Multiple sequence alignment - TraesCS5B01G149100

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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 TraesCS5B01G149100 chr5B 100.000 2428 0 0 1 2428 276959119 276961546 0.000000e+00 4484.0
1 TraesCS5B01G149100 chr5B 81.864 397 64 6 2028 2421 681096631 681096240 6.470000e-86 327.0
2 TraesCS5B01G149100 chr5B 81.734 323 48 6 2107 2421 700042426 700042745 2.390000e-65 259.0
3 TraesCS5B01G149100 chr5A 97.642 1739 41 0 1 1739 328007946 328009684 0.000000e+00 2985.0
4 TraesCS5B01G149100 chr5D 97.039 1756 50 1 1 1756 243833020 243834773 0.000000e+00 2953.0
5 TraesCS5B01G149100 chr5D 85.268 448 47 11 1985 2421 485378978 485379417 6.160000e-121 444.0
6 TraesCS5B01G149100 chr1D 83.048 525 77 11 1911 2425 445650171 445649649 1.310000e-127 466.0
7 TraesCS5B01G149100 chr6B 83.450 429 61 8 1997 2421 529866094 529865672 8.140000e-105 390.0
8 TraesCS5B01G149100 chrUn 82.629 426 62 4 2011 2428 97298971 97298550 1.370000e-97 366.0
9 TraesCS5B01G149100 chrUn 79.433 141 20 7 1868 2002 97204127 97203990 9.240000e-15 91.6
10 TraesCS5B01G149100 chr6A 82.270 423 45 14 1997 2407 493974456 493974052 2.990000e-89 339.0
11 TraesCS5B01G149100 chr3D 81.771 384 47 13 2037 2411 326223334 326222965 1.410000e-77 300.0
12 TraesCS5B01G149100 chr3D 79.853 407 67 10 1973 2367 438062939 438063342 1.420000e-72 283.0
13 TraesCS5B01G149100 chr3D 79.096 177 20 7 1955 2115 116477624 116477799 3.300000e-19 106.0
14 TraesCS5B01G149100 chr2D 84.727 275 34 5 2155 2421 432865269 432865543 3.980000e-68 268.0
15 TraesCS5B01G149100 chr3B 77.262 409 56 21 2025 2423 11085499 11085880 3.160000e-49 206.0
16 TraesCS5B01G149100 chr3B 72.515 342 76 15 2017 2351 757718062 757718392 7.150000e-16 95.3
17 TraesCS5B01G149100 chr3B 75.824 182 36 6 2017 2194 757723049 757723226 4.300000e-13 86.1


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 TraesCS5B01G149100 chr5B 276959119 276961546 2427 False 4484 4484 100.000 1 2428 1 chr5B.!!$F1 2427
1 TraesCS5B01G149100 chr5A 328007946 328009684 1738 False 2985 2985 97.642 1 1739 1 chr5A.!!$F1 1738
2 TraesCS5B01G149100 chr5D 243833020 243834773 1753 False 2953 2953 97.039 1 1756 1 chr5D.!!$F1 1755
3 TraesCS5B01G149100 chr1D 445649649 445650171 522 True 466 466 83.048 1911 2425 1 chr1D.!!$R1 514

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
39 40 0.178533 TGTCCGTTCGGTTGGTCTTT 59.821 50.0 11.04 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1785 0.099613 TTGTTCTTTTTGCAGCGCGA 59.9 45.0 12.1 0.0 0.0 5.87 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
39 40 0.178533 TGTCCGTTCGGTTGGTCTTT 59.821 50.000 11.04 0.00 0.00 2.52
145 146 0.892755 ATGACTTCGTCGGGCTTGTA 59.107 50.000 0.00 0.00 34.95 2.41
161 162 6.293955 CGGGCTTGTATATTCCATCGAAAATT 60.294 38.462 0.00 0.00 0.00 1.82
533 534 3.261580 TGAATTGAGCACCACAGTATCG 58.738 45.455 0.00 0.00 0.00 2.92
575 576 0.179089 CTCGACAAGCATCCTCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
871 872 6.831868 ACCCTATCAAAAATATGTAACGCCTT 59.168 34.615 0.00 0.00 0.00 4.35
887 888 1.156736 CCTTGTTTAGCTGTCCACGG 58.843 55.000 0.00 0.00 0.00 4.94
1051 1052 0.396435 TTGGCAGTCACCATTCGACT 59.604 50.000 0.00 0.00 44.55 4.18
1072 1073 5.079643 ACTATGCACTTGTCTCCCAAAATT 58.920 37.500 0.00 0.00 31.20 1.82
1229 1230 2.028476 GCACCGGACATACCTATGCATA 60.028 50.000 9.46 6.20 42.74 3.14
1281 1282 0.805322 CATCTCGTCCAGCAGACTGC 60.805 60.000 20.12 20.12 43.91 4.40
1334 1335 0.792640 CTGTGATCACTGCGTTCCAC 59.207 55.000 25.55 0.00 0.00 4.02
1372 1373 1.519719 GCATGGAGCGGAAGAGACT 59.480 57.895 0.00 0.00 0.00 3.24
1697 1698 2.955660 CAGTTAAACCCCAGAAAGTGCA 59.044 45.455 0.00 0.00 0.00 4.57
1700 1701 4.468153 AGTTAAACCCCAGAAAGTGCAAAA 59.532 37.500 0.00 0.00 0.00 2.44
1739 1740 1.069296 CACGGGTGTGCTGTACAAATG 60.069 52.381 0.00 0.00 41.89 2.32
1741 1742 1.196808 CGGGTGTGCTGTACAAATGAC 59.803 52.381 0.00 0.00 41.89 3.06
1745 1746 2.616376 GTGTGCTGTACAAATGACCACA 59.384 45.455 0.00 1.57 41.89 4.17
1746 1747 2.616376 TGTGCTGTACAAATGACCACAC 59.384 45.455 0.00 0.00 36.06 3.82
1751 1752 4.454161 GCTGTACAAATGACCACACATACA 59.546 41.667 0.00 0.00 0.00 2.29
1752 1753 5.616866 GCTGTACAAATGACCACACATACAC 60.617 44.000 0.00 0.00 0.00 2.90
1753 1754 5.616270 TGTACAAATGACCACACATACACT 58.384 37.500 0.00 0.00 0.00 3.55
1754 1755 5.468409 TGTACAAATGACCACACATACACTG 59.532 40.000 0.00 0.00 0.00 3.66
1755 1756 4.713553 ACAAATGACCACACATACACTGA 58.286 39.130 0.00 0.00 0.00 3.41
1756 1757 4.756642 ACAAATGACCACACATACACTGAG 59.243 41.667 0.00 0.00 0.00 3.35
1757 1758 4.890158 AATGACCACACATACACTGAGA 57.110 40.909 0.00 0.00 0.00 3.27
1758 1759 3.942130 TGACCACACATACACTGAGAG 57.058 47.619 0.00 0.00 0.00 3.20
1759 1760 2.029020 TGACCACACATACACTGAGAGC 60.029 50.000 0.00 0.00 0.00 4.09
1760 1761 1.970640 ACCACACATACACTGAGAGCA 59.029 47.619 0.00 0.00 0.00 4.26
1761 1762 2.568956 ACCACACATACACTGAGAGCAT 59.431 45.455 0.00 0.00 0.00 3.79
1762 1763 3.193263 CCACACATACACTGAGAGCATC 58.807 50.000 0.00 0.00 0.00 3.91
1783 1784 3.042059 TCCAATGGGGAGGTAGAGTAC 57.958 52.381 0.00 0.00 42.15 2.73
1784 1785 2.590611 TCCAATGGGGAGGTAGAGTACT 59.409 50.000 0.00 0.00 42.15 2.73
1785 1786 2.966516 CCAATGGGGAGGTAGAGTACTC 59.033 54.545 15.41 15.41 40.01 2.59
1786 1787 2.623889 CAATGGGGAGGTAGAGTACTCG 59.376 54.545 17.07 0.00 34.58 4.18
1787 1788 0.106819 TGGGGAGGTAGAGTACTCGC 60.107 60.000 17.07 13.49 43.51 5.03
1788 1789 1.165284 GGGGAGGTAGAGTACTCGCG 61.165 65.000 17.07 0.00 44.70 5.87
1789 1790 1.648174 GGAGGTAGAGTACTCGCGC 59.352 63.158 17.07 10.81 34.58 6.86
1790 1791 0.814812 GGAGGTAGAGTACTCGCGCT 60.815 60.000 17.07 12.35 34.58 5.92
1791 1792 0.305313 GAGGTAGAGTACTCGCGCTG 59.695 60.000 17.07 0.00 34.09 5.18
1792 1793 1.298488 GGTAGAGTACTCGCGCTGC 60.298 63.158 17.07 3.49 34.09 5.25
1793 1794 1.428219 GTAGAGTACTCGCGCTGCA 59.572 57.895 17.07 0.00 34.09 4.41
1794 1795 0.179171 GTAGAGTACTCGCGCTGCAA 60.179 55.000 17.07 0.00 34.09 4.08
1795 1796 0.524414 TAGAGTACTCGCGCTGCAAA 59.476 50.000 17.07 0.00 34.09 3.68
1796 1797 0.319555 AGAGTACTCGCGCTGCAAAA 60.320 50.000 17.07 0.00 34.09 2.44
1797 1798 0.511221 GAGTACTCGCGCTGCAAAAA 59.489 50.000 7.22 0.00 0.00 1.94
1798 1799 0.512952 AGTACTCGCGCTGCAAAAAG 59.487 50.000 5.56 0.00 0.00 2.27
1799 1800 0.511221 GTACTCGCGCTGCAAAAAGA 59.489 50.000 5.56 0.00 0.00 2.52
1800 1801 1.070175 GTACTCGCGCTGCAAAAAGAA 60.070 47.619 5.56 0.00 0.00 2.52
1801 1802 0.317020 ACTCGCGCTGCAAAAAGAAC 60.317 50.000 5.56 0.00 0.00 3.01
1802 1803 0.316937 CTCGCGCTGCAAAAAGAACA 60.317 50.000 5.56 0.00 0.00 3.18
1803 1804 0.099613 TCGCGCTGCAAAAAGAACAA 59.900 45.000 5.56 0.00 0.00 2.83
1804 1805 0.226984 CGCGCTGCAAAAAGAACAAC 59.773 50.000 5.56 0.00 0.00 3.32
1805 1806 1.276415 GCGCTGCAAAAAGAACAACA 58.724 45.000 0.00 0.00 0.00 3.33
1806 1807 1.860326 GCGCTGCAAAAAGAACAACAT 59.140 42.857 0.00 0.00 0.00 2.71
1807 1808 2.284952 GCGCTGCAAAAAGAACAACATT 59.715 40.909 0.00 0.00 0.00 2.71
1808 1809 3.242381 GCGCTGCAAAAAGAACAACATTT 60.242 39.130 0.00 0.00 0.00 2.32
1809 1810 4.727448 GCGCTGCAAAAAGAACAACATTTT 60.727 37.500 0.00 0.00 30.99 1.82
1810 1811 5.501574 GCGCTGCAAAAAGAACAACATTTTA 60.502 36.000 0.00 0.00 30.02 1.52
1811 1812 6.122125 CGCTGCAAAAAGAACAACATTTTAG 58.878 36.000 0.00 0.00 30.02 1.85
1812 1813 6.237808 CGCTGCAAAAAGAACAACATTTTAGT 60.238 34.615 0.00 0.00 30.02 2.24
1813 1814 7.043722 CGCTGCAAAAAGAACAACATTTTAGTA 60.044 33.333 0.00 0.00 30.02 1.82
1814 1815 8.764287 GCTGCAAAAAGAACAACATTTTAGTAT 58.236 29.630 0.00 0.00 30.02 2.12
1816 1817 8.547069 TGCAAAAAGAACAACATTTTAGTATGC 58.453 29.630 0.00 0.00 32.77 3.14
1817 1818 7.735586 GCAAAAAGAACAACATTTTAGTATGCG 59.264 33.333 0.00 0.00 30.02 4.73
1818 1819 6.927933 AAAGAACAACATTTTAGTATGCGC 57.072 33.333 0.00 0.00 0.00 6.09
1819 1820 5.621197 AGAACAACATTTTAGTATGCGCA 57.379 34.783 14.96 14.96 0.00 6.09
1820 1821 6.194796 AGAACAACATTTTAGTATGCGCAT 57.805 33.333 28.23 28.23 0.00 4.73
1821 1822 6.029607 AGAACAACATTTTAGTATGCGCATG 58.970 36.000 32.48 17.12 0.00 4.06
1822 1823 4.671377 ACAACATTTTAGTATGCGCATGG 58.329 39.130 32.48 13.02 0.00 3.66
1823 1824 3.354089 ACATTTTAGTATGCGCATGGC 57.646 42.857 32.48 23.24 43.96 4.40
1824 1825 2.034558 ACATTTTAGTATGCGCATGGCC 59.965 45.455 32.48 19.10 42.61 5.36
1825 1826 1.756430 TTTTAGTATGCGCATGGCCA 58.244 45.000 32.48 8.56 42.61 5.36
1826 1827 1.979855 TTTAGTATGCGCATGGCCAT 58.020 45.000 32.48 14.09 42.61 4.40
1827 1828 1.979855 TTAGTATGCGCATGGCCATT 58.020 45.000 32.48 11.96 42.61 3.16
1828 1829 1.979855 TAGTATGCGCATGGCCATTT 58.020 45.000 32.48 7.17 42.61 2.32
1829 1830 0.386476 AGTATGCGCATGGCCATTTG 59.614 50.000 32.48 12.77 42.61 2.32
1830 1831 0.598158 GTATGCGCATGGCCATTTGG 60.598 55.000 32.48 9.35 42.61 3.28
1840 1841 4.001248 CCATTTGGCGAGCTCCAA 57.999 55.556 8.47 5.35 43.84 3.53
1841 1842 2.496942 CCATTTGGCGAGCTCCAAT 58.503 52.632 8.47 0.00 44.78 3.16
1842 1843 1.679139 CCATTTGGCGAGCTCCAATA 58.321 50.000 8.47 0.43 44.78 1.90
1843 1844 1.605710 CCATTTGGCGAGCTCCAATAG 59.394 52.381 8.47 4.08 44.78 1.73
1844 1845 2.564771 CATTTGGCGAGCTCCAATAGA 58.435 47.619 8.47 0.00 44.78 1.98
1845 1846 2.024176 TTTGGCGAGCTCCAATAGAC 57.976 50.000 8.47 0.00 44.78 2.59
1846 1847 0.179111 TTGGCGAGCTCCAATAGACG 60.179 55.000 8.47 0.00 40.92 4.18
1847 1848 1.951631 GGCGAGCTCCAATAGACGC 60.952 63.158 8.47 5.84 45.22 5.19
1848 1849 2.296480 GCGAGCTCCAATAGACGCG 61.296 63.158 8.47 3.53 40.54 6.01
1849 1850 1.064296 CGAGCTCCAATAGACGCGT 59.936 57.895 13.85 13.85 0.00 6.01
1850 1851 0.306840 CGAGCTCCAATAGACGCGTA 59.693 55.000 13.97 0.00 0.00 4.42
1851 1852 1.268386 CGAGCTCCAATAGACGCGTAA 60.268 52.381 13.97 3.35 0.00 3.18
1852 1853 2.793585 CGAGCTCCAATAGACGCGTAAA 60.794 50.000 13.97 2.88 0.00 2.01
1853 1854 3.184541 GAGCTCCAATAGACGCGTAAAA 58.815 45.455 13.97 0.00 0.00 1.52
1854 1855 3.592059 AGCTCCAATAGACGCGTAAAAA 58.408 40.909 13.97 0.00 0.00 1.94
1872 1873 3.687340 AAAAATAAGAACGCGGGCG 57.313 47.368 12.47 12.04 46.03 6.13
1873 1874 0.169451 AAAAATAAGAACGCGGGCGG 59.831 50.000 18.03 0.00 44.69 6.13
1874 1875 0.674269 AAAATAAGAACGCGGGCGGA 60.674 50.000 18.03 0.00 44.69 5.54
1875 1876 0.674269 AAATAAGAACGCGGGCGGAA 60.674 50.000 18.03 0.00 44.69 4.30
1876 1877 0.674269 AATAAGAACGCGGGCGGAAA 60.674 50.000 18.03 0.00 44.69 3.13
1877 1878 0.674269 ATAAGAACGCGGGCGGAAAA 60.674 50.000 18.03 0.00 44.69 2.29
1878 1879 1.293267 TAAGAACGCGGGCGGAAAAG 61.293 55.000 18.03 0.00 44.69 2.27
1879 1880 4.753877 GAACGCGGGCGGAAAAGC 62.754 66.667 18.03 0.00 44.69 3.51
1885 1886 4.193334 GGGCGGAAAAGCGGCATC 62.193 66.667 1.45 0.00 43.94 3.91
1886 1887 4.536687 GGCGGAAAAGCGGCATCG 62.537 66.667 1.45 0.00 43.94 3.84
1916 1917 1.025113 TTTTGGCACGTGTCGTCCAA 61.025 50.000 16.50 17.36 41.37 3.53
1919 1920 2.958016 GCACGTGTCGTCCAACGT 60.958 61.111 18.38 0.00 43.14 3.99
1923 1924 2.235016 CGTGTCGTCCAACGTGCTT 61.235 57.895 0.00 0.00 43.14 3.91
1924 1925 1.275657 GTGTCGTCCAACGTGCTTG 59.724 57.895 0.00 0.00 43.14 4.01
1931 1932 3.185594 TCGTCCAACGTGCTTGATAAAAG 59.814 43.478 0.00 0.00 43.14 2.27
1939 1940 1.934476 CTTGATAAAAGCCGCGCGC 60.934 57.895 27.36 23.91 37.98 6.86
1962 1963 3.061848 CCCGCAAACCGCCATCTT 61.062 61.111 0.00 0.00 37.30 2.40
1964 1965 2.040544 CCGCAAACCGCCATCTTCT 61.041 57.895 0.00 0.00 37.30 2.85
1965 1966 1.425428 CGCAAACCGCCATCTTCTC 59.575 57.895 0.00 0.00 37.30 2.87
1966 1967 1.425428 GCAAACCGCCATCTTCTCG 59.575 57.895 0.00 0.00 32.94 4.04
1967 1968 1.425428 CAAACCGCCATCTTCTCGC 59.575 57.895 0.00 0.00 0.00 5.03
1969 1970 2.185310 AAACCGCCATCTTCTCGCCT 62.185 55.000 0.00 0.00 0.00 5.52
1970 1971 2.279784 CCGCCATCTTCTCGCCTC 60.280 66.667 0.00 0.00 0.00 4.70
1971 1972 2.656651 CGCCATCTTCTCGCCTCG 60.657 66.667 0.00 0.00 0.00 4.63
1977 1984 1.040339 ATCTTCTCGCCTCGCCTTCT 61.040 55.000 0.00 0.00 0.00 2.85
1985 1992 2.716017 CCTCGCCTTCTTCCTCGCT 61.716 63.158 0.00 0.00 0.00 4.93
1989 1996 0.390472 CGCCTTCTTCCTCGCTTCTT 60.390 55.000 0.00 0.00 0.00 2.52
2065 2075 3.775654 GCACCTCAGGCTACCGCT 61.776 66.667 0.00 0.00 36.09 5.52
2075 2085 3.812019 CTACCGCTGCGTCCGTCT 61.812 66.667 21.59 0.00 0.00 4.18
2099 2109 0.949105 CCCTCCGGCATGTATTACGC 60.949 60.000 0.00 0.00 0.00 4.42
2100 2110 1.282248 CCTCCGGCATGTATTACGCG 61.282 60.000 3.53 3.53 0.00 6.01
2103 2113 1.282248 CCGGCATGTATTACGCGGAG 61.282 60.000 12.47 0.00 0.00 4.63
2125 2135 2.267642 GCTCCGGTGGTACATGCA 59.732 61.111 0.00 0.00 44.52 3.96
2130 2140 1.887242 CGGTGGTACATGCATCGGG 60.887 63.158 0.00 0.00 44.52 5.14
2135 2145 1.956170 GTACATGCATCGGGCTCGG 60.956 63.158 5.94 0.00 45.15 4.63
2136 2146 2.131067 TACATGCATCGGGCTCGGA 61.131 57.895 5.94 0.00 45.15 4.55
2138 2148 1.819208 CATGCATCGGGCTCGGAAA 60.819 57.895 5.94 0.00 45.15 3.13
2151 2161 1.372499 CGGAAAGTTCGAGACCGCA 60.372 57.895 0.00 0.00 37.32 5.69
2154 2164 1.214367 GAAAGTTCGAGACCGCACAA 58.786 50.000 0.00 0.00 34.44 3.33
2223 2233 1.858091 AGGCGCATATGAACTTCTCG 58.142 50.000 10.83 0.00 0.00 4.04
2224 2234 1.409064 AGGCGCATATGAACTTCTCGA 59.591 47.619 10.83 0.00 0.00 4.04
2231 2241 1.674611 ATGAACTTCTCGAACGCGCG 61.675 55.000 30.96 30.96 37.46 6.86
2249 2259 1.669115 GAGCAAGCGCAGGAACTCA 60.669 57.895 11.47 0.00 42.27 3.41
2257 2267 2.266055 CAGGAACTCACGCCTCCC 59.734 66.667 0.00 0.00 34.60 4.30
2272 2282 4.929707 CCCCCGCGGCTAATCACC 62.930 72.222 22.85 0.00 0.00 4.02
2281 2291 0.674534 GGCTAATCACCGACGAGGAT 59.325 55.000 8.56 0.00 45.00 3.24
2371 2381 3.043713 CGCGAGCACTTCCAGCAA 61.044 61.111 0.00 0.00 0.00 3.91
2379 2389 1.800805 CACTTCCAGCAAGATGTCGT 58.199 50.000 0.00 0.00 35.82 4.34
2393 2403 3.046087 TCGTCGCCGAGAACGAGT 61.046 61.111 0.00 0.00 40.80 4.18
2411 2421 2.596851 TTCTGGGTGCAGAGGAGGC 61.597 63.158 0.00 0.00 32.21 4.70
2421 2431 3.453679 GAGGAGGCCGAAGCGAGT 61.454 66.667 0.00 0.00 41.24 4.18
2425 2435 3.282745 GAGGCCGAAGCGAGTCACA 62.283 63.158 0.00 0.00 41.24 3.58
2426 2436 3.112709 GGCCGAAGCGAGTCACAC 61.113 66.667 0.00 0.00 41.24 3.82
2427 2437 3.470567 GCCGAAGCGAGTCACACG 61.471 66.667 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.135139 GCTGATGAGAGTTAGCGGTGA 59.865 52.381 0.00 0.00 0.00 4.02
145 146 7.102346 TGGTTGCAAAATTTTCGATGGAATAT 58.898 30.769 0.00 0.00 30.88 1.28
161 162 0.835941 ACTTGGCCAATGGTTGCAAA 59.164 45.000 20.85 0.00 0.00 3.68
344 345 1.065273 CAAGATGCATCGCCTTGGC 59.935 57.895 20.67 0.75 35.05 4.52
533 534 4.319839 GCTTTCAGTGAGCTTAGGTTTCAC 60.320 45.833 0.00 4.27 41.10 3.18
575 576 4.327680 ACTTCTACTCAAAATGCACCCTC 58.672 43.478 0.00 0.00 0.00 4.30
579 580 6.902341 TCATTGACTTCTACTCAAAATGCAC 58.098 36.000 0.00 0.00 31.48 4.57
851 852 9.567848 CTAAACAAGGCGTTACATATTTTTGAT 57.432 29.630 0.00 0.00 36.59 2.57
871 872 0.759959 TTCCCGTGGACAGCTAAACA 59.240 50.000 0.00 0.00 0.00 2.83
887 888 2.289945 CCTGGTCTATGGCTATGCTTCC 60.290 54.545 0.00 0.00 0.00 3.46
1051 1052 4.832266 ACAATTTTGGGAGACAAGTGCATA 59.168 37.500 0.00 0.00 40.82 3.14
1072 1073 1.067142 GTGCTGACCGGATGAAGTACA 60.067 52.381 9.46 0.00 0.00 2.90
1159 1160 1.066858 TCAGAGAGATTGGTTCGGCAC 60.067 52.381 0.00 0.00 0.00 5.01
1229 1230 1.439353 CTGTGGCTGTCAACGCTGTT 61.439 55.000 0.00 0.00 0.00 3.16
1281 1282 3.131478 GGATTTGGACACCGCCCG 61.131 66.667 0.00 0.00 0.00 6.13
1490 1491 0.892755 TCATGTACGCCCGTTTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
1547 1548 2.266055 CTCCTCAAGTCCGGCCAC 59.734 66.667 2.24 0.00 0.00 5.01
1697 1698 4.405358 TGAGTCCAGCAGTCCAAAAATTTT 59.595 37.500 0.00 0.00 0.00 1.82
1700 1701 2.887152 GTGAGTCCAGCAGTCCAAAAAT 59.113 45.455 0.00 0.00 0.00 1.82
1712 1713 2.357517 GCACACCCGTGAGTCCAG 60.358 66.667 0.96 0.00 46.80 3.86
1739 1740 2.029020 TGCTCTCAGTGTATGTGTGGTC 60.029 50.000 0.00 0.00 0.00 4.02
1741 1742 2.749280 TGCTCTCAGTGTATGTGTGG 57.251 50.000 0.00 0.00 0.00 4.17
1745 1746 3.369175 TGGAGATGCTCTCAGTGTATGT 58.631 45.455 13.06 0.00 45.12 2.29
1746 1747 4.397481 TTGGAGATGCTCTCAGTGTATG 57.603 45.455 13.06 0.00 45.12 2.39
1751 1752 1.489649 CCCATTGGAGATGCTCTCAGT 59.510 52.381 3.62 0.00 45.12 3.41
1752 1753 1.202782 CCCCATTGGAGATGCTCTCAG 60.203 57.143 3.62 3.04 45.12 3.35
1753 1754 0.841961 CCCCATTGGAGATGCTCTCA 59.158 55.000 3.62 0.00 45.12 3.27
1754 1755 1.135094 TCCCCATTGGAGATGCTCTC 58.865 55.000 3.62 5.01 42.66 3.20
1755 1756 3.347158 TCCCCATTGGAGATGCTCT 57.653 52.632 3.62 0.00 38.61 4.09
1763 1764 2.590611 AGTACTCTACCTCCCCATTGGA 59.409 50.000 3.62 0.00 42.41 3.53
1764 1765 2.966516 GAGTACTCTACCTCCCCATTGG 59.033 54.545 15.91 0.00 0.00 3.16
1765 1766 2.623889 CGAGTACTCTACCTCCCCATTG 59.376 54.545 20.34 0.00 0.00 2.82
1766 1767 2.946785 CGAGTACTCTACCTCCCCATT 58.053 52.381 20.34 0.00 0.00 3.16
1767 1768 1.479021 GCGAGTACTCTACCTCCCCAT 60.479 57.143 20.34 0.00 0.00 4.00
1768 1769 0.106819 GCGAGTACTCTACCTCCCCA 60.107 60.000 20.34 0.00 0.00 4.96
1769 1770 1.165284 CGCGAGTACTCTACCTCCCC 61.165 65.000 20.34 0.00 0.00 4.81
1770 1771 1.784036 GCGCGAGTACTCTACCTCCC 61.784 65.000 20.34 0.00 0.00 4.30
1771 1772 0.814812 AGCGCGAGTACTCTACCTCC 60.815 60.000 20.34 3.54 0.00 4.30
1772 1773 0.305313 CAGCGCGAGTACTCTACCTC 59.695 60.000 20.34 4.46 0.00 3.85
1773 1774 1.716826 GCAGCGCGAGTACTCTACCT 61.717 60.000 20.34 10.16 0.00 3.08
1774 1775 1.298488 GCAGCGCGAGTACTCTACC 60.298 63.158 20.34 8.13 0.00 3.18
1775 1776 0.179171 TTGCAGCGCGAGTACTCTAC 60.179 55.000 20.34 11.37 0.00 2.59
1776 1777 0.524414 TTTGCAGCGCGAGTACTCTA 59.476 50.000 20.34 0.00 0.00 2.43
1777 1778 0.319555 TTTTGCAGCGCGAGTACTCT 60.320 50.000 20.34 0.00 0.00 3.24
1778 1779 0.511221 TTTTTGCAGCGCGAGTACTC 59.489 50.000 12.10 13.18 0.00 2.59
1779 1780 0.512952 CTTTTTGCAGCGCGAGTACT 59.487 50.000 12.10 0.00 0.00 2.73
1780 1781 0.511221 TCTTTTTGCAGCGCGAGTAC 59.489 50.000 12.10 0.00 0.00 2.73
1781 1782 1.070175 GTTCTTTTTGCAGCGCGAGTA 60.070 47.619 12.10 0.00 0.00 2.59
1782 1783 0.317020 GTTCTTTTTGCAGCGCGAGT 60.317 50.000 12.10 0.00 0.00 4.18
1783 1784 0.316937 TGTTCTTTTTGCAGCGCGAG 60.317 50.000 12.10 1.41 0.00 5.03
1784 1785 0.099613 TTGTTCTTTTTGCAGCGCGA 59.900 45.000 12.10 0.00 0.00 5.87
1785 1786 0.226984 GTTGTTCTTTTTGCAGCGCG 59.773 50.000 0.00 0.00 0.00 6.86
1786 1787 1.276415 TGTTGTTCTTTTTGCAGCGC 58.724 45.000 0.00 0.00 0.00 5.92
1787 1788 4.519191 AAATGTTGTTCTTTTTGCAGCG 57.481 36.364 0.00 0.00 0.00 5.18
1788 1789 7.003939 ACTAAAATGTTGTTCTTTTTGCAGC 57.996 32.000 0.00 0.00 35.79 5.25
1790 1791 8.547069 GCATACTAAAATGTTGTTCTTTTTGCA 58.453 29.630 0.00 0.00 35.79 4.08
1791 1792 7.735586 CGCATACTAAAATGTTGTTCTTTTTGC 59.264 33.333 0.00 0.00 35.79 3.68
1792 1793 7.735586 GCGCATACTAAAATGTTGTTCTTTTTG 59.264 33.333 0.30 0.00 35.79 2.44
1793 1794 7.436673 TGCGCATACTAAAATGTTGTTCTTTTT 59.563 29.630 5.66 0.00 37.26 1.94
1794 1795 6.920758 TGCGCATACTAAAATGTTGTTCTTTT 59.079 30.769 5.66 0.00 0.00 2.27
1795 1796 6.442952 TGCGCATACTAAAATGTTGTTCTTT 58.557 32.000 5.66 0.00 0.00 2.52
1796 1797 6.007936 TGCGCATACTAAAATGTTGTTCTT 57.992 33.333 5.66 0.00 0.00 2.52
1797 1798 5.621197 TGCGCATACTAAAATGTTGTTCT 57.379 34.783 5.66 0.00 0.00 3.01
1798 1799 5.229887 CCATGCGCATACTAAAATGTTGTTC 59.770 40.000 24.84 0.00 0.00 3.18
1799 1800 5.101628 CCATGCGCATACTAAAATGTTGTT 58.898 37.500 24.84 0.00 0.00 2.83
1800 1801 4.671377 CCATGCGCATACTAAAATGTTGT 58.329 39.130 24.84 0.00 0.00 3.32
1801 1802 3.486841 GCCATGCGCATACTAAAATGTTG 59.513 43.478 24.84 7.45 37.47 3.33
1802 1803 3.490761 GGCCATGCGCATACTAAAATGTT 60.491 43.478 24.84 0.00 40.31 2.71
1803 1804 2.034558 GGCCATGCGCATACTAAAATGT 59.965 45.455 24.84 0.00 40.31 2.71
1804 1805 2.034432 TGGCCATGCGCATACTAAAATG 59.966 45.455 24.84 9.66 40.31 2.32
1805 1806 2.305928 TGGCCATGCGCATACTAAAAT 58.694 42.857 24.84 0.00 40.31 1.82
1806 1807 1.756430 TGGCCATGCGCATACTAAAA 58.244 45.000 24.84 4.01 40.31 1.52
1807 1808 1.979855 ATGGCCATGCGCATACTAAA 58.020 45.000 24.84 8.48 40.31 1.85
1808 1809 1.979855 AATGGCCATGCGCATACTAA 58.020 45.000 24.84 10.02 40.31 2.24
1809 1810 1.608109 CAAATGGCCATGCGCATACTA 59.392 47.619 24.84 16.51 40.31 1.82
1810 1811 0.386476 CAAATGGCCATGCGCATACT 59.614 50.000 24.84 0.00 40.31 2.12
1811 1812 0.598158 CCAAATGGCCATGCGCATAC 60.598 55.000 24.84 17.94 40.31 2.39
1812 1813 1.740905 CCAAATGGCCATGCGCATA 59.259 52.632 24.84 7.98 40.31 3.14
1813 1814 2.502093 CCAAATGGCCATGCGCAT 59.498 55.556 21.63 19.28 40.31 4.73
1823 1824 4.001248 TTGGAGCTCGCCAAATGG 57.999 55.556 7.83 0.00 44.55 3.16
1828 1829 1.437573 CGTCTATTGGAGCTCGCCA 59.562 57.895 7.83 0.00 35.78 5.69
1829 1830 1.951631 GCGTCTATTGGAGCTCGCC 60.952 63.158 7.83 0.00 40.09 5.54
1830 1831 2.296480 CGCGTCTATTGGAGCTCGC 61.296 63.158 7.83 4.79 41.43 5.03
1831 1832 0.306840 TACGCGTCTATTGGAGCTCG 59.693 55.000 18.63 0.00 0.00 5.03
1832 1833 2.486951 TTACGCGTCTATTGGAGCTC 57.513 50.000 18.63 4.71 0.00 4.09
1833 1834 2.953466 TTTACGCGTCTATTGGAGCT 57.047 45.000 18.63 0.00 0.00 4.09
1854 1855 0.169451 CCGCCCGCGTTCTTATTTTT 59.831 50.000 4.92 0.00 37.81 1.94
1855 1856 0.674269 TCCGCCCGCGTTCTTATTTT 60.674 50.000 4.92 0.00 37.81 1.82
1856 1857 0.674269 TTCCGCCCGCGTTCTTATTT 60.674 50.000 4.92 0.00 37.81 1.40
1857 1858 0.674269 TTTCCGCCCGCGTTCTTATT 60.674 50.000 4.92 0.00 37.81 1.40
1858 1859 0.674269 TTTTCCGCCCGCGTTCTTAT 60.674 50.000 4.92 0.00 37.81 1.73
1859 1860 1.293267 CTTTTCCGCCCGCGTTCTTA 61.293 55.000 4.92 0.00 37.81 2.10
1860 1861 2.592287 TTTTCCGCCCGCGTTCTT 60.592 55.556 4.92 0.00 37.81 2.52
1861 1862 3.047877 CTTTTCCGCCCGCGTTCT 61.048 61.111 4.92 0.00 37.81 3.01
1862 1863 4.753877 GCTTTTCCGCCCGCGTTC 62.754 66.667 4.92 0.00 37.81 3.95
1868 1869 4.193334 GATGCCGCTTTTCCGCCC 62.193 66.667 0.00 0.00 0.00 6.13
1869 1870 4.536687 CGATGCCGCTTTTCCGCC 62.537 66.667 0.00 0.00 0.00 6.13
1888 1889 4.662961 GTGCCAAAACTGCCGGGC 62.663 66.667 13.32 13.32 46.58 6.13
1889 1890 4.341502 CGTGCCAAAACTGCCGGG 62.342 66.667 2.18 0.00 0.00 5.73
1890 1891 3.591835 ACGTGCCAAAACTGCCGG 61.592 61.111 0.00 0.00 0.00 6.13
1891 1892 2.353376 CACGTGCCAAAACTGCCG 60.353 61.111 0.82 0.00 0.00 5.69
1892 1893 1.299089 GACACGTGCCAAAACTGCC 60.299 57.895 17.22 0.00 0.00 4.85
1893 1894 1.654137 CGACACGTGCCAAAACTGC 60.654 57.895 17.22 0.00 0.00 4.40
1894 1895 0.315869 GACGACACGTGCCAAAACTG 60.316 55.000 17.22 0.00 41.37 3.16
1895 1896 1.433837 GGACGACACGTGCCAAAACT 61.434 55.000 17.22 0.00 42.09 2.66
1896 1897 1.010462 GGACGACACGTGCCAAAAC 60.010 57.895 17.22 2.53 42.09 2.43
1897 1898 3.412061 GGACGACACGTGCCAAAA 58.588 55.556 17.22 0.00 42.09 2.44
1902 1903 2.958016 ACGTTGGACGACACGTGC 60.958 61.111 17.22 7.72 46.05 5.34
1903 1904 2.917901 CACGTTGGACGACACGTG 59.082 61.111 15.48 15.48 46.05 4.49
1904 1905 2.894240 AAGCACGTTGGACGACACGT 62.894 55.000 7.54 0.00 46.05 4.49
1905 1906 2.235016 AAGCACGTTGGACGACACG 61.235 57.895 7.54 0.00 46.05 4.49
1906 1907 1.149361 TCAAGCACGTTGGACGACAC 61.149 55.000 7.54 0.00 46.05 3.67
1907 1908 0.249699 ATCAAGCACGTTGGACGACA 60.250 50.000 7.54 0.00 46.05 4.35
1908 1909 1.705256 TATCAAGCACGTTGGACGAC 58.295 50.000 7.54 0.00 46.05 4.34
1909 1910 2.442212 TTATCAAGCACGTTGGACGA 57.558 45.000 7.54 0.00 46.05 4.20
1916 1917 0.168128 GCGGCTTTTATCAAGCACGT 59.832 50.000 8.74 0.00 44.71 4.49
1919 1920 1.136565 GCGCGGCTTTTATCAAGCA 59.863 52.632 8.83 0.00 44.71 3.91
1923 1924 4.217111 CGCGCGCGGCTTTTATCA 62.217 61.111 43.28 0.00 40.44 2.15
1950 1951 1.745489 GGCGAGAAGATGGCGGTTT 60.745 57.895 0.00 0.00 32.50 3.27
1954 1955 2.656651 CGAGGCGAGAAGATGGCG 60.657 66.667 0.00 0.00 32.50 5.69
1958 1959 1.040339 AGAAGGCGAGGCGAGAAGAT 61.040 55.000 0.00 0.00 0.00 2.40
1962 1963 2.711922 GGAAGAAGGCGAGGCGAGA 61.712 63.158 0.00 0.00 0.00 4.04
1964 1965 2.680352 AGGAAGAAGGCGAGGCGA 60.680 61.111 0.00 0.00 0.00 5.54
1965 1966 2.202810 GAGGAAGAAGGCGAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
1966 1967 2.202810 CGAGGAAGAAGGCGAGGC 60.203 66.667 0.00 0.00 0.00 4.70
1967 1968 2.202810 GCGAGGAAGAAGGCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
1969 1970 1.215647 GAAGCGAGGAAGAAGGCGA 59.784 57.895 0.00 0.00 0.00 5.54
1970 1971 0.390472 AAGAAGCGAGGAAGAAGGCG 60.390 55.000 0.00 0.00 0.00 5.52
1971 1972 1.364721 GAAGAAGCGAGGAAGAAGGC 58.635 55.000 0.00 0.00 0.00 4.35
1977 1984 1.292223 CACCGGAAGAAGCGAGGAA 59.708 57.895 9.46 0.00 0.00 3.36
2051 2061 4.880537 CGCAGCGGTAGCCTGAGG 62.881 72.222 7.00 0.00 46.67 3.86
2114 2124 1.153168 AGCCCGATGCATGTACCAC 60.153 57.895 2.46 0.00 44.83 4.16
2117 2127 1.956170 CCGAGCCCGATGCATGTAC 60.956 63.158 2.46 0.00 44.83 2.90
2125 2135 1.153628 CGAACTTTCCGAGCCCGAT 60.154 57.895 0.00 0.00 38.22 4.18
2135 2145 1.192534 CTTGTGCGGTCTCGAACTTTC 59.807 52.381 0.00 0.00 44.96 2.62
2136 2146 1.202486 TCTTGTGCGGTCTCGAACTTT 60.202 47.619 0.00 0.00 44.96 2.66
2138 2148 0.039074 CTCTTGTGCGGTCTCGAACT 60.039 55.000 0.00 0.00 44.96 3.01
2203 2213 2.621526 TCGAGAAGTTCATATGCGCCTA 59.378 45.455 4.18 0.00 0.00 3.93
2204 2214 1.409064 TCGAGAAGTTCATATGCGCCT 59.591 47.619 4.18 0.00 0.00 5.52
2205 2215 1.852942 TCGAGAAGTTCATATGCGCC 58.147 50.000 4.18 0.00 0.00 6.53
2211 2221 1.265568 GCGCGTTCGAGAAGTTCATA 58.734 50.000 8.43 0.00 38.10 2.15
2231 2241 1.669115 TGAGTTCCTGCGCTTGCTC 60.669 57.895 9.73 9.73 40.12 4.26
2274 2284 4.286320 GGATGCGGCGATCCTCGT 62.286 66.667 22.66 3.91 42.81 4.18
2275 2285 4.284860 TGGATGCGGCGATCCTCG 62.285 66.667 26.88 0.00 42.36 4.63
2361 2371 1.670087 CGACGACATCTTGCTGGAAGT 60.670 52.381 8.80 0.00 35.30 3.01
2379 2389 1.209383 CAGAACTCGTTCTCGGCGA 59.791 57.895 10.14 10.14 46.13 5.54
2393 2403 2.596851 GCCTCCTCTGCACCCAGAA 61.597 63.158 0.00 0.00 46.84 3.02
2400 2410 4.087892 GCTTCGGCCTCCTCTGCA 62.088 66.667 0.00 0.00 34.32 4.41


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

AutoCloner maintained by Alex Coulton.