Multiple sequence alignment - TraesCS3A01G480700

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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 TraesCS3A01G480700 chr3A 100.000 2529 0 0 1 2529 711409396 711406868 0 4671
1 TraesCS3A01G480700 chr3D 88.906 1893 104 54 660 2529 575854564 575852755 0 2235
2 TraesCS3A01G480700 chr3B 90.211 950 44 20 847 1758 768249203 768250141 0 1194
3 TraesCS3A01G480700 chr3B 90.000 690 46 12 1840 2529 768250439 768251105 0 870


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 TraesCS3A01G480700 chr3A 711406868 711409396 2528 True 4671 4671 100.0000 1 2529 1 chr3A.!!$R1 2528
1 TraesCS3A01G480700 chr3D 575852755 575854564 1809 True 2235 2235 88.9060 660 2529 1 chr3D.!!$R1 1869
2 TraesCS3A01G480700 chr3B 768249203 768251105 1902 False 1032 1194 90.1055 847 2529 2 chr3B.!!$F1 1682

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
68 69 0.036732 ATTCTTGAAGCTGCCGGTCA 59.963 50.0 1.9 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 2077 0.603569 AAAGACTGCGGATCGACAGT 59.396 50.0 16.59 16.59 42.87 3.55 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
35 36 5.784578 AAAAGCTTCCAATACGGTTTTCT 57.215 34.783 0.00 0.00 34.42 2.52
36 37 5.784578 AAAGCTTCCAATACGGTTTTCTT 57.215 34.783 0.00 0.00 35.57 2.52
37 38 4.766404 AGCTTCCAATACGGTTTTCTTG 57.234 40.909 0.00 0.00 35.57 3.02
38 39 3.057526 AGCTTCCAATACGGTTTTCTTGC 60.058 43.478 0.00 0.00 35.57 4.01
39 40 3.057526 GCTTCCAATACGGTTTTCTTGCT 60.058 43.478 0.00 0.00 35.57 3.91
40 41 4.558697 GCTTCCAATACGGTTTTCTTGCTT 60.559 41.667 0.00 0.00 35.57 3.91
41 42 5.523438 TTCCAATACGGTTTTCTTGCTTT 57.477 34.783 0.00 0.00 35.57 3.51
42 43 5.523438 TCCAATACGGTTTTCTTGCTTTT 57.477 34.783 0.00 0.00 35.57 2.27
43 44 6.636562 TCCAATACGGTTTTCTTGCTTTTA 57.363 33.333 0.00 0.00 35.57 1.52
44 45 6.674066 TCCAATACGGTTTTCTTGCTTTTAG 58.326 36.000 0.00 0.00 35.57 1.85
45 46 5.861787 CCAATACGGTTTTCTTGCTTTTAGG 59.138 40.000 0.00 0.00 0.00 2.69
46 47 6.294286 CCAATACGGTTTTCTTGCTTTTAGGA 60.294 38.462 0.00 0.00 0.00 2.94
47 48 6.887626 ATACGGTTTTCTTGCTTTTAGGAA 57.112 33.333 0.00 0.00 0.00 3.36
48 49 4.928601 ACGGTTTTCTTGCTTTTAGGAAC 58.071 39.130 0.00 0.00 0.00 3.62
49 50 4.399934 ACGGTTTTCTTGCTTTTAGGAACA 59.600 37.500 0.00 0.00 0.00 3.18
50 51 5.068591 ACGGTTTTCTTGCTTTTAGGAACAT 59.931 36.000 0.00 0.00 0.00 2.71
51 52 5.983118 CGGTTTTCTTGCTTTTAGGAACATT 59.017 36.000 0.00 0.00 0.00 2.71
52 53 6.143919 CGGTTTTCTTGCTTTTAGGAACATTC 59.856 38.462 0.00 0.00 0.00 2.67
53 54 7.210174 GGTTTTCTTGCTTTTAGGAACATTCT 58.790 34.615 0.00 0.00 0.00 2.40
54 55 7.710907 GGTTTTCTTGCTTTTAGGAACATTCTT 59.289 33.333 0.00 0.00 0.00 2.52
55 56 8.542953 GTTTTCTTGCTTTTAGGAACATTCTTG 58.457 33.333 0.00 0.00 0.00 3.02
56 57 7.581213 TTCTTGCTTTTAGGAACATTCTTGA 57.419 32.000 0.00 0.00 0.00 3.02
57 58 7.581213 TCTTGCTTTTAGGAACATTCTTGAA 57.419 32.000 0.00 0.00 0.00 2.69
58 59 7.651808 TCTTGCTTTTAGGAACATTCTTGAAG 58.348 34.615 0.00 0.00 0.00 3.02
59 60 5.772521 TGCTTTTAGGAACATTCTTGAAGC 58.227 37.500 14.35 14.35 37.32 3.86
60 61 5.536161 TGCTTTTAGGAACATTCTTGAAGCT 59.464 36.000 18.48 0.00 37.50 3.74
61 62 5.860716 GCTTTTAGGAACATTCTTGAAGCTG 59.139 40.000 14.13 0.00 35.70 4.24
62 63 5.376854 TTTAGGAACATTCTTGAAGCTGC 57.623 39.130 0.00 0.00 0.00 5.25
63 64 2.165998 AGGAACATTCTTGAAGCTGCC 58.834 47.619 0.00 0.00 0.00 4.85
64 65 1.135575 GGAACATTCTTGAAGCTGCCG 60.136 52.381 0.00 0.00 0.00 5.69
65 66 0.883833 AACATTCTTGAAGCTGCCGG 59.116 50.000 0.00 0.00 0.00 6.13
66 67 0.250901 ACATTCTTGAAGCTGCCGGT 60.251 50.000 1.90 0.00 0.00 5.28
67 68 0.449388 CATTCTTGAAGCTGCCGGTC 59.551 55.000 1.90 0.00 0.00 4.79
68 69 0.036732 ATTCTTGAAGCTGCCGGTCA 59.963 50.000 1.90 0.00 0.00 4.02
69 70 0.179032 TTCTTGAAGCTGCCGGTCAA 60.179 50.000 1.90 3.55 0.00 3.18
70 71 0.036732 TCTTGAAGCTGCCGGTCAAT 59.963 50.000 1.90 0.00 0.00 2.57
71 72 0.883833 CTTGAAGCTGCCGGTCAATT 59.116 50.000 1.90 0.00 0.00 2.32
72 73 1.270550 CTTGAAGCTGCCGGTCAATTT 59.729 47.619 1.90 0.00 0.00 1.82
73 74 1.327303 TGAAGCTGCCGGTCAATTTT 58.673 45.000 1.90 0.00 0.00 1.82
74 75 1.686052 TGAAGCTGCCGGTCAATTTTT 59.314 42.857 1.90 0.00 0.00 1.94
146 147 5.893897 TGCAATTTCCCAAATATTTTGGC 57.106 34.783 12.48 1.31 38.23 4.52
147 148 5.568392 TGCAATTTCCCAAATATTTTGGCT 58.432 33.333 12.48 0.00 38.23 4.75
148 149 6.008960 TGCAATTTCCCAAATATTTTGGCTT 58.991 32.000 12.48 4.71 38.23 4.35
149 150 6.492772 TGCAATTTCCCAAATATTTTGGCTTT 59.507 30.769 12.48 4.56 38.23 3.51
150 151 7.015001 TGCAATTTCCCAAATATTTTGGCTTTT 59.985 29.630 12.48 4.28 38.23 2.27
151 152 7.328982 GCAATTTCCCAAATATTTTGGCTTTTG 59.671 33.333 12.48 14.16 38.23 2.44
152 153 8.574737 CAATTTCCCAAATATTTTGGCTTTTGA 58.425 29.630 12.48 2.97 38.23 2.69
153 154 8.703378 ATTTCCCAAATATTTTGGCTTTTGAA 57.297 26.923 12.48 8.06 38.23 2.69
154 155 7.742556 TTCCCAAATATTTTGGCTTTTGAAG 57.257 32.000 12.48 0.00 38.23 3.02
155 156 7.072263 TCCCAAATATTTTGGCTTTTGAAGA 57.928 32.000 12.48 1.14 38.23 2.87
156 157 7.160726 TCCCAAATATTTTGGCTTTTGAAGAG 58.839 34.615 12.48 0.00 38.23 2.85
157 158 7.016072 TCCCAAATATTTTGGCTTTTGAAGAGA 59.984 33.333 12.48 0.00 38.23 3.10
158 159 7.661027 CCCAAATATTTTGGCTTTTGAAGAGAA 59.339 33.333 12.53 0.00 38.23 2.87
159 160 9.223099 CCAAATATTTTGGCTTTTGAAGAGAAT 57.777 29.630 6.11 0.00 32.17 2.40
166 167 8.816640 TTTGGCTTTTGAAGAGAATCATTAAC 57.183 30.769 0.00 0.00 37.82 2.01
167 168 7.765695 TGGCTTTTGAAGAGAATCATTAACT 57.234 32.000 0.00 0.00 37.82 2.24
168 169 8.181904 TGGCTTTTGAAGAGAATCATTAACTT 57.818 30.769 0.00 0.00 37.82 2.66
169 170 8.641541 TGGCTTTTGAAGAGAATCATTAACTTT 58.358 29.630 0.00 0.00 37.82 2.66
170 171 9.481340 GGCTTTTGAAGAGAATCATTAACTTTT 57.519 29.630 0.00 0.00 37.82 2.27
176 177 9.354673 TGAAGAGAATCATTAACTTTTTGGAGT 57.645 29.630 0.00 0.00 37.82 3.85
204 205 5.813513 AAAATCCAGTTTCCAGAATTGCT 57.186 34.783 0.00 0.00 0.00 3.91
205 206 5.397142 AAATCCAGTTTCCAGAATTGCTC 57.603 39.130 0.00 0.00 0.00 4.26
206 207 3.507162 TCCAGTTTCCAGAATTGCTCA 57.493 42.857 0.00 0.00 0.00 4.26
207 208 3.415212 TCCAGTTTCCAGAATTGCTCAG 58.585 45.455 0.00 0.00 0.00 3.35
208 209 3.072915 TCCAGTTTCCAGAATTGCTCAGA 59.927 43.478 0.00 0.00 0.00 3.27
209 210 3.822735 CCAGTTTCCAGAATTGCTCAGAA 59.177 43.478 0.00 0.00 0.00 3.02
210 211 4.461781 CCAGTTTCCAGAATTGCTCAGAAT 59.538 41.667 0.00 0.00 0.00 2.40
211 212 5.047519 CCAGTTTCCAGAATTGCTCAGAATT 60.048 40.000 0.00 0.00 0.00 2.17
212 213 6.453092 CAGTTTCCAGAATTGCTCAGAATTT 58.547 36.000 0.00 0.00 0.00 1.82
213 214 6.927381 CAGTTTCCAGAATTGCTCAGAATTTT 59.073 34.615 0.00 0.00 0.00 1.82
214 215 8.084073 CAGTTTCCAGAATTGCTCAGAATTTTA 58.916 33.333 0.00 0.00 0.00 1.52
215 216 8.810041 AGTTTCCAGAATTGCTCAGAATTTTAT 58.190 29.630 0.00 0.00 0.00 1.40
287 288 9.918630 AGTCAGAATTTTCATAAATGGTTTGAG 57.081 29.630 0.00 0.00 34.27 3.02
288 289 9.912634 GTCAGAATTTTCATAAATGGTTTGAGA 57.087 29.630 0.00 0.00 34.27 3.27
317 318 5.841267 AAAAATGCCCCCAATTTAGAAGT 57.159 34.783 0.00 0.00 0.00 3.01
318 319 6.943899 AAAAATGCCCCCAATTTAGAAGTA 57.056 33.333 0.00 0.00 0.00 2.24
319 320 7.509236 AAAAATGCCCCCAATTTAGAAGTAT 57.491 32.000 0.00 0.00 0.00 2.12
320 321 8.616799 AAAAATGCCCCCAATTTAGAAGTATA 57.383 30.769 0.00 0.00 0.00 1.47
321 322 8.797436 AAAATGCCCCCAATTTAGAAGTATAT 57.203 30.769 0.00 0.00 0.00 0.86
322 323 8.797436 AAATGCCCCCAATTTAGAAGTATATT 57.203 30.769 0.00 0.00 0.00 1.28
323 324 8.422577 AATGCCCCCAATTTAGAAGTATATTC 57.577 34.615 0.00 0.00 0.00 1.75
324 325 6.001460 TGCCCCCAATTTAGAAGTATATTCG 58.999 40.000 0.00 0.00 0.00 3.34
325 326 5.414765 GCCCCCAATTTAGAAGTATATTCGG 59.585 44.000 0.00 0.00 0.00 4.30
326 327 6.746043 GCCCCCAATTTAGAAGTATATTCGGA 60.746 42.308 0.00 0.00 0.00 4.55
327 328 7.228590 CCCCCAATTTAGAAGTATATTCGGAA 58.771 38.462 0.00 0.00 0.00 4.30
328 329 7.888546 CCCCCAATTTAGAAGTATATTCGGAAT 59.111 37.037 8.49 8.49 0.00 3.01
329 330 9.953565 CCCCAATTTAGAAGTATATTCGGAATA 57.046 33.333 12.50 12.50 0.00 1.75
371 372 8.961294 TGTTGGAATTTCACAAAAATTGTTTG 57.039 26.923 0.78 0.00 43.23 2.93
372 373 8.786898 TGTTGGAATTTCACAAAAATTGTTTGA 58.213 25.926 6.31 5.18 43.23 2.69
373 374 9.617975 GTTGGAATTTCACAAAAATTGTTTGAA 57.382 25.926 6.31 9.56 43.23 2.69
445 446 7.826260 AAAATGTTCATGTTTCGAAAACTGT 57.174 28.000 13.10 0.00 0.00 3.55
446 447 7.826260 AAATGTTCATGTTTCGAAAACTGTT 57.174 28.000 13.10 4.07 0.00 3.16
447 448 7.449934 AATGTTCATGTTTCGAAAACTGTTC 57.550 32.000 13.10 10.35 0.00 3.18
448 449 5.944013 TGTTCATGTTTCGAAAACTGTTCA 58.056 33.333 13.10 5.61 0.00 3.18
449 450 5.797934 TGTTCATGTTTCGAAAACTGTTCAC 59.202 36.000 13.10 11.23 0.00 3.18
450 451 4.583426 TCATGTTTCGAAAACTGTTCACG 58.417 39.130 13.10 11.21 0.00 4.35
451 452 4.093703 TCATGTTTCGAAAACTGTTCACGT 59.906 37.500 13.10 0.00 0.00 4.49
452 453 3.738399 TGTTTCGAAAACTGTTCACGTG 58.262 40.909 13.10 9.94 0.00 4.49
453 454 3.186817 TGTTTCGAAAACTGTTCACGTGT 59.813 39.130 16.51 0.00 0.00 4.49
454 455 4.153256 GTTTCGAAAACTGTTCACGTGTT 58.847 39.130 16.51 0.00 0.00 3.32
455 456 4.407496 TTCGAAAACTGTTCACGTGTTT 57.593 36.364 16.51 7.37 35.71 2.83
456 457 5.527511 TTCGAAAACTGTTCACGTGTTTA 57.472 34.783 16.51 1.89 34.09 2.01
457 458 5.527511 TCGAAAACTGTTCACGTGTTTAA 57.472 34.783 16.51 0.00 34.09 1.52
458 459 5.924786 TCGAAAACTGTTCACGTGTTTAAA 58.075 33.333 16.51 0.00 34.09 1.52
459 460 6.369005 TCGAAAACTGTTCACGTGTTTAAAA 58.631 32.000 16.51 0.00 34.09 1.52
460 461 6.854892 TCGAAAACTGTTCACGTGTTTAAAAA 59.145 30.769 16.51 0.00 34.09 1.94
461 462 7.537991 TCGAAAACTGTTCACGTGTTTAAAAAT 59.462 29.630 16.51 0.00 34.09 1.82
462 463 8.157183 CGAAAACTGTTCACGTGTTTAAAAATT 58.843 29.630 16.51 3.65 34.09 1.82
465 466 9.628746 AAACTGTTCACGTGTTTAAAAATTACT 57.371 25.926 16.51 0.00 32.92 2.24
466 467 8.831000 ACTGTTCACGTGTTTAAAAATTACTC 57.169 30.769 16.51 0.00 0.00 2.59
467 468 8.671028 ACTGTTCACGTGTTTAAAAATTACTCT 58.329 29.630 16.51 0.00 0.00 3.24
468 469 9.155053 CTGTTCACGTGTTTAAAAATTACTCTC 57.845 33.333 16.51 0.00 0.00 3.20
469 470 8.666573 TGTTCACGTGTTTAAAAATTACTCTCA 58.333 29.630 16.51 0.00 0.00 3.27
470 471 9.493206 GTTCACGTGTTTAAAAATTACTCTCAA 57.507 29.630 16.51 0.00 0.00 3.02
489 490 9.037737 ACTCTCAATTTGAAAACAATGTTCATG 57.962 29.630 0.00 0.00 35.03 3.07
490 491 8.945481 TCTCAATTTGAAAACAATGTTCATGT 57.055 26.923 0.00 0.00 35.03 3.21
491 492 9.381033 TCTCAATTTGAAAACAATGTTCATGTT 57.619 25.926 0.00 0.00 42.56 2.71
592 593 9.684448 TTTTTAAATACATTCTTCACGATTGCA 57.316 25.926 0.00 0.00 0.00 4.08
593 594 8.894409 TTTAAATACATTCTTCACGATTGCAG 57.106 30.769 0.00 0.00 0.00 4.41
594 595 5.490139 AATACATTCTTCACGATTGCAGG 57.510 39.130 0.00 0.00 0.00 4.85
595 596 3.057969 ACATTCTTCACGATTGCAGGA 57.942 42.857 0.00 0.00 0.00 3.86
596 597 3.411446 ACATTCTTCACGATTGCAGGAA 58.589 40.909 0.00 0.00 0.00 3.36
597 598 3.820467 ACATTCTTCACGATTGCAGGAAA 59.180 39.130 0.00 0.00 0.00 3.13
598 599 4.278170 ACATTCTTCACGATTGCAGGAAAA 59.722 37.500 0.00 0.00 0.00 2.29
599 600 4.909696 TTCTTCACGATTGCAGGAAAAA 57.090 36.364 0.00 0.00 0.00 1.94
627 628 9.695884 TCGAAATTTTAAAATGTCTTGTTTTGC 57.304 25.926 22.82 2.37 31.73 3.68
628 629 9.483062 CGAAATTTTAAAATGTCTTGTTTTGCA 57.517 25.926 22.82 0.00 31.73 4.08
643 644 9.651913 TCTTGTTTTGCAAAAGAAATATATCCC 57.348 29.630 27.98 12.92 36.53 3.85
644 645 9.657419 CTTGTTTTGCAAAAGAAATATATCCCT 57.343 29.630 27.98 0.00 36.53 4.20
650 651 8.245195 TGCAAAAGAAATATATCCCTTTACCC 57.755 34.615 10.75 5.66 0.00 3.69
651 652 7.841729 TGCAAAAGAAATATATCCCTTTACCCA 59.158 33.333 10.75 7.31 0.00 4.51
652 653 8.700973 GCAAAAGAAATATATCCCTTTACCCAA 58.299 33.333 10.75 0.00 0.00 4.12
682 683 3.251043 GCTGCGTGCTAGAGCGAC 61.251 66.667 9.97 0.00 45.83 5.19
683 684 2.487428 CTGCGTGCTAGAGCGACT 59.513 61.111 9.97 0.00 45.83 4.18
691 692 1.071605 GCTAGAGCGACTTGTTGTGG 58.928 55.000 0.00 0.00 0.00 4.17
698 708 0.099791 CGACTTGTTGTGGGCGTTTT 59.900 50.000 0.00 0.00 0.00 2.43
721 731 1.473965 CGCAGTGAGCATCCAATAGGT 60.474 52.381 0.00 0.00 46.13 3.08
724 734 1.133976 AGTGAGCATCCAATAGGTGCC 60.134 52.381 0.00 0.00 40.54 5.01
729 739 1.689258 GCATCCAATAGGTGCCCCTTT 60.689 52.381 0.00 0.00 42.66 3.11
762 772 1.083401 CTGTTCGTCTTGTGCACGC 60.083 57.895 13.13 1.44 37.18 5.34
766 776 1.771073 TTCGTCTTGTGCACGCTTGG 61.771 55.000 13.13 1.38 37.18 3.61
799 809 3.197790 CGTTGGCCGCTGAGATGG 61.198 66.667 0.00 0.00 0.00 3.51
818 835 1.102978 GTCGTAGGGCCTAACGGTTA 58.897 55.000 24.96 11.28 0.00 2.85
819 836 1.476488 GTCGTAGGGCCTAACGGTTAA 59.524 52.381 24.96 11.02 0.00 2.01
820 837 1.750778 TCGTAGGGCCTAACGGTTAAG 59.249 52.381 24.96 6.33 0.00 1.85
821 838 1.803998 CGTAGGGCCTAACGGTTAAGC 60.804 57.143 16.44 12.06 0.00 3.09
822 839 1.207811 GTAGGGCCTAACGGTTAAGCA 59.792 52.381 16.44 0.85 0.00 3.91
823 840 0.916809 AGGGCCTAACGGTTAAGCAT 59.083 50.000 19.83 7.88 0.00 3.79
824 841 1.021968 GGGCCTAACGGTTAAGCATG 58.978 55.000 19.83 1.34 0.00 4.06
825 842 0.380733 GGCCTAACGGTTAAGCATGC 59.619 55.000 19.83 10.51 0.00 4.06
826 843 1.091537 GCCTAACGGTTAAGCATGCA 58.908 50.000 21.98 0.00 0.00 3.96
827 844 1.470890 GCCTAACGGTTAAGCATGCAA 59.529 47.619 21.98 2.93 0.00 4.08
828 845 2.477863 GCCTAACGGTTAAGCATGCAAG 60.478 50.000 21.98 6.50 0.00 4.01
829 846 2.747446 CCTAACGGTTAAGCATGCAAGT 59.253 45.455 21.98 7.14 0.00 3.16
830 847 3.936453 CCTAACGGTTAAGCATGCAAGTA 59.064 43.478 21.98 6.05 0.00 2.24
831 848 3.824414 AACGGTTAAGCATGCAAGTAC 57.176 42.857 21.98 11.65 0.00 2.73
832 849 3.053831 ACGGTTAAGCATGCAAGTACT 57.946 42.857 21.98 0.00 0.00 2.73
833 850 3.000727 ACGGTTAAGCATGCAAGTACTC 58.999 45.455 21.98 3.25 0.00 2.59
834 851 3.262420 CGGTTAAGCATGCAAGTACTCT 58.738 45.455 21.98 0.00 0.00 3.24
835 852 3.307242 CGGTTAAGCATGCAAGTACTCTC 59.693 47.826 21.98 0.15 0.00 3.20
836 853 3.307242 GGTTAAGCATGCAAGTACTCTCG 59.693 47.826 21.98 0.00 0.00 4.04
837 854 1.363744 AAGCATGCAAGTACTCTCGC 58.636 50.000 21.98 0.00 0.00 5.03
838 855 0.460987 AGCATGCAAGTACTCTCGCC 60.461 55.000 21.98 0.00 0.00 5.54
839 856 0.740868 GCATGCAAGTACTCTCGCCA 60.741 55.000 14.21 0.00 0.00 5.69
840 857 1.725641 CATGCAAGTACTCTCGCCAA 58.274 50.000 0.00 0.00 0.00 4.52
841 858 1.394917 CATGCAAGTACTCTCGCCAAC 59.605 52.381 0.00 0.00 0.00 3.77
842 859 0.391228 TGCAAGTACTCTCGCCAACA 59.609 50.000 0.00 0.00 0.00 3.33
843 860 1.202592 TGCAAGTACTCTCGCCAACAA 60.203 47.619 0.00 0.00 0.00 2.83
844 861 1.871039 GCAAGTACTCTCGCCAACAAA 59.129 47.619 0.00 0.00 0.00 2.83
845 862 2.289547 GCAAGTACTCTCGCCAACAAAA 59.710 45.455 0.00 0.00 0.00 2.44
878 895 3.667282 GCTACGATCGGGCGGCTA 61.667 66.667 20.98 0.10 35.12 3.93
950 967 2.294791 CCATCGTCCTATCACACTCTCC 59.705 54.545 0.00 0.00 0.00 3.71
1277 1328 6.103997 AGGTACGTATTGTGTATGAACAAGG 58.896 40.000 0.00 0.00 42.99 3.61
1301 1352 2.086094 TGCTGATTGGCATGTACTGTG 58.914 47.619 0.00 0.00 37.29 3.66
1422 1477 4.233635 CGGAGAGTACGTCGGCGG 62.234 72.222 16.39 0.00 43.45 6.13
1480 1535 1.600916 GGTCCTTGTCACAGCCACC 60.601 63.158 0.00 0.00 0.00 4.61
1519 1574 0.960861 GGAACAGGCCGAAAAGGGAG 60.961 60.000 0.00 0.00 41.48 4.30
1604 1661 6.524586 CCGTCAATCAGCTTGTAAATCTTTTC 59.475 38.462 0.00 0.00 36.20 2.29
1611 1668 7.589395 TCAGCTTGTAAATCTTTTCGCAAATA 58.411 30.769 0.00 0.00 0.00 1.40
1653 1710 2.758356 GCAAGTTAATGCGCGATCG 58.242 52.632 12.10 11.69 36.45 3.69
1656 1713 2.618419 CAAGTTAATGCGCGATCGAAG 58.382 47.619 21.57 13.01 38.10 3.79
1659 1716 3.123804 AGTTAATGCGCGATCGAAGAAT 58.876 40.909 21.57 9.06 43.58 2.40
1681 1738 2.519771 ATATATACCCGAGGCGACCA 57.480 50.000 0.00 0.00 0.00 4.02
1691 1748 1.223187 GAGGCGACCAAAGAACGAAA 58.777 50.000 0.00 0.00 0.00 3.46
1693 1750 0.040692 GGCGACCAAAGAACGAAACC 60.041 55.000 0.00 0.00 0.00 3.27
1761 2065 7.148507 CGCTTCAGAACTGTTTTTCAGAGATAT 60.149 37.037 0.00 0.00 46.27 1.63
1785 2089 1.000163 ACATCCATACTGTCGATCCGC 60.000 52.381 0.00 0.00 0.00 5.54
1795 2099 1.000394 TGTCGATCCGCAGTCTTTTCA 60.000 47.619 0.00 0.00 0.00 2.69
1805 2109 4.272018 CCGCAGTCTTTTCATAGAAGGATG 59.728 45.833 0.00 0.00 0.00 3.51
1809 2113 7.601886 CGCAGTCTTTTCATAGAAGGATGATAT 59.398 37.037 0.00 0.00 35.77 1.63
1810 2114 9.282569 GCAGTCTTTTCATAGAAGGATGATATT 57.717 33.333 0.00 0.00 35.77 1.28
1832 2136 9.760077 ATATTACTACATGCTAAAGTGGTGTAC 57.240 33.333 0.00 0.00 31.66 2.90
1865 2169 4.336993 AGAAAGTTGTGCAACGGTGAAATA 59.663 37.500 3.55 0.00 45.50 1.40
1929 2233 2.022195 AGGCATAGCACATCAAAGCTG 58.978 47.619 0.00 0.00 41.97 4.24
1952 2262 6.380995 TGTATGCACATTTCAGACAACATTC 58.619 36.000 0.00 0.00 33.38 2.67
1956 2266 5.067544 TGCACATTTCAGACAACATTCTCAA 59.932 36.000 0.00 0.00 0.00 3.02
1960 2270 7.377928 CACATTTCAGACAACATTCTCAAGTTC 59.622 37.037 0.00 0.00 0.00 3.01
1982 2312 5.548406 TCTACAACTAGGGAGAAGCAAAAC 58.452 41.667 0.00 0.00 0.00 2.43
1991 2321 3.363178 GGAGAAGCAAAACAAACAGACG 58.637 45.455 0.00 0.00 0.00 4.18
2006 2336 6.970613 ACAAACAGACGTTTATTCCAACTTTC 59.029 34.615 0.00 0.00 43.57 2.62
2018 2350 4.457834 TCCAACTTTCTTTTTGCGGAAA 57.542 36.364 0.00 0.00 0.00 3.13
2083 2415 1.896220 ACCACATGCTTGTACCAGTG 58.104 50.000 4.73 0.00 33.76 3.66
2087 2419 2.031769 CACATGCTTGTACCAGTGTGTG 60.032 50.000 14.65 14.65 33.76 3.82
2088 2420 2.221169 CATGCTTGTACCAGTGTGTGT 58.779 47.619 0.00 0.00 0.00 3.72
2089 2421 1.662517 TGCTTGTACCAGTGTGTGTG 58.337 50.000 0.00 0.00 0.00 3.82
2090 2422 1.065782 TGCTTGTACCAGTGTGTGTGT 60.066 47.619 0.00 0.00 0.00 3.72
2091 2423 1.330521 GCTTGTACCAGTGTGTGTGTG 59.669 52.381 0.00 0.00 0.00 3.82
2092 2424 2.627945 CTTGTACCAGTGTGTGTGTGT 58.372 47.619 0.00 0.00 0.00 3.72
2160 2492 5.527582 ACATACAGTGTTGTCCTTCTTTGTC 59.472 40.000 0.00 0.00 38.01 3.18
2181 2515 4.871993 CACATCTGGTGCAGTTCTAATC 57.128 45.455 0.00 0.00 41.36 1.75
2184 2518 5.413833 CACATCTGGTGCAGTTCTAATCTTT 59.586 40.000 0.00 0.00 41.36 2.52
2190 2524 7.500892 TCTGGTGCAGTTCTAATCTTTAAAACA 59.499 33.333 0.00 0.00 32.61 2.83
2193 2527 7.918562 GGTGCAGTTCTAATCTTTAAAACAACA 59.081 33.333 0.00 0.00 0.00 3.33
2486 2820 2.369860 TGTCAACCATTCAGCTCTCAGT 59.630 45.455 0.00 0.00 0.00 3.41
2487 2821 2.999355 GTCAACCATTCAGCTCTCAGTC 59.001 50.000 0.00 0.00 0.00 3.51
2488 2822 2.902486 TCAACCATTCAGCTCTCAGTCT 59.098 45.455 0.00 0.00 0.00 3.24
2489 2823 3.056250 TCAACCATTCAGCTCTCAGTCTC 60.056 47.826 0.00 0.00 0.00 3.36
2490 2824 2.533916 ACCATTCAGCTCTCAGTCTCA 58.466 47.619 0.00 0.00 0.00 3.27
2491 2825 2.496871 ACCATTCAGCTCTCAGTCTCAG 59.503 50.000 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.156748 AGAAAACCGTATTGGAAGCTTTTT 57.843 33.333 0.00 0.00 42.00 1.94
13 14 5.784578 AGAAAACCGTATTGGAAGCTTTT 57.215 34.783 0.00 0.00 42.00 2.27
14 15 5.528870 CAAGAAAACCGTATTGGAAGCTTT 58.471 37.500 0.00 0.00 42.00 3.51
15 16 4.558697 GCAAGAAAACCGTATTGGAAGCTT 60.559 41.667 0.00 0.00 42.00 3.74
16 17 3.057526 GCAAGAAAACCGTATTGGAAGCT 60.058 43.478 0.00 0.00 42.00 3.74
17 18 3.057526 AGCAAGAAAACCGTATTGGAAGC 60.058 43.478 0.00 0.00 42.00 3.86
18 19 4.766404 AGCAAGAAAACCGTATTGGAAG 57.234 40.909 0.00 0.00 42.00 3.46
19 20 5.523438 AAAGCAAGAAAACCGTATTGGAA 57.477 34.783 0.00 0.00 42.00 3.53
20 21 5.523438 AAAAGCAAGAAAACCGTATTGGA 57.477 34.783 0.00 0.00 42.00 3.53
21 22 5.861787 CCTAAAAGCAAGAAAACCGTATTGG 59.138 40.000 0.00 0.00 46.41 3.16
22 23 6.674066 TCCTAAAAGCAAGAAAACCGTATTG 58.326 36.000 0.00 0.00 0.00 1.90
23 24 6.887626 TCCTAAAAGCAAGAAAACCGTATT 57.112 33.333 0.00 0.00 0.00 1.89
24 25 6.263617 TGTTCCTAAAAGCAAGAAAACCGTAT 59.736 34.615 0.00 0.00 0.00 3.06
25 26 5.589452 TGTTCCTAAAAGCAAGAAAACCGTA 59.411 36.000 0.00 0.00 0.00 4.02
26 27 4.399934 TGTTCCTAAAAGCAAGAAAACCGT 59.600 37.500 0.00 0.00 0.00 4.83
27 28 4.927422 TGTTCCTAAAAGCAAGAAAACCG 58.073 39.130 0.00 0.00 0.00 4.44
28 29 7.210174 AGAATGTTCCTAAAAGCAAGAAAACC 58.790 34.615 0.00 0.00 0.00 3.27
29 30 8.542953 CAAGAATGTTCCTAAAAGCAAGAAAAC 58.457 33.333 0.00 0.00 0.00 2.43
30 31 8.474025 TCAAGAATGTTCCTAAAAGCAAGAAAA 58.526 29.630 0.00 0.00 0.00 2.29
31 32 8.006298 TCAAGAATGTTCCTAAAAGCAAGAAA 57.994 30.769 0.00 0.00 0.00 2.52
32 33 7.581213 TCAAGAATGTTCCTAAAAGCAAGAA 57.419 32.000 0.00 0.00 0.00 2.52
33 34 7.581213 TTCAAGAATGTTCCTAAAAGCAAGA 57.419 32.000 0.00 0.00 0.00 3.02
34 35 6.364435 GCTTCAAGAATGTTCCTAAAAGCAAG 59.636 38.462 0.00 0.00 0.00 4.01
35 36 6.040842 AGCTTCAAGAATGTTCCTAAAAGCAA 59.959 34.615 15.65 0.00 0.00 3.91
36 37 5.536161 AGCTTCAAGAATGTTCCTAAAAGCA 59.464 36.000 15.65 0.00 0.00 3.91
37 38 5.860716 CAGCTTCAAGAATGTTCCTAAAAGC 59.139 40.000 0.00 0.00 0.00 3.51
38 39 5.860716 GCAGCTTCAAGAATGTTCCTAAAAG 59.139 40.000 0.00 0.00 0.00 2.27
39 40 5.278957 GGCAGCTTCAAGAATGTTCCTAAAA 60.279 40.000 0.00 0.00 0.00 1.52
40 41 4.218417 GGCAGCTTCAAGAATGTTCCTAAA 59.782 41.667 0.00 0.00 0.00 1.85
41 42 3.758554 GGCAGCTTCAAGAATGTTCCTAA 59.241 43.478 0.00 0.00 0.00 2.69
42 43 3.347216 GGCAGCTTCAAGAATGTTCCTA 58.653 45.455 0.00 0.00 0.00 2.94
43 44 2.165998 GGCAGCTTCAAGAATGTTCCT 58.834 47.619 0.00 0.00 0.00 3.36
44 45 1.135575 CGGCAGCTTCAAGAATGTTCC 60.136 52.381 0.00 0.00 0.00 3.62
45 46 1.135575 CCGGCAGCTTCAAGAATGTTC 60.136 52.381 0.00 0.00 0.00 3.18
46 47 0.883833 CCGGCAGCTTCAAGAATGTT 59.116 50.000 0.00 0.00 0.00 2.71
47 48 0.250901 ACCGGCAGCTTCAAGAATGT 60.251 50.000 0.00 0.00 0.00 2.71
48 49 0.449388 GACCGGCAGCTTCAAGAATG 59.551 55.000 0.00 0.00 0.00 2.67
49 50 0.036732 TGACCGGCAGCTTCAAGAAT 59.963 50.000 0.00 0.00 0.00 2.40
50 51 0.179032 TTGACCGGCAGCTTCAAGAA 60.179 50.000 0.00 0.00 0.00 2.52
51 52 0.036732 ATTGACCGGCAGCTTCAAGA 59.963 50.000 0.00 0.00 32.91 3.02
52 53 0.883833 AATTGACCGGCAGCTTCAAG 59.116 50.000 0.00 0.00 32.91 3.02
53 54 1.327303 AAATTGACCGGCAGCTTCAA 58.673 45.000 0.00 3.72 33.89 2.69
54 55 1.327303 AAAATTGACCGGCAGCTTCA 58.673 45.000 0.00 0.00 0.00 3.02
55 56 2.438868 AAAAATTGACCGGCAGCTTC 57.561 45.000 0.00 0.00 0.00 3.86
120 121 7.818446 GCCAAAATATTTGGGAAATTGCATTTT 59.182 29.630 23.67 6.29 39.90 1.82
121 122 7.178805 AGCCAAAATATTTGGGAAATTGCATTT 59.821 29.630 23.67 0.00 39.90 2.32
122 123 6.664384 AGCCAAAATATTTGGGAAATTGCATT 59.336 30.769 23.67 0.00 39.90 3.56
123 124 6.189133 AGCCAAAATATTTGGGAAATTGCAT 58.811 32.000 23.67 0.00 39.90 3.96
124 125 5.568392 AGCCAAAATATTTGGGAAATTGCA 58.432 33.333 23.67 0.00 39.90 4.08
125 126 6.513806 AAGCCAAAATATTTGGGAAATTGC 57.486 33.333 23.67 8.21 39.90 3.56
126 127 8.574737 TCAAAAGCCAAAATATTTGGGAAATTG 58.425 29.630 23.67 20.53 39.90 2.32
127 128 8.703378 TCAAAAGCCAAAATATTTGGGAAATT 57.297 26.923 23.67 12.18 39.90 1.82
128 129 8.703378 TTCAAAAGCCAAAATATTTGGGAAAT 57.297 26.923 23.67 7.12 39.90 2.17
129 130 7.995488 TCTTCAAAAGCCAAAATATTTGGGAAA 59.005 29.630 23.67 7.50 39.90 3.13
130 131 7.512992 TCTTCAAAAGCCAAAATATTTGGGAA 58.487 30.769 23.67 13.93 39.90 3.97
131 132 7.016072 TCTCTTCAAAAGCCAAAATATTTGGGA 59.984 33.333 23.67 8.33 39.90 4.37
132 133 7.160726 TCTCTTCAAAAGCCAAAATATTTGGG 58.839 34.615 16.35 16.35 39.90 4.12
133 134 8.606040 TTCTCTTCAAAAGCCAAAATATTTGG 57.394 30.769 15.80 15.80 42.37 3.28
140 141 9.260002 GTTAATGATTCTCTTCAAAAGCCAAAA 57.740 29.630 0.00 0.00 0.00 2.44
141 142 8.641541 AGTTAATGATTCTCTTCAAAAGCCAAA 58.358 29.630 0.00 0.00 0.00 3.28
142 143 8.181904 AGTTAATGATTCTCTTCAAAAGCCAA 57.818 30.769 0.00 0.00 0.00 4.52
143 144 7.765695 AGTTAATGATTCTCTTCAAAAGCCA 57.234 32.000 0.00 0.00 0.00 4.75
144 145 9.481340 AAAAGTTAATGATTCTCTTCAAAAGCC 57.519 29.630 0.00 0.00 0.00 4.35
150 151 9.354673 ACTCCAAAAAGTTAATGATTCTCTTCA 57.645 29.630 0.00 0.00 0.00 3.02
181 182 6.178607 AGCAATTCTGGAAACTGGATTTTT 57.821 33.333 0.00 0.00 35.48 1.94
182 183 5.305128 TGAGCAATTCTGGAAACTGGATTTT 59.695 36.000 0.00 0.00 35.48 1.82
183 184 4.834496 TGAGCAATTCTGGAAACTGGATTT 59.166 37.500 0.00 0.00 35.48 2.17
184 185 4.410099 TGAGCAATTCTGGAAACTGGATT 58.590 39.130 0.00 0.00 37.94 3.01
185 186 4.015084 CTGAGCAATTCTGGAAACTGGAT 58.985 43.478 0.00 0.00 0.00 3.41
186 187 3.072915 TCTGAGCAATTCTGGAAACTGGA 59.927 43.478 0.00 0.00 0.00 3.86
187 188 3.415212 TCTGAGCAATTCTGGAAACTGG 58.585 45.455 0.00 0.00 0.00 4.00
188 189 5.640189 ATTCTGAGCAATTCTGGAAACTG 57.360 39.130 0.00 0.00 0.00 3.16
189 190 6.661304 AAATTCTGAGCAATTCTGGAAACT 57.339 33.333 0.00 0.00 0.00 2.66
190 191 8.992835 ATAAAATTCTGAGCAATTCTGGAAAC 57.007 30.769 0.00 0.00 0.00 2.78
261 262 9.918630 CTCAAACCATTTATGAAAATTCTGACT 57.081 29.630 0.00 0.00 32.87 3.41
262 263 9.912634 TCTCAAACCATTTATGAAAATTCTGAC 57.087 29.630 0.00 0.00 32.87 3.51
295 296 5.841267 ACTTCTAAATTGGGGGCATTTTT 57.159 34.783 0.00 0.00 0.00 1.94
296 297 8.797436 ATATACTTCTAAATTGGGGGCATTTT 57.203 30.769 0.00 0.00 0.00 1.82
297 298 8.797436 AATATACTTCTAAATTGGGGGCATTT 57.203 30.769 0.00 0.00 0.00 2.32
298 299 7.176690 CGAATATACTTCTAAATTGGGGGCATT 59.823 37.037 0.00 0.00 0.00 3.56
299 300 6.659242 CGAATATACTTCTAAATTGGGGGCAT 59.341 38.462 0.00 0.00 0.00 4.40
300 301 6.001460 CGAATATACTTCTAAATTGGGGGCA 58.999 40.000 0.00 0.00 0.00 5.36
301 302 5.414765 CCGAATATACTTCTAAATTGGGGGC 59.585 44.000 0.00 0.00 0.00 5.80
302 303 6.775708 TCCGAATATACTTCTAAATTGGGGG 58.224 40.000 0.00 0.00 30.64 5.40
303 304 8.863872 ATTCCGAATATACTTCTAAATTGGGG 57.136 34.615 0.00 0.00 30.64 4.96
345 346 9.570488 CAAACAATTTTTGTGAAATTCCAACAT 57.430 25.926 0.00 0.00 44.59 2.71
346 347 8.786898 TCAAACAATTTTTGTGAAATTCCAACA 58.213 25.926 10.72 0.00 44.59 3.33
347 348 9.617975 TTCAAACAATTTTTGTGAAATTCCAAC 57.382 25.926 10.72 0.00 44.59 3.77
420 421 8.250538 ACAGTTTTCGAAACATGAACATTTTT 57.749 26.923 22.03 0.00 0.00 1.94
421 422 7.826260 ACAGTTTTCGAAACATGAACATTTT 57.174 28.000 22.03 0.00 0.00 1.82
422 423 7.543868 TGAACAGTTTTCGAAACATGAACATTT 59.456 29.630 22.03 10.42 0.00 2.32
423 424 7.009174 GTGAACAGTTTTCGAAACATGAACATT 59.991 33.333 22.03 11.60 0.00 2.71
424 425 6.472163 GTGAACAGTTTTCGAAACATGAACAT 59.528 34.615 22.03 9.56 0.00 2.71
425 426 5.797934 GTGAACAGTTTTCGAAACATGAACA 59.202 36.000 22.03 17.74 0.00 3.18
426 427 5.053286 CGTGAACAGTTTTCGAAACATGAAC 60.053 40.000 22.03 13.20 0.00 3.18
427 428 5.025190 CGTGAACAGTTTTCGAAACATGAA 58.975 37.500 22.03 2.29 0.00 2.57
428 429 4.093703 ACGTGAACAGTTTTCGAAACATGA 59.906 37.500 22.03 2.64 0.00 3.07
429 430 4.202158 CACGTGAACAGTTTTCGAAACATG 59.798 41.667 10.90 14.20 0.00 3.21
430 431 4.142773 ACACGTGAACAGTTTTCGAAACAT 60.143 37.500 25.01 0.00 0.00 2.71
431 432 3.186817 ACACGTGAACAGTTTTCGAAACA 59.813 39.130 25.01 1.00 0.00 2.83
432 433 3.739494 ACACGTGAACAGTTTTCGAAAC 58.261 40.909 25.01 6.25 0.00 2.78
433 434 4.407496 AACACGTGAACAGTTTTCGAAA 57.593 36.364 25.01 6.47 0.00 3.46
434 435 4.407496 AAACACGTGAACAGTTTTCGAA 57.593 36.364 25.01 0.00 31.95 3.71
435 436 5.527511 TTAAACACGTGAACAGTTTTCGA 57.472 34.783 25.01 1.20 36.85 3.71
436 437 6.599637 TTTTAAACACGTGAACAGTTTTCG 57.400 33.333 25.01 8.76 36.85 3.46
439 440 9.628746 AGTAATTTTTAAACACGTGAACAGTTT 57.371 25.926 25.01 14.10 38.79 2.66
440 441 9.281075 GAGTAATTTTTAAACACGTGAACAGTT 57.719 29.630 25.01 10.06 0.00 3.16
441 442 8.671028 AGAGTAATTTTTAAACACGTGAACAGT 58.329 29.630 25.01 0.62 0.00 3.55
442 443 9.155053 GAGAGTAATTTTTAAACACGTGAACAG 57.845 33.333 25.01 0.00 0.00 3.16
443 444 8.666573 TGAGAGTAATTTTTAAACACGTGAACA 58.333 29.630 25.01 2.84 0.00 3.18
444 445 9.493206 TTGAGAGTAATTTTTAAACACGTGAAC 57.507 29.630 25.01 4.25 0.00 3.18
463 464 9.037737 CATGAACATTGTTTTCAAATTGAGAGT 57.962 29.630 3.08 0.00 43.39 3.24
464 465 9.037737 ACATGAACATTGTTTTCAAATTGAGAG 57.962 29.630 0.00 0.00 43.39 3.20
465 466 8.945481 ACATGAACATTGTTTTCAAATTGAGA 57.055 26.923 0.00 0.00 43.39 3.27
466 467 9.991388 AAACATGAACATTGTTTTCAAATTGAG 57.009 25.926 0.00 0.00 43.39 3.02
566 567 9.684448 TGCAATCGTGAAGAATGTATTTAAAAA 57.316 25.926 0.00 0.00 32.44 1.94
567 568 9.340695 CTGCAATCGTGAAGAATGTATTTAAAA 57.659 29.630 0.00 0.00 30.87 1.52
568 569 7.967854 CCTGCAATCGTGAAGAATGTATTTAAA 59.032 33.333 0.00 0.00 30.87 1.52
569 570 7.335673 TCCTGCAATCGTGAAGAATGTATTTAA 59.664 33.333 0.00 0.00 30.87 1.52
570 571 6.821160 TCCTGCAATCGTGAAGAATGTATTTA 59.179 34.615 0.00 0.00 30.87 1.40
571 572 5.647658 TCCTGCAATCGTGAAGAATGTATTT 59.352 36.000 0.00 0.00 30.87 1.40
572 573 5.185454 TCCTGCAATCGTGAAGAATGTATT 58.815 37.500 0.00 0.00 30.87 1.89
573 574 4.769688 TCCTGCAATCGTGAAGAATGTAT 58.230 39.130 0.00 0.00 30.87 2.29
574 575 4.200838 TCCTGCAATCGTGAAGAATGTA 57.799 40.909 0.00 0.00 30.87 2.29
575 576 3.057969 TCCTGCAATCGTGAAGAATGT 57.942 42.857 0.00 0.00 30.87 2.71
576 577 4.424061 TTTCCTGCAATCGTGAAGAATG 57.576 40.909 0.00 0.00 30.87 2.67
577 578 5.452078 TTTTTCCTGCAATCGTGAAGAAT 57.548 34.783 0.00 0.00 30.87 2.40
578 579 4.909696 TTTTTCCTGCAATCGTGAAGAA 57.090 36.364 0.00 0.00 30.87 2.52
601 602 9.695884 GCAAAACAAGACATTTTAAAATTTCGA 57.304 25.926 17.24 0.00 31.97 3.71
602 603 9.483062 TGCAAAACAAGACATTTTAAAATTTCG 57.517 25.926 17.24 9.65 31.97 3.46
617 618 9.651913 GGGATATATTTCTTTTGCAAAACAAGA 57.348 29.630 20.46 13.65 40.06 3.02
618 619 9.657419 AGGGATATATTTCTTTTGCAAAACAAG 57.343 29.630 20.46 11.47 40.06 3.16
624 625 8.700973 GGGTAAAGGGATATATTTCTTTTGCAA 58.299 33.333 14.98 0.00 32.53 4.08
625 626 7.841729 TGGGTAAAGGGATATATTTCTTTTGCA 59.158 33.333 14.98 0.00 32.53 4.08
626 627 8.245195 TGGGTAAAGGGATATATTTCTTTTGC 57.755 34.615 14.98 9.92 32.53 3.68
655 656 3.845625 GCACGCAGCACTACTTTTT 57.154 47.368 0.00 0.00 44.79 1.94
670 671 1.457303 CACAACAAGTCGCTCTAGCAC 59.543 52.381 2.44 0.20 42.21 4.40
682 683 1.555477 GTCAAAACGCCCACAACAAG 58.445 50.000 0.00 0.00 0.00 3.16
683 684 0.179161 CGTCAAAACGCCCACAACAA 60.179 50.000 0.00 0.00 42.82 2.83
734 744 6.816140 TGCACAAGACGAACAGAATAATATCA 59.184 34.615 0.00 0.00 0.00 2.15
735 745 7.119997 GTGCACAAGACGAACAGAATAATATC 58.880 38.462 13.17 0.00 0.00 1.63
737 747 5.061684 CGTGCACAAGACGAACAGAATAATA 59.938 40.000 18.64 0.00 39.21 0.98
738 748 4.143115 CGTGCACAAGACGAACAGAATAAT 60.143 41.667 18.64 0.00 39.21 1.28
739 749 3.183574 CGTGCACAAGACGAACAGAATAA 59.816 43.478 18.64 0.00 39.21 1.40
740 750 2.729360 CGTGCACAAGACGAACAGAATA 59.271 45.455 18.64 0.00 39.21 1.75
741 751 1.526887 CGTGCACAAGACGAACAGAAT 59.473 47.619 18.64 0.00 39.21 2.40
745 755 1.087202 AAGCGTGCACAAGACGAACA 61.087 50.000 18.64 0.00 39.21 3.18
746 756 0.654472 CAAGCGTGCACAAGACGAAC 60.654 55.000 18.64 0.00 39.21 3.95
747 757 1.641140 CAAGCGTGCACAAGACGAA 59.359 52.632 18.64 0.00 39.21 3.85
748 758 2.243957 CCAAGCGTGCACAAGACGA 61.244 57.895 18.64 0.00 39.21 4.20
749 759 2.249309 CCAAGCGTGCACAAGACG 59.751 61.111 18.64 3.11 39.87 4.18
750 760 2.050985 GCCAAGCGTGCACAAGAC 60.051 61.111 18.64 2.71 0.00 3.01
783 793 2.045926 ACCATCTCAGCGGCCAAC 60.046 61.111 2.24 0.00 0.00 3.77
791 801 0.757188 AGGCCCTACGACCATCTCAG 60.757 60.000 0.00 0.00 0.00 3.35
794 804 1.411041 GTTAGGCCCTACGACCATCT 58.589 55.000 0.00 0.00 0.00 2.90
796 806 1.397390 CCGTTAGGCCCTACGACCAT 61.397 60.000 24.24 0.00 0.00 3.55
799 809 1.102978 TAACCGTTAGGCCCTACGAC 58.897 55.000 24.24 5.34 42.76 4.34
825 842 4.545823 TTTTTGTTGGCGAGAGTACTTG 57.454 40.909 0.00 0.00 0.00 3.16
844 861 1.616159 AGCGGTACCTGCATGTTTTT 58.384 45.000 24.11 5.40 33.85 1.94
845 862 2.081462 GTAGCGGTACCTGCATGTTTT 58.919 47.619 24.11 10.01 33.85 2.43
848 865 1.141019 CGTAGCGGTACCTGCATGT 59.859 57.895 24.11 11.13 33.85 3.21
878 895 1.366366 CGTCGCCCCGATTAATCCT 59.634 57.895 9.87 0.00 38.42 3.24
1264 1288 2.417933 CAGCAGAGCCTTGTTCATACAC 59.582 50.000 0.00 0.00 32.98 2.90
1301 1352 9.197694 ACACGTATTTTATCTCTGAATGATAGC 57.802 33.333 0.00 0.00 0.00 2.97
1401 1456 3.494336 CGACGTACTCTCCGCCGT 61.494 66.667 0.00 0.00 36.04 5.68
1519 1574 6.706270 TGCAAATCTAGCTAAGCTAATACACC 59.294 38.462 0.00 0.00 40.82 4.16
1604 1661 8.474577 GCTATCAATCAAACTGAAATATTTGCG 58.525 33.333 5.17 0.00 36.06 4.85
1611 1668 8.635328 TGCATATGCTATCAATCAAACTGAAAT 58.365 29.630 27.13 0.00 42.66 2.17
1619 1676 9.902196 CATTAACTTGCATATGCTATCAATCAA 57.098 29.630 27.13 10.45 42.66 2.57
1653 1710 8.235905 GTCGCCTCGGGTATATATATATTCTTC 58.764 40.741 10.48 2.96 0.00 2.87
1656 1713 6.432162 TGGTCGCCTCGGGTATATATATATTC 59.568 42.308 10.48 5.77 0.00 1.75
1659 1716 5.308976 TGGTCGCCTCGGGTATATATATA 57.691 43.478 0.00 0.00 0.00 0.86
1706 1763 6.883217 CAGCTCCTTGTTATATATGCCTCAAT 59.117 38.462 0.00 0.00 0.00 2.57
1713 1770 5.163913 GCGCTTCAGCTCCTTGTTATATATG 60.164 44.000 0.00 0.00 39.32 1.78
1721 1778 2.746359 AGCGCTTCAGCTCCTTGT 59.254 55.556 2.64 0.00 45.67 3.16
1761 2065 4.156008 CGGATCGACAGTATGGATGTATGA 59.844 45.833 0.00 0.00 43.62 2.15
1773 2077 0.603569 AAAGACTGCGGATCGACAGT 59.396 50.000 16.59 16.59 42.87 3.55
1805 2109 8.888579 ACACCACTTTAGCATGTAGTAATATC 57.111 34.615 0.00 0.00 0.00 1.63
1809 2113 7.039574 TCAGTACACCACTTTAGCATGTAGTAA 60.040 37.037 0.00 0.00 34.26 2.24
1810 2114 6.434965 TCAGTACACCACTTTAGCATGTAGTA 59.565 38.462 0.00 0.00 34.26 1.82
1811 2115 5.245301 TCAGTACACCACTTTAGCATGTAGT 59.755 40.000 0.00 0.00 34.26 2.73
1812 2116 5.577164 GTCAGTACACCACTTTAGCATGTAG 59.423 44.000 0.00 0.00 34.26 2.74
1813 2117 5.245301 AGTCAGTACACCACTTTAGCATGTA 59.755 40.000 0.00 0.00 34.26 2.29
1814 2118 4.040461 AGTCAGTACACCACTTTAGCATGT 59.960 41.667 0.00 0.00 34.26 3.21
1815 2119 4.569943 AGTCAGTACACCACTTTAGCATG 58.430 43.478 0.00 0.00 34.26 4.06
1816 2120 4.891992 AGTCAGTACACCACTTTAGCAT 57.108 40.909 0.00 0.00 34.26 3.79
1817 2121 5.794726 TTAGTCAGTACACCACTTTAGCA 57.205 39.130 0.00 0.00 34.26 3.49
1818 2122 6.395629 TCATTAGTCAGTACACCACTTTAGC 58.604 40.000 0.00 0.00 34.26 3.09
1819 2123 7.827701 TCTCATTAGTCAGTACACCACTTTAG 58.172 38.462 0.00 0.00 34.26 1.85
1820 2124 7.770366 TCTCATTAGTCAGTACACCACTTTA 57.230 36.000 0.00 0.00 34.26 1.85
1821 2125 6.665992 TCTCATTAGTCAGTACACCACTTT 57.334 37.500 0.00 0.00 34.26 2.66
1822 2126 6.665992 TTCTCATTAGTCAGTACACCACTT 57.334 37.500 0.00 0.00 34.26 3.16
1832 2136 5.929697 TGCACAACTTTCTCATTAGTCAG 57.070 39.130 0.00 0.00 0.00 3.51
1865 2169 6.655078 ACAATGTTCTCTTAAAAGCCACAT 57.345 33.333 0.00 0.00 0.00 3.21
1914 2218 3.374988 GTGCATACAGCTTTGATGTGCTA 59.625 43.478 0.00 0.00 45.94 3.49
1919 2223 5.404096 TGAAATGTGCATACAGCTTTGATG 58.596 37.500 0.00 0.00 45.94 3.07
1929 2233 6.615088 AGAATGTTGTCTGAAATGTGCATAC 58.385 36.000 0.00 0.00 0.00 2.39
1952 2262 6.591750 TTCTCCCTAGTTGTAGAACTTGAG 57.408 41.667 10.92 13.53 39.56 3.02
1956 2266 4.417437 TGCTTCTCCCTAGTTGTAGAACT 58.583 43.478 10.46 10.46 44.90 3.01
1960 2270 5.305585 TGTTTTGCTTCTCCCTAGTTGTAG 58.694 41.667 0.00 0.00 0.00 2.74
1991 2321 6.477360 TCCGCAAAAAGAAAGTTGGAATAAAC 59.523 34.615 0.00 0.00 0.00 2.01
2006 2336 6.618379 GCTGGAATAAATGTTTCCGCAAAAAG 60.618 38.462 11.58 0.16 44.67 2.27
2083 2415 2.675844 TGCTTGAGTTACACACACACAC 59.324 45.455 0.00 0.00 0.00 3.82
2087 2419 3.248602 CCTCTTGCTTGAGTTACACACAC 59.751 47.826 5.96 0.00 32.50 3.82
2088 2420 3.118408 ACCTCTTGCTTGAGTTACACACA 60.118 43.478 5.96 0.00 32.50 3.72
2089 2421 3.248602 CACCTCTTGCTTGAGTTACACAC 59.751 47.826 5.96 0.00 32.50 3.82
2090 2422 3.118408 ACACCTCTTGCTTGAGTTACACA 60.118 43.478 5.96 0.00 32.50 3.72
2091 2423 3.467803 ACACCTCTTGCTTGAGTTACAC 58.532 45.455 5.96 0.00 32.50 2.90
2092 2424 3.838244 ACACCTCTTGCTTGAGTTACA 57.162 42.857 5.96 0.00 32.50 2.41
2184 2518 8.666573 TCGTGTAAGATGTTTTCTGTTGTTTTA 58.333 29.630 0.00 0.00 33.93 1.52
2190 2524 5.465724 GGTCTCGTGTAAGATGTTTTCTGTT 59.534 40.000 0.00 0.00 33.93 3.16
2193 2527 5.221461 ACAGGTCTCGTGTAAGATGTTTTCT 60.221 40.000 0.00 0.00 35.70 2.52
2377 2711 4.593864 GAGGACGAGCGGGCCATC 62.594 72.222 4.39 0.00 0.00 3.51
2486 2820 2.560504 TGCTTTGCGTTTCTTCTGAGA 58.439 42.857 0.00 0.00 0.00 3.27
2487 2821 3.338818 TTGCTTTGCGTTTCTTCTGAG 57.661 42.857 0.00 0.00 0.00 3.35
2488 2822 3.376859 TCTTTGCTTTGCGTTTCTTCTGA 59.623 39.130 0.00 0.00 0.00 3.27
2489 2823 3.694734 TCTTTGCTTTGCGTTTCTTCTG 58.305 40.909 0.00 0.00 0.00 3.02
2490 2824 4.370364 TTCTTTGCTTTGCGTTTCTTCT 57.630 36.364 0.00 0.00 0.00 2.85
2491 2825 4.798387 TCTTTCTTTGCTTTGCGTTTCTTC 59.202 37.500 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.