Multiple sequence alignment - TraesCS1B01G418700

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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 TraesCS1B01G418700 chr1B 100.000 2885 0 0 1 2885 642490679 642487795 0.000000e+00 5328.0
1 TraesCS1B01G418700 chr1B 80.982 1588 273 21 106 1686 642597916 642599481 0.000000e+00 1232.0
2 TraesCS1B01G418700 chr1B 73.317 416 103 7 530 941 531006159 531005748 2.320000e-31 147.0
3 TraesCS1B01G418700 chr1D 93.224 2066 101 8 106 2160 465552167 465550130 0.000000e+00 3003.0
4 TraesCS1B01G418700 chr1D 94.118 102 6 0 2 103 465567917 465567816 3.850000e-34 156.0
5 TraesCS1B01G418700 chr1A 93.822 1748 93 4 2 1737 557976859 557975115 0.000000e+00 2615.0
6 TraesCS1B01G418700 chr1A 80.547 1609 269 32 106 1686 558032108 558033700 0.000000e+00 1197.0
7 TraesCS1B01G418700 chr1A 91.377 835 40 15 1736 2542 557968029 557967199 0.000000e+00 1114.0
8 TraesCS1B01G418700 chr1A 90.244 82 8 0 1758 1839 558033736 558033817 1.090000e-19 108.0
9 TraesCS1B01G418700 chr1A 97.561 41 1 0 2539 2579 557966246 557966206 1.430000e-08 71.3
10 TraesCS1B01G418700 chr5B 75.181 415 97 6 530 941 26305647 26305236 1.060000e-44 191.0
11 TraesCS1B01G418700 chr3A 74.185 368 89 5 578 941 621846429 621846064 6.440000e-32 148.0
12 TraesCS1B01G418700 chr3B 73.494 415 98 10 530 941 638311733 638311328 2.320000e-31 147.0
13 TraesCS1B01G418700 chrUn 80.531 113 22 0 829 941 477970298 477970410 1.420000e-13 87.9


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 TraesCS1B01G418700 chr1B 642487795 642490679 2884 True 5328.00 5328 100.0000 1 2885 1 chr1B.!!$R2 2884
1 TraesCS1B01G418700 chr1B 642597916 642599481 1565 False 1232.00 1232 80.9820 106 1686 1 chr1B.!!$F1 1580
2 TraesCS1B01G418700 chr1D 465550130 465552167 2037 True 3003.00 3003 93.2240 106 2160 1 chr1D.!!$R1 2054
3 TraesCS1B01G418700 chr1A 557975115 557976859 1744 True 2615.00 2615 93.8220 2 1737 1 chr1A.!!$R1 1735
4 TraesCS1B01G418700 chr1A 558032108 558033817 1709 False 652.50 1197 85.3955 106 1839 2 chr1A.!!$F1 1733
5 TraesCS1B01G418700 chr1A 557966206 557968029 1823 True 592.65 1114 94.4690 1736 2579 2 chr1A.!!$R2 843

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
70 71 0.107214 GGATGGATTTCTGCCACCGA 60.107 55.0 0.0 0.0 38.44 4.69 F
1532 1585 0.107017 TCAGGCTATTCCCTTGCAGC 60.107 55.0 0.0 0.0 31.24 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1896 0.110486 AAACCCCATGAACTCTGCGT 59.89 50.0 0.00 0.0 0.00 5.24 R
2741 3780 0.239879 CAAGGCAACCGCGTGTTATT 59.76 50.0 4.92 2.7 39.92 1.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.499696 GCCATTATAACAGCAACATGGACC 60.500 45.833 0.00 0.00 34.21 4.46
34 35 2.817839 GCAACATGGACCCAAGGTAAGT 60.818 50.000 0.00 0.00 35.25 2.24
36 37 3.154827 ACATGGACCCAAGGTAAGTTG 57.845 47.619 0.00 0.00 35.25 3.16
39 40 0.958876 GGACCCAAGGTAAGTTGCCG 60.959 60.000 4.17 0.00 35.25 5.69
70 71 0.107214 GGATGGATTTCTGCCACCGA 60.107 55.000 0.00 0.00 38.44 4.69
75 76 3.476552 TGGATTTCTGCCACCGATATTC 58.523 45.455 0.00 0.00 0.00 1.75
103 104 4.887071 ACGGATTTCTGCATTGGCTTATTA 59.113 37.500 0.00 0.00 41.91 0.98
104 105 5.536161 ACGGATTTCTGCATTGGCTTATTAT 59.464 36.000 0.00 0.00 41.91 1.28
192 205 1.812686 TTGAGGAACCACGACCCGAG 61.813 60.000 0.00 0.00 0.00 4.63
287 306 3.951037 GAGATCTGGAACTACAGCTCTGA 59.049 47.826 0.00 0.00 42.25 3.27
327 349 0.526096 GCATTGATTTGTCGCGGCAT 60.526 50.000 16.97 0.00 0.00 4.40
355 377 2.483889 GGAGATTCTTTGCTAGGTCCGG 60.484 54.545 0.00 0.00 0.00 5.14
356 378 2.168728 GAGATTCTTTGCTAGGTCCGGT 59.831 50.000 0.00 0.00 0.00 5.28
377 399 4.926238 GGTGATTATCAGAGCTATCGGTTG 59.074 45.833 0.00 0.00 0.00 3.77
402 424 2.567049 GACTGTGGACCGACGGAG 59.433 66.667 23.38 9.60 0.00 4.63
510 549 6.198591 CGGAGACTTCATTTTATAAGACCGAC 59.801 42.308 0.00 0.00 38.39 4.79
511 550 6.198591 GGAGACTTCATTTTATAAGACCGACG 59.801 42.308 0.00 0.00 0.00 5.12
512 551 6.860080 AGACTTCATTTTATAAGACCGACGA 58.140 36.000 0.00 0.00 0.00 4.20
742 787 3.708890 CATGCGCATAACAACATGGATT 58.291 40.909 24.84 0.00 36.98 3.01
768 813 2.758009 CCAAAAGTCATGCTTGTTGGG 58.242 47.619 20.39 11.35 39.24 4.12
840 891 1.972660 GCGATGGTCCTAGCCAAGGT 61.973 60.000 2.79 0.00 46.62 3.50
894 945 2.422803 GCCTTGCCATGGTATGAACCTA 60.423 50.000 14.67 0.00 46.91 3.08
1077 1130 2.999185 ATGTTGGTCTGGGGTTCAAT 57.001 45.000 0.00 0.00 0.00 2.57
1104 1157 2.831685 AACAGGAGCATGTTGTCGTA 57.168 45.000 0.00 0.00 41.76 3.43
1105 1158 2.370281 ACAGGAGCATGTTGTCGTAG 57.630 50.000 0.00 0.00 0.00 3.51
1434 1487 2.892425 GCGGTCCTTGCAGATCCG 60.892 66.667 14.25 14.25 43.37 4.18
1438 1491 1.596934 GTCCTTGCAGATCCGGTCA 59.403 57.895 0.00 0.00 0.00 4.02
1473 1526 0.405198 TTTGGAAGCTGGAGCATGGA 59.595 50.000 0.65 0.00 45.16 3.41
1474 1527 0.405198 TTGGAAGCTGGAGCATGGAA 59.595 50.000 0.65 0.00 45.16 3.53
1475 1528 0.627451 TGGAAGCTGGAGCATGGAAT 59.373 50.000 0.65 0.00 45.16 3.01
1480 1533 0.182061 GCTGGAGCATGGAATCTGGA 59.818 55.000 0.00 0.00 41.59 3.86
1532 1585 0.107017 TCAGGCTATTCCCTTGCAGC 60.107 55.000 0.00 0.00 31.24 5.25
1537 1590 1.545582 GCTATTCCCTTGCAGCAAACA 59.454 47.619 9.65 0.00 34.13 2.83
1582 1635 3.393089 CCAGAGACGGGAGAATATTGG 57.607 52.381 0.00 0.00 0.00 3.16
1602 1655 3.118334 TGGTCAACACGGGAAGAAAACTA 60.118 43.478 0.00 0.00 0.00 2.24
1628 1681 2.395988 TATGATCCGGCAAGGCGCAT 62.396 55.000 10.83 0.00 45.17 4.73
1636 1689 1.065273 GCAAGGCGCATGATTGAGG 59.935 57.895 10.83 0.00 41.79 3.86
1723 1776 4.875536 TGAATCAAGATGGACACATTACGG 59.124 41.667 0.00 0.00 37.47 4.02
1756 1809 6.934083 ACAATCTTTCAAAAAGTGTGTGGTTT 59.066 30.769 8.76 0.00 0.00 3.27
1843 1896 3.961408 GAGTCTGGCAAGTTATCCTCCTA 59.039 47.826 0.00 0.00 0.00 2.94
1866 1919 1.542915 CAGAGTTCATGGGGTTTGCAG 59.457 52.381 0.00 0.00 0.00 4.41
1873 1926 1.617850 CATGGGGTTTGCAGCAGTTAA 59.382 47.619 0.00 0.00 0.00 2.01
1877 1930 2.562738 GGGGTTTGCAGCAGTTAAATCT 59.437 45.455 0.00 0.00 0.00 2.40
1885 1938 4.994852 TGCAGCAGTTAAATCTTCGTTAGT 59.005 37.500 0.00 0.00 0.00 2.24
1984 2039 8.506168 TGCTCCCTTAGTTTGTTTGAATATAG 57.494 34.615 0.00 0.00 0.00 1.31
2138 2194 2.292292 CGACAGGTGAAAACGGGATTTT 59.708 45.455 0.00 0.00 43.44 1.82
2160 2216 8.483743 TTTTAGTGAAAATCTTAAAACTCGCG 57.516 30.769 0.00 0.00 29.38 5.87
2161 2217 5.030874 AGTGAAAATCTTAAAACTCGCGG 57.969 39.130 6.13 0.00 0.00 6.46
2162 2218 4.753107 AGTGAAAATCTTAAAACTCGCGGA 59.247 37.500 6.13 0.00 0.00 5.54
2163 2219 5.080068 GTGAAAATCTTAAAACTCGCGGAG 58.920 41.667 6.13 5.03 35.52 4.63
2164 2220 4.153475 TGAAAATCTTAAAACTCGCGGAGG 59.847 41.667 6.13 0.00 33.35 4.30
2165 2221 3.604875 AATCTTAAAACTCGCGGAGGA 57.395 42.857 6.13 0.00 33.35 3.71
2166 2222 2.358939 TCTTAAAACTCGCGGAGGAC 57.641 50.000 6.13 0.00 33.35 3.85
2167 2223 1.891150 TCTTAAAACTCGCGGAGGACT 59.109 47.619 6.13 0.00 33.35 3.85
2168 2224 1.993370 CTTAAAACTCGCGGAGGACTG 59.007 52.381 6.13 0.00 33.35 3.51
2169 2225 0.963962 TAAAACTCGCGGAGGACTGT 59.036 50.000 6.13 0.00 33.35 3.55
2170 2226 0.600255 AAAACTCGCGGAGGACTGTG 60.600 55.000 6.13 0.00 33.35 3.66
2171 2227 2.436087 AAACTCGCGGAGGACTGTGG 62.436 60.000 6.13 0.00 33.35 4.17
2172 2228 4.803426 CTCGCGGAGGACTGTGGC 62.803 72.222 6.13 0.00 34.10 5.01
2201 2281 2.224793 GGACAAAAGTTGAGGTAGGGCT 60.225 50.000 0.00 0.00 0.00 5.19
2224 2305 3.605749 TTAGCCACTCGCCACCAGC 62.606 63.158 0.00 0.00 38.78 4.85
2254 2335 4.785453 CCGCCTTCCACCCTGCTC 62.785 72.222 0.00 0.00 0.00 4.26
2271 2353 1.304630 TCCACCGGACGGATCAAGA 60.305 57.895 18.80 3.58 38.96 3.02
2276 2358 1.329256 CCGGACGGATCAAGATAGGT 58.671 55.000 4.40 0.00 37.50 3.08
2300 2382 1.021390 CGCCAACCCTTGCTCTACTG 61.021 60.000 0.00 0.00 0.00 2.74
2308 2390 0.827368 CTTGCTCTACTGGGTCCTCC 59.173 60.000 0.00 0.00 0.00 4.30
2313 2395 0.323178 TCTACTGGGTCCTCCGTCAC 60.323 60.000 0.00 0.00 38.76 3.67
2320 2402 1.911766 GTCCTCCGTCACTGGGGAA 60.912 63.158 0.00 0.00 32.39 3.97
2358 2440 2.029020 TCGGGTTCAGACTGTCATTCTG 60.029 50.000 12.79 12.79 41.72 3.02
2374 2456 7.307694 TGTCATTCTGATACAATGCAAACTTC 58.692 34.615 0.00 0.00 32.17 3.01
2377 2459 3.689161 TCTGATACAATGCAAACTTCGGG 59.311 43.478 0.00 0.00 0.00 5.14
2378 2460 2.752354 TGATACAATGCAAACTTCGGGG 59.248 45.455 0.00 0.00 0.00 5.73
2379 2461 2.570415 TACAATGCAAACTTCGGGGA 57.430 45.000 0.00 0.00 0.00 4.81
2426 2508 7.934855 AACAAATGAGATGACAAGCTATCTT 57.065 32.000 0.00 0.00 33.97 2.40
2508 2590 4.464951 TGGAGCATCAGAAGCAATGAATTT 59.535 37.500 0.00 0.00 36.25 1.82
2523 2605 9.932207 AGCAATGAATTTGAAAGACAATGATAA 57.068 25.926 6.44 0.00 37.53 1.75
2533 2615 7.988737 TGAAAGACAATGATAATGCTTGGTAG 58.011 34.615 0.00 0.00 0.00 3.18
2575 3614 8.387190 ACTACAAGGTGTTTGGTAAATACTTC 57.613 34.615 0.00 0.00 41.25 3.01
2579 3618 7.340999 ACAAGGTGTTTGGTAAATACTTCAAGT 59.659 33.333 0.00 0.00 41.25 3.16
2580 3619 7.891498 AGGTGTTTGGTAAATACTTCAAGTT 57.109 32.000 0.00 0.00 33.58 2.66
2581 3620 7.712797 AGGTGTTTGGTAAATACTTCAAGTTG 58.287 34.615 0.00 0.00 33.58 3.16
2582 3621 6.419710 GGTGTTTGGTAAATACTTCAAGTTGC 59.580 38.462 0.00 0.00 33.58 4.17
2583 3622 6.975772 GTGTTTGGTAAATACTTCAAGTTGCA 59.024 34.615 0.00 0.00 30.81 4.08
2584 3623 7.489757 GTGTTTGGTAAATACTTCAAGTTGCAA 59.510 33.333 0.00 0.00 30.81 4.08
2585 3624 7.704472 TGTTTGGTAAATACTTCAAGTTGCAAG 59.296 33.333 0.00 5.85 0.00 4.01
2586 3625 6.325919 TGGTAAATACTTCAAGTTGCAAGG 57.674 37.500 0.00 0.00 0.00 3.61
2587 3626 6.065374 TGGTAAATACTTCAAGTTGCAAGGA 58.935 36.000 0.00 9.81 0.00 3.36
2588 3627 6.547880 TGGTAAATACTTCAAGTTGCAAGGAA 59.452 34.615 0.00 3.62 0.00 3.36
2589 3628 6.861572 GGTAAATACTTCAAGTTGCAAGGAAC 59.138 38.462 0.00 0.00 0.00 3.62
2590 3629 6.463995 AAATACTTCAAGTTGCAAGGAACA 57.536 33.333 0.00 0.00 0.00 3.18
2591 3630 5.695851 ATACTTCAAGTTGCAAGGAACAG 57.304 39.130 0.00 0.00 0.00 3.16
2592 3631 2.689983 ACTTCAAGTTGCAAGGAACAGG 59.310 45.455 0.00 0.00 0.00 4.00
2593 3632 2.435372 TCAAGTTGCAAGGAACAGGT 57.565 45.000 0.00 0.00 0.00 4.00
2594 3633 2.733956 TCAAGTTGCAAGGAACAGGTT 58.266 42.857 0.00 0.00 0.00 3.50
2595 3634 2.687935 TCAAGTTGCAAGGAACAGGTTC 59.312 45.455 0.00 3.58 38.80 3.62
2596 3635 1.308998 AGTTGCAAGGAACAGGTTCG 58.691 50.000 0.00 0.00 40.37 3.95
2597 3636 0.310854 GTTGCAAGGAACAGGTTCGG 59.689 55.000 0.00 0.53 40.37 4.30
2598 3637 0.821711 TTGCAAGGAACAGGTTCGGG 60.822 55.000 0.00 0.22 40.37 5.14
2599 3638 2.626780 GCAAGGAACAGGTTCGGGC 61.627 63.158 6.12 5.97 40.37 6.13
2600 3639 1.073199 CAAGGAACAGGTTCGGGCT 59.927 57.895 6.12 0.00 40.37 5.19
2601 3640 0.323629 CAAGGAACAGGTTCGGGCTA 59.676 55.000 6.12 0.00 40.37 3.93
2602 3641 0.323957 AAGGAACAGGTTCGGGCTAC 59.676 55.000 6.12 0.00 40.37 3.58
2603 3642 0.834687 AGGAACAGGTTCGGGCTACA 60.835 55.000 6.12 0.00 40.37 2.74
2604 3643 0.252197 GGAACAGGTTCGGGCTACAT 59.748 55.000 6.12 0.00 40.37 2.29
2605 3644 1.483415 GGAACAGGTTCGGGCTACATA 59.517 52.381 6.12 0.00 40.37 2.29
2606 3645 2.093341 GGAACAGGTTCGGGCTACATAA 60.093 50.000 6.12 0.00 40.37 1.90
2607 3646 2.981859 ACAGGTTCGGGCTACATAAG 57.018 50.000 0.00 0.00 0.00 1.73
2608 3647 2.463752 ACAGGTTCGGGCTACATAAGA 58.536 47.619 0.00 0.00 0.00 2.10
2609 3648 2.835764 ACAGGTTCGGGCTACATAAGAA 59.164 45.455 0.00 0.00 0.00 2.52
2610 3649 3.118738 ACAGGTTCGGGCTACATAAGAAG 60.119 47.826 0.00 0.00 0.00 2.85
2611 3650 3.132289 CAGGTTCGGGCTACATAAGAAGA 59.868 47.826 0.00 0.00 0.00 2.87
2612 3651 3.132467 AGGTTCGGGCTACATAAGAAGAC 59.868 47.826 0.00 0.00 0.00 3.01
2613 3652 3.118884 GGTTCGGGCTACATAAGAAGACA 60.119 47.826 0.00 0.00 0.00 3.41
2614 3653 4.443034 GGTTCGGGCTACATAAGAAGACAT 60.443 45.833 0.00 0.00 0.00 3.06
2615 3654 4.585955 TCGGGCTACATAAGAAGACATC 57.414 45.455 0.00 0.00 0.00 3.06
2616 3655 4.215908 TCGGGCTACATAAGAAGACATCT 58.784 43.478 0.00 0.00 41.32 2.90
2617 3656 4.278669 TCGGGCTACATAAGAAGACATCTC 59.721 45.833 0.00 0.00 37.42 2.75
2618 3657 4.279671 CGGGCTACATAAGAAGACATCTCT 59.720 45.833 0.00 0.00 37.42 3.10
2619 3658 5.563867 CGGGCTACATAAGAAGACATCTCTC 60.564 48.000 0.00 0.00 37.42 3.20
2620 3659 5.303078 GGGCTACATAAGAAGACATCTCTCA 59.697 44.000 0.00 0.00 37.42 3.27
2621 3660 6.446318 GGCTACATAAGAAGACATCTCTCAG 58.554 44.000 0.00 0.00 37.42 3.35
2622 3661 6.264292 GGCTACATAAGAAGACATCTCTCAGA 59.736 42.308 0.00 0.00 37.42 3.27
2623 3662 7.201866 GGCTACATAAGAAGACATCTCTCAGAA 60.202 40.741 0.00 0.00 37.42 3.02
2624 3663 7.862372 GCTACATAAGAAGACATCTCTCAGAAG 59.138 40.741 0.00 0.00 37.42 2.85
2625 3664 7.716799 ACATAAGAAGACATCTCTCAGAAGT 57.283 36.000 0.00 0.00 37.42 3.01
2626 3665 8.815565 ACATAAGAAGACATCTCTCAGAAGTA 57.184 34.615 0.00 0.00 37.42 2.24
2627 3666 8.682710 ACATAAGAAGACATCTCTCAGAAGTAC 58.317 37.037 0.00 0.00 37.42 2.73
2628 3667 8.681806 CATAAGAAGACATCTCTCAGAAGTACA 58.318 37.037 0.00 0.00 37.42 2.90
2629 3668 7.531857 AAGAAGACATCTCTCAGAAGTACAA 57.468 36.000 0.00 0.00 37.42 2.41
2630 3669 7.531857 AGAAGACATCTCTCAGAAGTACAAA 57.468 36.000 0.00 0.00 30.46 2.83
2631 3670 7.957002 AGAAGACATCTCTCAGAAGTACAAAA 58.043 34.615 0.00 0.00 30.46 2.44
2632 3671 8.592809 AGAAGACATCTCTCAGAAGTACAAAAT 58.407 33.333 0.00 0.00 30.46 1.82
2633 3672 9.213799 GAAGACATCTCTCAGAAGTACAAAATT 57.786 33.333 0.00 0.00 0.00 1.82
2634 3673 8.770438 AGACATCTCTCAGAAGTACAAAATTC 57.230 34.615 0.00 0.00 0.00 2.17
2635 3674 8.370940 AGACATCTCTCAGAAGTACAAAATTCA 58.629 33.333 0.00 0.00 0.00 2.57
2636 3675 8.545229 ACATCTCTCAGAAGTACAAAATTCAG 57.455 34.615 0.00 0.00 0.00 3.02
2637 3676 8.370940 ACATCTCTCAGAAGTACAAAATTCAGA 58.629 33.333 0.00 0.00 0.00 3.27
2638 3677 9.212641 CATCTCTCAGAAGTACAAAATTCAGAA 57.787 33.333 0.00 0.00 0.00 3.02
2639 3678 9.784531 ATCTCTCAGAAGTACAAAATTCAGAAA 57.215 29.630 0.00 0.00 0.00 2.52
2640 3679 9.784531 TCTCTCAGAAGTACAAAATTCAGAAAT 57.215 29.630 0.00 0.00 0.00 2.17
2641 3680 9.823098 CTCTCAGAAGTACAAAATTCAGAAATG 57.177 33.333 0.00 0.00 0.00 2.32
2642 3681 9.342308 TCTCAGAAGTACAAAATTCAGAAATGT 57.658 29.630 0.00 5.31 0.00 2.71
2673 3712 7.790823 TTAGTAATCCAAGTAAAATACCGGC 57.209 36.000 0.00 0.00 0.00 6.13
2674 3713 5.747342 AGTAATCCAAGTAAAATACCGGCA 58.253 37.500 0.00 0.00 0.00 5.69
2675 3714 4.976224 AATCCAAGTAAAATACCGGCAC 57.024 40.909 0.00 0.00 0.00 5.01
2676 3715 3.420300 TCCAAGTAAAATACCGGCACA 57.580 42.857 0.00 0.00 0.00 4.57
2677 3716 3.752665 TCCAAGTAAAATACCGGCACAA 58.247 40.909 0.00 0.00 0.00 3.33
2678 3717 3.754323 TCCAAGTAAAATACCGGCACAAG 59.246 43.478 0.00 0.00 0.00 3.16
2679 3718 3.498082 CAAGTAAAATACCGGCACAAGC 58.502 45.455 0.00 0.00 41.10 4.01
2693 3732 4.439305 GCACAAGCCAGTAATGAATGAA 57.561 40.909 0.00 0.00 33.58 2.57
2694 3733 4.168760 GCACAAGCCAGTAATGAATGAAC 58.831 43.478 0.00 0.00 33.58 3.18
2695 3734 4.082571 GCACAAGCCAGTAATGAATGAACT 60.083 41.667 0.00 0.00 33.58 3.01
2696 3735 5.565439 GCACAAGCCAGTAATGAATGAACTT 60.565 40.000 0.00 0.00 33.58 2.66
2697 3736 6.088824 CACAAGCCAGTAATGAATGAACTTC 58.911 40.000 0.00 0.00 0.00 3.01
2698 3737 9.594093 GCACAAGCCAGTAATGAATGAACTTCA 62.594 40.741 0.00 0.00 40.63 3.02
2699 3738 6.265196 ACAAGCCAGTAATGAATGAACTTCAA 59.735 34.615 0.00 0.00 46.62 2.69
2700 3739 6.506500 AGCCAGTAATGAATGAACTTCAAG 57.493 37.500 0.00 0.00 46.62 3.02
2701 3740 5.098211 GCCAGTAATGAATGAACTTCAAGC 58.902 41.667 0.00 0.00 46.62 4.01
2702 3741 5.105997 GCCAGTAATGAATGAACTTCAAGCT 60.106 40.000 0.00 0.00 46.62 3.74
2703 3742 6.549952 CCAGTAATGAATGAACTTCAAGCTC 58.450 40.000 0.00 0.00 46.62 4.09
2704 3743 6.404074 CCAGTAATGAATGAACTTCAAGCTCC 60.404 42.308 0.00 0.00 46.62 4.70
2705 3744 5.649831 AGTAATGAATGAACTTCAAGCTCCC 59.350 40.000 0.00 0.00 46.62 4.30
2706 3745 3.507162 TGAATGAACTTCAAGCTCCCA 57.493 42.857 0.00 0.00 40.92 4.37
2707 3746 3.415212 TGAATGAACTTCAAGCTCCCAG 58.585 45.455 0.00 0.00 40.92 4.45
2708 3747 3.181440 TGAATGAACTTCAAGCTCCCAGT 60.181 43.478 0.00 0.00 40.92 4.00
2709 3748 4.041567 TGAATGAACTTCAAGCTCCCAGTA 59.958 41.667 0.00 0.00 40.92 2.74
2710 3749 3.685139 TGAACTTCAAGCTCCCAGTAG 57.315 47.619 0.00 0.00 0.00 2.57
2711 3750 2.289694 TGAACTTCAAGCTCCCAGTAGC 60.290 50.000 0.00 0.00 43.11 3.58
2722 3761 5.897377 GCTCCCAGTAGCTTTGAATTTAA 57.103 39.130 0.00 0.00 39.50 1.52
2723 3762 6.456795 GCTCCCAGTAGCTTTGAATTTAAT 57.543 37.500 0.00 0.00 39.50 1.40
2724 3763 6.499172 GCTCCCAGTAGCTTTGAATTTAATC 58.501 40.000 0.00 0.00 39.50 1.75
2725 3764 6.319911 GCTCCCAGTAGCTTTGAATTTAATCT 59.680 38.462 0.00 0.00 39.50 2.40
2726 3765 7.148000 GCTCCCAGTAGCTTTGAATTTAATCTT 60.148 37.037 0.00 0.00 39.50 2.40
2727 3766 8.055279 TCCCAGTAGCTTTGAATTTAATCTTG 57.945 34.615 0.00 0.00 0.00 3.02
2728 3767 7.669722 TCCCAGTAGCTTTGAATTTAATCTTGT 59.330 33.333 0.00 0.00 0.00 3.16
2729 3768 7.756722 CCCAGTAGCTTTGAATTTAATCTTGTG 59.243 37.037 0.00 0.00 0.00 3.33
2730 3769 7.274250 CCAGTAGCTTTGAATTTAATCTTGTGC 59.726 37.037 0.00 0.00 0.00 4.57
2731 3770 8.025445 CAGTAGCTTTGAATTTAATCTTGTGCT 58.975 33.333 0.00 0.00 0.00 4.40
2732 3771 9.231297 AGTAGCTTTGAATTTAATCTTGTGCTA 57.769 29.630 0.00 0.00 0.00 3.49
2733 3772 9.278734 GTAGCTTTGAATTTAATCTTGTGCTAC 57.721 33.333 0.00 0.00 40.30 3.58
2734 3773 7.315890 AGCTTTGAATTTAATCTTGTGCTACC 58.684 34.615 0.00 0.00 0.00 3.18
2735 3774 6.531594 GCTTTGAATTTAATCTTGTGCTACCC 59.468 38.462 0.00 0.00 0.00 3.69
2736 3775 7.531857 TTTGAATTTAATCTTGTGCTACCCA 57.468 32.000 0.00 0.00 0.00 4.51
2737 3776 7.531857 TTGAATTTAATCTTGTGCTACCCAA 57.468 32.000 0.00 0.00 0.00 4.12
2738 3777 7.531857 TGAATTTAATCTTGTGCTACCCAAA 57.468 32.000 0.00 0.00 0.00 3.28
2739 3778 7.957002 TGAATTTAATCTTGTGCTACCCAAAA 58.043 30.769 0.00 0.00 0.00 2.44
2740 3779 8.592809 TGAATTTAATCTTGTGCTACCCAAAAT 58.407 29.630 0.00 0.00 0.00 1.82
2747 3786 8.588290 ATCTTGTGCTACCCAAAATAATAACA 57.412 30.769 0.00 0.00 0.00 2.41
2748 3787 7.822658 TCTTGTGCTACCCAAAATAATAACAC 58.177 34.615 0.00 0.00 0.00 3.32
2749 3788 6.184580 TGTGCTACCCAAAATAATAACACG 57.815 37.500 0.00 0.00 0.00 4.49
2750 3789 5.032220 GTGCTACCCAAAATAATAACACGC 58.968 41.667 0.00 0.00 0.00 5.34
2751 3790 4.201832 TGCTACCCAAAATAATAACACGCG 60.202 41.667 3.53 3.53 0.00 6.01
2752 3791 3.768468 ACCCAAAATAATAACACGCGG 57.232 42.857 12.47 1.27 0.00 6.46
2753 3792 3.083293 ACCCAAAATAATAACACGCGGT 58.917 40.909 12.47 2.05 0.00 5.68
2754 3793 3.506844 ACCCAAAATAATAACACGCGGTT 59.493 39.130 12.47 14.39 43.62 4.44
2755 3794 3.854809 CCCAAAATAATAACACGCGGTTG 59.145 43.478 12.47 2.37 40.73 3.77
2756 3795 3.302170 CCAAAATAATAACACGCGGTTGC 59.698 43.478 12.47 0.00 40.73 4.17
2757 3796 2.836479 AATAATAACACGCGGTTGCC 57.164 45.000 12.47 0.00 40.73 4.52
2758 3797 2.032680 ATAATAACACGCGGTTGCCT 57.967 45.000 12.47 3.95 40.73 4.75
2759 3798 1.810959 TAATAACACGCGGTTGCCTT 58.189 45.000 12.47 9.72 40.73 4.35
2760 3799 0.239879 AATAACACGCGGTTGCCTTG 59.760 50.000 12.47 0.00 40.73 3.61
2761 3800 0.604243 ATAACACGCGGTTGCCTTGA 60.604 50.000 12.47 0.00 40.73 3.02
2762 3801 0.814410 TAACACGCGGTTGCCTTGAA 60.814 50.000 12.47 0.00 40.73 2.69
2763 3802 1.452145 AACACGCGGTTGCCTTGAAT 61.452 50.000 12.47 0.00 38.60 2.57
2764 3803 1.154225 CACGCGGTTGCCTTGAATC 60.154 57.895 12.47 0.00 38.08 2.52
2765 3804 2.098298 CGCGGTTGCCTTGAATCG 59.902 61.111 0.00 0.00 38.08 3.34
2766 3805 2.387445 CGCGGTTGCCTTGAATCGA 61.387 57.895 0.00 0.00 38.08 3.59
2767 3806 1.873165 GCGGTTGCCTTGAATCGAA 59.127 52.632 0.00 0.00 30.69 3.71
2768 3807 0.239879 GCGGTTGCCTTGAATCGAAA 59.760 50.000 0.00 0.00 30.69 3.46
2769 3808 1.135402 GCGGTTGCCTTGAATCGAAAT 60.135 47.619 0.00 0.00 30.69 2.17
2770 3809 2.096819 GCGGTTGCCTTGAATCGAAATA 59.903 45.455 0.00 0.00 30.69 1.40
2771 3810 3.426963 GCGGTTGCCTTGAATCGAAATAA 60.427 43.478 0.00 0.00 30.69 1.40
2772 3811 4.728534 CGGTTGCCTTGAATCGAAATAAA 58.271 39.130 0.00 0.00 30.69 1.40
2773 3812 5.157781 CGGTTGCCTTGAATCGAAATAAAA 58.842 37.500 0.00 0.00 30.69 1.52
2774 3813 5.286082 CGGTTGCCTTGAATCGAAATAAAAG 59.714 40.000 0.00 0.00 30.69 2.27
2775 3814 6.386654 GGTTGCCTTGAATCGAAATAAAAGA 58.613 36.000 0.00 0.00 0.00 2.52
2776 3815 6.866248 GGTTGCCTTGAATCGAAATAAAAGAA 59.134 34.615 0.00 0.00 0.00 2.52
2777 3816 7.148804 GGTTGCCTTGAATCGAAATAAAAGAAC 60.149 37.037 0.00 0.00 0.00 3.01
2778 3817 6.386654 TGCCTTGAATCGAAATAAAAGAACC 58.613 36.000 0.00 0.00 0.00 3.62
2779 3818 6.208599 TGCCTTGAATCGAAATAAAAGAACCT 59.791 34.615 0.00 0.00 0.00 3.50
2780 3819 6.528072 GCCTTGAATCGAAATAAAAGAACCTG 59.472 38.462 0.00 0.00 0.00 4.00
2781 3820 6.528072 CCTTGAATCGAAATAAAAGAACCTGC 59.472 38.462 0.00 0.00 0.00 4.85
2782 3821 5.627172 TGAATCGAAATAAAAGAACCTGCG 58.373 37.500 0.00 0.00 0.00 5.18
2783 3822 4.616181 ATCGAAATAAAAGAACCTGCGG 57.384 40.909 0.00 0.00 0.00 5.69
2784 3823 2.745281 TCGAAATAAAAGAACCTGCGGG 59.255 45.455 11.02 11.02 38.88 6.13
2786 3825 3.685756 CGAAATAAAAGAACCTGCGGGTA 59.314 43.478 20.05 0.19 46.67 3.69
2787 3826 4.154556 CGAAATAAAAGAACCTGCGGGTAA 59.845 41.667 20.05 0.00 46.67 2.85
2788 3827 5.335035 CGAAATAAAAGAACCTGCGGGTAAA 60.335 40.000 20.05 0.10 46.67 2.01
2789 3828 5.381174 AATAAAAGAACCTGCGGGTAAAC 57.619 39.130 20.05 12.71 46.67 2.01
2790 3829 2.351706 AAAGAACCTGCGGGTAAACA 57.648 45.000 20.05 0.00 46.67 2.83
2791 3830 2.351706 AAGAACCTGCGGGTAAACAA 57.648 45.000 20.05 0.00 46.67 2.83
2792 3831 1.601166 AGAACCTGCGGGTAAACAAC 58.399 50.000 20.05 5.80 46.67 3.32
2793 3832 1.142262 AGAACCTGCGGGTAAACAACT 59.858 47.619 20.05 0.00 46.67 3.16
2794 3833 2.369532 AGAACCTGCGGGTAAACAACTA 59.630 45.455 20.05 0.00 46.67 2.24
2795 3834 2.934886 ACCTGCGGGTAAACAACTAA 57.065 45.000 18.00 0.00 45.32 2.24
2796 3835 3.428413 ACCTGCGGGTAAACAACTAAT 57.572 42.857 18.00 0.00 45.32 1.73
2797 3836 4.556592 ACCTGCGGGTAAACAACTAATA 57.443 40.909 18.00 0.00 45.32 0.98
2798 3837 4.909001 ACCTGCGGGTAAACAACTAATAA 58.091 39.130 18.00 0.00 45.32 1.40
2799 3838 5.315348 ACCTGCGGGTAAACAACTAATAAA 58.685 37.500 18.00 0.00 45.32 1.40
2800 3839 5.181811 ACCTGCGGGTAAACAACTAATAAAC 59.818 40.000 18.00 0.00 45.32 2.01
2801 3840 5.181622 CCTGCGGGTAAACAACTAATAAACA 59.818 40.000 2.29 0.00 0.00 2.83
2802 3841 6.127842 CCTGCGGGTAAACAACTAATAAACAT 60.128 38.462 2.29 0.00 0.00 2.71
2803 3842 6.613233 TGCGGGTAAACAACTAATAAACATG 58.387 36.000 0.00 0.00 0.00 3.21
2804 3843 6.031471 GCGGGTAAACAACTAATAAACATGG 58.969 40.000 0.00 0.00 0.00 3.66
2805 3844 6.127952 GCGGGTAAACAACTAATAAACATGGA 60.128 38.462 0.00 0.00 0.00 3.41
2806 3845 7.575343 GCGGGTAAACAACTAATAAACATGGAA 60.575 37.037 0.00 0.00 0.00 3.53
2807 3846 8.298140 CGGGTAAACAACTAATAAACATGGAAA 58.702 33.333 0.00 0.00 0.00 3.13
2808 3847 9.984190 GGGTAAACAACTAATAAACATGGAAAA 57.016 29.630 0.00 0.00 0.00 2.29
2829 3868 6.909550 AAAAACACTTAGAATGGGCATACA 57.090 33.333 0.00 0.00 0.00 2.29
2830 3869 6.909550 AAAACACTTAGAATGGGCATACAA 57.090 33.333 0.00 0.00 0.00 2.41
2831 3870 6.909550 AAACACTTAGAATGGGCATACAAA 57.090 33.333 0.00 0.00 0.00 2.83
2832 3871 7.480760 AAACACTTAGAATGGGCATACAAAT 57.519 32.000 0.00 0.00 0.00 2.32
2833 3872 7.480760 AACACTTAGAATGGGCATACAAATT 57.519 32.000 0.00 0.00 0.00 1.82
2834 3873 8.588290 AACACTTAGAATGGGCATACAAATTA 57.412 30.769 0.00 0.00 0.00 1.40
2835 3874 8.766994 ACACTTAGAATGGGCATACAAATTAT 57.233 30.769 0.00 0.00 0.00 1.28
2836 3875 8.632679 ACACTTAGAATGGGCATACAAATTATG 58.367 33.333 0.00 0.00 0.00 1.90
2837 3876 8.849168 CACTTAGAATGGGCATACAAATTATGA 58.151 33.333 0.00 0.00 0.00 2.15
2838 3877 9.420118 ACTTAGAATGGGCATACAAATTATGAA 57.580 29.630 0.00 0.00 0.00 2.57
2872 3911 9.725206 TTTCTTTGGGGAATATAGTCTACTACT 57.275 33.333 0.00 0.00 42.62 2.57
2874 3913 9.804977 TCTTTGGGGAATATAGTCTACTACTAC 57.195 37.037 0.00 0.00 43.47 2.73
2875 3914 9.810870 CTTTGGGGAATATAGTCTACTACTACT 57.189 37.037 0.00 0.00 43.47 2.57
2876 3915 9.804977 TTTGGGGAATATAGTCTACTACTACTC 57.195 37.037 0.00 0.00 43.47 2.59
2877 3916 8.754258 TGGGGAATATAGTCTACTACTACTCT 57.246 38.462 0.00 0.00 43.47 3.24
2878 3917 8.824783 TGGGGAATATAGTCTACTACTACTCTC 58.175 40.741 0.00 0.00 43.47 3.20
2879 3918 8.824783 GGGGAATATAGTCTACTACTACTCTCA 58.175 40.741 0.00 0.00 43.47 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.097741 GTCCATGTTGCTGTTATAATGGCA 59.902 41.667 10.05 10.05 35.56 4.92
24 25 2.686816 CGGCGGCAACTTACCTTGG 61.687 63.158 10.53 0.00 0.00 3.61
39 40 1.453155 ATCCATCCGCAAATATCGGC 58.547 50.000 0.00 0.00 46.05 5.54
192 205 1.600916 GAGGTCCACCAAGTGCACC 60.601 63.158 14.63 0.00 44.13 5.01
287 306 4.913335 CTATGCAGCAAAGACCAATCAT 57.087 40.909 0.00 0.00 0.00 2.45
327 349 5.249393 ACCTAGCAAAGAATCTCCTTCAAGA 59.751 40.000 0.00 0.00 36.24 3.02
355 377 5.403766 CACAACCGATAGCTCTGATAATCAC 59.596 44.000 0.00 0.00 0.00 3.06
356 378 5.069119 ACACAACCGATAGCTCTGATAATCA 59.931 40.000 0.00 0.00 0.00 2.57
377 399 2.251642 GGTCCACAGTCGCCAACAC 61.252 63.158 0.00 0.00 0.00 3.32
402 424 2.087646 GAAGTGGCCAAGATCACCTTC 58.912 52.381 7.24 10.82 34.67 3.46
534 573 7.174080 GGAGCAAGACTCTCTTTGAATAAACTT 59.826 37.037 0.00 0.00 45.48 2.66
574 613 3.079960 TGATAACGCCATCTCTTCGTC 57.920 47.619 0.00 0.00 35.18 4.20
742 787 0.112995 AGCATGACTTTTGGCTCCCA 59.887 50.000 0.00 0.00 28.71 4.37
768 813 2.285743 AGTCCTCCTGGCCCCTTC 60.286 66.667 0.00 0.00 0.00 3.46
840 891 1.075374 ACCTTTGTATCAAGCCAGGCA 59.925 47.619 15.80 0.00 0.00 4.75
894 945 4.857679 AGTCCTCGGTCTCAGTACTTATT 58.142 43.478 0.00 0.00 0.00 1.40
1061 1114 3.039252 ACAAATTGAACCCCAGACCAA 57.961 42.857 0.00 0.00 0.00 3.67
1077 1130 4.081752 ACAACATGCTCCTGTTTCAACAAA 60.082 37.500 0.00 0.00 37.25 2.83
1104 1157 8.144862 AGTCCTTCAAGTGATAGAAAATCTCT 57.855 34.615 0.00 0.00 38.28 3.10
1105 1158 8.785329 AAGTCCTTCAAGTGATAGAAAATCTC 57.215 34.615 0.00 0.00 0.00 2.75
1434 1487 8.964476 TCCAAATATCTAATTCTTCTGTGACC 57.036 34.615 0.00 0.00 0.00 4.02
1438 1491 9.118300 CAGCTTCCAAATATCTAATTCTTCTGT 57.882 33.333 0.00 0.00 0.00 3.41
1473 1526 3.678056 TTGTACGCTCTGTTCCAGATT 57.322 42.857 0.00 0.00 39.92 2.40
1474 1527 3.006967 ACTTTGTACGCTCTGTTCCAGAT 59.993 43.478 0.00 0.00 39.92 2.90
1475 1528 2.364324 ACTTTGTACGCTCTGTTCCAGA 59.636 45.455 0.00 0.00 38.25 3.86
1480 1533 5.408604 CCAAATAGACTTTGTACGCTCTGTT 59.591 40.000 0.00 0.00 0.00 3.16
1488 1541 6.489022 ACCAACCTTCCAAATAGACTTTGTAC 59.511 38.462 0.00 0.00 0.00 2.90
1491 1544 5.534654 TGACCAACCTTCCAAATAGACTTTG 59.465 40.000 0.00 0.00 0.00 2.77
1532 1585 1.202348 TCAACGGCACCACAATGTTTG 60.202 47.619 0.00 0.00 0.00 2.93
1537 1590 1.269448 GACAATCAACGGCACCACAAT 59.731 47.619 0.00 0.00 0.00 2.71
1578 1631 2.649531 TTCTTCCCGTGTTGACCAAT 57.350 45.000 0.00 0.00 0.00 3.16
1582 1635 3.497262 CCTAGTTTTCTTCCCGTGTTGAC 59.503 47.826 0.00 0.00 0.00 3.18
1602 1655 2.158755 CCTTGCCGGATCATAAAGACCT 60.159 50.000 5.05 0.00 33.16 3.85
1628 1681 7.186570 TCAAGATCATACAAGTCCTCAATCA 57.813 36.000 0.00 0.00 0.00 2.57
1636 1689 4.818546 CACCCCATCAAGATCATACAAGTC 59.181 45.833 0.00 0.00 0.00 3.01
1676 1729 3.502572 GGCGTGAAGATTGCCCTC 58.497 61.111 0.00 0.00 43.06 4.30
1723 1776 5.748630 ACTTTTTGAAAGATTGTTCGCCTTC 59.251 36.000 7.37 0.00 0.00 3.46
1843 1896 0.110486 AAACCCCATGAACTCTGCGT 59.890 50.000 0.00 0.00 0.00 5.24
2070 2125 9.567848 AAAGTATTACAACACAAACACAGAAAG 57.432 29.630 0.00 0.00 0.00 2.62
2115 2171 1.597027 CCCGTTTTCACCTGTCGCT 60.597 57.895 0.00 0.00 0.00 4.93
2138 2194 5.927689 TCCGCGAGTTTTAAGATTTTCACTA 59.072 36.000 8.23 0.00 0.00 2.74
2150 2206 0.963962 ACAGTCCTCCGCGAGTTTTA 59.036 50.000 8.23 0.00 0.00 1.52
2151 2207 0.600255 CACAGTCCTCCGCGAGTTTT 60.600 55.000 8.23 0.00 0.00 2.43
2160 2216 3.775654 CCTCCGCCACAGTCCTCC 61.776 72.222 0.00 0.00 0.00 4.30
2161 2217 2.680352 TCCTCCGCCACAGTCCTC 60.680 66.667 0.00 0.00 0.00 3.71
2162 2218 2.997897 GTCCTCCGCCACAGTCCT 60.998 66.667 0.00 0.00 0.00 3.85
2163 2219 4.436998 CGTCCTCCGCCACAGTCC 62.437 72.222 0.00 0.00 0.00 3.85
2164 2220 4.436998 CCGTCCTCCGCCACAGTC 62.437 72.222 0.00 0.00 34.38 3.51
2165 2221 4.988716 TCCGTCCTCCGCCACAGT 62.989 66.667 0.00 0.00 34.38 3.55
2166 2222 4.436998 GTCCGTCCTCCGCCACAG 62.437 72.222 0.00 0.00 34.38 3.66
2168 2224 2.999739 TTTTGTCCGTCCTCCGCCAC 63.000 60.000 0.00 0.00 34.38 5.01
2169 2225 2.725203 CTTTTGTCCGTCCTCCGCCA 62.725 60.000 0.00 0.00 34.38 5.69
2170 2226 2.031465 TTTTGTCCGTCCTCCGCC 59.969 61.111 0.00 0.00 34.38 6.13
2171 2227 0.883370 AACTTTTGTCCGTCCTCCGC 60.883 55.000 0.00 0.00 34.38 5.54
2172 2228 0.865769 CAACTTTTGTCCGTCCTCCG 59.134 55.000 0.00 0.00 0.00 4.63
2253 2334 0.686441 ATCTTGATCCGTCCGGTGGA 60.686 55.000 18.30 18.30 40.46 4.02
2254 2335 1.000163 CTATCTTGATCCGTCCGGTGG 60.000 57.143 0.00 5.07 36.47 4.61
2263 2345 0.038159 CGGCCGACCTATCTTGATCC 60.038 60.000 24.07 0.00 0.00 3.36
2264 2346 0.667792 GCGGCCGACCTATCTTGATC 60.668 60.000 33.48 1.16 0.00 2.92
2292 2374 1.380112 ACGGAGGACCCAGTAGAGC 60.380 63.158 0.00 0.00 34.14 4.09
2300 2382 3.391382 CCCAGTGACGGAGGACCC 61.391 72.222 0.00 0.00 0.00 4.46
2308 2390 4.308458 TGCCGTTCCCCAGTGACG 62.308 66.667 0.00 0.00 36.61 4.35
2313 2395 0.469917 AGATATGTGCCGTTCCCCAG 59.530 55.000 0.00 0.00 0.00 4.45
2320 2402 0.528466 CGAGTGCAGATATGTGCCGT 60.528 55.000 21.02 8.89 43.28 5.68
2358 2440 3.013921 TCCCCGAAGTTTGCATTGTATC 58.986 45.455 0.00 0.00 0.00 2.24
2387 2469 4.517453 TCATTTGTTTTCTGTCCCTAACGG 59.483 41.667 0.00 0.00 35.38 4.44
2426 2508 1.275291 GCTGGTTGTAGTCAGGTAGCA 59.725 52.381 0.00 0.00 0.00 3.49
2429 2511 4.606210 TGATAGCTGGTTGTAGTCAGGTA 58.394 43.478 0.00 0.00 44.55 3.08
2508 2590 6.839124 ACCAAGCATTATCATTGTCTTTCA 57.161 33.333 0.00 0.00 0.00 2.69
2575 3614 2.541588 CGAACCTGTTCCTTGCAACTTG 60.542 50.000 0.00 0.00 36.27 3.16
2579 3618 0.821711 CCCGAACCTGTTCCTTGCAA 60.822 55.000 0.00 0.00 36.27 4.08
2580 3619 1.228124 CCCGAACCTGTTCCTTGCA 60.228 57.895 4.54 0.00 36.27 4.08
2581 3620 2.626780 GCCCGAACCTGTTCCTTGC 61.627 63.158 4.54 1.78 36.27 4.01
2582 3621 0.323629 TAGCCCGAACCTGTTCCTTG 59.676 55.000 4.54 0.00 36.27 3.61
2583 3622 0.323957 GTAGCCCGAACCTGTTCCTT 59.676 55.000 4.54 0.00 36.27 3.36
2584 3623 0.834687 TGTAGCCCGAACCTGTTCCT 60.835 55.000 4.54 0.00 36.27 3.36
2585 3624 0.252197 ATGTAGCCCGAACCTGTTCC 59.748 55.000 4.54 0.00 36.27 3.62
2586 3625 2.973694 TATGTAGCCCGAACCTGTTC 57.026 50.000 0.00 0.00 36.29 3.18
2587 3626 2.835764 TCTTATGTAGCCCGAACCTGTT 59.164 45.455 0.00 0.00 0.00 3.16
2588 3627 2.463752 TCTTATGTAGCCCGAACCTGT 58.536 47.619 0.00 0.00 0.00 4.00
2589 3628 3.132289 TCTTCTTATGTAGCCCGAACCTG 59.868 47.826 0.00 0.00 0.00 4.00
2590 3629 3.132467 GTCTTCTTATGTAGCCCGAACCT 59.868 47.826 0.00 0.00 0.00 3.50
2591 3630 3.118884 TGTCTTCTTATGTAGCCCGAACC 60.119 47.826 0.00 0.00 0.00 3.62
2592 3631 4.119442 TGTCTTCTTATGTAGCCCGAAC 57.881 45.455 0.00 0.00 0.00 3.95
2593 3632 4.649674 AGATGTCTTCTTATGTAGCCCGAA 59.350 41.667 0.00 0.00 0.00 4.30
2594 3633 4.215908 AGATGTCTTCTTATGTAGCCCGA 58.784 43.478 0.00 0.00 0.00 5.14
2595 3634 4.279671 AGAGATGTCTTCTTATGTAGCCCG 59.720 45.833 0.00 0.00 33.74 6.13
2596 3635 5.303078 TGAGAGATGTCTTCTTATGTAGCCC 59.697 44.000 0.00 0.00 33.74 5.19
2597 3636 6.264292 TCTGAGAGATGTCTTCTTATGTAGCC 59.736 42.308 0.00 0.00 33.74 3.93
2598 3637 7.270757 TCTGAGAGATGTCTTCTTATGTAGC 57.729 40.000 0.00 0.00 33.74 3.58
2599 3638 8.902806 ACTTCTGAGAGATGTCTTCTTATGTAG 58.097 37.037 0.00 0.00 33.74 2.74
2600 3639 8.815565 ACTTCTGAGAGATGTCTTCTTATGTA 57.184 34.615 0.00 0.00 33.74 2.29
2601 3640 7.716799 ACTTCTGAGAGATGTCTTCTTATGT 57.283 36.000 0.00 0.00 33.74 2.29
2602 3641 8.681806 TGTACTTCTGAGAGATGTCTTCTTATG 58.318 37.037 0.00 0.00 34.84 1.90
2603 3642 8.815565 TGTACTTCTGAGAGATGTCTTCTTAT 57.184 34.615 0.00 0.00 34.84 1.73
2604 3643 8.637196 TTGTACTTCTGAGAGATGTCTTCTTA 57.363 34.615 0.00 0.00 34.84 2.10
2605 3644 7.531857 TTGTACTTCTGAGAGATGTCTTCTT 57.468 36.000 0.00 0.00 34.84 2.52
2606 3645 7.531857 TTTGTACTTCTGAGAGATGTCTTCT 57.468 36.000 0.00 0.00 34.84 2.85
2607 3646 8.770438 ATTTTGTACTTCTGAGAGATGTCTTC 57.230 34.615 0.00 0.00 34.84 2.87
2608 3647 9.213799 GAATTTTGTACTTCTGAGAGATGTCTT 57.786 33.333 0.00 0.00 34.84 3.01
2609 3648 8.370940 TGAATTTTGTACTTCTGAGAGATGTCT 58.629 33.333 0.00 0.00 34.84 3.41
2610 3649 8.539770 TGAATTTTGTACTTCTGAGAGATGTC 57.460 34.615 0.00 0.00 34.84 3.06
2611 3650 8.370940 TCTGAATTTTGTACTTCTGAGAGATGT 58.629 33.333 0.00 0.00 36.67 3.06
2612 3651 8.768957 TCTGAATTTTGTACTTCTGAGAGATG 57.231 34.615 0.00 0.00 0.00 2.90
2613 3652 9.784531 TTTCTGAATTTTGTACTTCTGAGAGAT 57.215 29.630 0.00 0.00 32.98 2.75
2614 3653 9.784531 ATTTCTGAATTTTGTACTTCTGAGAGA 57.215 29.630 0.00 0.00 32.98 3.10
2615 3654 9.823098 CATTTCTGAATTTTGTACTTCTGAGAG 57.177 33.333 0.00 0.00 32.98 3.20
2616 3655 9.342308 ACATTTCTGAATTTTGTACTTCTGAGA 57.658 29.630 0.00 0.00 32.98 3.27
2647 3686 8.843262 GCCGGTATTTTACTTGGATTACTAATT 58.157 33.333 1.90 0.00 0.00 1.40
2648 3687 7.994334 TGCCGGTATTTTACTTGGATTACTAAT 59.006 33.333 1.90 0.00 0.00 1.73
2649 3688 7.280652 GTGCCGGTATTTTACTTGGATTACTAA 59.719 37.037 1.90 0.00 0.00 2.24
2650 3689 6.762661 GTGCCGGTATTTTACTTGGATTACTA 59.237 38.462 1.90 0.00 0.00 1.82
2651 3690 5.587443 GTGCCGGTATTTTACTTGGATTACT 59.413 40.000 1.90 0.00 0.00 2.24
2652 3691 5.354792 TGTGCCGGTATTTTACTTGGATTAC 59.645 40.000 1.90 0.00 0.00 1.89
2653 3692 5.498393 TGTGCCGGTATTTTACTTGGATTA 58.502 37.500 1.90 0.00 0.00 1.75
2654 3693 4.337145 TGTGCCGGTATTTTACTTGGATT 58.663 39.130 1.90 0.00 0.00 3.01
2655 3694 3.958018 TGTGCCGGTATTTTACTTGGAT 58.042 40.909 1.90 0.00 0.00 3.41
2656 3695 3.420300 TGTGCCGGTATTTTACTTGGA 57.580 42.857 1.90 0.00 0.00 3.53
2657 3696 3.672241 GCTTGTGCCGGTATTTTACTTGG 60.672 47.826 1.90 0.00 0.00 3.61
2658 3697 3.498082 GCTTGTGCCGGTATTTTACTTG 58.502 45.455 1.90 0.00 0.00 3.16
2659 3698 3.842732 GCTTGTGCCGGTATTTTACTT 57.157 42.857 1.90 0.00 0.00 2.24
2672 3711 4.082571 AGTTCATTCATTACTGGCTTGTGC 60.083 41.667 0.00 0.00 38.76 4.57
2673 3712 5.633830 AGTTCATTCATTACTGGCTTGTG 57.366 39.130 0.00 0.00 0.00 3.33
2674 3713 5.769662 TGAAGTTCATTCATTACTGGCTTGT 59.230 36.000 0.08 0.00 43.09 3.16
2675 3714 6.258230 TGAAGTTCATTCATTACTGGCTTG 57.742 37.500 0.08 0.00 43.09 4.01
2686 3725 3.181440 ACTGGGAGCTTGAAGTTCATTCA 60.181 43.478 11.13 5.37 46.31 2.57
2687 3726 3.416156 ACTGGGAGCTTGAAGTTCATTC 58.584 45.455 11.13 5.34 38.50 2.67
2688 3727 3.515602 ACTGGGAGCTTGAAGTTCATT 57.484 42.857 11.13 0.00 0.00 2.57
2689 3728 3.620966 GCTACTGGGAGCTTGAAGTTCAT 60.621 47.826 11.13 0.00 39.50 2.57
2690 3729 2.289694 GCTACTGGGAGCTTGAAGTTCA 60.290 50.000 11.13 0.08 39.50 3.18
2691 3730 2.351455 GCTACTGGGAGCTTGAAGTTC 58.649 52.381 0.00 0.00 39.50 3.01
2692 3731 2.481289 GCTACTGGGAGCTTGAAGTT 57.519 50.000 0.00 0.00 39.50 2.66
2700 3739 5.897377 TTAAATTCAAAGCTACTGGGAGC 57.103 39.130 0.00 0.00 43.19 4.70
2701 3740 7.872113 AGATTAAATTCAAAGCTACTGGGAG 57.128 36.000 0.00 0.00 0.00 4.30
2702 3741 7.669722 ACAAGATTAAATTCAAAGCTACTGGGA 59.330 33.333 0.00 0.00 0.00 4.37
2703 3742 7.756722 CACAAGATTAAATTCAAAGCTACTGGG 59.243 37.037 0.00 0.00 0.00 4.45
2704 3743 7.274250 GCACAAGATTAAATTCAAAGCTACTGG 59.726 37.037 0.00 0.00 0.00 4.00
2705 3744 8.025445 AGCACAAGATTAAATTCAAAGCTACTG 58.975 33.333 0.00 0.00 0.00 2.74
2706 3745 8.115490 AGCACAAGATTAAATTCAAAGCTACT 57.885 30.769 0.00 0.00 0.00 2.57
2707 3746 9.278734 GTAGCACAAGATTAAATTCAAAGCTAC 57.721 33.333 0.00 0.00 41.51 3.58
2708 3747 8.458843 GGTAGCACAAGATTAAATTCAAAGCTA 58.541 33.333 0.00 0.00 0.00 3.32
2709 3748 7.315890 GGTAGCACAAGATTAAATTCAAAGCT 58.684 34.615 0.00 0.00 0.00 3.74
2710 3749 6.531594 GGGTAGCACAAGATTAAATTCAAAGC 59.468 38.462 0.00 0.00 0.00 3.51
2711 3750 7.601856 TGGGTAGCACAAGATTAAATTCAAAG 58.398 34.615 0.00 0.00 0.00 2.77
2712 3751 7.531857 TGGGTAGCACAAGATTAAATTCAAA 57.468 32.000 0.00 0.00 0.00 2.69
2713 3752 7.531857 TTGGGTAGCACAAGATTAAATTCAA 57.468 32.000 0.00 0.00 0.00 2.69
2714 3753 7.531857 TTTGGGTAGCACAAGATTAAATTCA 57.468 32.000 0.00 0.00 0.00 2.57
2721 3760 9.030452 TGTTATTATTTTGGGTAGCACAAGATT 57.970 29.630 0.00 0.00 0.00 2.40
2722 3761 8.466798 GTGTTATTATTTTGGGTAGCACAAGAT 58.533 33.333 0.00 0.05 31.32 2.40
2723 3762 7.361371 CGTGTTATTATTTTGGGTAGCACAAGA 60.361 37.037 0.00 0.00 31.32 3.02
2724 3763 6.745450 CGTGTTATTATTTTGGGTAGCACAAG 59.255 38.462 0.00 0.00 31.32 3.16
2725 3764 6.613233 CGTGTTATTATTTTGGGTAGCACAA 58.387 36.000 0.00 0.00 31.32 3.33
2726 3765 5.392165 GCGTGTTATTATTTTGGGTAGCACA 60.392 40.000 0.00 0.00 31.32 4.57
2727 3766 5.032220 GCGTGTTATTATTTTGGGTAGCAC 58.968 41.667 0.00 0.00 0.00 4.40
2728 3767 4.201832 CGCGTGTTATTATTTTGGGTAGCA 60.202 41.667 0.00 0.00 0.00 3.49
2729 3768 4.276460 CGCGTGTTATTATTTTGGGTAGC 58.724 43.478 0.00 0.00 0.00 3.58
2730 3769 4.333372 ACCGCGTGTTATTATTTTGGGTAG 59.667 41.667 4.92 0.00 0.00 3.18
2731 3770 4.260170 ACCGCGTGTTATTATTTTGGGTA 58.740 39.130 4.92 0.00 0.00 3.69
2732 3771 3.083293 ACCGCGTGTTATTATTTTGGGT 58.917 40.909 4.92 0.00 0.00 4.51
2733 3772 3.768468 ACCGCGTGTTATTATTTTGGG 57.232 42.857 4.92 0.00 0.00 4.12
2734 3773 3.302170 GCAACCGCGTGTTATTATTTTGG 59.698 43.478 4.92 0.00 34.69 3.28
2735 3774 3.302170 GGCAACCGCGTGTTATTATTTTG 59.698 43.478 4.92 0.00 39.92 2.44
2736 3775 3.191791 AGGCAACCGCGTGTTATTATTTT 59.808 39.130 4.92 0.00 39.92 1.82
2737 3776 2.750712 AGGCAACCGCGTGTTATTATTT 59.249 40.909 4.92 0.00 39.92 1.40
2738 3777 2.361789 AGGCAACCGCGTGTTATTATT 58.638 42.857 4.92 0.00 39.92 1.40
2739 3778 2.032680 AGGCAACCGCGTGTTATTAT 57.967 45.000 4.92 0.00 39.92 1.28
2740 3779 1.465387 CAAGGCAACCGCGTGTTATTA 59.535 47.619 4.92 0.00 39.92 0.98
2741 3780 0.239879 CAAGGCAACCGCGTGTTATT 59.760 50.000 4.92 2.70 39.92 1.40
2742 3781 0.604243 TCAAGGCAACCGCGTGTTAT 60.604 50.000 4.92 0.00 39.92 1.89
2743 3782 0.814410 TTCAAGGCAACCGCGTGTTA 60.814 50.000 4.92 0.00 39.92 2.41
2744 3783 1.452145 ATTCAAGGCAACCGCGTGTT 61.452 50.000 4.92 6.23 39.92 3.32
2745 3784 1.852067 GATTCAAGGCAACCGCGTGT 61.852 55.000 4.92 0.00 39.92 4.49
2746 3785 1.154225 GATTCAAGGCAACCGCGTG 60.154 57.895 4.92 0.00 39.92 5.34
2747 3786 2.677003 CGATTCAAGGCAACCGCGT 61.677 57.895 4.92 0.00 39.92 6.01
2748 3787 1.906994 TTCGATTCAAGGCAACCGCG 61.907 55.000 0.00 0.00 39.92 6.46
2749 3788 0.239879 TTTCGATTCAAGGCAACCGC 59.760 50.000 0.00 0.00 37.44 5.68
2750 3789 2.919666 ATTTCGATTCAAGGCAACCG 57.080 45.000 0.00 0.00 37.17 4.44
2751 3790 6.386654 TCTTTTATTTCGATTCAAGGCAACC 58.613 36.000 0.00 0.00 37.17 3.77
2752 3791 7.148804 GGTTCTTTTATTTCGATTCAAGGCAAC 60.149 37.037 0.00 0.00 0.00 4.17
2753 3792 6.866248 GGTTCTTTTATTTCGATTCAAGGCAA 59.134 34.615 0.00 0.00 0.00 4.52
2754 3793 6.208599 AGGTTCTTTTATTTCGATTCAAGGCA 59.791 34.615 0.00 0.00 0.00 4.75
2755 3794 6.528072 CAGGTTCTTTTATTTCGATTCAAGGC 59.472 38.462 0.00 0.00 0.00 4.35
2756 3795 6.528072 GCAGGTTCTTTTATTTCGATTCAAGG 59.472 38.462 0.00 0.00 0.00 3.61
2757 3796 6.249260 CGCAGGTTCTTTTATTTCGATTCAAG 59.751 38.462 0.00 0.00 0.00 3.02
2758 3797 6.083630 CGCAGGTTCTTTTATTTCGATTCAA 58.916 36.000 0.00 0.00 0.00 2.69
2759 3798 5.627172 CGCAGGTTCTTTTATTTCGATTCA 58.373 37.500 0.00 0.00 0.00 2.57
2778 3817 6.243811 TGTTTATTAGTTGTTTACCCGCAG 57.756 37.500 0.00 0.00 0.00 5.18
2779 3818 6.349445 CCATGTTTATTAGTTGTTTACCCGCA 60.349 38.462 0.00 0.00 0.00 5.69
2780 3819 6.031471 CCATGTTTATTAGTTGTTTACCCGC 58.969 40.000 0.00 0.00 0.00 6.13
2781 3820 7.380431 TCCATGTTTATTAGTTGTTTACCCG 57.620 36.000 0.00 0.00 0.00 5.28
2782 3821 9.984190 TTTTCCATGTTTATTAGTTGTTTACCC 57.016 29.630 0.00 0.00 0.00 3.69
2806 3845 6.909550 TGTATGCCCATTCTAAGTGTTTTT 57.090 33.333 0.00 0.00 0.00 1.94
2807 3846 6.909550 TTGTATGCCCATTCTAAGTGTTTT 57.090 33.333 0.00 0.00 0.00 2.43
2808 3847 6.909550 TTTGTATGCCCATTCTAAGTGTTT 57.090 33.333 0.00 0.00 0.00 2.83
2809 3848 7.480760 AATTTGTATGCCCATTCTAAGTGTT 57.519 32.000 0.00 0.00 0.00 3.32
2810 3849 8.632679 CATAATTTGTATGCCCATTCTAAGTGT 58.367 33.333 0.00 0.00 0.00 3.55
2811 3850 8.849168 TCATAATTTGTATGCCCATTCTAAGTG 58.151 33.333 0.00 0.00 0.00 3.16
2812 3851 8.995027 TCATAATTTGTATGCCCATTCTAAGT 57.005 30.769 0.00 0.00 0.00 2.24
2846 3885 9.725206 AGTAGTAGACTATATTCCCCAAAGAAA 57.275 33.333 0.00 0.00 36.27 2.52
2848 3887 9.804977 GTAGTAGTAGACTATATTCCCCAAAGA 57.195 37.037 0.00 0.00 42.69 2.52
2849 3888 9.810870 AGTAGTAGTAGACTATATTCCCCAAAG 57.189 37.037 0.00 0.00 42.69 2.77
2850 3889 9.804977 GAGTAGTAGTAGACTATATTCCCCAAA 57.195 37.037 0.00 0.00 42.69 3.28
2851 3890 9.180282 AGAGTAGTAGTAGACTATATTCCCCAA 57.820 37.037 0.00 0.00 42.69 4.12
2852 3891 8.754258 AGAGTAGTAGTAGACTATATTCCCCA 57.246 38.462 0.00 0.00 42.69 4.96
2853 3892 8.824783 TGAGAGTAGTAGTAGACTATATTCCCC 58.175 40.741 0.00 0.00 42.69 4.81


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

AutoCloner maintained by Alex Coulton.