Multiple sequence alignment - TraesCS6A01G366200

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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 TraesCS6A01G366200 chr6A 100.000 2555 0 0 1 2555 593993331 593990777 0.000000e+00 4719.0
1 TraesCS6A01G366200 chr6A 89.931 1162 85 18 824 1976 594254350 594253212 0.000000e+00 1469.0
2 TraesCS6A01G366200 chr6A 80.000 1560 162 70 877 2349 594319185 594320681 0.000000e+00 1014.0
3 TraesCS6A01G366200 chr6A 84.815 810 72 30 867 1645 594365616 594366405 0.000000e+00 767.0
4 TraesCS6A01G366200 chr6A 78.436 895 116 48 1321 2176 593929573 593928717 1.750000e-141 512.0
5 TraesCS6A01G366200 chr6A 85.422 391 32 8 1963 2352 594253192 594252826 1.430000e-102 383.0
6 TraesCS6A01G366200 chr6A 75.424 472 67 26 1330 1775 569678741 569678293 1.560000e-42 183.0
7 TraesCS6A01G366200 chr6A 98.684 76 1 0 2480 2555 454803426 454803501 4.430000e-28 135.0
8 TraesCS6A01G366200 chr6B 86.894 1526 115 32 867 2349 678174635 678176118 0.000000e+00 1631.0
9 TraesCS6A01G366200 chr6B 84.290 1585 132 52 815 2349 678356835 678358352 0.000000e+00 1439.0
10 TraesCS6A01G366200 chr6B 85.812 1022 108 27 815 1810 678092874 678091864 0.000000e+00 1050.0
11 TraesCS6A01G366200 chr6B 88.152 844 56 18 5 806 299044324 299045165 0.000000e+00 965.0
12 TraesCS6A01G366200 chr6B 83.348 1117 110 43 867 1943 677045688 677044608 0.000000e+00 963.0
13 TraesCS6A01G366200 chr6B 80.854 1358 140 66 922 2205 678542623 678543934 0.000000e+00 957.0
14 TraesCS6A01G366200 chr6B 82.318 1018 104 34 815 1787 676865978 676864992 0.000000e+00 813.0
15 TraesCS6A01G366200 chr6B 84.238 755 77 25 815 1531 677088456 677087706 0.000000e+00 697.0
16 TraesCS6A01G366200 chr6B 86.719 640 50 16 1327 1943 677336576 677335949 0.000000e+00 678.0
17 TraesCS6A01G366200 chr6B 87.145 599 71 6 5 600 107880870 107881465 0.000000e+00 675.0
18 TraesCS6A01G366200 chr6B 86.213 602 48 19 1651 2229 677087688 677087099 1.000000e-173 619.0
19 TraesCS6A01G366200 chr6B 85.739 568 45 22 1686 2230 677777854 677777300 3.690000e-158 568.0
20 TraesCS6A01G366200 chr6B 85.714 567 46 21 1686 2229 677910135 677909581 1.330000e-157 566.0
21 TraesCS6A01G366200 chr6B 86.085 539 49 16 1816 2349 678091819 678091302 7.990000e-155 556.0
22 TraesCS6A01G366200 chr6B 87.315 473 33 16 1773 2230 676865043 676864583 1.360000e-142 516.0
23 TraesCS6A01G366200 chr6B 80.349 458 50 18 867 1287 676492769 676492315 6.860000e-81 311.0
24 TraesCS6A01G366200 chr6B 78.701 385 51 22 1785 2160 676124196 676124558 7.110000e-56 228.0
25 TraesCS6A01G366200 chr6B 96.250 80 3 0 2476 2555 655972782 655972703 5.740000e-27 132.0
26 TraesCS6A01G366200 chr6B 94.444 54 3 0 2296 2349 677079706 677079653 1.630000e-12 84.2
27 TraesCS6A01G366200 chr6B 94.444 54 3 0 2296 2349 677906750 677906697 1.630000e-12 84.2
28 TraesCS6A01G366200 chr6B 94.118 51 3 0 2299 2349 677774639 677774589 7.580000e-11 78.7
29 TraesCS6A01G366200 chr7A 94.132 818 42 4 1 814 33074417 33073602 0.000000e+00 1240.0
30 TraesCS6A01G366200 chr7A 92.972 811 44 6 1 810 32687376 32688174 0.000000e+00 1170.0
31 TraesCS6A01G366200 chr6D 79.623 1644 168 73 815 2349 447737589 447739174 0.000000e+00 1026.0
32 TraesCS6A01G366200 chr6D 88.670 812 63 16 1544 2349 447278122 447277334 0.000000e+00 963.0
33 TraesCS6A01G366200 chr6D 84.972 885 79 29 815 1650 447279009 447278130 0.000000e+00 848.0
34 TraesCS6A01G366200 chr6D 88.809 277 22 5 1017 1287 447761176 447761449 5.270000e-87 331.0
35 TraesCS6A01G366200 chr5B 88.702 832 68 11 1 810 350367075 350366248 0.000000e+00 992.0
36 TraesCS6A01G366200 chr5B 98.684 76 1 0 2480 2555 17715347 17715272 4.430000e-28 135.0
37 TraesCS6A01G366200 chr4A 80.588 340 55 7 204 537 193100331 193100665 4.220000e-63 252.0
38 TraesCS6A01G366200 chr2A 80.236 339 57 8 204 537 15465452 15465785 1.960000e-61 246.0
39 TraesCS6A01G366200 chr2A 91.304 92 8 0 2464 2555 220576263 220576354 2.670000e-25 126.0
40 TraesCS6A01G366200 chr2A 78.462 130 17 8 669 790 36637060 36636934 9.800000e-10 75.0
41 TraesCS6A01G366200 chr7B 78.961 385 57 14 209 584 4798917 4799286 9.130000e-60 241.0
42 TraesCS6A01G366200 chrUn 79.208 303 52 7 205 499 225564962 225564663 1.550000e-47 200.0
43 TraesCS6A01G366200 chrUn 79.333 300 51 7 205 496 237459408 237459704 1.550000e-47 200.0
44 TraesCS6A01G366200 chrUn 79.333 300 51 7 205 496 257671124 257671420 1.550000e-47 200.0
45 TraesCS6A01G366200 chrUn 79.333 300 51 7 205 496 279681265 279681561 1.550000e-47 200.0
46 TraesCS6A01G366200 chr5D 98.684 76 1 0 2480 2555 542622699 542622624 4.430000e-28 135.0
47 TraesCS6A01G366200 chr5D 96.250 80 3 0 2476 2555 230391959 230392038 5.740000e-27 132.0
48 TraesCS6A01G366200 chr3A 98.684 76 1 0 2480 2555 215352024 215352099 4.430000e-28 135.0
49 TraesCS6A01G366200 chr4D 97.436 78 2 0 2478 2555 82851635 82851558 1.590000e-27 134.0
50 TraesCS6A01G366200 chr2B 94.253 87 4 1 2470 2555 406931226 406931140 5.740000e-27 132.0
51 TraesCS6A01G366200 chr5A 81.333 75 9 5 744 814 604234001 604233928 3.550000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G366200 chr6A 593990777 593993331 2554 True 4719.00 4719 100.0000 1 2555 1 chr6A.!!$R3 2554
1 TraesCS6A01G366200 chr6A 594319185 594320681 1496 False 1014.00 1014 80.0000 877 2349 1 chr6A.!!$F2 1472
2 TraesCS6A01G366200 chr6A 594252826 594254350 1524 True 926.00 1469 87.6765 824 2352 2 chr6A.!!$R4 1528
3 TraesCS6A01G366200 chr6A 594365616 594366405 789 False 767.00 767 84.8150 867 1645 1 chr6A.!!$F3 778
4 TraesCS6A01G366200 chr6A 593928717 593929573 856 True 512.00 512 78.4360 1321 2176 1 chr6A.!!$R2 855
5 TraesCS6A01G366200 chr6B 678174635 678176118 1483 False 1631.00 1631 86.8940 867 2349 1 chr6B.!!$F4 1482
6 TraesCS6A01G366200 chr6B 678356835 678358352 1517 False 1439.00 1439 84.2900 815 2349 1 chr6B.!!$F5 1534
7 TraesCS6A01G366200 chr6B 299044324 299045165 841 False 965.00 965 88.1520 5 806 1 chr6B.!!$F2 801
8 TraesCS6A01G366200 chr6B 677044608 677045688 1080 True 963.00 963 83.3480 867 1943 1 chr6B.!!$R3 1076
9 TraesCS6A01G366200 chr6B 678542623 678543934 1311 False 957.00 957 80.8540 922 2205 1 chr6B.!!$F6 1283
10 TraesCS6A01G366200 chr6B 678091302 678092874 1572 True 803.00 1050 85.9485 815 2349 2 chr6B.!!$R10 1534
11 TraesCS6A01G366200 chr6B 677335949 677336576 627 True 678.00 678 86.7190 1327 1943 1 chr6B.!!$R5 616
12 TraesCS6A01G366200 chr6B 107880870 107881465 595 False 675.00 675 87.1450 5 600 1 chr6B.!!$F1 595
13 TraesCS6A01G366200 chr6B 676864583 676865978 1395 True 664.50 813 84.8165 815 2230 2 chr6B.!!$R6 1415
14 TraesCS6A01G366200 chr6B 677087099 677088456 1357 True 658.00 697 85.2255 815 2229 2 chr6B.!!$R7 1414
15 TraesCS6A01G366200 chr6B 677906697 677910135 3438 True 325.10 566 90.0790 1686 2349 2 chr6B.!!$R9 663
16 TraesCS6A01G366200 chr6B 677774589 677777854 3265 True 323.35 568 89.9285 1686 2349 2 chr6B.!!$R8 663
17 TraesCS6A01G366200 chr7A 33073602 33074417 815 True 1240.00 1240 94.1320 1 814 1 chr7A.!!$R1 813
18 TraesCS6A01G366200 chr7A 32687376 32688174 798 False 1170.00 1170 92.9720 1 810 1 chr7A.!!$F1 809
19 TraesCS6A01G366200 chr6D 447737589 447739174 1585 False 1026.00 1026 79.6230 815 2349 1 chr6D.!!$F1 1534
20 TraesCS6A01G366200 chr6D 447277334 447279009 1675 True 905.50 963 86.8210 815 2349 2 chr6D.!!$R1 1534
21 TraesCS6A01G366200 chr5B 350366248 350367075 827 True 992.00 992 88.7020 1 810 1 chr5B.!!$R2 809

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
908 984 0.179936 CCAACAGGCTCCCATCTCTC 59.82 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2416 0.321996 GATGGATAAGCCTCCCGTCC 59.678 60.0 0.0 0.0 37.63 4.79 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
68 69 4.553156 GCAAAAACACCGAGATGTCGTTTA 60.553 41.667 11.66 0.00 45.30 2.01
190 194 2.628106 CAAATCTCGCCCGCATCG 59.372 61.111 0.00 0.00 0.00 3.84
273 278 2.920524 TGAAGCTTTTTACCACCGTCA 58.079 42.857 0.00 0.00 0.00 4.35
411 438 3.103911 GTCGTCCCAAGTCGCACG 61.104 66.667 0.00 0.00 0.00 5.34
476 503 5.101628 GCAAAATCCGATTACAATTGCAGA 58.898 37.500 17.58 0.00 40.86 4.26
572 599 1.942657 ACATGCAATCACTATGGTCGC 59.057 47.619 0.00 0.00 0.00 5.19
574 601 2.106477 TGCAATCACTATGGTCGCAA 57.894 45.000 0.00 0.00 0.00 4.85
722 784 1.067915 CAAACGTGGATTGCCCGATTT 60.068 47.619 0.00 0.00 37.93 2.17
811 874 3.006003 GGTGCCAAACGATTCCCTTTTAA 59.994 43.478 0.00 0.00 0.00 1.52
812 875 4.322424 GGTGCCAAACGATTCCCTTTTAAT 60.322 41.667 0.00 0.00 0.00 1.40
833 896 0.606604 TTAACTCGGCCAGACTCCAC 59.393 55.000 2.24 0.00 0.00 4.02
834 897 0.541063 TAACTCGGCCAGACTCCACA 60.541 55.000 2.24 0.00 0.00 4.17
849 912 0.872388 CCACAGTTCTTAACGCCCAC 59.128 55.000 0.00 0.00 36.23 4.61
865 939 2.224161 GCCCACAATTTACCAAACTGCA 60.224 45.455 0.00 0.00 0.00 4.41
894 970 1.407258 GCCTATAAATTGCGGCCAACA 59.593 47.619 2.24 0.00 36.56 3.33
908 984 0.179936 CCAACAGGCTCCCATCTCTC 59.820 60.000 0.00 0.00 0.00 3.20
925 1006 1.571215 CTCGTTACCCAAACCGGCAC 61.571 60.000 0.00 0.00 34.33 5.01
931 1012 2.902846 CCAAACCGGCACCGAACA 60.903 61.111 11.42 0.00 42.83 3.18
966 1063 2.437716 ATACCAAAGCCACCGCCG 60.438 61.111 0.00 0.00 34.57 6.46
986 1112 2.882137 CGGAGTCCACCTCTCTAATCTC 59.118 54.545 10.49 0.00 40.30 2.75
987 1113 3.434453 CGGAGTCCACCTCTCTAATCTCT 60.434 52.174 10.49 0.00 40.30 3.10
988 1114 4.142038 GGAGTCCACCTCTCTAATCTCTC 58.858 52.174 3.60 0.00 40.30 3.20
989 1115 4.385865 GGAGTCCACCTCTCTAATCTCTCA 60.386 50.000 3.60 0.00 40.30 3.27
990 1116 5.385198 GAGTCCACCTCTCTAATCTCTCAT 58.615 45.833 0.00 0.00 37.22 2.90
991 1117 5.385198 AGTCCACCTCTCTAATCTCTCATC 58.615 45.833 0.00 0.00 0.00 2.92
992 1118 5.103728 AGTCCACCTCTCTAATCTCTCATCA 60.104 44.000 0.00 0.00 0.00 3.07
995 1121 5.774184 CCACCTCTCTAATCTCTCATCATCA 59.226 44.000 0.00 0.00 0.00 3.07
1007 1133 6.827727 TCTCTCATCATCACATCATGTCAAT 58.172 36.000 0.00 0.00 0.00 2.57
1010 1136 5.442391 TCATCATCACATCATGTCAATGGT 58.558 37.500 9.00 0.96 34.30 3.55
1044 1170 2.038975 AGCGGCCCTGTCCTTCTA 59.961 61.111 0.00 0.00 0.00 2.10
1066 1192 1.919240 CCCCTTTCCCAACTACCAAC 58.081 55.000 0.00 0.00 0.00 3.77
1322 1493 3.782244 CCTGTTCACGCAGCTCGC 61.782 66.667 5.63 2.29 43.23 5.03
1529 1732 0.031449 GCCGCAGCAACCAGTAAAAA 59.969 50.000 0.00 0.00 39.53 1.94
1530 1733 1.766069 CCGCAGCAACCAGTAAAAAC 58.234 50.000 0.00 0.00 0.00 2.43
1540 1747 5.578727 GCAACCAGTAAAAACAACAACATCA 59.421 36.000 0.00 0.00 0.00 3.07
1567 1895 1.871080 ACCATAGCAGCAAGATACGC 58.129 50.000 0.00 0.00 0.00 4.42
1645 1987 2.840640 TAGAAGGAAGATCGGTGGGA 57.159 50.000 0.00 0.00 0.00 4.37
1646 1988 2.182516 AGAAGGAAGATCGGTGGGAT 57.817 50.000 0.00 0.00 38.35 3.85
1739 2140 1.077828 TGAGCCTCTTCTTCCTCTCCA 59.922 52.381 0.00 0.00 0.00 3.86
1743 2144 2.888069 GCCTCTTCTTCCTCTCCACTCT 60.888 54.545 0.00 0.00 0.00 3.24
1771 2179 3.125487 ACATAGAGTGAGTTCGTCGTCTG 59.875 47.826 0.00 0.00 0.00 3.51
1812 2226 1.064758 TGAGCTCTCTCCTCTCTGTCC 60.065 57.143 16.19 0.00 38.58 4.02
1884 2387 6.092944 ACAACGAGTCACAAATTGTAGACAAA 59.907 34.615 21.46 0.00 39.55 2.83
1885 2388 6.861065 ACGAGTCACAAATTGTAGACAAAT 57.139 33.333 21.46 8.83 39.55 2.32
1886 2389 7.956420 ACGAGTCACAAATTGTAGACAAATA 57.044 32.000 21.46 0.00 39.55 1.40
1887 2390 7.793902 ACGAGTCACAAATTGTAGACAAATAC 58.206 34.615 21.46 11.53 39.55 1.89
1888 2391 7.656137 ACGAGTCACAAATTGTAGACAAATACT 59.344 33.333 21.46 8.08 39.55 2.12
1912 2416 1.871676 CATGCATCTGATCTGTTCCGG 59.128 52.381 0.00 0.00 0.00 5.14
1958 2486 2.023673 TCATGGATGATTTGCCGAACC 58.976 47.619 0.00 0.00 0.00 3.62
1970 2534 1.202710 TGCCGAACCACTTTCTGCTTA 60.203 47.619 2.74 0.00 43.10 3.09
1999 2581 0.320683 TTCTGGAGTGTGGATGCGTG 60.321 55.000 0.00 0.00 0.00 5.34
2015 2597 1.006571 GTGTCGCCTCTGTTTCGGA 60.007 57.895 0.00 0.00 0.00 4.55
2029 2611 2.417339 TTCGGATTCGGATAAGCTCG 57.583 50.000 0.00 0.00 36.95 5.03
2050 2632 1.066573 AGAAAGGATCAGTGGCGTCTG 60.067 52.381 0.00 3.60 36.85 3.51
2177 2764 1.301322 TGGAACTTCATGACGCGCA 60.301 52.632 5.73 5.73 0.00 6.09
2217 2804 4.937201 TTTTTCTTCTTCTTTCCCTGCC 57.063 40.909 0.00 0.00 0.00 4.85
2221 2808 2.443255 TCTTCTTCTTTCCCTGCCTGTT 59.557 45.455 0.00 0.00 0.00 3.16
2230 2901 5.724854 TCTTTCCCTGCCTGTTAAGTACTAT 59.275 40.000 0.00 0.00 0.00 2.12
2231 2902 6.214819 TCTTTCCCTGCCTGTTAAGTACTATT 59.785 38.462 0.00 0.00 0.00 1.73
2352 5717 7.385267 GCTCAACTGATGAACTGAGGATATAT 58.615 38.462 0.00 0.00 37.67 0.86
2353 5718 7.545265 GCTCAACTGATGAACTGAGGATATATC 59.455 40.741 3.96 3.96 37.67 1.63
2354 5719 8.482852 TCAACTGATGAACTGAGGATATATCA 57.517 34.615 14.60 0.00 34.30 2.15
2355 5720 8.927411 TCAACTGATGAACTGAGGATATATCAA 58.073 33.333 14.60 0.00 34.30 2.57
2356 5721 9.722184 CAACTGATGAACTGAGGATATATCAAT 57.278 33.333 14.60 2.37 0.00 2.57
2368 5733 9.866655 TGAGGATATATCAATTTTAACCTTGCT 57.133 29.630 14.60 0.00 0.00 3.91
2385 5750 8.691661 AACCTTGCTATTTTACTCTTCTTTCA 57.308 30.769 0.00 0.00 0.00 2.69
2386 5751 8.691661 ACCTTGCTATTTTACTCTTCTTTCAA 57.308 30.769 0.00 0.00 0.00 2.69
2387 5752 9.131791 ACCTTGCTATTTTACTCTTCTTTCAAA 57.868 29.630 0.00 0.00 0.00 2.69
2388 5753 9.617975 CCTTGCTATTTTACTCTTCTTTCAAAG 57.382 33.333 0.00 0.00 0.00 2.77
2389 5754 9.122613 CTTGCTATTTTACTCTTCTTTCAAAGC 57.877 33.333 0.00 0.00 0.00 3.51
2390 5755 8.165239 TGCTATTTTACTCTTCTTTCAAAGCA 57.835 30.769 0.00 0.00 0.00 3.91
2391 5756 8.292448 TGCTATTTTACTCTTCTTTCAAAGCAG 58.708 33.333 0.00 0.00 0.00 4.24
2392 5757 8.293157 GCTATTTTACTCTTCTTTCAAAGCAGT 58.707 33.333 0.00 0.06 0.00 4.40
2393 5758 9.604626 CTATTTTACTCTTCTTTCAAAGCAGTG 57.395 33.333 0.00 0.00 0.00 3.66
2394 5759 6.377327 TTTACTCTTCTTTCAAAGCAGTGG 57.623 37.500 4.28 0.00 0.00 4.00
2395 5760 2.620585 ACTCTTCTTTCAAAGCAGTGGC 59.379 45.455 4.28 0.00 41.61 5.01
2396 5761 2.620115 CTCTTCTTTCAAAGCAGTGGCA 59.380 45.455 0.00 0.00 44.61 4.92
2397 5762 3.225104 TCTTCTTTCAAAGCAGTGGCAT 58.775 40.909 0.00 0.00 44.61 4.40
2398 5763 3.005050 TCTTCTTTCAAAGCAGTGGCATG 59.995 43.478 0.00 0.00 44.61 4.06
2399 5764 2.585330 TCTTTCAAAGCAGTGGCATGA 58.415 42.857 0.00 0.00 44.61 3.07
2400 5765 2.555325 TCTTTCAAAGCAGTGGCATGAG 59.445 45.455 0.00 0.00 44.61 2.90
2401 5766 1.250328 TTCAAAGCAGTGGCATGAGG 58.750 50.000 0.00 0.00 44.61 3.86
2402 5767 0.609957 TCAAAGCAGTGGCATGAGGG 60.610 55.000 0.00 0.00 44.61 4.30
2403 5768 0.609957 CAAAGCAGTGGCATGAGGGA 60.610 55.000 0.00 0.00 44.61 4.20
2404 5769 0.610232 AAAGCAGTGGCATGAGGGAC 60.610 55.000 0.00 0.00 44.61 4.46
2405 5770 1.782201 AAGCAGTGGCATGAGGGACA 61.782 55.000 0.00 0.00 44.61 4.02
2406 5771 1.748122 GCAGTGGCATGAGGGACAG 60.748 63.158 0.00 0.00 40.72 3.51
2407 5772 1.748122 CAGTGGCATGAGGGACAGC 60.748 63.158 0.00 0.00 0.00 4.40
2408 5773 2.821366 GTGGCATGAGGGACAGCG 60.821 66.667 0.00 0.00 0.00 5.18
2409 5774 3.321648 TGGCATGAGGGACAGCGT 61.322 61.111 0.00 0.00 0.00 5.07
2410 5775 1.987306 TGGCATGAGGGACAGCGTA 60.987 57.895 0.00 0.00 0.00 4.42
2411 5776 1.227380 GGCATGAGGGACAGCGTAG 60.227 63.158 0.00 0.00 0.00 3.51
2424 5789 4.120085 CGTAGCGGTTGGGATTCC 57.880 61.111 0.00 0.00 0.00 3.01
2425 5790 1.523032 CGTAGCGGTTGGGATTCCC 60.523 63.158 15.40 15.40 45.71 3.97
2436 5801 3.850454 GGATTCCCCCTCCCAAATC 57.150 57.895 0.00 0.00 0.00 2.17
2437 5802 1.235756 GGATTCCCCCTCCCAAATCT 58.764 55.000 0.00 0.00 0.00 2.40
2438 5803 1.575788 GGATTCCCCCTCCCAAATCTT 59.424 52.381 0.00 0.00 0.00 2.40
2439 5804 2.789399 GGATTCCCCCTCCCAAATCTTA 59.211 50.000 0.00 0.00 0.00 2.10
2440 5805 3.206639 GGATTCCCCCTCCCAAATCTTAA 59.793 47.826 0.00 0.00 0.00 1.85
2441 5806 4.326610 GGATTCCCCCTCCCAAATCTTAAA 60.327 45.833 0.00 0.00 0.00 1.52
2442 5807 4.984642 TTCCCCCTCCCAAATCTTAAAT 57.015 40.909 0.00 0.00 0.00 1.40
2443 5808 4.984642 TCCCCCTCCCAAATCTTAAATT 57.015 40.909 0.00 0.00 0.00 1.82
2444 5809 4.619679 TCCCCCTCCCAAATCTTAAATTG 58.380 43.478 0.00 0.00 0.00 2.32
2445 5810 3.134623 CCCCCTCCCAAATCTTAAATTGC 59.865 47.826 0.00 0.00 0.00 3.56
2446 5811 3.774216 CCCCTCCCAAATCTTAAATTGCA 59.226 43.478 0.00 0.00 0.00 4.08
2447 5812 4.383010 CCCCTCCCAAATCTTAAATTGCAC 60.383 45.833 0.00 0.00 0.00 4.57
2448 5813 4.222588 CCCTCCCAAATCTTAAATTGCACA 59.777 41.667 0.00 0.00 0.00 4.57
2449 5814 5.413499 CCTCCCAAATCTTAAATTGCACAG 58.587 41.667 0.00 0.00 0.00 3.66
2450 5815 5.404466 TCCCAAATCTTAAATTGCACAGG 57.596 39.130 0.00 0.00 0.00 4.00
2451 5816 5.083122 TCCCAAATCTTAAATTGCACAGGA 58.917 37.500 0.00 0.00 0.00 3.86
2452 5817 5.541868 TCCCAAATCTTAAATTGCACAGGAA 59.458 36.000 0.00 0.00 0.00 3.36
2453 5818 5.870978 CCCAAATCTTAAATTGCACAGGAAG 59.129 40.000 0.00 0.00 0.00 3.46
2454 5819 5.870978 CCAAATCTTAAATTGCACAGGAAGG 59.129 40.000 0.00 0.00 0.00 3.46
2455 5820 6.295236 CCAAATCTTAAATTGCACAGGAAGGA 60.295 38.462 0.00 0.00 0.00 3.36
2456 5821 6.916360 AATCTTAAATTGCACAGGAAGGAA 57.084 33.333 0.00 0.00 0.00 3.36
2457 5822 5.964958 TCTTAAATTGCACAGGAAGGAAG 57.035 39.130 0.00 0.00 0.00 3.46
2458 5823 5.630121 TCTTAAATTGCACAGGAAGGAAGA 58.370 37.500 0.00 0.00 0.00 2.87
2459 5824 6.248433 TCTTAAATTGCACAGGAAGGAAGAT 58.752 36.000 0.00 0.00 0.00 2.40
2460 5825 4.796038 AAATTGCACAGGAAGGAAGATG 57.204 40.909 0.00 0.00 0.00 2.90
2461 5826 2.205022 TTGCACAGGAAGGAAGATGG 57.795 50.000 0.00 0.00 0.00 3.51
2462 5827 1.067295 TGCACAGGAAGGAAGATGGT 58.933 50.000 0.00 0.00 0.00 3.55
2463 5828 1.271543 TGCACAGGAAGGAAGATGGTG 60.272 52.381 0.00 0.00 0.00 4.17
2464 5829 1.271597 GCACAGGAAGGAAGATGGTGT 60.272 52.381 0.00 0.00 0.00 4.16
2465 5830 2.815589 GCACAGGAAGGAAGATGGTGTT 60.816 50.000 0.00 0.00 0.00 3.32
2466 5831 2.816087 CACAGGAAGGAAGATGGTGTTG 59.184 50.000 0.00 0.00 0.00 3.33
2467 5832 2.224867 ACAGGAAGGAAGATGGTGTTGG 60.225 50.000 0.00 0.00 0.00 3.77
2468 5833 2.040278 CAGGAAGGAAGATGGTGTTGGA 59.960 50.000 0.00 0.00 0.00 3.53
2469 5834 2.716424 AGGAAGGAAGATGGTGTTGGAA 59.284 45.455 0.00 0.00 0.00 3.53
2470 5835 3.140144 AGGAAGGAAGATGGTGTTGGAAA 59.860 43.478 0.00 0.00 0.00 3.13
2471 5836 3.895041 GGAAGGAAGATGGTGTTGGAAAA 59.105 43.478 0.00 0.00 0.00 2.29
2472 5837 4.528206 GGAAGGAAGATGGTGTTGGAAAAT 59.472 41.667 0.00 0.00 0.00 1.82
2473 5838 5.336770 GGAAGGAAGATGGTGTTGGAAAATC 60.337 44.000 0.00 0.00 0.00 2.17
2474 5839 3.758554 AGGAAGATGGTGTTGGAAAATCG 59.241 43.478 0.00 0.00 0.00 3.34
2475 5840 3.119495 GGAAGATGGTGTTGGAAAATCGG 60.119 47.826 0.00 0.00 0.00 4.18
2476 5841 3.154827 AGATGGTGTTGGAAAATCGGT 57.845 42.857 0.00 0.00 0.00 4.69
2477 5842 2.819608 AGATGGTGTTGGAAAATCGGTG 59.180 45.455 0.00 0.00 0.00 4.94
2478 5843 1.323412 TGGTGTTGGAAAATCGGTGG 58.677 50.000 0.00 0.00 0.00 4.61
2479 5844 1.324383 GGTGTTGGAAAATCGGTGGT 58.676 50.000 0.00 0.00 0.00 4.16
2480 5845 2.158652 TGGTGTTGGAAAATCGGTGGTA 60.159 45.455 0.00 0.00 0.00 3.25
2481 5846 2.227149 GGTGTTGGAAAATCGGTGGTAC 59.773 50.000 0.00 0.00 0.00 3.34
2482 5847 3.143728 GTGTTGGAAAATCGGTGGTACT 58.856 45.455 0.00 0.00 0.00 2.73
2483 5848 3.187842 GTGTTGGAAAATCGGTGGTACTC 59.812 47.826 0.00 0.00 0.00 2.59
2484 5849 2.745821 GTTGGAAAATCGGTGGTACTCC 59.254 50.000 0.00 0.00 38.86 3.85
2485 5850 1.279846 TGGAAAATCGGTGGTACTCCC 59.720 52.381 0.00 0.00 39.09 4.30
2486 5851 1.558294 GGAAAATCGGTGGTACTCCCT 59.442 52.381 0.00 0.00 39.09 4.20
2487 5852 2.419713 GGAAAATCGGTGGTACTCCCTC 60.420 54.545 0.00 0.00 39.09 4.30
2488 5853 1.201424 AAATCGGTGGTACTCCCTCC 58.799 55.000 0.00 0.00 42.51 4.30
2489 5854 0.338814 AATCGGTGGTACTCCCTCCT 59.661 55.000 0.00 0.00 43.57 3.69
2490 5855 0.338814 ATCGGTGGTACTCCCTCCTT 59.661 55.000 0.00 0.00 43.57 3.36
2491 5856 0.115745 TCGGTGGTACTCCCTCCTTT 59.884 55.000 0.00 0.00 43.57 3.11
2492 5857 0.981943 CGGTGGTACTCCCTCCTTTT 59.018 55.000 0.00 0.00 43.57 2.27
2493 5858 1.066358 CGGTGGTACTCCCTCCTTTTC 60.066 57.143 0.00 0.00 43.57 2.29
2494 5859 1.066358 GGTGGTACTCCCTCCTTTTCG 60.066 57.143 0.00 0.00 42.63 3.46
2495 5860 1.066358 GTGGTACTCCCTCCTTTTCGG 60.066 57.143 0.00 0.00 0.00 4.30
2496 5861 1.273759 GGTACTCCCTCCTTTTCGGT 58.726 55.000 0.00 0.00 0.00 4.69
2497 5862 1.627329 GGTACTCCCTCCTTTTCGGTT 59.373 52.381 0.00 0.00 0.00 4.44
2498 5863 2.039480 GGTACTCCCTCCTTTTCGGTTT 59.961 50.000 0.00 0.00 0.00 3.27
2499 5864 3.261643 GGTACTCCCTCCTTTTCGGTTTA 59.738 47.826 0.00 0.00 0.00 2.01
2500 5865 4.080695 GGTACTCCCTCCTTTTCGGTTTAT 60.081 45.833 0.00 0.00 0.00 1.40
2501 5866 5.129320 GGTACTCCCTCCTTTTCGGTTTATA 59.871 44.000 0.00 0.00 0.00 0.98
2502 5867 5.354842 ACTCCCTCCTTTTCGGTTTATAG 57.645 43.478 0.00 0.00 0.00 1.31
2503 5868 5.028131 ACTCCCTCCTTTTCGGTTTATAGA 58.972 41.667 0.00 0.00 0.00 1.98
2504 5869 5.128991 ACTCCCTCCTTTTCGGTTTATAGAG 59.871 44.000 0.00 0.00 0.00 2.43
2505 5870 4.127907 CCCTCCTTTTCGGTTTATAGAGC 58.872 47.826 0.00 0.00 0.00 4.09
2506 5871 4.141688 CCCTCCTTTTCGGTTTATAGAGCT 60.142 45.833 0.00 0.00 0.00 4.09
2507 5872 5.429130 CCTCCTTTTCGGTTTATAGAGCTT 58.571 41.667 0.00 0.00 0.00 3.74
2508 5873 6.407752 CCCTCCTTTTCGGTTTATAGAGCTTA 60.408 42.308 0.00 0.00 0.00 3.09
2509 5874 7.217906 CCTCCTTTTCGGTTTATAGAGCTTAT 58.782 38.462 0.00 0.00 0.00 1.73
2510 5875 7.385478 CCTCCTTTTCGGTTTATAGAGCTTATC 59.615 40.741 0.00 0.00 0.00 1.75
2511 5876 8.019656 TCCTTTTCGGTTTATAGAGCTTATCT 57.980 34.615 0.00 0.00 42.47 1.98
2512 5877 8.483758 TCCTTTTCGGTTTATAGAGCTTATCTT 58.516 33.333 0.00 0.00 39.64 2.40
2513 5878 9.760077 CCTTTTCGGTTTATAGAGCTTATCTTA 57.240 33.333 0.00 0.00 39.64 2.10
2550 5915 9.447157 TTTTCCATTTTATAAGGCTCAATTTGG 57.553 29.630 0.00 0.00 0.00 3.28
2551 5916 7.732222 TCCATTTTATAAGGCTCAATTTGGT 57.268 32.000 0.00 0.00 0.00 3.67
2552 5917 8.144862 TCCATTTTATAAGGCTCAATTTGGTT 57.855 30.769 0.00 0.00 0.00 3.67
2553 5918 8.040132 TCCATTTTATAAGGCTCAATTTGGTTG 58.960 33.333 0.00 0.00 39.25 3.77
2554 5919 7.823799 CCATTTTATAAGGCTCAATTTGGTTGT 59.176 33.333 0.00 0.00 38.95 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 2.094390 ACTGCATTTTGCTTCATCGCAT 60.094 40.909 0.75 0.00 45.31 4.73
115 118 2.032117 CACATCGCAAAGTGCTACAACA 60.032 45.455 0.00 0.00 42.25 3.33
201 205 1.963515 AGAAAAAGCTTCAACGGGCAT 59.036 42.857 0.00 0.00 0.00 4.40
286 291 0.899720 CCCTAGTTCGTGCAACCCTA 59.100 55.000 0.00 0.00 35.28 3.53
346 373 0.169230 TGTTGTCTTTTTGTGCGCGT 59.831 45.000 8.43 0.00 0.00 6.01
347 374 1.007524 GTTGTTGTCTTTTTGTGCGCG 60.008 47.619 0.00 0.00 0.00 6.86
348 375 1.989165 TGTTGTTGTCTTTTTGTGCGC 59.011 42.857 0.00 0.00 0.00 6.09
411 438 4.132336 TGCTAGATCAATTCATGGCAGAC 58.868 43.478 0.00 0.00 0.00 3.51
492 519 3.792047 CTACGACCCGCGACGACA 61.792 66.667 21.82 11.14 44.57 4.35
549 576 3.699067 GACCATAGTGATTGCATGTTGC 58.301 45.455 0.00 0.00 45.29 4.17
612 650 9.144747 CTCGTTCAGATTTCTTCTTATCTTCAA 57.855 33.333 0.00 0.00 29.93 2.69
811 874 2.304761 TGGAGTCTGGCCGAGTTAAAAT 59.695 45.455 0.00 0.00 0.00 1.82
812 875 1.695242 TGGAGTCTGGCCGAGTTAAAA 59.305 47.619 0.00 0.00 0.00 1.52
833 896 3.915437 AATTGTGGGCGTTAAGAACTG 57.085 42.857 0.00 0.00 0.00 3.16
834 897 4.216902 GGTAAATTGTGGGCGTTAAGAACT 59.783 41.667 0.00 0.00 0.00 3.01
849 912 4.306600 GGAAGGTGCAGTTTGGTAAATTG 58.693 43.478 0.00 0.00 0.00 2.32
865 939 2.751816 GCAATTTATAGGCCGGGAAGGT 60.752 50.000 2.18 0.00 43.70 3.50
894 970 1.404843 GTAACGAGAGATGGGAGCCT 58.595 55.000 0.00 0.00 0.00 4.58
908 984 2.619165 GGTGCCGGTTTGGGTAACG 61.619 63.158 1.90 0.00 37.64 3.18
931 1012 0.687354 ATGTGAGTTGAGCTCCGGTT 59.313 50.000 12.15 0.00 43.48 4.44
968 1065 4.871871 TGAGAGATTAGAGAGGTGGACT 57.128 45.455 0.00 0.00 0.00 3.85
969 1066 5.136828 TGATGAGAGATTAGAGAGGTGGAC 58.863 45.833 0.00 0.00 0.00 4.02
986 1112 5.531287 ACCATTGACATGATGTGATGATGAG 59.469 40.000 15.94 5.88 31.07 2.90
987 1113 5.298276 CACCATTGACATGATGTGATGATGA 59.702 40.000 15.94 0.00 31.07 2.92
988 1114 5.507315 CCACCATTGACATGATGTGATGATG 60.507 44.000 15.94 11.14 31.07 3.07
989 1115 4.583073 CCACCATTGACATGATGTGATGAT 59.417 41.667 15.94 1.08 31.07 2.45
990 1116 3.949113 CCACCATTGACATGATGTGATGA 59.051 43.478 15.94 0.00 31.07 2.92
991 1117 3.697542 ACCACCATTGACATGATGTGATG 59.302 43.478 1.23 7.14 31.07 3.07
992 1118 3.972133 ACCACCATTGACATGATGTGAT 58.028 40.909 1.23 0.00 31.07 3.06
995 1121 2.231964 GCAACCACCATTGACATGATGT 59.768 45.455 0.00 0.00 31.07 3.06
1007 1133 2.359850 GCCGAGATGCAACCACCA 60.360 61.111 0.00 0.00 0.00 4.17
1010 1136 3.626996 CTGGGCCGAGATGCAACCA 62.627 63.158 9.58 0.00 0.00 3.67
1044 1170 0.408309 GGTAGTTGGGAAAGGGGCTT 59.592 55.000 0.00 0.00 0.00 4.35
1488 1678 4.161295 CATGGAGGCGGCGGAGAA 62.161 66.667 9.78 0.00 0.00 2.87
1529 1732 4.574892 TGGTATGTCGATGATGTTGTTGT 58.425 39.130 0.00 0.00 0.00 3.32
1530 1733 5.739752 ATGGTATGTCGATGATGTTGTTG 57.260 39.130 0.00 0.00 0.00 3.33
1540 1747 3.321968 TCTTGCTGCTATGGTATGTCGAT 59.678 43.478 0.00 0.00 0.00 3.59
1567 1895 5.611796 ATGTACAGTTTGTGCAGTATGTG 57.388 39.130 0.33 0.00 45.60 3.21
1645 1987 5.319043 TGGGTCTTAAAACTCCAACTGAT 57.681 39.130 0.00 0.00 0.00 2.90
1646 1988 4.781775 TGGGTCTTAAAACTCCAACTGA 57.218 40.909 0.00 0.00 0.00 3.41
1647 1989 6.405278 AATTGGGTCTTAAAACTCCAACTG 57.595 37.500 4.58 0.00 39.85 3.16
1743 2144 2.672195 CGAACTCACTCTATGTGCAGCA 60.672 50.000 0.00 0.00 45.81 4.41
1771 2179 4.082190 TCACTCTATGTACAAGTGGAGCAC 60.082 45.833 20.69 0.00 40.60 4.40
1802 2216 1.034838 ACAGCTAGCGGACAGAGAGG 61.035 60.000 22.16 0.00 0.00 3.69
1804 2218 0.609406 ACACAGCTAGCGGACAGAGA 60.609 55.000 22.16 0.00 0.00 3.10
1806 2220 1.763968 ATACACAGCTAGCGGACAGA 58.236 50.000 22.16 4.12 0.00 3.41
1812 2226 0.962489 AGGGCTATACACAGCTAGCG 59.038 55.000 9.55 7.05 41.01 4.26
1884 2387 6.416631 ACAGATCAGATGCATGTACAGTAT 57.583 37.500 2.46 0.00 0.00 2.12
1885 2388 5.859205 ACAGATCAGATGCATGTACAGTA 57.141 39.130 2.46 0.00 0.00 2.74
1886 2389 4.750021 ACAGATCAGATGCATGTACAGT 57.250 40.909 2.46 0.00 0.00 3.55
1887 2390 4.510711 GGAACAGATCAGATGCATGTACAG 59.489 45.833 2.46 0.00 0.00 2.74
1888 2391 4.445453 GGAACAGATCAGATGCATGTACA 58.555 43.478 2.46 0.00 0.00 2.90
1912 2416 0.321996 GATGGATAAGCCTCCCGTCC 59.678 60.000 0.00 0.00 37.63 4.79
1958 2486 7.377928 CAGAAACAGAAACATAAGCAGAAAGTG 59.622 37.037 0.00 0.00 0.00 3.16
1970 2534 3.885297 CCACACTCCAGAAACAGAAACAT 59.115 43.478 0.00 0.00 0.00 2.71
1999 2581 1.000145 GAATCCGAAACAGAGGCGAC 59.000 55.000 0.00 0.00 0.00 5.19
2015 2597 3.637229 TCCTTTCTCGAGCTTATCCGAAT 59.363 43.478 7.81 0.00 34.17 3.34
2029 2611 1.205893 AGACGCCACTGATCCTTTCTC 59.794 52.381 0.00 0.00 0.00 2.87
2112 2698 3.952675 CGCCGTGCTGCAAGTTGT 61.953 61.111 14.22 0.00 35.30 3.32
2177 2764 3.703001 AATCCTCGGTTCATCAGTTGT 57.297 42.857 0.00 0.00 0.00 3.32
2359 5724 9.787435 TGAAAGAAGAGTAAAATAGCAAGGTTA 57.213 29.630 0.00 0.00 0.00 2.85
2360 5725 8.691661 TGAAAGAAGAGTAAAATAGCAAGGTT 57.308 30.769 0.00 0.00 0.00 3.50
2361 5726 8.691661 TTGAAAGAAGAGTAAAATAGCAAGGT 57.308 30.769 0.00 0.00 0.00 3.50
2362 5727 9.617975 CTTTGAAAGAAGAGTAAAATAGCAAGG 57.382 33.333 0.00 0.00 0.00 3.61
2363 5728 9.122613 GCTTTGAAAGAAGAGTAAAATAGCAAG 57.877 33.333 9.48 0.00 0.00 4.01
2364 5729 8.629158 TGCTTTGAAAGAAGAGTAAAATAGCAA 58.371 29.630 9.48 0.00 0.00 3.91
2365 5730 8.165239 TGCTTTGAAAGAAGAGTAAAATAGCA 57.835 30.769 9.48 0.00 0.00 3.49
2366 5731 8.293157 ACTGCTTTGAAAGAAGAGTAAAATAGC 58.707 33.333 19.49 0.00 36.13 2.97
2367 5732 9.604626 CACTGCTTTGAAAGAAGAGTAAAATAG 57.395 33.333 19.49 0.00 36.13 1.73
2368 5733 8.567948 CCACTGCTTTGAAAGAAGAGTAAAATA 58.432 33.333 19.49 0.00 36.13 1.40
2369 5734 7.428826 CCACTGCTTTGAAAGAAGAGTAAAAT 58.571 34.615 19.49 0.00 36.13 1.82
2370 5735 6.680378 GCCACTGCTTTGAAAGAAGAGTAAAA 60.680 38.462 19.49 0.00 36.13 1.52
2371 5736 5.221048 GCCACTGCTTTGAAAGAAGAGTAAA 60.221 40.000 19.49 0.00 36.13 2.01
2372 5737 4.275936 GCCACTGCTTTGAAAGAAGAGTAA 59.724 41.667 19.49 0.00 36.13 2.24
2373 5738 3.815401 GCCACTGCTTTGAAAGAAGAGTA 59.185 43.478 19.49 0.00 36.13 2.59
2374 5739 2.620585 GCCACTGCTTTGAAAGAAGAGT 59.379 45.455 19.49 9.02 36.13 3.24
2375 5740 2.620115 TGCCACTGCTTTGAAAGAAGAG 59.380 45.455 19.49 11.37 36.13 2.85
2376 5741 2.653726 TGCCACTGCTTTGAAAGAAGA 58.346 42.857 19.49 0.00 36.13 2.87
2377 5742 3.005050 TCATGCCACTGCTTTGAAAGAAG 59.995 43.478 11.37 11.37 40.26 2.85
2378 5743 2.957680 TCATGCCACTGCTTTGAAAGAA 59.042 40.909 9.48 0.00 38.71 2.52
2379 5744 2.555325 CTCATGCCACTGCTTTGAAAGA 59.445 45.455 9.48 0.00 38.71 2.52
2380 5745 2.352421 CCTCATGCCACTGCTTTGAAAG 60.352 50.000 0.00 0.00 38.71 2.62
2381 5746 1.614903 CCTCATGCCACTGCTTTGAAA 59.385 47.619 0.00 0.00 38.71 2.69
2382 5747 1.250328 CCTCATGCCACTGCTTTGAA 58.750 50.000 0.00 0.00 38.71 2.69
2383 5748 0.609957 CCCTCATGCCACTGCTTTGA 60.610 55.000 0.00 0.00 38.71 2.69
2384 5749 0.609957 TCCCTCATGCCACTGCTTTG 60.610 55.000 0.00 0.00 38.71 2.77
2385 5750 0.610232 GTCCCTCATGCCACTGCTTT 60.610 55.000 0.00 0.00 38.71 3.51
2386 5751 1.001641 GTCCCTCATGCCACTGCTT 60.002 57.895 0.00 0.00 38.71 3.91
2387 5752 2.194388 CTGTCCCTCATGCCACTGCT 62.194 60.000 0.00 0.00 38.71 4.24
2388 5753 1.748122 CTGTCCCTCATGCCACTGC 60.748 63.158 0.00 0.00 38.26 4.40
2389 5754 1.748122 GCTGTCCCTCATGCCACTG 60.748 63.158 0.00 0.00 0.00 3.66
2390 5755 2.673523 GCTGTCCCTCATGCCACT 59.326 61.111 0.00 0.00 0.00 4.00
2391 5756 2.238847 TACGCTGTCCCTCATGCCAC 62.239 60.000 0.00 0.00 0.00 5.01
2392 5757 1.960040 CTACGCTGTCCCTCATGCCA 61.960 60.000 0.00 0.00 0.00 4.92
2393 5758 1.227380 CTACGCTGTCCCTCATGCC 60.227 63.158 0.00 0.00 0.00 4.40
2394 5759 1.884926 GCTACGCTGTCCCTCATGC 60.885 63.158 0.00 0.00 0.00 4.06
2395 5760 1.589993 CGCTACGCTGTCCCTCATG 60.590 63.158 0.00 0.00 0.00 3.07
2396 5761 2.786495 CCGCTACGCTGTCCCTCAT 61.786 63.158 0.00 0.00 0.00 2.90
2397 5762 3.449227 CCGCTACGCTGTCCCTCA 61.449 66.667 0.00 0.00 0.00 3.86
2398 5763 3.003113 AACCGCTACGCTGTCCCTC 62.003 63.158 0.00 0.00 0.00 4.30
2399 5764 2.995574 AACCGCTACGCTGTCCCT 60.996 61.111 0.00 0.00 0.00 4.20
2400 5765 2.813908 CAACCGCTACGCTGTCCC 60.814 66.667 0.00 0.00 0.00 4.46
2401 5766 2.813908 CCAACCGCTACGCTGTCC 60.814 66.667 0.00 0.00 0.00 4.02
2402 5767 2.573609 ATCCCAACCGCTACGCTGTC 62.574 60.000 0.00 0.00 0.00 3.51
2403 5768 2.180159 AATCCCAACCGCTACGCTGT 62.180 55.000 0.00 0.00 0.00 4.40
2404 5769 1.429148 GAATCCCAACCGCTACGCTG 61.429 60.000 0.00 0.00 0.00 5.18
2405 5770 1.153429 GAATCCCAACCGCTACGCT 60.153 57.895 0.00 0.00 0.00 5.07
2406 5771 2.178235 GGAATCCCAACCGCTACGC 61.178 63.158 0.00 0.00 0.00 4.42
2407 5772 1.523032 GGGAATCCCAACCGCTACG 60.523 63.158 14.67 0.00 44.65 3.51
2408 5773 4.553668 GGGAATCCCAACCGCTAC 57.446 61.111 14.67 0.00 44.65 3.58
2418 5783 1.235756 AGATTTGGGAGGGGGAATCC 58.764 55.000 0.00 0.00 35.99 3.01
2419 5784 4.536295 TTAAGATTTGGGAGGGGGAATC 57.464 45.455 0.00 0.00 0.00 2.52
2420 5785 4.984642 TTTAAGATTTGGGAGGGGGAAT 57.015 40.909 0.00 0.00 0.00 3.01
2421 5786 4.984642 ATTTAAGATTTGGGAGGGGGAA 57.015 40.909 0.00 0.00 0.00 3.97
2422 5787 4.619679 CAATTTAAGATTTGGGAGGGGGA 58.380 43.478 0.00 0.00 0.00 4.81
2423 5788 3.134623 GCAATTTAAGATTTGGGAGGGGG 59.865 47.826 0.00 0.00 0.00 5.40
2424 5789 3.774216 TGCAATTTAAGATTTGGGAGGGG 59.226 43.478 0.00 0.00 0.00 4.79
2425 5790 4.222588 TGTGCAATTTAAGATTTGGGAGGG 59.777 41.667 0.00 0.00 0.00 4.30
2426 5791 5.404466 TGTGCAATTTAAGATTTGGGAGG 57.596 39.130 0.00 0.00 0.00 4.30
2427 5792 5.185635 TCCTGTGCAATTTAAGATTTGGGAG 59.814 40.000 0.00 0.00 0.00 4.30
2428 5793 5.083122 TCCTGTGCAATTTAAGATTTGGGA 58.917 37.500 0.00 0.00 0.00 4.37
2429 5794 5.404466 TCCTGTGCAATTTAAGATTTGGG 57.596 39.130 0.00 0.00 0.00 4.12
2430 5795 5.870978 CCTTCCTGTGCAATTTAAGATTTGG 59.129 40.000 0.00 0.00 0.00 3.28
2431 5796 6.690530 TCCTTCCTGTGCAATTTAAGATTTG 58.309 36.000 0.00 0.00 0.00 2.32
2432 5797 6.916360 TCCTTCCTGTGCAATTTAAGATTT 57.084 33.333 0.00 0.00 0.00 2.17
2433 5798 6.721208 TCTTCCTTCCTGTGCAATTTAAGATT 59.279 34.615 0.00 0.00 0.00 2.40
2434 5799 6.248433 TCTTCCTTCCTGTGCAATTTAAGAT 58.752 36.000 0.00 0.00 0.00 2.40
2435 5800 5.630121 TCTTCCTTCCTGTGCAATTTAAGA 58.370 37.500 0.00 0.00 0.00 2.10
2436 5801 5.964958 TCTTCCTTCCTGTGCAATTTAAG 57.035 39.130 0.00 0.00 0.00 1.85
2437 5802 5.185635 CCATCTTCCTTCCTGTGCAATTTAA 59.814 40.000 0.00 0.00 0.00 1.52
2438 5803 4.706476 CCATCTTCCTTCCTGTGCAATTTA 59.294 41.667 0.00 0.00 0.00 1.40
2439 5804 3.512724 CCATCTTCCTTCCTGTGCAATTT 59.487 43.478 0.00 0.00 0.00 1.82
2440 5805 3.094572 CCATCTTCCTTCCTGTGCAATT 58.905 45.455 0.00 0.00 0.00 2.32
2441 5806 2.042162 ACCATCTTCCTTCCTGTGCAAT 59.958 45.455 0.00 0.00 0.00 3.56
2442 5807 1.425066 ACCATCTTCCTTCCTGTGCAA 59.575 47.619 0.00 0.00 0.00 4.08
2443 5808 1.067295 ACCATCTTCCTTCCTGTGCA 58.933 50.000 0.00 0.00 0.00 4.57
2444 5809 1.271597 ACACCATCTTCCTTCCTGTGC 60.272 52.381 0.00 0.00 0.00 4.57
2445 5810 2.816087 CAACACCATCTTCCTTCCTGTG 59.184 50.000 0.00 0.00 0.00 3.66
2446 5811 2.224867 CCAACACCATCTTCCTTCCTGT 60.225 50.000 0.00 0.00 0.00 4.00
2447 5812 2.040278 TCCAACACCATCTTCCTTCCTG 59.960 50.000 0.00 0.00 0.00 3.86
2448 5813 2.348472 TCCAACACCATCTTCCTTCCT 58.652 47.619 0.00 0.00 0.00 3.36
2449 5814 2.879103 TCCAACACCATCTTCCTTCC 57.121 50.000 0.00 0.00 0.00 3.46
2450 5815 5.619981 CGATTTTCCAACACCATCTTCCTTC 60.620 44.000 0.00 0.00 0.00 3.46
2451 5816 4.218417 CGATTTTCCAACACCATCTTCCTT 59.782 41.667 0.00 0.00 0.00 3.36
2452 5817 3.758554 CGATTTTCCAACACCATCTTCCT 59.241 43.478 0.00 0.00 0.00 3.36
2453 5818 3.119495 CCGATTTTCCAACACCATCTTCC 60.119 47.826 0.00 0.00 0.00 3.46
2454 5819 3.506067 ACCGATTTTCCAACACCATCTTC 59.494 43.478 0.00 0.00 0.00 2.87
2455 5820 3.255642 CACCGATTTTCCAACACCATCTT 59.744 43.478 0.00 0.00 0.00 2.40
2456 5821 2.819608 CACCGATTTTCCAACACCATCT 59.180 45.455 0.00 0.00 0.00 2.90
2457 5822 2.094752 CCACCGATTTTCCAACACCATC 60.095 50.000 0.00 0.00 0.00 3.51
2458 5823 1.892474 CCACCGATTTTCCAACACCAT 59.108 47.619 0.00 0.00 0.00 3.55
2459 5824 1.323412 CCACCGATTTTCCAACACCA 58.677 50.000 0.00 0.00 0.00 4.17
2460 5825 1.324383 ACCACCGATTTTCCAACACC 58.676 50.000 0.00 0.00 0.00 4.16
2461 5826 3.143728 AGTACCACCGATTTTCCAACAC 58.856 45.455 0.00 0.00 0.00 3.32
2462 5827 3.404899 GAGTACCACCGATTTTCCAACA 58.595 45.455 0.00 0.00 0.00 3.33
2463 5828 2.745821 GGAGTACCACCGATTTTCCAAC 59.254 50.000 0.00 0.00 35.97 3.77
2464 5829 2.290450 GGGAGTACCACCGATTTTCCAA 60.290 50.000 0.00 0.00 39.85 3.53
2465 5830 1.279846 GGGAGTACCACCGATTTTCCA 59.720 52.381 0.00 0.00 39.85 3.53
2466 5831 1.558294 AGGGAGTACCACCGATTTTCC 59.442 52.381 0.00 0.00 43.89 3.13
2467 5832 2.419713 GGAGGGAGTACCACCGATTTTC 60.420 54.545 0.00 0.00 40.33 2.29
2468 5833 1.558294 GGAGGGAGTACCACCGATTTT 59.442 52.381 0.00 0.00 40.33 1.82
2469 5834 1.201424 GGAGGGAGTACCACCGATTT 58.799 55.000 0.00 0.00 40.33 2.17
2470 5835 2.912020 GGAGGGAGTACCACCGATT 58.088 57.895 0.00 0.00 40.33 3.34
2471 5836 4.701286 GGAGGGAGTACCACCGAT 57.299 61.111 0.00 0.00 40.33 4.18
2475 5840 1.066358 CCGAAAAGGAGGGAGTACCAC 60.066 57.143 0.00 0.00 45.00 4.16
2476 5841 1.272807 CCGAAAAGGAGGGAGTACCA 58.727 55.000 0.00 0.00 45.00 3.25
2477 5842 1.273759 ACCGAAAAGGAGGGAGTACC 58.726 55.000 0.00 0.00 45.00 3.34
2478 5843 3.413846 AAACCGAAAAGGAGGGAGTAC 57.586 47.619 0.00 0.00 45.00 2.73
2479 5844 6.197168 TCTATAAACCGAAAAGGAGGGAGTA 58.803 40.000 0.00 0.00 45.00 2.59
2480 5845 5.028131 TCTATAAACCGAAAAGGAGGGAGT 58.972 41.667 0.00 0.00 45.00 3.85
2481 5846 5.602628 CTCTATAAACCGAAAAGGAGGGAG 58.397 45.833 0.00 0.00 45.00 4.30
2482 5847 4.141779 GCTCTATAAACCGAAAAGGAGGGA 60.142 45.833 0.00 0.00 45.00 4.20
2483 5848 4.127907 GCTCTATAAACCGAAAAGGAGGG 58.872 47.826 0.00 0.00 45.00 4.30
2484 5849 5.024785 AGCTCTATAAACCGAAAAGGAGG 57.975 43.478 0.00 0.00 45.00 4.30
2485 5850 8.145122 AGATAAGCTCTATAAACCGAAAAGGAG 58.855 37.037 0.00 0.00 36.42 3.69
2486 5851 8.019656 AGATAAGCTCTATAAACCGAAAAGGA 57.980 34.615 0.00 0.00 36.42 3.36
2487 5852 8.664211 AAGATAAGCTCTATAAACCGAAAAGG 57.336 34.615 0.00 0.00 38.86 3.11
2524 5889 9.447157 CCAAATTGAGCCTTATAAAATGGAAAA 57.553 29.630 0.00 0.00 0.00 2.29
2525 5890 8.601546 ACCAAATTGAGCCTTATAAAATGGAAA 58.398 29.630 0.00 0.00 0.00 3.13
2526 5891 8.144862 ACCAAATTGAGCCTTATAAAATGGAA 57.855 30.769 0.00 0.00 0.00 3.53
2527 5892 7.732222 ACCAAATTGAGCCTTATAAAATGGA 57.268 32.000 0.00 0.00 0.00 3.41
2528 5893 7.823799 ACAACCAAATTGAGCCTTATAAAATGG 59.176 33.333 0.00 0.00 41.23 3.16
2529 5894 8.776376 ACAACCAAATTGAGCCTTATAAAATG 57.224 30.769 0.00 0.00 41.23 2.32


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

AutoCloner maintained by Alex Coulton.