Multiple sequence alignment - TraesCS6B01G049500

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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 TraesCS6B01G049500 chr6B 100.000 2531 0 0 1 2531 29069389 29066859 0.000000e+00 4674.0
1 TraesCS6B01G049500 chr6B 85.221 1042 89 40 749 1745 29060856 29059835 0.000000e+00 1011.0
2 TraesCS6B01G049500 chr6B 92.941 680 42 3 874 1547 28713936 28714615 0.000000e+00 985.0
3 TraesCS6B01G049500 chr6B 92.782 665 38 7 873 1532 59232678 59233337 0.000000e+00 953.0
4 TraesCS6B01G049500 chr6B 91.825 685 46 8 871 1547 59294821 59295503 0.000000e+00 946.0
5 TraesCS6B01G049500 chr6B 91.483 681 49 6 876 1547 28517449 28516769 0.000000e+00 928.0
6 TraesCS6B01G049500 chr6B 86.255 713 65 19 854 1535 38877580 38878290 0.000000e+00 743.0
7 TraesCS6B01G049500 chr6D 92.627 1709 92 17 1 1686 16530517 16528820 0.000000e+00 2427.0
8 TraesCS6B01G049500 chr6D 89.350 723 59 13 840 1545 16307401 16306680 0.000000e+00 893.0
9 TraesCS6B01G049500 chr6D 90.303 165 12 4 2273 2436 16528529 16528368 1.970000e-51 213.0
10 TraesCS6B01G049500 chr6D 89.286 140 13 2 1 139 136124826 136124688 9.310000e-40 174.0
11 TraesCS6B01G049500 chr6D 75.446 224 39 10 136 356 5906536 5906326 7.450000e-16 95.3
12 TraesCS6B01G049500 chr6A 88.633 1258 74 21 519 1745 16802496 16801277 0.000000e+00 1467.0
13 TraesCS6B01G049500 chr6A 84.747 1049 97 37 739 1740 16720468 16719436 0.000000e+00 992.0
14 TraesCS6B01G049500 chr6A 90.960 708 49 11 841 1534 16658846 16658140 0.000000e+00 939.0
15 TraesCS6B01G049500 chr6A 89.617 183 15 4 2273 2454 16800846 16800667 1.960000e-56 230.0
16 TraesCS6B01G049500 chr2D 85.526 228 18 11 136 350 56643432 56643657 9.110000e-55 224.0
17 TraesCS6B01G049500 chr5D 85.268 224 17 9 138 350 42084137 42084355 1.520000e-52 217.0
18 TraesCS6B01G049500 chr4B 89.143 175 16 2 138 311 112038146 112038318 5.480000e-52 215.0
19 TraesCS6B01G049500 chr1D 85.646 209 22 4 138 344 465130920 465131122 1.970000e-51 213.0
20 TraesCS6B01G049500 chr1D 88.571 140 14 2 1 139 266230902 266231040 4.330000e-38 169.0
21 TraesCS6B01G049500 chr5A 84.821 224 19 6 138 350 30657175 30657394 7.090000e-51 211.0
22 TraesCS6B01G049500 chr7A 88.571 175 16 4 172 344 20777583 20777755 2.550000e-50 209.0
23 TraesCS6B01G049500 chr1B 84.932 219 18 8 138 344 533803314 533803529 9.180000e-50 207.0
24 TraesCS6B01G049500 chr1B 90.000 60 6 0 291 350 197830893 197830952 7.510000e-11 78.7
25 TraesCS6B01G049500 chr4D 91.549 142 10 2 1 141 264483968 264483828 7.140000e-46 195.0
26 TraesCS6B01G049500 chr4D 89.437 142 12 3 1 141 318598755 318598894 2.590000e-40 176.0
27 TraesCS6B01G049500 chr7B 85.204 196 20 7 138 329 158043592 158043782 2.570000e-45 193.0
28 TraesCS6B01G049500 chr2B 89.437 142 13 2 1 141 667095612 667095752 7.190000e-41 178.0
29 TraesCS6B01G049500 chr2B 81.517 211 30 6 146 350 741971694 741971901 5.600000e-37 165.0
30 TraesCS6B01G049500 chr1A 89.437 142 12 3 1 141 354203899 354203760 2.590000e-40 176.0
31 TraesCS6B01G049500 chr2A 82.297 209 29 6 146 349 740047740 740047945 9.310000e-40 174.0
32 TraesCS6B01G049500 chr3B 89.286 140 12 3 1 139 273339756 273339893 3.350000e-39 172.0
33 TraesCS6B01G049500 chr3D 88.571 140 14 2 3 141 254036858 254036996 4.330000e-38 169.0


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 TraesCS6B01G049500 chr6B 29066859 29069389 2530 True 4674.0 4674 100.000 1 2531 1 chr6B.!!$R3 2530
1 TraesCS6B01G049500 chr6B 29059835 29060856 1021 True 1011.0 1011 85.221 749 1745 1 chr6B.!!$R2 996
2 TraesCS6B01G049500 chr6B 28713936 28714615 679 False 985.0 985 92.941 874 1547 1 chr6B.!!$F1 673
3 TraesCS6B01G049500 chr6B 59232678 59233337 659 False 953.0 953 92.782 873 1532 1 chr6B.!!$F3 659
4 TraesCS6B01G049500 chr6B 59294821 59295503 682 False 946.0 946 91.825 871 1547 1 chr6B.!!$F4 676
5 TraesCS6B01G049500 chr6B 28516769 28517449 680 True 928.0 928 91.483 876 1547 1 chr6B.!!$R1 671
6 TraesCS6B01G049500 chr6B 38877580 38878290 710 False 743.0 743 86.255 854 1535 1 chr6B.!!$F2 681
7 TraesCS6B01G049500 chr6D 16528368 16530517 2149 True 1320.0 2427 91.465 1 2436 2 chr6D.!!$R4 2435
8 TraesCS6B01G049500 chr6D 16306680 16307401 721 True 893.0 893 89.350 840 1545 1 chr6D.!!$R2 705
9 TraesCS6B01G049500 chr6A 16719436 16720468 1032 True 992.0 992 84.747 739 1740 1 chr6A.!!$R2 1001
10 TraesCS6B01G049500 chr6A 16658140 16658846 706 True 939.0 939 90.960 841 1534 1 chr6A.!!$R1 693
11 TraesCS6B01G049500 chr6A 16800667 16802496 1829 True 848.5 1467 89.125 519 2454 2 chr6A.!!$R3 1935

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
976 1033 1.680651 CACACCTCGAGAGCCCTCT 60.681 63.158 15.71 0.0 43.78 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2234 2417 0.109597 CTTGTTGATGAGCGTTGCCC 60.11 55.0 0.0 0.0 0.0 5.36 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
75 76 6.290294 AGCCTTAGCAATTGAATTGTCAAT 57.710 33.333 18.12 6.15 45.67 2.57
109 110 4.655963 TGAGAAGTTATTTCCTTGCAGCT 58.344 39.130 0.00 0.00 36.40 4.24
185 186 8.491950 TGAACTTTCAACAAGTTTGTAAAAAGC 58.508 29.630 20.50 12.39 41.55 3.51
337 338 8.737168 TTGTCAAAGCTAATATGCAGAGTAAT 57.263 30.769 0.00 0.00 34.99 1.89
350 352 9.686683 ATATGCAGAGTAATTAAAAACAGAGGT 57.313 29.630 0.00 0.00 0.00 3.85
352 354 8.547967 TGCAGAGTAATTAAAAACAGAGGTAG 57.452 34.615 0.00 0.00 0.00 3.18
358 360 8.947115 AGTAATTAAAAACAGAGGTAGCACATC 58.053 33.333 0.00 0.00 0.00 3.06
380 382 3.604065 CATGAGATTCATGTGCCTTCG 57.396 47.619 10.20 0.00 46.80 3.79
407 410 7.336161 TCCTTCGTTTTCCAGTTTTAAATCA 57.664 32.000 0.00 0.00 0.00 2.57
434 437 3.958704 TGCCAAATTGAGTTGTACAACG 58.041 40.909 28.21 15.18 45.50 4.10
587 590 9.290988 TGATTAAGCTACTCAATTACCAAAACA 57.709 29.630 0.00 0.00 0.00 2.83
634 637 4.411256 AACTCCTGTACGTGGAAAAAGA 57.589 40.909 0.00 0.00 32.61 2.52
645 648 4.642885 ACGTGGAAAAAGAGATTTTGGACA 59.357 37.500 0.00 0.00 41.27 4.02
699 704 6.760291 TGTTCAAGTGTTAAAACAAAACCCT 58.240 32.000 0.00 0.00 41.21 4.34
700 705 7.217906 TGTTCAAGTGTTAAAACAAAACCCTT 58.782 30.769 0.00 0.00 41.21 3.95
756 761 2.037620 GCGTGATCCAGATCCCTGCT 62.038 60.000 5.22 0.00 39.07 4.24
802 807 4.899239 GGATCGCCACCCGCAGAG 62.899 72.222 0.00 0.00 37.30 3.35
833 838 3.610669 CCGCTCCCCTCAGATCCG 61.611 72.222 0.00 0.00 0.00 4.18
976 1033 1.680651 CACACCTCGAGAGCCCTCT 60.681 63.158 15.71 0.00 43.78 3.69
1065 1143 4.344865 GTCAAGGCCGGGCTCCAA 62.345 66.667 32.90 16.73 0.00 3.53
1332 1437 3.797353 ATCATCCCGCGCCACCTT 61.797 61.111 0.00 0.00 0.00 3.50
1579 1702 5.543405 AGTTCCATATCAGGGAGAAGATGAG 59.457 44.000 0.00 0.00 35.46 2.90
1581 1704 4.108614 TCCATATCAGGGAGAAGATGAGGA 59.891 45.833 0.00 0.00 0.00 3.71
1632 1758 2.215942 TGCTAGTCTGTAGTGGCTCA 57.784 50.000 0.00 0.00 33.85 4.26
1715 1845 2.332063 ATGGCTAAAGATGTGACCCG 57.668 50.000 0.00 0.00 0.00 5.28
1748 1878 9.347240 CATATTCTCTTGTTTATCCATGGAACT 57.653 33.333 20.67 5.70 0.00 3.01
1750 1880 6.373005 TCTCTTGTTTATCCATGGAACTGA 57.627 37.500 20.67 13.25 0.00 3.41
1751 1881 6.962182 TCTCTTGTTTATCCATGGAACTGAT 58.038 36.000 20.67 3.98 0.00 2.90
1752 1882 7.050377 TCTCTTGTTTATCCATGGAACTGATC 58.950 38.462 20.67 8.15 0.00 2.92
1753 1883 6.720309 TCTTGTTTATCCATGGAACTGATCA 58.280 36.000 20.67 10.63 0.00 2.92
1754 1884 7.174413 TCTTGTTTATCCATGGAACTGATCAA 58.826 34.615 20.67 16.74 0.00 2.57
1755 1885 6.757897 TGTTTATCCATGGAACTGATCAAC 57.242 37.500 20.67 10.18 0.00 3.18
1756 1886 6.244654 TGTTTATCCATGGAACTGATCAACA 58.755 36.000 20.67 12.69 32.90 3.33
1768 1898 4.647291 CTGATCAACAGTGTTCGTAACC 57.353 45.455 5.27 0.00 41.30 2.85
1769 1899 4.307432 CTGATCAACAGTGTTCGTAACCT 58.693 43.478 5.27 0.00 41.30 3.50
1770 1900 4.055360 TGATCAACAGTGTTCGTAACCTG 58.945 43.478 5.27 0.00 36.43 4.00
1771 1901 2.206750 TCAACAGTGTTCGTAACCTGC 58.793 47.619 5.27 0.00 34.85 4.85
1772 1902 1.263217 CAACAGTGTTCGTAACCTGCC 59.737 52.381 5.27 0.00 34.85 4.85
1773 1903 0.466543 ACAGTGTTCGTAACCTGCCA 59.533 50.000 0.00 0.00 34.85 4.92
1774 1904 1.071699 ACAGTGTTCGTAACCTGCCAT 59.928 47.619 0.00 0.00 34.85 4.40
1775 1905 2.151202 CAGTGTTCGTAACCTGCCATT 58.849 47.619 0.00 0.00 0.00 3.16
1776 1906 2.095768 CAGTGTTCGTAACCTGCCATTG 60.096 50.000 0.00 0.00 0.00 2.82
1777 1907 0.878416 TGTTCGTAACCTGCCATTGC 59.122 50.000 0.00 0.00 38.26 3.56
1778 1908 1.165270 GTTCGTAACCTGCCATTGCT 58.835 50.000 0.00 0.00 38.71 3.91
1779 1909 1.539827 GTTCGTAACCTGCCATTGCTT 59.460 47.619 0.00 0.00 38.71 3.91
1780 1910 1.904287 TCGTAACCTGCCATTGCTTT 58.096 45.000 0.00 0.00 38.71 3.51
1781 1911 2.235016 TCGTAACCTGCCATTGCTTTT 58.765 42.857 0.00 0.00 38.71 2.27
1782 1912 2.030363 TCGTAACCTGCCATTGCTTTTG 60.030 45.455 0.00 0.00 38.71 2.44
1783 1913 2.030363 CGTAACCTGCCATTGCTTTTGA 60.030 45.455 0.00 0.00 38.71 2.69
1784 1914 3.551863 CGTAACCTGCCATTGCTTTTGAA 60.552 43.478 0.00 0.00 38.71 2.69
1785 1915 3.557228 AACCTGCCATTGCTTTTGAAA 57.443 38.095 0.00 0.00 38.71 2.69
1786 1916 2.837498 ACCTGCCATTGCTTTTGAAAC 58.163 42.857 0.00 0.00 38.71 2.78
1787 1917 2.170187 ACCTGCCATTGCTTTTGAAACA 59.830 40.909 0.00 0.00 38.71 2.83
1788 1918 3.181452 ACCTGCCATTGCTTTTGAAACAT 60.181 39.130 0.00 0.00 38.71 2.71
1789 1919 3.816523 CCTGCCATTGCTTTTGAAACATT 59.183 39.130 0.00 0.00 38.71 2.71
1790 1920 4.276431 CCTGCCATTGCTTTTGAAACATTT 59.724 37.500 0.00 0.00 38.71 2.32
1791 1921 5.171147 TGCCATTGCTTTTGAAACATTTG 57.829 34.783 0.00 0.00 38.71 2.32
1792 1922 4.036498 TGCCATTGCTTTTGAAACATTTGG 59.964 37.500 0.00 0.00 38.71 3.28
1793 1923 4.036616 GCCATTGCTTTTGAAACATTTGGT 59.963 37.500 0.00 0.00 33.53 3.67
1794 1924 5.512473 CCATTGCTTTTGAAACATTTGGTG 58.488 37.500 0.00 0.00 0.00 4.17
1795 1925 5.066246 CCATTGCTTTTGAAACATTTGGTGT 59.934 36.000 0.00 0.00 44.84 4.16
1796 1926 9.696417 GCCATTGCTTTTGAAACATTTGGTGTT 62.696 37.037 0.00 0.00 43.02 3.32
1821 1951 7.688372 TCGATTAATCTTCTGAATGTTGCTTC 58.312 34.615 13.45 0.00 0.00 3.86
1826 1956 5.833406 TCTTCTGAATGTTGCTTCAAACA 57.167 34.783 0.00 0.00 43.82 2.83
1828 1958 5.357878 TCTTCTGAATGTTGCTTCAAACACT 59.642 36.000 0.00 0.00 42.56 3.55
1831 1961 4.923893 TGAATGTTGCTTCAAACACTCAG 58.076 39.130 0.00 0.00 40.32 3.35
1832 1962 2.849880 TGTTGCTTCAAACACTCAGC 57.150 45.000 0.00 0.00 35.16 4.26
1846 1976 3.501445 ACACTCAGCTTCTGCATCTTTTC 59.499 43.478 0.00 0.00 42.74 2.29
1847 1977 3.501062 CACTCAGCTTCTGCATCTTTTCA 59.499 43.478 0.00 0.00 42.74 2.69
1852 1982 2.800250 CTTCTGCATCTTTTCACCCCT 58.200 47.619 0.00 0.00 0.00 4.79
1868 1998 0.898320 CCCTGTACCCTCTGTCAGTG 59.102 60.000 0.00 0.00 0.00 3.66
1870 2000 1.971357 CCTGTACCCTCTGTCAGTGTT 59.029 52.381 0.00 0.00 0.00 3.32
1875 2005 3.107642 ACCCTCTGTCAGTGTTAAACG 57.892 47.619 0.00 0.00 0.00 3.60
1876 2006 2.696707 ACCCTCTGTCAGTGTTAAACGA 59.303 45.455 0.00 0.00 0.00 3.85
1877 2007 3.323979 ACCCTCTGTCAGTGTTAAACGAT 59.676 43.478 0.00 0.00 0.00 3.73
1878 2008 3.679980 CCCTCTGTCAGTGTTAAACGATG 59.320 47.826 0.00 0.00 0.00 3.84
1879 2009 3.679980 CCTCTGTCAGTGTTAAACGATGG 59.320 47.826 0.00 0.00 0.00 3.51
1880 2010 3.064207 TCTGTCAGTGTTAAACGATGGC 58.936 45.455 0.00 0.00 0.00 4.40
1881 2011 2.805671 CTGTCAGTGTTAAACGATGGCA 59.194 45.455 0.00 0.00 0.00 4.92
1882 2012 2.805671 TGTCAGTGTTAAACGATGGCAG 59.194 45.455 0.00 0.00 0.00 4.85
1883 2013 2.806244 GTCAGTGTTAAACGATGGCAGT 59.194 45.455 0.00 0.00 0.00 4.40
1884 2014 3.991773 GTCAGTGTTAAACGATGGCAGTA 59.008 43.478 0.00 0.00 0.00 2.74
1885 2015 3.991773 TCAGTGTTAAACGATGGCAGTAC 59.008 43.478 0.00 0.00 0.00 2.73
1886 2016 3.994392 CAGTGTTAAACGATGGCAGTACT 59.006 43.478 0.00 0.00 0.00 2.73
1887 2017 5.047872 TCAGTGTTAAACGATGGCAGTACTA 60.048 40.000 0.00 0.00 0.00 1.82
1888 2018 5.636121 CAGTGTTAAACGATGGCAGTACTAA 59.364 40.000 0.00 0.00 0.00 2.24
1889 2019 6.146510 CAGTGTTAAACGATGGCAGTACTAAA 59.853 38.462 0.00 0.00 0.00 1.85
1890 2020 6.877322 AGTGTTAAACGATGGCAGTACTAAAT 59.123 34.615 0.00 0.00 0.00 1.40
1891 2021 7.389607 AGTGTTAAACGATGGCAGTACTAAATT 59.610 33.333 0.00 0.00 0.00 1.82
1892 2022 7.480542 GTGTTAAACGATGGCAGTACTAAATTG 59.519 37.037 0.00 0.00 0.00 2.32
1893 2023 5.560966 AAACGATGGCAGTACTAAATTGG 57.439 39.130 0.00 0.00 0.00 3.16
1894 2024 4.481368 ACGATGGCAGTACTAAATTGGA 57.519 40.909 0.00 0.00 0.00 3.53
1895 2025 5.036117 ACGATGGCAGTACTAAATTGGAT 57.964 39.130 0.00 0.00 0.00 3.41
1896 2026 6.169557 ACGATGGCAGTACTAAATTGGATA 57.830 37.500 0.00 0.00 0.00 2.59
1897 2027 6.588204 ACGATGGCAGTACTAAATTGGATAA 58.412 36.000 0.00 0.00 0.00 1.75
1898 2028 7.051623 ACGATGGCAGTACTAAATTGGATAAA 58.948 34.615 0.00 0.00 0.00 1.40
1899 2029 7.226720 ACGATGGCAGTACTAAATTGGATAAAG 59.773 37.037 0.00 0.00 0.00 1.85
1900 2030 7.441157 CGATGGCAGTACTAAATTGGATAAAGA 59.559 37.037 0.00 0.00 0.00 2.52
1901 2031 9.120538 GATGGCAGTACTAAATTGGATAAAGAA 57.879 33.333 0.00 0.00 0.00 2.52
1902 2032 8.506168 TGGCAGTACTAAATTGGATAAAGAAG 57.494 34.615 0.00 0.00 0.00 2.85
1903 2033 7.556275 TGGCAGTACTAAATTGGATAAAGAAGG 59.444 37.037 0.00 0.00 0.00 3.46
1904 2034 7.013369 GGCAGTACTAAATTGGATAAAGAAGGG 59.987 40.741 0.00 0.00 0.00 3.95
1905 2035 7.556635 GCAGTACTAAATTGGATAAAGAAGGGT 59.443 37.037 0.00 0.00 0.00 4.34
1906 2036 9.462606 CAGTACTAAATTGGATAAAGAAGGGTT 57.537 33.333 0.00 0.00 0.00 4.11
1907 2037 9.682465 AGTACTAAATTGGATAAAGAAGGGTTC 57.318 33.333 0.00 0.00 0.00 3.62
1908 2038 9.457436 GTACTAAATTGGATAAAGAAGGGTTCA 57.543 33.333 0.00 0.00 0.00 3.18
1909 2039 8.950007 ACTAAATTGGATAAAGAAGGGTTCAA 57.050 30.769 0.00 0.00 0.00 2.69
1910 2040 9.374711 ACTAAATTGGATAAAGAAGGGTTCAAA 57.625 29.630 0.00 0.00 0.00 2.69
1912 2042 8.902540 AAATTGGATAAAGAAGGGTTCAAAAC 57.097 30.769 0.00 0.00 0.00 2.43
1924 2054 2.159114 GGTTCAAAACTCTTGCAGGCAA 60.159 45.455 6.53 6.53 0.00 4.52
1927 2057 2.495270 TCAAAACTCTTGCAGGCAAACA 59.505 40.909 8.20 0.00 35.33 2.83
1940 2070 2.825532 AGGCAAACATGGCGAATTAAGT 59.174 40.909 0.00 0.00 39.53 2.24
1942 2072 3.179048 GCAAACATGGCGAATTAAGTCC 58.821 45.455 0.00 0.00 0.00 3.85
1947 2077 3.270027 CATGGCGAATTAAGTCCTGACA 58.730 45.455 0.00 0.00 0.00 3.58
1953 2083 4.728882 GCGAATTAAGTCCTGACAATGCTG 60.729 45.833 0.00 0.00 0.00 4.41
1968 2099 5.430886 ACAATGCTGAATCATGTGCTAGTA 58.569 37.500 0.00 0.00 0.00 1.82
1973 2104 6.114767 TGCTGAATCATGTGCTAGTAATTGA 58.885 36.000 0.00 0.00 0.00 2.57
1976 2107 7.414429 GCTGAATCATGTGCTAGTAATTGACAA 60.414 37.037 0.00 0.00 0.00 3.18
1989 2120 7.894376 AGTAATTGACAAATTTGATGCCAAG 57.106 32.000 24.64 0.00 37.23 3.61
1990 2121 6.875195 AGTAATTGACAAATTTGATGCCAAGG 59.125 34.615 24.64 0.00 37.23 3.61
1992 2123 4.524316 TGACAAATTTGATGCCAAGGAG 57.476 40.909 24.64 0.00 33.23 3.69
1994 2125 2.264813 CAAATTTGATGCCAAGGAGCG 58.735 47.619 13.08 0.00 33.23 5.03
1997 2128 0.597568 TTTGATGCCAAGGAGCGTTG 59.402 50.000 0.00 0.00 33.23 4.10
1998 2129 0.537143 TTGATGCCAAGGAGCGTTGT 60.537 50.000 2.74 0.00 34.65 3.32
1999 2130 0.537143 TGATGCCAAGGAGCGTTGTT 60.537 50.000 2.74 0.00 34.65 2.83
2000 2131 0.169009 GATGCCAAGGAGCGTTGTTC 59.831 55.000 2.74 0.00 34.65 3.18
2001 2132 1.244019 ATGCCAAGGAGCGTTGTTCC 61.244 55.000 2.74 0.00 34.65 3.62
2002 2133 1.896660 GCCAAGGAGCGTTGTTCCA 60.897 57.895 2.51 0.00 35.33 3.53
2003 2134 1.452145 GCCAAGGAGCGTTGTTCCAA 61.452 55.000 2.51 0.00 35.33 3.53
2004 2135 1.028905 CCAAGGAGCGTTGTTCCAAA 58.971 50.000 2.51 0.00 35.33 3.28
2005 2136 1.269051 CCAAGGAGCGTTGTTCCAAAC 60.269 52.381 2.51 0.00 35.33 2.93
2006 2137 1.403679 CAAGGAGCGTTGTTCCAAACA 59.596 47.619 2.51 0.00 40.21 2.83
2018 2149 6.522625 TTGTTCCAAACAATTGAACTCTGA 57.477 33.333 13.59 0.00 45.79 3.27
2019 2150 5.890334 TGTTCCAAACAATTGAACTCTGAC 58.110 37.500 13.59 3.39 38.72 3.51
2020 2151 5.652014 TGTTCCAAACAATTGAACTCTGACT 59.348 36.000 13.59 0.00 38.72 3.41
2021 2152 6.152661 TGTTCCAAACAATTGAACTCTGACTT 59.847 34.615 13.59 0.00 38.72 3.01
2022 2153 6.773976 TCCAAACAATTGAACTCTGACTTT 57.226 33.333 13.59 0.00 38.94 2.66
2023 2154 7.873719 TCCAAACAATTGAACTCTGACTTTA 57.126 32.000 13.59 0.00 38.94 1.85
2024 2155 8.287439 TCCAAACAATTGAACTCTGACTTTAA 57.713 30.769 13.59 0.00 38.94 1.52
2025 2156 8.912988 TCCAAACAATTGAACTCTGACTTTAAT 58.087 29.630 13.59 0.00 38.94 1.40
2026 2157 9.533253 CCAAACAATTGAACTCTGACTTTAATT 57.467 29.630 13.59 0.00 38.94 1.40
2029 2160 9.736023 AACAATTGAACTCTGACTTTAATTGTC 57.264 29.630 21.43 0.00 42.81 3.18
2030 2161 8.902806 ACAATTGAACTCTGACTTTAATTGTCA 58.097 29.630 13.59 10.20 40.96 3.58
2031 2162 9.173939 CAATTGAACTCTGACTTTAATTGTCAC 57.826 33.333 0.00 0.97 39.23 3.67
2032 2163 7.857734 TTGAACTCTGACTTTAATTGTCACA 57.142 32.000 7.47 2.98 39.23 3.58
2033 2164 7.857734 TGAACTCTGACTTTAATTGTCACAA 57.142 32.000 0.00 0.00 39.23 3.33
2034 2165 8.275015 TGAACTCTGACTTTAATTGTCACAAA 57.725 30.769 0.00 0.00 39.23 2.83
2035 2166 8.397906 TGAACTCTGACTTTAATTGTCACAAAG 58.602 33.333 0.00 0.00 39.23 2.77
2036 2167 6.729187 ACTCTGACTTTAATTGTCACAAAGC 58.271 36.000 0.00 0.00 39.23 3.51
2037 2168 6.318648 ACTCTGACTTTAATTGTCACAAAGCA 59.681 34.615 0.00 0.00 39.23 3.91
2038 2169 7.094508 TCTGACTTTAATTGTCACAAAGCAA 57.905 32.000 0.00 0.00 39.23 3.91
2039 2170 7.542890 TCTGACTTTAATTGTCACAAAGCAAA 58.457 30.769 0.00 0.00 39.23 3.68
2040 2171 8.031864 TCTGACTTTAATTGTCACAAAGCAAAA 58.968 29.630 0.00 0.00 39.23 2.44
2041 2172 8.539770 TGACTTTAATTGTCACAAAGCAAAAA 57.460 26.923 0.00 0.00 39.23 1.94
2063 2194 6.908870 AAATTCTTTTGGTTTGAGTTGAGC 57.091 33.333 0.00 0.00 0.00 4.26
2064 2195 5.859205 ATTCTTTTGGTTTGAGTTGAGCT 57.141 34.783 0.00 0.00 0.00 4.09
2065 2196 4.637483 TCTTTTGGTTTGAGTTGAGCTG 57.363 40.909 0.00 0.00 0.00 4.24
2066 2197 3.381272 TCTTTTGGTTTGAGTTGAGCTGG 59.619 43.478 0.00 0.00 0.00 4.85
2067 2198 2.727123 TTGGTTTGAGTTGAGCTGGA 57.273 45.000 0.00 0.00 0.00 3.86
2068 2199 2.727123 TGGTTTGAGTTGAGCTGGAA 57.273 45.000 0.00 0.00 0.00 3.53
2069 2200 3.011566 TGGTTTGAGTTGAGCTGGAAA 57.988 42.857 0.00 0.00 0.00 3.13
2070 2201 2.687935 TGGTTTGAGTTGAGCTGGAAAC 59.312 45.455 0.00 0.00 0.00 2.78
2071 2202 2.952310 GGTTTGAGTTGAGCTGGAAACT 59.048 45.455 0.00 0.00 39.31 2.66
2075 2206 4.689612 TGAGTTGAGCTGGAAACTAACT 57.310 40.909 0.00 0.00 36.77 2.24
2076 2207 5.036117 TGAGTTGAGCTGGAAACTAACTT 57.964 39.130 0.00 0.00 36.77 2.66
2128 2289 0.612174 AGGCTGACTCGTGAAGGCTA 60.612 55.000 15.40 0.00 44.23 3.93
2153 2314 1.518325 TATGTGCCACTGACCAAACG 58.482 50.000 0.00 0.00 0.00 3.60
2183 2344 8.517047 TCCTCCCTCTGTAGGTTAATATAAGAA 58.483 37.037 0.00 0.00 41.89 2.52
2184 2345 9.155785 CCTCCCTCTGTAGGTTAATATAAGAAA 57.844 37.037 0.00 0.00 41.89 2.52
2213 2396 8.842358 TTTAGACTAACCGAAAACAGAATCAT 57.158 30.769 0.00 0.00 0.00 2.45
2217 2400 9.530633 AGACTAACCGAAAACAGAATCATATAC 57.469 33.333 0.00 0.00 0.00 1.47
2223 2406 6.936900 CCGAAAACAGAATCATATACTGGGAT 59.063 38.462 0.00 0.00 36.17 3.85
2224 2407 8.094548 CCGAAAACAGAATCATATACTGGGATA 58.905 37.037 0.00 0.00 36.17 2.59
2225 2408 9.658799 CGAAAACAGAATCATATACTGGGATAT 57.341 33.333 0.00 0.00 36.17 1.63
2236 2419 8.992349 TCATATACTGGGATATTAAGACATGGG 58.008 37.037 0.00 0.00 0.00 4.00
2237 2420 4.373156 ACTGGGATATTAAGACATGGGC 57.627 45.455 0.00 0.00 0.00 5.36
2238 2421 3.721575 ACTGGGATATTAAGACATGGGCA 59.278 43.478 0.00 0.00 0.00 5.36
2239 2422 4.167892 ACTGGGATATTAAGACATGGGCAA 59.832 41.667 0.00 0.00 0.00 4.52
2240 2423 4.469657 TGGGATATTAAGACATGGGCAAC 58.530 43.478 0.00 0.00 0.00 4.17
2241 2424 3.502211 GGGATATTAAGACATGGGCAACG 59.498 47.826 0.00 0.00 37.60 4.10
2252 2435 0.821301 TGGGCAACGCTCATCAACAA 60.821 50.000 0.00 0.00 32.27 2.83
2253 2436 0.109597 GGGCAACGCTCATCAACAAG 60.110 55.000 0.00 0.00 37.60 3.16
2262 2455 0.770499 TCATCAACAAGTCAGGCCCA 59.230 50.000 0.00 0.00 0.00 5.36
2266 2459 1.171308 CAACAAGTCAGGCCCATCAG 58.829 55.000 0.00 0.00 0.00 2.90
2314 2558 6.155136 TGCGCTTCATGTTCATCAATAAAAA 58.845 32.000 9.73 0.00 0.00 1.94
2402 2647 0.250770 AGAGGTTTCGTTCTTGGCCC 60.251 55.000 0.00 0.00 0.00 5.80
2443 2688 1.392510 CGCTAACCGTAACTTTGCTCC 59.607 52.381 0.00 0.00 0.00 4.70
2446 2691 1.601166 AACCGTAACTTTGCTCCCAC 58.399 50.000 0.00 0.00 0.00 4.61
2454 2699 5.627780 CGTAACTTTGCTCCCACAATAAAAC 59.372 40.000 0.00 0.00 0.00 2.43
2455 2700 5.606348 AACTTTGCTCCCACAATAAAACA 57.394 34.783 0.00 0.00 0.00 2.83
2456 2701 5.606348 ACTTTGCTCCCACAATAAAACAA 57.394 34.783 0.00 0.00 0.00 2.83
2457 2702 6.173427 ACTTTGCTCCCACAATAAAACAAT 57.827 33.333 0.00 0.00 0.00 2.71
2458 2703 7.296628 ACTTTGCTCCCACAATAAAACAATA 57.703 32.000 0.00 0.00 0.00 1.90
2459 2704 7.378181 ACTTTGCTCCCACAATAAAACAATAG 58.622 34.615 0.00 0.00 0.00 1.73
2460 2705 6.909550 TTGCTCCCACAATAAAACAATAGT 57.090 33.333 0.00 0.00 0.00 2.12
2461 2706 6.909550 TGCTCCCACAATAAAACAATAGTT 57.090 33.333 0.00 0.00 40.40 2.24
2462 2707 6.686630 TGCTCCCACAATAAAACAATAGTTG 58.313 36.000 0.00 0.00 38.17 3.16
2526 2771 9.979578 TTTTTCTACTAACGTTGGAAGTATACA 57.020 29.630 19.29 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 3.644966 AACTTCTCAGGTGTGGTTGAA 57.355 42.857 0.00 0.00 0.00 2.69
313 314 8.737168 AATTACTCTGCATATTAGCTTTGACA 57.263 30.769 0.00 0.00 34.99 3.58
337 338 4.153475 GCGATGTGCTACCTCTGTTTTTAA 59.847 41.667 0.00 0.00 41.73 1.52
350 352 3.457610 TGAATCTCATGCGATGTGCTA 57.542 42.857 0.00 0.00 46.63 3.49
352 354 2.917363 CATGAATCTCATGCGATGTGC 58.083 47.619 0.00 0.00 46.37 4.57
380 382 8.812147 ATTTAAAACTGGAAAACGAAGGAATC 57.188 30.769 0.00 0.00 0.00 2.52
407 410 7.856145 TGTACAACTCAATTTGGCAAATTTT 57.144 28.000 30.19 21.02 38.97 1.82
425 428 8.599055 TTTACATTGGTATGTACGTTGTACAA 57.401 30.769 13.18 3.59 44.73 2.41
460 463 4.750717 GCATTGATCAACATAGGGGATGGA 60.751 45.833 11.07 0.00 40.18 3.41
555 558 8.713271 GGTAATTGAGTAGCTTAATCATGTAGC 58.287 37.037 0.00 0.00 32.37 3.58
587 590 6.380846 TGCTCATTGTAGCTAATCCCAATTTT 59.619 34.615 0.00 0.00 43.19 1.82
656 659 6.590068 TGAACATGTGTTTTCATTTTCCCAT 58.410 32.000 0.00 0.00 38.56 4.00
700 705 7.915397 GCTGTGATCAGTTCTAAGAAACAAAAA 59.085 33.333 0.00 0.00 43.05 1.94
756 761 0.539518 TCGGATCGGCCAATCAGAAA 59.460 50.000 3.81 0.00 35.94 2.52
833 838 2.202756 GATCCGCGTGACAGGGTC 60.203 66.667 4.92 0.00 0.00 4.46
976 1033 0.669318 CTTGCTACTTCACCGGCGAA 60.669 55.000 9.30 1.96 0.00 4.70
984 1054 2.086869 GCCATCTTGCTTGCTACTTCA 58.913 47.619 0.00 0.00 0.00 3.02
1005 1083 2.121832 TCGCCTCCCTTCCTTCCA 59.878 61.111 0.00 0.00 0.00 3.53
1185 1263 3.146066 CAAGAAAGGACGGGAAACATCA 58.854 45.455 0.00 0.00 0.00 3.07
1452 1557 1.130054 ACTTGGCCTCCTTCTCTGCA 61.130 55.000 3.32 0.00 0.00 4.41
1579 1702 4.158579 GGATCCAATCAACCAAAAGTCTCC 59.841 45.833 6.95 0.00 0.00 3.71
1581 1704 4.768968 CAGGATCCAATCAACCAAAAGTCT 59.231 41.667 15.82 0.00 0.00 3.24
1632 1758 5.647658 TGGCTTGTTCATCGAACTAATGAAT 59.352 36.000 8.23 0.00 43.10 2.57
1690 1820 3.063997 GTCACATCTTTAGCCATTCCACG 59.936 47.826 0.00 0.00 0.00 4.94
1748 1878 4.055360 CAGGTTACGAACACTGTTGATCA 58.945 43.478 0.00 0.00 0.00 2.92
1750 1880 2.806244 GCAGGTTACGAACACTGTTGAT 59.194 45.455 0.00 0.00 34.34 2.57
1751 1881 2.206750 GCAGGTTACGAACACTGTTGA 58.793 47.619 0.00 0.00 34.34 3.18
1752 1882 1.263217 GGCAGGTTACGAACACTGTTG 59.737 52.381 0.00 0.00 34.34 3.33
1753 1883 1.134340 TGGCAGGTTACGAACACTGTT 60.134 47.619 0.00 0.00 34.34 3.16
1754 1884 0.466543 TGGCAGGTTACGAACACTGT 59.533 50.000 0.00 0.00 34.34 3.55
1755 1885 1.808411 ATGGCAGGTTACGAACACTG 58.192 50.000 0.00 1.29 34.70 3.66
1756 1886 2.151202 CAATGGCAGGTTACGAACACT 58.849 47.619 0.00 0.00 0.00 3.55
1757 1887 1.401018 GCAATGGCAGGTTACGAACAC 60.401 52.381 0.00 0.00 40.72 3.32
1758 1888 0.878416 GCAATGGCAGGTTACGAACA 59.122 50.000 0.00 0.00 40.72 3.18
1759 1889 1.165270 AGCAATGGCAGGTTACGAAC 58.835 50.000 0.00 0.00 44.61 3.95
1760 1890 1.904287 AAGCAATGGCAGGTTACGAA 58.096 45.000 0.00 0.00 44.61 3.85
1761 1891 1.904287 AAAGCAATGGCAGGTTACGA 58.096 45.000 0.00 0.00 44.61 3.43
1762 1892 2.030363 TCAAAAGCAATGGCAGGTTACG 60.030 45.455 0.00 0.00 44.61 3.18
1763 1893 3.658757 TCAAAAGCAATGGCAGGTTAC 57.341 42.857 0.00 0.00 44.61 2.50
1764 1894 4.141846 TGTTTCAAAAGCAATGGCAGGTTA 60.142 37.500 0.00 0.00 44.61 2.85
1765 1895 3.205338 GTTTCAAAAGCAATGGCAGGTT 58.795 40.909 0.00 0.00 44.61 3.50
1766 1896 2.170187 TGTTTCAAAAGCAATGGCAGGT 59.830 40.909 0.00 0.00 44.61 4.00
1767 1897 2.836262 TGTTTCAAAAGCAATGGCAGG 58.164 42.857 0.00 0.00 44.61 4.85
1768 1898 5.209240 CAAATGTTTCAAAAGCAATGGCAG 58.791 37.500 0.00 0.00 44.61 4.85
1769 1899 4.036498 CCAAATGTTTCAAAAGCAATGGCA 59.964 37.500 0.00 0.00 44.61 4.92
1770 1900 4.036616 ACCAAATGTTTCAAAAGCAATGGC 59.963 37.500 9.86 0.00 41.61 4.40
1771 1901 5.066246 ACACCAAATGTTTCAAAAGCAATGG 59.934 36.000 8.92 8.92 38.98 3.16
1772 1902 6.121613 ACACCAAATGTTTCAAAAGCAATG 57.878 33.333 0.00 0.00 38.98 2.82
1785 1915 7.390440 TCAGAAGATTAATCGAACACCAAATGT 59.610 33.333 9.78 0.00 46.42 2.71
1786 1916 7.751732 TCAGAAGATTAATCGAACACCAAATG 58.248 34.615 9.78 0.27 0.00 2.32
1787 1917 7.921786 TCAGAAGATTAATCGAACACCAAAT 57.078 32.000 9.78 0.00 0.00 2.32
1788 1918 7.737972 TTCAGAAGATTAATCGAACACCAAA 57.262 32.000 9.78 0.00 0.00 3.28
1789 1919 7.390440 ACATTCAGAAGATTAATCGAACACCAA 59.610 33.333 9.78 0.00 0.00 3.67
1790 1920 6.878923 ACATTCAGAAGATTAATCGAACACCA 59.121 34.615 9.78 0.00 0.00 4.17
1791 1921 7.308782 ACATTCAGAAGATTAATCGAACACC 57.691 36.000 9.78 0.00 0.00 4.16
1792 1922 7.217070 GCAACATTCAGAAGATTAATCGAACAC 59.783 37.037 9.78 1.99 0.00 3.32
1793 1923 7.119699 AGCAACATTCAGAAGATTAATCGAACA 59.880 33.333 9.78 0.00 0.00 3.18
1794 1924 7.467623 AGCAACATTCAGAAGATTAATCGAAC 58.532 34.615 9.78 5.79 0.00 3.95
1795 1925 7.615582 AGCAACATTCAGAAGATTAATCGAA 57.384 32.000 9.78 7.71 0.00 3.71
1796 1926 7.334171 TGAAGCAACATTCAGAAGATTAATCGA 59.666 33.333 9.78 0.00 34.31 3.59
1797 1927 7.466805 TGAAGCAACATTCAGAAGATTAATCG 58.533 34.615 9.78 0.00 34.31 3.34
1798 1928 9.630098 TTTGAAGCAACATTCAGAAGATTAATC 57.370 29.630 7.41 7.41 40.16 1.75
1799 1929 9.415544 GTTTGAAGCAACATTCAGAAGATTAAT 57.584 29.630 0.00 0.00 40.16 1.40
1821 1951 2.812591 AGATGCAGAAGCTGAGTGTTTG 59.187 45.455 0.00 0.00 42.74 2.93
1826 1956 3.501445 GTGAAAAGATGCAGAAGCTGAGT 59.499 43.478 0.00 0.00 42.74 3.41
1828 1958 2.816087 GGTGAAAAGATGCAGAAGCTGA 59.184 45.455 0.00 0.00 42.74 4.26
1831 1961 1.203287 GGGGTGAAAAGATGCAGAAGC 59.797 52.381 0.00 0.00 42.57 3.86
1832 1962 2.490903 CAGGGGTGAAAAGATGCAGAAG 59.509 50.000 0.00 0.00 0.00 2.85
1846 1976 0.544357 TGACAGAGGGTACAGGGGTG 60.544 60.000 0.00 0.00 0.00 4.61
1847 1977 0.252284 CTGACAGAGGGTACAGGGGT 60.252 60.000 0.00 0.00 0.00 4.95
1852 1982 4.500205 CGTTTAACACTGACAGAGGGTACA 60.500 45.833 10.08 0.00 37.31 2.90
1868 1998 6.964934 CCAATTTAGTACTGCCATCGTTTAAC 59.035 38.462 5.39 0.00 0.00 2.01
1870 2000 6.408035 TCCAATTTAGTACTGCCATCGTTTA 58.592 36.000 5.39 0.00 0.00 2.01
1875 2005 8.677148 TCTTTATCCAATTTAGTACTGCCATC 57.323 34.615 5.39 0.00 0.00 3.51
1876 2006 9.125026 CTTCTTTATCCAATTTAGTACTGCCAT 57.875 33.333 5.39 0.00 0.00 4.40
1877 2007 7.556275 CCTTCTTTATCCAATTTAGTACTGCCA 59.444 37.037 5.39 0.00 0.00 4.92
1878 2008 7.013369 CCCTTCTTTATCCAATTTAGTACTGCC 59.987 40.741 5.39 0.00 0.00 4.85
1879 2009 7.556635 ACCCTTCTTTATCCAATTTAGTACTGC 59.443 37.037 5.39 0.00 0.00 4.40
1880 2010 9.462606 AACCCTTCTTTATCCAATTTAGTACTG 57.537 33.333 5.39 0.00 0.00 2.74
1881 2011 9.682465 GAACCCTTCTTTATCCAATTTAGTACT 57.318 33.333 0.00 0.00 0.00 2.73
1882 2012 9.457436 TGAACCCTTCTTTATCCAATTTAGTAC 57.543 33.333 0.00 0.00 0.00 2.73
1884 2014 8.950007 TTGAACCCTTCTTTATCCAATTTAGT 57.050 30.769 0.00 0.00 0.00 2.24
1886 2016 9.990360 GTTTTGAACCCTTCTTTATCCAATTTA 57.010 29.630 0.00 0.00 0.00 1.40
1887 2017 8.713971 AGTTTTGAACCCTTCTTTATCCAATTT 58.286 29.630 0.00 0.00 0.00 1.82
1888 2018 8.262601 AGTTTTGAACCCTTCTTTATCCAATT 57.737 30.769 0.00 0.00 0.00 2.32
1889 2019 7.730332 AGAGTTTTGAACCCTTCTTTATCCAAT 59.270 33.333 0.00 0.00 0.00 3.16
1890 2020 7.066781 AGAGTTTTGAACCCTTCTTTATCCAA 58.933 34.615 0.00 0.00 0.00 3.53
1891 2021 6.610830 AGAGTTTTGAACCCTTCTTTATCCA 58.389 36.000 0.00 0.00 0.00 3.41
1892 2022 7.371159 CAAGAGTTTTGAACCCTTCTTTATCC 58.629 38.462 0.00 0.00 25.67 2.59
1893 2023 6.863645 GCAAGAGTTTTGAACCCTTCTTTATC 59.136 38.462 0.00 0.00 25.67 1.75
1894 2024 6.323739 TGCAAGAGTTTTGAACCCTTCTTTAT 59.676 34.615 0.00 0.00 25.67 1.40
1895 2025 5.654650 TGCAAGAGTTTTGAACCCTTCTTTA 59.345 36.000 0.00 0.00 25.67 1.85
1896 2026 4.466015 TGCAAGAGTTTTGAACCCTTCTTT 59.534 37.500 0.00 0.00 25.67 2.52
1897 2027 4.023291 TGCAAGAGTTTTGAACCCTTCTT 58.977 39.130 0.00 0.00 25.67 2.52
1898 2028 3.631250 TGCAAGAGTTTTGAACCCTTCT 58.369 40.909 0.00 0.00 25.67 2.85
1899 2029 3.243535 CCTGCAAGAGTTTTGAACCCTTC 60.244 47.826 0.00 0.00 34.07 3.46
1900 2030 2.695147 CCTGCAAGAGTTTTGAACCCTT 59.305 45.455 0.00 0.00 34.07 3.95
1901 2031 2.310538 CCTGCAAGAGTTTTGAACCCT 58.689 47.619 0.00 0.00 34.07 4.34
1902 2032 1.269778 GCCTGCAAGAGTTTTGAACCC 60.270 52.381 0.00 0.00 34.07 4.11
1903 2033 1.408702 TGCCTGCAAGAGTTTTGAACC 59.591 47.619 0.00 0.00 34.07 3.62
1904 2034 2.869233 TGCCTGCAAGAGTTTTGAAC 57.131 45.000 0.00 0.00 34.07 3.18
1905 2035 3.056250 TGTTTGCCTGCAAGAGTTTTGAA 60.056 39.130 4.58 0.00 37.24 2.69
1906 2036 2.495270 TGTTTGCCTGCAAGAGTTTTGA 59.505 40.909 4.58 0.00 37.24 2.69
1907 2037 2.891112 TGTTTGCCTGCAAGAGTTTTG 58.109 42.857 4.58 0.00 37.24 2.44
1908 2038 3.460103 CATGTTTGCCTGCAAGAGTTTT 58.540 40.909 4.58 0.00 37.24 2.43
1909 2039 2.224113 CCATGTTTGCCTGCAAGAGTTT 60.224 45.455 4.58 0.00 37.24 2.66
1910 2040 1.342174 CCATGTTTGCCTGCAAGAGTT 59.658 47.619 4.58 0.00 37.24 3.01
1911 2041 0.963962 CCATGTTTGCCTGCAAGAGT 59.036 50.000 4.58 0.00 37.24 3.24
1912 2042 0.389426 GCCATGTTTGCCTGCAAGAG 60.389 55.000 4.58 0.00 37.24 2.85
1924 2054 3.689649 GTCAGGACTTAATTCGCCATGTT 59.310 43.478 0.00 0.00 0.00 2.71
1927 2057 3.627395 TGTCAGGACTTAATTCGCCAT 57.373 42.857 0.65 0.00 0.00 4.40
1940 2070 3.692593 CACATGATTCAGCATTGTCAGGA 59.307 43.478 0.00 0.00 0.00 3.86
1942 2072 3.128764 AGCACATGATTCAGCATTGTCAG 59.871 43.478 0.00 0.00 0.00 3.51
1947 2077 7.283807 TCAATTACTAGCACATGATTCAGCATT 59.716 33.333 0.00 0.00 0.00 3.56
1953 2083 9.793252 AATTTGTCAATTACTAGCACATGATTC 57.207 29.630 0.00 0.00 30.22 2.52
1968 2099 5.867330 TCCTTGGCATCAAATTTGTCAATT 58.133 33.333 17.47 0.00 37.98 2.32
1973 2104 2.353011 CGCTCCTTGGCATCAAATTTGT 60.353 45.455 17.47 3.04 31.77 2.83
1976 2107 1.549203 ACGCTCCTTGGCATCAAATT 58.451 45.000 0.00 0.00 31.77 1.82
1997 2128 6.136541 AGTCAGAGTTCAATTGTTTGGAAC 57.863 37.500 5.13 2.16 33.44 3.62
1998 2129 6.773976 AAGTCAGAGTTCAATTGTTTGGAA 57.226 33.333 5.13 0.00 33.44 3.53
1999 2130 6.773976 AAAGTCAGAGTTCAATTGTTTGGA 57.226 33.333 5.13 0.00 33.44 3.53
2000 2131 9.533253 AATTAAAGTCAGAGTTCAATTGTTTGG 57.467 29.630 5.13 0.00 33.44 3.28
2003 2134 9.736023 GACAATTAAAGTCAGAGTTCAATTGTT 57.264 29.630 24.42 13.70 42.21 2.83
2004 2135 8.902806 TGACAATTAAAGTCAGAGTTCAATTGT 58.097 29.630 24.07 24.07 43.83 2.71
2005 2136 9.173939 GTGACAATTAAAGTCAGAGTTCAATTG 57.826 33.333 19.37 19.37 45.77 2.32
2006 2137 8.902806 TGTGACAATTAAAGTCAGAGTTCAATT 58.097 29.630 12.72 0.00 45.77 2.32
2007 2138 8.450578 TGTGACAATTAAAGTCAGAGTTCAAT 57.549 30.769 12.72 0.00 45.77 2.57
2008 2139 7.857734 TGTGACAATTAAAGTCAGAGTTCAA 57.142 32.000 12.72 0.00 45.77 2.69
2009 2140 7.857734 TTGTGACAATTAAAGTCAGAGTTCA 57.142 32.000 12.72 6.14 45.77 3.18
2010 2141 7.377131 GCTTTGTGACAATTAAAGTCAGAGTTC 59.623 37.037 12.72 4.11 45.77 3.01
2011 2142 7.148086 TGCTTTGTGACAATTAAAGTCAGAGTT 60.148 33.333 12.72 0.00 45.77 3.01
2012 2143 6.318648 TGCTTTGTGACAATTAAAGTCAGAGT 59.681 34.615 12.72 0.00 45.77 3.24
2013 2144 6.728200 TGCTTTGTGACAATTAAAGTCAGAG 58.272 36.000 12.72 11.82 45.77 3.35
2014 2145 6.691754 TGCTTTGTGACAATTAAAGTCAGA 57.308 33.333 12.72 9.83 45.77 3.27
2015 2146 7.754069 TTTGCTTTGTGACAATTAAAGTCAG 57.246 32.000 12.72 4.84 45.77 3.51
2016 2147 8.539770 TTTTTGCTTTGTGACAATTAAAGTCA 57.460 26.923 0.00 9.33 43.23 3.41
2040 2171 6.536224 CAGCTCAACTCAAACCAAAAGAATTT 59.464 34.615 0.00 0.00 42.41 1.82
2041 2172 6.044682 CAGCTCAACTCAAACCAAAAGAATT 58.955 36.000 0.00 0.00 0.00 2.17
2042 2173 5.452356 CCAGCTCAACTCAAACCAAAAGAAT 60.452 40.000 0.00 0.00 0.00 2.40
2043 2174 4.142182 CCAGCTCAACTCAAACCAAAAGAA 60.142 41.667 0.00 0.00 0.00 2.52
2044 2175 3.381272 CCAGCTCAACTCAAACCAAAAGA 59.619 43.478 0.00 0.00 0.00 2.52
2045 2176 3.381272 TCCAGCTCAACTCAAACCAAAAG 59.619 43.478 0.00 0.00 0.00 2.27
2046 2177 3.360867 TCCAGCTCAACTCAAACCAAAA 58.639 40.909 0.00 0.00 0.00 2.44
2047 2178 3.011566 TCCAGCTCAACTCAAACCAAA 57.988 42.857 0.00 0.00 0.00 3.28
2048 2179 2.727123 TCCAGCTCAACTCAAACCAA 57.273 45.000 0.00 0.00 0.00 3.67
2049 2180 2.687935 GTTTCCAGCTCAACTCAAACCA 59.312 45.455 0.00 0.00 0.00 3.67
2050 2181 2.952310 AGTTTCCAGCTCAACTCAAACC 59.048 45.455 0.00 0.00 32.10 3.27
2051 2182 5.297029 AGTTAGTTTCCAGCTCAACTCAAAC 59.703 40.000 5.87 6.62 34.92 2.93
2052 2183 5.437060 AGTTAGTTTCCAGCTCAACTCAAA 58.563 37.500 5.87 0.00 34.92 2.69
2053 2184 5.036117 AGTTAGTTTCCAGCTCAACTCAA 57.964 39.130 5.87 0.00 34.92 3.02
2054 2185 4.689612 AGTTAGTTTCCAGCTCAACTCA 57.310 40.909 5.87 0.00 34.92 3.41
2055 2186 5.278022 CCAAAGTTAGTTTCCAGCTCAACTC 60.278 44.000 5.87 0.00 34.92 3.01
2056 2187 4.580580 CCAAAGTTAGTTTCCAGCTCAACT 59.419 41.667 7.46 7.46 37.08 3.16
2057 2188 4.578928 TCCAAAGTTAGTTTCCAGCTCAAC 59.421 41.667 0.00 0.00 0.00 3.18
2058 2189 4.787551 TCCAAAGTTAGTTTCCAGCTCAA 58.212 39.130 0.00 0.00 0.00 3.02
2059 2190 4.431416 TCCAAAGTTAGTTTCCAGCTCA 57.569 40.909 0.00 0.00 0.00 4.26
2060 2191 6.174049 ACTATCCAAAGTTAGTTTCCAGCTC 58.826 40.000 0.00 0.00 0.00 4.09
2061 2192 6.128138 ACTATCCAAAGTTAGTTTCCAGCT 57.872 37.500 0.00 0.00 0.00 4.24
2062 2193 5.938125 TGACTATCCAAAGTTAGTTTCCAGC 59.062 40.000 0.00 0.00 30.27 4.85
2063 2194 7.386851 TCTGACTATCCAAAGTTAGTTTCCAG 58.613 38.462 0.00 0.00 35.27 3.86
2064 2195 7.311092 TCTGACTATCCAAAGTTAGTTTCCA 57.689 36.000 0.00 0.00 35.27 3.53
2065 2196 9.315525 GTATCTGACTATCCAAAGTTAGTTTCC 57.684 37.037 0.00 0.00 35.27 3.13
2066 2197 9.315525 GGTATCTGACTATCCAAAGTTAGTTTC 57.684 37.037 0.00 0.00 35.27 2.78
2067 2198 8.822805 TGGTATCTGACTATCCAAAGTTAGTTT 58.177 33.333 0.00 0.00 35.27 2.66
2068 2199 8.258708 GTGGTATCTGACTATCCAAAGTTAGTT 58.741 37.037 0.00 0.00 35.27 2.24
2069 2200 7.399191 TGTGGTATCTGACTATCCAAAGTTAGT 59.601 37.037 0.00 0.00 35.27 2.24
2070 2201 7.782049 TGTGGTATCTGACTATCCAAAGTTAG 58.218 38.462 0.00 0.00 35.10 2.34
2071 2202 7.727578 TGTGGTATCTGACTATCCAAAGTTA 57.272 36.000 0.00 0.00 0.00 2.24
2075 2206 7.390440 CAGTTTTGTGGTATCTGACTATCCAAA 59.610 37.037 0.00 0.00 0.00 3.28
2076 2207 6.878923 CAGTTTTGTGGTATCTGACTATCCAA 59.121 38.462 0.00 0.00 0.00 3.53
2128 2289 3.966979 TGGTCAGTGGCACATAAATCAT 58.033 40.909 21.41 0.00 44.52 2.45
2191 2374 9.530633 GTATATGATTCTGTTTTCGGTTAGTCT 57.469 33.333 0.00 0.00 0.00 3.24
2196 2379 6.542370 CCCAGTATATGATTCTGTTTTCGGTT 59.458 38.462 0.00 0.00 0.00 4.44
2213 2396 6.733334 TGCCCATGTCTTAATATCCCAGTATA 59.267 38.462 0.00 0.00 0.00 1.47
2217 2400 4.371624 TGCCCATGTCTTAATATCCCAG 57.628 45.455 0.00 0.00 0.00 4.45
2223 2406 3.202906 GAGCGTTGCCCATGTCTTAATA 58.797 45.455 0.00 0.00 0.00 0.98
2224 2407 2.017049 GAGCGTTGCCCATGTCTTAAT 58.983 47.619 0.00 0.00 0.00 1.40
2225 2408 1.271108 TGAGCGTTGCCCATGTCTTAA 60.271 47.619 0.00 0.00 0.00 1.85
2226 2409 0.323302 TGAGCGTTGCCCATGTCTTA 59.677 50.000 0.00 0.00 0.00 2.10
2227 2410 0.322816 ATGAGCGTTGCCCATGTCTT 60.323 50.000 0.00 0.00 0.00 3.01
2228 2411 0.745845 GATGAGCGTTGCCCATGTCT 60.746 55.000 0.00 0.00 0.00 3.41
2229 2412 1.026182 TGATGAGCGTTGCCCATGTC 61.026 55.000 0.00 0.00 0.00 3.06
2230 2413 0.608856 TTGATGAGCGTTGCCCATGT 60.609 50.000 0.00 0.00 0.00 3.21
2231 2414 0.179156 GTTGATGAGCGTTGCCCATG 60.179 55.000 0.00 0.00 0.00 3.66
2232 2415 0.608856 TGTTGATGAGCGTTGCCCAT 60.609 50.000 0.00 0.00 0.00 4.00
2233 2416 0.821301 TTGTTGATGAGCGTTGCCCA 60.821 50.000 0.00 0.00 0.00 5.36
2234 2417 0.109597 CTTGTTGATGAGCGTTGCCC 60.110 55.000 0.00 0.00 0.00 5.36
2235 2418 0.593128 ACTTGTTGATGAGCGTTGCC 59.407 50.000 0.00 0.00 0.00 4.52
2236 2419 1.264020 TGACTTGTTGATGAGCGTTGC 59.736 47.619 0.00 0.00 0.00 4.17
2237 2420 2.096069 CCTGACTTGTTGATGAGCGTTG 60.096 50.000 0.00 0.00 0.00 4.10
2238 2421 2.146342 CCTGACTTGTTGATGAGCGTT 58.854 47.619 0.00 0.00 0.00 4.84
2239 2422 1.800805 CCTGACTTGTTGATGAGCGT 58.199 50.000 0.00 0.00 0.00 5.07
2240 2423 0.445436 GCCTGACTTGTTGATGAGCG 59.555 55.000 0.00 0.00 0.00 5.03
2241 2424 0.807496 GGCCTGACTTGTTGATGAGC 59.193 55.000 0.00 0.00 0.00 4.26
2252 2435 0.980231 GTCCTCTGATGGGCCTGACT 60.980 60.000 4.53 0.00 0.00 3.41
2253 2436 1.267574 TGTCCTCTGATGGGCCTGAC 61.268 60.000 4.53 0.96 0.00 3.51
2262 2455 9.388506 CATCAACTTACTTATTTGTCCTCTGAT 57.611 33.333 0.00 0.00 0.00 2.90
2266 2459 7.467623 CAGCATCAACTTACTTATTTGTCCTC 58.532 38.462 0.00 0.00 0.00 3.71
2342 2586 7.753309 TTATTACATGTATATTTTGCGGCCT 57.247 32.000 6.36 0.00 0.00 5.19
2359 2604 7.068962 TCTGACCATTCACCGTAGATTATTACA 59.931 37.037 0.00 0.00 0.00 2.41
2379 2624 2.143925 CCAAGAACGAAACCTCTGACC 58.856 52.381 0.00 0.00 0.00 4.02
2414 2659 4.997565 AGTTACGGTTAGCGCTAAACATA 58.002 39.130 36.70 27.70 32.46 2.29
2415 2660 3.853475 AGTTACGGTTAGCGCTAAACAT 58.147 40.909 36.70 28.75 32.46 2.71
2416 2661 3.302365 AGTTACGGTTAGCGCTAAACA 57.698 42.857 36.70 21.07 32.46 2.83
2417 2662 4.388790 CAAAGTTACGGTTAGCGCTAAAC 58.611 43.478 30.99 30.99 0.00 2.01
2426 2671 2.104451 TGTGGGAGCAAAGTTACGGTTA 59.896 45.455 0.00 0.00 0.00 2.85
2430 2675 5.365403 TTTATTGTGGGAGCAAAGTTACG 57.635 39.130 0.00 0.00 31.63 3.18
2500 2745 9.979578 TGTATACTTCCAACGTTAGTAGAAAAA 57.020 29.630 13.29 2.50 0.00 1.94


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

AutoCloner maintained by Alex Coulton.