Multiple sequence alignment - TraesCS7B01G228500

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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 TraesCS7B01G228500 chr7B 100.000 2805 0 0 1 2805 428918847 428921651 0.000000e+00 5180
1 TraesCS7B01G228500 chr7B 87.621 824 96 6 2 824 499927673 499928491 0.000000e+00 952
2 TraesCS7B01G228500 chr7B 87.286 818 99 5 9 824 73486495 73485681 0.000000e+00 929
3 TraesCS7B01G228500 chr7D 95.013 1905 61 15 907 2805 414488138 414490014 0.000000e+00 2961
4 TraesCS7B01G228500 chr7D 86.972 829 104 3 1 826 543913769 543914596 0.000000e+00 929
5 TraesCS7B01G228500 chr7D 86.578 827 107 4 1 825 40387416 40388240 0.000000e+00 909
6 TraesCS7B01G228500 chr7A 93.050 1885 88 26 941 2805 476934672 476936533 0.000000e+00 2715
7 TraesCS7B01G228500 chr1D 87.319 828 103 2 1 827 1449152 1448326 0.000000e+00 946
8 TraesCS7B01G228500 chr1D 86.320 826 111 2 7 831 40177327 40176503 0.000000e+00 898
9 TraesCS7B01G228500 chr2D 87.349 830 96 8 1 824 609979930 609980756 0.000000e+00 942
10 TraesCS7B01G228500 chr2D 84.865 185 28 0 2173 2357 483786126 483785942 1.330000e-43 187
11 TraesCS7B01G228500 chr2D 87.582 153 19 0 2495 2647 483785633 483785481 7.980000e-41 178
12 TraesCS7B01G228500 chr6D 86.925 826 104 4 1 824 367429381 367428558 0.000000e+00 924
13 TraesCS7B01G228500 chr5D 86.788 825 107 2 1 824 543574317 543575140 0.000000e+00 918
14 TraesCS7B01G228500 chr2B 85.185 189 27 1 2173 2361 568635606 568635419 2.850000e-45 193
15 TraesCS7B01G228500 chr2B 86.275 153 21 0 2495 2647 568635116 568634964 1.730000e-37 167
16 TraesCS7B01G228500 chr2A 85.405 185 27 0 2173 2357 627611144 627610960 2.850000e-45 193
17 TraesCS7B01G228500 chr2A 85.621 153 22 0 2495 2647 627610645 627610493 8.040000e-36 161


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 TraesCS7B01G228500 chr7B 428918847 428921651 2804 False 5180 5180 100.000 1 2805 1 chr7B.!!$F1 2804
1 TraesCS7B01G228500 chr7B 499927673 499928491 818 False 952 952 87.621 2 824 1 chr7B.!!$F2 822
2 TraesCS7B01G228500 chr7B 73485681 73486495 814 True 929 929 87.286 9 824 1 chr7B.!!$R1 815
3 TraesCS7B01G228500 chr7D 414488138 414490014 1876 False 2961 2961 95.013 907 2805 1 chr7D.!!$F2 1898
4 TraesCS7B01G228500 chr7D 543913769 543914596 827 False 929 929 86.972 1 826 1 chr7D.!!$F3 825
5 TraesCS7B01G228500 chr7D 40387416 40388240 824 False 909 909 86.578 1 825 1 chr7D.!!$F1 824
6 TraesCS7B01G228500 chr7A 476934672 476936533 1861 False 2715 2715 93.050 941 2805 1 chr7A.!!$F1 1864
7 TraesCS7B01G228500 chr1D 1448326 1449152 826 True 946 946 87.319 1 827 1 chr1D.!!$R1 826
8 TraesCS7B01G228500 chr1D 40176503 40177327 824 True 898 898 86.320 7 831 1 chr1D.!!$R2 824
9 TraesCS7B01G228500 chr2D 609979930 609980756 826 False 942 942 87.349 1 824 1 chr2D.!!$F1 823
10 TraesCS7B01G228500 chr6D 367428558 367429381 823 True 924 924 86.925 1 824 1 chr6D.!!$R1 823
11 TraesCS7B01G228500 chr5D 543574317 543575140 823 False 918 918 86.788 1 824 1 chr5D.!!$F1 823

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
664 670 0.10339 TCTCGACAACGTCTTTGCCA 59.897 50.0 0.0 0.0 39.01 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2171 0.396695 AGGCAACGCTAGGCTACCTA 60.397 55.0 0.0 0.0 46.39 3.08 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
30 31 2.168947 GACATGTGTCAGCCTGCTG 58.831 57.895 12.91 12.91 44.18 4.41
104 108 1.300963 CTGGTCCCACATGTCAGGG 59.699 63.158 13.98 13.98 46.90 4.45
105 109 1.463214 TGGTCCCACATGTCAGGGT 60.463 57.895 18.35 0.00 45.64 4.34
106 110 1.065410 TGGTCCCACATGTCAGGGTT 61.065 55.000 18.35 0.00 45.64 4.11
107 111 0.322546 GGTCCCACATGTCAGGGTTC 60.323 60.000 18.35 13.18 45.64 3.62
123 127 1.512926 GTTCGACACATGTCAGCCTT 58.487 50.000 12.32 0.00 44.99 4.35
191 195 1.077501 CATGTTCGCCTGGTCCCAT 60.078 57.895 0.00 0.00 0.00 4.00
192 196 1.097547 CATGTTCGCCTGGTCCCATC 61.098 60.000 0.00 0.00 0.00 3.51
227 231 1.002366 CGTGTCAATCTGCTACTGGC 58.998 55.000 0.00 0.00 42.22 4.85
229 233 2.275318 GTGTCAATCTGCTACTGGCTC 58.725 52.381 0.00 0.00 42.39 4.70
261 265 1.449782 TGGCACTCGGCAAAGAAGA 59.550 52.632 0.00 0.00 46.20 2.87
556 560 2.351276 GGCAAAGAAGGCCCTCGA 59.649 61.111 0.00 0.00 45.87 4.04
563 567 2.930562 AAGGCCCTCGACCTGCTT 60.931 61.111 0.00 0.00 37.67 3.91
594 598 1.301479 GTGTCAGGAACCACCGTCC 60.301 63.158 0.00 0.00 44.74 4.79
629 633 5.577945 TCCGTTAGCTACTTTATTTTGTCGG 59.422 40.000 0.00 0.00 0.00 4.79
650 656 1.000506 GTGGTACTGTTTGGCTCTCGA 59.999 52.381 0.00 0.00 0.00 4.04
654 660 1.583054 ACTGTTTGGCTCTCGACAAC 58.417 50.000 0.00 0.00 38.04 3.32
664 670 0.103390 TCTCGACAACGTCTTTGCCA 59.897 50.000 0.00 0.00 39.01 4.92
694 700 3.251004 GTGTTCTGACTCTCGGCAAATTT 59.749 43.478 0.00 0.00 0.00 1.82
724 730 3.688159 GAGGTGTACGCCGGGTGT 61.688 66.667 19.53 18.47 0.00 4.16
779 785 2.257371 GCGGTTTTCGGCCCTTTC 59.743 61.111 0.00 0.00 39.70 2.62
788 794 2.434774 GGCCCTTTCCCGAGTGTT 59.565 61.111 0.00 0.00 0.00 3.32
790 796 0.826256 GGCCCTTTCCCGAGTGTTTT 60.826 55.000 0.00 0.00 0.00 2.43
801 807 3.184736 AGTGTTTTTGGCACTCGGT 57.815 47.368 0.00 0.00 42.90 4.69
806 812 3.499157 GTGTTTTTGGCACTCGGTATACA 59.501 43.478 5.01 0.00 34.30 2.29
831 837 4.466370 CAGAATTCCAGTAGTGACACCCTA 59.534 45.833 0.84 0.00 0.00 3.53
832 838 5.129485 CAGAATTCCAGTAGTGACACCCTAT 59.871 44.000 0.84 0.00 0.00 2.57
833 839 5.129485 AGAATTCCAGTAGTGACACCCTATG 59.871 44.000 0.84 0.00 0.00 2.23
834 840 3.750501 TCCAGTAGTGACACCCTATGA 57.249 47.619 0.84 0.00 0.00 2.15
835 841 4.055710 TCCAGTAGTGACACCCTATGAA 57.944 45.455 0.84 0.00 0.00 2.57
836 842 4.620723 TCCAGTAGTGACACCCTATGAAT 58.379 43.478 0.84 0.00 0.00 2.57
837 843 4.649674 TCCAGTAGTGACACCCTATGAATC 59.350 45.833 0.84 0.00 0.00 2.52
838 844 4.651503 CCAGTAGTGACACCCTATGAATCT 59.348 45.833 0.84 0.00 0.00 2.40
839 845 5.833667 CCAGTAGTGACACCCTATGAATCTA 59.166 44.000 0.84 0.00 0.00 1.98
840 846 6.495181 CCAGTAGTGACACCCTATGAATCTAT 59.505 42.308 0.84 0.00 0.00 1.98
841 847 7.670140 CCAGTAGTGACACCCTATGAATCTATA 59.330 40.741 0.84 0.00 0.00 1.31
842 848 9.249053 CAGTAGTGACACCCTATGAATCTATAT 57.751 37.037 0.84 0.00 0.00 0.86
843 849 9.830186 AGTAGTGACACCCTATGAATCTATATT 57.170 33.333 0.84 0.00 0.00 1.28
866 872 8.908786 ATTCACCACGATCATTATTATGAAGT 57.091 30.769 0.00 0.04 43.67 3.01
867 873 7.946655 TCACCACGATCATTATTATGAAGTC 57.053 36.000 0.00 0.00 43.67 3.01
868 874 6.640907 TCACCACGATCATTATTATGAAGTCG 59.359 38.462 13.38 13.38 43.67 4.18
873 879 8.642908 ACGATCATTATTATGAAGTCGTGAAA 57.357 30.769 17.73 0.00 46.59 2.69
874 880 9.261180 ACGATCATTATTATGAAGTCGTGAAAT 57.739 29.630 17.73 0.00 46.59 2.17
878 884 9.914923 TCATTATTATGAAGTCGTGAAATTTCG 57.085 29.630 13.34 3.42 37.83 3.46
879 885 9.914923 CATTATTATGAAGTCGTGAAATTTCGA 57.085 29.630 13.34 5.83 33.37 3.71
891 897 8.483743 TCGTGAAATTTCGACTAACAAAAATC 57.516 30.769 13.34 0.00 0.00 2.17
892 898 8.339714 TCGTGAAATTTCGACTAACAAAAATCT 58.660 29.630 13.34 0.00 0.00 2.40
893 899 9.588774 CGTGAAATTTCGACTAACAAAAATCTA 57.411 29.630 13.34 0.00 0.00 1.98
899 905 8.651391 TTTCGACTAACAAAAATCTACACTCA 57.349 30.769 0.00 0.00 0.00 3.41
900 906 8.827177 TTCGACTAACAAAAATCTACACTCAT 57.173 30.769 0.00 0.00 0.00 2.90
901 907 9.917129 TTCGACTAACAAAAATCTACACTCATA 57.083 29.630 0.00 0.00 0.00 2.15
902 908 9.917129 TCGACTAACAAAAATCTACACTCATAA 57.083 29.630 0.00 0.00 0.00 1.90
904 910 9.974750 GACTAACAAAAATCTACACTCATAAGC 57.025 33.333 0.00 0.00 0.00 3.09
905 911 8.947115 ACTAACAAAAATCTACACTCATAAGCC 58.053 33.333 0.00 0.00 0.00 4.35
944 950 9.216117 AGTTGCGTAAAGTATCAGTATTTTTCT 57.784 29.630 0.00 0.00 0.00 2.52
1052 1059 2.124983 CCATGGCCACAGGAGTCG 60.125 66.667 19.13 0.00 0.00 4.18
1229 1236 1.080434 GCTGACTGTGTCGGACTCC 60.080 63.158 9.88 0.77 41.05 3.85
1675 1682 4.293415 CAAAACCAGAAGCAACAGTGATC 58.707 43.478 0.00 0.00 0.00 2.92
1726 1748 5.779529 TCTCTGCTTTGCATTTCTTTCTT 57.220 34.783 0.00 0.00 38.13 2.52
1727 1749 6.152932 TCTCTGCTTTGCATTTCTTTCTTT 57.847 33.333 0.00 0.00 38.13 2.52
1728 1750 6.211515 TCTCTGCTTTGCATTTCTTTCTTTC 58.788 36.000 0.00 0.00 38.13 2.62
1729 1751 6.040166 TCTCTGCTTTGCATTTCTTTCTTTCT 59.960 34.615 0.00 0.00 38.13 2.52
1730 1752 6.576185 TCTGCTTTGCATTTCTTTCTTTCTT 58.424 32.000 0.00 0.00 38.13 2.52
1731 1753 7.043565 TCTGCTTTGCATTTCTTTCTTTCTTT 58.956 30.769 0.00 0.00 38.13 2.52
1732 1754 7.223387 TCTGCTTTGCATTTCTTTCTTTCTTTC 59.777 33.333 0.00 0.00 38.13 2.62
1733 1755 7.043565 TGCTTTGCATTTCTTTCTTTCTTTCT 58.956 30.769 0.00 0.00 31.71 2.52
1810 1832 8.900511 AATGTTGAAATTGATCGATACACTTG 57.099 30.769 0.00 0.00 0.00 3.16
1895 1919 2.880890 TCTCTCTTGTTTGCTTGCTTCC 59.119 45.455 0.00 0.00 0.00 3.46
1998 2024 2.431419 TGACGAACACCTTACACCAGAA 59.569 45.455 0.00 0.00 0.00 3.02
1999 2025 3.057734 GACGAACACCTTACACCAGAAG 58.942 50.000 0.00 0.00 0.00 2.85
2001 2027 3.243771 ACGAACACCTTACACCAGAAGAG 60.244 47.826 0.00 0.00 0.00 2.85
2002 2028 3.005472 CGAACACCTTACACCAGAAGAGA 59.995 47.826 0.00 0.00 0.00 3.10
2004 2030 5.365619 GAACACCTTACACCAGAAGAGAAA 58.634 41.667 0.00 0.00 0.00 2.52
2005 2031 4.962155 ACACCTTACACCAGAAGAGAAAG 58.038 43.478 0.00 0.00 0.00 2.62
2006 2032 4.654262 ACACCTTACACCAGAAGAGAAAGA 59.346 41.667 0.00 0.00 0.00 2.52
2007 2033 5.130477 ACACCTTACACCAGAAGAGAAAGAA 59.870 40.000 0.00 0.00 0.00 2.52
2008 2034 5.467063 CACCTTACACCAGAAGAGAAAGAAC 59.533 44.000 0.00 0.00 0.00 3.01
2009 2035 5.130477 ACCTTACACCAGAAGAGAAAGAACA 59.870 40.000 0.00 0.00 0.00 3.18
2010 2036 5.467063 CCTTACACCAGAAGAGAAAGAACAC 59.533 44.000 0.00 0.00 0.00 3.32
2011 2037 4.487714 ACACCAGAAGAGAAAGAACACA 57.512 40.909 0.00 0.00 0.00 3.72
2012 2038 4.446371 ACACCAGAAGAGAAAGAACACAG 58.554 43.478 0.00 0.00 0.00 3.66
2013 2039 3.812053 CACCAGAAGAGAAAGAACACAGG 59.188 47.826 0.00 0.00 0.00 4.00
2014 2040 3.711704 ACCAGAAGAGAAAGAACACAGGA 59.288 43.478 0.00 0.00 0.00 3.86
2015 2041 4.202305 ACCAGAAGAGAAAGAACACAGGAG 60.202 45.833 0.00 0.00 0.00 3.69
2016 2042 4.202305 CCAGAAGAGAAAGAACACAGGAGT 60.202 45.833 0.00 0.00 0.00 3.85
2017 2043 5.011125 CCAGAAGAGAAAGAACACAGGAGTA 59.989 44.000 0.00 0.00 0.00 2.59
2027 2053 9.303537 GAAAGAACACAGGAGTAAGTATATGAC 57.696 37.037 0.00 0.00 0.00 3.06
2032 2058 5.928839 CACAGGAGTAAGTATATGACATGGC 59.071 44.000 0.00 0.00 0.00 4.40
2054 2084 3.692576 GCAATTCACTCATGAGCATGAC 58.307 45.455 22.83 4.56 42.42 3.06
2092 2122 3.070018 AGAGAAAGCACAATCAAGACCG 58.930 45.455 0.00 0.00 0.00 4.79
2104 2134 1.134521 TCAAGACCGGAATGGATTCGG 60.135 52.381 9.46 0.00 42.00 4.30
2133 2163 3.599584 GACCTCGGTCGGTGATGA 58.400 61.111 0.00 0.00 37.42 2.92
2134 2164 2.116383 GACCTCGGTCGGTGATGAT 58.884 57.895 0.00 0.00 37.42 2.45
2135 2165 0.249073 GACCTCGGTCGGTGATGATG 60.249 60.000 0.00 0.00 37.42 3.07
2136 2166 1.068083 CCTCGGTCGGTGATGATGG 59.932 63.158 0.00 0.00 0.00 3.51
2137 2167 1.592669 CTCGGTCGGTGATGATGGC 60.593 63.158 0.00 0.00 0.00 4.40
2138 2168 2.186644 CGGTCGGTGATGATGGCA 59.813 61.111 0.00 0.00 0.00 4.92
2139 2169 2.173669 CGGTCGGTGATGATGGCAC 61.174 63.158 0.00 0.00 35.56 5.01
2141 2171 1.447838 GTCGGTGATGATGGCACGT 60.448 57.895 0.00 0.00 37.13 4.49
2142 2172 0.179121 GTCGGTGATGATGGCACGTA 60.179 55.000 0.00 0.00 37.13 3.57
2143 2173 0.102300 TCGGTGATGATGGCACGTAG 59.898 55.000 0.00 0.00 37.13 3.51
2155 2188 1.722636 GCACGTAGGTAGCCTAGCGT 61.723 60.000 13.11 13.11 41.04 5.07
2158 2191 0.594284 CGTAGGTAGCCTAGCGTTGC 60.594 60.000 0.00 0.00 36.71 4.17
2167 2200 1.815421 CTAGCGTTGCCTGCGGATT 60.815 57.895 0.00 0.00 37.44 3.01
2278 2311 0.394762 GGAACTGCATGCAGATGGGA 60.395 55.000 45.50 13.04 46.30 4.37
2279 2312 1.466856 GAACTGCATGCAGATGGGAA 58.533 50.000 45.50 12.26 46.30 3.97
2422 2455 3.436728 GCCTTTGGCCGGATGATC 58.563 61.111 5.05 0.00 44.06 2.92
2557 2590 1.289380 GGTGAAGACGGAGAGCGTT 59.711 57.895 0.00 0.00 0.00 4.84
2769 2805 4.195334 CATAGCCGGGGCCTTGCT 62.195 66.667 20.92 20.92 43.17 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 89 1.492133 CCCTGACATGTGGGACCAGT 61.492 60.000 14.85 0.00 46.15 4.00
123 127 3.073798 TCTTGGCAAACTCACCCAATAGA 59.926 43.478 0.00 0.00 37.92 1.98
247 251 0.321996 GAGGGTCTTCTTTGCCGAGT 59.678 55.000 0.00 0.00 0.00 4.18
261 265 4.778143 GGCGAACATGCCGAGGGT 62.778 66.667 11.63 0.00 46.75 4.34
282 286 2.608988 AGCTCCTGACAGGTGGGG 60.609 66.667 21.06 10.85 36.53 4.96
314 318 3.517296 TGGCAAACTCACCCAATAGAA 57.483 42.857 0.00 0.00 0.00 2.10
315 319 3.073798 TCTTGGCAAACTCACCCAATAGA 59.926 43.478 0.00 0.00 37.92 1.98
373 377 1.843376 CCTGACAGGTGGGACCAGT 60.843 63.158 13.84 0.00 40.96 4.00
530 534 0.962356 CCTTCTTTGCCGAGTGCCAT 60.962 55.000 0.00 0.00 40.16 4.40
556 560 2.936032 GGGACCAGGGAAGCAGGT 60.936 66.667 0.00 0.00 38.63 4.00
563 567 2.920912 GACACGTGGGACCAGGGA 60.921 66.667 21.57 0.00 36.28 4.20
594 598 3.867723 CTAACGGATAGCAGACGGG 57.132 57.895 0.00 0.00 0.00 5.28
629 633 1.809684 GAGAGCCAAACAGTACCACC 58.190 55.000 0.00 0.00 0.00 4.61
650 656 0.100503 GCACTTGGCAAAGACGTTGT 59.899 50.000 8.15 0.00 43.97 3.32
664 670 0.249911 GAGTCAGAACACGGGCACTT 60.250 55.000 0.00 0.00 0.00 3.16
694 700 0.468226 ACACCTCTTCGGCAAACAGA 59.532 50.000 0.00 0.00 35.61 3.41
724 730 0.534203 GTGTCACCCTCGGCAAAAGA 60.534 55.000 0.00 0.00 0.00 2.52
779 785 2.414750 AGTGCCAAAAACACTCGGG 58.585 52.632 0.00 0.00 45.06 5.14
788 794 4.081365 TCTGATGTATACCGAGTGCCAAAA 60.081 41.667 0.00 0.00 0.00 2.44
790 796 3.028130 TCTGATGTATACCGAGTGCCAA 58.972 45.455 0.00 0.00 0.00 4.52
801 807 8.414003 GTGTCACTACTGGAATTCTGATGTATA 58.586 37.037 5.23 0.00 0.00 1.47
806 812 4.080863 GGGTGTCACTACTGGAATTCTGAT 60.081 45.833 5.23 0.00 0.00 2.90
840 846 9.996554 ACTTCATAATAATGATCGTGGTGAATA 57.003 29.630 0.00 0.00 41.73 1.75
841 847 8.908786 ACTTCATAATAATGATCGTGGTGAAT 57.091 30.769 0.00 0.00 41.73 2.57
842 848 7.169140 CGACTTCATAATAATGATCGTGGTGAA 59.831 37.037 0.00 0.00 41.73 3.18
843 849 6.640907 CGACTTCATAATAATGATCGTGGTGA 59.359 38.462 0.00 0.00 41.73 4.02
844 850 6.811299 CGACTTCATAATAATGATCGTGGTG 58.189 40.000 0.00 0.00 41.73 4.17
852 858 9.914923 CGAAATTTCACGACTTCATAATAATGA 57.085 29.630 17.99 0.00 40.43 2.57
853 859 9.914923 TCGAAATTTCACGACTTCATAATAATG 57.085 29.630 17.99 0.00 33.62 1.90
866 872 8.339714 AGATTTTTGTTAGTCGAAATTTCACGA 58.660 29.630 17.99 8.32 36.18 4.35
867 873 8.488979 AGATTTTTGTTAGTCGAAATTTCACG 57.511 30.769 17.99 6.00 30.53 4.35
873 879 9.268268 TGAGTGTAGATTTTTGTTAGTCGAAAT 57.732 29.630 0.00 0.00 30.53 2.17
874 880 8.651391 TGAGTGTAGATTTTTGTTAGTCGAAA 57.349 30.769 0.00 0.00 0.00 3.46
875 881 8.827177 ATGAGTGTAGATTTTTGTTAGTCGAA 57.173 30.769 0.00 0.00 0.00 3.71
876 882 9.917129 TTATGAGTGTAGATTTTTGTTAGTCGA 57.083 29.630 0.00 0.00 0.00 4.20
878 884 9.974750 GCTTATGAGTGTAGATTTTTGTTAGTC 57.025 33.333 0.00 0.00 0.00 2.59
879 885 8.947115 GGCTTATGAGTGTAGATTTTTGTTAGT 58.053 33.333 0.00 0.00 0.00 2.24
880 886 9.167311 AGGCTTATGAGTGTAGATTTTTGTTAG 57.833 33.333 0.00 0.00 0.00 2.34
882 888 9.515226 TTAGGCTTATGAGTGTAGATTTTTGTT 57.485 29.630 0.00 0.00 0.00 2.83
883 889 9.167311 CTTAGGCTTATGAGTGTAGATTTTTGT 57.833 33.333 0.00 0.00 0.00 2.83
884 890 8.125448 GCTTAGGCTTATGAGTGTAGATTTTTG 58.875 37.037 0.00 0.00 35.22 2.44
885 891 8.214721 GCTTAGGCTTATGAGTGTAGATTTTT 57.785 34.615 0.00 0.00 35.22 1.94
886 892 7.793927 GCTTAGGCTTATGAGTGTAGATTTT 57.206 36.000 0.00 0.00 35.22 1.82
903 909 2.094417 CGCAACTAGTTTCAGCTTAGGC 59.906 50.000 5.07 2.07 39.06 3.93
904 910 3.326747 ACGCAACTAGTTTCAGCTTAGG 58.673 45.455 5.07 0.00 0.00 2.69
905 911 6.145696 ACTTTACGCAACTAGTTTCAGCTTAG 59.854 38.462 5.07 1.59 0.00 2.18
943 949 5.995282 TGTCGGGGTTATCTGCAAATATTAG 59.005 40.000 0.00 0.00 0.00 1.73
944 950 5.931294 TGTCGGGGTTATCTGCAAATATTA 58.069 37.500 0.00 0.00 0.00 0.98
1052 1059 3.512516 GGTGCGCTGATGGCTTCC 61.513 66.667 9.73 0.00 39.13 3.46
1065 1072 1.665599 GTTGTTGCATGGCTGGTGC 60.666 57.895 0.00 3.68 42.81 5.01
1068 1075 2.259204 CGGTTGTTGCATGGCTGG 59.741 61.111 0.00 0.00 0.00 4.85
1128 1135 4.379243 CGGGCTGAGCTTGACGGT 62.379 66.667 3.72 0.00 0.00 4.83
1427 1434 3.708734 GCGTTGAACACCCCGTCG 61.709 66.667 0.00 0.00 0.00 5.12
1675 1682 6.412214 TGGATGAATGATGATGGCAGTATAG 58.588 40.000 0.00 0.00 0.00 1.31
1726 1748 9.471084 ACAAACGAAAAAGAAAGAAAGAAAGAA 57.529 25.926 0.00 0.00 0.00 2.52
1727 1749 9.471084 AACAAACGAAAAAGAAAGAAAGAAAGA 57.529 25.926 0.00 0.00 0.00 2.52
1728 1750 9.727403 GAACAAACGAAAAAGAAAGAAAGAAAG 57.273 29.630 0.00 0.00 0.00 2.62
1729 1751 9.471084 AGAACAAACGAAAAAGAAAGAAAGAAA 57.529 25.926 0.00 0.00 0.00 2.52
1730 1752 8.911662 CAGAACAAACGAAAAAGAAAGAAAGAA 58.088 29.630 0.00 0.00 0.00 2.52
1731 1753 7.061789 GCAGAACAAACGAAAAAGAAAGAAAGA 59.938 33.333 0.00 0.00 0.00 2.52
1732 1754 7.166824 GCAGAACAAACGAAAAAGAAAGAAAG 58.833 34.615 0.00 0.00 0.00 2.62
1733 1755 6.090223 GGCAGAACAAACGAAAAAGAAAGAAA 59.910 34.615 0.00 0.00 0.00 2.52
1740 1762 2.535574 GCTGGCAGAACAAACGAAAAAG 59.464 45.455 20.86 0.00 0.00 2.27
1895 1919 2.919666 ACATTTTCGATTTCCAGCGG 57.080 45.000 0.00 0.00 0.00 5.52
1928 1954 9.607988 TGGAATGTAACTATGTAAGTGTATTGG 57.392 33.333 0.00 0.00 38.88 3.16
1998 2024 7.784470 ATACTTACTCCTGTGTTCTTTCTCT 57.216 36.000 0.00 0.00 0.00 3.10
1999 2025 9.522804 CATATACTTACTCCTGTGTTCTTTCTC 57.477 37.037 0.00 0.00 0.00 2.87
2001 2027 9.303537 GTCATATACTTACTCCTGTGTTCTTTC 57.696 37.037 0.00 0.00 0.00 2.62
2002 2028 8.812972 TGTCATATACTTACTCCTGTGTTCTTT 58.187 33.333 0.00 0.00 0.00 2.52
2004 2030 7.956328 TGTCATATACTTACTCCTGTGTTCT 57.044 36.000 0.00 0.00 0.00 3.01
2005 2031 7.653713 CCATGTCATATACTTACTCCTGTGTTC 59.346 40.741 0.00 0.00 0.00 3.18
2006 2032 7.500992 CCATGTCATATACTTACTCCTGTGTT 58.499 38.462 0.00 0.00 0.00 3.32
2007 2033 6.463049 GCCATGTCATATACTTACTCCTGTGT 60.463 42.308 0.00 0.00 0.00 3.72
2008 2034 5.928839 GCCATGTCATATACTTACTCCTGTG 59.071 44.000 0.00 0.00 0.00 3.66
2009 2035 5.279006 CGCCATGTCATATACTTACTCCTGT 60.279 44.000 0.00 0.00 0.00 4.00
2010 2036 5.164233 CGCCATGTCATATACTTACTCCTG 58.836 45.833 0.00 0.00 0.00 3.86
2011 2037 4.322049 GCGCCATGTCATATACTTACTCCT 60.322 45.833 0.00 0.00 0.00 3.69
2012 2038 3.927142 GCGCCATGTCATATACTTACTCC 59.073 47.826 0.00 0.00 0.00 3.85
2013 2039 4.556233 TGCGCCATGTCATATACTTACTC 58.444 43.478 4.18 0.00 0.00 2.59
2014 2040 4.600692 TGCGCCATGTCATATACTTACT 57.399 40.909 4.18 0.00 0.00 2.24
2015 2041 5.862924 ATTGCGCCATGTCATATACTTAC 57.137 39.130 4.18 0.00 0.00 2.34
2016 2042 5.994668 TGAATTGCGCCATGTCATATACTTA 59.005 36.000 4.18 0.00 0.00 2.24
2017 2043 4.821260 TGAATTGCGCCATGTCATATACTT 59.179 37.500 4.18 0.00 0.00 2.24
2027 2053 1.402613 TCATGAGTGAATTGCGCCATG 59.597 47.619 4.18 8.83 37.19 3.66
2032 2058 2.353579 TCATGCTCATGAGTGAATTGCG 59.646 45.455 23.38 4.94 42.42 4.85
2054 2084 8.567948 TGCTTTCTCTACTTTACTTTGATTTGG 58.432 33.333 0.00 0.00 0.00 3.28
2092 2122 1.532868 CGATGCTTCCGAATCCATTCC 59.467 52.381 0.00 0.00 33.28 3.01
2104 2134 4.005032 GAGGTCGCTCGATGCTTC 57.995 61.111 0.00 0.00 40.11 3.86
2135 2165 1.363080 GCTAGGCTACCTACGTGCC 59.637 63.158 5.74 5.74 46.42 5.01
2136 2166 1.008767 CGCTAGGCTACCTACGTGC 60.009 63.158 0.00 0.00 34.61 5.34
2137 2167 0.737219 AACGCTAGGCTACCTACGTG 59.263 55.000 16.43 10.18 40.24 4.49
2138 2168 0.737219 CAACGCTAGGCTACCTACGT 59.263 55.000 12.42 12.42 41.61 3.57
2139 2169 0.594284 GCAACGCTAGGCTACCTACG 60.594 60.000 11.50 11.50 37.00 3.51
2141 2171 0.396695 AGGCAACGCTAGGCTACCTA 60.397 55.000 0.00 0.00 46.39 3.08
2142 2172 1.686110 AGGCAACGCTAGGCTACCT 60.686 57.895 0.00 0.00 46.39 3.08
2143 2173 1.521681 CAGGCAACGCTAGGCTACC 60.522 63.158 0.00 0.00 40.22 3.18
2347 2380 1.675641 GATGGTGGTGCTGGTGACC 60.676 63.158 0.00 0.00 0.00 4.02
2422 2455 2.797278 CCCCTTCTCCATCGTCGGG 61.797 68.421 0.00 0.00 0.00 5.14
2727 2763 4.680237 CACCGTCAGGAGCCGCAA 62.680 66.667 0.00 0.00 41.02 4.85
2753 2789 4.195334 CAGCAAGGCCCCGGCTAT 62.195 66.667 12.49 0.00 37.50 2.97
2769 2805 1.070615 CACATGGACGACACCACCA 59.929 57.895 0.00 0.00 43.03 4.17


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

AutoCloner maintained by Alex Coulton.