Multiple sequence alignment - TraesCS2A01G250300

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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 TraesCS2A01G250300 chr2A 100.000 2237 0 0 1 2237 377137522 377135286 0.000000e+00 4132.0
1 TraesCS2A01G250300 chr2A 74.227 582 110 23 68 617 689953729 689954302 8.100000e-50 207.0
2 TraesCS2A01G250300 chr2A 93.694 111 6 1 1905 2015 61487233 61487342 4.940000e-37 165.0
3 TraesCS2A01G250300 chr2A 80.882 204 29 7 416 616 683137328 683137132 3.850000e-33 152.0
4 TraesCS2A01G250300 chr2A 81.152 191 29 5 134 320 81104675 81104862 1.790000e-31 147.0
5 TraesCS2A01G250300 chr2D 90.627 1835 86 28 110 1910 300890512 300888730 0.000000e+00 2357.0
6 TraesCS2A01G250300 chr2D 93.991 233 2 2 2006 2237 300888732 300888511 2.130000e-90 342.0
7 TraesCS2A01G250300 chr2B 95.822 1149 21 7 766 1910 358774981 358773856 0.000000e+00 1831.0
8 TraesCS2A01G250300 chr2B 95.833 240 3 5 2002 2237 358773856 358773620 4.510000e-102 381.0
9 TraesCS2A01G250300 chr2B 80.827 266 43 7 69 330 120246506 120246767 3.770000e-48 202.0
10 TraesCS2A01G250300 chr4B 75.571 569 114 17 70 617 660873728 660873164 7.930000e-65 257.0
11 TraesCS2A01G250300 chr4B 84.264 197 24 7 427 619 136187207 136187014 3.790000e-43 185.0
12 TraesCS2A01G250300 chr4B 95.146 103 5 0 1907 2009 262872606 262872504 1.780000e-36 163.0
13 TraesCS2A01G250300 chr4B 84.158 101 9 7 11 107 417223818 417223721 8.510000e-15 91.6
14 TraesCS2A01G250300 chr3A 79.603 353 47 14 68 415 523335901 523335569 1.730000e-56 230.0
15 TraesCS2A01G250300 chr3A 94.444 108 5 1 1907 2014 424454775 424454669 4.940000e-37 165.0
16 TraesCS2A01G250300 chr3B 83.761 234 28 6 74 302 8858364 8858136 1.740000e-51 213.0
17 TraesCS2A01G250300 chr3B 96.154 104 4 0 1909 2012 479298379 479298482 1.060000e-38 171.0
18 TraesCS2A01G250300 chr3B 95.327 107 5 0 1900 2006 677322441 677322335 1.060000e-38 171.0
19 TraesCS2A01G250300 chr3B 81.905 105 10 5 11 107 7153074 7152971 1.840000e-11 80.5
20 TraesCS2A01G250300 chr5D 81.439 264 42 5 69 330 442484555 442484813 2.250000e-50 209.0
21 TraesCS2A01G250300 chr5D 81.439 264 40 7 74 330 476791115 476790854 8.100000e-50 207.0
22 TraesCS2A01G250300 chr5D 80.669 269 46 5 68 331 476791228 476790961 1.050000e-48 204.0
23 TraesCS2A01G250300 chr5D 97.087 103 3 0 1909 2011 301216109 301216211 8.210000e-40 174.0
24 TraesCS2A01G250300 chr4A 81.226 261 44 3 68 325 83744872 83744614 2.910000e-49 206.0
25 TraesCS2A01G250300 chr7D 75.541 462 72 24 162 615 548237819 548238247 2.930000e-44 189.0
26 TraesCS2A01G250300 chr7D 95.283 106 4 1 1900 2005 41596539 41596643 1.370000e-37 167.0
27 TraesCS2A01G250300 chr4D 96.190 105 4 0 1906 2010 179707534 179707430 2.950000e-39 172.0
28 TraesCS2A01G250300 chr4D 97.143 35 1 0 6 40 507969810 507969844 2.400000e-05 60.2
29 TraesCS2A01G250300 chrUn 86.928 153 18 2 467 617 260712307 260712155 1.060000e-38 171.0
30 TraesCS2A01G250300 chrUn 80.000 105 13 5 11 107 102576565 102576461 1.110000e-08 71.3
31 TraesCS2A01G250300 chr6D 95.327 107 4 1 1908 2014 467773477 467773582 3.820000e-38 169.0
32 TraesCS2A01G250300 chr6D 85.350 157 21 2 464 618 318968249 318968405 6.390000e-36 161.0
33 TraesCS2A01G250300 chr6A 85.119 168 21 4 455 618 559205907 559205740 3.820000e-38 169.0
34 TraesCS2A01G250300 chr1B 79.365 252 37 11 375 616 658793999 658794245 1.780000e-36 163.0
35 TraesCS2A01G250300 chr5B 81.218 197 31 5 424 617 559118880 559118687 1.070000e-33 154.0
36 TraesCS2A01G250300 chr6B 74.809 393 61 17 14 393 523052469 523052102 2.320000e-30 143.0
37 TraesCS2A01G250300 chr6B 81.905 105 11 6 11 107 234676024 234676128 5.120000e-12 82.4
38 TraesCS2A01G250300 chr7A 82.653 98 16 1 11 108 512444213 512444117 3.960000e-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 TraesCS2A01G250300 chr2A 377135286 377137522 2236 True 4132.0 4132 100.0000 1 2237 1 chr2A.!!$R1 2236
1 TraesCS2A01G250300 chr2A 689953729 689954302 573 False 207.0 207 74.2270 68 617 1 chr2A.!!$F3 549
2 TraesCS2A01G250300 chr2D 300888511 300890512 2001 True 1349.5 2357 92.3090 110 2237 2 chr2D.!!$R1 2127
3 TraesCS2A01G250300 chr2B 358773620 358774981 1361 True 1106.0 1831 95.8275 766 2237 2 chr2B.!!$R1 1471
4 TraesCS2A01G250300 chr4B 660873164 660873728 564 True 257.0 257 75.5710 70 617 1 chr4B.!!$R4 547

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
19 20 0.099436 GGTATGGCTTTGCTTCTGCG 59.901 55.0 0.0 0.0 43.34 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1801 0.038166 ACGAGGCAACACCATTGGAT 59.962 50.0 10.37 0.0 43.14 3.41 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 0.099436 GGTATGGCTTTGCTTCTGCG 59.901 55.000 0.00 0.00 43.34 5.18
20 21 1.086696 GTATGGCTTTGCTTCTGCGA 58.913 50.000 0.00 0.00 43.34 5.10
21 22 1.063174 GTATGGCTTTGCTTCTGCGAG 59.937 52.381 0.00 0.00 43.34 5.03
22 23 0.321919 ATGGCTTTGCTTCTGCGAGA 60.322 50.000 0.00 0.00 43.34 4.04
23 24 0.534877 TGGCTTTGCTTCTGCGAGAA 60.535 50.000 0.00 0.00 43.34 2.87
48 49 1.067354 GGCTGTGCCTCTTGAAAATGG 60.067 52.381 0.73 0.00 46.69 3.16
51 52 3.243839 GCTGTGCCTCTTGAAAATGGAAA 60.244 43.478 0.00 0.00 0.00 3.13
52 53 4.740334 GCTGTGCCTCTTGAAAATGGAAAA 60.740 41.667 0.00 0.00 0.00 2.29
53 54 5.350504 TGTGCCTCTTGAAAATGGAAAAA 57.649 34.783 0.00 0.00 0.00 1.94
179 233 1.594331 GTTTTGCTTCCACGAGAGGT 58.406 50.000 0.00 0.00 0.00 3.85
192 246 3.125316 CACGAGAGGTATGGTTTTGCTTC 59.875 47.826 0.00 0.00 0.00 3.86
317 371 3.680786 CCACGAGAGGCACGGTCA 61.681 66.667 0.00 0.00 34.93 4.02
337 391 3.055891 TCATGCATCTCGAAACCTCTCAA 60.056 43.478 0.00 0.00 0.00 3.02
390 464 2.559698 TTTTTCCATGAGAGGCACGA 57.440 45.000 0.00 0.00 0.00 4.35
392 466 2.315925 TTTCCATGAGAGGCACGATC 57.684 50.000 0.00 0.00 0.00 3.69
395 469 2.666317 TCCATGAGAGGCACGATCTTA 58.334 47.619 0.00 0.00 0.00 2.10
419 523 2.743928 CGAGAGGCAGCGGCTTTT 60.744 61.111 9.17 0.00 38.98 2.27
435 539 5.163804 GCGGCTTTTGAAAAAGAAAAGGAAA 60.164 36.000 17.58 0.00 46.39 3.13
436 540 6.621812 GCGGCTTTTGAAAAAGAAAAGGAAAA 60.622 34.615 17.58 0.00 46.39 2.29
437 541 6.740905 CGGCTTTTGAAAAAGAAAAGGAAAAC 59.259 34.615 17.58 0.00 46.39 2.43
438 542 7.572168 CGGCTTTTGAAAAAGAAAAGGAAAACA 60.572 33.333 17.58 0.00 46.39 2.83
446 550 5.612725 AAGAAAAGGAAAACATGCTCCAA 57.387 34.783 10.73 0.00 33.83 3.53
453 558 0.110486 AAACATGCTCCAAGTCCGGT 59.890 50.000 0.00 0.00 0.00 5.28
464 569 2.159572 CCAAGTCCGGTATTTTTGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
526 633 9.896645 AGCATGAATCTAGTTTTAAAGATCTGA 57.103 29.630 0.00 0.00 31.20 3.27
632 750 3.840124 AAAAAGAGTCTTGTCCCGACT 57.160 42.857 6.06 0.00 43.97 4.18
634 752 4.950205 AAAAGAGTCTTGTCCCGACTTA 57.050 40.909 6.06 0.00 41.53 2.24
636 754 4.950205 AAGAGTCTTGTCCCGACTTAAA 57.050 40.909 4.10 0.00 41.53 1.52
643 761 2.853705 TGTCCCGACTTAAAAAGGTGG 58.146 47.619 0.00 0.00 0.00 4.61
648 766 3.252458 CCCGACTTAAAAAGGTGGAAGTG 59.748 47.826 0.00 0.00 32.37 3.16
660 778 9.898152 AAAAAGGTGGAAGTGATTTTTATGAAA 57.102 25.926 0.00 0.00 32.80 2.69
661 779 9.546428 AAAAGGTGGAAGTGATTTTTATGAAAG 57.454 29.630 0.00 0.00 0.00 2.62
662 780 7.839680 AGGTGGAAGTGATTTTTATGAAAGT 57.160 32.000 0.00 0.00 0.00 2.66
663 781 8.934023 AGGTGGAAGTGATTTTTATGAAAGTA 57.066 30.769 0.00 0.00 0.00 2.24
664 782 8.793592 AGGTGGAAGTGATTTTTATGAAAGTAC 58.206 33.333 0.00 0.00 0.00 2.73
665 783 8.793592 GGTGGAAGTGATTTTTATGAAAGTACT 58.206 33.333 0.00 0.00 0.00 2.73
689 807 5.784750 TCTCAATTAGTGATTTCGCACAG 57.215 39.130 0.00 0.00 41.19 3.66
705 823 3.134127 AGCAATTTCCGGCGCTCC 61.134 61.111 7.64 0.00 34.54 4.70
968 1087 2.745884 CCAGATCCGCGTTTGGCA 60.746 61.111 4.92 0.00 43.84 4.92
1203 1322 1.820481 GCTACTCGCCGACCTCTCT 60.820 63.158 0.00 0.00 0.00 3.10
1385 1507 8.075574 TGTGACAAGAACTTGCTTTATGTTATG 58.924 33.333 13.50 0.00 44.03 1.90
1471 1593 5.249163 TGAATTCCTGATTGAGACTTCCAGA 59.751 40.000 2.27 0.00 0.00 3.86
1496 1618 5.557576 TCTATGCAAAGCAGATGATACCT 57.442 39.130 0.00 0.00 43.65 3.08
1532 1654 5.945191 TCTGAATTGGCATTTCAGTATGTCA 59.055 36.000 33.75 20.57 46.54 3.58
1535 1657 4.374843 TTGGCATTTCAGTATGTCATGC 57.625 40.909 0.00 0.00 45.54 4.06
1544 1666 0.806102 GTATGTCATGCGAGCACGGT 60.806 55.000 5.52 0.00 40.15 4.83
1545 1667 0.805711 TATGTCATGCGAGCACGGTG 60.806 55.000 5.52 3.15 40.15 4.94
1546 1668 2.738521 GTCATGCGAGCACGGTGT 60.739 61.111 10.24 0.00 40.15 4.16
1547 1669 2.738139 TCATGCGAGCACGGTGTG 60.738 61.111 10.24 0.00 40.15 3.82
1556 1678 4.970392 CACGGTGTGCATTGCAAT 57.030 50.000 13.94 5.99 41.47 3.56
1557 1679 2.436795 CACGGTGTGCATTGCAATG 58.563 52.632 30.92 30.92 41.47 2.82
1558 1680 0.318869 CACGGTGTGCATTGCAATGT 60.319 50.000 33.67 14.66 41.47 2.71
1559 1681 1.068679 CACGGTGTGCATTGCAATGTA 60.069 47.619 33.67 29.20 41.47 2.29
1566 1688 4.418013 GTGCATTGCAATGTACTGTACA 57.582 40.909 37.83 24.39 45.03 2.90
1652 1801 0.756294 ACCGTGTGTGAGGTCAATCA 59.244 50.000 0.00 0.00 35.50 2.57
1767 1916 0.810648 TTCTGCATCATTTGGGTCGC 59.189 50.000 0.00 0.00 0.00 5.19
1910 2060 6.749139 TGAGATATGGCTGATAGTGTTGTAC 58.251 40.000 0.00 0.00 0.00 2.90
1911 2061 6.551227 TGAGATATGGCTGATAGTGTTGTACT 59.449 38.462 0.00 0.00 43.56 2.73
1912 2062 6.987386 AGATATGGCTGATAGTGTTGTACTC 58.013 40.000 0.00 0.00 40.89 2.59
1913 2063 3.887621 TGGCTGATAGTGTTGTACTCC 57.112 47.619 0.00 0.00 40.89 3.85
1914 2064 2.500098 TGGCTGATAGTGTTGTACTCCC 59.500 50.000 0.00 0.00 40.89 4.30
1915 2065 2.766828 GGCTGATAGTGTTGTACTCCCT 59.233 50.000 0.00 0.00 40.89 4.20
1916 2066 3.181474 GGCTGATAGTGTTGTACTCCCTC 60.181 52.174 0.00 0.00 40.89 4.30
1917 2067 3.181474 GCTGATAGTGTTGTACTCCCTCC 60.181 52.174 0.00 0.00 40.89 4.30
1918 2068 3.021695 TGATAGTGTTGTACTCCCTCCG 58.978 50.000 0.00 0.00 40.89 4.63
1919 2069 2.592102 TAGTGTTGTACTCCCTCCGT 57.408 50.000 0.00 0.00 40.89 4.69
1920 2070 1.254954 AGTGTTGTACTCCCTCCGTC 58.745 55.000 0.00 0.00 33.17 4.79
1921 2071 1.203025 AGTGTTGTACTCCCTCCGTCT 60.203 52.381 0.00 0.00 33.17 4.18
1922 2072 1.201880 GTGTTGTACTCCCTCCGTCTC 59.798 57.143 0.00 0.00 0.00 3.36
1923 2073 1.202964 TGTTGTACTCCCTCCGTCTCA 60.203 52.381 0.00 0.00 0.00 3.27
1924 2074 1.891150 GTTGTACTCCCTCCGTCTCAA 59.109 52.381 0.00 0.00 0.00 3.02
1925 2075 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
1926 2076 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
1927 2077 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
1928 2078 4.346730 TGTACTCCCTCCGTCTCAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
1929 2079 4.773674 TGTACTCCCTCCGTCTCAAAATAA 59.226 41.667 0.00 0.00 0.00 1.40
1930 2080 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
1931 2081 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
1932 2082 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
1933 2083 3.835978 TCCCTCCGTCTCAAAATAAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
1934 2084 3.933332 CCCTCCGTCTCAAAATAAGTGAC 59.067 47.826 0.00 0.00 0.00 3.67
1935 2085 4.322801 CCCTCCGTCTCAAAATAAGTGACT 60.323 45.833 0.00 0.00 0.00 3.41
1936 2086 4.865365 CCTCCGTCTCAAAATAAGTGACTC 59.135 45.833 0.00 0.00 0.00 3.36
1937 2087 5.462530 TCCGTCTCAAAATAAGTGACTCA 57.537 39.130 0.00 0.00 0.00 3.41
1938 2088 5.849510 TCCGTCTCAAAATAAGTGACTCAA 58.150 37.500 0.00 0.00 0.00 3.02
1939 2089 5.694910 TCCGTCTCAAAATAAGTGACTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
1940 2090 5.696724 CCGTCTCAAAATAAGTGACTCAACT 59.303 40.000 0.00 0.00 0.00 3.16
1941 2091 6.202954 CCGTCTCAAAATAAGTGACTCAACTT 59.797 38.462 0.00 0.00 42.89 2.66
1942 2092 7.254795 CCGTCTCAAAATAAGTGACTCAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
1943 2093 7.584123 CGTCTCAAAATAAGTGACTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
1944 2094 8.398665 GTCTCAAAATAAGTGACTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
1945 2095 9.607988 TCTCAAAATAAGTGACTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
1946 2096 9.651718 CTCAAAATAAGTGACTCAACTTTGTAC 57.348 33.333 0.00 0.00 40.77 2.90
1947 2097 9.391006 TCAAAATAAGTGACTCAACTTTGTACT 57.609 29.630 0.00 0.00 40.77 2.73
1953 2103 8.788325 AAGTGACTCAACTTTGTACTAAGTTT 57.212 30.769 26.14 15.97 43.85 2.66
1954 2104 9.880157 AAGTGACTCAACTTTGTACTAAGTTTA 57.120 29.630 26.14 19.67 43.85 2.01
1955 2105 9.530633 AGTGACTCAACTTTGTACTAAGTTTAG 57.469 33.333 27.69 27.69 43.85 1.85
1956 2106 9.310716 GTGACTCAACTTTGTACTAAGTTTAGT 57.689 33.333 31.64 31.64 46.91 2.24
1980 2130 9.310716 AGTACAAAGTTAGTACAAAGTTGAGTC 57.689 33.333 6.30 0.00 43.24 3.36
1981 2131 9.090692 GTACAAAGTTAGTACAAAGTTGAGTCA 57.909 33.333 0.00 0.00 41.08 3.41
1982 2132 7.971455 ACAAAGTTAGTACAAAGTTGAGTCAC 58.029 34.615 0.00 0.00 0.00 3.67
1983 2133 7.822822 ACAAAGTTAGTACAAAGTTGAGTCACT 59.177 33.333 0.00 0.00 0.00 3.41
1984 2134 8.665685 CAAAGTTAGTACAAAGTTGAGTCACTT 58.334 33.333 0.00 0.00 38.74 3.16
1985 2135 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
1991 2141 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
1992 2142 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
1993 2143 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
1994 2144 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
1995 2145 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
1996 2146 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
1997 2147 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
1998 2148 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
1999 2149 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2000 2150 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2001 2151 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2002 2152 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2003 2153 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
2004 2154 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2005 2155 1.272807 TTTTGGGACGGAGGGAGTAG 58.727 55.000 0.00 0.00 0.00 2.57
2006 2156 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
2007 2157 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
2075 2232 7.435305 TGTGAAGAAATTGCAAATCAGATCAA 58.565 30.769 1.71 1.75 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.099436 CGCAGAAGCAAAGCCATACC 59.901 55.000 0.00 0.00 42.27 2.73
2 3 1.066215 TCTCGCAGAAGCAAAGCCATA 60.066 47.619 0.00 0.00 42.27 2.74
3 4 0.321919 TCTCGCAGAAGCAAAGCCAT 60.322 50.000 0.00 0.00 42.27 4.40
4 5 0.534877 TTCTCGCAGAAGCAAAGCCA 60.535 50.000 0.00 0.00 42.27 4.75
6 7 3.672361 CTTCTCGCAGAAGCAAAGC 57.328 52.632 11.34 0.00 44.35 3.51
17 18 3.782244 CACAGCCGTGCTTCTCGC 61.782 66.667 0.00 0.00 36.40 5.03
29 30 1.888512 TCCATTTTCAAGAGGCACAGC 59.111 47.619 0.00 0.00 0.00 4.40
31 32 5.350504 TTTTTCCATTTTCAAGAGGCACA 57.649 34.783 0.00 0.00 0.00 4.57
61 62 4.344448 CAAAACCGTGCTTCTCGTAAAAA 58.656 39.130 0.00 0.00 0.00 1.94
62 63 3.789459 GCAAAACCGTGCTTCTCGTAAAA 60.789 43.478 0.00 0.00 41.51 1.52
63 64 2.286536 GCAAAACCGTGCTTCTCGTAAA 60.287 45.455 0.00 0.00 41.51 2.01
64 65 1.262151 GCAAAACCGTGCTTCTCGTAA 59.738 47.619 0.00 0.00 41.51 3.18
65 66 0.863144 GCAAAACCGTGCTTCTCGTA 59.137 50.000 0.00 0.00 41.51 3.43
66 67 1.647084 GCAAAACCGTGCTTCTCGT 59.353 52.632 0.00 0.00 41.51 4.18
67 68 4.515107 GCAAAACCGTGCTTCTCG 57.485 55.556 0.00 0.00 41.51 4.04
78 102 0.110010 GCCTCTCGCAGAAGCAAAAC 60.110 55.000 2.95 0.00 42.27 2.43
317 371 3.616956 TTGAGAGGTTTCGAGATGCAT 57.383 42.857 0.00 0.00 0.00 3.96
373 447 1.833630 AGATCGTGCCTCTCATGGAAA 59.166 47.619 0.00 0.00 32.54 3.13
378 452 3.068873 GGAAGTAAGATCGTGCCTCTCAT 59.931 47.826 0.00 0.00 0.00 2.90
379 453 2.427453 GGAAGTAAGATCGTGCCTCTCA 59.573 50.000 0.00 0.00 0.00 3.27
390 464 0.386113 GCCTCTCGCGGAAGTAAGAT 59.614 55.000 6.13 0.00 0.00 2.40
392 466 1.511305 TGCCTCTCGCGGAAGTAAG 59.489 57.895 6.13 0.00 42.08 2.34
419 523 6.538381 GGAGCATGTTTTCCTTTTCTTTTTCA 59.462 34.615 0.00 0.00 0.00 2.69
435 539 0.981183 TACCGGACTTGGAGCATGTT 59.019 50.000 9.46 0.00 0.00 2.71
436 540 1.204146 ATACCGGACTTGGAGCATGT 58.796 50.000 9.46 0.00 0.00 3.21
437 541 2.332063 AATACCGGACTTGGAGCATG 57.668 50.000 9.46 0.00 0.00 4.06
438 542 3.366052 AAAATACCGGACTTGGAGCAT 57.634 42.857 9.46 0.00 0.00 3.79
446 550 1.002773 ACCGAGCAAAAATACCGGACT 59.997 47.619 9.46 0.00 42.49 3.85
486 592 9.716531 CTAGATTCATGCTGATAGGTTTTGATA 57.283 33.333 0.00 0.00 0.00 2.15
487 593 8.216423 ACTAGATTCATGCTGATAGGTTTTGAT 58.784 33.333 0.00 0.00 0.00 2.57
526 633 4.789012 TCACCGTTAGATTCCTTACGTT 57.211 40.909 0.00 0.00 42.03 3.99
531 638 5.321927 ACCATTTTCACCGTTAGATTCCTT 58.678 37.500 0.00 0.00 0.00 3.36
619 726 4.024302 CACCTTTTTAAGTCGGGACAAGAC 60.024 45.833 1.17 0.00 0.00 3.01
620 727 4.131596 CACCTTTTTAAGTCGGGACAAGA 58.868 43.478 1.17 0.00 0.00 3.02
621 728 3.252458 CCACCTTTTTAAGTCGGGACAAG 59.748 47.826 1.17 0.00 0.00 3.16
627 745 4.131596 TCACTTCCACCTTTTTAAGTCGG 58.868 43.478 0.00 0.00 29.93 4.79
634 752 9.898152 TTTCATAAAAATCACTTCCACCTTTTT 57.102 25.926 0.00 0.00 34.45 1.94
636 754 8.704668 ACTTTCATAAAAATCACTTCCACCTTT 58.295 29.630 0.00 0.00 0.00 3.11
659 777 8.443937 GCGAAATCACTAATTGAGAAAGTACTT 58.556 33.333 1.12 1.12 37.77 2.24
660 778 7.602644 TGCGAAATCACTAATTGAGAAAGTACT 59.397 33.333 0.00 0.00 37.77 2.73
661 779 7.688578 GTGCGAAATCACTAATTGAGAAAGTAC 59.311 37.037 0.00 0.00 37.77 2.73
662 780 7.386573 TGTGCGAAATCACTAATTGAGAAAGTA 59.613 33.333 0.00 0.00 37.77 2.24
663 781 6.204688 TGTGCGAAATCACTAATTGAGAAAGT 59.795 34.615 0.00 0.00 37.77 2.66
664 782 6.602179 TGTGCGAAATCACTAATTGAGAAAG 58.398 36.000 0.00 0.00 37.77 2.62
665 783 6.552859 TGTGCGAAATCACTAATTGAGAAA 57.447 33.333 0.00 0.00 37.77 2.52
667 785 4.093408 GCTGTGCGAAATCACTAATTGAGA 59.907 41.667 0.00 0.00 37.77 3.27
668 786 4.142838 TGCTGTGCGAAATCACTAATTGAG 60.143 41.667 0.00 0.00 37.77 3.02
669 787 3.750652 TGCTGTGCGAAATCACTAATTGA 59.249 39.130 0.00 0.00 39.11 2.57
670 788 4.082274 TGCTGTGCGAAATCACTAATTG 57.918 40.909 0.00 0.00 37.81 2.32
671 789 4.764679 TTGCTGTGCGAAATCACTAATT 57.235 36.364 0.00 0.00 37.81 1.40
672 790 4.970662 ATTGCTGTGCGAAATCACTAAT 57.029 36.364 0.00 0.00 37.81 1.73
673 791 4.764679 AATTGCTGTGCGAAATCACTAA 57.235 36.364 0.00 0.00 37.81 2.24
674 792 4.379394 GGAAATTGCTGTGCGAAATCACTA 60.379 41.667 0.00 0.00 37.81 2.74
675 793 3.568538 GAAATTGCTGTGCGAAATCACT 58.431 40.909 0.00 0.00 37.81 3.41
676 794 2.663119 GGAAATTGCTGTGCGAAATCAC 59.337 45.455 0.00 0.00 37.48 3.06
689 807 3.439540 TGGAGCGCCGGAAATTGC 61.440 61.111 5.05 0.00 36.79 3.56
705 823 3.375299 GTGAAAGAAATCGATCTGGGGTG 59.625 47.826 0.00 0.00 0.00 4.61
1385 1507 8.509690 CCACCATATCTCATTTCATAACATGTC 58.490 37.037 0.00 0.00 0.00 3.06
1471 1593 7.002879 AGGTATCATCTGCTTTGCATAGAAAT 58.997 34.615 8.49 2.51 38.13 2.17
1496 1618 7.649533 ATGCCAATTCAGAAATGTAGATCAA 57.350 32.000 0.00 0.00 0.00 2.57
1544 1666 3.817647 TGTACAGTACATTGCAATGCACA 59.182 39.130 33.62 24.55 40.04 4.57
1545 1667 4.418013 TGTACAGTACATTGCAATGCAC 57.582 40.909 33.94 30.93 40.04 4.57
1546 1668 5.645497 TGTATGTACAGTACATTGCAATGCA 59.355 36.000 33.94 22.51 46.69 3.96
1547 1669 6.117911 TGTATGTACAGTACATTGCAATGC 57.882 37.500 33.94 21.10 46.69 3.56
1548 1670 7.696755 ACATGTATGTACAGTACATTGCAATG 58.303 34.615 32.74 32.74 46.69 2.82
1549 1671 7.552330 TGACATGTATGTACAGTACATTGCAAT 59.448 33.333 27.51 18.53 46.69 3.56
1550 1672 6.876257 TGACATGTATGTACAGTACATTGCAA 59.124 34.615 27.51 10.16 46.69 4.08
1551 1673 6.402222 TGACATGTATGTACAGTACATTGCA 58.598 36.000 27.51 24.47 46.69 4.08
1552 1674 6.902224 TGACATGTATGTACAGTACATTGC 57.098 37.500 27.51 20.69 46.69 3.56
1553 1675 8.702163 TCTTGACATGTATGTACAGTACATTG 57.298 34.615 27.51 21.78 46.69 2.82
1554 1676 9.890629 ATTCTTGACATGTATGTACAGTACATT 57.109 29.630 27.51 12.21 46.69 2.71
1565 1687 9.726232 CCACAGATTTTATTCTTGACATGTATG 57.274 33.333 0.00 0.00 0.00 2.39
1566 1688 8.906867 CCCACAGATTTTATTCTTGACATGTAT 58.093 33.333 0.00 0.00 0.00 2.29
1567 1689 8.106462 TCCCACAGATTTTATTCTTGACATGTA 58.894 33.333 0.00 0.00 0.00 2.29
1568 1690 6.947733 TCCCACAGATTTTATTCTTGACATGT 59.052 34.615 0.00 0.00 0.00 3.21
1569 1691 7.094248 TGTCCCACAGATTTTATTCTTGACATG 60.094 37.037 0.00 0.00 0.00 3.21
1570 1692 6.947733 TGTCCCACAGATTTTATTCTTGACAT 59.052 34.615 0.00 0.00 0.00 3.06
1652 1801 0.038166 ACGAGGCAACACCATTGGAT 59.962 50.000 10.37 0.00 43.14 3.41
1910 2060 4.081642 TCACTTATTTTGAGACGGAGGGAG 60.082 45.833 0.00 0.00 0.00 4.30
1911 2061 3.835978 TCACTTATTTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
1912 2062 3.933332 GTCACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
1913 2063 4.822026 AGTCACTTATTTTGAGACGGAGG 58.178 43.478 0.00 0.00 34.56 4.30
1914 2064 5.470368 TGAGTCACTTATTTTGAGACGGAG 58.530 41.667 0.00 0.00 34.56 4.63
1915 2065 5.462530 TGAGTCACTTATTTTGAGACGGA 57.537 39.130 0.00 0.00 34.56 4.69
1916 2066 5.696724 AGTTGAGTCACTTATTTTGAGACGG 59.303 40.000 0.00 0.00 34.56 4.79
1917 2067 6.771188 AGTTGAGTCACTTATTTTGAGACG 57.229 37.500 0.00 0.00 34.56 4.18
1918 2068 8.398665 ACAAAGTTGAGTCACTTATTTTGAGAC 58.601 33.333 14.62 0.00 35.87 3.36
1919 2069 8.506168 ACAAAGTTGAGTCACTTATTTTGAGA 57.494 30.769 14.62 0.00 35.87 3.27
1920 2070 9.651718 GTACAAAGTTGAGTCACTTATTTTGAG 57.348 33.333 14.62 0.00 35.87 3.02
1921 2071 9.391006 AGTACAAAGTTGAGTCACTTATTTTGA 57.609 29.630 14.62 1.37 35.87 2.69
1927 2077 9.880157 AAACTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 2.97 0.00 46.40 2.24
1928 2078 8.788325 AAACTTAGTACAAAGTTGAGTCACTT 57.212 30.769 2.97 0.00 46.40 3.16
1929 2079 9.530633 CTAAACTTAGTACAAAGTTGAGTCACT 57.469 33.333 2.97 0.00 46.40 3.41
1954 2104 9.310716 GACTCAACTTTGTACTAACTTTGTACT 57.689 33.333 12.73 0.00 40.44 2.73
1955 2105 9.090692 TGACTCAACTTTGTACTAACTTTGTAC 57.909 33.333 6.58 6.58 40.27 2.90
1956 2106 9.090692 GTGACTCAACTTTGTACTAACTTTGTA 57.909 33.333 0.00 0.00 0.00 2.41
1957 2107 7.822822 AGTGACTCAACTTTGTACTAACTTTGT 59.177 33.333 0.00 0.00 0.00 2.83
1958 2108 8.197988 AGTGACTCAACTTTGTACTAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
1959 2109 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
1965 2115 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
1966 2116 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
1967 2117 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
1968 2118 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
1969 2119 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
1970 2120 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
1971 2121 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
1972 2122 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
1973 2123 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
1974 2124 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
1975 2125 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
1976 2126 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
1977 2127 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
1978 2128 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
1979 2129 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
1980 2130 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1981 2131 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1982 2132 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1983 2133 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1984 2134 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1985 2135 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
1986 2136 1.272807 CTACTCCCTCCGTCCCAAAA 58.727 55.000 0.00 0.00 0.00 2.44
1987 2137 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1988 2138 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
1989 2139 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
1990 2140 2.374839 AGTATACTACTCCCTCCGTCCC 59.625 54.545 2.75 0.00 32.47 4.46
1991 2141 3.786368 AGTATACTACTCCCTCCGTCC 57.214 52.381 2.75 0.00 32.47 4.79
1992 2142 5.863965 AGTTAGTATACTACTCCCTCCGTC 58.136 45.833 12.25 0.00 40.14 4.79
1993 2143 5.903198 AGTTAGTATACTACTCCCTCCGT 57.097 43.478 12.25 0.00 40.14 4.69
1994 2144 5.874261 GCTAGTTAGTATACTACTCCCTCCG 59.126 48.000 12.25 3.64 40.14 4.63
1995 2145 7.019656 AGCTAGTTAGTATACTACTCCCTCC 57.980 44.000 12.25 0.00 40.14 4.30
1996 2146 9.435688 GTTAGCTAGTTAGTATACTACTCCCTC 57.564 40.741 12.25 1.53 40.14 4.30
1997 2147 9.169721 AGTTAGCTAGTTAGTATACTACTCCCT 57.830 37.037 12.25 12.88 40.14 4.20
1998 2148 9.218440 CAGTTAGCTAGTTAGTATACTACTCCC 57.782 40.741 12.25 7.71 40.14 4.30
1999 2149 8.720562 GCAGTTAGCTAGTTAGTATACTACTCC 58.279 40.741 12.25 4.06 39.13 3.85
2000 2150 9.270640 TGCAGTTAGCTAGTTAGTATACTACTC 57.729 37.037 12.25 8.74 45.94 2.59
2001 2151 9.275398 CTGCAGTTAGCTAGTTAGTATACTACT 57.725 37.037 12.25 13.99 45.94 2.57
2002 2152 9.054922 ACTGCAGTTAGCTAGTTAGTATACTAC 57.945 37.037 15.25 7.98 45.94 2.73
2003 2153 9.270640 GACTGCAGTTAGCTAGTTAGTATACTA 57.729 37.037 22.65 8.59 45.94 1.82
2004 2154 7.994334 AGACTGCAGTTAGCTAGTTAGTATACT 59.006 37.037 22.65 10.87 45.94 2.12
2005 2155 8.071368 CAGACTGCAGTTAGCTAGTTAGTATAC 58.929 40.741 22.65 1.23 45.94 1.47
2006 2156 7.774157 ACAGACTGCAGTTAGCTAGTTAGTATA 59.226 37.037 22.65 0.00 45.94 1.47
2007 2157 6.603997 ACAGACTGCAGTTAGCTAGTTAGTAT 59.396 38.462 22.65 0.00 45.94 2.12
2075 2232 2.094752 GCGTTGCTGGATTGGTAAACAT 60.095 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.