Multiple sequence alignment - TraesCS6D01G239000

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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 TraesCS6D01G239000 chr6D 100.000 2351 0 0 1 2351 339394436 339396786 0.000000e+00 4342
1 TraesCS6D01G239000 chr2D 95.781 1683 68 3 1 1681 593126539 593128220 0.000000e+00 2712
2 TraesCS6D01G239000 chr2D 95.207 1690 73 6 1 1685 305961103 305959417 0.000000e+00 2665
3 TraesCS6D01G239000 chr2D 92.500 80 5 1 1747 1826 522903896 522903974 1.910000e-21 113
4 TraesCS6D01G239000 chr7D 95.730 1686 62 5 1 1681 31418820 31420500 0.000000e+00 2706
5 TraesCS6D01G239000 chr7D 95.258 1687 75 5 1 1684 589251033 589249349 0.000000e+00 2667
6 TraesCS6D01G239000 chr7D 95.015 1685 81 3 1 1684 16646481 16644799 0.000000e+00 2643
7 TraesCS6D01G239000 chr7D 96.203 79 2 1 1747 1825 495331165 495331088 6.820000e-26 128
8 TraesCS6D01G239000 chrUn 95.490 1685 74 2 1 1684 241760751 241759068 0.000000e+00 2689
9 TraesCS6D01G239000 chr5D 95.306 1683 76 3 1 1681 54749559 54751240 0.000000e+00 2667
10 TraesCS6D01G239000 chr4D 95.006 1682 82 2 1 1681 441127901 441129581 0.000000e+00 2639
11 TraesCS6D01G239000 chr3D 94.864 1694 79 4 1 1692 234618662 234620349 0.000000e+00 2639
12 TraesCS6D01G239000 chr2B 83.397 524 66 8 1848 2351 672710699 672711221 1.270000e-127 466
13 TraesCS6D01G239000 chr4B 92.500 80 5 1 1747 1826 593368233 593368311 1.910000e-21 113
14 TraesCS6D01G239000 chr1B 92.500 80 5 1 1747 1826 152318960 152319038 1.910000e-21 113
15 TraesCS6D01G239000 chr7A 91.250 80 6 1 1747 1826 238592920 238592998 8.880000e-20 108
16 TraesCS6D01G239000 chr7B 92.105 76 5 1 1751 1826 679785526 679785600 3.200000e-19 106
17 TraesCS6D01G239000 chr2A 90.123 81 7 1 1747 1827 270832142 270832063 1.150000e-18 104


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 TraesCS6D01G239000 chr6D 339394436 339396786 2350 False 4342 4342 100.000 1 2351 1 chr6D.!!$F1 2350
1 TraesCS6D01G239000 chr2D 593126539 593128220 1681 False 2712 2712 95.781 1 1681 1 chr2D.!!$F2 1680
2 TraesCS6D01G239000 chr2D 305959417 305961103 1686 True 2665 2665 95.207 1 1685 1 chr2D.!!$R1 1684
3 TraesCS6D01G239000 chr7D 31418820 31420500 1680 False 2706 2706 95.730 1 1681 1 chr7D.!!$F1 1680
4 TraesCS6D01G239000 chr7D 589249349 589251033 1684 True 2667 2667 95.258 1 1684 1 chr7D.!!$R3 1683
5 TraesCS6D01G239000 chr7D 16644799 16646481 1682 True 2643 2643 95.015 1 1684 1 chr7D.!!$R1 1683
6 TraesCS6D01G239000 chrUn 241759068 241760751 1683 True 2689 2689 95.490 1 1684 1 chrUn.!!$R1 1683
7 TraesCS6D01G239000 chr5D 54749559 54751240 1681 False 2667 2667 95.306 1 1681 1 chr5D.!!$F1 1680
8 TraesCS6D01G239000 chr4D 441127901 441129581 1680 False 2639 2639 95.006 1 1681 1 chr4D.!!$F1 1680
9 TraesCS6D01G239000 chr3D 234618662 234620349 1687 False 2639 2639 94.864 1 1692 1 chr3D.!!$F1 1691
10 TraesCS6D01G239000 chr2B 672710699 672711221 522 False 466 466 83.397 1848 2351 1 chr2B.!!$F1 503

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
847 848 0.107017 GTCCTGCTGCACCCACATAT 60.107 55.0 0.0 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1831 0.037734 GGAGGGAGCGGGAAAGAAAA 59.962 55.0 0.0 0.0 0.0 2.29 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
49 50 1.980052 CCGGTGTCCATGTACCAGT 59.020 57.895 10.48 0.00 36.76 4.00
227 228 2.749865 CGTCGTTGCCGATGCCAAT 61.750 57.895 0.00 0.00 46.30 3.16
543 544 0.179181 GATTGTCGTAGTCGGCGTCA 60.179 55.000 6.85 0.00 45.30 4.35
598 599 0.812412 GCTAAGCGGCCGACCAATAA 60.812 55.000 33.48 4.88 34.57 1.40
603 604 1.310216 GCGGCCGACCAATAAAGGTT 61.310 55.000 33.48 0.00 43.38 3.50
747 748 4.631740 TCCAGGGTCGTCCAGGCA 62.632 66.667 0.04 0.00 41.58 4.75
751 752 3.083997 GGGTCGTCCAGGCATCCT 61.084 66.667 0.04 0.00 35.00 3.24
847 848 0.107017 GTCCTGCTGCACCCACATAT 60.107 55.000 0.00 0.00 0.00 1.78
909 910 2.034532 TGCGGAGGACACGGTAGA 59.965 61.111 0.00 0.00 0.00 2.59
938 939 1.410004 ACAAACACGAGGAGAGACCA 58.590 50.000 0.00 0.00 42.04 4.02
989 990 2.547218 GCCAGAACAAGTAGTTGTCCGA 60.547 50.000 16.16 0.00 46.68 4.55
1035 1036 4.324991 AAGTGGAACGGCCCGGTC 62.325 66.667 14.15 14.15 45.86 4.79
1071 1072 2.517875 GCAGGGATGATTGGCGCT 60.518 61.111 7.64 0.00 0.00 5.92
1395 1397 2.610859 GGGAGGTTGAGGAGGGCA 60.611 66.667 0.00 0.00 0.00 5.36
1548 1551 6.445451 ACCTAGGTTAGACTCGATACCATA 57.555 41.667 9.21 0.00 33.02 2.74
1681 1689 5.041940 GGGCTACAATACGAAGTCTAACAG 58.958 45.833 0.00 0.00 43.93 3.16
1685 1693 6.810182 GCTACAATACGAAGTCTAACAGGAAA 59.190 38.462 0.00 0.00 43.93 3.13
1686 1694 7.201418 GCTACAATACGAAGTCTAACAGGAAAC 60.201 40.741 0.00 0.00 43.93 2.78
1687 1695 5.632347 ACAATACGAAGTCTAACAGGAAACG 59.368 40.000 0.00 0.00 43.93 3.60
1688 1696 3.722728 ACGAAGTCTAACAGGAAACGT 57.277 42.857 0.00 0.00 29.74 3.99
1690 1698 2.655474 CGAAGTCTAACAGGAAACGTCG 59.345 50.000 0.00 0.00 37.31 5.12
1691 1699 3.636381 GAAGTCTAACAGGAAACGTCGT 58.364 45.455 0.00 0.00 0.00 4.34
1692 1700 4.611355 CGAAGTCTAACAGGAAACGTCGTA 60.611 45.833 0.00 0.00 38.32 3.43
1693 1701 5.382618 AAGTCTAACAGGAAACGTCGTAT 57.617 39.130 0.00 0.00 0.00 3.06
1694 1702 4.730657 AGTCTAACAGGAAACGTCGTATG 58.269 43.478 0.00 0.00 0.00 2.39
1695 1703 3.302699 GTCTAACAGGAAACGTCGTATGC 59.697 47.826 0.00 0.00 0.00 3.14
1696 1704 2.157834 AACAGGAAACGTCGTATGCA 57.842 45.000 0.00 0.00 0.00 3.96
1697 1705 2.380084 ACAGGAAACGTCGTATGCAT 57.620 45.000 3.79 3.79 0.00 3.96
1698 1706 1.999735 ACAGGAAACGTCGTATGCATG 59.000 47.619 10.16 1.78 0.00 4.06
1699 1707 1.999735 CAGGAAACGTCGTATGCATGT 59.000 47.619 10.16 0.00 0.00 3.21
1700 1708 2.029244 CAGGAAACGTCGTATGCATGTC 59.971 50.000 10.16 1.37 0.00 3.06
1701 1709 1.006391 GGAAACGTCGTATGCATGTCG 60.006 52.381 10.16 14.02 0.00 4.35
1702 1710 1.652124 GAAACGTCGTATGCATGTCGT 59.348 47.619 10.16 11.38 37.09 4.34
1703 1711 1.265568 AACGTCGTATGCATGTCGTC 58.734 50.000 10.16 10.72 34.96 4.20
1704 1712 0.450583 ACGTCGTATGCATGTCGTCT 59.549 50.000 10.16 0.78 31.20 4.18
1705 1713 1.667212 ACGTCGTATGCATGTCGTCTA 59.333 47.619 10.16 0.00 31.20 2.59
1706 1714 2.096335 ACGTCGTATGCATGTCGTCTAA 59.904 45.455 10.16 0.00 31.20 2.10
1707 1715 3.103007 CGTCGTATGCATGTCGTCTAAA 58.897 45.455 10.16 0.00 0.00 1.85
1708 1716 3.544682 CGTCGTATGCATGTCGTCTAAAA 59.455 43.478 10.16 0.00 0.00 1.52
1709 1717 4.030865 CGTCGTATGCATGTCGTCTAAAAA 59.969 41.667 10.16 0.00 0.00 1.94
1740 1748 5.847304 CTGTATAGCAGTGCTAATCCTTGA 58.153 41.667 27.75 5.63 44.62 3.02
1741 1749 6.425210 TGTATAGCAGTGCTAATCCTTGAT 57.575 37.500 27.75 12.85 44.62 2.57
1742 1750 6.830912 TGTATAGCAGTGCTAATCCTTGATT 58.169 36.000 27.75 11.16 44.62 2.57
1743 1751 7.282585 TGTATAGCAGTGCTAATCCTTGATTT 58.717 34.615 27.75 10.46 44.62 2.17
1744 1752 4.978083 AGCAGTGCTAATCCTTGATTTG 57.022 40.909 18.11 0.00 36.99 2.32
1745 1753 4.338879 AGCAGTGCTAATCCTTGATTTGT 58.661 39.130 18.11 0.00 36.99 2.83
1746 1754 5.500234 AGCAGTGCTAATCCTTGATTTGTA 58.500 37.500 18.11 0.00 36.99 2.41
1747 1755 5.355350 AGCAGTGCTAATCCTTGATTTGTAC 59.645 40.000 18.11 9.95 39.20 2.90
1748 1756 5.123820 GCAGTGCTAATCCTTGATTTGTACA 59.876 40.000 8.18 0.00 40.40 2.90
1749 1757 6.546395 CAGTGCTAATCCTTGATTTGTACAC 58.454 40.000 16.58 9.76 40.40 2.90
1750 1758 6.149308 CAGTGCTAATCCTTGATTTGTACACA 59.851 38.462 16.58 0.00 40.40 3.72
1751 1759 6.714810 AGTGCTAATCCTTGATTTGTACACAA 59.285 34.615 16.58 0.00 40.40 3.33
1752 1760 7.394359 AGTGCTAATCCTTGATTTGTACACAAT 59.606 33.333 16.58 0.00 40.40 2.71
1753 1761 8.028938 GTGCTAATCCTTGATTTGTACACAATT 58.971 33.333 12.00 0.00 38.95 2.32
1754 1762 9.237187 TGCTAATCCTTGATTTGTACACAATTA 57.763 29.630 0.00 0.00 35.55 1.40
1759 1767 9.920946 ATCCTTGATTTGTACACAATTATACCT 57.079 29.630 0.00 0.00 35.55 3.08
1760 1768 9.173021 TCCTTGATTTGTACACAATTATACCTG 57.827 33.333 0.00 0.00 35.55 4.00
1761 1769 8.405531 CCTTGATTTGTACACAATTATACCTGG 58.594 37.037 0.00 0.00 35.55 4.45
1762 1770 9.173021 CTTGATTTGTACACAATTATACCTGGA 57.827 33.333 0.00 0.00 35.55 3.86
1763 1771 9.693739 TTGATTTGTACACAATTATACCTGGAT 57.306 29.630 0.00 0.00 35.55 3.41
1770 1778 9.924650 GTACACAATTATACCTGGATACTTAGG 57.075 37.037 0.00 0.00 40.01 2.69
1771 1779 8.792830 ACACAATTATACCTGGATACTTAGGA 57.207 34.615 0.00 0.00 37.52 2.94
1772 1780 9.220906 ACACAATTATACCTGGATACTTAGGAA 57.779 33.333 0.00 0.00 37.52 3.36
1773 1781 9.712305 CACAATTATACCTGGATACTTAGGAAG 57.288 37.037 0.00 0.00 37.52 3.46
1774 1782 8.881262 ACAATTATACCTGGATACTTAGGAAGG 58.119 37.037 0.00 0.00 37.52 3.46
1775 1783 8.322091 CAATTATACCTGGATACTTAGGAAGGG 58.678 40.741 0.00 0.00 37.52 3.95
1776 1784 3.797671 ACCTGGATACTTAGGAAGGGT 57.202 47.619 0.00 0.00 37.52 4.34
1777 1785 3.385115 ACCTGGATACTTAGGAAGGGTG 58.615 50.000 0.00 0.00 37.52 4.61
1778 1786 3.013648 ACCTGGATACTTAGGAAGGGTGA 59.986 47.826 0.00 0.00 37.52 4.02
1779 1787 3.643792 CCTGGATACTTAGGAAGGGTGAG 59.356 52.174 0.00 0.00 36.11 3.51
1780 1788 4.547671 CTGGATACTTAGGAAGGGTGAGA 58.452 47.826 0.00 0.00 37.61 3.27
1781 1789 4.955335 TGGATACTTAGGAAGGGTGAGAA 58.045 43.478 0.00 0.00 37.61 2.87
1782 1790 4.962995 TGGATACTTAGGAAGGGTGAGAAG 59.037 45.833 0.00 0.00 37.61 2.85
1783 1791 4.345547 GGATACTTAGGAAGGGTGAGAAGG 59.654 50.000 0.00 0.00 0.00 3.46
1784 1792 1.909986 ACTTAGGAAGGGTGAGAAGGC 59.090 52.381 0.00 0.00 0.00 4.35
1785 1793 0.902531 TTAGGAAGGGTGAGAAGGCG 59.097 55.000 0.00 0.00 0.00 5.52
1786 1794 0.040646 TAGGAAGGGTGAGAAGGCGA 59.959 55.000 0.00 0.00 0.00 5.54
1787 1795 1.219393 GGAAGGGTGAGAAGGCGAG 59.781 63.158 0.00 0.00 0.00 5.03
1788 1796 1.219393 GAAGGGTGAGAAGGCGAGG 59.781 63.158 0.00 0.00 0.00 4.63
1789 1797 1.536662 AAGGGTGAGAAGGCGAGGT 60.537 57.895 0.00 0.00 0.00 3.85
1790 1798 0.252103 AAGGGTGAGAAGGCGAGGTA 60.252 55.000 0.00 0.00 0.00 3.08
1791 1799 0.684805 AGGGTGAGAAGGCGAGGTAG 60.685 60.000 0.00 0.00 0.00 3.18
1792 1800 0.683504 GGGTGAGAAGGCGAGGTAGA 60.684 60.000 0.00 0.00 0.00 2.59
1793 1801 1.404843 GGTGAGAAGGCGAGGTAGAT 58.595 55.000 0.00 0.00 0.00 1.98
1794 1802 2.584236 GGTGAGAAGGCGAGGTAGATA 58.416 52.381 0.00 0.00 0.00 1.98
1795 1803 2.957006 GGTGAGAAGGCGAGGTAGATAA 59.043 50.000 0.00 0.00 0.00 1.75
1796 1804 3.243468 GGTGAGAAGGCGAGGTAGATAAC 60.243 52.174 0.00 0.00 0.00 1.89
1810 1818 5.070685 GGTAGATAACCCTTATGCCTTTGG 58.929 45.833 0.00 0.00 43.16 3.28
1811 1819 4.881157 AGATAACCCTTATGCCTTTGGT 57.119 40.909 0.00 0.00 0.00 3.67
1812 1820 4.536765 AGATAACCCTTATGCCTTTGGTG 58.463 43.478 0.00 0.00 0.00 4.17
1813 1821 2.990740 AACCCTTATGCCTTTGGTGA 57.009 45.000 0.00 0.00 0.00 4.02
1814 1822 2.514458 ACCCTTATGCCTTTGGTGAG 57.486 50.000 0.00 0.00 0.00 3.51
1815 1823 1.992557 ACCCTTATGCCTTTGGTGAGA 59.007 47.619 0.00 0.00 0.00 3.27
1816 1824 2.378547 ACCCTTATGCCTTTGGTGAGAA 59.621 45.455 0.00 0.00 0.00 2.87
1817 1825 3.181423 ACCCTTATGCCTTTGGTGAGAAA 60.181 43.478 0.00 0.00 0.00 2.52
1818 1826 4.026052 CCCTTATGCCTTTGGTGAGAAAT 58.974 43.478 0.00 0.00 0.00 2.17
1819 1827 5.200483 CCCTTATGCCTTTGGTGAGAAATA 58.800 41.667 0.00 0.00 0.00 1.40
1820 1828 5.656416 CCCTTATGCCTTTGGTGAGAAATAA 59.344 40.000 0.00 0.00 0.00 1.40
1821 1829 6.154363 CCCTTATGCCTTTGGTGAGAAATAAA 59.846 38.462 0.00 0.00 0.00 1.40
1822 1830 7.035612 CCTTATGCCTTTGGTGAGAAATAAAC 58.964 38.462 0.00 0.00 0.00 2.01
1823 1831 7.093771 CCTTATGCCTTTGGTGAGAAATAAACT 60.094 37.037 0.00 0.00 0.00 2.66
1824 1832 6.670695 ATGCCTTTGGTGAGAAATAAACTT 57.329 33.333 0.00 0.00 0.00 2.66
1825 1833 6.478512 TGCCTTTGGTGAGAAATAAACTTT 57.521 33.333 0.00 0.00 0.00 2.66
1826 1834 6.883744 TGCCTTTGGTGAGAAATAAACTTTT 58.116 32.000 0.00 0.00 0.00 2.27
1827 1835 6.983890 TGCCTTTGGTGAGAAATAAACTTTTC 59.016 34.615 0.00 0.00 36.13 2.29
1828 1836 7.147742 TGCCTTTGGTGAGAAATAAACTTTTCT 60.148 33.333 0.00 0.00 46.08 2.52
1829 1837 7.710907 GCCTTTGGTGAGAAATAAACTTTTCTT 59.289 33.333 1.39 0.00 44.04 2.52
1830 1838 9.599866 CCTTTGGTGAGAAATAAACTTTTCTTT 57.400 29.630 1.39 0.00 44.04 2.52
1832 1840 9.594478 TTTGGTGAGAAATAAACTTTTCTTTCC 57.406 29.630 8.26 7.34 44.04 3.13
1833 1841 7.722363 TGGTGAGAAATAAACTTTTCTTTCCC 58.278 34.615 8.26 5.01 44.04 3.97
1834 1842 6.861572 GGTGAGAAATAAACTTTTCTTTCCCG 59.138 38.462 8.26 0.00 44.04 5.14
1835 1843 6.362551 GTGAGAAATAAACTTTTCTTTCCCGC 59.637 38.462 8.26 2.15 44.04 6.13
1836 1844 6.264518 TGAGAAATAAACTTTTCTTTCCCGCT 59.735 34.615 8.26 0.00 44.04 5.52
1837 1845 6.678878 AGAAATAAACTTTTCTTTCCCGCTC 58.321 36.000 8.26 0.00 41.95 5.03
1838 1846 5.386958 AATAAACTTTTCTTTCCCGCTCC 57.613 39.130 0.00 0.00 0.00 4.70
1839 1847 1.617322 AACTTTTCTTTCCCGCTCCC 58.383 50.000 0.00 0.00 0.00 4.30
1840 1848 0.771755 ACTTTTCTTTCCCGCTCCCT 59.228 50.000 0.00 0.00 0.00 4.20
1841 1849 1.271434 ACTTTTCTTTCCCGCTCCCTC 60.271 52.381 0.00 0.00 0.00 4.30
1842 1850 0.037734 TTTTCTTTCCCGCTCCCTCC 59.962 55.000 0.00 0.00 0.00 4.30
1843 1851 1.848886 TTTCTTTCCCGCTCCCTCCC 61.849 60.000 0.00 0.00 0.00 4.30
1844 1852 3.798511 CTTTCCCGCTCCCTCCCC 61.799 72.222 0.00 0.00 0.00 4.81
1966 1974 3.798650 CGCGCATGGCTTTCCGAA 61.799 61.111 8.75 0.00 40.44 4.30
1991 1999 0.738389 CTCTCAGGCTCGTTCTCCTC 59.262 60.000 0.00 0.00 0.00 3.71
1992 2000 0.329931 TCTCAGGCTCGTTCTCCTCT 59.670 55.000 0.00 0.00 0.00 3.69
1993 2001 0.455410 CTCAGGCTCGTTCTCCTCTG 59.545 60.000 0.00 0.00 0.00 3.35
2039 2048 3.774528 TCGCAGCTCCGCTCCATT 61.775 61.111 0.00 0.00 36.40 3.16
2042 2051 2.042831 GCAGCTCCGCTCCATTGTT 61.043 57.895 0.00 0.00 36.40 2.83
2055 2076 1.165270 CATTGTTGTTCCTCCGGTCC 58.835 55.000 0.00 0.00 0.00 4.46
2083 2104 3.451004 GCATGGGCCAATCGTGCA 61.451 61.111 21.74 0.00 44.14 4.57
2087 2108 4.424711 GGGCCAATCGTGCAGGGA 62.425 66.667 4.39 0.00 0.00 4.20
2091 2112 3.197790 CAATCGTGCAGGGAGGCG 61.198 66.667 6.56 0.00 36.28 5.52
2093 2114 3.254024 AATCGTGCAGGGAGGCGTT 62.254 57.895 6.56 0.00 36.28 4.84
2095 2116 4.988598 CGTGCAGGGAGGCGTTGT 62.989 66.667 0.00 0.00 36.28 3.32
2098 2119 4.329545 GCAGGGAGGCGTTGTGGA 62.330 66.667 0.00 0.00 0.00 4.02
2123 2144 3.402681 CCATCCCGTGCACCTCCT 61.403 66.667 12.15 0.00 0.00 3.69
2261 2289 2.586357 GGCCTGATTCGCGTCTCC 60.586 66.667 5.77 0.00 0.00 3.71
2299 2327 3.317608 CTGCTACAATTGCGGCAAG 57.682 52.632 21.11 10.75 34.21 4.01
2336 2364 2.029844 GAGTGCAGCAACCCGACTC 61.030 63.158 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.447663 CGCCACGGATCACATGACA 60.448 57.895 0.00 0.00 0.00 3.58
49 50 2.940514 TCCTACCCTGTTGATCCAGA 57.059 50.000 0.93 0.00 34.23 3.86
227 228 0.036952 CCGCTTTCAGAGGAGCTTCA 60.037 55.000 0.00 0.00 37.36 3.02
543 544 2.105766 GGCTTCATCATCAAAGGCCTT 58.894 47.619 13.78 13.78 40.97 4.35
557 558 3.296709 GAGGAGTTCGCCGGCTTCA 62.297 63.158 26.68 4.99 0.00 3.02
643 644 0.397816 AAGCTGGACTCCTCCGCTAT 60.398 55.000 7.30 0.00 42.21 2.97
747 748 4.115199 GCCGCCACCTCCAAGGAT 62.115 66.667 0.00 0.00 37.67 3.24
751 752 4.697756 CTTCGCCGCCACCTCCAA 62.698 66.667 0.00 0.00 0.00 3.53
847 848 1.074072 CCATCAACCCGGAACACCA 59.926 57.895 0.73 0.00 0.00 4.17
909 910 2.878406 CCTCGTGTTTGTTGATGGTTCT 59.122 45.455 0.00 0.00 0.00 3.01
925 926 2.347322 GCAGCTGGTCTCTCCTCGT 61.347 63.158 17.12 0.00 37.07 4.18
989 990 3.060000 TCGCCATCCGACTCACGT 61.060 61.111 0.00 0.00 41.89 4.49
1071 1072 3.838271 GATCCTGTCGCGGCTCCA 61.838 66.667 13.81 0.05 0.00 3.86
1120 1121 1.075525 TGATCCCGATCGTCCCCTT 60.076 57.895 15.09 0.00 40.63 3.95
1121 1122 1.833049 GTGATCCCGATCGTCCCCT 60.833 63.158 15.09 0.00 40.63 4.79
1266 1267 3.537206 GACGGCCTCAGCACCAGTT 62.537 63.158 0.00 0.00 42.56 3.16
1340 1341 2.289882 CCATCAGTGCCTCAGTTCTTCA 60.290 50.000 0.00 0.00 0.00 3.02
1465 1467 5.506708 CAAAACACTAAACCCTAGGGCTAT 58.493 41.667 28.88 16.24 39.32 2.97
1466 1468 4.263594 CCAAAACACTAAACCCTAGGGCTA 60.264 45.833 28.88 17.85 39.32 3.93
1654 1662 4.275810 AGACTTCGTATTGTAGCCCTACA 58.724 43.478 4.11 4.11 43.61 2.74
1681 1689 1.006391 CGACATGCATACGACGTTTCC 60.006 52.381 16.84 0.00 0.00 3.13
1685 1693 0.450583 AGACGACATGCATACGACGT 59.549 50.000 24.87 19.20 36.71 4.34
1686 1694 2.378507 TAGACGACATGCATACGACG 57.621 50.000 24.87 16.63 0.00 5.12
1687 1695 5.444586 TTTTTAGACGACATGCATACGAC 57.555 39.130 24.87 20.03 0.00 4.34
1716 1724 8.434416 AATCAAGGATTAGCACTGCTATACAGC 61.434 40.741 11.61 0.06 41.01 4.40
1717 1725 6.933521 AATCAAGGATTAGCACTGCTATACAG 59.066 38.462 11.61 1.48 41.01 2.74
1718 1726 5.869649 TCAAGGATTAGCACTGCTATACA 57.130 39.130 11.61 0.00 41.01 2.29
1719 1727 7.227512 ACAAATCAAGGATTAGCACTGCTATAC 59.772 37.037 11.61 8.59 41.01 1.47
1720 1728 7.282585 ACAAATCAAGGATTAGCACTGCTATA 58.717 34.615 11.61 3.89 41.01 1.31
1721 1729 6.125029 ACAAATCAAGGATTAGCACTGCTAT 58.875 36.000 11.61 2.61 41.01 2.97
1722 1730 5.500234 ACAAATCAAGGATTAGCACTGCTA 58.500 37.500 6.66 6.66 40.44 3.49
1723 1731 4.338879 ACAAATCAAGGATTAGCACTGCT 58.661 39.130 8.95 8.95 43.41 4.24
1724 1732 4.708726 ACAAATCAAGGATTAGCACTGC 57.291 40.909 0.00 0.00 31.46 4.40
1725 1733 6.149308 TGTGTACAAATCAAGGATTAGCACTG 59.851 38.462 0.00 0.00 31.46 3.66
1726 1734 6.237901 TGTGTACAAATCAAGGATTAGCACT 58.762 36.000 0.00 0.00 31.46 4.40
1727 1735 6.494893 TGTGTACAAATCAAGGATTAGCAC 57.505 37.500 0.00 0.00 31.46 4.40
1728 1736 7.701539 ATTGTGTACAAATCAAGGATTAGCA 57.298 32.000 0.00 0.00 39.55 3.49
1733 1741 9.920946 AGGTATAATTGTGTACAAATCAAGGAT 57.079 29.630 0.00 0.00 39.55 3.24
1734 1742 9.173021 CAGGTATAATTGTGTACAAATCAAGGA 57.827 33.333 0.00 0.00 39.55 3.36
1735 1743 8.405531 CCAGGTATAATTGTGTACAAATCAAGG 58.594 37.037 0.00 0.00 39.55 3.61
1736 1744 9.173021 TCCAGGTATAATTGTGTACAAATCAAG 57.827 33.333 0.00 0.00 39.55 3.02
1737 1745 9.693739 ATCCAGGTATAATTGTGTACAAATCAA 57.306 29.630 0.00 0.00 39.55 2.57
1744 1752 9.924650 CCTAAGTATCCAGGTATAATTGTGTAC 57.075 37.037 0.00 0.00 0.00 2.90
1745 1753 9.886337 TCCTAAGTATCCAGGTATAATTGTGTA 57.114 33.333 0.00 0.00 33.37 2.90
1746 1754 8.792830 TCCTAAGTATCCAGGTATAATTGTGT 57.207 34.615 0.00 0.00 33.37 3.72
1747 1755 9.712305 CTTCCTAAGTATCCAGGTATAATTGTG 57.288 37.037 0.00 0.00 33.37 3.33
1748 1756 8.881262 CCTTCCTAAGTATCCAGGTATAATTGT 58.119 37.037 0.00 0.00 33.37 2.71
1749 1757 8.322091 CCCTTCCTAAGTATCCAGGTATAATTG 58.678 40.741 0.00 0.00 33.37 2.32
1750 1758 8.023271 ACCCTTCCTAAGTATCCAGGTATAATT 58.977 37.037 0.00 0.00 33.37 1.40
1751 1759 7.458170 CACCCTTCCTAAGTATCCAGGTATAAT 59.542 40.741 0.00 0.00 33.37 1.28
1752 1760 6.785963 CACCCTTCCTAAGTATCCAGGTATAA 59.214 42.308 0.00 0.00 33.37 0.98
1753 1761 6.105139 TCACCCTTCCTAAGTATCCAGGTATA 59.895 42.308 0.00 0.00 33.37 1.47
1754 1762 5.102783 TCACCCTTCCTAAGTATCCAGGTAT 60.103 44.000 0.00 0.00 33.37 2.73
1755 1763 4.233521 TCACCCTTCCTAAGTATCCAGGTA 59.766 45.833 0.00 0.00 33.37 3.08
1756 1764 3.013648 TCACCCTTCCTAAGTATCCAGGT 59.986 47.826 0.00 0.00 33.37 4.00
1757 1765 3.643792 CTCACCCTTCCTAAGTATCCAGG 59.356 52.174 0.00 0.00 0.00 4.45
1758 1766 4.547671 TCTCACCCTTCCTAAGTATCCAG 58.452 47.826 0.00 0.00 0.00 3.86
1759 1767 4.620086 TCTCACCCTTCCTAAGTATCCA 57.380 45.455 0.00 0.00 0.00 3.41
1760 1768 4.345547 CCTTCTCACCCTTCCTAAGTATCC 59.654 50.000 0.00 0.00 0.00 2.59
1761 1769 4.202274 GCCTTCTCACCCTTCCTAAGTATC 60.202 50.000 0.00 0.00 0.00 2.24
1762 1770 3.712218 GCCTTCTCACCCTTCCTAAGTAT 59.288 47.826 0.00 0.00 0.00 2.12
1763 1771 3.105283 GCCTTCTCACCCTTCCTAAGTA 58.895 50.000 0.00 0.00 0.00 2.24
1764 1772 1.909986 GCCTTCTCACCCTTCCTAAGT 59.090 52.381 0.00 0.00 0.00 2.24
1765 1773 1.134670 CGCCTTCTCACCCTTCCTAAG 60.135 57.143 0.00 0.00 0.00 2.18
1766 1774 0.902531 CGCCTTCTCACCCTTCCTAA 59.097 55.000 0.00 0.00 0.00 2.69
1767 1775 0.040646 TCGCCTTCTCACCCTTCCTA 59.959 55.000 0.00 0.00 0.00 2.94
1768 1776 1.229209 TCGCCTTCTCACCCTTCCT 60.229 57.895 0.00 0.00 0.00 3.36
1769 1777 1.219393 CTCGCCTTCTCACCCTTCC 59.781 63.158 0.00 0.00 0.00 3.46
1770 1778 1.219393 CCTCGCCTTCTCACCCTTC 59.781 63.158 0.00 0.00 0.00 3.46
1771 1779 0.252103 TACCTCGCCTTCTCACCCTT 60.252 55.000 0.00 0.00 0.00 3.95
1772 1780 0.684805 CTACCTCGCCTTCTCACCCT 60.685 60.000 0.00 0.00 0.00 4.34
1773 1781 0.683504 TCTACCTCGCCTTCTCACCC 60.684 60.000 0.00 0.00 0.00 4.61
1774 1782 1.404843 ATCTACCTCGCCTTCTCACC 58.595 55.000 0.00 0.00 0.00 4.02
1775 1783 3.243468 GGTTATCTACCTCGCCTTCTCAC 60.243 52.174 0.00 0.00 44.10 3.51
1776 1784 2.957006 GGTTATCTACCTCGCCTTCTCA 59.043 50.000 0.00 0.00 44.10 3.27
1777 1785 2.296752 GGGTTATCTACCTCGCCTTCTC 59.703 54.545 0.00 0.00 46.86 2.87
1778 1786 2.091222 AGGGTTATCTACCTCGCCTTCT 60.091 50.000 0.00 0.00 46.86 2.85
1779 1787 2.317973 AGGGTTATCTACCTCGCCTTC 58.682 52.381 0.00 0.00 46.86 3.46
1780 1788 2.473576 AGGGTTATCTACCTCGCCTT 57.526 50.000 0.00 0.00 46.86 4.35
1781 1789 2.473576 AAGGGTTATCTACCTCGCCT 57.526 50.000 0.00 0.00 46.86 5.52
1782 1790 3.616802 GCATAAGGGTTATCTACCTCGCC 60.617 52.174 0.00 0.00 46.86 5.54
1783 1791 3.586892 GCATAAGGGTTATCTACCTCGC 58.413 50.000 0.00 0.00 46.86 5.03
1784 1792 3.833070 AGGCATAAGGGTTATCTACCTCG 59.167 47.826 0.00 0.00 46.86 4.63
1785 1793 5.827326 AAGGCATAAGGGTTATCTACCTC 57.173 43.478 0.00 0.00 46.86 3.85
1786 1794 5.163088 CCAAAGGCATAAGGGTTATCTACCT 60.163 44.000 0.00 0.00 46.86 3.08
1787 1795 5.070685 CCAAAGGCATAAGGGTTATCTACC 58.929 45.833 0.00 0.00 46.99 3.18
1788 1796 5.531287 CACCAAAGGCATAAGGGTTATCTAC 59.469 44.000 0.00 0.00 0.00 2.59
1789 1797 5.430417 TCACCAAAGGCATAAGGGTTATCTA 59.570 40.000 0.00 0.00 0.00 1.98
1790 1798 4.229582 TCACCAAAGGCATAAGGGTTATCT 59.770 41.667 0.00 0.00 0.00 1.98
1791 1799 4.532834 TCACCAAAGGCATAAGGGTTATC 58.467 43.478 0.00 0.00 0.00 1.75
1792 1800 4.229582 TCTCACCAAAGGCATAAGGGTTAT 59.770 41.667 0.00 0.00 0.00 1.89
1793 1801 3.589735 TCTCACCAAAGGCATAAGGGTTA 59.410 43.478 0.00 0.00 0.00 2.85
1794 1802 2.378547 TCTCACCAAAGGCATAAGGGTT 59.621 45.455 0.00 0.00 0.00 4.11
1795 1803 1.992557 TCTCACCAAAGGCATAAGGGT 59.007 47.619 0.00 0.00 0.00 4.34
1796 1804 2.806945 TCTCACCAAAGGCATAAGGG 57.193 50.000 0.00 0.00 0.00 3.95
1797 1805 6.773976 TTATTTCTCACCAAAGGCATAAGG 57.226 37.500 0.00 0.00 0.00 2.69
1798 1806 7.830739 AGTTTATTTCTCACCAAAGGCATAAG 58.169 34.615 0.00 0.00 0.00 1.73
1799 1807 7.775053 AGTTTATTTCTCACCAAAGGCATAA 57.225 32.000 0.00 0.00 0.00 1.90
1800 1808 7.775053 AAGTTTATTTCTCACCAAAGGCATA 57.225 32.000 0.00 0.00 0.00 3.14
1801 1809 6.670695 AAGTTTATTTCTCACCAAAGGCAT 57.329 33.333 0.00 0.00 0.00 4.40
1802 1810 6.478512 AAAGTTTATTTCTCACCAAAGGCA 57.521 33.333 0.00 0.00 0.00 4.75
1803 1811 7.210174 AGAAAAGTTTATTTCTCACCAAAGGC 58.790 34.615 0.00 0.00 44.28 4.35
1804 1812 9.599866 AAAGAAAAGTTTATTTCTCACCAAAGG 57.400 29.630 3.05 0.00 46.25 3.11
1806 1814 9.594478 GGAAAGAAAAGTTTATTTCTCACCAAA 57.406 29.630 18.30 0.00 46.25 3.28
1807 1815 8.201464 GGGAAAGAAAAGTTTATTTCTCACCAA 58.799 33.333 18.30 0.00 46.25 3.67
1808 1816 7.469456 CGGGAAAGAAAAGTTTATTTCTCACCA 60.469 37.037 18.74 0.00 44.77 4.17
1809 1817 6.861572 CGGGAAAGAAAAGTTTATTTCTCACC 59.138 38.462 18.74 12.72 44.77 4.02
1810 1818 6.362551 GCGGGAAAGAAAAGTTTATTTCTCAC 59.637 38.462 18.74 9.31 44.77 3.51
1811 1819 6.264518 AGCGGGAAAGAAAAGTTTATTTCTCA 59.735 34.615 18.74 0.00 44.77 3.27
1812 1820 6.678878 AGCGGGAAAGAAAAGTTTATTTCTC 58.321 36.000 18.30 15.25 46.25 2.87
1814 1822 5.862323 GGAGCGGGAAAGAAAAGTTTATTTC 59.138 40.000 13.09 13.09 43.76 2.17
1815 1823 5.279306 GGGAGCGGGAAAGAAAAGTTTATTT 60.279 40.000 0.00 0.00 34.62 1.40
1816 1824 4.219944 GGGAGCGGGAAAGAAAAGTTTATT 59.780 41.667 0.00 0.00 0.00 1.40
1817 1825 3.762288 GGGAGCGGGAAAGAAAAGTTTAT 59.238 43.478 0.00 0.00 0.00 1.40
1818 1826 3.151554 GGGAGCGGGAAAGAAAAGTTTA 58.848 45.455 0.00 0.00 0.00 2.01
1819 1827 1.961394 GGGAGCGGGAAAGAAAAGTTT 59.039 47.619 0.00 0.00 0.00 2.66
1820 1828 1.145119 AGGGAGCGGGAAAGAAAAGTT 59.855 47.619 0.00 0.00 0.00 2.66
1821 1829 0.771755 AGGGAGCGGGAAAGAAAAGT 59.228 50.000 0.00 0.00 0.00 2.66
1822 1830 1.454201 GAGGGAGCGGGAAAGAAAAG 58.546 55.000 0.00 0.00 0.00 2.27
1823 1831 0.037734 GGAGGGAGCGGGAAAGAAAA 59.962 55.000 0.00 0.00 0.00 2.29
1824 1832 1.683441 GGAGGGAGCGGGAAAGAAA 59.317 57.895 0.00 0.00 0.00 2.52
1825 1833 2.298661 GGGAGGGAGCGGGAAAGAA 61.299 63.158 0.00 0.00 0.00 2.52
1826 1834 2.687566 GGGAGGGAGCGGGAAAGA 60.688 66.667 0.00 0.00 0.00 2.52
1827 1835 3.798511 GGGGAGGGAGCGGGAAAG 61.799 72.222 0.00 0.00 0.00 2.62
1952 1960 2.424956 AGAGAAATTCGGAAAGCCATGC 59.575 45.455 0.00 0.00 0.00 4.06
1961 1969 2.428890 GAGCCTGAGAGAGAAATTCGGA 59.571 50.000 0.00 0.00 0.00 4.55
1963 1971 2.159310 ACGAGCCTGAGAGAGAAATTCG 60.159 50.000 0.00 0.00 0.00 3.34
1965 1973 3.513515 AGAACGAGCCTGAGAGAGAAATT 59.486 43.478 0.00 0.00 0.00 1.82
1966 1974 3.096092 AGAACGAGCCTGAGAGAGAAAT 58.904 45.455 0.00 0.00 0.00 2.17
2028 2037 0.804989 GGAACAACAATGGAGCGGAG 59.195 55.000 0.00 0.00 0.00 4.63
2069 2090 4.738998 CCCTGCACGATTGGCCCA 62.739 66.667 0.00 0.00 0.00 5.36
2075 2096 3.254024 AACGCCTCCCTGCACGATT 62.254 57.895 0.00 0.00 0.00 3.34
2083 2104 3.322466 CCTCCACAACGCCTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
2138 2159 2.955022 GATTCTGCCTCCGCTGCCAT 62.955 60.000 0.00 0.00 35.36 4.40
2153 2180 2.665185 CCCCCGAATCGGCGATTC 60.665 66.667 39.18 39.18 46.86 2.52
2248 2276 4.508128 GCCGGGAGACGCGAATCA 62.508 66.667 15.93 0.00 42.31 2.57
2299 2327 4.554036 GCGGAGATGTGGCCCTCC 62.554 72.222 14.17 14.17 44.18 4.30


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

AutoCloner maintained by Alex Coulton.