Multiple sequence alignment - TraesCS5B01G028400

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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 TraesCS5B01G028400 chr5B 100.000 2471 0 0 622 3092 27485988 27488458 0.000000e+00 4564.0
1 TraesCS5B01G028400 chr5B 100.000 323 0 0 1 323 27485367 27485689 5.710000e-167 597.0
2 TraesCS5B01G028400 chr5B 98.276 58 0 1 3036 3092 313074714 313074771 1.960000e-17 100.0
3 TraesCS5B01G028400 chr5D 91.564 2430 91 42 624 3004 36742761 36745125 0.000000e+00 3247.0
4 TraesCS5B01G028400 chr5D 86.577 149 10 1 175 323 36742564 36742702 4.130000e-34 156.0
5 TraesCS5B01G028400 chr5A 91.718 2258 92 35 806 3004 25863736 25865957 0.000000e+00 3046.0
6 TraesCS5B01G028400 chr5A 80.921 152 15 10 624 762 25863579 25863729 1.170000e-19 108.0
7 TraesCS5B01G028400 chr5A 92.424 66 5 0 3027 3092 379456323 379456388 9.130000e-16 95.3
8 TraesCS5B01G028400 chr2D 76.932 854 164 27 1242 2083 299552071 299551239 3.630000e-124 455.0
9 TraesCS5B01G028400 chr2D 85.119 168 17 5 1 160 370983931 370983764 6.860000e-37 165.0
10 TraesCS5B01G028400 chr2B 76.553 853 169 25 1242 2083 371562939 371562107 3.660000e-119 438.0
11 TraesCS5B01G028400 chr2A 76.257 855 168 27 1242 2083 374721652 374720820 3.690000e-114 422.0
12 TraesCS5B01G028400 chr7D 87.574 169 11 4 1 160 441858463 441858630 1.460000e-43 187.0
13 TraesCS5B01G028400 chr3A 87.574 169 11 4 1 160 368974498 368974665 1.460000e-43 187.0
14 TraesCS5B01G028400 chr3A 93.651 63 4 0 3030 3092 552188785 552188723 9.130000e-16 95.3
15 TraesCS5B01G028400 chr7A 88.199 161 12 2 1 154 213107557 213107397 5.270000e-43 185.0
16 TraesCS5B01G028400 chr7A 93.651 63 4 0 3030 3092 142928827 142928765 9.130000e-16 95.3
17 TraesCS5B01G028400 chr7A 92.424 66 5 0 3027 3092 265037134 265037069 9.130000e-16 95.3
18 TraesCS5B01G028400 chr6B 86.905 168 14 3 1 160 638849328 638849495 6.810000e-42 182.0
19 TraesCS5B01G028400 chr6B 86.310 168 15 3 1 160 519723217 519723384 3.170000e-40 176.0
20 TraesCS5B01G028400 chr4D 86.310 168 15 3 1 160 449199088 449198921 3.170000e-40 176.0
21 TraesCS5B01G028400 chr4A 86.391 169 13 4 1 160 128798409 128798576 3.170000e-40 176.0
22 TraesCS5B01G028400 chr4A 93.651 63 4 0 3030 3092 197756650 197756588 9.130000e-16 95.3
23 TraesCS5B01G028400 chr7B 86.667 165 12 4 1 156 105834312 105834475 1.140000e-39 174.0
24 TraesCS5B01G028400 chr6A 92.424 66 5 0 3027 3092 359997507 359997572 9.130000e-16 95.3
25 TraesCS5B01G028400 chr1A 93.651 63 4 0 3030 3092 473118445 473118383 9.130000e-16 95.3
26 TraesCS5B01G028400 chr3D 89.333 75 5 3 3020 3092 67439475 67439548 1.180000e-14 91.6


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 TraesCS5B01G028400 chr5B 27485367 27488458 3091 False 2580.5 4564 100.0000 1 3092 2 chr5B.!!$F2 3091
1 TraesCS5B01G028400 chr5D 36742564 36745125 2561 False 1701.5 3247 89.0705 175 3004 2 chr5D.!!$F1 2829
2 TraesCS5B01G028400 chr5A 25863579 25865957 2378 False 1577.0 3046 86.3195 624 3004 2 chr5A.!!$F2 2380
3 TraesCS5B01G028400 chr2D 299551239 299552071 832 True 455.0 455 76.9320 1242 2083 1 chr2D.!!$R1 841
4 TraesCS5B01G028400 chr2B 371562107 371562939 832 True 438.0 438 76.5530 1242 2083 1 chr2B.!!$R1 841
5 TraesCS5B01G028400 chr2A 374720820 374721652 832 True 422.0 422 76.2570 1242 2083 1 chr2A.!!$R1 841

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
276 277 0.249573 GGAGCAGATGAGAGCAGAGC 60.25 60.0 0.0 0.0 0.0 4.09 F
906 930 0.250081 GGATTCCTCTGTGATCCGGC 60.25 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1675 1.670949 GCTCGCTGTCCAGGATCTCA 61.671 60.0 0.0 0.0 0.0 3.27 R
2619 2712 0.041312 CGGAACAACAAGGCGAAGTG 60.041 55.0 0.0 0.0 0.0 3.16 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
22 23 2.911198 CGTTCCTACGCGCAAAATG 58.089 52.632 5.73 0.00 41.41 2.32
23 24 0.440758 CGTTCCTACGCGCAAAATGA 59.559 50.000 5.73 0.00 41.41 2.57
24 25 1.526986 CGTTCCTACGCGCAAAATGAG 60.527 52.381 5.73 0.00 41.41 2.90
25 26 0.446222 TTCCTACGCGCAAAATGAGC 59.554 50.000 5.73 0.00 39.86 4.26
26 27 0.391130 TCCTACGCGCAAAATGAGCT 60.391 50.000 5.73 0.00 41.12 4.09
27 28 0.447801 CCTACGCGCAAAATGAGCTT 59.552 50.000 5.73 0.00 41.12 3.74
28 29 1.135689 CCTACGCGCAAAATGAGCTTT 60.136 47.619 5.73 0.00 41.12 3.51
29 30 1.906966 CTACGCGCAAAATGAGCTTTG 59.093 47.619 5.73 0.00 41.12 2.77
30 31 0.310543 ACGCGCAAAATGAGCTTTGA 59.689 45.000 5.73 0.00 41.12 2.69
31 32 0.979811 CGCGCAAAATGAGCTTTGAG 59.020 50.000 8.75 0.00 41.12 3.02
32 33 1.664016 CGCGCAAAATGAGCTTTGAGT 60.664 47.619 8.75 0.00 41.12 3.41
33 34 1.717645 GCGCAAAATGAGCTTTGAGTG 59.282 47.619 0.30 0.00 40.12 3.51
34 35 2.322161 CGCAAAATGAGCTTTGAGTGG 58.678 47.619 0.00 0.00 38.35 4.00
35 36 2.030893 CGCAAAATGAGCTTTGAGTGGA 60.031 45.455 0.00 0.00 38.35 4.02
36 37 3.366679 CGCAAAATGAGCTTTGAGTGGAT 60.367 43.478 0.00 0.00 38.35 3.41
37 38 3.924686 GCAAAATGAGCTTTGAGTGGATG 59.075 43.478 0.00 0.00 38.35 3.51
38 39 4.560108 GCAAAATGAGCTTTGAGTGGATGT 60.560 41.667 0.00 0.00 38.35 3.06
39 40 4.778534 AAATGAGCTTTGAGTGGATGTG 57.221 40.909 0.00 0.00 0.00 3.21
40 41 2.936919 TGAGCTTTGAGTGGATGTGT 57.063 45.000 0.00 0.00 0.00 3.72
41 42 4.558226 ATGAGCTTTGAGTGGATGTGTA 57.442 40.909 0.00 0.00 0.00 2.90
42 43 3.930336 TGAGCTTTGAGTGGATGTGTAG 58.070 45.455 0.00 0.00 0.00 2.74
43 44 2.675348 GAGCTTTGAGTGGATGTGTAGC 59.325 50.000 0.00 0.00 0.00 3.58
44 45 2.304180 AGCTTTGAGTGGATGTGTAGCT 59.696 45.455 0.00 0.00 33.22 3.32
45 46 3.077359 GCTTTGAGTGGATGTGTAGCTT 58.923 45.455 0.00 0.00 0.00 3.74
46 47 3.503748 GCTTTGAGTGGATGTGTAGCTTT 59.496 43.478 0.00 0.00 0.00 3.51
47 48 4.378874 GCTTTGAGTGGATGTGTAGCTTTC 60.379 45.833 0.00 0.00 0.00 2.62
48 49 4.623932 TTGAGTGGATGTGTAGCTTTCT 57.376 40.909 0.00 0.00 0.00 2.52
49 50 4.193826 TGAGTGGATGTGTAGCTTTCTC 57.806 45.455 0.00 0.00 0.00 2.87
50 51 3.578282 TGAGTGGATGTGTAGCTTTCTCA 59.422 43.478 0.00 0.00 0.00 3.27
51 52 4.040339 TGAGTGGATGTGTAGCTTTCTCAA 59.960 41.667 0.00 0.00 0.00 3.02
52 53 4.973168 AGTGGATGTGTAGCTTTCTCAAA 58.027 39.130 0.00 0.00 0.00 2.69
53 54 5.376625 AGTGGATGTGTAGCTTTCTCAAAA 58.623 37.500 0.00 0.00 0.00 2.44
54 55 5.827797 AGTGGATGTGTAGCTTTCTCAAAAA 59.172 36.000 0.00 0.00 0.00 1.94
55 56 6.016777 AGTGGATGTGTAGCTTTCTCAAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
56 57 5.241506 TGGATGTGTAGCTTTCTCAAAAAGG 59.758 40.000 0.00 0.00 0.00 3.11
57 58 4.568152 TGTGTAGCTTTCTCAAAAAGGC 57.432 40.909 0.00 0.00 0.00 4.35
58 59 3.951037 TGTGTAGCTTTCTCAAAAAGGCA 59.049 39.130 0.00 0.00 33.96 4.75
59 60 4.400884 TGTGTAGCTTTCTCAAAAAGGCAA 59.599 37.500 0.00 0.00 33.96 4.52
60 61 5.105554 TGTGTAGCTTTCTCAAAAAGGCAAA 60.106 36.000 0.00 0.00 33.96 3.68
61 62 5.460091 GTGTAGCTTTCTCAAAAAGGCAAAG 59.540 40.000 0.00 0.00 33.96 2.77
62 63 5.359576 TGTAGCTTTCTCAAAAAGGCAAAGA 59.640 36.000 0.00 0.00 33.96 2.52
63 64 5.343307 AGCTTTCTCAAAAAGGCAAAGAA 57.657 34.783 0.00 0.00 33.96 2.52
64 65 5.922053 AGCTTTCTCAAAAAGGCAAAGAAT 58.078 33.333 0.00 0.00 33.96 2.40
65 66 5.756833 AGCTTTCTCAAAAAGGCAAAGAATG 59.243 36.000 0.00 0.00 33.96 2.67
66 67 5.754890 GCTTTCTCAAAAAGGCAAAGAATGA 59.245 36.000 0.00 0.00 32.00 2.57
67 68 6.073927 GCTTTCTCAAAAAGGCAAAGAATGAG 60.074 38.462 0.00 0.00 35.35 2.90
68 69 6.469782 TTCTCAAAAAGGCAAAGAATGAGT 57.530 33.333 0.00 0.00 35.50 3.41
69 70 7.581213 TTCTCAAAAAGGCAAAGAATGAGTA 57.419 32.000 0.00 0.00 35.50 2.59
70 71 7.206981 TCTCAAAAAGGCAAAGAATGAGTAG 57.793 36.000 0.00 0.00 35.50 2.57
71 72 6.772716 TCTCAAAAAGGCAAAGAATGAGTAGT 59.227 34.615 0.00 0.00 35.50 2.73
72 73 7.936847 TCTCAAAAAGGCAAAGAATGAGTAGTA 59.063 33.333 0.00 0.00 35.50 1.82
73 74 8.635765 TCAAAAAGGCAAAGAATGAGTAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
74 75 9.077885 TCAAAAAGGCAAAGAATGAGTAGTATT 57.922 29.630 0.00 0.00 0.00 1.89
75 76 9.346725 CAAAAAGGCAAAGAATGAGTAGTATTC 57.653 33.333 0.00 0.00 35.32 1.75
76 77 7.631717 AAAGGCAAAGAATGAGTAGTATTCC 57.368 36.000 0.00 0.00 35.62 3.01
77 78 6.567602 AGGCAAAGAATGAGTAGTATTCCT 57.432 37.500 0.00 0.00 35.62 3.36
78 79 7.676683 AGGCAAAGAATGAGTAGTATTCCTA 57.323 36.000 0.00 0.00 35.62 2.94
79 80 7.501844 AGGCAAAGAATGAGTAGTATTCCTAC 58.498 38.462 0.00 0.00 45.47 3.18
93 94 7.375106 AGTATTCCTACGATATTCCTGTACG 57.625 40.000 0.00 0.00 32.82 3.67
94 95 4.494350 TTCCTACGATATTCCTGTACGC 57.506 45.455 0.00 0.00 0.00 4.42
95 96 3.748083 TCCTACGATATTCCTGTACGCT 58.252 45.455 0.00 0.00 0.00 5.07
96 97 4.898320 TCCTACGATATTCCTGTACGCTA 58.102 43.478 0.00 0.00 0.00 4.26
97 98 4.692625 TCCTACGATATTCCTGTACGCTAC 59.307 45.833 0.00 0.00 0.00 3.58
98 99 4.453478 CCTACGATATTCCTGTACGCTACA 59.547 45.833 0.00 0.00 37.13 2.74
99 100 4.906065 ACGATATTCCTGTACGCTACAA 57.094 40.909 0.00 0.00 38.38 2.41
100 101 5.252969 ACGATATTCCTGTACGCTACAAA 57.747 39.130 0.00 0.00 38.38 2.83
101 102 5.039333 ACGATATTCCTGTACGCTACAAAC 58.961 41.667 0.00 0.00 38.38 2.93
102 103 4.443394 CGATATTCCTGTACGCTACAAACC 59.557 45.833 0.00 0.00 38.38 3.27
103 104 2.068837 TTCCTGTACGCTACAAACCG 57.931 50.000 0.00 0.00 38.38 4.44
104 105 1.246649 TCCTGTACGCTACAAACCGA 58.753 50.000 0.00 0.00 38.38 4.69
105 106 1.612950 TCCTGTACGCTACAAACCGAA 59.387 47.619 0.00 0.00 38.38 4.30
106 107 2.231964 TCCTGTACGCTACAAACCGAAT 59.768 45.455 0.00 0.00 38.38 3.34
107 108 2.347452 CCTGTACGCTACAAACCGAATG 59.653 50.000 0.00 0.00 38.38 2.67
108 109 1.727880 TGTACGCTACAAACCGAATGC 59.272 47.619 0.00 0.00 35.38 3.56
109 110 1.727880 GTACGCTACAAACCGAATGCA 59.272 47.619 0.00 0.00 0.00 3.96
110 111 1.448985 ACGCTACAAACCGAATGCAT 58.551 45.000 0.00 0.00 0.00 3.96
111 112 2.623535 ACGCTACAAACCGAATGCATA 58.376 42.857 0.00 0.00 0.00 3.14
112 113 3.202906 ACGCTACAAACCGAATGCATAT 58.797 40.909 0.00 0.00 0.00 1.78
113 114 4.373527 ACGCTACAAACCGAATGCATATA 58.626 39.130 0.00 0.00 0.00 0.86
114 115 4.994852 ACGCTACAAACCGAATGCATATAT 59.005 37.500 0.00 0.00 0.00 0.86
115 116 6.160684 ACGCTACAAACCGAATGCATATATA 58.839 36.000 0.00 0.00 0.00 0.86
116 117 6.310467 ACGCTACAAACCGAATGCATATATAG 59.690 38.462 0.00 0.00 0.00 1.31
117 118 6.530181 CGCTACAAACCGAATGCATATATAGA 59.470 38.462 0.00 0.00 0.00 1.98
118 119 7.062956 CGCTACAAACCGAATGCATATATAGAA 59.937 37.037 0.00 0.00 0.00 2.10
119 120 8.717821 GCTACAAACCGAATGCATATATAGAAA 58.282 33.333 0.00 0.00 0.00 2.52
148 149 9.768215 TTTTCTCCAAAATCCTTATTCCTATGT 57.232 29.630 0.00 0.00 0.00 2.29
149 150 9.768215 TTTCTCCAAAATCCTTATTCCTATGTT 57.232 29.630 0.00 0.00 0.00 2.71
150 151 9.768215 TTCTCCAAAATCCTTATTCCTATGTTT 57.232 29.630 0.00 0.00 0.00 2.83
151 152 9.768215 TCTCCAAAATCCTTATTCCTATGTTTT 57.232 29.630 0.00 0.00 0.00 2.43
166 167 9.567776 TTCCTATGTTTTTCTATGAACAGAACA 57.432 29.630 0.00 0.00 38.95 3.18
167 168 9.567776 TCCTATGTTTTTCTATGAACAGAACAA 57.432 29.630 0.00 0.00 38.95 2.83
171 172 8.925161 TGTTTTTCTATGAACAGAACAAAAGG 57.075 30.769 0.00 0.00 34.31 3.11
172 173 8.527810 TGTTTTTCTATGAACAGAACAAAAGGT 58.472 29.630 0.00 0.00 34.31 3.50
178 179 9.349713 TCTATGAACAGAACAAAAGGTAATTGT 57.650 29.630 0.00 0.00 42.56 2.71
189 190 8.106247 ACAAAAGGTAATTGTACGTCATGAAT 57.894 30.769 0.00 0.00 39.14 2.57
248 249 7.244558 TGATAGATGATGAGATTAGGACAGGT 58.755 38.462 0.00 0.00 0.00 4.00
254 255 2.237143 TGAGATTAGGACAGGTTGCAGG 59.763 50.000 0.00 0.00 0.00 4.85
276 277 0.249573 GGAGCAGATGAGAGCAGAGC 60.250 60.000 0.00 0.00 0.00 4.09
277 278 0.460722 GAGCAGATGAGAGCAGAGCA 59.539 55.000 0.00 0.00 0.00 4.26
278 279 0.462375 AGCAGATGAGAGCAGAGCAG 59.538 55.000 0.00 0.00 0.00 4.24
279 280 0.460722 GCAGATGAGAGCAGAGCAGA 59.539 55.000 0.00 0.00 0.00 4.26
280 281 1.537348 GCAGATGAGAGCAGAGCAGAG 60.537 57.143 0.00 0.00 0.00 3.35
281 282 0.748450 AGATGAGAGCAGAGCAGAGC 59.252 55.000 0.00 0.00 0.00 4.09
282 283 0.460722 GATGAGAGCAGAGCAGAGCA 59.539 55.000 0.00 0.00 0.00 4.26
283 284 0.462375 ATGAGAGCAGAGCAGAGCAG 59.538 55.000 0.00 0.00 0.00 4.24
284 285 0.611340 TGAGAGCAGAGCAGAGCAGA 60.611 55.000 0.00 0.00 0.00 4.26
285 286 0.531657 GAGAGCAGAGCAGAGCAGAA 59.468 55.000 0.00 0.00 0.00 3.02
307 308 1.032014 GAGTCCCACAAAAGCAGCAA 58.968 50.000 0.00 0.00 0.00 3.91
314 315 1.325338 CACAAAAGCAGCAAAGCACAC 59.675 47.619 0.00 0.00 36.85 3.82
647 648 2.117423 CCCCTCCAAACACCACCC 59.883 66.667 0.00 0.00 0.00 4.61
649 650 2.773527 CCCTCCAAACACCACCCCA 61.774 63.158 0.00 0.00 0.00 4.96
650 651 1.464722 CCTCCAAACACCACCCCAT 59.535 57.895 0.00 0.00 0.00 4.00
651 652 0.611896 CCTCCAAACACCACCCCATC 60.612 60.000 0.00 0.00 0.00 3.51
652 653 0.960364 CTCCAAACACCACCCCATCG 60.960 60.000 0.00 0.00 0.00 3.84
654 655 0.323360 CCAAACACCACCCCATCGAT 60.323 55.000 0.00 0.00 0.00 3.59
655 656 1.544724 CAAACACCACCCCATCGATT 58.455 50.000 0.00 0.00 0.00 3.34
699 707 2.131294 GAGATCCGATCCGACCACCG 62.131 65.000 4.67 0.00 38.18 4.94
713 724 2.437359 ACCGCCAGCAGCAGATTC 60.437 61.111 0.00 0.00 44.04 2.52
746 757 2.781158 GGAGCTCGCCTCTGTCCTC 61.781 68.421 7.83 0.00 40.57 3.71
747 758 2.757917 AGCTCGCCTCTGTCCTCC 60.758 66.667 0.00 0.00 0.00 4.30
748 759 2.757917 GCTCGCCTCTGTCCTCCT 60.758 66.667 0.00 0.00 0.00 3.69
891 915 2.363795 TCCGTCCGGAGCAGGATT 60.364 61.111 16.70 0.00 43.04 3.01
892 916 2.107141 CCGTCCGGAGCAGGATTC 59.893 66.667 3.06 0.00 43.04 2.52
904 928 1.539929 GCAGGATTCCTCTGTGATCCG 60.540 57.143 0.98 0.00 36.57 4.18
905 929 1.069823 CAGGATTCCTCTGTGATCCGG 59.930 57.143 0.98 0.00 36.57 5.14
906 930 0.250081 GGATTCCTCTGTGATCCGGC 60.250 60.000 0.00 0.00 0.00 6.13
907 931 0.598680 GATTCCTCTGTGATCCGGCG 60.599 60.000 0.00 0.00 0.00 6.46
913 937 4.492160 TGTGATCCGGCGCGTCTC 62.492 66.667 9.90 0.00 0.00 3.36
946 970 0.250510 GGAGCCAAGATCCGGGATTC 60.251 60.000 11.57 3.30 0.00 2.52
962 992 3.561528 GGGATTCCCTTTTCGGTTTCTCT 60.562 47.826 14.98 0.00 41.34 3.10
963 993 4.079970 GGATTCCCTTTTCGGTTTCTCTT 58.920 43.478 0.00 0.00 0.00 2.85
964 994 4.523173 GGATTCCCTTTTCGGTTTCTCTTT 59.477 41.667 0.00 0.00 0.00 2.52
965 995 5.335740 GGATTCCCTTTTCGGTTTCTCTTTC 60.336 44.000 0.00 0.00 0.00 2.62
966 996 4.432980 TCCCTTTTCGGTTTCTCTTTCT 57.567 40.909 0.00 0.00 0.00 2.52
967 997 4.386711 TCCCTTTTCGGTTTCTCTTTCTC 58.613 43.478 0.00 0.00 0.00 2.87
968 998 3.186613 CCCTTTTCGGTTTCTCTTTCTCG 59.813 47.826 0.00 0.00 0.00 4.04
969 999 4.056050 CCTTTTCGGTTTCTCTTTCTCGA 58.944 43.478 0.00 0.00 0.00 4.04
970 1000 4.150804 CCTTTTCGGTTTCTCTTTCTCGAG 59.849 45.833 5.93 5.93 0.00 4.04
971 1001 2.349297 TCGGTTTCTCTTTCTCGAGC 57.651 50.000 7.81 0.00 0.00 5.03
972 1002 0.985549 CGGTTTCTCTTTCTCGAGCG 59.014 55.000 7.81 0.00 0.00 5.03
1579 1634 1.442769 CCTCCTCACCGACAACAATG 58.557 55.000 0.00 0.00 0.00 2.82
1580 1635 0.798776 CTCCTCACCGACAACAATGC 59.201 55.000 0.00 0.00 0.00 3.56
1581 1636 0.605319 TCCTCACCGACAACAATGCC 60.605 55.000 0.00 0.00 0.00 4.40
1582 1637 1.497278 CTCACCGACAACAATGCCG 59.503 57.895 0.00 0.00 31.63 5.69
1583 1638 2.126888 CACCGACAACAATGCCGC 60.127 61.111 0.00 0.00 30.32 6.53
1584 1639 3.361977 ACCGACAACAATGCCGCC 61.362 61.111 0.00 0.00 30.32 6.13
1585 1640 4.459331 CCGACAACAATGCCGCCG 62.459 66.667 0.00 0.00 30.32 6.46
1586 1641 4.459331 CGACAACAATGCCGCCGG 62.459 66.667 0.00 0.00 0.00 6.13
1620 1675 3.434319 CGCCACCGCAGCTTCATT 61.434 61.111 0.00 0.00 34.03 2.57
2065 2123 2.733301 CGCCGCTCATGGAGATCT 59.267 61.111 0.00 0.00 0.00 2.75
2096 2154 4.554363 CCTCCGTGACTAGGCGCG 62.554 72.222 24.69 24.69 41.13 6.86
2152 2210 8.748179 AAGGAAGAGATATATCATCCCTTTGA 57.252 34.615 16.07 0.00 30.98 2.69
2202 2263 4.529897 TCTGCAATGCAAAGTCCTATCAT 58.470 39.130 9.92 0.00 38.41 2.45
2212 2273 8.177119 TGCAAAGTCCTATCATGTTTTACTTT 57.823 30.769 0.00 1.89 36.43 2.66
2213 2274 8.637986 TGCAAAGTCCTATCATGTTTTACTTTT 58.362 29.630 10.84 0.00 34.43 2.27
2250 2318 4.202040 TGTGCCAAGTCTCATCAGTTTTTG 60.202 41.667 0.00 0.00 0.00 2.44
2253 2321 4.516698 GCCAAGTCTCATCAGTTTTTGAGA 59.483 41.667 0.00 0.00 44.55 3.27
2277 2346 2.636647 TCAACTGTGCCATGTCTCAA 57.363 45.000 0.00 0.00 0.00 3.02
2314 2383 8.143193 TGCAAGTTACAATGAGAATGAACAATT 58.857 29.630 0.00 0.00 0.00 2.32
2315 2384 8.642020 GCAAGTTACAATGAGAATGAACAATTC 58.358 33.333 0.00 0.00 44.44 2.17
2316 2385 9.132521 CAAGTTACAATGAGAATGAACAATTCC 57.867 33.333 0.00 0.00 45.10 3.01
2317 2386 7.830739 AGTTACAATGAGAATGAACAATTCCC 58.169 34.615 0.00 0.00 45.10 3.97
2318 2387 7.451255 AGTTACAATGAGAATGAACAATTCCCA 59.549 33.333 0.00 0.00 45.10 4.37
2319 2388 6.862469 ACAATGAGAATGAACAATTCCCAT 57.138 33.333 0.00 0.00 45.10 4.00
2322 2391 8.984855 ACAATGAGAATGAACAATTCCCATAAT 58.015 29.630 0.00 0.00 45.10 1.28
2359 2428 8.445275 TGGTAGCCATTTTATATTACAGTGTG 57.555 34.615 5.88 0.00 0.00 3.82
2474 2555 7.211966 AGTAAAAGGATGCTGATGATATTGC 57.788 36.000 0.00 0.00 0.00 3.56
2516 2604 4.012374 TGGAAATCTCACAGCAATTCTCC 58.988 43.478 0.00 0.00 0.00 3.71
2518 2606 4.142513 GGAAATCTCACAGCAATTCTCCAC 60.143 45.833 0.00 0.00 0.00 4.02
2555 2644 3.076621 TGGTGATGTGATGAAGAAGCAC 58.923 45.455 0.00 0.00 0.00 4.40
2590 2683 1.975660 TCCCCTTTGTGGTTTCTTCG 58.024 50.000 0.00 0.00 0.00 3.79
2619 2712 2.421314 GCAACCAGCACCAAACCC 59.579 61.111 0.00 0.00 44.79 4.11
2675 2772 3.834799 GGGATGCTGCTGCTTGCC 61.835 66.667 21.91 21.91 44.66 4.52
2741 2839 4.709397 GCTGCCTCTATCCTATGTGAGTAT 59.291 45.833 0.00 0.00 0.00 2.12
2742 2840 5.186797 GCTGCCTCTATCCTATGTGAGTATT 59.813 44.000 0.00 0.00 0.00 1.89
2743 2841 6.295575 GCTGCCTCTATCCTATGTGAGTATTT 60.296 42.308 0.00 0.00 0.00 1.40
2744 2842 6.997655 TGCCTCTATCCTATGTGAGTATTTG 58.002 40.000 0.00 0.00 0.00 2.32
2779 2877 4.729227 TGGTGTTTTTCCTTTCCACTTC 57.271 40.909 0.00 0.00 0.00 3.01
2781 2879 3.113322 GTGTTTTTCCTTTCCACTTCGC 58.887 45.455 0.00 0.00 0.00 4.70
2789 2888 2.094757 TTTCCACTTCGCTCCGAGCA 62.095 55.000 20.22 4.94 42.58 4.26
2844 2943 0.801067 CGCTGGTAGTTAGCACGGAC 60.801 60.000 0.00 0.00 41.18 4.79
2845 2944 0.531200 GCTGGTAGTTAGCACGGACT 59.469 55.000 0.00 0.00 40.81 3.85
2892 2991 2.540101 GCAACCTGTCGATACATGTAGC 59.460 50.000 11.14 11.14 33.88 3.58
2920 3019 6.660094 TGGTTTTTGTAGTGTATGTTATCCCC 59.340 38.462 0.00 0.00 0.00 4.81
2921 3020 6.660094 GGTTTTTGTAGTGTATGTTATCCCCA 59.340 38.462 0.00 0.00 0.00 4.96
2922 3021 7.362315 GGTTTTTGTAGTGTATGTTATCCCCAC 60.362 40.741 0.00 0.00 0.00 4.61
2963 3062 8.960591 CAATATCACACACCTTTTCCTCTAAAT 58.039 33.333 0.00 0.00 0.00 1.40
2964 3063 6.824305 ATCACACACCTTTTCCTCTAAATG 57.176 37.500 0.00 0.00 0.00 2.32
2966 3065 6.833041 TCACACACCTTTTCCTCTAAATGTA 58.167 36.000 0.00 0.00 0.00 2.29
2968 3067 7.606456 TCACACACCTTTTCCTCTAAATGTATC 59.394 37.037 0.00 0.00 0.00 2.24
3004 3106 2.680339 GGCACCACTATCTTCTTGCTTC 59.320 50.000 0.00 0.00 0.00 3.86
3005 3107 2.680339 GCACCACTATCTTCTTGCTTCC 59.320 50.000 0.00 0.00 0.00 3.46
3006 3108 2.932614 CACCACTATCTTCTTGCTTCCG 59.067 50.000 0.00 0.00 0.00 4.30
3007 3109 2.093447 ACCACTATCTTCTTGCTTCCGG 60.093 50.000 0.00 0.00 0.00 5.14
3008 3110 1.936547 CACTATCTTCTTGCTTCCGGC 59.063 52.381 0.00 0.00 42.22 6.13
3009 3111 1.834263 ACTATCTTCTTGCTTCCGGCT 59.166 47.619 0.00 0.00 42.39 5.52
3010 3112 2.237392 ACTATCTTCTTGCTTCCGGCTT 59.763 45.455 0.00 0.00 42.39 4.35
3011 3113 2.206576 ATCTTCTTGCTTCCGGCTTT 57.793 45.000 0.00 0.00 42.39 3.51
3012 3114 1.981256 TCTTCTTGCTTCCGGCTTTT 58.019 45.000 0.00 0.00 42.39 2.27
3013 3115 3.134574 TCTTCTTGCTTCCGGCTTTTA 57.865 42.857 0.00 0.00 42.39 1.52
3014 3116 3.074412 TCTTCTTGCTTCCGGCTTTTAG 58.926 45.455 0.00 0.00 42.39 1.85
3015 3117 1.821216 TCTTGCTTCCGGCTTTTAGG 58.179 50.000 0.00 0.00 42.39 2.69
3016 3118 1.073284 TCTTGCTTCCGGCTTTTAGGT 59.927 47.619 0.00 0.00 42.39 3.08
3017 3119 1.200020 CTTGCTTCCGGCTTTTAGGTG 59.800 52.381 0.00 0.00 42.39 4.00
3018 3120 0.608035 TGCTTCCGGCTTTTAGGTGG 60.608 55.000 0.00 0.00 42.39 4.61
3019 3121 1.934220 GCTTCCGGCTTTTAGGTGGC 61.934 60.000 0.00 0.00 38.06 5.01
3020 3122 0.608035 CTTCCGGCTTTTAGGTGGCA 60.608 55.000 0.00 0.00 0.00 4.92
3021 3123 0.178987 TTCCGGCTTTTAGGTGGCAA 60.179 50.000 0.00 0.00 0.00 4.52
3022 3124 0.891904 TCCGGCTTTTAGGTGGCAAC 60.892 55.000 0.00 0.00 0.00 4.17
3035 3137 2.671619 GCAACCGCACCTGCCTTA 60.672 61.111 0.00 0.00 38.36 2.69
3036 3138 2.690778 GCAACCGCACCTGCCTTAG 61.691 63.158 0.00 0.00 38.36 2.18
3037 3139 2.359975 AACCGCACCTGCCTTAGC 60.360 61.111 0.00 0.00 37.91 3.09
3050 3152 3.173965 TGCCTTAGCATATACTCCCTCC 58.826 50.000 0.00 0.00 46.52 4.30
3051 3153 2.166664 GCCTTAGCATATACTCCCTCCG 59.833 54.545 0.00 0.00 39.53 4.63
3052 3154 3.432378 CCTTAGCATATACTCCCTCCGT 58.568 50.000 0.00 0.00 0.00 4.69
3053 3155 3.444388 CCTTAGCATATACTCCCTCCGTC 59.556 52.174 0.00 0.00 0.00 4.79
3054 3156 1.926108 AGCATATACTCCCTCCGTCC 58.074 55.000 0.00 0.00 0.00 4.79
3055 3157 0.526662 GCATATACTCCCTCCGTCCG 59.473 60.000 0.00 0.00 0.00 4.79
3056 3158 1.174783 CATATACTCCCTCCGTCCGG 58.825 60.000 0.00 0.00 0.00 5.14
3057 3159 0.039326 ATATACTCCCTCCGTCCGGG 59.961 60.000 0.00 0.00 43.38 5.73
3058 3160 1.355718 TATACTCCCTCCGTCCGGGT 61.356 60.000 0.00 0.00 42.56 5.28
3059 3161 2.234246 ATACTCCCTCCGTCCGGGTT 62.234 60.000 0.00 0.00 42.56 4.11
3060 3162 2.445492 TACTCCCTCCGTCCGGGTTT 62.445 60.000 0.00 0.00 42.56 3.27
3061 3163 1.683365 CTCCCTCCGTCCGGGTTTA 60.683 63.158 0.00 0.00 42.56 2.01
3062 3164 1.002017 TCCCTCCGTCCGGGTTTAT 59.998 57.895 0.00 0.00 42.56 1.40
3063 3165 0.618393 TCCCTCCGTCCGGGTTTATT 60.618 55.000 0.00 0.00 42.56 1.40
3064 3166 1.122227 CCCTCCGTCCGGGTTTATTA 58.878 55.000 0.00 0.00 36.91 0.98
3065 3167 1.069668 CCCTCCGTCCGGGTTTATTAG 59.930 57.143 0.00 0.00 36.91 1.73
3066 3168 1.069668 CCTCCGTCCGGGTTTATTAGG 59.930 57.143 0.00 0.00 37.00 2.69
3067 3169 0.465287 TCCGTCCGGGTTTATTAGGC 59.535 55.000 0.00 0.00 37.00 3.93
3068 3170 0.533531 CCGTCCGGGTTTATTAGGCC 60.534 60.000 0.00 0.00 0.00 5.19
3069 3171 0.466963 CGTCCGGGTTTATTAGGCCT 59.533 55.000 11.78 11.78 0.00 5.19
3070 3172 1.688197 CGTCCGGGTTTATTAGGCCTA 59.312 52.381 8.91 8.91 0.00 3.93
3071 3173 2.102925 CGTCCGGGTTTATTAGGCCTAA 59.897 50.000 27.11 27.11 0.00 2.69
3072 3174 3.432046 CGTCCGGGTTTATTAGGCCTAAA 60.432 47.826 28.50 12.25 0.00 1.85
3073 3175 4.132336 GTCCGGGTTTATTAGGCCTAAAG 58.868 47.826 28.50 13.19 0.00 1.85
3074 3176 4.039339 TCCGGGTTTATTAGGCCTAAAGA 58.961 43.478 28.50 16.79 0.00 2.52
3075 3177 4.132336 CCGGGTTTATTAGGCCTAAAGAC 58.868 47.826 28.50 23.35 0.00 3.01
3076 3178 4.384427 CCGGGTTTATTAGGCCTAAAGACA 60.384 45.833 28.50 10.52 0.00 3.41
3077 3179 5.187687 CGGGTTTATTAGGCCTAAAGACAA 58.812 41.667 28.50 16.49 0.00 3.18
3078 3180 5.065602 CGGGTTTATTAGGCCTAAAGACAAC 59.934 44.000 28.50 23.66 0.00 3.32
3079 3181 6.185511 GGGTTTATTAGGCCTAAAGACAACT 58.814 40.000 28.50 13.03 0.00 3.16
3080 3182 6.662234 GGGTTTATTAGGCCTAAAGACAACTT 59.338 38.462 28.50 12.30 38.05 2.66
3081 3183 7.177921 GGGTTTATTAGGCCTAAAGACAACTTT 59.822 37.037 28.50 11.58 46.36 2.66
3082 3184 8.582437 GGTTTATTAGGCCTAAAGACAACTTTT 58.418 33.333 28.50 10.86 42.79 2.27
3083 3185 9.622004 GTTTATTAGGCCTAAAGACAACTTTTC 57.378 33.333 28.50 6.62 42.79 2.29
3084 3186 9.582648 TTTATTAGGCCTAAAGACAACTTTTCT 57.417 29.630 28.50 10.16 42.79 2.52
3085 3187 9.582648 TTATTAGGCCTAAAGACAACTTTTCTT 57.417 29.630 28.50 9.73 42.79 2.52
3087 3189 8.617290 TTAGGCCTAAAGACAACTTTTCTTAG 57.383 34.615 23.21 0.00 42.79 2.18
3088 3190 6.838382 AGGCCTAAAGACAACTTTTCTTAGA 58.162 36.000 1.29 0.00 42.79 2.10
3089 3191 6.711194 AGGCCTAAAGACAACTTTTCTTAGAC 59.289 38.462 1.29 0.00 42.79 2.59
3090 3192 6.072618 GGCCTAAAGACAACTTTTCTTAGACC 60.073 42.308 0.00 0.00 42.79 3.85
3091 3193 6.485648 GCCTAAAGACAACTTTTCTTAGACCA 59.514 38.462 0.00 0.00 42.79 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.790481 GCTCATTTTGCGCGTAGGAAC 60.790 52.381 8.43 0.00 0.00 3.62
6 7 0.446222 GCTCATTTTGCGCGTAGGAA 59.554 50.000 8.43 2.45 0.00 3.36
7 8 0.391130 AGCTCATTTTGCGCGTAGGA 60.391 50.000 8.43 0.00 32.55 2.94
8 9 0.447801 AAGCTCATTTTGCGCGTAGG 59.552 50.000 8.43 0.00 32.55 3.18
9 10 1.906966 CAAAGCTCATTTTGCGCGTAG 59.093 47.619 8.43 0.00 32.55 3.51
10 11 1.533299 TCAAAGCTCATTTTGCGCGTA 59.467 42.857 8.43 0.00 37.83 4.42
11 12 0.310543 TCAAAGCTCATTTTGCGCGT 59.689 45.000 8.43 0.00 37.83 6.01
12 13 0.979811 CTCAAAGCTCATTTTGCGCG 59.020 50.000 0.00 0.00 37.83 6.86
13 14 1.717645 CACTCAAAGCTCATTTTGCGC 59.282 47.619 0.00 0.00 37.83 6.09
14 15 2.030893 TCCACTCAAAGCTCATTTTGCG 60.031 45.455 0.00 0.00 37.83 4.85
15 16 3.648339 TCCACTCAAAGCTCATTTTGC 57.352 42.857 0.00 0.00 37.83 3.68
16 17 4.921515 CACATCCACTCAAAGCTCATTTTG 59.078 41.667 0.00 0.00 38.97 2.44
17 18 4.586001 ACACATCCACTCAAAGCTCATTTT 59.414 37.500 0.00 0.00 0.00 1.82
18 19 4.147321 ACACATCCACTCAAAGCTCATTT 58.853 39.130 0.00 0.00 0.00 2.32
19 20 3.759581 ACACATCCACTCAAAGCTCATT 58.240 40.909 0.00 0.00 0.00 2.57
20 21 3.430042 ACACATCCACTCAAAGCTCAT 57.570 42.857 0.00 0.00 0.00 2.90
21 22 2.936919 ACACATCCACTCAAAGCTCA 57.063 45.000 0.00 0.00 0.00 4.26
22 23 2.675348 GCTACACATCCACTCAAAGCTC 59.325 50.000 0.00 0.00 0.00 4.09
23 24 2.304180 AGCTACACATCCACTCAAAGCT 59.696 45.455 0.00 0.00 34.37 3.74
24 25 2.704572 AGCTACACATCCACTCAAAGC 58.295 47.619 0.00 0.00 0.00 3.51
25 26 4.999950 AGAAAGCTACACATCCACTCAAAG 59.000 41.667 0.00 0.00 0.00 2.77
26 27 4.973168 AGAAAGCTACACATCCACTCAAA 58.027 39.130 0.00 0.00 0.00 2.69
27 28 4.040339 TGAGAAAGCTACACATCCACTCAA 59.960 41.667 0.00 0.00 0.00 3.02
28 29 3.578282 TGAGAAAGCTACACATCCACTCA 59.422 43.478 0.00 0.00 0.00 3.41
29 30 4.193826 TGAGAAAGCTACACATCCACTC 57.806 45.455 0.00 0.00 0.00 3.51
30 31 4.623932 TTGAGAAAGCTACACATCCACT 57.376 40.909 0.00 0.00 0.00 4.00
31 32 5.689383 TTTTGAGAAAGCTACACATCCAC 57.311 39.130 0.00 0.00 0.00 4.02
32 33 5.241506 CCTTTTTGAGAAAGCTACACATCCA 59.758 40.000 0.00 0.00 0.00 3.41
33 34 5.703876 CCTTTTTGAGAAAGCTACACATCC 58.296 41.667 0.00 0.00 0.00 3.51
34 35 5.157067 GCCTTTTTGAGAAAGCTACACATC 58.843 41.667 0.00 0.00 0.00 3.06
35 36 4.584325 TGCCTTTTTGAGAAAGCTACACAT 59.416 37.500 0.00 0.00 0.00 3.21
36 37 3.951037 TGCCTTTTTGAGAAAGCTACACA 59.049 39.130 0.00 0.00 0.00 3.72
37 38 4.568152 TGCCTTTTTGAGAAAGCTACAC 57.432 40.909 0.00 0.00 0.00 2.90
38 39 5.359576 TCTTTGCCTTTTTGAGAAAGCTACA 59.640 36.000 0.00 0.00 0.00 2.74
39 40 5.831997 TCTTTGCCTTTTTGAGAAAGCTAC 58.168 37.500 0.00 0.00 0.00 3.58
40 41 6.463995 TTCTTTGCCTTTTTGAGAAAGCTA 57.536 33.333 0.00 0.00 0.00 3.32
41 42 5.343307 TTCTTTGCCTTTTTGAGAAAGCT 57.657 34.783 0.00 0.00 0.00 3.74
42 43 5.754890 TCATTCTTTGCCTTTTTGAGAAAGC 59.245 36.000 0.00 0.00 30.96 3.51
43 44 6.982724 ACTCATTCTTTGCCTTTTTGAGAAAG 59.017 34.615 4.21 0.00 34.62 2.62
44 45 6.877236 ACTCATTCTTTGCCTTTTTGAGAAA 58.123 32.000 4.21 0.00 34.62 2.52
45 46 6.469782 ACTCATTCTTTGCCTTTTTGAGAA 57.530 33.333 4.21 0.00 34.62 2.87
46 47 6.772716 ACTACTCATTCTTTGCCTTTTTGAGA 59.227 34.615 4.21 0.00 34.62 3.27
47 48 6.974965 ACTACTCATTCTTTGCCTTTTTGAG 58.025 36.000 0.00 0.00 36.17 3.02
48 49 6.959639 ACTACTCATTCTTTGCCTTTTTGA 57.040 33.333 0.00 0.00 0.00 2.69
49 50 9.346725 GAATACTACTCATTCTTTGCCTTTTTG 57.653 33.333 0.00 0.00 31.09 2.44
50 51 8.523658 GGAATACTACTCATTCTTTGCCTTTTT 58.476 33.333 0.00 0.00 33.70 1.94
51 52 7.890655 AGGAATACTACTCATTCTTTGCCTTTT 59.109 33.333 0.00 0.00 33.70 2.27
52 53 7.406104 AGGAATACTACTCATTCTTTGCCTTT 58.594 34.615 0.00 0.00 33.70 3.11
53 54 6.963322 AGGAATACTACTCATTCTTTGCCTT 58.037 36.000 0.00 0.00 33.70 4.35
54 55 6.567602 AGGAATACTACTCATTCTTTGCCT 57.432 37.500 0.00 0.00 33.70 4.75
55 56 7.716768 GTAGGAATACTACTCATTCTTTGCC 57.283 40.000 0.00 0.00 46.89 4.52
67 68 8.386606 CGTACAGGAATATCGTAGGAATACTAC 58.613 40.741 0.00 0.00 46.94 2.73
68 69 7.065085 GCGTACAGGAATATCGTAGGAATACTA 59.935 40.741 0.00 0.00 0.00 1.82
69 70 6.128063 GCGTACAGGAATATCGTAGGAATACT 60.128 42.308 0.00 0.00 0.00 2.12
70 71 6.026513 GCGTACAGGAATATCGTAGGAATAC 58.973 44.000 0.00 0.00 0.00 1.89
71 72 5.942236 AGCGTACAGGAATATCGTAGGAATA 59.058 40.000 0.00 0.00 0.00 1.75
72 73 4.765856 AGCGTACAGGAATATCGTAGGAAT 59.234 41.667 0.00 0.00 0.00 3.01
73 74 4.139786 AGCGTACAGGAATATCGTAGGAA 58.860 43.478 0.00 0.00 0.00 3.36
74 75 3.748083 AGCGTACAGGAATATCGTAGGA 58.252 45.455 0.00 0.00 0.00 2.94
75 76 4.453478 TGTAGCGTACAGGAATATCGTAGG 59.547 45.833 0.00 0.00 34.06 3.18
76 77 5.602458 TGTAGCGTACAGGAATATCGTAG 57.398 43.478 0.00 0.00 34.06 3.51
77 78 6.201517 GTTTGTAGCGTACAGGAATATCGTA 58.798 40.000 0.00 0.00 40.24 3.43
78 79 4.906065 TTGTAGCGTACAGGAATATCGT 57.094 40.909 0.00 0.00 40.24 3.73
79 80 4.443394 GGTTTGTAGCGTACAGGAATATCG 59.557 45.833 0.00 0.00 40.24 2.92
80 81 4.443394 CGGTTTGTAGCGTACAGGAATATC 59.557 45.833 0.00 0.00 40.24 1.63
81 82 4.098349 TCGGTTTGTAGCGTACAGGAATAT 59.902 41.667 0.00 0.00 45.09 1.28
82 83 3.443329 TCGGTTTGTAGCGTACAGGAATA 59.557 43.478 0.00 0.00 45.09 1.75
83 84 2.231964 TCGGTTTGTAGCGTACAGGAAT 59.768 45.455 0.00 0.00 45.09 3.01
84 85 1.612950 TCGGTTTGTAGCGTACAGGAA 59.387 47.619 0.00 0.00 45.09 3.36
85 86 1.246649 TCGGTTTGTAGCGTACAGGA 58.753 50.000 0.00 0.00 45.09 3.86
86 87 2.068837 TTCGGTTTGTAGCGTACAGG 57.931 50.000 0.00 0.00 45.09 4.00
87 88 2.222729 GCATTCGGTTTGTAGCGTACAG 60.223 50.000 0.00 0.00 45.09 2.74
88 89 1.727880 GCATTCGGTTTGTAGCGTACA 59.272 47.619 0.00 0.00 45.09 2.90
89 90 1.727880 TGCATTCGGTTTGTAGCGTAC 59.272 47.619 0.00 0.00 45.09 3.67
90 91 2.081725 TGCATTCGGTTTGTAGCGTA 57.918 45.000 0.00 0.00 45.09 4.42
91 92 1.448985 ATGCATTCGGTTTGTAGCGT 58.551 45.000 0.00 0.00 45.09 5.07
92 93 3.878086 ATATGCATTCGGTTTGTAGCG 57.122 42.857 3.54 0.00 46.15 4.26
93 94 7.827819 TCTATATATGCATTCGGTTTGTAGC 57.172 36.000 3.54 0.00 0.00 3.58
122 123 9.768215 ACATAGGAATAAGGATTTTGGAGAAAA 57.232 29.630 0.00 0.00 35.52 2.29
123 124 9.768215 AACATAGGAATAAGGATTTTGGAGAAA 57.232 29.630 0.00 0.00 0.00 2.52
124 125 9.768215 AAACATAGGAATAAGGATTTTGGAGAA 57.232 29.630 0.00 0.00 0.00 2.87
125 126 9.768215 AAAACATAGGAATAAGGATTTTGGAGA 57.232 29.630 0.00 0.00 0.00 3.71
140 141 9.567776 TGTTCTGTTCATAGAAAAACATAGGAA 57.432 29.630 0.00 0.00 38.33 3.36
141 142 9.567776 TTGTTCTGTTCATAGAAAAACATAGGA 57.432 29.630 0.00 0.00 38.33 2.94
145 146 9.533253 CCTTTTGTTCTGTTCATAGAAAAACAT 57.467 29.630 0.00 0.00 38.33 2.71
146 147 8.527810 ACCTTTTGTTCTGTTCATAGAAAAACA 58.472 29.630 0.00 0.00 38.33 2.83
147 148 8.926715 ACCTTTTGTTCTGTTCATAGAAAAAC 57.073 30.769 0.00 0.00 38.33 2.43
152 153 9.349713 ACAATTACCTTTTGTTCTGTTCATAGA 57.650 29.630 0.00 0.00 33.64 1.98
155 156 8.073768 CGTACAATTACCTTTTGTTCTGTTCAT 58.926 33.333 0.00 0.00 38.26 2.57
156 157 7.066043 ACGTACAATTACCTTTTGTTCTGTTCA 59.934 33.333 0.00 0.00 38.26 3.18
157 158 7.412063 ACGTACAATTACCTTTTGTTCTGTTC 58.588 34.615 0.00 0.00 38.26 3.18
158 159 7.066043 TGACGTACAATTACCTTTTGTTCTGTT 59.934 33.333 0.00 0.00 38.26 3.16
159 160 6.539464 TGACGTACAATTACCTTTTGTTCTGT 59.461 34.615 0.00 0.00 38.26 3.41
160 161 6.950545 TGACGTACAATTACCTTTTGTTCTG 58.049 36.000 0.00 0.00 38.26 3.02
161 162 7.442969 TCATGACGTACAATTACCTTTTGTTCT 59.557 33.333 0.00 0.00 38.26 3.01
162 163 7.577979 TCATGACGTACAATTACCTTTTGTTC 58.422 34.615 0.00 0.00 38.26 3.18
163 164 7.499321 TCATGACGTACAATTACCTTTTGTT 57.501 32.000 0.00 0.00 38.26 2.83
164 165 7.499321 TTCATGACGTACAATTACCTTTTGT 57.501 32.000 0.00 0.00 40.30 2.83
165 166 8.233868 TCATTCATGACGTACAATTACCTTTTG 58.766 33.333 0.00 0.00 0.00 2.44
166 167 8.330466 TCATTCATGACGTACAATTACCTTTT 57.670 30.769 0.00 0.00 0.00 2.27
167 168 7.915293 TCATTCATGACGTACAATTACCTTT 57.085 32.000 0.00 0.00 0.00 3.11
168 169 7.065803 CCTTCATTCATGACGTACAATTACCTT 59.934 37.037 0.00 0.00 36.36 3.50
169 170 6.538742 CCTTCATTCATGACGTACAATTACCT 59.461 38.462 0.00 0.00 36.36 3.08
170 171 6.315393 ACCTTCATTCATGACGTACAATTACC 59.685 38.462 0.00 0.00 36.36 2.85
171 172 7.303634 ACCTTCATTCATGACGTACAATTAC 57.696 36.000 0.00 0.00 36.36 1.89
172 173 9.607988 ATTACCTTCATTCATGACGTACAATTA 57.392 29.630 0.00 0.00 36.36 1.40
173 174 7.915293 TTACCTTCATTCATGACGTACAATT 57.085 32.000 0.00 0.00 36.36 2.32
174 175 8.397906 CAATTACCTTCATTCATGACGTACAAT 58.602 33.333 0.00 0.00 36.36 2.71
175 176 7.389330 ACAATTACCTTCATTCATGACGTACAA 59.611 33.333 0.00 0.00 36.36 2.41
176 177 6.876789 ACAATTACCTTCATTCATGACGTACA 59.123 34.615 0.00 0.00 36.36 2.90
177 178 7.303634 ACAATTACCTTCATTCATGACGTAC 57.696 36.000 0.00 0.00 36.36 3.67
178 179 7.493320 GGTACAATTACCTTCATTCATGACGTA 59.507 37.037 0.00 0.00 44.24 3.57
224 225 7.716799 ACCTGTCCTAATCTCATCATCTATC 57.283 40.000 0.00 0.00 0.00 2.08
227 228 5.454471 GCAACCTGTCCTAATCTCATCATCT 60.454 44.000 0.00 0.00 0.00 2.90
232 233 3.118112 CCTGCAACCTGTCCTAATCTCAT 60.118 47.826 0.00 0.00 0.00 2.90
235 236 1.561542 CCCTGCAACCTGTCCTAATCT 59.438 52.381 0.00 0.00 0.00 2.40
248 249 1.001764 CATCTGCTCCACCCTGCAA 60.002 57.895 0.00 0.00 38.81 4.08
254 255 0.179078 CTGCTCTCATCTGCTCCACC 60.179 60.000 0.00 0.00 0.00 4.61
276 277 0.972134 TGGGACTCTGTTCTGCTCTG 59.028 55.000 0.00 0.00 0.00 3.35
277 278 0.972883 GTGGGACTCTGTTCTGCTCT 59.027 55.000 0.00 0.00 0.00 4.09
278 279 0.681733 TGTGGGACTCTGTTCTGCTC 59.318 55.000 0.00 0.00 0.00 4.26
279 280 1.131638 TTGTGGGACTCTGTTCTGCT 58.868 50.000 0.00 0.00 0.00 4.24
280 281 1.967319 TTTGTGGGACTCTGTTCTGC 58.033 50.000 0.00 0.00 0.00 4.26
281 282 2.291741 GCTTTTGTGGGACTCTGTTCTG 59.708 50.000 0.00 0.00 0.00 3.02
282 283 2.092429 TGCTTTTGTGGGACTCTGTTCT 60.092 45.455 0.00 0.00 0.00 3.01
283 284 2.291741 CTGCTTTTGTGGGACTCTGTTC 59.708 50.000 0.00 0.00 0.00 3.18
284 285 2.301346 CTGCTTTTGTGGGACTCTGTT 58.699 47.619 0.00 0.00 0.00 3.16
285 286 1.972872 CTGCTTTTGTGGGACTCTGT 58.027 50.000 0.00 0.00 0.00 3.41
630 631 2.117423 GGGTGGTGTTTGGAGGGG 59.883 66.667 0.00 0.00 0.00 4.79
647 648 1.442526 GACTGGGCTGCAATCGATGG 61.443 60.000 0.00 0.00 0.00 3.51
649 650 1.153086 GGACTGGGCTGCAATCGAT 60.153 57.895 0.50 0.00 0.00 3.59
650 651 2.268920 GGACTGGGCTGCAATCGA 59.731 61.111 0.50 0.00 0.00 3.59
651 652 2.825836 GGGACTGGGCTGCAATCG 60.826 66.667 0.50 0.00 0.00 3.34
652 653 2.825836 CGGGACTGGGCTGCAATC 60.826 66.667 0.50 0.00 0.00 2.67
699 707 3.885521 GCCGAATCTGCTGCTGGC 61.886 66.667 6.69 4.13 42.22 4.85
725 736 3.404141 GACAGAGGCGAGCTCCGTC 62.404 68.421 8.47 11.79 44.58 4.79
726 737 3.444805 GACAGAGGCGAGCTCCGT 61.445 66.667 8.47 2.50 41.15 4.69
768 779 3.976701 ATGAAACCAGCCTCCGCGG 62.977 63.158 22.12 22.12 41.18 6.46
769 780 2.436646 ATGAAACCAGCCTCCGCG 60.437 61.111 0.00 0.00 41.18 6.46
770 781 2.115291 GGATGAAACCAGCCTCCGC 61.115 63.158 0.00 0.00 37.16 5.54
771 782 1.604378 AGGATGAAACCAGCCTCCG 59.396 57.895 0.00 0.00 46.72 4.63
775 786 0.394899 CCTGGAGGATGAAACCAGCC 60.395 60.000 0.00 0.00 46.65 4.85
776 787 0.329596 ACCTGGAGGATGAAACCAGC 59.670 55.000 0.00 0.00 46.65 4.85
778 789 0.038166 GCACCTGGAGGATGAAACCA 59.962 55.000 0.00 0.00 38.94 3.67
779 790 1.026718 CGCACCTGGAGGATGAAACC 61.027 60.000 0.00 0.00 38.94 3.27
784 795 4.147449 TCGCGCACCTGGAGGATG 62.147 66.667 8.75 0.00 38.94 3.51
810 821 4.065088 CAGGGAGAAAGATTTCACGAACA 58.935 43.478 7.97 0.00 39.61 3.18
812 823 3.074412 GCAGGGAGAAAGATTTCACGAA 58.926 45.455 7.97 0.00 39.61 3.85
870 882 2.427245 CCTGCTCCGGACGGATCTT 61.427 63.158 14.50 0.00 44.24 2.40
891 915 3.838271 GCGCCGGATCACAGAGGA 61.838 66.667 5.05 0.00 0.00 3.71
906 930 4.856607 GAGGAAGGCCGAGACGCG 62.857 72.222 3.53 3.53 39.96 6.01
907 931 4.516195 GGAGGAAGGCCGAGACGC 62.516 72.222 0.00 0.00 39.96 5.19
921 945 2.812619 GGATCTTGGCTCCGGGGAG 61.813 68.421 4.80 10.44 44.56 4.30
929 953 1.709994 GGGAATCCCGGATCTTGGCT 61.710 60.000 0.90 0.00 32.13 4.75
946 970 3.186613 CGAGAAAGAGAAACCGAAAAGGG 59.813 47.826 0.00 0.00 46.96 3.95
1116 1159 2.045143 AGGTCCTCCGTCTCGTCC 60.045 66.667 0.00 0.00 39.05 4.79
1496 1551 2.797462 GAGAGCAGCGCGAAGAAGC 61.797 63.158 12.10 5.32 0.00 3.86
1620 1675 1.670949 GCTCGCTGTCCAGGATCTCA 61.671 60.000 0.00 0.00 0.00 3.27
2096 2154 3.390135 TGTTCATCTCCACGAACACTTC 58.610 45.455 1.03 0.00 44.88 3.01
2110 2168 6.231211 TCTTCCTTACCTTGTTCTGTTCATC 58.769 40.000 0.00 0.00 0.00 2.92
2202 2263 9.515020 CAGCTGAAATGTCTAAAAAGTAAAACA 57.485 29.630 8.42 0.00 0.00 2.83
2212 2273 3.485394 TGGCACAGCTGAAATGTCTAAA 58.515 40.909 23.35 0.00 0.00 1.85
2213 2274 3.138884 TGGCACAGCTGAAATGTCTAA 57.861 42.857 23.35 0.00 0.00 2.10
2250 2318 6.772452 AGACATGGCACAGTTGAAATGTCTC 61.772 44.000 0.00 0.00 45.33 3.36
2314 2383 9.077885 GCTACCAAATCAGATTAAATTATGGGA 57.922 33.333 12.15 4.66 0.00 4.37
2315 2384 8.306761 GGCTACCAAATCAGATTAAATTATGGG 58.693 37.037 12.15 0.07 0.00 4.00
2316 2385 8.859090 TGGCTACCAAATCAGATTAAATTATGG 58.141 33.333 7.49 7.49 0.00 2.74
2351 2420 5.736486 TGCGTTGAATTAAACACACTGTA 57.264 34.783 6.49 0.00 0.00 2.74
2359 2428 4.855531 AGGACACTTGCGTTGAATTAAAC 58.144 39.130 0.00 0.00 0.00 2.01
2443 2524 7.394016 TCATCAGCATCCTTTTACTAAGACAA 58.606 34.615 0.00 0.00 0.00 3.18
2474 2555 2.357034 CACCAACCGACACCCGAG 60.357 66.667 0.00 0.00 41.76 4.63
2555 2644 1.547223 GGGGATGGATGGATCAGCTTG 60.547 57.143 0.00 0.00 0.00 4.01
2590 2683 0.676151 CTGGTTGCTTGCTCCTCTCC 60.676 60.000 8.26 0.00 0.00 3.71
2619 2712 0.041312 CGGAACAACAAGGCGAAGTG 60.041 55.000 0.00 0.00 0.00 3.16
2675 2772 1.134759 CACATCACTCTCTGAGCCTGG 60.135 57.143 0.00 0.00 32.04 4.45
2679 2776 1.274728 ACACCACATCACTCTCTGAGC 59.725 52.381 0.00 0.00 32.04 4.26
2718 2816 2.896685 ACTCACATAGGATAGAGGCAGC 59.103 50.000 0.00 0.00 32.52 5.25
2741 2839 4.950050 ACACCAAGAAACACAACAACAAA 58.050 34.783 0.00 0.00 0.00 2.83
2742 2840 4.592485 ACACCAAGAAACACAACAACAA 57.408 36.364 0.00 0.00 0.00 2.83
2743 2841 4.592485 AACACCAAGAAACACAACAACA 57.408 36.364 0.00 0.00 0.00 3.33
2744 2842 5.915812 AAAACACCAAGAAACACAACAAC 57.084 34.783 0.00 0.00 0.00 3.32
2779 2877 1.518133 CTTCCTCTTGCTCGGAGCG 60.518 63.158 23.72 11.58 46.26 5.03
2781 2879 0.179150 CGACTTCCTCTTGCTCGGAG 60.179 60.000 0.00 0.00 0.00 4.63
2789 2888 1.289380 GTGCCGACGACTTCCTCTT 59.711 57.895 0.00 0.00 0.00 2.85
2822 2921 2.165301 GTGCTAACTACCAGCGGCG 61.165 63.158 0.51 0.51 42.13 6.46
2824 2923 1.518572 CCGTGCTAACTACCAGCGG 60.519 63.158 0.00 0.00 42.13 5.52
2844 2943 7.602753 TCCGTTGTGAATACATAGGATGATAG 58.397 38.462 0.00 0.00 37.62 2.08
2845 2944 7.309805 CCTCCGTTGTGAATACATAGGATGATA 60.310 40.741 0.00 0.00 39.98 2.15
2892 2991 8.120465 GGATAACATACACTACAAAAACCATCG 58.880 37.037 0.00 0.00 0.00 3.84
2920 3019 6.748658 GTGATATTGACAATGACAACATGGTG 59.251 38.462 9.83 9.83 40.37 4.17
2921 3020 6.433716 TGTGATATTGACAATGACAACATGGT 59.566 34.615 11.05 0.00 42.66 3.55
2922 3021 6.748658 GTGTGATATTGACAATGACAACATGG 59.251 38.462 11.05 0.00 36.79 3.66
2963 3062 6.168389 GTGCCATGATACAGATGATGATACA 58.832 40.000 0.00 0.00 28.72 2.29
2964 3063 5.583854 GGTGCCATGATACAGATGATGATAC 59.416 44.000 0.00 0.00 28.72 2.24
2966 3065 4.042435 TGGTGCCATGATACAGATGATGAT 59.958 41.667 0.00 0.00 28.72 2.45
2968 3067 3.501062 GTGGTGCCATGATACAGATGATG 59.499 47.826 0.00 0.00 0.00 3.07
3004 3106 1.584495 GTTGCCACCTAAAAGCCGG 59.416 57.895 0.00 0.00 0.00 6.13
3005 3107 1.584495 GGTTGCCACCTAAAAGCCG 59.416 57.895 0.00 0.00 40.44 5.52
3006 3108 1.584495 CGGTTGCCACCTAAAAGCC 59.416 57.895 5.29 0.00 41.64 4.35
3007 3109 1.080772 GCGGTTGCCACCTAAAAGC 60.081 57.895 5.29 0.00 41.64 3.51
3008 3110 0.039527 GTGCGGTTGCCACCTAAAAG 60.040 55.000 5.29 0.00 41.64 2.27
3009 3111 1.457009 GGTGCGGTTGCCACCTAAAA 61.457 55.000 5.29 0.00 41.64 1.52
3010 3112 1.899534 GGTGCGGTTGCCACCTAAA 60.900 57.895 5.29 0.00 41.64 1.85
3011 3113 2.281900 GGTGCGGTTGCCACCTAA 60.282 61.111 5.29 0.00 41.64 2.69
3012 3114 3.246112 AGGTGCGGTTGCCACCTA 61.246 61.111 11.10 0.00 45.04 3.08
3013 3115 4.954970 CAGGTGCGGTTGCCACCT 62.955 66.667 7.24 7.24 46.63 4.00
3018 3120 2.671619 TAAGGCAGGTGCGGTTGC 60.672 61.111 0.00 0.00 43.26 4.17
3019 3121 2.690778 GCTAAGGCAGGTGCGGTTG 61.691 63.158 0.00 0.00 43.26 3.77
3020 3122 2.359975 GCTAAGGCAGGTGCGGTT 60.360 61.111 0.00 0.00 43.26 4.44
3021 3123 3.636231 TGCTAAGGCAGGTGCGGT 61.636 61.111 0.00 0.00 44.28 5.68
3030 3132 2.166664 CGGAGGGAGTATATGCTAAGGC 59.833 54.545 0.00 0.00 39.26 4.35
3031 3133 3.432378 ACGGAGGGAGTATATGCTAAGG 58.568 50.000 0.00 0.00 0.00 2.69
3032 3134 3.444388 GGACGGAGGGAGTATATGCTAAG 59.556 52.174 0.00 0.00 0.00 2.18
3033 3135 3.428532 GGACGGAGGGAGTATATGCTAA 58.571 50.000 0.00 0.00 0.00 3.09
3034 3136 2.617276 CGGACGGAGGGAGTATATGCTA 60.617 54.545 0.00 0.00 0.00 3.49
3035 3137 1.887088 CGGACGGAGGGAGTATATGCT 60.887 57.143 0.00 0.00 0.00 3.79
3036 3138 0.526662 CGGACGGAGGGAGTATATGC 59.473 60.000 0.00 0.00 0.00 3.14
3037 3139 1.174783 CCGGACGGAGGGAGTATATG 58.825 60.000 4.40 0.00 37.50 1.78
3038 3140 3.666192 CCGGACGGAGGGAGTATAT 57.334 57.895 4.40 0.00 37.50 0.86
3046 3148 1.069668 CCTAATAAACCCGGACGGAGG 59.930 57.143 13.13 5.18 37.50 4.30
3047 3149 1.539712 GCCTAATAAACCCGGACGGAG 60.540 57.143 13.13 5.04 37.50 4.63
3048 3150 0.465287 GCCTAATAAACCCGGACGGA 59.535 55.000 13.13 0.00 37.50 4.69
3049 3151 0.533531 GGCCTAATAAACCCGGACGG 60.534 60.000 0.73 3.25 37.81 4.79
3050 3152 0.466963 AGGCCTAATAAACCCGGACG 59.533 55.000 1.29 0.00 0.00 4.79
3051 3153 3.843893 TTAGGCCTAATAAACCCGGAC 57.156 47.619 21.68 0.00 0.00 4.79
3052 3154 4.039339 TCTTTAGGCCTAATAAACCCGGA 58.961 43.478 25.70 6.80 0.00 5.14
3053 3155 4.132336 GTCTTTAGGCCTAATAAACCCGG 58.868 47.826 25.70 8.87 0.00 5.73
3054 3156 4.773013 TGTCTTTAGGCCTAATAAACCCG 58.227 43.478 25.70 8.69 0.00 5.28
3055 3157 6.185511 AGTTGTCTTTAGGCCTAATAAACCC 58.814 40.000 25.70 15.18 0.00 4.11
3056 3158 7.698506 AAGTTGTCTTTAGGCCTAATAAACC 57.301 36.000 25.70 12.16 0.00 3.27
3057 3159 9.622004 GAAAAGTTGTCTTTAGGCCTAATAAAC 57.378 33.333 25.70 22.86 42.26 2.01
3058 3160 9.582648 AGAAAAGTTGTCTTTAGGCCTAATAAA 57.417 29.630 25.70 12.32 42.26 1.40
3059 3161 9.582648 AAGAAAAGTTGTCTTTAGGCCTAATAA 57.417 29.630 25.70 13.92 42.26 1.40
3061 3163 9.232473 CTAAGAAAAGTTGTCTTTAGGCCTAAT 57.768 33.333 25.70 6.84 42.26 1.73
3062 3164 8.434392 TCTAAGAAAAGTTGTCTTTAGGCCTAA 58.566 33.333 21.68 21.68 42.26 2.69
3063 3165 7.876582 GTCTAAGAAAAGTTGTCTTTAGGCCTA 59.123 37.037 13.54 8.91 42.26 3.93
3064 3166 6.711194 GTCTAAGAAAAGTTGTCTTTAGGCCT 59.289 38.462 13.54 11.78 42.26 5.19
3065 3167 6.072618 GGTCTAAGAAAAGTTGTCTTTAGGCC 60.073 42.308 13.54 14.30 42.26 5.19
3066 3168 6.485648 TGGTCTAAGAAAAGTTGTCTTTAGGC 59.514 38.462 13.54 9.98 42.26 3.93


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

AutoCloner maintained by Alex Coulton.