Multiple sequence alignment - TraesCS3B01G319100

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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 TraesCS3B01G319100 chr3B 100.000 7255 0 0 1 7255 513989377 513996631 0.000000e+00 13398
1 TraesCS3B01G319100 chr3D 95.949 6517 136 45 807 7255 394748531 394754987 0.000000e+00 10455
2 TraesCS3B01G319100 chr3D 93.579 732 27 7 90 802 394747763 394748493 0.000000e+00 1074
3 TraesCS3B01G319100 chr3A 94.925 6049 188 51 1251 7255 514105526 514111499 0.000000e+00 9359
4 TraesCS3B01G319100 chr3A 89.041 438 14 16 806 1242 514105031 514105435 5.020000e-141 512
5 TraesCS3B01G319100 chr3A 90.663 332 20 7 93 417 514095952 514096279 1.450000e-116 431
6 TraesCS3B01G319100 chr7A 84.818 303 44 2 3090 3392 216341146 216340846 3.290000e-78 303


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 TraesCS3B01G319100 chr3B 513989377 513996631 7254 False 13398.0 13398 100.000 1 7255 1 chr3B.!!$F1 7254
1 TraesCS3B01G319100 chr3D 394747763 394754987 7224 False 5764.5 10455 94.764 90 7255 2 chr3D.!!$F1 7165
2 TraesCS3B01G319100 chr3A 514105031 514111499 6468 False 4935.5 9359 91.983 806 7255 2 chr3A.!!$F2 6449

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
584 600 0.317519 CCAACCGGTTCTTTCGTTGC 60.318 55.000 19.24 0.0 0.00 4.17 F
1415 1574 0.031857 TGTTGCCTCCATTTTGCGTG 59.968 50.000 0.00 0.0 0.00 5.34 F
1485 1644 0.323087 GGCGTCCATGGGTAAACCTT 60.323 55.000 13.02 0.0 41.11 3.50 F
2707 2909 0.408700 ACCTTCTGTACCTCTCCCGT 59.591 55.000 0.00 0.0 0.00 5.28 F
3628 3830 0.694444 TGGGGCTTCCTGAGGGATAC 60.694 60.000 0.00 0.0 41.87 2.24 F
4361 4569 0.617413 AGCAAGCACTCATAGGCAGT 59.383 50.000 0.00 0.0 0.00 4.40 F
4592 4800 1.799181 CGTATCCGAGTCCAAGTGCTG 60.799 57.143 0.00 0.0 35.63 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 2024 0.317186 GAAGACTAGCTAGCGCGTCC 60.317 60.000 25.73 14.14 42.32 4.79 R
2403 2598 0.868406 CGGCACAAAGGTTCTGTCTC 59.132 55.000 0.00 0.00 0.00 3.36 R
2968 3170 1.045407 TTCCTGCGGCGTATATCCTT 58.955 50.000 9.37 0.00 0.00 3.36 R
4025 4233 1.338674 TGATCGGCATTCTTCACGGTT 60.339 47.619 0.00 0.00 0.00 4.44 R
4745 4953 0.451783 GTCCCATTGTCACCGCAATC 59.548 55.000 0.00 0.00 37.00 2.67 R
6203 6411 2.373169 TGCTCCCTTCTTGTTCATGAGT 59.627 45.455 0.00 0.00 0.00 3.41 R
6499 6707 7.514721 TGTTCAGTTGTAGGTATTCCTTCTTT 58.485 34.615 0.00 0.00 42.12 2.52 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 1.761174 AGTGTGTAGTGGGCCTTGG 59.239 57.895 4.53 0.00 0.00 3.61
19 20 0.766674 AGTGTGTAGTGGGCCTTGGA 60.767 55.000 4.53 0.00 0.00 3.53
20 21 0.328258 GTGTGTAGTGGGCCTTGGAT 59.672 55.000 4.53 0.00 0.00 3.41
21 22 0.327924 TGTGTAGTGGGCCTTGGATG 59.672 55.000 4.53 0.00 0.00 3.51
22 23 0.328258 GTGTAGTGGGCCTTGGATGT 59.672 55.000 4.53 0.00 0.00 3.06
23 24 1.557832 GTGTAGTGGGCCTTGGATGTA 59.442 52.381 4.53 0.00 0.00 2.29
24 25 2.026636 GTGTAGTGGGCCTTGGATGTAA 60.027 50.000 4.53 0.00 0.00 2.41
25 26 2.238646 TGTAGTGGGCCTTGGATGTAAG 59.761 50.000 4.53 0.00 0.00 2.34
36 37 5.880901 CCTTGGATGTAAGGTATATTGCCT 58.119 41.667 0.00 0.00 41.85 4.75
37 38 5.707298 CCTTGGATGTAAGGTATATTGCCTG 59.293 44.000 0.00 0.00 41.85 4.85
38 39 6.465751 CCTTGGATGTAAGGTATATTGCCTGA 60.466 42.308 0.00 0.00 41.85 3.86
39 40 6.702449 TGGATGTAAGGTATATTGCCTGAT 57.298 37.500 0.02 0.00 36.30 2.90
40 41 6.711277 TGGATGTAAGGTATATTGCCTGATC 58.289 40.000 0.02 0.00 36.30 2.92
41 42 6.116126 GGATGTAAGGTATATTGCCTGATCC 58.884 44.000 11.78 11.78 36.30 3.36
42 43 6.296432 GGATGTAAGGTATATTGCCTGATCCA 60.296 42.308 16.86 7.59 37.27 3.41
43 44 6.114187 TGTAAGGTATATTGCCTGATCCAG 57.886 41.667 0.00 0.00 36.30 3.86
44 45 3.710209 AGGTATATTGCCTGATCCAGC 57.290 47.619 0.00 0.00 34.56 4.85
45 46 2.027745 AGGTATATTGCCTGATCCAGCG 60.028 50.000 0.00 0.00 34.56 5.18
46 47 2.350522 GTATATTGCCTGATCCAGCGG 58.649 52.381 0.00 0.00 0.00 5.52
47 48 0.607489 ATATTGCCTGATCCAGCGGC 60.607 55.000 0.00 0.00 44.02 6.53
50 51 2.517875 GCCTGATCCAGCGGCAAT 60.518 61.111 1.45 0.00 43.25 3.56
51 52 2.550101 GCCTGATCCAGCGGCAATC 61.550 63.158 1.45 2.97 43.25 2.67
52 53 2.249535 CCTGATCCAGCGGCAATCG 61.250 63.158 1.45 0.02 42.76 3.34
61 62 3.093278 CGGCAATCGCTTGACCTC 58.907 61.111 2.58 0.00 37.04 3.85
62 63 2.464459 CGGCAATCGCTTGACCTCC 61.464 63.158 2.58 0.00 37.04 4.30
63 64 1.377202 GGCAATCGCTTGACCTCCA 60.377 57.895 2.58 0.00 33.98 3.86
64 65 1.372087 GGCAATCGCTTGACCTCCAG 61.372 60.000 2.58 0.00 33.98 3.86
65 66 0.391661 GCAATCGCTTGACCTCCAGA 60.392 55.000 2.58 0.00 34.04 3.86
66 67 1.945819 GCAATCGCTTGACCTCCAGAA 60.946 52.381 2.58 0.00 34.04 3.02
67 68 2.636830 CAATCGCTTGACCTCCAGAAT 58.363 47.619 0.00 0.00 34.04 2.40
68 69 2.611225 ATCGCTTGACCTCCAGAATC 57.389 50.000 0.00 0.00 0.00 2.52
69 70 1.561643 TCGCTTGACCTCCAGAATCT 58.438 50.000 0.00 0.00 0.00 2.40
70 71 1.478510 TCGCTTGACCTCCAGAATCTC 59.521 52.381 0.00 0.00 0.00 2.75
71 72 1.800655 CGCTTGACCTCCAGAATCTCG 60.801 57.143 0.00 0.00 0.00 4.04
72 73 1.478510 GCTTGACCTCCAGAATCTCGA 59.521 52.381 0.00 0.00 0.00 4.04
73 74 2.093973 GCTTGACCTCCAGAATCTCGAA 60.094 50.000 0.00 0.00 0.00 3.71
74 75 3.431486 GCTTGACCTCCAGAATCTCGAAT 60.431 47.826 0.00 0.00 0.00 3.34
75 76 3.808466 TGACCTCCAGAATCTCGAATG 57.192 47.619 0.00 0.00 0.00 2.67
76 77 3.365472 TGACCTCCAGAATCTCGAATGA 58.635 45.455 0.00 0.00 0.00 2.57
77 78 3.963374 TGACCTCCAGAATCTCGAATGAT 59.037 43.478 0.00 0.00 0.00 2.45
78 79 4.202192 TGACCTCCAGAATCTCGAATGATG 60.202 45.833 0.00 0.00 0.00 3.07
79 80 3.963374 ACCTCCAGAATCTCGAATGATGA 59.037 43.478 0.00 0.00 0.00 2.92
80 81 4.406972 ACCTCCAGAATCTCGAATGATGAA 59.593 41.667 0.00 0.00 0.00 2.57
81 82 4.749099 CCTCCAGAATCTCGAATGATGAAC 59.251 45.833 0.00 0.00 0.00 3.18
82 83 4.697514 TCCAGAATCTCGAATGATGAACC 58.302 43.478 0.00 0.00 0.00 3.62
83 84 3.812053 CCAGAATCTCGAATGATGAACCC 59.188 47.826 0.00 0.00 0.00 4.11
84 85 3.492383 CAGAATCTCGAATGATGAACCCG 59.508 47.826 0.00 0.00 0.00 5.28
85 86 3.133003 AGAATCTCGAATGATGAACCCGT 59.867 43.478 0.00 0.00 0.00 5.28
86 87 4.341235 AGAATCTCGAATGATGAACCCGTA 59.659 41.667 0.00 0.00 0.00 4.02
87 88 4.665833 ATCTCGAATGATGAACCCGTAA 57.334 40.909 0.00 0.00 0.00 3.18
88 89 3.777478 TCTCGAATGATGAACCCGTAAC 58.223 45.455 0.00 0.00 0.00 2.50
89 90 2.864343 CTCGAATGATGAACCCGTAACC 59.136 50.000 0.00 0.00 0.00 2.85
90 91 2.234168 TCGAATGATGAACCCGTAACCA 59.766 45.455 0.00 0.00 0.00 3.67
91 92 3.118555 TCGAATGATGAACCCGTAACCAT 60.119 43.478 0.00 0.00 0.00 3.55
159 160 7.475015 CGACAGATAATTTTGTGATGGACAAT 58.525 34.615 0.05 0.00 44.23 2.71
171 172 1.200519 TGGACAATCTCCTAACCGGG 58.799 55.000 6.32 0.00 40.26 5.73
277 290 1.084954 ACTTTATACCCCCTCCCCCAA 59.915 52.381 0.00 0.00 0.00 4.12
547 561 3.019564 GCAGCCAACTTTCTCCATGTAT 58.980 45.455 0.00 0.00 0.00 2.29
548 562 3.181493 GCAGCCAACTTTCTCCATGTATG 60.181 47.826 0.00 0.00 0.00 2.39
549 563 3.019564 AGCCAACTTTCTCCATGTATGC 58.980 45.455 0.00 0.00 0.00 3.14
570 586 3.792401 CTTTTGAGTTTGAACCCCAACC 58.208 45.455 0.00 0.00 33.85 3.77
582 598 0.820482 CCCCAACCGGTTCTTTCGTT 60.820 55.000 19.24 0.00 0.00 3.85
584 600 0.317519 CCAACCGGTTCTTTCGTTGC 60.318 55.000 19.24 0.00 0.00 4.17
585 601 0.378962 CAACCGGTTCTTTCGTTGCA 59.621 50.000 19.24 0.00 0.00 4.08
589 605 0.655733 CGGTTCTTTCGTTGCAGTGT 59.344 50.000 0.00 0.00 0.00 3.55
594 610 2.560504 TCTTTCGTTGCAGTGTGATGT 58.439 42.857 0.00 0.00 0.00 3.06
601 617 1.154338 GCAGTGTGATGTCTTGCGC 60.154 57.895 0.00 0.00 0.00 6.09
699 718 8.704668 AGGTAAATGAAAAATTGATATGGGGTC 58.295 33.333 0.00 0.00 0.00 4.46
700 719 8.704668 GGTAAATGAAAAATTGATATGGGGTCT 58.295 33.333 0.00 0.00 0.00 3.85
710 729 2.787473 TATGGGGTCTCAAAGTGCAG 57.213 50.000 0.00 0.00 0.00 4.41
713 732 0.823356 GGGGTCTCAAAGTGCAGCAA 60.823 55.000 0.00 0.00 0.00 3.91
773 792 1.606480 GCTTTTGCTTTCTGGGCCTTC 60.606 52.381 4.53 0.00 43.35 3.46
840 893 4.561735 TTCCAAGGCAAAGTTAAGAACG 57.438 40.909 0.00 0.00 36.23 3.95
1013 1077 3.101796 TAAAGATGAGCCCCGGCCG 62.102 63.158 21.04 21.04 43.17 6.13
1242 1315 3.384467 TCATGCATGACATCGAGAAGGTA 59.616 43.478 25.42 0.00 36.64 3.08
1300 1459 5.335976 GGAAATTCACTGGGATTCACACTTC 60.336 44.000 0.00 0.00 0.00 3.01
1415 1574 0.031857 TGTTGCCTCCATTTTGCGTG 59.968 50.000 0.00 0.00 0.00 5.34
1416 1575 0.667184 GTTGCCTCCATTTTGCGTGG 60.667 55.000 0.00 0.00 38.11 4.94
1483 1642 1.001887 TGGCGTCCATGGGTAAACC 60.002 57.895 13.02 7.53 40.81 3.27
1485 1644 0.323087 GGCGTCCATGGGTAAACCTT 60.323 55.000 13.02 0.00 41.11 3.50
1486 1645 1.541379 GCGTCCATGGGTAAACCTTT 58.459 50.000 13.02 0.00 41.11 3.11
1487 1646 1.890489 GCGTCCATGGGTAAACCTTTT 59.110 47.619 13.02 0.00 41.11 2.27
1489 1648 3.150767 CGTCCATGGGTAAACCTTTTGA 58.849 45.455 13.02 0.00 41.11 2.69
1490 1649 3.190535 CGTCCATGGGTAAACCTTTTGAG 59.809 47.826 13.02 0.00 41.11 3.02
1493 1652 5.069914 GTCCATGGGTAAACCTTTTGAGTTT 59.930 40.000 13.02 0.00 41.11 2.66
1494 1653 5.663556 TCCATGGGTAAACCTTTTGAGTTTT 59.336 36.000 13.02 0.00 41.11 2.43
1497 1656 5.179533 TGGGTAAACCTTTTGAGTTTTTGC 58.820 37.500 0.00 0.00 41.11 3.68
1498 1657 5.046231 TGGGTAAACCTTTTGAGTTTTTGCT 60.046 36.000 0.00 0.00 41.11 3.91
1499 1658 5.293324 GGGTAAACCTTTTGAGTTTTTGCTG 59.707 40.000 0.00 0.00 38.37 4.41
1500 1659 4.944962 AAACCTTTTGAGTTTTTGCTGC 57.055 36.364 0.00 0.00 33.73 5.25
1501 1660 3.893326 ACCTTTTGAGTTTTTGCTGCT 57.107 38.095 0.00 0.00 0.00 4.24
1502 1661 5.337578 AACCTTTTGAGTTTTTGCTGCTA 57.662 34.783 0.00 0.00 0.00 3.49
1503 1662 4.682787 ACCTTTTGAGTTTTTGCTGCTAC 58.317 39.130 0.00 0.00 0.00 3.58
1504 1663 4.159506 ACCTTTTGAGTTTTTGCTGCTACA 59.840 37.500 0.00 0.00 0.00 2.74
1505 1664 5.163416 ACCTTTTGAGTTTTTGCTGCTACAT 60.163 36.000 0.00 0.00 0.00 2.29
1506 1665 6.040391 ACCTTTTGAGTTTTTGCTGCTACATA 59.960 34.615 0.00 0.00 0.00 2.29
1507 1666 6.583806 CCTTTTGAGTTTTTGCTGCTACATAG 59.416 38.462 0.00 0.00 0.00 2.23
1508 1667 6.875948 TTTGAGTTTTTGCTGCTACATAGA 57.124 33.333 0.00 0.00 0.00 1.98
1509 1668 7.452880 TTTGAGTTTTTGCTGCTACATAGAT 57.547 32.000 0.00 0.00 0.00 1.98
1510 1669 7.452880 TTGAGTTTTTGCTGCTACATAGATT 57.547 32.000 0.00 0.00 0.00 2.40
1511 1670 7.452880 TGAGTTTTTGCTGCTACATAGATTT 57.547 32.000 0.00 0.00 0.00 2.17
1512 1671 7.307694 TGAGTTTTTGCTGCTACATAGATTTG 58.692 34.615 0.00 0.00 0.00 2.32
1518 1677 4.453478 TGCTGCTACATAGATTTGCATAGC 59.547 41.667 0.00 5.02 36.43 2.97
1521 1680 6.549912 TGCTACATAGATTTGCATAGCTTG 57.450 37.500 11.71 7.73 36.75 4.01
1556 1715 8.801882 TTCAACAAGGGATAATACTAACTTGG 57.198 34.615 0.00 0.00 39.53 3.61
1572 1731 2.193127 CTTGGTGTACCCCTATGGACA 58.807 52.381 0.00 0.00 38.00 4.02
1573 1732 2.579624 TGGTGTACCCCTATGGACAT 57.420 50.000 0.00 0.00 38.00 3.06
1574 1733 2.123589 TGGTGTACCCCTATGGACATG 58.876 52.381 0.00 0.00 38.00 3.21
1575 1734 1.420138 GGTGTACCCCTATGGACATGG 59.580 57.143 0.00 0.00 38.00 3.66
1576 1735 2.404559 GTGTACCCCTATGGACATGGA 58.595 52.381 0.00 0.00 38.00 3.41
1577 1736 2.104281 GTGTACCCCTATGGACATGGAC 59.896 54.545 0.00 0.00 38.00 4.02
1773 1936 0.458716 GTGCTCAGCGAGAAGGTACC 60.459 60.000 2.73 2.73 0.00 3.34
1788 1960 1.542547 GGTACCACCACACCAGTCAAG 60.543 57.143 7.15 0.00 38.42 3.02
1791 1963 1.898574 CACCACACCAGTCAAGCCC 60.899 63.158 0.00 0.00 0.00 5.19
1798 1970 2.845345 CCAGTCAAGCCCCCTTGGT 61.845 63.158 3.86 0.00 46.69 3.67
1799 1971 1.303643 CAGTCAAGCCCCCTTGGTC 60.304 63.158 3.86 0.00 46.69 4.02
1800 1972 1.464198 AGTCAAGCCCCCTTGGTCT 60.464 57.895 3.86 1.36 46.69 3.85
1801 1973 1.068352 AGTCAAGCCCCCTTGGTCTT 61.068 55.000 3.86 0.00 46.69 3.01
1802 1974 0.895559 GTCAAGCCCCCTTGGTCTTG 60.896 60.000 3.86 0.00 46.69 3.02
1803 1975 1.065410 TCAAGCCCCCTTGGTCTTGA 61.065 55.000 1.22 1.22 46.14 3.02
1837 2009 7.465353 TTGCTTTTCAATGACCTTGATCATA 57.535 32.000 0.00 0.00 43.30 2.15
1840 2012 6.435430 TTTTCAATGACCTTGATCATACGG 57.565 37.500 0.00 0.12 43.30 4.02
1843 2015 4.651962 TCAATGACCTTGATCATACGGGTA 59.348 41.667 0.00 0.00 38.97 3.69
1844 2016 4.602340 ATGACCTTGATCATACGGGTAC 57.398 45.455 0.00 0.00 37.56 3.34
1845 2017 3.367321 TGACCTTGATCATACGGGTACA 58.633 45.455 0.00 2.06 0.00 2.90
1846 2018 3.131577 TGACCTTGATCATACGGGTACAC 59.868 47.826 0.00 0.00 0.00 2.90
1847 2019 3.101437 ACCTTGATCATACGGGTACACA 58.899 45.455 0.00 0.00 0.00 3.72
1848 2020 3.516300 ACCTTGATCATACGGGTACACAA 59.484 43.478 0.00 0.00 0.00 3.33
1849 2021 4.020039 ACCTTGATCATACGGGTACACAAA 60.020 41.667 0.00 0.00 0.00 2.83
1850 2022 4.570772 CCTTGATCATACGGGTACACAAAG 59.429 45.833 0.00 0.00 0.00 2.77
1851 2023 3.527533 TGATCATACGGGTACACAAAGC 58.472 45.455 0.00 0.00 0.00 3.51
1852 2024 1.999048 TCATACGGGTACACAAAGCG 58.001 50.000 0.00 0.00 0.00 4.68
1853 2025 1.003851 CATACGGGTACACAAAGCGG 58.996 55.000 0.00 0.00 0.00 5.52
1864 2036 4.436998 AAAGCGGACGCGCTAGCT 62.437 61.111 13.93 15.44 45.26 3.32
1991 2166 6.480981 TGTACTAGCAGTGGTTTGTTTAAGAC 59.519 38.462 0.00 0.00 0.00 3.01
2014 2189 3.493767 ACCAAGGACAGGAGAAAAGTC 57.506 47.619 0.00 0.00 0.00 3.01
2017 2192 3.959433 GGACAGGAGAAAAGTCCCC 57.041 57.895 0.00 0.00 44.72 4.81
2031 2214 2.361610 CCCCTGTCATGGTGGCAC 60.362 66.667 9.70 9.70 0.00 5.01
2141 2328 9.959721 AATCAGGAGAGATAGAGAGATTAGTAC 57.040 37.037 0.00 0.00 0.00 2.73
2183 2370 5.242434 ACATGCAAATGAAACAATGATGCT 58.758 33.333 0.00 0.00 33.66 3.79
2184 2371 6.399743 ACATGCAAATGAAACAATGATGCTA 58.600 32.000 0.00 0.00 33.66 3.49
2185 2372 6.533723 ACATGCAAATGAAACAATGATGCTAG 59.466 34.615 0.00 0.00 33.66 3.42
2217 2404 8.279103 GCATATTCTTGCTTCTGTGATTAGTAC 58.721 37.037 0.00 0.00 39.57 2.73
2221 2408 7.704578 TCTTGCTTCTGTGATTAGTACTAGT 57.295 36.000 0.00 0.00 0.00 2.57
2222 2409 8.803397 TCTTGCTTCTGTGATTAGTACTAGTA 57.197 34.615 2.23 0.00 0.00 1.82
2248 2438 9.734984 AGTATCTACCTTAAGCTCTCTAGATTC 57.265 37.037 0.00 0.63 32.49 2.52
2249 2439 9.509956 GTATCTACCTTAAGCTCTCTAGATTCA 57.490 37.037 0.00 0.00 32.49 2.57
2290 2485 3.066208 AGAGAGGGAATATGGGAGCAA 57.934 47.619 0.00 0.00 0.00 3.91
2307 2502 4.184629 GAGCAAATGAGAGTTCCGTATGT 58.815 43.478 0.00 0.00 0.00 2.29
2403 2598 4.649692 ACATATCTTAGCTGGAGCCATTG 58.350 43.478 0.00 0.00 43.38 2.82
2412 2607 2.354259 CTGGAGCCATTGAGACAGAAC 58.646 52.381 0.00 0.00 0.00 3.01
2416 2611 3.416156 GAGCCATTGAGACAGAACCTTT 58.584 45.455 0.00 0.00 0.00 3.11
2417 2612 3.152341 AGCCATTGAGACAGAACCTTTG 58.848 45.455 0.00 0.00 0.00 2.77
2420 2615 3.304928 CCATTGAGACAGAACCTTTGTGC 60.305 47.826 0.00 0.00 0.00 4.57
2421 2616 1.967319 TGAGACAGAACCTTTGTGCC 58.033 50.000 0.00 0.00 0.00 5.01
2427 2622 0.470766 AGAACCTTTGTGCCGTGGTA 59.529 50.000 0.00 0.00 31.82 3.25
2436 2635 2.032620 TGTGCCGTGGTAAATTTTGGT 58.967 42.857 0.00 0.00 0.00 3.67
2522 2724 8.730680 TGAAAAGAAATAATAGCAGAACTGACC 58.269 33.333 5.97 0.00 0.00 4.02
2528 2730 6.663944 ATAATAGCAGAACTGACCGTTTTC 57.336 37.500 5.97 0.00 35.56 2.29
2531 2733 1.531578 GCAGAACTGACCGTTTTCCTC 59.468 52.381 5.97 0.00 35.56 3.71
2536 2738 3.947910 ACTGACCGTTTTCCTCGATTA 57.052 42.857 0.00 0.00 0.00 1.75
2707 2909 0.408700 ACCTTCTGTACCTCTCCCGT 59.591 55.000 0.00 0.00 0.00 5.28
2824 3026 1.855295 TCCAGAGGTACACGGCAATA 58.145 50.000 0.00 0.00 0.00 1.90
2968 3170 0.911769 ACCATCATGAAAGCGGAGGA 59.088 50.000 0.00 0.00 0.00 3.71
3048 3250 3.307762 CCTCCTCCCTTACTGACTTTTGG 60.308 52.174 0.00 0.00 0.00 3.28
3205 3407 1.069204 CCCCAGATCAACGACGATGAT 59.931 52.381 19.08 19.08 40.14 2.45
3298 3500 2.368875 CAGGCCTAATATGACGGTCCTT 59.631 50.000 3.98 0.00 0.00 3.36
3557 3759 1.526575 CGGCAAACCAGATGCAACCT 61.527 55.000 0.00 0.00 45.60 3.50
3628 3830 0.694444 TGGGGCTTCCTGAGGGATAC 60.694 60.000 0.00 0.00 41.87 2.24
3667 3873 7.451255 TGTTCATCATAAGGAAAACATTCAGGT 59.549 33.333 0.00 0.00 33.10 4.00
3907 4113 7.260387 TGGGAAGAACAACACTGGTATATTA 57.740 36.000 0.00 0.00 0.00 0.98
3911 4117 9.880157 GGAAGAACAACACTGGTATATTAACTA 57.120 33.333 0.00 0.00 0.00 2.24
3932 4138 3.644335 ACCTCGGCTCTTCCTACTTTAT 58.356 45.455 0.00 0.00 0.00 1.40
4361 4569 0.617413 AGCAAGCACTCATAGGCAGT 59.383 50.000 0.00 0.00 0.00 4.40
4592 4800 1.799181 CGTATCCGAGTCCAAGTGCTG 60.799 57.143 0.00 0.00 35.63 4.41
4745 4953 2.361757 TCAAACAGCCTGTGGAATTGTG 59.638 45.455 0.00 0.00 0.00 3.33
5292 5500 4.616802 CGCAAAATTCACAGGTAACACATC 59.383 41.667 0.00 0.00 41.41 3.06
5404 5612 2.567169 ACTAACATGGCTACACTGCAGA 59.433 45.455 23.35 0.00 34.04 4.26
6299 6507 4.572389 CGGCAATAAGTGATATCATAGCCC 59.428 45.833 9.02 3.19 35.09 5.19
6499 6707 3.181445 ACAACAGAGTGGAACATAGCCAA 60.181 43.478 0.00 0.00 44.52 4.52
6643 6851 5.566395 CCAATGCATCGACATCAATTAATCG 59.434 40.000 0.00 0.00 35.91 3.34
6933 7141 4.524316 TCAAATTCCAAGGAAGTGCATG 57.476 40.909 7.69 0.94 37.56 4.06
7236 7444 7.095816 TGTCACGTTGAATATGAAGTAACACAG 60.096 37.037 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.766674 TCCAAGGCCCACTACACACT 60.767 55.000 0.00 0.00 0.00 3.55
1 2 0.328258 ATCCAAGGCCCACTACACAC 59.672 55.000 0.00 0.00 0.00 3.82
2 3 0.327924 CATCCAAGGCCCACTACACA 59.672 55.000 0.00 0.00 0.00 3.72
3 4 0.328258 ACATCCAAGGCCCACTACAC 59.672 55.000 0.00 0.00 0.00 2.90
4 5 1.959710 TACATCCAAGGCCCACTACA 58.040 50.000 0.00 0.00 0.00 2.74
5 6 2.421529 CCTTACATCCAAGGCCCACTAC 60.422 54.545 0.00 0.00 38.80 2.73
6 7 1.843851 CCTTACATCCAAGGCCCACTA 59.156 52.381 0.00 0.00 38.80 2.74
7 8 0.625849 CCTTACATCCAAGGCCCACT 59.374 55.000 0.00 0.00 38.80 4.00
8 9 3.191182 CCTTACATCCAAGGCCCAC 57.809 57.895 0.00 0.00 38.80 4.61
14 15 6.533730 TCAGGCAATATACCTTACATCCAAG 58.466 40.000 0.00 0.00 34.42 3.61
15 16 6.508030 TCAGGCAATATACCTTACATCCAA 57.492 37.500 0.00 0.00 34.42 3.53
16 17 6.296432 GGATCAGGCAATATACCTTACATCCA 60.296 42.308 15.05 0.00 36.38 3.41
17 18 6.116126 GGATCAGGCAATATACCTTACATCC 58.884 44.000 0.00 9.38 34.42 3.51
18 19 6.711277 TGGATCAGGCAATATACCTTACATC 58.289 40.000 0.00 0.00 34.42 3.06
19 20 6.702449 TGGATCAGGCAATATACCTTACAT 57.298 37.500 0.00 0.00 34.42 2.29
20 21 5.513094 GCTGGATCAGGCAATATACCTTACA 60.513 44.000 0.00 0.00 34.42 2.41
21 22 4.938226 GCTGGATCAGGCAATATACCTTAC 59.062 45.833 0.00 0.00 34.42 2.34
22 23 4.322725 CGCTGGATCAGGCAATATACCTTA 60.323 45.833 9.27 0.00 34.42 2.69
23 24 3.557898 CGCTGGATCAGGCAATATACCTT 60.558 47.826 9.27 0.00 34.42 3.50
24 25 2.027745 CGCTGGATCAGGCAATATACCT 60.028 50.000 9.27 0.00 38.35 3.08
25 26 2.350522 CGCTGGATCAGGCAATATACC 58.649 52.381 9.27 0.00 31.21 2.73
26 27 2.350522 CCGCTGGATCAGGCAATATAC 58.649 52.381 9.27 0.00 31.21 1.47
27 28 2.768253 CCGCTGGATCAGGCAATATA 57.232 50.000 9.27 0.00 31.21 0.86
28 29 3.639099 CCGCTGGATCAGGCAATAT 57.361 52.632 9.27 0.00 31.21 1.28
34 35 2.249535 CGATTGCCGCTGGATCAGG 61.250 63.158 0.00 0.00 31.21 3.86
35 36 3.327148 CGATTGCCGCTGGATCAG 58.673 61.111 0.00 0.00 34.12 2.90
44 45 2.464459 GGAGGTCAAGCGATTGCCG 61.464 63.158 8.91 0.00 44.31 5.69
45 46 1.372087 CTGGAGGTCAAGCGATTGCC 61.372 60.000 8.91 13.20 44.31 4.52
46 47 0.391661 TCTGGAGGTCAAGCGATTGC 60.392 55.000 8.91 3.87 43.24 3.56
47 48 2.099141 TTCTGGAGGTCAAGCGATTG 57.901 50.000 7.17 7.17 0.00 2.67
48 49 2.503356 AGATTCTGGAGGTCAAGCGATT 59.497 45.455 0.00 0.00 0.00 3.34
49 50 2.102252 GAGATTCTGGAGGTCAAGCGAT 59.898 50.000 0.00 0.00 0.00 4.58
50 51 1.478510 GAGATTCTGGAGGTCAAGCGA 59.521 52.381 0.00 0.00 0.00 4.93
51 52 1.800655 CGAGATTCTGGAGGTCAAGCG 60.801 57.143 0.00 0.00 0.00 4.68
52 53 1.478510 TCGAGATTCTGGAGGTCAAGC 59.521 52.381 0.00 0.00 0.00 4.01
53 54 3.876274 TTCGAGATTCTGGAGGTCAAG 57.124 47.619 0.00 0.00 0.00 3.02
54 55 3.769300 TCATTCGAGATTCTGGAGGTCAA 59.231 43.478 0.00 0.00 0.00 3.18
55 56 3.365472 TCATTCGAGATTCTGGAGGTCA 58.635 45.455 0.00 0.00 0.00 4.02
56 57 4.038522 TCATCATTCGAGATTCTGGAGGTC 59.961 45.833 0.00 0.00 0.00 3.85
57 58 3.963374 TCATCATTCGAGATTCTGGAGGT 59.037 43.478 0.00 0.00 0.00 3.85
58 59 4.597404 TCATCATTCGAGATTCTGGAGG 57.403 45.455 0.00 0.00 0.00 4.30
59 60 4.749099 GGTTCATCATTCGAGATTCTGGAG 59.251 45.833 0.00 0.00 0.00 3.86
60 61 4.443457 GGGTTCATCATTCGAGATTCTGGA 60.443 45.833 0.00 0.00 0.00 3.86
61 62 3.812053 GGGTTCATCATTCGAGATTCTGG 59.188 47.826 0.00 0.00 0.00 3.86
62 63 3.492383 CGGGTTCATCATTCGAGATTCTG 59.508 47.826 0.00 0.00 0.00 3.02
63 64 3.133003 ACGGGTTCATCATTCGAGATTCT 59.867 43.478 0.00 0.00 0.00 2.40
64 65 3.458189 ACGGGTTCATCATTCGAGATTC 58.542 45.455 0.00 0.00 0.00 2.52
65 66 3.543680 ACGGGTTCATCATTCGAGATT 57.456 42.857 0.00 0.00 0.00 2.40
66 67 4.369182 GTTACGGGTTCATCATTCGAGAT 58.631 43.478 0.00 0.00 0.00 2.75
67 68 3.429822 GGTTACGGGTTCATCATTCGAGA 60.430 47.826 0.00 0.00 0.00 4.04
68 69 2.864343 GGTTACGGGTTCATCATTCGAG 59.136 50.000 0.00 0.00 0.00 4.04
69 70 2.234168 TGGTTACGGGTTCATCATTCGA 59.766 45.455 0.00 0.00 0.00 3.71
70 71 2.623535 TGGTTACGGGTTCATCATTCG 58.376 47.619 0.00 0.00 0.00 3.34
71 72 4.196193 TGATGGTTACGGGTTCATCATTC 58.804 43.478 8.84 0.00 40.41 2.67
72 73 4.229304 TGATGGTTACGGGTTCATCATT 57.771 40.909 8.84 0.00 40.41 2.57
73 74 3.924114 TGATGGTTACGGGTTCATCAT 57.076 42.857 8.84 0.00 40.41 2.45
74 75 3.924114 ATGATGGTTACGGGTTCATCA 57.076 42.857 13.30 13.30 46.38 3.07
75 76 4.035208 GTCAATGATGGTTACGGGTTCATC 59.965 45.833 0.00 0.00 37.21 2.92
76 77 3.945285 GTCAATGATGGTTACGGGTTCAT 59.055 43.478 0.00 0.00 0.00 2.57
77 78 3.244596 TGTCAATGATGGTTACGGGTTCA 60.245 43.478 0.00 0.00 0.00 3.18
78 79 3.340034 TGTCAATGATGGTTACGGGTTC 58.660 45.455 0.00 0.00 0.00 3.62
79 80 3.426787 TGTCAATGATGGTTACGGGTT 57.573 42.857 0.00 0.00 0.00 4.11
80 81 3.644966 ATGTCAATGATGGTTACGGGT 57.355 42.857 0.00 0.00 0.00 5.28
81 82 4.447290 TGTATGTCAATGATGGTTACGGG 58.553 43.478 0.00 0.00 0.00 5.28
82 83 4.511454 CCTGTATGTCAATGATGGTTACGG 59.489 45.833 0.00 0.00 0.00 4.02
83 84 4.024893 GCCTGTATGTCAATGATGGTTACG 60.025 45.833 0.00 0.00 0.00 3.18
84 85 4.881273 TGCCTGTATGTCAATGATGGTTAC 59.119 41.667 0.00 0.00 0.00 2.50
85 86 4.881273 GTGCCTGTATGTCAATGATGGTTA 59.119 41.667 0.00 0.00 0.00 2.85
86 87 3.696051 GTGCCTGTATGTCAATGATGGTT 59.304 43.478 0.00 0.00 0.00 3.67
87 88 3.282021 GTGCCTGTATGTCAATGATGGT 58.718 45.455 0.00 0.00 0.00 3.55
88 89 2.288729 CGTGCCTGTATGTCAATGATGG 59.711 50.000 0.00 0.00 0.00 3.51
89 90 2.286595 GCGTGCCTGTATGTCAATGATG 60.287 50.000 0.00 0.00 0.00 3.07
90 91 1.942657 GCGTGCCTGTATGTCAATGAT 59.057 47.619 0.00 0.00 0.00 2.45
91 92 1.338579 TGCGTGCCTGTATGTCAATGA 60.339 47.619 0.00 0.00 0.00 2.57
122 123 9.950680 CAAAATTATCTGTCGCCTATTACAATT 57.049 29.630 0.00 0.00 0.00 2.32
171 172 3.793559 ACCGTGCCATACTTGAATACTC 58.206 45.455 0.00 0.00 0.00 2.59
437 450 7.671495 ATCACAGTGTTTTTGCTTTTCTTTT 57.329 28.000 0.00 0.00 0.00 2.27
469 482 4.142773 ACGAGGGTTGTTATGCGTTTAATG 60.143 41.667 0.00 0.00 0.00 1.90
484 497 3.692406 GCCTGGTCGACGAGGGTT 61.692 66.667 37.57 0.00 41.51 4.11
506 519 3.243737 TGCGAGACTGAAACTGTATGTGT 60.244 43.478 0.00 0.00 0.00 3.72
547 561 2.461695 TGGGGTTCAAACTCAAAAGCA 58.538 42.857 0.00 0.00 0.00 3.91
548 562 3.194861 GTTGGGGTTCAAACTCAAAAGC 58.805 45.455 0.00 0.00 37.08 3.51
549 563 3.736740 CGGTTGGGGTTCAAACTCAAAAG 60.737 47.826 0.00 0.00 40.79 2.27
570 586 0.655733 ACACTGCAACGAAAGAACCG 59.344 50.000 0.00 0.00 0.00 4.44
582 598 1.844771 GCGCAAGACATCACACTGCA 61.845 55.000 0.30 0.00 43.02 4.41
594 610 2.428890 TGAAAAGAAAAAGGGCGCAAGA 59.571 40.909 10.83 0.00 43.02 3.02
644 661 7.180866 TGCTACCGCCGTTTACATATGTAAAT 61.181 38.462 32.85 22.29 42.30 1.40
674 693 8.704668 AGACCCCATATCAATTTTTCATTTACC 58.295 33.333 0.00 0.00 0.00 2.85
696 715 1.597742 TCTTGCTGCACTTTGAGACC 58.402 50.000 0.00 0.00 0.00 3.85
699 718 3.772932 TGTTTTCTTGCTGCACTTTGAG 58.227 40.909 0.00 0.00 0.00 3.02
700 719 3.772932 CTGTTTTCTTGCTGCACTTTGA 58.227 40.909 0.00 0.00 0.00 2.69
710 729 6.030228 GGAGTATACATTGCTGTTTTCTTGC 58.970 40.000 5.50 0.00 36.79 4.01
713 732 7.944729 AATGGAGTATACATTGCTGTTTTCT 57.055 32.000 5.50 0.00 37.18 2.52
802 821 0.658897 GAAAAGTTGGTCGGTTGCGA 59.341 50.000 0.00 0.00 0.00 5.10
803 822 0.317519 GGAAAAGTTGGTCGGTTGCG 60.318 55.000 0.00 0.00 0.00 4.85
804 823 0.741915 TGGAAAAGTTGGTCGGTTGC 59.258 50.000 0.00 0.00 0.00 4.17
840 893 2.161486 GCGTGTGTGCTCTCCGATC 61.161 63.158 0.00 0.00 0.00 3.69
865 918 5.337652 GGGGCTTTATATAGCACAGGACTAG 60.338 48.000 17.67 0.00 46.54 2.57
938 996 2.032528 GTAGCACTGGCCAGCACA 59.967 61.111 33.06 12.70 42.56 4.57
1044 1117 1.228154 GAACTTGAACAGGCCCCGT 60.228 57.895 0.00 0.00 0.00 5.28
1242 1315 6.545666 TCATTCATGTGTTCCAACAGTAACTT 59.454 34.615 0.00 0.00 40.05 2.66
1300 1459 6.216750 TGTTCCGTTTTGTTTTTGTTTCTG 57.783 33.333 0.00 0.00 0.00 3.02
1385 1544 4.002906 TGGAGGCAACAACTTAGTGTAG 57.997 45.455 0.00 0.00 41.41 2.74
1415 1574 2.280797 TTCAGGCACGACTGCACC 60.281 61.111 0.00 0.00 46.28 5.01
1416 1575 1.160329 AAGTTCAGGCACGACTGCAC 61.160 55.000 0.00 0.00 46.28 4.57
1483 1642 7.362662 TCTATGTAGCAGCAAAAACTCAAAAG 58.637 34.615 0.00 0.00 0.00 2.27
1485 1644 6.875948 TCTATGTAGCAGCAAAAACTCAAA 57.124 33.333 0.00 0.00 0.00 2.69
1486 1645 7.452880 AATCTATGTAGCAGCAAAAACTCAA 57.547 32.000 0.00 0.00 0.00 3.02
1487 1646 7.307694 CAAATCTATGTAGCAGCAAAAACTCA 58.692 34.615 0.00 0.00 0.00 3.41
1489 1648 6.095377 GCAAATCTATGTAGCAGCAAAAACT 58.905 36.000 0.00 0.00 0.00 2.66
1490 1649 5.863397 TGCAAATCTATGTAGCAGCAAAAAC 59.137 36.000 0.00 0.00 0.00 2.43
1493 1652 5.840243 ATGCAAATCTATGTAGCAGCAAA 57.160 34.783 0.00 0.00 38.75 3.68
1494 1653 5.049198 GCTATGCAAATCTATGTAGCAGCAA 60.049 40.000 6.78 0.00 38.75 3.91
1497 1656 6.600350 CAAGCTATGCAAATCTATGTAGCAG 58.400 40.000 12.73 3.19 38.75 4.24
1498 1657 6.549912 CAAGCTATGCAAATCTATGTAGCA 57.450 37.500 12.73 0.00 37.57 3.49
1512 1671 8.933181 TGTTGAAACAATCTGGCAAGCTATGC 62.933 42.308 11.11 11.11 44.63 3.14
1518 1677 4.053295 CCTTGTTGAAACAATCTGGCAAG 58.947 43.478 8.94 0.00 46.71 4.01
1521 1680 2.627699 TCCCTTGTTGAAACAATCTGGC 59.372 45.455 8.94 0.00 46.71 4.85
1539 1698 6.464892 GGGGTACACCAAGTTAGTATTATCCC 60.465 46.154 10.04 0.00 42.91 3.85
1540 1699 6.328410 AGGGGTACACCAAGTTAGTATTATCC 59.672 42.308 18.57 0.00 42.91 2.59
1542 1701 8.877195 CATAGGGGTACACCAAGTTAGTATTAT 58.123 37.037 18.57 0.00 42.91 1.28
1543 1702 7.290714 CCATAGGGGTACACCAAGTTAGTATTA 59.709 40.741 18.57 0.00 42.91 0.98
1544 1703 6.100714 CCATAGGGGTACACCAAGTTAGTATT 59.899 42.308 18.57 0.00 42.91 1.89
1546 1705 4.964262 CCATAGGGGTACACCAAGTTAGTA 59.036 45.833 18.57 0.00 42.91 1.82
1547 1706 3.778629 CCATAGGGGTACACCAAGTTAGT 59.221 47.826 18.57 0.00 42.91 2.24
1548 1707 4.035112 TCCATAGGGGTACACCAAGTTAG 58.965 47.826 18.57 0.00 42.91 2.34
1550 1709 2.574824 GTCCATAGGGGTACACCAAGTT 59.425 50.000 18.57 0.00 42.91 2.66
1552 1711 2.193127 TGTCCATAGGGGTACACCAAG 58.807 52.381 18.57 5.16 42.91 3.61
1555 1714 1.420138 CCATGTCCATAGGGGTACACC 59.580 57.143 5.83 5.83 38.11 4.16
1556 1715 2.104281 GTCCATGTCCATAGGGGTACAC 59.896 54.545 0.00 0.00 38.11 2.90
1773 1936 1.898574 GGGCTTGACTGGTGTGGTG 60.899 63.158 0.00 0.00 0.00 4.17
1788 1960 0.972471 CCAATCAAGACCAAGGGGGC 60.972 60.000 0.00 0.00 45.66 5.80
1791 1963 6.165577 CAAATTAACCAATCAAGACCAAGGG 58.834 40.000 0.00 0.00 0.00 3.95
1798 1970 8.954950 TTGAAAAGCAAATTAACCAATCAAGA 57.045 26.923 0.00 0.00 32.46 3.02
1799 1971 9.601971 CATTGAAAAGCAAATTAACCAATCAAG 57.398 29.630 0.00 0.00 40.48 3.02
1800 1972 9.334947 TCATTGAAAAGCAAATTAACCAATCAA 57.665 25.926 0.00 0.00 40.48 2.57
1801 1973 8.772705 GTCATTGAAAAGCAAATTAACCAATCA 58.227 29.630 0.00 0.00 40.48 2.57
1802 1974 8.229811 GGTCATTGAAAAGCAAATTAACCAATC 58.770 33.333 0.00 0.00 40.48 2.67
1803 1975 7.938490 AGGTCATTGAAAAGCAAATTAACCAAT 59.062 29.630 0.00 0.00 40.48 3.16
1837 2009 1.301165 GTCCGCTTTGTGTACCCGT 60.301 57.895 0.00 0.00 0.00 5.28
1840 2012 2.858158 GCGTCCGCTTTGTGTACC 59.142 61.111 4.10 0.00 38.26 3.34
1851 2023 2.049475 AAGACTAGCTAGCGCGTCCG 62.049 60.000 25.73 9.91 42.32 4.79
1852 2024 0.317186 GAAGACTAGCTAGCGCGTCC 60.317 60.000 25.73 14.14 42.32 4.79
1853 2025 0.377554 TGAAGACTAGCTAGCGCGTC 59.622 55.000 20.91 23.48 42.32 5.19
1864 2036 2.739292 GTGCGTGACTTGTGAAGACTA 58.261 47.619 0.00 0.00 0.00 2.59
1918 2090 1.953559 TCCAAGGCGAATCTACATGC 58.046 50.000 0.00 0.00 0.00 4.06
1919 2091 3.535561 AGTTCCAAGGCGAATCTACATG 58.464 45.455 0.00 0.00 0.00 3.21
1991 2166 2.543777 TTTCTCCTGTCCTTGGTTCG 57.456 50.000 0.00 0.00 0.00 3.95
2014 2189 2.361610 GTGCCACCATGACAGGGG 60.362 66.667 11.48 2.61 0.00 4.79
2015 2190 1.973281 GTGTGCCACCATGACAGGG 60.973 63.158 4.17 4.17 0.00 4.45
2031 2214 1.207329 GAGTGGCAAGGTAGGTAGGTG 59.793 57.143 0.00 0.00 0.00 4.00
2146 2333 8.114331 TCATTTGCATGTTCTTAGAACAAGAT 57.886 30.769 28.17 12.20 33.42 2.40
2147 2334 7.509141 TCATTTGCATGTTCTTAGAACAAGA 57.491 32.000 28.17 14.12 33.42 3.02
2148 2335 8.482429 GTTTCATTTGCATGTTCTTAGAACAAG 58.518 33.333 28.17 24.64 33.42 3.16
2151 2338 7.928908 TGTTTCATTTGCATGTTCTTAGAAC 57.071 32.000 17.34 17.34 0.00 3.01
2152 2339 8.980610 CATTGTTTCATTTGCATGTTCTTAGAA 58.019 29.630 0.00 0.00 0.00 2.10
2153 2340 8.358895 TCATTGTTTCATTTGCATGTTCTTAGA 58.641 29.630 0.00 0.00 0.00 2.10
2154 2341 8.523523 TCATTGTTTCATTTGCATGTTCTTAG 57.476 30.769 0.00 0.00 0.00 2.18
2155 2342 8.927721 CATCATTGTTTCATTTGCATGTTCTTA 58.072 29.630 0.00 0.00 0.00 2.10
2161 2348 5.794687 AGCATCATTGTTTCATTTGCATG 57.205 34.783 0.00 0.00 0.00 4.06
2164 2351 7.028962 TGTACTAGCATCATTGTTTCATTTGC 58.971 34.615 0.00 0.00 0.00 3.68
2167 2354 7.094248 TGCTTGTACTAGCATCATTGTTTCATT 60.094 33.333 25.07 0.00 45.72 2.57
2197 2384 7.704578 ACTAGTACTAATCACAGAAGCAAGA 57.295 36.000 3.76 0.00 0.00 3.02
2199 2386 8.577048 ACTACTAGTACTAATCACAGAAGCAA 57.423 34.615 3.76 0.00 0.00 3.91
2222 2409 9.734984 GAATCTAGAGAGCTTAAGGTAGATACT 57.265 37.037 14.85 5.55 0.00 2.12
2271 2461 3.864789 TTTGCTCCCATATTCCCTCTC 57.135 47.619 0.00 0.00 0.00 3.20
2290 2485 4.801330 TGTCACATACGGAACTCTCATT 57.199 40.909 0.00 0.00 0.00 2.57
2307 2502 3.635836 TGTCAACATTCCATGCTTTGTCA 59.364 39.130 0.00 0.00 0.00 3.58
2338 2533 9.826574 TTTAATGCAGTCGTTATTATAGGAACT 57.173 29.630 0.00 0.00 46.37 3.01
2369 2564 9.956720 CCAGCTAAGATATGTTTATTTTTGGAG 57.043 33.333 0.00 0.00 0.00 3.86
2385 2580 3.044156 TCTCAATGGCTCCAGCTAAGAT 58.956 45.455 0.00 0.00 41.70 2.40
2403 2598 0.868406 CGGCACAAAGGTTCTGTCTC 59.132 55.000 0.00 0.00 0.00 3.36
2412 2607 3.378911 AAATTTACCACGGCACAAAGG 57.621 42.857 0.00 0.00 0.00 3.11
2416 2611 2.032620 ACCAAAATTTACCACGGCACA 58.967 42.857 0.00 0.00 0.00 4.57
2417 2612 2.804697 ACCAAAATTTACCACGGCAC 57.195 45.000 0.00 0.00 0.00 5.01
2420 2615 4.548494 GGTGTTACCAAAATTTACCACGG 58.452 43.478 0.00 0.00 38.42 4.94
2421 2616 4.024218 TCGGTGTTACCAAAATTTACCACG 60.024 41.667 5.21 1.67 38.47 4.94
2427 2622 3.243134 CCACGTCGGTGTTACCAAAATTT 60.243 43.478 0.00 0.00 42.80 1.82
2442 2641 7.854934 TTCCAAAATTATTTTTACCACGTCG 57.145 32.000 0.00 0.00 33.29 5.12
2469 2668 7.733773 TTCCAGATCTAGTTCTTATTGTCCA 57.266 36.000 0.00 0.00 0.00 4.02
2509 2711 2.367567 AGGAAAACGGTCAGTTCTGCTA 59.632 45.455 0.00 0.00 43.37 3.49
2517 2719 5.796350 AAATAATCGAGGAAAACGGTCAG 57.204 39.130 0.00 0.00 0.00 3.51
2522 2724 7.745015 TCAAGGTAAAATAATCGAGGAAAACG 58.255 34.615 0.00 0.00 0.00 3.60
2528 2730 7.016361 CCTGTTCAAGGTAAAATAATCGAGG 57.984 40.000 0.00 0.00 41.74 4.63
2707 2909 3.051479 TACTCGTGGCGCGACTCA 61.051 61.111 20.52 2.87 45.68 3.41
2718 2920 1.070105 TTTGCCTTGGCGTACTCGT 59.930 52.632 7.18 0.00 39.49 4.18
2824 3026 1.971357 AGGTTGATGGTCTTGTCGAGT 59.029 47.619 0.00 0.00 0.00 4.18
2968 3170 1.045407 TTCCTGCGGCGTATATCCTT 58.955 50.000 9.37 0.00 0.00 3.36
3298 3500 5.548056 AGGAATCTGGAGGTTGAAGTCTTTA 59.452 40.000 0.00 0.00 0.00 1.85
3496 3698 1.588824 ATGTGCCGAACAGTGCATGG 61.589 55.000 0.00 0.00 43.64 3.66
3557 3759 3.538591 CTGCTGCATAGAGTTCATCCAA 58.461 45.455 1.31 0.00 0.00 3.53
3628 3830 7.810282 CCTTATGATGAACATACCTTAGTCTCG 59.190 40.741 0.00 0.00 40.62 4.04
3667 3873 3.460825 AGGGAGACAGGTTATTAAGGCA 58.539 45.455 0.00 0.00 0.00 4.75
3907 4113 2.025131 AGTAGGAAGAGCCGAGGTAGTT 60.025 50.000 0.00 0.00 43.43 2.24
3911 4117 1.939980 AAAGTAGGAAGAGCCGAGGT 58.060 50.000 0.00 0.00 43.43 3.85
3932 4138 7.136822 TCAGGAAATCCTAAGCTTAGCATTA 57.863 36.000 25.38 12.01 46.65 1.90
4025 4233 1.338674 TGATCGGCATTCTTCACGGTT 60.339 47.619 0.00 0.00 0.00 4.44
4361 4569 5.368145 GAACCATACACCAATGCAGAGATA 58.632 41.667 0.00 0.00 0.00 1.98
4592 4800 4.878971 GCCTCAAAGGTTAAGATCTTCTCC 59.121 45.833 12.24 14.92 37.80 3.71
4745 4953 0.451783 GTCCCATTGTCACCGCAATC 59.548 55.000 0.00 0.00 37.00 2.67
5292 5500 5.642491 CCATACAATGCTCATGAGAGTATGG 59.358 44.000 33.34 33.34 44.98 2.74
5404 5612 4.265073 CTCTTCGGATTGTCCTTTTCCAT 58.735 43.478 0.00 0.00 33.30 3.41
5861 6069 9.383519 CTGTAAGTTTCATATGTTGGATACTGT 57.616 33.333 1.90 0.00 37.61 3.55
6203 6411 2.373169 TGCTCCCTTCTTGTTCATGAGT 59.627 45.455 0.00 0.00 0.00 3.41
6499 6707 7.514721 TGTTCAGTTGTAGGTATTCCTTCTTT 58.485 34.615 0.00 0.00 42.12 2.52
6643 6851 2.801342 CGGCTAGCCTCTGATGAACTTC 60.801 54.545 30.55 0.00 0.00 3.01
6933 7141 1.664302 GCTCAAAGAACTGGAAAGCGC 60.664 52.381 0.00 0.00 0.00 5.92
7171 7379 3.253188 CACACACGTTCAGGGAATCATTT 59.747 43.478 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.