Multiple sequence alignment - TraesCS2A01G192300

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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 TraesCS2A01G192300 chr2A 100.000 2531 0 0 1 2531 159879610 159877080 0.000000e+00 4674
1 TraesCS2A01G192300 chr2D 93.839 1818 65 14 1 1774 141474376 141476190 0.000000e+00 2693
2 TraesCS2A01G192300 chr2D 94.721 341 12 3 2196 2531 141476473 141476812 2.230000e-145 525
3 TraesCS2A01G192300 chr2D 84.923 325 17 3 1481 1774 553366191 553365868 1.470000e-77 300
4 TraesCS2A01G192300 chr2D 82.432 148 18 5 1927 2074 141476248 141476387 3.420000e-24 122
5 TraesCS2A01G192300 chr2B 90.791 1770 95 26 1 1736 199022018 199020283 0.000000e+00 2303
6 TraesCS2A01G192300 chr2B 94.463 307 11 2 2222 2525 199019656 199019353 3.810000e-128 468
7 TraesCS2A01G192300 chr2B 83.459 266 17 12 1938 2178 199020187 199019924 3.280000e-54 222
8 TraesCS2A01G192300 chr2B 93.162 117 7 1 1773 1888 144610027 144610143 1.200000e-38 171
9 TraesCS2A01G192300 chr2B 91.453 117 9 1 1773 1888 144610144 144610028 2.610000e-35 159
10 TraesCS2A01G192300 chr1A 85.276 326 15 11 1481 1774 451521516 451521840 3.160000e-79 305
11 TraesCS2A01G192300 chr1A 83.228 316 22 12 1481 1766 552087274 552086960 6.940000e-66 261
12 TraesCS2A01G192300 chr1A 92.308 117 7 2 1773 1888 72678885 72678770 5.600000e-37 165
13 TraesCS2A01G192300 chr1A 93.578 109 5 2 1927 2034 552086892 552086785 7.250000e-36 161
14 TraesCS2A01G192300 chr1A 91.453 117 8 2 1773 1888 72678769 72678884 2.610000e-35 159
15 TraesCS2A01G192300 chr1A 93.519 108 5 1 1927 2034 451521900 451522005 2.610000e-35 159
16 TraesCS2A01G192300 chr1A 89.600 125 10 2 1768 1891 53467642 53467520 3.370000e-34 156
17 TraesCS2A01G192300 chr1A 82.270 141 13 4 1771 1900 87518921 87518782 7.400000e-21 111
18 TraesCS2A01G192300 chr6D 84.615 325 18 3 1481 1774 19564535 19564858 6.850000e-76 294
19 TraesCS2A01G192300 chr6D 93.578 109 5 2 1927 2034 19564917 19565024 7.250000e-36 161
20 TraesCS2A01G192300 chrUn 84.098 327 18 6 1481 1774 22375513 22375838 4.120000e-73 285
21 TraesCS2A01G192300 chrUn 95.283 106 5 0 1927 2032 22375898 22376003 4.330000e-38 169
22 TraesCS2A01G192300 chr7A 83.540 322 23 11 1481 1774 110399076 110398757 8.920000e-70 274
23 TraesCS2A01G192300 chr7A 81.846 325 27 4 1481 1774 606317396 606317719 6.990000e-61 244
24 TraesCS2A01G192300 chr7A 92.727 110 6 1 1927 2034 606317779 606317888 9.370000e-35 158
25 TraesCS2A01G192300 chr7A 84.962 133 9 3 1773 1894 664847564 664847696 9.510000e-25 124
26 TraesCS2A01G192300 chr5A 83.077 325 23 4 1481 1774 19264853 19264530 1.490000e-67 267
27 TraesCS2A01G192300 chr4B 82.769 325 24 9 1481 1774 279320433 279320756 6.940000e-66 261
28 TraesCS2A01G192300 chr5D 82.943 299 18 5 1501 1767 485907524 485907227 3.250000e-59 239
29 TraesCS2A01G192300 chr4D 95.370 108 5 0 1927 2034 346188685 346188792 3.350000e-39 172
30 TraesCS2A01G192300 chr3B 91.870 123 9 1 1773 1894 346682715 346682593 1.200000e-38 171
31 TraesCS2A01G192300 chr3B 92.562 121 6 3 1770 1888 346682595 346682714 1.200000e-38 171
32 TraesCS2A01G192300 chr6A 92.308 117 6 2 1773 1888 543531543 543531429 2.010000e-36 163
33 TraesCS2A01G192300 chr6A 90.984 122 7 4 1773 1892 543531428 543531547 7.250000e-36 161
34 TraesCS2A01G192300 chr3A 84.615 143 9 7 1773 1903 584748652 584748793 2.040000e-26 130
35 TraesCS2A01G192300 chr3A 83.206 131 10 3 1773 1892 234955477 234955606 2.660000e-20 110
36 TraesCS2A01G192300 chr5B 83.453 139 12 3 1773 1900 697172410 697172548 4.420000e-23 119


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 TraesCS2A01G192300 chr2A 159877080 159879610 2530 True 4674.000000 4674 100.000000 1 2531 1 chr2A.!!$R1 2530
1 TraesCS2A01G192300 chr2D 141474376 141476812 2436 False 1113.333333 2693 90.330667 1 2531 3 chr2D.!!$F1 2530
2 TraesCS2A01G192300 chr2B 199019353 199022018 2665 True 997.666667 2303 89.571000 1 2525 3 chr2B.!!$R2 2524

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
404 405 0.590732 GCAAGAATCAGCCAATCGCG 60.591 55.0 0.0 0.0 44.76 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 2283 0.041312 TTTCTTGAGCTCAAACGCGC 60.041 50.0 28.16 0.0 35.15 6.86 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
201 202 2.866156 CAGACAAGAGAAGCAAACGACA 59.134 45.455 0.00 0.00 0.00 4.35
404 405 0.590732 GCAAGAATCAGCCAATCGCG 60.591 55.000 0.00 0.00 44.76 5.87
576 577 4.420168 ACAAGGTGTTGATTTGTTGTTCG 58.580 39.130 0.00 0.00 37.10 3.95
701 702 6.669125 TGATGGAATGTTGGAGAACAATTT 57.331 33.333 0.00 0.00 45.23 1.82
706 707 7.507829 TGGAATGTTGGAGAACAATTTGATTT 58.492 30.769 2.79 0.00 45.23 2.17
860 869 4.944317 AGCAGAGCAATTACCTCTAAAACC 59.056 41.667 7.31 0.00 37.57 3.27
867 876 5.358160 GCAATTACCTCTAAAACCTGCAGAT 59.642 40.000 17.39 0.00 0.00 2.90
883 892 2.663602 GCAGATAGAACACACGTGTCAG 59.336 50.000 20.49 11.62 44.13 3.51
929 938 2.591715 CGCCTCCGCCTATTTGGG 60.592 66.667 0.00 0.00 36.00 4.12
968 977 4.933064 CATCCGAGGACGCGAGCC 62.933 72.222 15.93 14.43 38.29 4.70
1272 1297 2.183046 GTGCTGCTCGTCCTCTCC 59.817 66.667 0.00 0.00 0.00 3.71
1517 1542 3.011583 CCGGAAATTAGCGCGGAC 58.988 61.111 8.83 0.00 0.00 4.79
1538 1563 5.415701 GGACTTTCCTGCACTGATTGATTTA 59.584 40.000 0.00 0.00 32.53 1.40
1638 1686 2.253452 GTTGCGGCTGCTGTTCTG 59.747 61.111 20.27 0.00 43.34 3.02
1712 1762 3.013921 TCTTGTTCGTCTGGTTTTGCTT 58.986 40.909 0.00 0.00 0.00 3.91
1725 1775 3.243839 GGTTTTGCTTGCTGAGATGGAAA 60.244 43.478 0.00 0.00 0.00 3.13
1726 1776 3.928727 TTTGCTTGCTGAGATGGAAAG 57.071 42.857 0.00 0.00 0.00 2.62
1727 1777 1.171308 TGCTTGCTGAGATGGAAAGC 58.829 50.000 0.00 0.00 43.59 3.51
1728 1778 0.098376 GCTTGCTGAGATGGAAAGCG 59.902 55.000 0.00 0.00 39.88 4.68
1750 1800 2.475111 TCAACGAGCGAACTTGTTCATC 59.525 45.455 13.05 9.15 45.75 2.92
1762 1812 3.006110 ACTTGTTCATCTGTTGCATTGGG 59.994 43.478 0.00 0.00 0.00 4.12
1770 1827 4.293662 TCTGTTGCATTGGGTATGTGTA 57.706 40.909 0.00 0.00 36.57 2.90
1771 1828 4.854173 TCTGTTGCATTGGGTATGTGTAT 58.146 39.130 0.00 0.00 36.57 2.29
1772 1829 5.260424 TCTGTTGCATTGGGTATGTGTATT 58.740 37.500 0.00 0.00 36.57 1.89
1773 1830 6.418946 TCTGTTGCATTGGGTATGTGTATTA 58.581 36.000 0.00 0.00 36.57 0.98
1774 1831 6.317642 TCTGTTGCATTGGGTATGTGTATTAC 59.682 38.462 0.00 0.00 36.57 1.89
1775 1832 6.184068 TGTTGCATTGGGTATGTGTATTACT 58.816 36.000 0.00 0.00 36.57 2.24
1776 1833 6.317642 TGTTGCATTGGGTATGTGTATTACTC 59.682 38.462 0.00 0.00 36.57 2.59
1777 1834 6.247229 TGCATTGGGTATGTGTATTACTCT 57.753 37.500 0.00 0.00 36.57 3.24
1778 1835 6.288294 TGCATTGGGTATGTGTATTACTCTC 58.712 40.000 0.00 0.00 36.57 3.20
1779 1836 6.099701 TGCATTGGGTATGTGTATTACTCTCT 59.900 38.462 0.00 0.00 36.57 3.10
1780 1837 6.647067 GCATTGGGTATGTGTATTACTCTCTC 59.353 42.308 0.00 0.00 36.57 3.20
1781 1838 6.726490 TTGGGTATGTGTATTACTCTCTCC 57.274 41.667 0.00 0.00 0.00 3.71
1782 1839 4.825634 TGGGTATGTGTATTACTCTCTCCG 59.174 45.833 0.00 0.00 0.00 4.63
1783 1840 4.826183 GGGTATGTGTATTACTCTCTCCGT 59.174 45.833 0.00 0.00 0.00 4.69
1784 1841 5.301298 GGGTATGTGTATTACTCTCTCCGTT 59.699 44.000 0.00 0.00 0.00 4.44
1785 1842 6.437094 GGTATGTGTATTACTCTCTCCGTTC 58.563 44.000 0.00 0.00 0.00 3.95
1786 1843 4.978083 TGTGTATTACTCTCTCCGTTCC 57.022 45.455 0.00 0.00 0.00 3.62
1787 1844 3.376234 TGTGTATTACTCTCTCCGTTCCG 59.624 47.826 0.00 0.00 0.00 4.30
1788 1845 3.624861 GTGTATTACTCTCTCCGTTCCGA 59.375 47.826 0.00 0.00 0.00 4.55
1789 1846 4.095483 GTGTATTACTCTCTCCGTTCCGAA 59.905 45.833 0.00 0.00 0.00 4.30
1790 1847 4.885907 TGTATTACTCTCTCCGTTCCGAAT 59.114 41.667 0.00 0.00 0.00 3.34
1791 1848 5.359009 TGTATTACTCTCTCCGTTCCGAATT 59.641 40.000 0.00 0.00 0.00 2.17
1792 1849 6.543465 TGTATTACTCTCTCCGTTCCGAATTA 59.457 38.462 0.00 0.00 0.00 1.40
1793 1850 3.779271 ACTCTCTCCGTTCCGAATTAC 57.221 47.619 0.00 0.00 0.00 1.89
1794 1851 3.354467 ACTCTCTCCGTTCCGAATTACT 58.646 45.455 0.00 0.00 0.00 2.24
1795 1852 3.762823 ACTCTCTCCGTTCCGAATTACTT 59.237 43.478 0.00 0.00 0.00 2.24
1796 1853 4.106029 TCTCTCCGTTCCGAATTACTTG 57.894 45.455 0.00 0.00 0.00 3.16
1797 1854 3.508793 TCTCTCCGTTCCGAATTACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
1798 1855 3.841643 TCTCCGTTCCGAATTACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
1799 1856 3.508793 TCTCCGTTCCGAATTACTTGTCT 59.491 43.478 0.00 0.00 0.00 3.41
1800 1857 4.021719 TCTCCGTTCCGAATTACTTGTCTT 60.022 41.667 0.00 0.00 0.00 3.01
1801 1858 5.183713 TCTCCGTTCCGAATTACTTGTCTTA 59.816 40.000 0.00 0.00 0.00 2.10
1802 1859 5.969423 TCCGTTCCGAATTACTTGTCTTAT 58.031 37.500 0.00 0.00 0.00 1.73
1803 1860 7.067372 TCTCCGTTCCGAATTACTTGTCTTATA 59.933 37.037 0.00 0.00 0.00 0.98
1804 1861 7.719483 TCCGTTCCGAATTACTTGTCTTATAT 58.281 34.615 0.00 0.00 0.00 0.86
1805 1862 8.199449 TCCGTTCCGAATTACTTGTCTTATATT 58.801 33.333 0.00 0.00 0.00 1.28
1806 1863 8.823818 CCGTTCCGAATTACTTGTCTTATATTT 58.176 33.333 0.00 0.00 0.00 1.40
1807 1864 9.632969 CGTTCCGAATTACTTGTCTTATATTTG 57.367 33.333 0.00 0.00 0.00 2.32
1828 1885 7.408132 TTTGTCTAAATACGATGCATCTAGC 57.592 36.000 23.73 13.55 45.96 3.42
1829 1886 7.657354 ATTTGTCTAAATACGATGCATCTAGCA 59.343 33.333 23.73 15.47 45.26 3.49
1845 1902 5.230323 TCTAGCACTCTAGATACATCCGT 57.770 43.478 0.00 0.00 44.65 4.69
1846 1903 6.356186 TCTAGCACTCTAGATACATCCGTA 57.644 41.667 0.00 0.00 44.65 4.02
1847 1904 6.948589 TCTAGCACTCTAGATACATCCGTAT 58.051 40.000 0.00 0.00 44.65 3.06
1862 1919 9.698309 ATACATCCGTATCTAGACAAATTCAAG 57.302 33.333 0.00 0.00 32.66 3.02
1863 1920 7.782049 ACATCCGTATCTAGACAAATTCAAGA 58.218 34.615 0.00 0.00 0.00 3.02
1864 1921 7.707035 ACATCCGTATCTAGACAAATTCAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
1865 1922 7.165460 TCCGTATCTAGACAAATTCAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
1866 1923 7.608153 TCCGTATCTAGACAAATTCAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
1867 1924 7.759886 TCCGTATCTAGACAAATTCAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
1868 1925 7.545965 CCGTATCTAGACAAATTCAAGACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
1869 1926 9.569167 CGTATCTAGACAAATTCAAGACAAGTA 57.431 33.333 0.00 0.00 0.00 2.24
1874 1931 9.746711 CTAGACAAATTCAAGACAAGTAATTCG 57.253 33.333 0.00 0.00 0.00 3.34
1875 1932 7.584987 AGACAAATTCAAGACAAGTAATTCGG 58.415 34.615 0.00 0.00 0.00 4.30
1876 1933 7.444183 AGACAAATTCAAGACAAGTAATTCGGA 59.556 33.333 0.00 0.00 0.00 4.55
1877 1934 7.936584 ACAAATTCAAGACAAGTAATTCGGAA 58.063 30.769 0.00 0.00 0.00 4.30
1878 1935 7.860872 ACAAATTCAAGACAAGTAATTCGGAAC 59.139 33.333 0.00 0.00 0.00 3.62
1898 1955 2.289565 CGGAGGGAGTTCTAAAATGGC 58.710 52.381 0.00 0.00 0.00 4.40
1908 1965 6.076981 AGTTCTAAAATGGCAGTTCAGTTG 57.923 37.500 0.00 0.00 0.00 3.16
1957 2034 9.799106 TGGAGATTTTTCTTAGAATCAACTCTT 57.201 29.630 0.00 0.00 35.28 2.85
2035 2112 6.763303 AGAAACAAAACATAACCGAAATGC 57.237 33.333 0.00 0.00 0.00 3.56
2038 2115 4.861210 ACAAAACATAACCGAAATGCGAA 58.139 34.783 0.00 0.00 44.57 4.70
2040 2117 2.798834 ACATAACCGAAATGCGAACG 57.201 45.000 0.00 0.00 44.57 3.95
2041 2118 2.339418 ACATAACCGAAATGCGAACGA 58.661 42.857 0.00 0.00 44.57 3.85
2102 2203 2.766313 TCTTCGGGACAACATTGACAG 58.234 47.619 0.00 0.00 0.00 3.51
2110 2211 4.338118 GGGACAACATTGACAGTTTCTTCA 59.662 41.667 0.00 0.00 0.00 3.02
2153 2254 3.377253 ACTGCCACCATTTGATCTCAT 57.623 42.857 0.00 0.00 0.00 2.90
2174 2275 1.337703 CAGCAACTAAAACAGCCAGCA 59.662 47.619 0.00 0.00 0.00 4.41
2176 2277 2.035066 AGCAACTAAAACAGCCAGCAAG 59.965 45.455 0.00 0.00 0.00 4.01
2178 2279 3.305608 GCAACTAAAACAGCCAGCAAGAT 60.306 43.478 0.00 0.00 0.00 2.40
2179 2280 4.479619 CAACTAAAACAGCCAGCAAGATC 58.520 43.478 0.00 0.00 0.00 2.75
2180 2281 4.026356 ACTAAAACAGCCAGCAAGATCT 57.974 40.909 0.00 0.00 0.00 2.75
2181 2282 4.006319 ACTAAAACAGCCAGCAAGATCTC 58.994 43.478 0.00 0.00 0.00 2.75
2182 2283 1.446907 AAACAGCCAGCAAGATCTCG 58.553 50.000 0.00 0.00 0.00 4.04
2183 2284 1.023513 AACAGCCAGCAAGATCTCGC 61.024 55.000 0.00 0.00 0.00 5.03
2225 2556 2.094675 CATTCGCTTGTCATTCCCCTT 58.905 47.619 0.00 0.00 0.00 3.95
2234 2565 1.004745 GTCATTCCCCTTCCAGCTGAA 59.995 52.381 17.39 6.85 0.00 3.02
2245 2576 1.376037 CAGCTGAAGTTCCCCCGAC 60.376 63.158 8.42 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 1.134128 TCCACATATGGCTGATGCGTT 60.134 47.619 7.80 0.00 46.80 4.84
223 224 4.122776 GCAGTACCCATTATCTGTCACTG 58.877 47.826 0.00 0.00 36.18 3.66
261 262 0.392998 TCGCATCTTTCCCTTCCTGC 60.393 55.000 0.00 0.00 0.00 4.85
404 405 1.144936 CGCACATCTCTTCCTCCCC 59.855 63.158 0.00 0.00 0.00 4.81
701 702 1.327303 GGTGGTCACAGGCAAAATCA 58.673 50.000 3.40 0.00 0.00 2.57
706 707 1.770110 AGAGGGTGGTCACAGGCAA 60.770 57.895 3.40 0.00 0.00 4.52
741 743 8.236586 TCAAAATCGTGTTATCCAGAAATCAAG 58.763 33.333 0.00 0.00 0.00 3.02
860 869 2.663602 GACACGTGTGTTCTATCTGCAG 59.336 50.000 28.82 7.63 45.05 4.41
867 876 0.318360 CGCCTGACACGTGTGTTCTA 60.318 55.000 28.82 5.99 45.05 2.10
883 892 1.673808 AAGGATGACGTCTACCCGCC 61.674 60.000 17.92 8.68 0.00 6.13
929 938 2.256306 TCCCTTTTGATTTTGGAGGCC 58.744 47.619 0.00 0.00 0.00 5.19
1107 1132 4.365111 ATGGGCTTGGGCTTCGCA 62.365 61.111 0.00 0.00 38.73 5.10
1365 1390 1.076339 CTTCCTCCTCCTCGCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
1366 1391 1.076632 TCTTCCTCCTCCTCGCTCC 60.077 63.158 0.00 0.00 0.00 4.70
1517 1542 6.506500 ACTAAATCAATCAGTGCAGGAAAG 57.493 37.500 0.00 0.00 0.00 2.62
1538 1563 4.714632 TCAAGAAATCGAACAGGGAAACT 58.285 39.130 0.00 0.00 0.00 2.66
1638 1686 0.529378 CCAACAGAATGCCTTCCAGC 59.471 55.000 0.00 0.00 42.53 4.85
1712 1762 0.321346 TGACGCTTTCCATCTCAGCA 59.679 50.000 0.00 0.00 32.71 4.41
1725 1775 1.299926 AAGTTCGCTCGTTGACGCT 60.300 52.632 0.00 0.00 39.60 5.07
1726 1776 1.154836 CAAGTTCGCTCGTTGACGC 60.155 57.895 0.00 0.00 39.60 5.19
1727 1777 0.575390 AACAAGTTCGCTCGTTGACG 59.425 50.000 0.00 0.00 41.45 4.35
1728 1778 1.591158 TGAACAAGTTCGCTCGTTGAC 59.409 47.619 8.28 0.00 42.28 3.18
1750 1800 5.581126 AATACACATACCCAATGCAACAG 57.419 39.130 0.00 0.00 39.39 3.16
1762 1812 6.437094 GGAACGGAGAGAGTAATACACATAC 58.563 44.000 0.00 0.00 0.00 2.39
1802 1859 9.140286 GCTAGATGCATCGTATTTAGACAAATA 57.860 33.333 20.67 2.13 42.31 1.40
1803 1860 8.023050 GCTAGATGCATCGTATTTAGACAAAT 57.977 34.615 20.67 0.98 42.31 2.32
1804 1861 7.408132 GCTAGATGCATCGTATTTAGACAAA 57.592 36.000 20.67 0.00 42.31 2.83
1836 1893 9.698309 CTTGAATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
1837 1894 8.909923 TCTTGAATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 33.79 2.29
1838 1895 7.707035 GTCTTGAATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 39.77 3.06
1839 1896 7.706607 TGTCTTGAATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 39.77 3.51
1840 1897 7.782049 TGTCTTGAATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 39.77 4.18
1841 1898 7.165460 TGTCTTGAATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 39.77 4.69
1842 1899 7.545965 ACTTGTCTTGAATTTGTCTAGATACGG 59.454 37.037 0.00 0.00 39.77 4.02
1843 1900 8.467402 ACTTGTCTTGAATTTGTCTAGATACG 57.533 34.615 0.00 0.00 39.77 3.06
1848 1905 9.746711 CGAATTACTTGTCTTGAATTTGTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
1849 1906 8.717821 CCGAATTACTTGTCTTGAATTTGTCTA 58.282 33.333 0.00 0.00 0.00 2.59
1850 1907 7.444183 TCCGAATTACTTGTCTTGAATTTGTCT 59.556 33.333 0.00 0.00 0.00 3.41
1851 1908 7.581476 TCCGAATTACTTGTCTTGAATTTGTC 58.419 34.615 0.00 0.00 0.00 3.18
1852 1909 7.504924 TCCGAATTACTTGTCTTGAATTTGT 57.495 32.000 0.00 0.00 0.00 2.83
1853 1910 7.059488 CGTTCCGAATTACTTGTCTTGAATTTG 59.941 37.037 0.00 0.00 0.00 2.32
1854 1911 7.075741 CGTTCCGAATTACTTGTCTTGAATTT 58.924 34.615 0.00 0.00 0.00 1.82
1855 1912 6.348213 CCGTTCCGAATTACTTGTCTTGAATT 60.348 38.462 0.00 0.00 0.00 2.17
1856 1913 5.121768 CCGTTCCGAATTACTTGTCTTGAAT 59.878 40.000 0.00 0.00 0.00 2.57
1857 1914 4.449743 CCGTTCCGAATTACTTGTCTTGAA 59.550 41.667 0.00 0.00 0.00 2.69
1858 1915 3.991773 CCGTTCCGAATTACTTGTCTTGA 59.008 43.478 0.00 0.00 0.00 3.02
1859 1916 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
1860 1917 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
1861 1918 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
1862 1919 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1863 1920 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1864 1921 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1865 1922 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1866 1923 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1867 1924 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1868 1925 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1869 1926 0.981943 AACTCCCTCCGTTCCGAATT 59.018 50.000 0.00 0.00 0.00 2.17
1870 1927 0.535797 GAACTCCCTCCGTTCCGAAT 59.464 55.000 0.00 0.00 35.81 3.34
1871 1928 0.541296 AGAACTCCCTCCGTTCCGAA 60.541 55.000 0.00 0.00 41.19 4.30
1872 1929 0.329261 TAGAACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 41.19 4.55
1873 1930 1.180029 TTAGAACTCCCTCCGTTCCG 58.820 55.000 0.00 0.00 41.19 4.30
1874 1931 3.690475 TTTTAGAACTCCCTCCGTTCC 57.310 47.619 0.00 0.00 41.19 3.62
1875 1932 3.939592 CCATTTTAGAACTCCCTCCGTTC 59.060 47.826 0.00 0.00 40.72 3.95
1876 1933 3.872630 GCCATTTTAGAACTCCCTCCGTT 60.873 47.826 0.00 0.00 0.00 4.44
1877 1934 2.355818 GCCATTTTAGAACTCCCTCCGT 60.356 50.000 0.00 0.00 0.00 4.69
1878 1935 2.289565 GCCATTTTAGAACTCCCTCCG 58.710 52.381 0.00 0.00 0.00 4.63
1879 1936 3.282885 CTGCCATTTTAGAACTCCCTCC 58.717 50.000 0.00 0.00 0.00 4.30
1880 1937 3.956744 ACTGCCATTTTAGAACTCCCTC 58.043 45.455 0.00 0.00 0.00 4.30
1881 1938 4.202567 TGAACTGCCATTTTAGAACTCCCT 60.203 41.667 0.00 0.00 0.00 4.20
1882 1939 4.079253 TGAACTGCCATTTTAGAACTCCC 58.921 43.478 0.00 0.00 0.00 4.30
1883 1940 4.762251 ACTGAACTGCCATTTTAGAACTCC 59.238 41.667 0.00 0.00 0.00 3.85
1884 1941 5.948992 ACTGAACTGCCATTTTAGAACTC 57.051 39.130 0.00 0.00 0.00 3.01
1885 1942 5.594317 ACAACTGAACTGCCATTTTAGAACT 59.406 36.000 0.00 0.00 0.00 3.01
1886 1943 5.831997 ACAACTGAACTGCCATTTTAGAAC 58.168 37.500 0.00 0.00 0.00 3.01
1887 1944 6.463995 AACAACTGAACTGCCATTTTAGAA 57.536 33.333 0.00 0.00 0.00 2.10
1888 1945 6.272318 CAAACAACTGAACTGCCATTTTAGA 58.728 36.000 0.00 0.00 0.00 2.10
1891 1948 3.622612 GCAAACAACTGAACTGCCATTTT 59.377 39.130 0.00 0.00 0.00 1.82
1898 1955 1.843992 GGCAGCAAACAACTGAACTG 58.156 50.000 0.00 0.00 37.32 3.16
1957 2034 2.832733 TGCATCCAATTTGCCAAGATCA 59.167 40.909 0.00 0.00 39.39 2.92
1969 2046 7.989416 AAAAATCAAACAATCTGCATCCAAT 57.011 28.000 0.00 0.00 0.00 3.16
2038 2115 0.976073 ACCTCATCCCACCGAATCGT 60.976 55.000 0.82 0.00 0.00 3.73
2040 2117 0.179045 CCACCTCATCCCACCGAATC 60.179 60.000 0.00 0.00 0.00 2.52
2041 2118 1.635817 CCCACCTCATCCCACCGAAT 61.636 60.000 0.00 0.00 0.00 3.34
2046 2138 4.489771 CGGCCCACCTCATCCCAC 62.490 72.222 0.00 0.00 0.00 4.61
2077 2169 3.813166 TCAATGTTGTCCCGAAGAAGTTC 59.187 43.478 0.00 0.00 0.00 3.01
2089 2190 7.250569 TCTTTGAAGAAACTGTCAATGTTGTC 58.749 34.615 0.00 0.00 33.90 3.18
2125 2226 4.954875 TCAAATGGTGGCAGTTTTAAAGG 58.045 39.130 0.00 0.00 0.00 3.11
2126 2227 6.458210 AGATCAAATGGTGGCAGTTTTAAAG 58.542 36.000 0.00 0.00 0.00 1.85
2127 2228 6.041409 TGAGATCAAATGGTGGCAGTTTTAAA 59.959 34.615 0.00 0.00 0.00 1.52
2128 2229 5.538053 TGAGATCAAATGGTGGCAGTTTTAA 59.462 36.000 0.00 0.00 0.00 1.52
2129 2230 5.076182 TGAGATCAAATGGTGGCAGTTTTA 58.924 37.500 0.00 0.00 0.00 1.52
2153 2254 1.608590 GCTGGCTGTTTTAGTTGCTGA 59.391 47.619 0.00 0.00 0.00 4.26
2174 2275 1.687494 GCTCAAACGCGCGAGATCTT 61.687 55.000 39.36 17.68 0.00 2.40
2176 2277 2.072038 GAGCTCAAACGCGCGAGATC 62.072 60.000 39.36 26.65 37.49 2.75
2178 2279 2.805353 GAGCTCAAACGCGCGAGA 60.805 61.111 39.36 27.26 34.40 4.04
2179 2280 2.539972 CTTGAGCTCAAACGCGCGAG 62.540 60.000 39.36 24.31 35.41 5.03
2180 2281 2.657757 CTTGAGCTCAAACGCGCGA 61.658 57.895 39.36 13.65 35.15 5.87
2181 2282 2.158058 TTCTTGAGCTCAAACGCGCG 62.158 55.000 30.96 30.96 35.15 6.86
2182 2283 0.041312 TTTCTTGAGCTCAAACGCGC 60.041 50.000 28.16 0.00 35.15 6.86
2183 2284 2.383298 TTTTCTTGAGCTCAAACGCG 57.617 45.000 28.16 17.28 35.15 6.01
2215 2329 1.371467 TTCAGCTGGAAGGGGAATGA 58.629 50.000 15.13 0.00 0.00 2.57
2225 2556 2.592993 CGGGGGAACTTCAGCTGGA 61.593 63.158 15.13 3.47 0.00 3.86
2234 2565 1.003928 GGTAATGTTGTCGGGGGAACT 59.996 52.381 0.00 0.00 0.00 3.01
2239 2570 2.610374 CGTATTGGTAATGTTGTCGGGG 59.390 50.000 0.00 0.00 0.00 5.73
2245 2576 9.093970 TCTTTCTGTATCGTATTGGTAATGTTG 57.906 33.333 0.00 0.00 0.00 3.33
2286 2619 5.965033 TTCTCTGCTAAGGAGAATGGATT 57.035 39.130 2.54 0.00 42.59 3.01
2300 2633 5.140454 AGGGTAAAATTGTGTTTCTCTGCT 58.860 37.500 0.00 0.00 0.00 4.24
2341 2674 0.978146 ACAGGAGCGACTAATGCCCT 60.978 55.000 0.00 0.00 34.61 5.19
2417 2750 2.250273 AGTGACTACCCCTGGGACATAT 59.750 50.000 16.20 0.00 38.20 1.78


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

AutoCloner maintained by Alex Coulton.