Multiple sequence alignment - TraesCS5A01G494500

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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 TraesCS5A01G494500 chr5A 100.000 2153 0 0 478 2630 663190777 663188625 0.000000e+00 3976.0
1 TraesCS5A01G494500 chr5A 100.000 110 0 0 1 110 663191254 663191145 1.230000e-48 204.0
2 TraesCS5A01G494500 chr4D 87.279 1863 99 44 775 2553 483041897 483040089 0.000000e+00 2001.0
3 TraesCS5A01G494500 chr4D 86.463 229 19 5 540 766 483042265 483042047 9.410000e-60 241.0
4 TraesCS5A01G494500 chr4B 83.725 1745 108 78 801 2407 612878013 612876307 0.000000e+00 1487.0
5 TraesCS5A01G494500 chr6A 84.733 131 20 0 1347 1477 617097557 617097687 5.910000e-27 132.0
6 TraesCS5A01G494500 chr6A 97.297 37 1 0 1894 1930 39864894 39864858 2.190000e-06 63.9
7 TraesCS5A01G494500 chr6B 84.328 134 15 3 1347 1477 717596746 717596616 2.750000e-25 126.0
8 TraesCS5A01G494500 chr6B 91.379 58 3 2 2185 2241 49553388 49553332 7.800000e-11 78.7
9 TraesCS5A01G494500 chr6B 90.000 60 3 3 2180 2238 48674230 48674287 1.010000e-09 75.0
10 TraesCS5A01G494500 chr7B 81.481 135 23 2 1343 1476 734430594 734430727 2.770000e-20 110.0
11 TraesCS5A01G494500 chr7B 100.000 28 0 0 1826 1853 671704630 671704603 5.000000e-03 52.8
12 TraesCS5A01G494500 chr6D 81.538 130 24 0 1347 1476 472568632 472568503 9.950000e-20 108.0
13 TraesCS5A01G494500 chr4A 91.525 59 3 2 2181 2238 738033377 738033434 2.170000e-11 80.5
14 TraesCS5A01G494500 chr4A 91.228 57 3 2 2186 2241 660130545 660130490 2.810000e-10 76.8
15 TraesCS5A01G494500 chr3B 92.727 55 2 2 2188 2241 775576402 775576349 7.800000e-11 78.7
16 TraesCS5A01G494500 chr3B 97.368 38 1 0 1891 1928 513807532 513807569 6.080000e-07 65.8
17 TraesCS5A01G494500 chr2A 88.710 62 7 0 2177 2238 4139208 4139269 2.810000e-10 76.8
18 TraesCS5A01G494500 chr2A 97.368 38 1 0 1891 1928 173359035 173358998 6.080000e-07 65.8
19 TraesCS5A01G494500 chrUn 90.000 60 3 3 2180 2238 205782104 205782161 1.010000e-09 75.0
20 TraesCS5A01G494500 chr3D 87.500 64 5 3 2179 2241 22679152 22679091 1.310000e-08 71.3
21 TraesCS5A01G494500 chr3D 88.525 61 4 3 2179 2238 22767806 22767864 1.310000e-08 71.3
22 TraesCS5A01G494500 chr3D 97.368 38 1 0 1891 1928 394187394 394187431 6.080000e-07 65.8
23 TraesCS5A01G494500 chr3D 97.297 37 1 0 1890 1926 554793643 554793607 2.190000e-06 63.9
24 TraesCS5A01G494500 chr3D 100.000 28 0 0 1826 1853 55347658 55347685 5.000000e-03 52.8
25 TraesCS5A01G494500 chr3A 97.368 38 1 0 1891 1928 513924217 513924254 6.080000e-07 65.8
26 TraesCS5A01G494500 chr2B 97.297 37 1 0 1891 1927 470473463 470473499 2.190000e-06 63.9
27 TraesCS5A01G494500 chr7D 100.000 28 0 0 1826 1853 531593712 531593685 5.000000e-03 52.8
28 TraesCS5A01G494500 chr7A 100.000 28 0 0 1826 1853 682896620 682896647 5.000000e-03 52.8


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 TraesCS5A01G494500 chr5A 663188625 663191254 2629 True 2090 3976 100.000 1 2630 2 chr5A.!!$R1 2629
1 TraesCS5A01G494500 chr4D 483040089 483042265 2176 True 1121 2001 86.871 540 2553 2 chr4D.!!$R1 2013
2 TraesCS5A01G494500 chr4B 612876307 612878013 1706 True 1487 1487 83.725 801 2407 1 chr4B.!!$R1 1606

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
109 110 0.032815 GAAGAGCAGATAGACGGCCC 59.967 60.0 0.0 0.0 40.39 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1848 0.179124 GGGACTCACTTGCTAGAGCG 60.179 60.0 1.04 0.0 45.83 5.03 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
18 19 1.981636 TGGGTGATGCAAAATGGGC 59.018 52.632 0.00 0.00 0.00 5.36
19 20 0.835115 TGGGTGATGCAAAATGGGCA 60.835 50.000 0.00 0.00 46.66 5.36
20 21 0.324285 GGGTGATGCAAAATGGGCAA 59.676 50.000 0.00 0.00 45.60 4.52
21 22 1.441738 GGTGATGCAAAATGGGCAAC 58.558 50.000 0.00 0.00 45.60 4.17
35 36 2.262572 GGCAACCAAAGTCTTATGCG 57.737 50.000 0.00 0.00 34.73 4.73
36 37 1.539827 GGCAACCAAAGTCTTATGCGT 59.460 47.619 0.00 0.00 34.73 5.24
37 38 2.030274 GGCAACCAAAGTCTTATGCGTT 60.030 45.455 0.00 0.00 34.73 4.84
38 39 3.234386 GCAACCAAAGTCTTATGCGTTC 58.766 45.455 0.00 0.00 0.00 3.95
39 40 3.304391 GCAACCAAAGTCTTATGCGTTCA 60.304 43.478 0.00 0.00 0.00 3.18
40 41 4.615912 GCAACCAAAGTCTTATGCGTTCAT 60.616 41.667 0.00 0.00 36.73 2.57
41 42 4.946784 ACCAAAGTCTTATGCGTTCATC 57.053 40.909 0.00 0.00 34.22 2.92
42 43 4.323417 ACCAAAGTCTTATGCGTTCATCA 58.677 39.130 0.00 0.00 34.22 3.07
43 44 4.154195 ACCAAAGTCTTATGCGTTCATCAC 59.846 41.667 0.00 0.00 34.22 3.06
52 53 3.713936 CGTTCATCACGGCACTAGA 57.286 52.632 0.00 0.00 45.89 2.43
53 54 1.990799 CGTTCATCACGGCACTAGAA 58.009 50.000 0.00 0.00 45.89 2.10
54 55 2.333926 CGTTCATCACGGCACTAGAAA 58.666 47.619 0.00 0.00 45.89 2.52
55 56 2.345641 CGTTCATCACGGCACTAGAAAG 59.654 50.000 0.00 0.00 45.89 2.62
56 57 3.585862 GTTCATCACGGCACTAGAAAGA 58.414 45.455 0.00 0.00 0.00 2.52
57 58 3.953712 TCATCACGGCACTAGAAAGAA 57.046 42.857 0.00 0.00 0.00 2.52
58 59 3.849911 TCATCACGGCACTAGAAAGAAG 58.150 45.455 0.00 0.00 0.00 2.85
59 60 3.509967 TCATCACGGCACTAGAAAGAAGA 59.490 43.478 0.00 0.00 0.00 2.87
60 61 3.577649 TCACGGCACTAGAAAGAAGAG 57.422 47.619 0.00 0.00 0.00 2.85
61 62 1.996191 CACGGCACTAGAAAGAAGAGC 59.004 52.381 0.00 0.00 0.00 4.09
62 63 1.618837 ACGGCACTAGAAAGAAGAGCA 59.381 47.619 0.00 0.00 0.00 4.26
63 64 2.266554 CGGCACTAGAAAGAAGAGCAG 58.733 52.381 0.00 0.00 0.00 4.24
64 65 2.094494 CGGCACTAGAAAGAAGAGCAGA 60.094 50.000 0.00 0.00 0.00 4.26
65 66 3.430098 CGGCACTAGAAAGAAGAGCAGAT 60.430 47.826 0.00 0.00 0.00 2.90
66 67 4.202060 CGGCACTAGAAAGAAGAGCAGATA 60.202 45.833 0.00 0.00 0.00 1.98
67 68 5.665459 GGCACTAGAAAGAAGAGCAGATAA 58.335 41.667 0.00 0.00 0.00 1.75
68 69 5.522097 GGCACTAGAAAGAAGAGCAGATAAC 59.478 44.000 0.00 0.00 0.00 1.89
69 70 5.522097 GCACTAGAAAGAAGAGCAGATAACC 59.478 44.000 0.00 0.00 0.00 2.85
70 71 6.045955 CACTAGAAAGAAGAGCAGATAACCC 58.954 44.000 0.00 0.00 0.00 4.11
71 72 5.961421 ACTAGAAAGAAGAGCAGATAACCCT 59.039 40.000 0.00 0.00 0.00 4.34
72 73 5.351948 AGAAAGAAGAGCAGATAACCCTC 57.648 43.478 0.00 0.00 0.00 4.30
73 74 4.780021 AGAAAGAAGAGCAGATAACCCTCA 59.220 41.667 0.00 0.00 0.00 3.86
74 75 5.249393 AGAAAGAAGAGCAGATAACCCTCAA 59.751 40.000 0.00 0.00 0.00 3.02
75 76 5.505181 AAGAAGAGCAGATAACCCTCAAA 57.495 39.130 0.00 0.00 0.00 2.69
76 77 5.505181 AGAAGAGCAGATAACCCTCAAAA 57.495 39.130 0.00 0.00 0.00 2.44
77 78 5.880901 AGAAGAGCAGATAACCCTCAAAAA 58.119 37.500 0.00 0.00 0.00 1.94
105 106 6.959671 AAAAGAAAGAAGAGCAGATAGACG 57.040 37.500 0.00 0.00 0.00 4.18
106 107 4.647424 AGAAAGAAGAGCAGATAGACGG 57.353 45.455 0.00 0.00 0.00 4.79
107 108 2.880963 AAGAAGAGCAGATAGACGGC 57.119 50.000 0.00 0.00 39.85 5.68
108 109 1.036707 AGAAGAGCAGATAGACGGCC 58.963 55.000 0.00 0.00 40.39 6.13
109 110 0.032815 GAAGAGCAGATAGACGGCCC 59.967 60.000 0.00 0.00 40.39 5.80
494 495 2.507102 CTCATTGCGGACGCTCGT 60.507 61.111 18.04 0.00 42.51 4.18
495 496 2.048597 TCATTGCGGACGCTCGTT 60.049 55.556 18.04 0.00 42.51 3.85
496 497 1.626654 CTCATTGCGGACGCTCGTTT 61.627 55.000 18.04 0.00 42.51 3.60
497 498 1.225745 CATTGCGGACGCTCGTTTC 60.226 57.895 18.04 0.00 42.51 2.78
498 499 2.726691 ATTGCGGACGCTCGTTTCG 61.727 57.895 18.04 12.22 42.51 3.46
499 500 4.634133 TGCGGACGCTCGTTTCGT 62.634 61.111 18.04 0.00 43.49 3.85
500 501 3.400590 GCGGACGCTCGTTTCGTT 61.401 61.111 9.76 0.00 40.59 3.85
501 502 2.935446 GCGGACGCTCGTTTCGTTT 61.935 57.895 9.76 0.00 40.59 3.60
502 503 1.127225 CGGACGCTCGTTTCGTTTC 59.873 57.895 0.00 0.00 40.59 2.78
503 504 1.273455 CGGACGCTCGTTTCGTTTCT 61.273 55.000 0.00 0.00 40.59 2.52
504 505 1.689959 GGACGCTCGTTTCGTTTCTA 58.310 50.000 0.00 0.00 40.59 2.10
505 506 1.647702 GGACGCTCGTTTCGTTTCTAG 59.352 52.381 0.00 0.00 40.59 2.43
506 507 2.578495 GACGCTCGTTTCGTTTCTAGA 58.422 47.619 0.00 0.00 40.59 2.43
507 508 2.314122 ACGCTCGTTTCGTTTCTAGAC 58.686 47.619 0.00 0.00 36.72 2.59
508 509 1.647702 CGCTCGTTTCGTTTCTAGACC 59.352 52.381 0.00 0.00 0.00 3.85
509 510 1.991264 GCTCGTTTCGTTTCTAGACCC 59.009 52.381 0.00 0.00 0.00 4.46
510 511 2.352519 GCTCGTTTCGTTTCTAGACCCT 60.353 50.000 0.00 0.00 0.00 4.34
511 512 3.243336 CTCGTTTCGTTTCTAGACCCTG 58.757 50.000 0.00 0.00 0.00 4.45
512 513 1.725164 CGTTTCGTTTCTAGACCCTGC 59.275 52.381 0.00 0.00 0.00 4.85
513 514 1.725164 GTTTCGTTTCTAGACCCTGCG 59.275 52.381 0.00 0.00 0.00 5.18
514 515 1.250328 TTCGTTTCTAGACCCTGCGA 58.750 50.000 0.00 0.00 0.00 5.10
515 516 0.809385 TCGTTTCTAGACCCTGCGAG 59.191 55.000 0.00 0.00 0.00 5.03
516 517 0.809385 CGTTTCTAGACCCTGCGAGA 59.191 55.000 0.00 0.00 0.00 4.04
517 518 1.202200 CGTTTCTAGACCCTGCGAGAG 60.202 57.143 0.00 0.00 0.00 3.20
518 519 2.093106 GTTTCTAGACCCTGCGAGAGA 58.907 52.381 0.00 0.00 0.00 3.10
519 520 2.045561 TTCTAGACCCTGCGAGAGAG 57.954 55.000 0.00 0.00 0.00 3.20
520 521 0.181587 TCTAGACCCTGCGAGAGAGG 59.818 60.000 0.00 0.00 0.00 3.69
522 523 2.285889 TAGACCCTGCGAGAGAGGGG 62.286 65.000 10.64 1.18 46.45 4.79
523 524 3.663815 GACCCTGCGAGAGAGGGGA 62.664 68.421 10.64 0.00 46.45 4.81
524 525 3.151022 CCCTGCGAGAGAGGGGAC 61.151 72.222 0.00 0.00 43.86 4.46
525 526 2.363018 CCTGCGAGAGAGGGGACA 60.363 66.667 0.00 0.00 0.00 4.02
526 527 2.716017 CCTGCGAGAGAGGGGACAC 61.716 68.421 0.00 0.00 0.00 3.67
527 528 3.057547 CTGCGAGAGAGGGGACACG 62.058 68.421 0.00 0.00 0.00 4.49
528 529 3.827898 GCGAGAGAGGGGACACGG 61.828 72.222 0.00 0.00 0.00 4.94
529 530 3.827898 CGAGAGAGGGGACACGGC 61.828 72.222 0.00 0.00 0.00 5.68
530 531 2.363147 GAGAGAGGGGACACGGCT 60.363 66.667 0.00 0.00 0.00 5.52
531 532 2.363147 AGAGAGGGGACACGGCTC 60.363 66.667 0.00 0.00 0.00 4.70
532 533 3.462678 GAGAGGGGACACGGCTCC 61.463 72.222 0.00 0.00 0.00 4.70
533 534 4.316823 AGAGGGGACACGGCTCCA 62.317 66.667 0.00 0.00 30.97 3.86
534 535 3.083997 GAGGGGACACGGCTCCAT 61.084 66.667 0.00 0.00 30.97 3.41
535 536 3.391665 GAGGGGACACGGCTCCATG 62.392 68.421 0.00 0.00 30.97 3.66
536 537 4.489771 GGGGACACGGCTCCATGG 62.490 72.222 4.97 4.97 30.97 3.66
537 538 3.399181 GGGACACGGCTCCATGGA 61.399 66.667 15.27 15.27 30.97 3.41
538 539 2.746375 GGGACACGGCTCCATGGAT 61.746 63.158 16.63 0.00 30.97 3.41
539 540 1.524621 GGACACGGCTCCATGGATG 60.525 63.158 16.63 13.28 0.00 3.51
632 633 3.499737 CGAGCCACGGATTGCACC 61.500 66.667 0.00 0.00 38.46 5.01
688 690 3.115892 CGCCGGTACACGCATGTT 61.116 61.111 1.90 0.00 40.48 2.71
689 691 2.782615 GCCGGTACACGCATGTTC 59.217 61.111 1.90 0.00 40.48 3.18
690 692 3.077705 CCGGTACACGCATGTTCG 58.922 61.111 0.00 0.00 40.48 3.95
691 693 1.735198 CCGGTACACGCATGTTCGT 60.735 57.895 0.00 0.00 44.35 3.85
708 710 0.875728 CGTAATGACCACGGCCAAAA 59.124 50.000 2.24 0.00 35.78 2.44
719 721 2.995258 CACGGCCAAAAGAATCAAATGG 59.005 45.455 2.24 0.00 0.00 3.16
726 728 4.758165 CCAAAAGAATCAAATGGCAAAGCT 59.242 37.500 0.00 0.00 0.00 3.74
728 730 6.091713 CCAAAAGAATCAAATGGCAAAGCTAG 59.908 38.462 0.00 0.00 0.00 3.42
729 731 4.382345 AGAATCAAATGGCAAAGCTAGC 57.618 40.909 6.62 6.62 0.00 3.42
740 742 1.728971 CAAAGCTAGCCAAGTGACGAG 59.271 52.381 12.13 0.00 0.00 4.18
755 757 1.005630 CGAGCCCCGGATTCTCATC 60.006 63.158 0.73 0.00 33.91 2.92
757 759 2.118233 GAGCCCCGGATTCTCATCCC 62.118 65.000 0.73 0.00 46.06 3.85
766 768 1.630878 GATTCTCATCCCCCGGCTTAT 59.369 52.381 0.00 0.00 0.00 1.73
768 770 2.642171 TCTCATCCCCCGGCTTATAT 57.358 50.000 0.00 0.00 0.00 0.86
770 772 2.044492 TCTCATCCCCCGGCTTATATCT 59.956 50.000 0.00 0.00 0.00 1.98
771 773 2.432510 CTCATCCCCCGGCTTATATCTC 59.567 54.545 0.00 0.00 0.00 2.75
772 774 1.137086 CATCCCCCGGCTTATATCTCG 59.863 57.143 0.00 0.00 0.00 4.04
773 775 1.218316 CCCCCGGCTTATATCTCGC 59.782 63.158 0.00 0.00 0.00 5.03
850 1000 0.979665 AGTGAGTGAGTGACCATGGG 59.020 55.000 18.09 0.00 0.00 4.00
873 1034 3.447634 CTCTCGGCTGTCGCTCTCG 62.448 68.421 0.00 0.00 39.05 4.04
918 1082 5.278561 CCATTACTAGTAGGAGTACTGCTGC 60.279 48.000 25.58 23.76 42.50 5.25
943 1111 3.093172 CTCCAGCCCCTTCCCCTC 61.093 72.222 0.00 0.00 0.00 4.30
944 1112 4.760220 TCCAGCCCCTTCCCCTCC 62.760 72.222 0.00 0.00 0.00 4.30
949 1117 4.845307 CCCCTTCCCCTCCCCCTC 62.845 77.778 0.00 0.00 0.00 4.30
978 1166 4.996434 CTGCCATCCCGATCCGGC 62.996 72.222 0.00 0.00 46.86 6.13
1376 1592 3.744719 CCTGTCGGAGTTCGCGGA 61.745 66.667 6.13 0.00 39.05 5.54
1581 1797 2.835895 GAGGCGTCCTCCTCCTCC 60.836 72.222 13.12 0.00 44.36 4.30
1621 1837 4.595538 ACGGTGCCGCTCGTTTCA 62.596 61.111 10.87 0.00 44.19 2.69
1632 1848 0.163788 CTCGTTTCATGCCGTGACAC 59.836 55.000 0.00 0.00 36.32 3.67
1724 1940 6.063640 TGTGAATCAGTGAATGTGAGTTTG 57.936 37.500 0.00 0.00 0.00 2.93
1725 1941 5.008911 TGTGAATCAGTGAATGTGAGTTTGG 59.991 40.000 0.00 0.00 0.00 3.28
1781 1998 3.599343 CCTGTTTTCATGGACTCGATCA 58.401 45.455 0.00 0.00 0.00 2.92
1854 2087 4.670621 GCAATTTCAGTACAACACAAGACG 59.329 41.667 0.00 0.00 0.00 4.18
1856 2089 6.255215 CAATTTCAGTACAACACAAGACGTT 58.745 36.000 0.00 0.00 0.00 3.99
1857 2090 5.866335 TTTCAGTACAACACAAGACGTTT 57.134 34.783 0.00 0.00 0.00 3.60
1858 2091 5.866335 TTCAGTACAACACAAGACGTTTT 57.134 34.783 0.00 0.00 0.00 2.43
1894 2131 7.527084 AAAAATTTGGTCGAATTCGTTTTGA 57.473 28.000 25.93 12.03 40.80 2.69
1916 2153 2.661195 CCGAAATGCAAACCGAAATCAC 59.339 45.455 0.00 0.00 0.00 3.06
1924 2161 4.981674 TGCAAACCGAAATCACTGAAATTC 59.018 37.500 0.00 0.00 0.00 2.17
1929 2166 6.002062 ACCGAAATCACTGAAATTCACTTC 57.998 37.500 0.00 0.00 0.00 3.01
1979 2216 2.106683 CGTGGCCTCGATTTGGTCC 61.107 63.158 22.35 0.00 0.00 4.46
1980 2217 1.749258 GTGGCCTCGATTTGGTCCC 60.749 63.158 3.32 0.00 0.00 4.46
1981 2218 2.227757 TGGCCTCGATTTGGTCCCA 61.228 57.895 3.32 0.00 0.00 4.37
1982 2219 1.001393 GGCCTCGATTTGGTCCCAA 60.001 57.895 0.00 0.00 0.00 4.12
1983 2220 0.395724 GGCCTCGATTTGGTCCCAAT 60.396 55.000 0.00 0.00 35.70 3.16
1984 2221 0.740737 GCCTCGATTTGGTCCCAATG 59.259 55.000 0.00 0.00 35.70 2.82
2054 2297 3.016736 AGTTTTCTGCCCATATCAACCG 58.983 45.455 0.00 0.00 0.00 4.44
2077 2323 5.278266 CGTTTTTCCTGGCAAAGTTATCAGA 60.278 40.000 0.00 0.00 0.00 3.27
2088 2334 5.855395 GCAAAGTTATCAGAAAAGCTCACAG 59.145 40.000 0.00 0.00 0.00 3.66
2103 2349 4.713814 AGCTCACAGAAGGATTAGTGATCA 59.286 41.667 0.00 0.00 40.76 2.92
2104 2350 5.049167 GCTCACAGAAGGATTAGTGATCAG 58.951 45.833 0.00 0.00 40.76 2.90
2127 2376 6.205658 CAGGCTTATATAGTTTTCTTCCAGCC 59.794 42.308 6.65 6.65 36.55 4.85
2177 2436 4.184629 GTGTGGCTACTTAACCTCTGATG 58.815 47.826 0.64 0.00 0.00 3.07
2178 2437 4.081642 GTGTGGCTACTTAACCTCTGATGA 60.082 45.833 0.64 0.00 0.00 2.92
2179 2438 4.716784 TGTGGCTACTTAACCTCTGATGAT 59.283 41.667 0.64 0.00 0.00 2.45
2254 2569 4.640647 GTGTGATTTAGGATTTCAGGGGAC 59.359 45.833 0.00 0.00 0.00 4.46
2258 2573 5.893255 TGATTTAGGATTTCAGGGGACAATG 59.107 40.000 0.00 0.00 0.00 2.82
2267 2582 0.257039 AGGGGACAATGTGATGCCTC 59.743 55.000 0.00 0.00 0.00 4.70
2281 2596 0.817654 TGCCTCTCATACCACACTCG 59.182 55.000 0.00 0.00 0.00 4.18
2284 2607 0.248661 CTCTCATACCACACTCGCGG 60.249 60.000 6.13 0.00 0.00 6.46
2291 2614 1.809619 CCACACTCGCGGTACATGG 60.810 63.158 6.13 4.51 0.00 3.66
2327 2650 7.020827 ACTAATTTGGTCAGGAGATCAAGAA 57.979 36.000 0.00 0.00 45.08 2.52
2390 2713 8.068380 GGTTACATTGCTACGGATTATTTTCTC 58.932 37.037 0.00 0.00 0.00 2.87
2399 2722 5.983540 ACGGATTATTTTCTCAAGAGCTCT 58.016 37.500 11.45 11.45 0.00 4.09
2433 2756 9.194972 TGTTATCAGAATTATTGCCACCATTTA 57.805 29.630 0.00 0.00 0.00 1.40
2451 2774 9.831737 CACCATTTAGTGTTCTTTTTAGAGATG 57.168 33.333 0.00 0.00 32.89 2.90
2473 2796 5.308825 TGAAAAAGGCTTTTTGTTGGTTCA 58.691 33.333 35.28 24.04 42.51 3.18
2484 2807 4.553330 TTGTTGGTTCATACTCCCTCTC 57.447 45.455 0.00 0.00 0.00 3.20
2502 2825 9.921637 CTCCCTCTCTGTATCAAAATATAAGAC 57.078 37.037 0.00 0.00 0.00 3.01
2564 2888 9.760077 ACCCTAAGATAGTGTAAAAATATGTCG 57.240 33.333 0.00 0.00 0.00 4.35
2565 2889 9.204570 CCCTAAGATAGTGTAAAAATATGTCGG 57.795 37.037 0.00 0.00 0.00 4.79
2566 2890 9.976511 CCTAAGATAGTGTAAAAATATGTCGGA 57.023 33.333 0.00 0.00 0.00 4.55
2584 2908 7.562259 TGTCGGATATTTTAATATGGAGGGA 57.438 36.000 0.00 0.00 31.96 4.20
2585 2909 8.158025 TGTCGGATATTTTAATATGGAGGGAT 57.842 34.615 0.00 0.00 31.96 3.85
2586 2910 8.046708 TGTCGGATATTTTAATATGGAGGGATG 58.953 37.037 0.00 0.00 31.96 3.51
2587 2911 7.499232 GTCGGATATTTTAATATGGAGGGATGG 59.501 40.741 0.00 0.00 31.96 3.51
2588 2912 7.404688 TCGGATATTTTAATATGGAGGGATGGA 59.595 37.037 0.00 0.00 31.96 3.41
2589 2913 7.716998 CGGATATTTTAATATGGAGGGATGGAG 59.283 40.741 0.00 0.00 31.96 3.86
2590 2914 8.560903 GGATATTTTAATATGGAGGGATGGAGT 58.439 37.037 0.00 0.00 31.96 3.85
2593 2917 7.947782 TTTTAATATGGAGGGATGGAGTACT 57.052 36.000 0.00 0.00 0.00 2.73
2594 2918 7.947782 TTTAATATGGAGGGATGGAGTACTT 57.052 36.000 0.00 0.00 0.00 2.24
2595 2919 9.455144 TTTTAATATGGAGGGATGGAGTACTTA 57.545 33.333 0.00 0.00 0.00 2.24
2596 2920 8.666129 TTAATATGGAGGGATGGAGTACTTAG 57.334 38.462 0.00 0.00 0.00 2.18
2597 2921 3.330126 TGGAGGGATGGAGTACTTAGG 57.670 52.381 0.00 0.00 0.00 2.69
2598 2922 1.972075 GGAGGGATGGAGTACTTAGGC 59.028 57.143 0.00 0.00 0.00 3.93
2599 2923 1.614413 GAGGGATGGAGTACTTAGGCG 59.386 57.143 0.00 0.00 0.00 5.52
2600 2924 1.063114 AGGGATGGAGTACTTAGGCGT 60.063 52.381 0.00 0.00 0.00 5.68
2601 2925 1.068741 GGGATGGAGTACTTAGGCGTG 59.931 57.143 0.00 0.00 0.00 5.34
2602 2926 1.755380 GGATGGAGTACTTAGGCGTGT 59.245 52.381 0.00 0.00 0.00 4.49
2603 2927 2.167900 GGATGGAGTACTTAGGCGTGTT 59.832 50.000 0.00 0.00 0.00 3.32
2604 2928 3.369157 GGATGGAGTACTTAGGCGTGTTT 60.369 47.826 0.00 0.00 0.00 2.83
2605 2929 3.034721 TGGAGTACTTAGGCGTGTTTG 57.965 47.619 0.00 0.00 0.00 2.93
2606 2930 2.289195 TGGAGTACTTAGGCGTGTTTGG 60.289 50.000 0.00 0.00 0.00 3.28
2607 2931 2.289257 GGAGTACTTAGGCGTGTTTGGT 60.289 50.000 0.00 0.00 0.00 3.67
2608 2932 3.396560 GAGTACTTAGGCGTGTTTGGTT 58.603 45.455 0.00 0.00 0.00 3.67
2609 2933 3.135994 AGTACTTAGGCGTGTTTGGTTG 58.864 45.455 0.00 0.00 0.00 3.77
2610 2934 2.047002 ACTTAGGCGTGTTTGGTTGT 57.953 45.000 0.00 0.00 0.00 3.32
2611 2935 1.944709 ACTTAGGCGTGTTTGGTTGTC 59.055 47.619 0.00 0.00 0.00 3.18
2612 2936 2.218603 CTTAGGCGTGTTTGGTTGTCT 58.781 47.619 0.00 0.00 0.00 3.41
2613 2937 1.588674 TAGGCGTGTTTGGTTGTCTG 58.411 50.000 0.00 0.00 0.00 3.51
2614 2938 0.393808 AGGCGTGTTTGGTTGTCTGT 60.394 50.000 0.00 0.00 0.00 3.41
2615 2939 1.134340 AGGCGTGTTTGGTTGTCTGTA 60.134 47.619 0.00 0.00 0.00 2.74
2616 2940 1.003223 GGCGTGTTTGGTTGTCTGTAC 60.003 52.381 0.00 0.00 0.00 2.90
2617 2941 1.937899 GCGTGTTTGGTTGTCTGTACT 59.062 47.619 0.00 0.00 0.00 2.73
2618 2942 2.286184 GCGTGTTTGGTTGTCTGTACTG 60.286 50.000 0.00 0.00 0.00 2.74
2619 2943 3.191669 CGTGTTTGGTTGTCTGTACTGA 58.808 45.455 0.00 0.00 0.00 3.41
2620 2944 3.807622 CGTGTTTGGTTGTCTGTACTGAT 59.192 43.478 5.69 0.00 0.00 2.90
2621 2945 4.272504 CGTGTTTGGTTGTCTGTACTGATT 59.727 41.667 5.69 0.00 0.00 2.57
2622 2946 5.220777 CGTGTTTGGTTGTCTGTACTGATTT 60.221 40.000 5.69 0.00 0.00 2.17
2623 2947 6.560711 GTGTTTGGTTGTCTGTACTGATTTT 58.439 36.000 5.69 0.00 0.00 1.82
2624 2948 6.472163 GTGTTTGGTTGTCTGTACTGATTTTG 59.528 38.462 5.69 0.00 0.00 2.44
2625 2949 4.829064 TGGTTGTCTGTACTGATTTTGC 57.171 40.909 5.69 0.00 0.00 3.68
2626 2950 3.568007 TGGTTGTCTGTACTGATTTTGCC 59.432 43.478 5.69 5.57 0.00 4.52
2627 2951 3.821033 GGTTGTCTGTACTGATTTTGCCT 59.179 43.478 5.69 0.00 0.00 4.75
2628 2952 4.320494 GGTTGTCTGTACTGATTTTGCCTG 60.320 45.833 5.69 0.00 0.00 4.85
2629 2953 2.813754 TGTCTGTACTGATTTTGCCTGC 59.186 45.455 5.69 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.835115 TGCCCATTTTGCATCACCCA 60.835 50.000 0.00 0.00 32.85 4.51
3 4 1.270732 TGGTTGCCCATTTTGCATCAC 60.271 47.619 0.00 0.00 38.76 3.06
4 5 1.054231 TGGTTGCCCATTTTGCATCA 58.946 45.000 0.00 0.00 38.76 3.07
5 6 2.181954 TTGGTTGCCCATTTTGCATC 57.818 45.000 0.00 0.00 41.49 3.91
7 8 1.211457 ACTTTGGTTGCCCATTTTGCA 59.789 42.857 0.00 0.00 41.49 4.08
8 9 1.872952 GACTTTGGTTGCCCATTTTGC 59.127 47.619 0.00 0.00 41.49 3.68
9 10 3.473923 AGACTTTGGTTGCCCATTTTG 57.526 42.857 0.00 0.00 41.49 2.44
10 11 5.550290 CATAAGACTTTGGTTGCCCATTTT 58.450 37.500 0.00 0.00 41.49 1.82
11 12 4.563374 GCATAAGACTTTGGTTGCCCATTT 60.563 41.667 0.00 0.00 41.49 2.32
12 13 3.055891 GCATAAGACTTTGGTTGCCCATT 60.056 43.478 0.00 0.00 41.49 3.16
13 14 2.497273 GCATAAGACTTTGGTTGCCCAT 59.503 45.455 0.00 0.00 41.49 4.00
14 15 1.892474 GCATAAGACTTTGGTTGCCCA 59.108 47.619 0.00 0.00 39.65 5.36
15 16 1.135402 CGCATAAGACTTTGGTTGCCC 60.135 52.381 0.00 0.00 0.00 5.36
16 17 1.539827 ACGCATAAGACTTTGGTTGCC 59.460 47.619 0.00 0.00 0.00 4.52
17 18 2.989422 ACGCATAAGACTTTGGTTGC 57.011 45.000 0.00 0.00 0.00 4.17
18 19 4.481930 TGAACGCATAAGACTTTGGTTG 57.518 40.909 0.00 0.00 0.00 3.77
19 20 4.759693 TGATGAACGCATAAGACTTTGGTT 59.240 37.500 0.00 0.00 34.11 3.67
20 21 4.154195 GTGATGAACGCATAAGACTTTGGT 59.846 41.667 0.00 0.00 34.11 3.67
21 22 4.651994 GTGATGAACGCATAAGACTTTGG 58.348 43.478 0.00 0.00 34.11 3.28
22 23 4.326205 CGTGATGAACGCATAAGACTTTG 58.674 43.478 0.00 0.00 46.99 2.77
23 24 4.584029 CGTGATGAACGCATAAGACTTT 57.416 40.909 0.00 0.00 46.99 2.66
35 36 3.585862 TCTTTCTAGTGCCGTGATGAAC 58.414 45.455 0.00 0.00 0.00 3.18
36 37 3.953712 TCTTTCTAGTGCCGTGATGAA 57.046 42.857 0.00 0.00 0.00 2.57
37 38 3.509967 TCTTCTTTCTAGTGCCGTGATGA 59.490 43.478 0.00 0.00 0.00 2.92
38 39 3.849911 TCTTCTTTCTAGTGCCGTGATG 58.150 45.455 0.00 0.00 0.00 3.07
39 40 3.677424 GCTCTTCTTTCTAGTGCCGTGAT 60.677 47.826 0.00 0.00 0.00 3.06
40 41 2.352814 GCTCTTCTTTCTAGTGCCGTGA 60.353 50.000 0.00 0.00 0.00 4.35
41 42 1.996191 GCTCTTCTTTCTAGTGCCGTG 59.004 52.381 0.00 0.00 0.00 4.94
42 43 1.618837 TGCTCTTCTTTCTAGTGCCGT 59.381 47.619 0.00 0.00 32.62 5.68
43 44 2.094494 TCTGCTCTTCTTTCTAGTGCCG 60.094 50.000 0.00 0.00 32.62 5.69
44 45 3.601443 TCTGCTCTTCTTTCTAGTGCC 57.399 47.619 0.00 0.00 32.62 5.01
45 46 5.522097 GGTTATCTGCTCTTCTTTCTAGTGC 59.478 44.000 0.00 0.00 33.84 4.40
46 47 6.045955 GGGTTATCTGCTCTTCTTTCTAGTG 58.954 44.000 0.00 0.00 0.00 2.74
47 48 5.961421 AGGGTTATCTGCTCTTCTTTCTAGT 59.039 40.000 0.00 0.00 0.00 2.57
48 49 6.097554 TGAGGGTTATCTGCTCTTCTTTCTAG 59.902 42.308 0.00 0.00 0.00 2.43
49 50 5.958380 TGAGGGTTATCTGCTCTTCTTTCTA 59.042 40.000 0.00 0.00 0.00 2.10
50 51 4.780021 TGAGGGTTATCTGCTCTTCTTTCT 59.220 41.667 0.00 0.00 0.00 2.52
51 52 5.091261 TGAGGGTTATCTGCTCTTCTTTC 57.909 43.478 0.00 0.00 0.00 2.62
52 53 5.505181 TTGAGGGTTATCTGCTCTTCTTT 57.495 39.130 0.00 0.00 0.00 2.52
53 54 5.505181 TTTGAGGGTTATCTGCTCTTCTT 57.495 39.130 0.00 0.00 0.00 2.52
54 55 5.505181 TTTTGAGGGTTATCTGCTCTTCT 57.495 39.130 0.00 0.00 0.00 2.85
81 82 6.370166 CCGTCTATCTGCTCTTCTTTCTTTTT 59.630 38.462 0.00 0.00 0.00 1.94
82 83 5.872070 CCGTCTATCTGCTCTTCTTTCTTTT 59.128 40.000 0.00 0.00 0.00 2.27
83 84 5.415221 CCGTCTATCTGCTCTTCTTTCTTT 58.585 41.667 0.00 0.00 0.00 2.52
84 85 4.679372 GCCGTCTATCTGCTCTTCTTTCTT 60.679 45.833 0.00 0.00 0.00 2.52
85 86 3.181480 GCCGTCTATCTGCTCTTCTTTCT 60.181 47.826 0.00 0.00 0.00 2.52
86 87 3.120041 GCCGTCTATCTGCTCTTCTTTC 58.880 50.000 0.00 0.00 0.00 2.62
87 88 2.159028 GGCCGTCTATCTGCTCTTCTTT 60.159 50.000 0.00 0.00 0.00 2.52
88 89 1.410882 GGCCGTCTATCTGCTCTTCTT 59.589 52.381 0.00 0.00 0.00 2.52
89 90 1.036707 GGCCGTCTATCTGCTCTTCT 58.963 55.000 0.00 0.00 0.00 2.85
90 91 0.032815 GGGCCGTCTATCTGCTCTTC 59.967 60.000 0.00 0.00 0.00 2.87
91 92 2.128729 GGGCCGTCTATCTGCTCTT 58.871 57.895 0.00 0.00 0.00 2.85
92 93 3.863606 GGGCCGTCTATCTGCTCT 58.136 61.111 0.00 0.00 0.00 4.09
477 478 1.626654 AAACGAGCGTCCGCAATGAG 61.627 55.000 14.70 2.83 44.88 2.90
478 479 1.623081 GAAACGAGCGTCCGCAATGA 61.623 55.000 14.70 0.00 44.88 2.57
479 480 1.225745 GAAACGAGCGTCCGCAATG 60.226 57.895 14.70 5.45 44.88 2.82
480 481 2.726691 CGAAACGAGCGTCCGCAAT 61.727 57.895 14.70 0.00 44.88 3.56
481 482 3.399770 CGAAACGAGCGTCCGCAA 61.400 61.111 14.70 0.00 44.88 4.85
482 483 4.634133 ACGAAACGAGCGTCCGCA 62.634 61.111 14.70 0.00 44.88 5.69
483 484 2.791295 GAAACGAAACGAGCGTCCGC 62.791 60.000 2.94 2.94 41.75 5.54
484 485 1.127225 GAAACGAAACGAGCGTCCG 59.873 57.895 13.41 13.41 41.75 4.79
485 486 1.647702 CTAGAAACGAAACGAGCGTCC 59.352 52.381 0.00 0.00 41.75 4.79
486 487 2.337936 GTCTAGAAACGAAACGAGCGTC 59.662 50.000 0.00 0.00 41.75 5.19
487 488 2.314122 GTCTAGAAACGAAACGAGCGT 58.686 47.619 0.00 0.00 44.94 5.07
488 489 1.647702 GGTCTAGAAACGAAACGAGCG 59.352 52.381 0.00 0.00 0.00 5.03
489 490 1.991264 GGGTCTAGAAACGAAACGAGC 59.009 52.381 0.00 0.00 0.00 5.03
490 491 3.243336 CAGGGTCTAGAAACGAAACGAG 58.757 50.000 0.00 0.00 0.00 4.18
491 492 2.608752 GCAGGGTCTAGAAACGAAACGA 60.609 50.000 0.00 0.00 0.00 3.85
492 493 1.725164 GCAGGGTCTAGAAACGAAACG 59.275 52.381 0.00 0.00 0.00 3.60
493 494 1.725164 CGCAGGGTCTAGAAACGAAAC 59.275 52.381 0.00 0.00 0.00 2.78
494 495 1.614903 TCGCAGGGTCTAGAAACGAAA 59.385 47.619 0.00 0.00 0.00 3.46
495 496 1.201647 CTCGCAGGGTCTAGAAACGAA 59.798 52.381 0.00 0.00 0.00 3.85
496 497 0.809385 CTCGCAGGGTCTAGAAACGA 59.191 55.000 0.00 0.00 0.00 3.85
497 498 0.809385 TCTCGCAGGGTCTAGAAACG 59.191 55.000 0.00 0.00 0.00 3.60
498 499 2.093106 TCTCTCGCAGGGTCTAGAAAC 58.907 52.381 0.00 0.00 0.00 2.78
499 500 2.370349 CTCTCTCGCAGGGTCTAGAAA 58.630 52.381 0.00 0.00 0.00 2.52
500 501 1.408961 CCTCTCTCGCAGGGTCTAGAA 60.409 57.143 0.00 0.00 0.00 2.10
501 502 0.181587 CCTCTCTCGCAGGGTCTAGA 59.818 60.000 0.00 0.00 0.00 2.43
502 503 0.821711 CCCTCTCTCGCAGGGTCTAG 60.822 65.000 0.00 0.00 45.35 2.43
503 504 1.227664 CCCTCTCTCGCAGGGTCTA 59.772 63.158 0.00 0.00 45.35 2.59
504 505 2.043450 CCCTCTCTCGCAGGGTCT 60.043 66.667 0.00 0.00 45.35 3.85
508 509 2.363018 TGTCCCCTCTCTCGCAGG 60.363 66.667 0.00 0.00 0.00 4.85
509 510 2.888863 GTGTCCCCTCTCTCGCAG 59.111 66.667 0.00 0.00 0.00 5.18
510 511 3.062466 CGTGTCCCCTCTCTCGCA 61.062 66.667 0.00 0.00 0.00 5.10
511 512 3.827898 CCGTGTCCCCTCTCTCGC 61.828 72.222 0.00 0.00 0.00 5.03
512 513 3.827898 GCCGTGTCCCCTCTCTCG 61.828 72.222 0.00 0.00 0.00 4.04
513 514 2.363147 AGCCGTGTCCCCTCTCTC 60.363 66.667 0.00 0.00 0.00 3.20
514 515 2.363147 GAGCCGTGTCCCCTCTCT 60.363 66.667 0.00 0.00 0.00 3.10
515 516 3.462678 GGAGCCGTGTCCCCTCTC 61.463 72.222 0.00 0.00 0.00 3.20
516 517 3.625632 ATGGAGCCGTGTCCCCTCT 62.626 63.158 0.00 0.00 35.49 3.69
517 518 3.083997 ATGGAGCCGTGTCCCCTC 61.084 66.667 0.00 0.00 35.49 4.30
518 519 3.402681 CATGGAGCCGTGTCCCCT 61.403 66.667 0.45 0.00 35.49 4.79
519 520 4.489771 CCATGGAGCCGTGTCCCC 62.490 72.222 5.56 0.00 35.49 4.81
520 521 2.746375 ATCCATGGAGCCGTGTCCC 61.746 63.158 21.33 0.00 35.49 4.46
521 522 1.524621 CATCCATGGAGCCGTGTCC 60.525 63.158 21.33 0.00 37.10 4.02
522 523 4.131376 CATCCATGGAGCCGTGTC 57.869 61.111 21.33 0.00 0.00 3.67
532 533 3.635373 CACCTTCTCATTTCCCATCCATG 59.365 47.826 0.00 0.00 0.00 3.66
533 534 3.528905 TCACCTTCTCATTTCCCATCCAT 59.471 43.478 0.00 0.00 0.00 3.41
534 535 2.918934 TCACCTTCTCATTTCCCATCCA 59.081 45.455 0.00 0.00 0.00 3.41
535 536 3.282885 GTCACCTTCTCATTTCCCATCC 58.717 50.000 0.00 0.00 0.00 3.51
536 537 2.939103 CGTCACCTTCTCATTTCCCATC 59.061 50.000 0.00 0.00 0.00 3.51
537 538 2.305927 ACGTCACCTTCTCATTTCCCAT 59.694 45.455 0.00 0.00 0.00 4.00
538 539 1.697432 ACGTCACCTTCTCATTTCCCA 59.303 47.619 0.00 0.00 0.00 4.37
539 540 2.076863 CACGTCACCTTCTCATTTCCC 58.923 52.381 0.00 0.00 0.00 3.97
540 541 2.737252 GTCACGTCACCTTCTCATTTCC 59.263 50.000 0.00 0.00 0.00 3.13
541 542 2.737252 GGTCACGTCACCTTCTCATTTC 59.263 50.000 0.00 0.00 33.08 2.17
542 543 2.767505 GGTCACGTCACCTTCTCATTT 58.232 47.619 0.00 0.00 33.08 2.32
543 544 1.336887 CGGTCACGTCACCTTCTCATT 60.337 52.381 7.15 0.00 33.77 2.57
544 545 0.243907 CGGTCACGTCACCTTCTCAT 59.756 55.000 7.15 0.00 33.77 2.90
545 546 1.658114 CGGTCACGTCACCTTCTCA 59.342 57.895 7.15 0.00 33.77 3.27
582 583 2.586079 CGATGCAGGCGTAGGTGG 60.586 66.667 3.80 0.00 0.00 4.61
583 584 3.264897 GCGATGCAGGCGTAGGTG 61.265 66.667 12.49 0.00 0.00 4.00
688 690 0.035036 TTTGGCCGTGGTCATTACGA 59.965 50.000 0.00 0.00 43.82 3.43
689 691 0.875728 TTTTGGCCGTGGTCATTACG 59.124 50.000 0.00 0.00 40.98 3.18
690 692 2.156098 TCTTTTGGCCGTGGTCATTAC 58.844 47.619 0.00 0.00 0.00 1.89
691 693 2.570415 TCTTTTGGCCGTGGTCATTA 57.430 45.000 0.00 0.00 0.00 1.90
708 710 4.382345 GCTAGCTTTGCCATTTGATTCT 57.618 40.909 7.70 0.00 0.00 2.40
719 721 0.166814 CGTCACTTGGCTAGCTTTGC 59.833 55.000 15.72 0.00 0.00 3.68
726 728 2.656069 GGGGCTCGTCACTTGGCTA 61.656 63.158 0.00 0.00 0.00 3.93
729 731 4.760047 CCGGGGCTCGTCACTTGG 62.760 72.222 5.83 0.00 37.11 3.61
730 732 2.521958 AATCCGGGGCTCGTCACTTG 62.522 60.000 5.83 0.00 37.11 3.16
737 739 1.005630 GATGAGAATCCGGGGCTCG 60.006 63.158 0.00 0.00 38.88 5.03
740 742 2.432123 GGGATGAGAATCCGGGGC 59.568 66.667 0.00 0.00 41.63 5.80
755 757 1.218316 GCGAGATATAAGCCGGGGG 59.782 63.158 2.18 0.00 0.00 5.40
757 759 0.179161 CGAGCGAGATATAAGCCGGG 60.179 60.000 2.18 0.00 0.00 5.73
766 768 1.352056 CAGTGACGCGAGCGAGATA 59.648 57.895 24.72 4.25 42.83 1.98
768 770 4.103103 CCAGTGACGCGAGCGAGA 62.103 66.667 24.72 6.79 42.83 4.04
770 772 4.700365 CACCAGTGACGCGAGCGA 62.700 66.667 24.72 0.00 42.83 4.93
771 773 4.700365 TCACCAGTGACGCGAGCG 62.700 66.667 15.93 16.38 46.03 5.03
795 938 3.418068 GTCTGCAGCGTGCTCCAC 61.418 66.667 9.47 0.00 45.31 4.02
796 939 3.927548 TGTCTGCAGCGTGCTCCA 61.928 61.111 9.47 0.00 45.31 3.86
797 940 3.418068 GTGTCTGCAGCGTGCTCC 61.418 66.667 9.47 0.00 45.31 4.70
798 941 2.662857 TGTGTCTGCAGCGTGCTC 60.663 61.111 9.47 1.13 45.31 4.26
799 942 2.969238 GTGTGTCTGCAGCGTGCT 60.969 61.111 9.47 0.00 45.31 4.40
1026 1230 2.530916 AACTGGCCCGGGTAGGTT 60.531 61.111 24.63 20.01 38.74 3.50
1260 1464 1.805945 GTCCTCGTACGCCAGCTTG 60.806 63.158 11.24 0.00 0.00 4.01
1376 1592 1.076632 ACGCGGATCTCCTCCTTCT 60.077 57.895 12.47 0.00 42.47 2.85
1554 1770 3.474570 GACGCCTCCTCCATGGCT 61.475 66.667 6.96 0.00 46.42 4.75
1608 1824 3.430862 GGCATGAAACGAGCGGCA 61.431 61.111 1.45 0.00 0.00 5.69
1614 1830 2.230892 GTGTCACGGCATGAAACGA 58.769 52.632 11.05 0.00 39.72 3.85
1621 1837 1.139734 CTAGAGCGTGTCACGGCAT 59.860 57.895 25.70 13.05 42.82 4.40
1632 1848 0.179124 GGGACTCACTTGCTAGAGCG 60.179 60.000 1.04 0.00 45.83 5.03
1660 1876 1.066752 CATGCCATTGCCATGTCCG 59.933 57.895 0.00 0.00 36.33 4.79
1701 1917 5.008911 CCAAACTCACATTCACTGATTCACA 59.991 40.000 0.00 0.00 0.00 3.58
1724 1940 3.722147 AGAATGTACAGACATCGATGCC 58.278 45.455 25.11 14.96 45.93 4.40
1725 1941 4.615949 AGAGAATGTACAGACATCGATGC 58.384 43.478 25.11 17.04 45.93 3.91
1808 2025 6.698329 TGCTGAAATGTCAACTGAAATTCAAG 59.302 34.615 0.00 0.00 31.04 3.02
1894 2131 2.294791 TGATTTCGGTTTGCATTTCGGT 59.705 40.909 0.00 0.00 0.00 4.69
1961 2198 2.106683 GGACCAAATCGAGGCCACG 61.107 63.158 17.19 17.19 0.00 4.94
1963 2200 1.784301 TTGGGACCAAATCGAGGCCA 61.784 55.000 5.01 0.00 32.44 5.36
1979 2216 0.319727 ACGCATGCAAACCACATTGG 60.320 50.000 19.57 0.00 45.02 3.16
1980 2217 0.785378 CACGCATGCAAACCACATTG 59.215 50.000 19.57 0.00 0.00 2.82
1981 2218 0.388659 ACACGCATGCAAACCACATT 59.611 45.000 19.57 0.00 0.00 2.71
1982 2219 0.318869 CACACGCATGCAAACCACAT 60.319 50.000 19.57 0.00 0.00 3.21
1983 2220 1.065436 CACACGCATGCAAACCACA 59.935 52.632 19.57 0.00 0.00 4.17
1984 2221 2.302230 GCACACGCATGCAAACCAC 61.302 57.895 19.57 0.00 45.39 4.16
2054 2297 6.084326 TCTGATAACTTTGCCAGGAAAAAC 57.916 37.500 0.00 0.00 0.00 2.43
2077 2323 5.869579 TCACTAATCCTTCTGTGAGCTTTT 58.130 37.500 0.00 0.00 34.94 2.27
2103 2349 6.299922 GGCTGGAAGAAAACTATATAAGCCT 58.700 40.000 7.29 0.00 42.51 4.58
2104 2350 5.179555 CGGCTGGAAGAAAACTATATAAGCC 59.820 44.000 0.00 0.00 42.40 4.35
2142 2391 5.560724 AGTAGCCACACACAATTGAACTAT 58.439 37.500 13.59 0.00 0.00 2.12
2150 2409 4.041691 AGAGGTTAAGTAGCCACACACAAT 59.958 41.667 0.00 0.00 0.00 2.71
2208 2523 9.944376 ACACTTTTACTGATCTAAATGCTCTTA 57.056 29.630 0.00 0.00 0.00 2.10
2209 2524 8.725148 CACACTTTTACTGATCTAAATGCTCTT 58.275 33.333 0.00 0.00 0.00 2.85
2210 2525 8.097038 TCACACTTTTACTGATCTAAATGCTCT 58.903 33.333 0.00 0.00 0.00 4.09
2211 2526 8.256611 TCACACTTTTACTGATCTAAATGCTC 57.743 34.615 0.00 0.00 0.00 4.26
2212 2527 8.798859 ATCACACTTTTACTGATCTAAATGCT 57.201 30.769 0.00 0.00 0.00 3.79
2213 2528 9.846248 AAATCACACTTTTACTGATCTAAATGC 57.154 29.630 0.00 0.00 0.00 3.56
2219 2534 9.965902 AATCCTAAATCACACTTTTACTGATCT 57.034 29.630 0.00 0.00 0.00 2.75
2222 2537 9.567776 TGAAATCCTAAATCACACTTTTACTGA 57.432 29.630 0.00 0.00 0.00 3.41
2223 2538 9.831737 CTGAAATCCTAAATCACACTTTTACTG 57.168 33.333 0.00 0.00 0.00 2.74
2224 2539 9.014297 CCTGAAATCCTAAATCACACTTTTACT 57.986 33.333 0.00 0.00 0.00 2.24
2225 2540 8.244113 CCCTGAAATCCTAAATCACACTTTTAC 58.756 37.037 0.00 0.00 0.00 2.01
2226 2541 7.396055 CCCCTGAAATCCTAAATCACACTTTTA 59.604 37.037 0.00 0.00 0.00 1.52
2229 2544 5.015178 TCCCCTGAAATCCTAAATCACACTT 59.985 40.000 0.00 0.00 0.00 3.16
2254 2569 3.562973 GTGGTATGAGAGGCATCACATTG 59.437 47.826 16.17 0.00 37.78 2.82
2258 2573 2.169352 AGTGTGGTATGAGAGGCATCAC 59.831 50.000 0.00 0.00 38.44 3.06
2267 2582 4.402192 CCGCGAGTGTGGTATGAG 57.598 61.111 8.23 0.00 41.05 2.90
2281 2596 2.224670 TGGAATTATCCCCATGTACCGC 60.225 50.000 0.00 0.00 45.95 5.68
2284 2607 8.706322 AATTAGTTGGAATTATCCCCATGTAC 57.294 34.615 0.00 0.00 45.95 2.90
2405 2728 7.041635 TGGTGGCAATAATTCTGATAACATG 57.958 36.000 0.00 0.00 0.00 3.21
2413 2736 6.866480 ACACTAAATGGTGGCAATAATTCTG 58.134 36.000 1.94 0.00 41.09 3.02
2414 2737 7.397192 AGAACACTAAATGGTGGCAATAATTCT 59.603 33.333 1.94 0.00 41.09 2.40
2451 2774 5.871465 TGAACCAACAAAAAGCCTTTTTC 57.129 34.783 12.11 0.91 40.65 2.29
2455 2778 5.221441 GGAGTATGAACCAACAAAAAGCCTT 60.221 40.000 0.00 0.00 0.00 4.35
2464 2787 3.515502 CAGAGAGGGAGTATGAACCAACA 59.484 47.826 0.00 0.00 0.00 3.33
2540 2864 9.976511 TCCGACATATTTTTACACTATCTTAGG 57.023 33.333 0.00 0.00 0.00 2.69
2558 2882 9.274354 TCCCTCCATATTAAAATATCCGACATA 57.726 33.333 0.00 0.00 29.35 2.29
2559 2883 8.158025 TCCCTCCATATTAAAATATCCGACAT 57.842 34.615 0.00 0.00 29.35 3.06
2560 2884 7.562259 TCCCTCCATATTAAAATATCCGACA 57.438 36.000 0.00 0.00 29.35 4.35
2561 2885 7.499232 CCATCCCTCCATATTAAAATATCCGAC 59.501 40.741 0.00 0.00 29.35 4.79
2562 2886 7.404688 TCCATCCCTCCATATTAAAATATCCGA 59.595 37.037 0.00 0.00 29.35 4.55
2563 2887 7.573710 TCCATCCCTCCATATTAAAATATCCG 58.426 38.462 0.00 0.00 29.35 4.18
2564 2888 8.560903 ACTCCATCCCTCCATATTAAAATATCC 58.439 37.037 0.00 0.00 29.35 2.59
2567 2891 9.629649 AGTACTCCATCCCTCCATATTAAAATA 57.370 33.333 0.00 0.00 0.00 1.40
2568 2892 8.525729 AGTACTCCATCCCTCCATATTAAAAT 57.474 34.615 0.00 0.00 0.00 1.82
2569 2893 7.947782 AGTACTCCATCCCTCCATATTAAAA 57.052 36.000 0.00 0.00 0.00 1.52
2570 2894 7.947782 AAGTACTCCATCCCTCCATATTAAA 57.052 36.000 0.00 0.00 0.00 1.52
2571 2895 7.678598 CCTAAGTACTCCATCCCTCCATATTAA 59.321 40.741 0.00 0.00 0.00 1.40
2572 2896 7.189794 CCTAAGTACTCCATCCCTCCATATTA 58.810 42.308 0.00 0.00 0.00 0.98
2573 2897 6.026186 CCTAAGTACTCCATCCCTCCATATT 58.974 44.000 0.00 0.00 0.00 1.28
2574 2898 5.594777 CCTAAGTACTCCATCCCTCCATAT 58.405 45.833 0.00 0.00 0.00 1.78
2575 2899 4.756372 GCCTAAGTACTCCATCCCTCCATA 60.756 50.000 0.00 0.00 0.00 2.74
2576 2900 3.863086 CCTAAGTACTCCATCCCTCCAT 58.137 50.000 0.00 0.00 0.00 3.41
2577 2901 2.693074 GCCTAAGTACTCCATCCCTCCA 60.693 54.545 0.00 0.00 0.00 3.86
2578 2902 1.972075 GCCTAAGTACTCCATCCCTCC 59.028 57.143 0.00 0.00 0.00 4.30
2579 2903 1.614413 CGCCTAAGTACTCCATCCCTC 59.386 57.143 0.00 0.00 0.00 4.30
2580 2904 1.063114 ACGCCTAAGTACTCCATCCCT 60.063 52.381 0.00 0.00 0.00 4.20
2581 2905 1.068741 CACGCCTAAGTACTCCATCCC 59.931 57.143 0.00 0.00 0.00 3.85
2582 2906 1.755380 ACACGCCTAAGTACTCCATCC 59.245 52.381 0.00 0.00 0.00 3.51
2583 2907 3.521947 AACACGCCTAAGTACTCCATC 57.478 47.619 0.00 0.00 0.00 3.51
2584 2908 3.596214 CAAACACGCCTAAGTACTCCAT 58.404 45.455 0.00 0.00 0.00 3.41
2585 2909 2.289195 CCAAACACGCCTAAGTACTCCA 60.289 50.000 0.00 0.00 0.00 3.86
2586 2910 2.289257 ACCAAACACGCCTAAGTACTCC 60.289 50.000 0.00 0.00 0.00 3.85
2587 2911 3.036075 ACCAAACACGCCTAAGTACTC 57.964 47.619 0.00 0.00 0.00 2.59
2588 2912 3.135994 CAACCAAACACGCCTAAGTACT 58.864 45.455 0.00 0.00 0.00 2.73
2589 2913 2.874086 ACAACCAAACACGCCTAAGTAC 59.126 45.455 0.00 0.00 0.00 2.73
2590 2914 3.132925 GACAACCAAACACGCCTAAGTA 58.867 45.455 0.00 0.00 0.00 2.24
2591 2915 1.944709 GACAACCAAACACGCCTAAGT 59.055 47.619 0.00 0.00 0.00 2.24
2592 2916 2.032030 CAGACAACCAAACACGCCTAAG 60.032 50.000 0.00 0.00 0.00 2.18
2593 2917 1.944024 CAGACAACCAAACACGCCTAA 59.056 47.619 0.00 0.00 0.00 2.69
2594 2918 1.134340 ACAGACAACCAAACACGCCTA 60.134 47.619 0.00 0.00 0.00 3.93
2595 2919 0.393808 ACAGACAACCAAACACGCCT 60.394 50.000 0.00 0.00 0.00 5.52
2596 2920 1.003223 GTACAGACAACCAAACACGCC 60.003 52.381 0.00 0.00 0.00 5.68
2597 2921 1.937899 AGTACAGACAACCAAACACGC 59.062 47.619 0.00 0.00 0.00 5.34
2598 2922 3.191669 TCAGTACAGACAACCAAACACG 58.808 45.455 0.00 0.00 0.00 4.49
2599 2923 5.751243 AATCAGTACAGACAACCAAACAC 57.249 39.130 0.00 0.00 0.00 3.32
2600 2924 6.559810 CAAAATCAGTACAGACAACCAAACA 58.440 36.000 0.00 0.00 0.00 2.83
2601 2925 5.458779 GCAAAATCAGTACAGACAACCAAAC 59.541 40.000 0.00 0.00 0.00 2.93
2602 2926 5.451242 GGCAAAATCAGTACAGACAACCAAA 60.451 40.000 0.00 0.00 0.00 3.28
2603 2927 4.037446 GGCAAAATCAGTACAGACAACCAA 59.963 41.667 0.00 0.00 0.00 3.67
2604 2928 3.568007 GGCAAAATCAGTACAGACAACCA 59.432 43.478 0.00 0.00 0.00 3.67
2605 2929 3.821033 AGGCAAAATCAGTACAGACAACC 59.179 43.478 0.00 0.00 0.00 3.77
2606 2930 4.787598 CAGGCAAAATCAGTACAGACAAC 58.212 43.478 0.00 0.00 0.00 3.32
2607 2931 3.253188 GCAGGCAAAATCAGTACAGACAA 59.747 43.478 0.00 0.00 0.00 3.18
2608 2932 2.813754 GCAGGCAAAATCAGTACAGACA 59.186 45.455 0.00 0.00 0.00 3.41
2609 2933 3.477899 GCAGGCAAAATCAGTACAGAC 57.522 47.619 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.