Multiple sequence alignment - TraesCS6D01G276500

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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 TraesCS6D01G276500 chr6D 100.000 2237 0 0 1 2237 385234848 385232612 0.000000e+00 4132.0
1 TraesCS6D01G276500 chr6B 87.175 1731 91 52 20 1663 575332227 575330541 0.000000e+00 1845.0
2 TraesCS6D01G276500 chr6B 87.674 430 43 7 1812 2237 575330342 575329919 2.000000e-135 492.0
3 TraesCS6D01G276500 chr6A 86.445 1741 85 52 1 1663 529602346 529600679 0.000000e+00 1768.0
4 TraesCS6D01G276500 chr6A 92.973 185 12 1 2053 2237 529568101 529567918 3.660000e-68 268.0
5 TraesCS6D01G276500 chr6A 83.019 212 13 13 1835 2043 529600502 529600311 1.060000e-38 171.0
6 TraesCS6D01G276500 chr4A 100.000 28 0 0 1699 1726 739641821 739641794 4.000000e-03 52.8
7 TraesCS6D01G276500 chr4A 100.000 28 0 0 1699 1726 742046944 742046917 4.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G276500 chr6D 385232612 385234848 2236 True 4132.0 4132 100.0000 1 2237 1 chr6D.!!$R1 2236
1 TraesCS6D01G276500 chr6B 575329919 575332227 2308 True 1168.5 1845 87.4245 20 2237 2 chr6B.!!$R1 2217
2 TraesCS6D01G276500 chr6A 529600311 529602346 2035 True 969.5 1768 84.7320 1 2043 2 chr6A.!!$R2 2042

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
982 1064 0.038159 AGAAGAAGAAGCCACGTCCG 60.038 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2264 0.539051 ATATAGCCTGCCTGATCCGC 59.461 55.0 0.0 0.0 0.0 5.54 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
35 36 2.203015 ACACACACACCTGTCCGC 60.203 61.111 0.00 0.00 0.00 5.54
37 38 4.250305 ACACACACCTGTCCGCCC 62.250 66.667 0.00 0.00 0.00 6.13
38 39 4.248842 CACACACCTGTCCGCCCA 62.249 66.667 0.00 0.00 0.00 5.36
95 116 2.892425 GCACCCTTCGCCTCGATG 60.892 66.667 0.00 0.00 35.23 3.84
201 224 1.676968 CCTCCCCGATCACACAACA 59.323 57.895 0.00 0.00 0.00 3.33
314 340 2.111999 CTGTTCCTCGGCTCCCACAA 62.112 60.000 0.00 0.00 0.00 3.33
315 341 1.671379 GTTCCTCGGCTCCCACAAC 60.671 63.158 0.00 0.00 0.00 3.32
316 342 1.841556 TTCCTCGGCTCCCACAACT 60.842 57.895 0.00 0.00 0.00 3.16
340 367 0.855349 CGCACAACTGACTGACTGAC 59.145 55.000 0.00 0.00 0.00 3.51
341 368 1.536922 CGCACAACTGACTGACTGACT 60.537 52.381 0.00 0.00 0.00 3.41
342 369 1.863454 GCACAACTGACTGACTGACTG 59.137 52.381 0.00 0.00 0.00 3.51
346 373 4.631377 CACAACTGACTGACTGACTGAAAA 59.369 41.667 0.00 0.00 0.00 2.29
347 374 4.631813 ACAACTGACTGACTGACTGAAAAC 59.368 41.667 0.00 0.00 0.00 2.43
353 380 5.471797 TGACTGACTGACTGAAAACAAAACA 59.528 36.000 0.00 0.00 0.00 2.83
358 385 4.022416 ACTGACTGAAAACAAAACAGCACA 60.022 37.500 0.00 0.00 35.38 4.57
394 440 5.576563 TTAGAAGACCAGTTGGATTGGAA 57.423 39.130 4.92 0.00 39.08 3.53
421 467 6.275305 GATAGACGAGCTATCCAAACAAAC 57.725 41.667 14.81 0.00 46.47 2.93
579 645 6.721704 GGATATGCATCCCTTTTCTTTCTT 57.278 37.500 0.19 0.00 44.55 2.52
620 700 1.135489 CGTCCCTTTTCACGAGATCGA 60.135 52.381 9.58 0.00 43.02 3.59
817 899 1.234615 CGTGGCCCCTATTTATGCGG 61.235 60.000 0.00 0.00 0.00 5.69
852 934 4.066139 ATGGGCTGGGCTGGGTTC 62.066 66.667 0.00 0.00 0.00 3.62
890 972 4.274459 GTGCATTTACACATCTCCCATCTC 59.726 45.833 0.00 0.00 40.40 2.75
891 973 3.817647 GCATTTACACATCTCCCATCTCC 59.182 47.826 0.00 0.00 0.00 3.71
892 974 4.392940 CATTTACACATCTCCCATCTCCC 58.607 47.826 0.00 0.00 0.00 4.30
893 975 2.866923 TACACATCTCCCATCTCCCA 57.133 50.000 0.00 0.00 0.00 4.37
894 976 2.203120 ACACATCTCCCATCTCCCAT 57.797 50.000 0.00 0.00 0.00 4.00
895 977 2.053244 ACACATCTCCCATCTCCCATC 58.947 52.381 0.00 0.00 0.00 3.51
896 978 2.336891 CACATCTCCCATCTCCCATCT 58.663 52.381 0.00 0.00 0.00 2.90
908 990 0.810426 TCCCATCTCGTCTCGTCTCG 60.810 60.000 0.00 0.00 0.00 4.04
922 1004 2.024871 CTCGTCTCATCGGCGGTC 59.975 66.667 7.21 0.00 0.00 4.79
937 1019 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
938 1020 3.029735 TCGTCGTCGTCGTCGTCA 61.030 61.111 18.44 1.12 45.27 4.35
939 1021 2.095282 CGTCGTCGTCGTCGTCAT 59.905 61.111 12.51 0.00 41.73 3.06
960 1042 3.804193 CCGGAGGCGCAAGAAAGC 61.804 66.667 10.83 0.00 46.14 3.51
980 1062 2.333014 CTCAGAAGAAGAAGCCACGTC 58.667 52.381 0.00 0.00 0.00 4.34
981 1063 1.000955 TCAGAAGAAGAAGCCACGTCC 59.999 52.381 0.00 0.00 0.00 4.79
982 1064 0.038159 AGAAGAAGAAGCCACGTCCG 60.038 55.000 0.00 0.00 0.00 4.79
983 1065 1.004918 AAGAAGAAGCCACGTCCGG 60.005 57.895 0.00 0.00 0.00 5.14
1011 1093 0.880718 GTCCGGCGATGGAGAATTCC 60.881 60.000 9.30 0.00 44.31 3.01
1023 1105 1.410882 GAGAATTCCTGGGACGAGGAG 59.589 57.143 0.65 0.00 43.26 3.69
1251 1333 3.751049 CTAGTCCTAGGGCCGGCCA 62.751 68.421 44.46 26.34 37.98 5.36
1294 1379 4.687215 TCGTCGTCGTCCCCTCGT 62.687 66.667 1.33 0.00 38.33 4.18
1298 1383 4.351938 CGTCGTCCCCTCGTGCAA 62.352 66.667 0.00 0.00 0.00 4.08
1304 1389 2.892425 CCCCTCGTGCAATCTCGC 60.892 66.667 0.00 0.00 0.00 5.03
1328 1432 6.750501 GCCGTGTATTAGGATTTTCTTTTTCC 59.249 38.462 0.00 0.00 0.00 3.13
1356 1460 1.342574 TGGTGATCCTGTCCATCCGTA 60.343 52.381 0.00 0.00 34.23 4.02
1387 1491 1.489649 AGGATCATCTTCTGCTGGTGG 59.510 52.381 0.00 0.00 0.00 4.61
1440 1548 9.378551 GATGGTTGTGTAAATACTTCATACTCA 57.621 33.333 0.00 0.00 0.00 3.41
1442 1550 9.733556 TGGTTGTGTAAATACTTCATACTCATT 57.266 29.630 0.00 0.00 0.00 2.57
1466 1574 3.068873 GTGTGAGTTGTCAGTCTCTTCCT 59.931 47.826 8.06 0.00 31.53 3.36
1526 1634 7.148490 GGATGGTGCTGCGTTTTTATTTTATTT 60.148 33.333 0.00 0.00 0.00 1.40
1565 1673 5.039480 ACTGCGATTGTGAAAAGAGATTG 57.961 39.130 0.00 0.00 0.00 2.67
1588 1701 4.685628 GTGCATAGAGCTTTAGATCAGAGC 59.314 45.833 0.00 0.96 45.94 4.09
1605 1718 3.677002 GCTCTGTGCTATGGGTCTC 57.323 57.895 0.00 0.00 38.95 3.36
1609 1722 1.833630 TCTGTGCTATGGGTCTCAAGG 59.166 52.381 0.00 0.00 0.00 3.61
1655 1806 7.497249 GCCTGAAGATGTATGTCAACTCTTATT 59.503 37.037 0.00 0.00 0.00 1.40
1665 1816 9.136952 GTATGTCAACTCTTATTTGAACTACGT 57.863 33.333 0.00 0.00 34.78 3.57
1666 1817 7.633361 TGTCAACTCTTATTTGAACTACGTC 57.367 36.000 0.00 0.00 34.78 4.34
1667 1818 6.643770 TGTCAACTCTTATTTGAACTACGTCC 59.356 38.462 0.00 0.00 34.78 4.79
1668 1819 5.860182 TCAACTCTTATTTGAACTACGTCCG 59.140 40.000 0.00 0.00 29.89 4.79
1669 1820 4.171754 ACTCTTATTTGAACTACGTCCGC 58.828 43.478 0.00 0.00 0.00 5.54
1670 1821 3.514645 TCTTATTTGAACTACGTCCGCC 58.485 45.455 0.00 0.00 0.00 6.13
1671 1822 3.056678 TCTTATTTGAACTACGTCCGCCA 60.057 43.478 0.00 0.00 0.00 5.69
1672 1823 2.172851 ATTTGAACTACGTCCGCCAA 57.827 45.000 0.00 0.00 0.00 4.52
1673 1824 2.172851 TTTGAACTACGTCCGCCAAT 57.827 45.000 0.00 0.00 0.00 3.16
1674 1825 3.316071 TTTGAACTACGTCCGCCAATA 57.684 42.857 0.00 0.00 0.00 1.90
1675 1826 2.282701 TGAACTACGTCCGCCAATAC 57.717 50.000 0.00 0.00 0.00 1.89
1676 1827 1.135024 TGAACTACGTCCGCCAATACC 60.135 52.381 0.00 0.00 0.00 2.73
1677 1828 0.896923 AACTACGTCCGCCAATACCA 59.103 50.000 0.00 0.00 0.00 3.25
1678 1829 0.896923 ACTACGTCCGCCAATACCAA 59.103 50.000 0.00 0.00 0.00 3.67
1679 1830 1.483415 ACTACGTCCGCCAATACCAAT 59.517 47.619 0.00 0.00 0.00 3.16
1680 1831 2.694628 ACTACGTCCGCCAATACCAATA 59.305 45.455 0.00 0.00 0.00 1.90
1681 1832 2.695127 ACGTCCGCCAATACCAATAA 57.305 45.000 0.00 0.00 0.00 1.40
1682 1833 2.988570 ACGTCCGCCAATACCAATAAA 58.011 42.857 0.00 0.00 0.00 1.40
1683 1834 3.547746 ACGTCCGCCAATACCAATAAAT 58.452 40.909 0.00 0.00 0.00 1.40
1684 1835 3.562557 ACGTCCGCCAATACCAATAAATC 59.437 43.478 0.00 0.00 0.00 2.17
1685 1836 3.562141 CGTCCGCCAATACCAATAAATCA 59.438 43.478 0.00 0.00 0.00 2.57
1686 1837 4.319477 CGTCCGCCAATACCAATAAATCAG 60.319 45.833 0.00 0.00 0.00 2.90
1687 1838 4.819630 GTCCGCCAATACCAATAAATCAGA 59.180 41.667 0.00 0.00 0.00 3.27
1688 1839 5.298276 GTCCGCCAATACCAATAAATCAGAA 59.702 40.000 0.00 0.00 0.00 3.02
1689 1840 5.298276 TCCGCCAATACCAATAAATCAGAAC 59.702 40.000 0.00 0.00 0.00 3.01
1690 1841 5.299279 CCGCCAATACCAATAAATCAGAACT 59.701 40.000 0.00 0.00 0.00 3.01
1691 1842 6.201517 CGCCAATACCAATAAATCAGAACTG 58.798 40.000 0.00 0.00 0.00 3.16
1692 1843 6.183360 CGCCAATACCAATAAATCAGAACTGT 60.183 38.462 1.73 0.00 0.00 3.55
1693 1844 7.196331 GCCAATACCAATAAATCAGAACTGTC 58.804 38.462 1.73 0.00 0.00 3.51
1694 1845 7.682021 GCCAATACCAATAAATCAGAACTGTCC 60.682 40.741 1.73 0.00 0.00 4.02
1695 1846 7.409697 CAATACCAATAAATCAGAACTGTCCG 58.590 38.462 1.73 0.00 0.00 4.79
1696 1847 3.689649 ACCAATAAATCAGAACTGTCCGC 59.310 43.478 1.73 0.00 0.00 5.54
1697 1848 3.065371 CCAATAAATCAGAACTGTCCGCC 59.935 47.826 1.73 0.00 0.00 6.13
1698 1849 3.627395 ATAAATCAGAACTGTCCGCCA 57.373 42.857 1.73 0.00 0.00 5.69
1699 1850 2.270352 AAATCAGAACTGTCCGCCAA 57.730 45.000 1.73 0.00 0.00 4.52
1700 1851 2.270352 AATCAGAACTGTCCGCCAAA 57.730 45.000 1.73 0.00 0.00 3.28
1701 1852 2.496899 ATCAGAACTGTCCGCCAAAT 57.503 45.000 1.73 0.00 0.00 2.32
1702 1853 3.627395 ATCAGAACTGTCCGCCAAATA 57.373 42.857 1.73 0.00 0.00 1.40
1703 1854 2.695359 TCAGAACTGTCCGCCAAATAC 58.305 47.619 1.73 0.00 0.00 1.89
1704 1855 1.393539 CAGAACTGTCCGCCAAATACG 59.606 52.381 0.00 0.00 0.00 3.06
1705 1856 1.274167 AGAACTGTCCGCCAAATACGA 59.726 47.619 0.00 0.00 0.00 3.43
1706 1857 2.070783 GAACTGTCCGCCAAATACGAA 58.929 47.619 0.00 0.00 0.00 3.85
1707 1858 1.722011 ACTGTCCGCCAAATACGAAG 58.278 50.000 0.00 0.00 0.00 3.79
1708 1859 1.006832 CTGTCCGCCAAATACGAAGG 58.993 55.000 0.00 0.00 0.00 3.46
1709 1860 0.609151 TGTCCGCCAAATACGAAGGA 59.391 50.000 0.00 0.00 0.00 3.36
1710 1861 1.287425 GTCCGCCAAATACGAAGGAG 58.713 55.000 0.00 0.00 0.00 3.69
1711 1862 1.134907 GTCCGCCAAATACGAAGGAGA 60.135 52.381 0.00 0.00 0.00 3.71
1712 1863 1.134907 TCCGCCAAATACGAAGGAGAC 60.135 52.381 0.00 0.00 0.00 3.36
1713 1864 1.287425 CGCCAAATACGAAGGAGACC 58.713 55.000 0.00 0.00 0.00 3.85
1714 1865 1.404986 CGCCAAATACGAAGGAGACCA 60.405 52.381 0.00 0.00 0.00 4.02
1715 1866 2.706890 GCCAAATACGAAGGAGACCAA 58.293 47.619 0.00 0.00 0.00 3.67
1716 1867 3.279434 GCCAAATACGAAGGAGACCAAT 58.721 45.455 0.00 0.00 0.00 3.16
1717 1868 4.448210 GCCAAATACGAAGGAGACCAATA 58.552 43.478 0.00 0.00 0.00 1.90
1718 1869 4.879545 GCCAAATACGAAGGAGACCAATAA 59.120 41.667 0.00 0.00 0.00 1.40
1719 1870 5.355910 GCCAAATACGAAGGAGACCAATAAA 59.644 40.000 0.00 0.00 0.00 1.40
1720 1871 6.677187 GCCAAATACGAAGGAGACCAATAAAC 60.677 42.308 0.00 0.00 0.00 2.01
1721 1872 6.183360 CCAAATACGAAGGAGACCAATAAACC 60.183 42.308 0.00 0.00 0.00 3.27
1722 1873 5.687166 ATACGAAGGAGACCAATAAACCA 57.313 39.130 0.00 0.00 0.00 3.67
1723 1874 3.939066 ACGAAGGAGACCAATAAACCAG 58.061 45.455 0.00 0.00 0.00 4.00
1724 1875 3.581332 ACGAAGGAGACCAATAAACCAGA 59.419 43.478 0.00 0.00 0.00 3.86
1725 1876 4.041198 ACGAAGGAGACCAATAAACCAGAA 59.959 41.667 0.00 0.00 0.00 3.02
1726 1877 4.392138 CGAAGGAGACCAATAAACCAGAAC 59.608 45.833 0.00 0.00 0.00 3.01
1727 1878 3.939066 AGGAGACCAATAAACCAGAACG 58.061 45.455 0.00 0.00 0.00 3.95
1728 1879 3.007635 GGAGACCAATAAACCAGAACGG 58.992 50.000 0.00 0.00 42.50 4.44
1729 1880 3.307199 GGAGACCAATAAACCAGAACGGA 60.307 47.826 0.00 0.00 38.63 4.69
1730 1881 3.933332 GAGACCAATAAACCAGAACGGAG 59.067 47.826 0.00 0.00 38.63 4.63
1731 1882 3.007635 GACCAATAAACCAGAACGGAGG 58.992 50.000 0.00 0.00 38.63 4.30
1732 1883 1.743394 CCAATAAACCAGAACGGAGGC 59.257 52.381 0.00 0.00 38.63 4.70
1733 1884 2.432444 CAATAAACCAGAACGGAGGCA 58.568 47.619 0.00 0.00 38.63 4.75
1734 1885 2.403252 ATAAACCAGAACGGAGGCAG 57.597 50.000 0.00 0.00 38.63 4.85
1735 1886 1.053424 TAAACCAGAACGGAGGCAGT 58.947 50.000 0.00 0.00 38.63 4.40
1736 1887 1.053424 AAACCAGAACGGAGGCAGTA 58.947 50.000 0.00 0.00 38.63 2.74
1737 1888 0.320697 AACCAGAACGGAGGCAGTAC 59.679 55.000 0.00 0.00 38.63 2.73
1738 1889 1.218316 CCAGAACGGAGGCAGTACC 59.782 63.158 0.00 0.00 36.56 3.34
1751 1902 1.394917 GCAGTACCTCTCAACAATGCG 59.605 52.381 0.00 0.00 0.00 4.73
1761 1915 4.130857 TCTCAACAATGCGGTTCAGTTAA 58.869 39.130 0.00 0.00 0.00 2.01
1762 1916 4.576873 TCTCAACAATGCGGTTCAGTTAAA 59.423 37.500 0.00 0.00 0.00 1.52
1770 1924 3.242518 GCGGTTCAGTTAAAAGATTGCC 58.757 45.455 0.00 0.00 0.00 4.52
1771 1925 3.057526 GCGGTTCAGTTAAAAGATTGCCT 60.058 43.478 0.00 0.00 0.00 4.75
1778 1932 8.957466 GTTCAGTTAAAAGATTGCCTATTACCT 58.043 33.333 0.00 0.00 0.00 3.08
1780 1934 7.556275 TCAGTTAAAAGATTGCCTATTACCTGG 59.444 37.037 0.00 0.00 0.00 4.45
1785 1942 6.521527 AAGATTGCCTATTACCTGGAGAAT 57.478 37.500 0.00 2.20 0.00 2.40
1787 1944 4.336889 TTGCCTATTACCTGGAGAATCG 57.663 45.455 0.00 0.00 34.37 3.34
1789 1946 2.633481 GCCTATTACCTGGAGAATCGGT 59.367 50.000 0.00 0.00 34.37 4.69
1793 1950 6.221659 CCTATTACCTGGAGAATCGGTTAAC 58.778 44.000 0.00 0.00 34.37 2.01
1814 2096 2.719556 CGATAACGCGACAGGATTAGTG 59.280 50.000 15.93 0.00 0.00 2.74
1844 2158 6.932901 ACATTTCTTTGTACATTCATTGCG 57.067 33.333 0.00 0.00 0.00 4.85
1946 2263 4.630069 ACATGTGTAAAACGCCTCTCATAC 59.370 41.667 0.00 0.00 0.00 2.39
1947 2264 3.247442 TGTGTAAAACGCCTCTCATACG 58.753 45.455 0.00 0.00 0.00 3.06
1955 2272 0.387878 GCCTCTCATACGCGGATCAG 60.388 60.000 12.47 2.23 0.00 2.90
1971 2288 4.584743 CGGATCAGGCAGGCTATATATACA 59.415 45.833 0.00 0.00 0.00 2.29
1982 2299 8.037758 GCAGGCTATATATACACATTCAGTTCT 58.962 37.037 0.00 0.00 0.00 3.01
1992 2309 1.610038 CATTCAGTTCTGGTTGCTGCA 59.390 47.619 0.00 0.00 0.00 4.41
2039 2356 9.154847 GAAAGATCAAAACTGGGGATTTATTTG 57.845 33.333 0.00 0.00 0.00 2.32
2105 2424 7.411486 TGTTCAAAAGGGAGTTATCACAAAA 57.589 32.000 0.00 0.00 0.00 2.44
2110 2429 8.482128 TCAAAAGGGAGTTATCACAAAATGTTT 58.518 29.630 0.00 0.00 0.00 2.83
2134 2453 5.463154 ACATCCTAGGCAGTAGATTTCTCT 58.537 41.667 2.96 0.00 35.39 3.10
2140 2459 4.555689 AGGCAGTAGATTTCTCTGGAGAT 58.444 43.478 0.88 0.00 37.29 2.75
2145 2464 5.471797 CAGTAGATTTCTCTGGAGATAGCGA 59.528 44.000 0.88 0.00 37.29 4.93
2167 2486 6.037098 CGACTTGATTCTCCGACTAAGATTT 58.963 40.000 0.00 0.00 0.00 2.17
2227 2546 3.236391 TGGACGGCCAGTTCAGTT 58.764 55.556 5.41 0.00 39.92 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.153449 CGGACAGGTGTGTGTGTGT 60.153 57.895 0.00 0.00 36.88 3.72
18 19 2.203015 GCGGACAGGTGTGTGTGT 60.203 61.111 0.00 0.00 36.88 3.72
35 36 4.402528 TTCGTGTGGCCGGATGGG 62.403 66.667 5.05 0.00 39.58 4.00
37 38 3.487202 CGTTCGTGTGGCCGGATG 61.487 66.667 5.05 0.00 0.00 3.51
116 137 1.557832 TGGATAGAAACGGGAAGGGTG 59.442 52.381 0.00 0.00 0.00 4.61
117 138 1.961133 TGGATAGAAACGGGAAGGGT 58.039 50.000 0.00 0.00 0.00 4.34
201 224 2.514803 GTCAGGTTTTATGTGGTGGCT 58.485 47.619 0.00 0.00 0.00 4.75
234 257 1.443194 GCGCTGTTGATTGCAGGTG 60.443 57.895 0.00 0.00 34.73 4.00
314 340 0.175760 AGTCAGTTGTGCGTGTGAGT 59.824 50.000 0.00 0.00 0.00 3.41
315 341 0.578683 CAGTCAGTTGTGCGTGTGAG 59.421 55.000 0.00 0.00 0.00 3.51
316 342 0.174617 TCAGTCAGTTGTGCGTGTGA 59.825 50.000 0.00 0.00 0.00 3.58
340 367 6.464895 TTTTCTGTGCTGTTTTGTTTTCAG 57.535 33.333 0.00 0.00 0.00 3.02
341 368 5.107143 GCTTTTCTGTGCTGTTTTGTTTTCA 60.107 36.000 0.00 0.00 0.00 2.69
342 369 5.120674 AGCTTTTCTGTGCTGTTTTGTTTTC 59.879 36.000 0.00 0.00 38.21 2.29
346 373 3.874392 AGCTTTTCTGTGCTGTTTTGT 57.126 38.095 0.00 0.00 38.21 2.83
347 374 6.833342 AATAAGCTTTTCTGTGCTGTTTTG 57.167 33.333 3.20 0.00 39.71 2.44
353 380 8.850156 TCTTCTAAAAATAAGCTTTTCTGTGCT 58.150 29.630 3.20 0.00 41.82 4.40
358 385 9.355916 ACTGGTCTTCTAAAAATAAGCTTTTCT 57.644 29.630 3.20 0.00 31.15 2.52
520 578 1.008538 GTGTACGGGTCGACGTTGT 60.009 57.895 9.92 10.09 46.25 3.32
522 580 2.252260 CGTGTACGGGTCGACGTT 59.748 61.111 9.92 0.00 46.25 3.99
528 586 2.202222 CGTCGACGTGTACGGGTC 60.202 66.667 29.08 6.14 44.95 4.46
576 642 7.119699 ACGCATATCATGTCAGAAAAAGAAAGA 59.880 33.333 0.00 0.00 0.00 2.52
577 643 7.246311 ACGCATATCATGTCAGAAAAAGAAAG 58.754 34.615 0.00 0.00 0.00 2.62
578 644 7.144722 ACGCATATCATGTCAGAAAAAGAAA 57.855 32.000 0.00 0.00 0.00 2.52
579 645 6.183360 GGACGCATATCATGTCAGAAAAAGAA 60.183 38.462 0.00 0.00 34.32 2.52
620 700 3.041940 CGCCGTCGCTTTCTTGGT 61.042 61.111 0.00 0.00 0.00 3.67
852 934 3.966215 CACCAGTGCTACCGGTTG 58.034 61.111 15.04 13.30 0.00 3.77
890 972 1.090625 ACGAGACGAGACGAGATGGG 61.091 60.000 0.00 0.00 0.00 4.00
891 973 0.302288 GACGAGACGAGACGAGATGG 59.698 60.000 0.00 0.00 0.00 3.51
892 974 1.256895 GAGACGAGACGAGACGAGATG 59.743 57.143 0.00 0.00 0.00 2.90
893 975 1.135053 TGAGACGAGACGAGACGAGAT 60.135 52.381 0.00 0.00 0.00 2.75
894 976 0.243095 TGAGACGAGACGAGACGAGA 59.757 55.000 0.00 0.00 0.00 4.04
895 977 1.256895 GATGAGACGAGACGAGACGAG 59.743 57.143 0.00 0.00 0.00 4.18
896 978 1.279152 GATGAGACGAGACGAGACGA 58.721 55.000 0.00 0.00 0.00 4.20
908 990 2.278013 GACGACCGCCGATGAGAC 60.278 66.667 0.00 0.00 41.76 3.36
937 1019 2.203056 TTGCGCCTCCGGATGATG 60.203 61.111 11.34 3.09 33.87 3.07
938 1020 1.971505 TTCTTGCGCCTCCGGATGAT 61.972 55.000 11.34 0.00 38.40 2.45
939 1021 2.178876 TTTCTTGCGCCTCCGGATGA 62.179 55.000 11.34 0.00 37.23 2.92
953 1035 4.071423 GGCTTCTTCTTCTGAGCTTTCTT 58.929 43.478 0.00 0.00 0.00 2.52
960 1042 2.333014 GACGTGGCTTCTTCTTCTGAG 58.667 52.381 0.00 0.00 0.00 3.35
983 1065 3.711541 ATCGCCGGACCTTACGTGC 62.712 63.158 5.05 0.00 0.00 5.34
984 1066 1.876714 CATCGCCGGACCTTACGTG 60.877 63.158 5.05 0.00 0.00 4.49
985 1067 2.493030 CATCGCCGGACCTTACGT 59.507 61.111 5.05 0.00 0.00 3.57
986 1068 2.279252 CCATCGCCGGACCTTACG 60.279 66.667 5.05 0.00 0.00 3.18
987 1069 1.067582 CTCCATCGCCGGACCTTAC 59.932 63.158 5.05 0.00 0.00 2.34
988 1070 0.685131 TTCTCCATCGCCGGACCTTA 60.685 55.000 5.05 0.00 0.00 2.69
989 1071 1.338136 ATTCTCCATCGCCGGACCTT 61.338 55.000 5.05 0.00 0.00 3.50
1294 1379 2.469826 CTAATACACGGCGAGATTGCA 58.530 47.619 16.62 0.00 36.28 4.08
1297 1382 4.602340 AATCCTAATACACGGCGAGATT 57.398 40.909 16.62 12.09 0.00 2.40
1298 1383 4.602340 AAATCCTAATACACGGCGAGAT 57.398 40.909 16.62 0.00 0.00 2.75
1304 1389 8.051901 AGGAAAAAGAAAATCCTAATACACGG 57.948 34.615 0.00 0.00 41.74 4.94
1328 1432 4.144297 TGGACAGGATCACCAAAGAAAAG 58.856 43.478 0.00 0.00 38.94 2.27
1356 1460 1.132462 AGATGATCCTCTGCCCCATCT 60.132 52.381 0.00 0.00 39.10 2.90
1387 1491 0.808847 GATGGGAACGACGCCCTAAC 60.809 60.000 11.28 0.00 46.19 2.34
1440 1548 5.028549 AGAGACTGACAACTCACACAAAT 57.971 39.130 10.55 0.00 35.83 2.32
1442 1550 4.433615 GAAGAGACTGACAACTCACACAA 58.566 43.478 10.55 0.00 35.83 3.33
1489 1597 3.652274 CAGCACCATCCAAAATTCGTTT 58.348 40.909 0.00 0.00 0.00 3.60
1491 1599 1.067635 GCAGCACCATCCAAAATTCGT 60.068 47.619 0.00 0.00 0.00 3.85
1492 1600 1.632422 GCAGCACCATCCAAAATTCG 58.368 50.000 0.00 0.00 0.00 3.34
1493 1601 1.067635 ACGCAGCACCATCCAAAATTC 60.068 47.619 0.00 0.00 0.00 2.17
1495 1603 0.968405 AACGCAGCACCATCCAAAAT 59.032 45.000 0.00 0.00 0.00 1.82
1536 1644 7.763985 TCTCTTTTCACAATCGCAGTCATAATA 59.236 33.333 0.00 0.00 0.00 0.98
1537 1645 6.595326 TCTCTTTTCACAATCGCAGTCATAAT 59.405 34.615 0.00 0.00 0.00 1.28
1543 1651 4.516698 ACAATCTCTTTTCACAATCGCAGT 59.483 37.500 0.00 0.00 0.00 4.40
1565 1673 4.685628 GCTCTGATCTAAAGCTCTATGCAC 59.314 45.833 0.00 0.00 45.94 4.57
1588 1701 2.158986 CCTTGAGACCCATAGCACAGAG 60.159 54.545 0.00 0.00 0.00 3.35
1605 1718 6.348050 GCAAGATAAGAAGAGTTGACACCTTG 60.348 42.308 0.00 0.00 0.00 3.61
1609 1722 5.121454 CAGGCAAGATAAGAAGAGTTGACAC 59.879 44.000 0.00 0.00 0.00 3.67
1663 1814 3.562141 TGATTTATTGGTATTGGCGGACG 59.438 43.478 0.00 0.00 0.00 4.79
1665 1816 5.042463 TCTGATTTATTGGTATTGGCGGA 57.958 39.130 0.00 0.00 0.00 5.54
1666 1817 5.299279 AGTTCTGATTTATTGGTATTGGCGG 59.701 40.000 0.00 0.00 0.00 6.13
1667 1818 6.183360 ACAGTTCTGATTTATTGGTATTGGCG 60.183 38.462 6.83 0.00 0.00 5.69
1668 1819 7.100458 ACAGTTCTGATTTATTGGTATTGGC 57.900 36.000 6.83 0.00 0.00 4.52
1669 1820 7.467267 CGGACAGTTCTGATTTATTGGTATTGG 60.467 40.741 6.83 0.00 0.00 3.16
1670 1821 7.409697 CGGACAGTTCTGATTTATTGGTATTG 58.590 38.462 6.83 0.00 0.00 1.90
1671 1822 6.038271 GCGGACAGTTCTGATTTATTGGTATT 59.962 38.462 6.83 0.00 0.00 1.89
1672 1823 5.527582 GCGGACAGTTCTGATTTATTGGTAT 59.472 40.000 6.83 0.00 0.00 2.73
1673 1824 4.873827 GCGGACAGTTCTGATTTATTGGTA 59.126 41.667 6.83 0.00 0.00 3.25
1674 1825 3.689649 GCGGACAGTTCTGATTTATTGGT 59.310 43.478 6.83 0.00 0.00 3.67
1675 1826 3.065371 GGCGGACAGTTCTGATTTATTGG 59.935 47.826 6.83 0.00 0.00 3.16
1676 1827 3.689161 TGGCGGACAGTTCTGATTTATTG 59.311 43.478 6.83 0.00 0.00 1.90
1677 1828 3.950397 TGGCGGACAGTTCTGATTTATT 58.050 40.909 6.83 0.00 0.00 1.40
1678 1829 3.627395 TGGCGGACAGTTCTGATTTAT 57.373 42.857 6.83 0.00 0.00 1.40
1679 1830 3.410631 TTGGCGGACAGTTCTGATTTA 57.589 42.857 6.83 0.00 0.00 1.40
1680 1831 2.270352 TTGGCGGACAGTTCTGATTT 57.730 45.000 6.83 0.00 0.00 2.17
1681 1832 2.270352 TTTGGCGGACAGTTCTGATT 57.730 45.000 6.83 0.00 0.00 2.57
1682 1833 2.496899 ATTTGGCGGACAGTTCTGAT 57.503 45.000 6.83 0.00 0.00 2.90
1683 1834 2.695359 GTATTTGGCGGACAGTTCTGA 58.305 47.619 6.83 0.00 0.00 3.27
1684 1835 1.393539 CGTATTTGGCGGACAGTTCTG 59.606 52.381 0.00 0.00 0.00 3.02
1685 1836 1.274167 TCGTATTTGGCGGACAGTTCT 59.726 47.619 0.00 0.00 0.00 3.01
1686 1837 1.717194 TCGTATTTGGCGGACAGTTC 58.283 50.000 0.00 0.00 0.00 3.01
1687 1838 2.073816 CTTCGTATTTGGCGGACAGTT 58.926 47.619 0.00 0.00 0.00 3.16
1688 1839 1.674817 CCTTCGTATTTGGCGGACAGT 60.675 52.381 0.00 0.00 0.00 3.55
1689 1840 1.006832 CCTTCGTATTTGGCGGACAG 58.993 55.000 0.00 0.00 0.00 3.51
1690 1841 0.609151 TCCTTCGTATTTGGCGGACA 59.391 50.000 0.00 0.00 0.00 4.02
1691 1842 1.134907 TCTCCTTCGTATTTGGCGGAC 60.135 52.381 0.00 0.00 0.00 4.79
1692 1843 1.134907 GTCTCCTTCGTATTTGGCGGA 60.135 52.381 0.00 0.00 0.00 5.54
1693 1844 1.287425 GTCTCCTTCGTATTTGGCGG 58.713 55.000 0.00 0.00 0.00 6.13
1694 1845 1.287425 GGTCTCCTTCGTATTTGGCG 58.713 55.000 0.00 0.00 0.00 5.69
1695 1846 2.396590 TGGTCTCCTTCGTATTTGGC 57.603 50.000 0.00 0.00 0.00 4.52
1696 1847 6.183360 GGTTTATTGGTCTCCTTCGTATTTGG 60.183 42.308 0.00 0.00 0.00 3.28
1697 1848 6.373216 TGGTTTATTGGTCTCCTTCGTATTTG 59.627 38.462 0.00 0.00 0.00 2.32
1698 1849 6.478129 TGGTTTATTGGTCTCCTTCGTATTT 58.522 36.000 0.00 0.00 0.00 1.40
1699 1850 6.057321 TGGTTTATTGGTCTCCTTCGTATT 57.943 37.500 0.00 0.00 0.00 1.89
1700 1851 5.424252 TCTGGTTTATTGGTCTCCTTCGTAT 59.576 40.000 0.00 0.00 0.00 3.06
1701 1852 4.773674 TCTGGTTTATTGGTCTCCTTCGTA 59.226 41.667 0.00 0.00 0.00 3.43
1702 1853 3.581332 TCTGGTTTATTGGTCTCCTTCGT 59.419 43.478 0.00 0.00 0.00 3.85
1703 1854 4.202245 TCTGGTTTATTGGTCTCCTTCG 57.798 45.455 0.00 0.00 0.00 3.79
1704 1855 4.392138 CGTTCTGGTTTATTGGTCTCCTTC 59.608 45.833 0.00 0.00 0.00 3.46
1705 1856 4.324267 CGTTCTGGTTTATTGGTCTCCTT 58.676 43.478 0.00 0.00 0.00 3.36
1706 1857 3.307480 CCGTTCTGGTTTATTGGTCTCCT 60.307 47.826 0.00 0.00 0.00 3.69
1707 1858 3.007635 CCGTTCTGGTTTATTGGTCTCC 58.992 50.000 0.00 0.00 0.00 3.71
1708 1859 3.933332 CTCCGTTCTGGTTTATTGGTCTC 59.067 47.826 0.00 0.00 39.52 3.36
1709 1860 3.307480 CCTCCGTTCTGGTTTATTGGTCT 60.307 47.826 0.00 0.00 39.52 3.85
1710 1861 3.007635 CCTCCGTTCTGGTTTATTGGTC 58.992 50.000 0.00 0.00 39.52 4.02
1711 1862 2.878526 GCCTCCGTTCTGGTTTATTGGT 60.879 50.000 0.00 0.00 39.52 3.67
1712 1863 1.743394 GCCTCCGTTCTGGTTTATTGG 59.257 52.381 0.00 0.00 39.52 3.16
1713 1864 2.420022 CTGCCTCCGTTCTGGTTTATTG 59.580 50.000 0.00 0.00 39.52 1.90
1714 1865 2.039879 ACTGCCTCCGTTCTGGTTTATT 59.960 45.455 0.00 0.00 39.52 1.40
1715 1866 1.628846 ACTGCCTCCGTTCTGGTTTAT 59.371 47.619 0.00 0.00 39.52 1.40
1716 1867 1.053424 ACTGCCTCCGTTCTGGTTTA 58.947 50.000 0.00 0.00 39.52 2.01
1717 1868 1.053424 TACTGCCTCCGTTCTGGTTT 58.947 50.000 0.00 0.00 39.52 3.27
1718 1869 0.320697 GTACTGCCTCCGTTCTGGTT 59.679 55.000 0.00 0.00 39.52 3.67
1719 1870 1.542187 GGTACTGCCTCCGTTCTGGT 61.542 60.000 0.00 0.00 39.52 4.00
1720 1871 1.218316 GGTACTGCCTCCGTTCTGG 59.782 63.158 0.00 0.00 40.09 3.86
1721 1872 2.277858 AGGTACTGCCTCCGTTCTG 58.722 57.895 0.00 0.00 46.96 3.02
1722 1873 4.867847 AGGTACTGCCTCCGTTCT 57.132 55.556 0.00 0.00 46.96 3.01
1730 1881 1.740025 GCATTGTTGAGAGGTACTGCC 59.260 52.381 0.00 0.00 41.55 4.85
1731 1882 1.394917 CGCATTGTTGAGAGGTACTGC 59.605 52.381 0.00 0.00 41.55 4.40
1732 1883 2.002586 CCGCATTGTTGAGAGGTACTG 58.997 52.381 0.00 0.00 41.55 2.74
1734 1885 2.094762 ACCGCATTGTTGAGAGGTAC 57.905 50.000 0.00 0.00 0.00 3.34
1735 1886 2.037902 TGAACCGCATTGTTGAGAGGTA 59.962 45.455 0.00 0.00 0.00 3.08
1736 1887 1.202758 TGAACCGCATTGTTGAGAGGT 60.203 47.619 0.00 0.00 0.00 3.85
1737 1888 1.466167 CTGAACCGCATTGTTGAGAGG 59.534 52.381 0.00 0.00 32.02 3.69
1738 1889 2.146342 ACTGAACCGCATTGTTGAGAG 58.854 47.619 4.65 0.00 33.76 3.20
1739 1890 2.254546 ACTGAACCGCATTGTTGAGA 57.745 45.000 4.65 0.00 33.76 3.27
1751 1902 8.188799 GGTAATAGGCAATCTTTTAACTGAACC 58.811 37.037 0.00 0.00 0.00 3.62
1761 1915 5.975988 TCTCCAGGTAATAGGCAATCTTT 57.024 39.130 0.00 0.00 0.00 2.52
1762 1916 5.975988 TTCTCCAGGTAATAGGCAATCTT 57.024 39.130 0.00 0.00 0.00 2.40
1770 1924 5.919141 CGTTAACCGATTCTCCAGGTAATAG 59.081 44.000 0.00 0.00 37.26 1.73
1771 1925 5.593909 TCGTTAACCGATTCTCCAGGTAATA 59.406 40.000 0.00 0.00 41.60 0.98
1787 1944 1.585214 CCTGTCGCGTTATCGTTAACC 59.415 52.381 5.77 3.71 39.49 2.85
1789 1946 2.917701 TCCTGTCGCGTTATCGTTAA 57.082 45.000 5.77 0.00 39.49 2.01
1793 1950 2.719556 CACTAATCCTGTCGCGTTATCG 59.280 50.000 5.77 0.00 40.37 2.92
1800 1957 1.726853 AGTTGCACTAATCCTGTCGC 58.273 50.000 0.00 0.00 0.00 5.19
1814 2096 8.795786 TGAATGTACAAAGAAATGTAAGTTGC 57.204 30.769 0.00 0.00 37.52 4.17
1885 2202 6.884832 TGTGTTAGTATTAGATCAAGGGGTG 58.115 40.000 0.00 0.00 0.00 4.61
1946 2263 1.877576 TATAGCCTGCCTGATCCGCG 61.878 60.000 0.00 0.00 0.00 6.46
1947 2264 0.539051 ATATAGCCTGCCTGATCCGC 59.461 55.000 0.00 0.00 0.00 5.54
1949 2266 5.363868 TGTGTATATATAGCCTGCCTGATCC 59.636 44.000 0.00 0.00 0.00 3.36
1955 2272 6.644347 ACTGAATGTGTATATATAGCCTGCC 58.356 40.000 0.00 0.00 0.00 4.85
1971 2288 1.610522 GCAGCAACCAGAACTGAATGT 59.389 47.619 3.19 0.00 33.10 2.71
1982 2299 2.954989 TCTATTTTGTGTGCAGCAACCA 59.045 40.909 0.00 0.00 0.00 3.67
1992 2309 7.505585 TCTTTCACCATTTCCTCTATTTTGTGT 59.494 33.333 0.00 0.00 0.00 3.72
2066 2385 9.626045 CCCTTTTGAACATTCAACTACTATTTC 57.374 33.333 6.55 0.00 45.99 2.17
2069 2388 8.164070 ACTCCCTTTTGAACATTCAACTACTAT 58.836 33.333 6.55 0.00 45.99 2.12
2070 2389 7.514721 ACTCCCTTTTGAACATTCAACTACTA 58.485 34.615 6.55 0.00 45.99 1.82
2071 2390 6.365520 ACTCCCTTTTGAACATTCAACTACT 58.634 36.000 6.55 0.00 45.99 2.57
2072 2391 6.635030 ACTCCCTTTTGAACATTCAACTAC 57.365 37.500 6.55 0.00 45.99 2.73
2073 2392 8.934023 ATAACTCCCTTTTGAACATTCAACTA 57.066 30.769 6.55 0.00 45.99 2.24
2074 2393 7.505585 TGATAACTCCCTTTTGAACATTCAACT 59.494 33.333 6.55 0.00 45.99 3.16
2075 2394 7.595130 GTGATAACTCCCTTTTGAACATTCAAC 59.405 37.037 6.55 0.00 45.99 3.18
2076 2395 7.286546 TGTGATAACTCCCTTTTGAACATTCAA 59.713 33.333 2.89 2.89 44.78 2.69
2077 2396 6.775142 TGTGATAACTCCCTTTTGAACATTCA 59.225 34.615 0.00 0.00 34.92 2.57
2078 2397 7.214467 TGTGATAACTCCCTTTTGAACATTC 57.786 36.000 0.00 0.00 0.00 2.67
2079 2398 7.595819 TTGTGATAACTCCCTTTTGAACATT 57.404 32.000 0.00 0.00 0.00 2.71
2080 2399 7.595819 TTTGTGATAACTCCCTTTTGAACAT 57.404 32.000 0.00 0.00 0.00 2.71
2082 2401 7.926018 ACATTTTGTGATAACTCCCTTTTGAAC 59.074 33.333 0.00 0.00 0.00 3.18
2083 2402 8.017418 ACATTTTGTGATAACTCCCTTTTGAA 57.983 30.769 0.00 0.00 0.00 2.69
2084 2403 7.595819 ACATTTTGTGATAACTCCCTTTTGA 57.404 32.000 0.00 0.00 0.00 2.69
2085 2404 8.661352 AAACATTTTGTGATAACTCCCTTTTG 57.339 30.769 0.00 0.00 0.00 2.44
2086 2405 9.758651 GTAAACATTTTGTGATAACTCCCTTTT 57.241 29.630 0.00 0.00 0.00 2.27
2090 2409 7.973944 GGATGTAAACATTTTGTGATAACTCCC 59.026 37.037 0.00 0.00 36.57 4.30
2105 2424 7.380423 AATCTACTGCCTAGGATGTAAACAT 57.620 36.000 14.75 0.00 39.70 2.71
2110 2429 6.491745 CAGAGAAATCTACTGCCTAGGATGTA 59.508 42.308 14.75 12.97 0.00 2.29
2134 2453 4.576216 GAGAATCAAGTCGCTATCTCCA 57.424 45.455 0.00 0.00 33.17 3.86
2140 2459 2.366533 AGTCGGAGAATCAAGTCGCTA 58.633 47.619 0.00 0.00 39.69 4.26
2145 2464 6.092807 GCAAAATCTTAGTCGGAGAATCAAGT 59.907 38.462 0.00 0.00 39.69 3.16
2167 2486 2.003196 TGCTCGTCGACATAATGCAA 57.997 45.000 17.16 1.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.