Multiple sequence alignment - TraesCS3D01G259200

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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 TraesCS3D01G259200 chr3D 100.000 2123 0 0 1 2123 361145785 361147907 0.000000e+00 3921.0
1 TraesCS3D01G259200 chr3B 92.284 1607 89 19 112 1703 470501805 470503391 0.000000e+00 2248.0
2 TraesCS3D01G259200 chr3B 90.580 138 12 1 1754 1891 470514527 470514663 4.650000e-42 182.0
3 TraesCS3D01G259200 chr3A 88.139 1779 100 45 147 1889 481092327 481094030 0.000000e+00 2013.0
4 TraesCS3D01G259200 chr1D 93.671 79 5 0 1033 1111 453269181 453269259 3.700000e-23 119.0
5 TraesCS3D01G259200 chr1B 93.671 79 5 0 1033 1111 623766360 623766438 3.700000e-23 119.0
6 TraesCS3D01G259200 chr1B 81.818 110 13 6 1003 1109 608379857 608379752 3.750000e-13 86.1
7 TraesCS3D01G259200 chr5B 88.000 100 11 1 1 100 691589130 691589032 1.330000e-22 117.0


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 TraesCS3D01G259200 chr3D 361145785 361147907 2122 False 3921 3921 100.000 1 2123 1 chr3D.!!$F1 2122
1 TraesCS3D01G259200 chr3B 470501805 470503391 1586 False 2248 2248 92.284 112 1703 1 chr3B.!!$F1 1591
2 TraesCS3D01G259200 chr3A 481092327 481094030 1703 False 2013 2013 88.139 147 1889 1 chr3A.!!$F1 1742

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
425 440 0.458669 GCGAGATCAGTTACCCGGAA 59.541 55.0 0.73 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1845 1.003839 TGGTTGGCTAGCAGAACCG 60.004 57.895 29.04 0.0 41.85 4.44 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
19 20 1.734163 AATGGTTAAAGGCGTCTCCG 58.266 50.000 0.00 0.00 40.77 4.63
33 34 4.427096 CGTCTCCGCTAATCATGTATCT 57.573 45.455 0.00 0.00 0.00 1.98
34 35 4.799678 CGTCTCCGCTAATCATGTATCTT 58.200 43.478 0.00 0.00 0.00 2.40
35 36 4.854291 CGTCTCCGCTAATCATGTATCTTC 59.146 45.833 0.00 0.00 0.00 2.87
36 37 5.164954 GTCTCCGCTAATCATGTATCTTCC 58.835 45.833 0.00 0.00 0.00 3.46
37 38 4.220821 TCTCCGCTAATCATGTATCTTCCC 59.779 45.833 0.00 0.00 0.00 3.97
38 39 3.901222 TCCGCTAATCATGTATCTTCCCA 59.099 43.478 0.00 0.00 0.00 4.37
39 40 4.021104 TCCGCTAATCATGTATCTTCCCAG 60.021 45.833 0.00 0.00 0.00 4.45
40 41 4.021104 CCGCTAATCATGTATCTTCCCAGA 60.021 45.833 0.00 0.00 0.00 3.86
41 42 5.511373 CCGCTAATCATGTATCTTCCCAGAA 60.511 44.000 0.00 0.00 30.76 3.02
42 43 6.169094 CGCTAATCATGTATCTTCCCAGAAT 58.831 40.000 0.00 0.00 30.76 2.40
43 44 6.312426 CGCTAATCATGTATCTTCCCAGAATC 59.688 42.308 0.00 0.00 30.76 2.52
44 45 7.393216 GCTAATCATGTATCTTCCCAGAATCT 58.607 38.462 0.00 0.00 30.76 2.40
45 46 7.333921 GCTAATCATGTATCTTCCCAGAATCTG 59.666 40.741 2.68 2.68 30.76 2.90
58 59 5.350504 CCAGAATCTGGTCATTCTACTGT 57.649 43.478 20.76 0.00 45.82 3.55
59 60 5.738909 CCAGAATCTGGTCATTCTACTGTT 58.261 41.667 20.76 0.00 45.82 3.16
60 61 6.176183 CCAGAATCTGGTCATTCTACTGTTT 58.824 40.000 20.76 0.00 45.82 2.83
61 62 6.656693 CCAGAATCTGGTCATTCTACTGTTTT 59.343 38.462 20.76 0.00 45.82 2.43
62 63 7.148340 CCAGAATCTGGTCATTCTACTGTTTTC 60.148 40.741 20.76 0.00 45.82 2.29
63 64 7.388776 CAGAATCTGGTCATTCTACTGTTTTCA 59.611 37.037 1.53 0.00 40.52 2.69
64 65 7.939039 AGAATCTGGTCATTCTACTGTTTTCAA 59.061 33.333 0.00 0.00 40.67 2.69
65 66 8.641498 AATCTGGTCATTCTACTGTTTTCAAT 57.359 30.769 0.00 0.00 0.00 2.57
66 67 9.739276 AATCTGGTCATTCTACTGTTTTCAATA 57.261 29.630 0.00 0.00 0.00 1.90
67 68 9.911788 ATCTGGTCATTCTACTGTTTTCAATAT 57.088 29.630 0.00 0.00 0.00 1.28
68 69 9.739276 TCTGGTCATTCTACTGTTTTCAATATT 57.261 29.630 0.00 0.00 0.00 1.28
80 81 9.143155 ACTGTTTTCAATATTAAACTTCACCCT 57.857 29.630 12.72 0.00 35.73 4.34
81 82 9.410556 CTGTTTTCAATATTAAACTTCACCCTG 57.589 33.333 12.72 0.00 35.73 4.45
82 83 8.919145 TGTTTTCAATATTAAACTTCACCCTGT 58.081 29.630 12.72 0.00 35.73 4.00
83 84 9.191995 GTTTTCAATATTAAACTTCACCCTGTG 57.808 33.333 6.59 0.00 32.79 3.66
84 85 7.461182 TTCAATATTAAACTTCACCCTGTGG 57.539 36.000 0.00 0.00 33.87 4.17
85 86 6.785076 TCAATATTAAACTTCACCCTGTGGA 58.215 36.000 0.00 0.00 33.87 4.02
86 87 7.235079 TCAATATTAAACTTCACCCTGTGGAA 58.765 34.615 0.00 0.00 33.87 3.53
87 88 7.726291 TCAATATTAAACTTCACCCTGTGGAAA 59.274 33.333 0.00 0.00 33.87 3.13
88 89 8.364142 CAATATTAAACTTCACCCTGTGGAAAA 58.636 33.333 0.00 0.00 33.87 2.29
89 90 6.800072 ATTAAACTTCACCCTGTGGAAAAA 57.200 33.333 0.00 0.00 33.87 1.94
90 91 4.736126 AAACTTCACCCTGTGGAAAAAG 57.264 40.909 0.00 0.00 33.87 2.27
91 92 3.382083 ACTTCACCCTGTGGAAAAAGT 57.618 42.857 0.00 0.00 33.87 2.66
92 93 3.708451 ACTTCACCCTGTGGAAAAAGTT 58.292 40.909 0.00 0.00 33.87 2.66
93 94 4.093743 ACTTCACCCTGTGGAAAAAGTTT 58.906 39.130 0.00 0.00 33.87 2.66
94 95 4.530553 ACTTCACCCTGTGGAAAAAGTTTT 59.469 37.500 0.00 0.00 33.87 2.43
95 96 5.012664 ACTTCACCCTGTGGAAAAAGTTTTT 59.987 36.000 13.35 13.35 33.87 1.94
144 145 7.484975 TGAAGTAATCCATGTTTTCACGTTTT 58.515 30.769 0.00 0.00 0.00 2.43
184 185 5.009010 GTGGTCACAACTTTGTCATTCTCAT 59.991 40.000 0.00 0.00 39.91 2.90
190 191 7.916977 TCACAACTTTGTCATTCTCATTTTCTG 59.083 33.333 0.00 0.00 39.91 3.02
316 327 5.399013 TGATACACATGTCTGTACAACTCG 58.601 41.667 0.00 0.00 39.58 4.18
334 349 8.317891 ACAACTCGATACAATTGATAAACACA 57.682 30.769 13.59 0.00 0.00 3.72
335 350 8.779303 ACAACTCGATACAATTGATAAACACAA 58.221 29.630 13.59 0.00 0.00 3.33
356 371 1.576356 GCGATCAGTTGCCTAGAAGG 58.424 55.000 0.00 0.00 38.80 3.46
418 433 4.097892 TGATAAGCACAGCGAGATCAGTTA 59.902 41.667 0.00 0.00 0.00 2.24
425 440 0.458669 GCGAGATCAGTTACCCGGAA 59.541 55.000 0.73 0.00 0.00 4.30
493 508 5.126869 TCAACTCACCAGAATCTCTCAGATC 59.873 44.000 0.00 0.00 32.89 2.75
593 612 1.603802 GCGGTCAATCCATACATGTGG 59.396 52.381 9.11 1.72 40.76 4.17
594 613 1.603802 CGGTCAATCCATACATGTGGC 59.396 52.381 9.11 0.00 39.19 5.01
595 614 2.746142 CGGTCAATCCATACATGTGGCT 60.746 50.000 9.11 0.00 39.19 4.75
596 615 2.620115 GGTCAATCCATACATGTGGCTG 59.380 50.000 9.11 3.31 39.19 4.85
597 616 3.544684 GTCAATCCATACATGTGGCTGA 58.455 45.455 9.11 5.84 39.19 4.26
686 707 3.691609 GGTCCACAGATTTTGGAGACATC 59.308 47.826 0.00 0.00 44.06 3.06
809 830 6.460676 GGAGAAGTGGCATATGATTTTTCTGG 60.461 42.308 6.97 0.00 0.00 3.86
845 871 1.128692 GTTGCAAGCTACAACTAGCCG 59.871 52.381 19.99 0.00 46.01 5.52
924 950 7.331934 TGAGATCAAAGCACACTAGACATAAAC 59.668 37.037 0.00 0.00 0.00 2.01
955 981 1.155042 CCAGACTCAGCAGAAACAGC 58.845 55.000 0.00 0.00 0.00 4.40
1016 1042 0.251474 AGGATGAGCAAGCCAAGCAA 60.251 50.000 0.00 0.00 0.00 3.91
1119 1145 2.267006 CTGCTCTGCCACCACGAT 59.733 61.111 0.00 0.00 0.00 3.73
1156 1187 2.736144 TCGGCGTATTCAGTTCAAGT 57.264 45.000 6.85 0.00 0.00 3.16
1335 1369 9.716531 CTTGGTAGATCAGAAATGCAATATCTA 57.283 33.333 0.00 0.00 0.00 1.98
1523 1577 2.554142 CATGATACTTCTGCGCCTCAA 58.446 47.619 4.18 0.00 0.00 3.02
1541 1595 3.734463 TCAATCAGGCGACAAGTTTACA 58.266 40.909 0.00 0.00 0.00 2.41
1594 1649 1.194547 GCCGTGTCCGTGCATATAATG 59.805 52.381 0.00 0.00 32.67 1.90
1597 1652 2.863740 CGTGTCCGTGCATATAATGTGT 59.136 45.455 0.00 0.00 0.00 3.72
1612 1667 3.594603 ATGTGTCCTTGACTCCTTACG 57.405 47.619 0.00 0.00 33.15 3.18
1619 1674 5.125097 TGTCCTTGACTCCTTACGAGATTAC 59.875 44.000 0.00 0.00 41.63 1.89
1621 1676 6.541641 GTCCTTGACTCCTTACGAGATTACTA 59.458 42.308 0.00 0.00 41.63 1.82
1661 1718 6.770746 TCAGATAGGTTGTACTAGTTGACC 57.229 41.667 0.00 7.28 0.00 4.02
1676 1733 0.928505 TGACCCATTCCTCATGCCAT 59.071 50.000 0.00 0.00 0.00 4.40
1681 1738 3.140707 ACCCATTCCTCATGCCATATTGA 59.859 43.478 0.00 0.00 0.00 2.57
1703 1760 0.249615 GCTACTCATGCATGCTCGGA 60.250 55.000 22.25 12.26 0.00 4.55
1719 1776 0.179065 CGGATGGCTGCAGAAGATCA 60.179 55.000 20.43 7.23 0.00 2.92
1775 1839 2.036346 GTCTGCAGGAGCCAAAATGTTT 59.964 45.455 15.13 0.00 41.13 2.83
1778 1842 2.061028 GCAGGAGCCAAAATGTTTTCG 58.939 47.619 0.00 0.00 33.58 3.46
1781 1845 2.029918 AGGAGCCAAAATGTTTTCGAGC 60.030 45.455 0.00 0.00 0.00 5.03
1828 1892 1.373497 GCACTGCACACTCTACGCT 60.373 57.895 0.00 0.00 0.00 5.07
1856 1920 7.857456 TCCGTATTCTGGGCAATGTATATATT 58.143 34.615 0.00 0.00 0.00 1.28
1858 1922 7.987458 CCGTATTCTGGGCAATGTATATATTCT 59.013 37.037 0.00 0.00 0.00 2.40
1864 1928 8.043113 TCTGGGCAATGTATATATTCTGATGTC 58.957 37.037 0.00 0.00 0.00 3.06
1938 2002 9.829507 AAGAAAAACAATACAAAATGATGTGGA 57.170 25.926 0.00 0.00 34.75 4.02
1939 2003 9.480053 AGAAAAACAATACAAAATGATGTGGAG 57.520 29.630 0.00 0.00 34.75 3.86
1940 2004 9.474920 GAAAAACAATACAAAATGATGTGGAGA 57.525 29.630 0.00 0.00 34.75 3.71
1944 2008 9.643693 AACAATACAAAATGATGTGGAGATTTC 57.356 29.630 0.00 0.00 34.75 2.17
1945 2009 8.805175 ACAATACAAAATGATGTGGAGATTTCA 58.195 29.630 0.00 0.00 34.75 2.69
1946 2010 9.811995 CAATACAAAATGATGTGGAGATTTCAT 57.188 29.630 0.00 0.00 34.75 2.57
1949 2013 8.542497 ACAAAATGATGTGGAGATTTCATTTG 57.458 30.769 9.69 7.41 44.05 2.32
1950 2014 8.152246 ACAAAATGATGTGGAGATTTCATTTGT 58.848 29.630 9.69 7.88 44.05 2.83
1951 2015 8.995220 CAAAATGATGTGGAGATTTCATTTGTT 58.005 29.630 9.69 0.00 44.05 2.83
1952 2016 9.563748 AAAATGATGTGGAGATTTCATTTGTTT 57.436 25.926 9.69 0.00 44.05 2.83
1953 2017 9.563748 AAATGATGTGGAGATTTCATTTGTTTT 57.436 25.926 8.48 0.00 43.50 2.43
1954 2018 8.767478 ATGATGTGGAGATTTCATTTGTTTTC 57.233 30.769 0.00 0.00 0.00 2.29
1955 2019 7.724287 TGATGTGGAGATTTCATTTGTTTTCA 58.276 30.769 0.00 0.00 0.00 2.69
1956 2020 8.202811 TGATGTGGAGATTTCATTTGTTTTCAA 58.797 29.630 0.00 0.00 38.10 2.69
1957 2021 7.769272 TGTGGAGATTTCATTTGTTTTCAAC 57.231 32.000 0.00 0.00 39.73 3.18
1958 2022 7.555087 TGTGGAGATTTCATTTGTTTTCAACT 58.445 30.769 0.00 0.00 39.73 3.16
1959 2023 8.690884 TGTGGAGATTTCATTTGTTTTCAACTA 58.309 29.630 0.00 0.00 39.73 2.24
1960 2024 9.696917 GTGGAGATTTCATTTGTTTTCAACTAT 57.303 29.630 0.00 0.00 39.73 2.12
1979 2043 9.868277 TCAACTATTTCACAATTCAAAAACAGT 57.132 25.926 0.00 0.00 0.00 3.55
1980 2044 9.904647 CAACTATTTCACAATTCAAAAACAGTG 57.095 29.630 0.00 0.00 0.00 3.66
1981 2045 8.647143 ACTATTTCACAATTCAAAAACAGTGG 57.353 30.769 0.00 0.00 0.00 4.00
1982 2046 8.257306 ACTATTTCACAATTCAAAAACAGTGGT 58.743 29.630 0.00 0.00 0.00 4.16
1983 2047 7.920160 ATTTCACAATTCAAAAACAGTGGTT 57.080 28.000 0.00 0.00 39.43 3.67
2072 2136 9.807649 ATAAAGCAATTTCAATTATCTCACCAC 57.192 29.630 0.00 0.00 0.00 4.16
2073 2137 6.839124 AGCAATTTCAATTATCTCACCACA 57.161 33.333 0.00 0.00 0.00 4.17
2074 2138 7.414222 AGCAATTTCAATTATCTCACCACAT 57.586 32.000 0.00 0.00 0.00 3.21
2075 2139 7.486647 AGCAATTTCAATTATCTCACCACATC 58.513 34.615 0.00 0.00 0.00 3.06
2076 2140 6.698766 GCAATTTCAATTATCTCACCACATCC 59.301 38.462 0.00 0.00 0.00 3.51
2077 2141 6.624352 ATTTCAATTATCTCACCACATCCG 57.376 37.500 0.00 0.00 0.00 4.18
2078 2142 4.753516 TCAATTATCTCACCACATCCGT 57.246 40.909 0.00 0.00 0.00 4.69
2079 2143 5.862678 TCAATTATCTCACCACATCCGTA 57.137 39.130 0.00 0.00 0.00 4.02
2080 2144 5.597806 TCAATTATCTCACCACATCCGTAC 58.402 41.667 0.00 0.00 0.00 3.67
2081 2145 5.128008 TCAATTATCTCACCACATCCGTACA 59.872 40.000 0.00 0.00 0.00 2.90
2082 2146 5.808366 ATTATCTCACCACATCCGTACAT 57.192 39.130 0.00 0.00 0.00 2.29
2083 2147 5.607939 TTATCTCACCACATCCGTACATT 57.392 39.130 0.00 0.00 0.00 2.71
2084 2148 3.973206 TCTCACCACATCCGTACATTT 57.027 42.857 0.00 0.00 0.00 2.32
2085 2149 4.280436 TCTCACCACATCCGTACATTTT 57.720 40.909 0.00 0.00 0.00 1.82
2086 2150 4.647611 TCTCACCACATCCGTACATTTTT 58.352 39.130 0.00 0.00 0.00 1.94
2108 2172 6.968263 TTTAAATATGATTTCGCCCCATCA 57.032 33.333 0.00 0.00 33.92 3.07
2109 2173 6.968263 TTAAATATGATTTCGCCCCATCAA 57.032 33.333 0.00 0.00 33.13 2.57
2110 2174 7.537596 TTAAATATGATTTCGCCCCATCAAT 57.462 32.000 0.00 0.00 33.13 2.57
2111 2175 8.642935 TTAAATATGATTTCGCCCCATCAATA 57.357 30.769 0.00 0.00 33.13 1.90
2112 2176 7.722949 AAATATGATTTCGCCCCATCAATAT 57.277 32.000 0.00 0.00 33.13 1.28
2113 2177 8.821686 AAATATGATTTCGCCCCATCAATATA 57.178 30.769 0.00 0.00 33.13 0.86
2114 2178 9.425248 AAATATGATTTCGCCCCATCAATATAT 57.575 29.630 0.00 0.00 33.13 0.86
2115 2179 9.425248 AATATGATTTCGCCCCATCAATATATT 57.575 29.630 0.00 0.00 33.13 1.28
2116 2180 7.722949 ATGATTTCGCCCCATCAATATATTT 57.277 32.000 0.00 0.00 33.13 1.40
2117 2181 7.156876 TGATTTCGCCCCATCAATATATTTC 57.843 36.000 0.00 0.00 0.00 2.17
2118 2182 6.718912 TGATTTCGCCCCATCAATATATTTCA 59.281 34.615 0.00 0.00 0.00 2.69
2119 2183 6.968263 TTTCGCCCCATCAATATATTTCAA 57.032 33.333 0.00 0.00 0.00 2.69
2120 2184 7.537596 TTTCGCCCCATCAATATATTTCAAT 57.462 32.000 0.00 0.00 0.00 2.57
2121 2185 7.537596 TTCGCCCCATCAATATATTTCAATT 57.462 32.000 0.00 0.00 0.00 2.32
2122 2186 8.642935 TTCGCCCCATCAATATATTTCAATTA 57.357 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.164954 GGAAGATACATGATTAGCGGAGAC 58.835 45.833 0.00 0.00 0.00 3.36
14 15 4.220821 GGGAAGATACATGATTAGCGGAGA 59.779 45.833 0.00 0.00 0.00 3.71
15 16 4.021104 TGGGAAGATACATGATTAGCGGAG 60.021 45.833 0.00 0.00 0.00 4.63
16 17 3.901222 TGGGAAGATACATGATTAGCGGA 59.099 43.478 0.00 0.00 0.00 5.54
17 18 4.021104 TCTGGGAAGATACATGATTAGCGG 60.021 45.833 0.00 0.00 0.00 5.52
18 19 5.139435 TCTGGGAAGATACATGATTAGCG 57.861 43.478 0.00 0.00 0.00 4.26
19 20 7.333921 CAGATTCTGGGAAGATACATGATTAGC 59.666 40.741 5.73 0.00 0.00 3.09
20 21 8.774890 CAGATTCTGGGAAGATACATGATTAG 57.225 38.462 5.73 0.00 0.00 1.73
37 38 7.388776 TGAAAACAGTAGAATGACCAGATTCTG 59.611 37.037 6.70 6.70 41.75 3.02
38 39 7.453393 TGAAAACAGTAGAATGACCAGATTCT 58.547 34.615 0.00 0.00 43.62 2.40
39 40 7.672983 TGAAAACAGTAGAATGACCAGATTC 57.327 36.000 0.00 0.00 33.21 2.52
40 41 8.641498 ATTGAAAACAGTAGAATGACCAGATT 57.359 30.769 0.00 0.00 0.00 2.40
41 42 9.911788 ATATTGAAAACAGTAGAATGACCAGAT 57.088 29.630 0.00 0.00 0.00 2.90
42 43 9.739276 AATATTGAAAACAGTAGAATGACCAGA 57.261 29.630 0.00 0.00 0.00 3.86
54 55 9.143155 AGGGTGAAGTTTAATATTGAAAACAGT 57.857 29.630 13.66 4.16 37.92 3.55
55 56 9.410556 CAGGGTGAAGTTTAATATTGAAAACAG 57.589 33.333 13.66 0.00 37.92 3.16
56 57 8.919145 ACAGGGTGAAGTTTAATATTGAAAACA 58.081 29.630 13.66 4.58 37.92 2.83
57 58 9.191995 CACAGGGTGAAGTTTAATATTGAAAAC 57.808 33.333 0.00 2.11 35.23 2.43
58 59 8.364142 CCACAGGGTGAAGTTTAATATTGAAAA 58.636 33.333 0.00 0.00 35.23 2.29
59 60 7.726291 TCCACAGGGTGAAGTTTAATATTGAAA 59.274 33.333 0.00 0.00 35.23 2.69
60 61 7.235079 TCCACAGGGTGAAGTTTAATATTGAA 58.765 34.615 0.00 0.00 35.23 2.69
61 62 6.785076 TCCACAGGGTGAAGTTTAATATTGA 58.215 36.000 0.00 0.00 35.23 2.57
62 63 7.461182 TTCCACAGGGTGAAGTTTAATATTG 57.539 36.000 0.00 0.00 35.23 1.90
63 64 8.485578 TTTTCCACAGGGTGAAGTTTAATATT 57.514 30.769 0.00 0.00 35.23 1.28
64 65 8.485578 TTTTTCCACAGGGTGAAGTTTAATAT 57.514 30.769 0.00 0.00 35.23 1.28
65 66 7.562088 ACTTTTTCCACAGGGTGAAGTTTAATA 59.438 33.333 0.00 0.00 35.23 0.98
66 67 6.382859 ACTTTTTCCACAGGGTGAAGTTTAAT 59.617 34.615 0.00 0.00 35.23 1.40
67 68 5.717654 ACTTTTTCCACAGGGTGAAGTTTAA 59.282 36.000 0.00 0.00 35.23 1.52
68 69 5.265989 ACTTTTTCCACAGGGTGAAGTTTA 58.734 37.500 0.00 0.00 35.23 2.01
69 70 4.093743 ACTTTTTCCACAGGGTGAAGTTT 58.906 39.130 0.00 0.00 35.23 2.66
70 71 3.708451 ACTTTTTCCACAGGGTGAAGTT 58.292 40.909 0.00 0.00 35.23 2.66
71 72 3.382083 ACTTTTTCCACAGGGTGAAGT 57.618 42.857 0.00 0.00 35.23 3.01
72 73 4.736126 AAACTTTTTCCACAGGGTGAAG 57.264 40.909 0.00 0.00 35.23 3.02
73 74 5.491323 AAAAACTTTTTCCACAGGGTGAA 57.509 34.783 0.00 0.00 35.23 3.18
95 96 9.958180 TCATCAGATGAGTTTAATACTGGAAAA 57.042 29.630 9.21 0.00 37.17 2.29
96 97 9.958180 TTCATCAGATGAGTTTAATACTGGAAA 57.042 29.630 12.97 0.00 40.94 3.13
97 98 9.605275 CTTCATCAGATGAGTTTAATACTGGAA 57.395 33.333 12.97 0.00 40.94 3.53
98 99 8.762645 ACTTCATCAGATGAGTTTAATACTGGA 58.237 33.333 12.97 0.00 40.94 3.86
99 100 8.954950 ACTTCATCAGATGAGTTTAATACTGG 57.045 34.615 12.97 0.00 40.94 4.00
106 107 9.551734 CATGGATTACTTCATCAGATGAGTTTA 57.448 33.333 12.97 3.89 40.94 2.01
107 108 8.051535 ACATGGATTACTTCATCAGATGAGTTT 58.948 33.333 12.97 4.77 40.94 2.66
108 109 7.571919 ACATGGATTACTTCATCAGATGAGTT 58.428 34.615 12.97 7.06 40.94 3.01
109 110 7.134362 ACATGGATTACTTCATCAGATGAGT 57.866 36.000 12.97 14.53 40.94 3.41
110 111 8.447924 AAACATGGATTACTTCATCAGATGAG 57.552 34.615 12.97 9.99 40.94 2.90
144 145 3.319689 TGACCACGAGACAGTACATTTCA 59.680 43.478 0.00 0.00 0.00 2.69
184 185 1.305201 GGACTGAACCACGCAGAAAA 58.695 50.000 0.00 0.00 36.86 2.29
190 191 2.047179 GGAGGGACTGAACCACGC 60.047 66.667 0.00 0.00 41.55 5.34
216 217 9.165014 CATGCATTTCACATTTTTCTTCAAAAG 57.835 29.630 0.00 0.00 37.79 2.27
218 219 7.133513 GCATGCATTTCACATTTTTCTTCAAA 58.866 30.769 14.21 0.00 0.00 2.69
220 221 5.758784 TGCATGCATTTCACATTTTTCTTCA 59.241 32.000 18.46 0.00 0.00 3.02
221 222 6.230849 TGCATGCATTTCACATTTTTCTTC 57.769 33.333 18.46 0.00 0.00 2.87
223 224 4.153475 GCTGCATGCATTTCACATTTTTCT 59.847 37.500 22.97 0.00 42.31 2.52
224 225 4.399978 GCTGCATGCATTTCACATTTTTC 58.600 39.130 22.97 0.00 42.31 2.29
225 226 3.189702 GGCTGCATGCATTTCACATTTTT 59.810 39.130 22.97 0.00 45.15 1.94
316 327 6.244999 TCGCGTTGTGTTTATCAATTGTATC 58.755 36.000 5.77 0.00 0.00 2.24
356 371 5.178797 ACAGACATGTGTATAAGTTCCAGC 58.821 41.667 1.15 0.00 38.57 4.85
418 433 1.286248 AGGCTAATCAAGTTCCGGGT 58.714 50.000 0.00 0.00 0.00 5.28
425 440 4.755266 ACGGTATCAAGGCTAATCAAGT 57.245 40.909 0.00 0.00 0.00 3.16
493 508 9.235537 CATGCATATCTCAGTTATCTATTCTCG 57.764 37.037 0.00 0.00 0.00 4.04
593 612 0.679002 TGGGATTTGCTCAGCTCAGC 60.679 55.000 1.01 1.01 40.13 4.26
594 613 1.380524 CTGGGATTTGCTCAGCTCAG 58.619 55.000 0.00 0.00 38.50 3.35
595 614 3.564262 CTGGGATTTGCTCAGCTCA 57.436 52.632 0.00 0.00 38.50 4.26
686 707 1.450531 GATGCAAGATCTTGGGGGCG 61.451 60.000 31.41 10.27 40.74 6.13
924 950 1.345741 TGAGTCTGGGCTCTTCAAGTG 59.654 52.381 3.85 0.00 36.51 3.16
955 981 5.389935 GGTGTTTCGCTTCAGAATAGAGTTG 60.390 44.000 0.00 0.00 0.00 3.16
1016 1042 3.330720 CTCCCCGCTTCCCTTGGT 61.331 66.667 0.00 0.00 0.00 3.67
1119 1145 3.256879 GCCGATCACTGATCCTGATCTAA 59.743 47.826 20.33 0.00 41.30 2.10
1156 1187 1.478654 GGCAAAACTGGGAGTCTTGGA 60.479 52.381 0.00 0.00 0.00 3.53
1335 1369 8.956426 TCAACTGATCAAGTGTAAGAAAAGTTT 58.044 29.630 0.00 0.00 39.81 2.66
1337 1371 8.562892 CATCAACTGATCAAGTGTAAGAAAAGT 58.437 33.333 0.00 0.00 39.81 2.66
1338 1372 8.562892 ACATCAACTGATCAAGTGTAAGAAAAG 58.437 33.333 0.00 0.00 39.81 2.27
1339 1373 8.450578 ACATCAACTGATCAAGTGTAAGAAAA 57.549 30.769 0.00 0.00 39.81 2.29
1340 1374 8.450578 AACATCAACTGATCAAGTGTAAGAAA 57.549 30.769 0.00 0.00 39.81 2.52
1341 1375 9.725019 ATAACATCAACTGATCAAGTGTAAGAA 57.275 29.630 0.00 0.00 39.81 2.52
1342 1376 9.725019 AATAACATCAACTGATCAAGTGTAAGA 57.275 29.630 0.00 0.00 39.81 2.10
1343 1377 9.764870 CAATAACATCAACTGATCAAGTGTAAG 57.235 33.333 0.00 0.00 39.81 2.34
1344 1378 9.283768 ACAATAACATCAACTGATCAAGTGTAA 57.716 29.630 0.00 0.00 39.81 2.41
1345 1379 8.720562 CACAATAACATCAACTGATCAAGTGTA 58.279 33.333 0.00 0.00 39.81 2.90
1346 1380 7.587629 CACAATAACATCAACTGATCAAGTGT 58.412 34.615 0.00 0.00 39.81 3.55
1347 1381 6.525628 GCACAATAACATCAACTGATCAAGTG 59.474 38.462 0.00 0.00 39.81 3.16
1356 1401 4.397420 TCCACAGCACAATAACATCAACT 58.603 39.130 0.00 0.00 0.00 3.16
1430 1483 3.174573 GGCAAACTTCGCATGCGC 61.175 61.111 34.45 18.39 40.94 6.09
1441 1495 1.792367 GTGCGGATTTTTCAGGCAAAC 59.208 47.619 0.00 0.00 35.10 2.93
1523 1577 3.067106 CTGTGTAAACTTGTCGCCTGAT 58.933 45.455 0.00 0.00 0.00 2.90
1541 1595 7.144722 TCGATTTGTTTCTGCAATATTCTGT 57.855 32.000 0.00 0.00 0.00 3.41
1594 1649 2.818432 TCTCGTAAGGAGTCAAGGACAC 59.182 50.000 0.00 0.00 43.60 3.67
1597 1652 5.507637 AGTAATCTCGTAAGGAGTCAAGGA 58.492 41.667 0.00 0.00 43.60 3.36
1661 1718 4.146564 TGTCAATATGGCATGAGGAATGG 58.853 43.478 10.98 0.00 36.71 3.16
1676 1733 3.811497 GCATGCATGAGTAGCTGTCAATA 59.189 43.478 30.64 0.00 0.00 1.90
1681 1738 1.805495 CGAGCATGCATGAGTAGCTGT 60.805 52.381 30.64 0.00 35.36 4.40
1703 1760 1.472904 CGTCTGATCTTCTGCAGCCAT 60.473 52.381 9.47 0.00 32.27 4.40
1719 1776 3.617263 GCCGAACTCAAATCATAACGTCT 59.383 43.478 0.00 0.00 0.00 4.18
1758 1815 2.061028 CGAAAACATTTTGGCTCCTGC 58.939 47.619 0.00 0.00 38.76 4.85
1759 1816 3.568538 CTCGAAAACATTTTGGCTCCTG 58.431 45.455 0.00 0.00 0.00 3.86
1763 1827 1.335872 CCGCTCGAAAACATTTTGGCT 60.336 47.619 0.00 0.00 0.00 4.75
1775 1839 1.153823 GCTAGCAGAACCGCTCGAA 60.154 57.895 10.63 0.00 42.62 3.71
1778 1842 1.079127 TTGGCTAGCAGAACCGCTC 60.079 57.895 18.24 0.00 42.62 5.03
1781 1845 1.003839 TGGTTGGCTAGCAGAACCG 60.004 57.895 29.04 0.00 41.85 4.44
1828 1892 1.140852 CATTGCCCAGAATACGGAGGA 59.859 52.381 0.00 0.00 0.00 3.71
1912 1976 9.829507 TCCACATCATTTTGTATTGTTTTTCTT 57.170 25.926 0.00 0.00 0.00 2.52
1913 1977 9.480053 CTCCACATCATTTTGTATTGTTTTTCT 57.520 29.630 0.00 0.00 0.00 2.52
1914 1978 9.474920 TCTCCACATCATTTTGTATTGTTTTTC 57.525 29.630 0.00 0.00 0.00 2.29
1918 1982 9.643693 GAAATCTCCACATCATTTTGTATTGTT 57.356 29.630 0.00 0.00 0.00 2.83
1919 1983 8.805175 TGAAATCTCCACATCATTTTGTATTGT 58.195 29.630 0.00 0.00 0.00 2.71
1920 1984 9.811995 ATGAAATCTCCACATCATTTTGTATTG 57.188 29.630 0.00 0.00 0.00 1.90
1923 1987 9.642327 CAAATGAAATCTCCACATCATTTTGTA 57.358 29.630 9.23 0.00 45.37 2.41
1924 1988 8.152246 ACAAATGAAATCTCCACATCATTTTGT 58.848 29.630 9.23 8.62 45.37 2.83
1925 1989 8.542497 ACAAATGAAATCTCCACATCATTTTG 57.458 30.769 9.23 8.16 45.37 2.44
1926 1990 9.563748 AAACAAATGAAATCTCCACATCATTTT 57.436 25.926 9.23 1.39 45.37 1.82
1928 1992 9.211485 GAAAACAAATGAAATCTCCACATCATT 57.789 29.630 0.00 0.00 42.61 2.57
1929 1993 8.369424 TGAAAACAAATGAAATCTCCACATCAT 58.631 29.630 0.00 0.00 34.11 2.45
1930 1994 7.724287 TGAAAACAAATGAAATCTCCACATCA 58.276 30.769 0.00 0.00 0.00 3.07
1931 1995 8.592105 TTGAAAACAAATGAAATCTCCACATC 57.408 30.769 0.00 0.00 0.00 3.06
1953 2017 9.868277 ACTGTTTTTGAATTGTGAAATAGTTGA 57.132 25.926 0.00 0.00 32.04 3.18
1954 2018 9.904647 CACTGTTTTTGAATTGTGAAATAGTTG 57.095 29.630 0.00 0.00 33.19 3.16
1955 2019 9.097257 CCACTGTTTTTGAATTGTGAAATAGTT 57.903 29.630 0.00 0.00 33.19 2.24
1956 2020 8.257306 ACCACTGTTTTTGAATTGTGAAATAGT 58.743 29.630 0.00 0.00 34.96 2.12
1957 2021 8.647143 ACCACTGTTTTTGAATTGTGAAATAG 57.353 30.769 0.00 0.00 0.00 1.73
1958 2022 9.442047 AAACCACTGTTTTTGAATTGTGAAATA 57.558 25.926 0.00 0.00 41.92 1.40
1959 2023 7.920160 AACCACTGTTTTTGAATTGTGAAAT 57.080 28.000 0.00 0.00 0.00 2.17
1960 2024 7.736447 AAACCACTGTTTTTGAATTGTGAAA 57.264 28.000 0.00 0.00 41.92 2.69
2046 2110 9.807649 GTGGTGAGATAATTGAAATTGCTTTAT 57.192 29.630 0.00 0.00 0.00 1.40
2047 2111 8.801299 TGTGGTGAGATAATTGAAATTGCTTTA 58.199 29.630 0.00 0.00 0.00 1.85
2048 2112 7.669427 TGTGGTGAGATAATTGAAATTGCTTT 58.331 30.769 0.00 0.00 0.00 3.51
2049 2113 7.230849 TGTGGTGAGATAATTGAAATTGCTT 57.769 32.000 0.00 0.00 0.00 3.91
2050 2114 6.839124 TGTGGTGAGATAATTGAAATTGCT 57.161 33.333 0.00 0.00 0.00 3.91
2051 2115 6.698766 GGATGTGGTGAGATAATTGAAATTGC 59.301 38.462 0.00 0.00 0.00 3.56
2052 2116 6.914215 CGGATGTGGTGAGATAATTGAAATTG 59.086 38.462 0.00 0.00 0.00 2.32
2053 2117 6.603201 ACGGATGTGGTGAGATAATTGAAATT 59.397 34.615 0.00 0.00 0.00 1.82
2054 2118 6.122277 ACGGATGTGGTGAGATAATTGAAAT 58.878 36.000 0.00 0.00 0.00 2.17
2055 2119 5.496556 ACGGATGTGGTGAGATAATTGAAA 58.503 37.500 0.00 0.00 0.00 2.69
2056 2120 5.097742 ACGGATGTGGTGAGATAATTGAA 57.902 39.130 0.00 0.00 0.00 2.69
2057 2121 4.753516 ACGGATGTGGTGAGATAATTGA 57.246 40.909 0.00 0.00 0.00 2.57
2058 2122 5.356426 TGTACGGATGTGGTGAGATAATTG 58.644 41.667 0.00 0.00 0.00 2.32
2059 2123 5.607939 TGTACGGATGTGGTGAGATAATT 57.392 39.130 0.00 0.00 0.00 1.40
2060 2124 5.808366 ATGTACGGATGTGGTGAGATAAT 57.192 39.130 0.00 0.00 0.00 1.28
2061 2125 5.607939 AATGTACGGATGTGGTGAGATAA 57.392 39.130 0.00 0.00 0.00 1.75
2062 2126 5.607939 AAATGTACGGATGTGGTGAGATA 57.392 39.130 0.00 0.00 0.00 1.98
2063 2127 4.487714 AAATGTACGGATGTGGTGAGAT 57.512 40.909 0.00 0.00 0.00 2.75
2064 2128 3.973206 AAATGTACGGATGTGGTGAGA 57.027 42.857 0.00 0.00 0.00 3.27
2083 2147 7.786030 TGATGGGGCGAAATCATATTTAAAAA 58.214 30.769 0.00 0.00 0.00 1.94
2084 2148 7.353414 TGATGGGGCGAAATCATATTTAAAA 57.647 32.000 0.00 0.00 0.00 1.52
2085 2149 6.968263 TGATGGGGCGAAATCATATTTAAA 57.032 33.333 0.00 0.00 0.00 1.52
2086 2150 6.968263 TTGATGGGGCGAAATCATATTTAA 57.032 33.333 0.00 0.00 33.01 1.52
2087 2151 8.821686 ATATTGATGGGGCGAAATCATATTTA 57.178 30.769 0.00 0.00 33.01 1.40
2088 2152 7.722949 ATATTGATGGGGCGAAATCATATTT 57.277 32.000 0.00 0.00 33.01 1.40
2089 2153 9.425248 AATATATTGATGGGGCGAAATCATATT 57.575 29.630 0.00 0.00 33.01 1.28
2090 2154 9.425248 AAATATATTGATGGGGCGAAATCATAT 57.575 29.630 0.00 0.00 33.01 1.78
2091 2155 8.821686 AAATATATTGATGGGGCGAAATCATA 57.178 30.769 0.00 0.00 33.01 2.15
2092 2156 7.396907 TGAAATATATTGATGGGGCGAAATCAT 59.603 33.333 0.00 0.00 33.01 2.45
2093 2157 6.718912 TGAAATATATTGATGGGGCGAAATCA 59.281 34.615 0.00 0.00 0.00 2.57
2094 2158 7.156876 TGAAATATATTGATGGGGCGAAATC 57.843 36.000 0.00 0.00 0.00 2.17
2095 2159 7.537596 TTGAAATATATTGATGGGGCGAAAT 57.462 32.000 0.00 0.00 0.00 2.17
2096 2160 6.968263 TTGAAATATATTGATGGGGCGAAA 57.032 33.333 0.00 0.00 0.00 3.46
2097 2161 7.537596 AATTGAAATATATTGATGGGGCGAA 57.462 32.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.