2734 5.042593 TGTGTCGAAATTAACACGTACTGT 58.957 37.500 11.71 0.00 46.91 3.55
2506 2735 5.564213 TGTGTCGAAATTAACACGTACTG 57.436 39.130 11.71 0.00 46.91 2.74
2507 2736 6.586868 TTTGTGTCGAAATTAACACGTACT 57.413 33.333 11.71 0.00 46.91 2.73
2508 2737 7.647780 TTTTTGTGTCGAAATTAACACGTAC 57.352 32.000 11.71 0.00 46.91 3.67
2529 2758 6.374333 ACACCGTAATGATCAGTAGCATTTTT 59.626 34.615 2.50 0.00 38.55 1.94
2530 2759 5.880332 ACACCGTAATGATCAGTAGCATTTT 59.120 36.000 2.50 0.00 38.55 1.82
2531 2760 5.428253 ACACCGTAATGATCAGTAGCATTT 58.572 37.500 2.50 0.00 38.55 2.32
2532 2761 5.023533 ACACCGTAATGATCAGTAGCATT 57.976 39.130 2.50 0.00 43.80 3.56
2533 2762 4.672587 ACACCGTAATGATCAGTAGCAT 57.327 40.909 2.50 0.00 31.60 3.79
2534 2763 4.180817 CAACACCGTAATGATCAGTAGCA 58.819 43.478 2.50 0.00 0.00 3.49
2535 2764 4.181578 ACAACACCGTAATGATCAGTAGC 58.818 43.478 2.50 0.00 0.00 3.58
2536 2765 6.691818 GTCTACAACACCGTAATGATCAGTAG 59.308 42.308 2.50 4.37 0.00 2.57
2537 2766 6.558009 GTCTACAACACCGTAATGATCAGTA 58.442 40.000 0.09 0.00 0.00 2.74
2538 2767 5.408356 GTCTACAACACCGTAATGATCAGT 58.592 41.667 0.09 0.00 0.00 3.41
2539 2768 4.499399 CGTCTACAACACCGTAATGATCAG 59.501 45.833 0.09 0.00 0.00 2.90
2540 2769 4.417506 CGTCTACAACACCGTAATGATCA 58.582 43.478 0.00 0.00 0.00 2.92
2541 2770 3.795101 CCGTCTACAACACCGTAATGATC 59.205 47.826 0.00 0.00 0.00 2.92
2542 2771 3.777478 CCGTCTACAACACCGTAATGAT 58.223 45.455 0.00 0.00 0.00 2.45
2543 2772 2.671914 GCCGTCTACAACACCGTAATGA 60.672 50.000 0.00 0.00 0.00 2.57
2544 2773 1.657094 GCCGTCTACAACACCGTAATG 59.343 52.381 0.00 0.00 0.00 1.90
2545 2774 1.273048 TGCCGTCTACAACACCGTAAT 59.727 47.619 0.00 0.00 0.00 1.89
2546 2775 0.672889 TGCCGTCTACAACACCGTAA 59.327 50.000 0.00 0.00 0.00 3.18
2547 2776 0.241749 CTGCCGTCTACAACACCGTA 59.758 55.000 0.00 0.00 0.00 4.02
2548 2777 1.006571 CTGCCGTCTACAACACCGT 60.007 57.895 0.00 0.00 0.00 4.83
2549 2778 1.736645 CCTGCCGTCTACAACACCG 60.737 63.158 0.00 0.00 0.00 4.94
2550 2779 2.033194 GCCTGCCGTCTACAACACC 61.033 63.158 0.00 0.00 0.00 4.16
2551 2780 2.033194 GGCCTGCCGTCTACAACAC 61.033 63.158 0.00 0.00 0.00 3.32
2552 2781 2.345991 GGCCTGCCGTCTACAACA 59.654 61.111 0.00 0.00 0.00 3.33
2553 2782 2.436115 GGGCCTGCCGTCTACAAC 60.436 66.667 0.84 0.00 36.85 3.32
2554 2783 1.847798 ATTGGGCCTGCCGTCTACAA 61.848 55.000 4.53 0.79 36.85 2.41
2555 2784 2.252072 GATTGGGCCTGCCGTCTACA 62.252 60.000 4.53 0.00 36.85 2.74
2556 2785 1.523938 GATTGGGCCTGCCGTCTAC 60.524 63.158 4.53 0.00 36.85 2.59
2557 2786 2.742116 GGATTGGGCCTGCCGTCTA 61.742 63.158 4.53 0.00 36.85 2.59
2558 2787 4.115199 GGATTGGGCCTGCCGTCT 62.115 66.667 4.53 0.00 36.85 4.18
2559 2788 3.645268 AAGGATTGGGCCTGCCGTC 62.645 63.158 4.53 0.54 38.58 4.79
2560 2789 3.661648 AAGGATTGGGCCTGCCGT 61.662 61.111 4.53 0.00 38.58 5.68
2561 2790 3.142838 CAAGGATTGGGCCTGCCG 61.143 66.667 4.53 0.00 43.94 5.69


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

AutoCloner maintained by Alex Coulton.