Multiple sequence alignment - TraesCS2D01G053500

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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 TraesCS2D01G053500 chr2D 100.000 2289 0 0 1 2289 20919041 20916753 0.000000e+00 4228.0
1 TraesCS2D01G053500 chr4D 92.474 1342 94 6 9 1347 414225602 414226939 0.000000e+00 1912.0
2 TraesCS2D01G053500 chr4D 91.412 1374 114 4 9 1381 421048632 421047262 0.000000e+00 1881.0
3 TraesCS2D01G053500 chr4D 91.247 1371 106 8 16 1381 493971098 493969737 0.000000e+00 1855.0
4 TraesCS2D01G053500 chr4D 91.433 1354 110 6 31 1381 48683904 48682554 0.000000e+00 1853.0
5 TraesCS2D01G053500 chr4D 90.843 1376 114 8 9 1381 116524553 116523187 0.000000e+00 1832.0
6 TraesCS2D01G053500 chr4D 93.960 298 16 2 1363 1659 116523133 116522837 1.250000e-122 449.0
7 TraesCS2D01G053500 chr4D 93.878 294 18 0 1363 1656 102105482 102105189 5.800000e-121 444.0
8 TraesCS2D01G053500 chr3A 91.557 1374 113 3 9 1381 418765656 418764285 0.000000e+00 1892.0
9 TraesCS2D01G053500 chr3A 94.558 294 16 0 1363 1656 418764231 418763938 2.680000e-124 455.0
10 TraesCS2D01G053500 chr3A 88.889 81 5 1 2184 2260 365361839 365361919 1.870000e-16 97.1
11 TraesCS2D01G053500 chr3B 91.213 1377 112 7 9 1381 478550949 478549578 0.000000e+00 1864.0
12 TraesCS2D01G053500 chr3B 97.183 71 2 0 1991 2061 672761234 672761304 1.110000e-23 121.0
13 TraesCS2D01G053500 chr1A 91.194 1374 116 4 9 1381 31810754 31812123 0.000000e+00 1862.0
14 TraesCS2D01G053500 chr4A 90.611 1374 125 4 9 1381 327748370 327747000 0.000000e+00 1820.0
15 TraesCS2D01G053500 chr4A 93.262 282 16 3 1932 2212 688787294 688787573 1.640000e-111 412.0
16 TraesCS2D01G053500 chr4A 92.754 69 5 0 1993 2061 486638119 486638051 1.450000e-17 100.0
17 TraesCS2D01G053500 chr5D 93.708 445 27 1 1841 2285 369559239 369559682 0.000000e+00 665.0
18 TraesCS2D01G053500 chr5D 93.377 302 18 2 1363 1662 369344992 369345293 1.610000e-121 446.0
19 TraesCS2D01G053500 chr5D 96.341 164 6 0 1656 1819 369559089 369559252 1.040000e-68 270.0
20 TraesCS2D01G053500 chr5B 94.237 295 17 0 1363 1657 641299176 641298882 3.470000e-123 451.0
21 TraesCS2D01G053500 chr1D 93.980 299 16 2 1363 1659 429021576 429021874 3.470000e-123 451.0
22 TraesCS2D01G053500 chr3D 93.898 295 18 0 1363 1657 515987559 515987265 1.610000e-121 446.0
23 TraesCS2D01G053500 chr3D 93.878 294 18 0 1363 1656 6289046 6289339 5.800000e-121 444.0
24 TraesCS2D01G053500 chr3D 89.024 82 4 2 2184 2260 274417240 274417321 1.870000e-16 97.1
25 TraesCS2D01G053500 chr3D 89.024 82 4 2 2184 2260 274629275 274629356 1.870000e-16 97.1
26 TraesCS2D01G053500 chr6D 93.624 298 18 1 1363 1659 450907386 450907683 5.800000e-121 444.0
27 TraesCS2D01G053500 chr4B 90.303 165 10 4 1991 2154 232120085 232120244 6.410000e-51 211.0
28 TraesCS2D01G053500 chr6A 92.105 114 5 3 2042 2154 349884309 349884419 8.470000e-35 158.0


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 TraesCS2D01G053500 chr2D 20916753 20919041 2288 True 4228.0 4228 100.0000 1 2289 1 chr2D.!!$R1 2288
1 TraesCS2D01G053500 chr4D 414225602 414226939 1337 False 1912.0 1912 92.4740 9 1347 1 chr4D.!!$F1 1338
2 TraesCS2D01G053500 chr4D 421047262 421048632 1370 True 1881.0 1881 91.4120 9 1381 1 chr4D.!!$R3 1372
3 TraesCS2D01G053500 chr4D 493969737 493971098 1361 True 1855.0 1855 91.2470 16 1381 1 chr4D.!!$R4 1365
4 TraesCS2D01G053500 chr4D 48682554 48683904 1350 True 1853.0 1853 91.4330 31 1381 1 chr4D.!!$R1 1350
5 TraesCS2D01G053500 chr4D 116522837 116524553 1716 True 1140.5 1832 92.4015 9 1659 2 chr4D.!!$R5 1650
6 TraesCS2D01G053500 chr3A 418763938 418765656 1718 True 1173.5 1892 93.0575 9 1656 2 chr3A.!!$R1 1647
7 TraesCS2D01G053500 chr3B 478549578 478550949 1371 True 1864.0 1864 91.2130 9 1381 1 chr3B.!!$R1 1372
8 TraesCS2D01G053500 chr1A 31810754 31812123 1369 False 1862.0 1862 91.1940 9 1381 1 chr1A.!!$F1 1372
9 TraesCS2D01G053500 chr4A 327747000 327748370 1370 True 1820.0 1820 90.6110 9 1381 1 chr4A.!!$R1 1372
10 TraesCS2D01G053500 chr5D 369559089 369559682 593 False 467.5 665 95.0245 1656 2285 2 chr5D.!!$F2 629

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
736 748 1.188863 GCCTGGCTCCATGAATTGTT 58.811 50.0 12.43 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2351 0.040204 AACCCATGGCCCAGAGAAAG 59.96 55.0 6.09 0.0 0.0 2.62 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
162 169 1.481363 CCGGTTCTTCCTCCTCCTTAC 59.519 57.143 0.00 0.00 0.00 2.34
180 187 3.083997 GCTCCCCACCGATGACCT 61.084 66.667 0.00 0.00 0.00 3.85
182 189 1.991230 CTCCCCACCGATGACCTTT 59.009 57.895 0.00 0.00 0.00 3.11
219 226 2.161211 GTCTCCCAGTACACTACGACAC 59.839 54.545 0.00 0.00 0.00 3.67
259 266 4.283722 CCCAGTAGTTCTTGTACTTGGACT 59.716 45.833 0.00 0.00 36.01 3.85
441 449 1.374252 GGAGCCGAAGTTCGAGCAA 60.374 57.895 28.36 0.00 43.74 3.91
507 515 1.553690 CGAGGAAGAAGGCCCTCCAA 61.554 60.000 0.00 0.00 44.66 3.53
518 526 1.226262 CCCTCCAACCAATACCCCG 59.774 63.158 0.00 0.00 0.00 5.73
535 543 3.327404 GAGGGAAGGGGTTGGCGA 61.327 66.667 0.00 0.00 0.00 5.54
631 640 1.229820 TGGTGGGCAGGGTGAGTAT 60.230 57.895 0.00 0.00 0.00 2.12
641 650 5.024118 GGCAGGGTGAGTATATATAGGTGT 58.976 45.833 0.00 0.00 0.00 4.16
668 680 1.822371 GAGGAGGAAGAGTGACAGTCC 59.178 57.143 6.67 0.00 0.00 3.85
706 718 5.419788 ACATGCTCTTCAATAAGCCATGAAA 59.580 36.000 17.56 0.00 40.65 2.69
736 748 1.188863 GCCTGGCTCCATGAATTGTT 58.811 50.000 12.43 0.00 0.00 2.83
739 751 2.827322 CCTGGCTCCATGAATTGTTTGA 59.173 45.455 0.00 0.00 0.00 2.69
863 875 1.676014 CGCCAAGGAAGAACCGAAGAT 60.676 52.381 0.00 0.00 44.74 2.40
866 878 1.394917 CAAGGAAGAACCGAAGATGCG 59.605 52.381 0.00 0.00 44.74 4.73
906 918 4.888325 ATGGAGGAGCCCCCGAGG 62.888 72.222 0.00 0.00 40.87 4.63
925 937 1.227823 AGCAAGCACCGCAACTACA 60.228 52.632 0.00 0.00 0.00 2.74
940 952 4.562757 GCAACTACAACCACTACCATGAGA 60.563 45.833 0.00 0.00 0.00 3.27
1012 1024 3.988151 ATCCCCATGCCCCTGGACA 62.988 63.158 0.00 0.00 38.69 4.02
1041 1053 4.893601 TTCGTCGCGGTGCCAACA 62.894 61.111 6.13 0.00 0.00 3.33
1055 1067 1.949525 GCCAACAGAGTTCAAGCTCAA 59.050 47.619 0.00 0.00 37.94 3.02
1066 1078 2.997980 TCAAGCTCAAGAACAACACCA 58.002 42.857 0.00 0.00 0.00 4.17
1171 1183 3.006217 CCAGATCAAGATCGGCTACATGA 59.994 47.826 0.00 0.00 42.48 3.07
1194 1206 0.734253 CGTTCAAGCTCCTGACTCCG 60.734 60.000 0.00 0.00 0.00 4.63
1290 1302 3.771160 CGCCGCCAAGGAGTAGGT 61.771 66.667 0.00 0.00 45.00 3.08
1316 1328 2.168728 GGCACCTCCTTCCTAAGTACTG 59.831 54.545 0.00 0.00 0.00 2.74
1374 1386 7.899178 TTTGAACTATCGTTATGATGTGTGT 57.101 32.000 0.00 0.00 37.99 3.72
1396 1481 1.202710 ACATGGTTGTGCCGAAGTGTA 60.203 47.619 0.00 0.00 41.21 2.90
1452 1537 0.955428 ACACCAGGCGTTGCATACAG 60.955 55.000 0.00 0.00 0.00 2.74
1491 1576 3.146066 GGTTTGTCCACTAACATGCAGA 58.854 45.455 6.41 0.00 34.16 4.26
1504 1589 1.682854 CATGCAGACAACCAAACACCT 59.317 47.619 0.00 0.00 0.00 4.00
1518 1603 1.149174 CACCTGGCAGTGTGGTTCT 59.851 57.895 21.34 0.00 32.89 3.01
1569 1654 3.561143 ACCAAACAACTTGCAGATGGTA 58.439 40.909 6.59 0.00 37.89 3.25
1574 1659 6.294453 CCAAACAACTTGCAGATGGTACATTA 60.294 38.462 0.00 0.00 37.03 1.90
1622 1707 4.194640 GAGTTGAGAAGGCTATGCAATGA 58.805 43.478 0.00 0.00 0.00 2.57
1708 1793 2.043953 GGGGCACAAGTGGGATCC 60.044 66.667 1.92 1.92 0.00 3.36
1710 1795 2.763215 GGCACAAGTGGGATCCCA 59.237 61.111 30.62 30.62 45.02 4.37
1807 1892 6.139679 ACATATTCTTCCTTCCCACTTGAA 57.860 37.500 0.00 0.00 0.00 2.69
1808 1893 6.552008 ACATATTCTTCCTTCCCACTTGAAA 58.448 36.000 0.00 0.00 0.00 2.69
1809 1894 7.184862 ACATATTCTTCCTTCCCACTTGAAAT 58.815 34.615 0.00 0.00 0.00 2.17
1810 1895 5.990120 ATTCTTCCTTCCCACTTGAAATG 57.010 39.130 0.00 0.00 0.00 2.32
1811 1896 3.157087 TCTTCCTTCCCACTTGAAATGC 58.843 45.455 0.00 0.00 0.00 3.56
1812 1897 2.673775 TCCTTCCCACTTGAAATGCA 57.326 45.000 0.00 0.00 0.00 3.96
1813 1898 3.173953 TCCTTCCCACTTGAAATGCAT 57.826 42.857 0.00 0.00 0.00 3.96
1814 1899 4.314522 TCCTTCCCACTTGAAATGCATA 57.685 40.909 0.00 0.00 0.00 3.14
1815 1900 4.671831 TCCTTCCCACTTGAAATGCATAA 58.328 39.130 0.00 0.00 0.00 1.90
1816 1901 4.462483 TCCTTCCCACTTGAAATGCATAAC 59.538 41.667 0.00 0.00 0.00 1.89
1817 1902 4.463891 CCTTCCCACTTGAAATGCATAACT 59.536 41.667 0.00 0.00 0.00 2.24
1818 1903 5.047092 CCTTCCCACTTGAAATGCATAACTT 60.047 40.000 0.00 0.00 0.00 2.66
1819 1904 6.418057 TTCCCACTTGAAATGCATAACTTT 57.582 33.333 0.00 0.00 0.00 2.66
1820 1905 6.024552 TCCCACTTGAAATGCATAACTTTC 57.975 37.500 0.00 1.07 33.06 2.62
1821 1906 5.774690 TCCCACTTGAAATGCATAACTTTCT 59.225 36.000 0.00 0.00 33.50 2.52
1822 1907 6.945435 TCCCACTTGAAATGCATAACTTTCTA 59.055 34.615 0.00 0.00 33.50 2.10
1823 1908 7.121168 TCCCACTTGAAATGCATAACTTTCTAG 59.879 37.037 15.70 15.70 38.96 2.43
1824 1909 6.749118 CCACTTGAAATGCATAACTTTCTAGC 59.251 38.462 16.65 0.00 37.58 3.42
1825 1910 6.749118 CACTTGAAATGCATAACTTTCTAGCC 59.251 38.462 16.65 0.00 37.58 3.93
1826 1911 5.835113 TGAAATGCATAACTTTCTAGCCC 57.165 39.130 0.00 0.00 33.50 5.19
1827 1912 4.335315 TGAAATGCATAACTTTCTAGCCCG 59.665 41.667 0.00 0.00 33.50 6.13
1828 1913 1.663695 TGCATAACTTTCTAGCCCGC 58.336 50.000 0.00 0.00 0.00 6.13
1829 1914 1.065782 TGCATAACTTTCTAGCCCGCA 60.066 47.619 0.00 0.00 0.00 5.69
1830 1915 2.014128 GCATAACTTTCTAGCCCGCAA 58.986 47.619 0.00 0.00 0.00 4.85
1831 1916 2.422127 GCATAACTTTCTAGCCCGCAAA 59.578 45.455 0.00 0.00 0.00 3.68
1832 1917 3.119637 GCATAACTTTCTAGCCCGCAAAA 60.120 43.478 0.00 0.00 0.00 2.44
1833 1918 4.617298 GCATAACTTTCTAGCCCGCAAAAA 60.617 41.667 0.00 0.00 0.00 1.94
1882 1967 8.684386 TTCACATGAACATACACTTAGGAAAA 57.316 30.769 0.00 0.00 0.00 2.29
1888 1973 6.425721 TGAACATACACTTAGGAAAAGGAACG 59.574 38.462 0.00 0.00 0.00 3.95
1919 2004 6.966435 ACTCCAACAAAACACAAATGAAAG 57.034 33.333 0.00 0.00 0.00 2.62
1923 2008 5.122082 CCAACAAAACACAAATGAAAGTGCT 59.878 36.000 0.00 0.00 39.30 4.40
1925 2010 5.237048 ACAAAACACAAATGAAAGTGCTGT 58.763 33.333 0.00 0.00 39.30 4.40
1952 2037 2.200373 GGCAACCACACACTTAGGAT 57.800 50.000 0.00 0.00 0.00 3.24
1962 2047 8.706322 ACCACACACTTAGGATAGAAAATTTT 57.294 30.769 2.28 2.28 0.00 1.82
1979 2064 8.415553 AGAAAATTTTCAGACATGAACATCACA 58.584 29.630 28.00 0.00 45.07 3.58
1989 2074 7.966753 CAGACATGAACATCACAAATTAAGAGG 59.033 37.037 0.00 0.00 0.00 3.69
2001 2086 7.023575 CACAAATTAAGAGGATTTTCAGTCCG 58.976 38.462 0.00 0.00 40.76 4.79
2003 2088 1.726853 AAGAGGATTTTCAGTCCGCG 58.273 50.000 0.00 0.00 40.07 6.46
2014 2099 0.735978 CAGTCCGCGATACTGCAACA 60.736 55.000 22.70 0.00 38.08 3.33
2107 2192 4.127171 TGACACCTTTTTCTTCTTCTCCG 58.873 43.478 0.00 0.00 0.00 4.63
2110 2195 5.377478 ACACCTTTTTCTTCTTCTCCGAAT 58.623 37.500 0.00 0.00 0.00 3.34
2116 2201 2.337583 TCTTCTTCTCCGAATGCAACG 58.662 47.619 9.21 9.21 0.00 4.10
2154 2239 5.643777 AGTAATTACTTGCACACATGAGACC 59.356 40.000 12.50 0.00 31.13 3.85
2168 2253 9.345517 CACACATGAGACCAAAAATATTAACTG 57.654 33.333 0.00 0.00 0.00 3.16
2215 2300 1.518903 GCACTGTTTCTGCCACTCCC 61.519 60.000 0.00 0.00 0.00 4.30
2249 2334 6.604735 ACTGAGTACTGAACAATTGAACAC 57.395 37.500 13.59 1.33 0.00 3.32
2250 2335 5.527582 ACTGAGTACTGAACAATTGAACACC 59.472 40.000 13.59 0.00 0.00 4.16
2256 2341 0.820074 AACAATTGAACACCGGGCGA 60.820 50.000 13.59 0.00 0.00 5.54
2262 2347 1.079405 GAACACCGGGCGATCTCAA 60.079 57.895 6.32 0.00 0.00 3.02
2266 2351 1.819632 ACCGGGCGATCTCAATTGC 60.820 57.895 6.32 0.00 41.00 3.56
2272 2357 2.032675 GGGCGATCTCAATTGCTTTCTC 59.967 50.000 0.00 0.00 41.41 2.87
2285 2370 0.040204 CTTTCTCTGGGCCATGGGTT 59.960 55.000 15.13 0.00 0.00 4.11
2286 2371 0.251742 TTTCTCTGGGCCATGGGTTG 60.252 55.000 15.13 0.00 0.00 3.77
2287 2372 1.139498 TTCTCTGGGCCATGGGTTGA 61.139 55.000 15.13 0.00 0.00 3.18
2288 2373 0.920763 TCTCTGGGCCATGGGTTGAT 60.921 55.000 15.13 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.043816 CACTCCATCCGCATCTACCT 58.956 55.000 0.00 0.00 0.00 3.08
1 2 0.034059 CCACTCCATCCGCATCTACC 59.966 60.000 0.00 0.00 0.00 3.18
2 3 0.601311 GCCACTCCATCCGCATCTAC 60.601 60.000 0.00 0.00 0.00 2.59
3 4 0.760567 AGCCACTCCATCCGCATCTA 60.761 55.000 0.00 0.00 0.00 1.98
4 5 2.068821 AGCCACTCCATCCGCATCT 61.069 57.895 0.00 0.00 0.00 2.90
5 6 1.890979 CAGCCACTCCATCCGCATC 60.891 63.158 0.00 0.00 0.00 3.91
6 7 2.191375 CAGCCACTCCATCCGCAT 59.809 61.111 0.00 0.00 0.00 4.73
7 8 4.100084 CCAGCCACTCCATCCGCA 62.100 66.667 0.00 0.00 0.00 5.69
12 13 1.578215 ATGAAGGCCAGCCACTCCAT 61.578 55.000 12.03 5.49 38.92 3.41
14 15 1.452833 GATGAAGGCCAGCCACTCC 60.453 63.158 12.03 0.00 38.92 3.85
68 72 0.177373 TCGACTCCTCCGAGATCGAA 59.823 55.000 13.65 0.00 41.43 3.71
162 169 4.530857 GGTCATCGGTGGGGAGCG 62.531 72.222 0.00 0.00 0.00 5.03
219 226 1.227674 GGCTCCTAATGACCGCCAG 60.228 63.158 0.00 0.00 40.41 4.85
259 266 4.039488 TGACGCTAAACAAAGGAAGAGGTA 59.961 41.667 0.00 0.00 0.00 3.08
326 333 1.302033 CCATAGGAGGGCACGATGC 60.302 63.158 0.00 0.00 44.08 3.91
338 346 2.170607 ACGTTGATTCCTGACCCATAGG 59.829 50.000 0.00 0.00 40.04 2.57
340 348 3.104512 AGACGTTGATTCCTGACCCATA 58.895 45.455 0.00 0.00 0.00 2.74
341 349 1.909302 AGACGTTGATTCCTGACCCAT 59.091 47.619 0.00 0.00 0.00 4.00
507 515 0.986550 CCTTCCCTCGGGGTATTGGT 60.987 60.000 0.00 0.00 44.74 3.67
518 526 2.680370 ATCGCCAACCCCTTCCCTC 61.680 63.158 0.00 0.00 0.00 4.30
550 558 1.536922 CGTCTACATCGCCATGAGCTT 60.537 52.381 0.00 0.00 40.39 3.74
565 573 4.851843 TCACTATCAACCTTCCTCGTCTA 58.148 43.478 0.00 0.00 0.00 2.59
569 577 3.948473 TCTCTCACTATCAACCTTCCTCG 59.052 47.826 0.00 0.00 0.00 4.63
631 640 5.555941 TCCTCCTCTCCATCACACCTATATA 59.444 44.000 0.00 0.00 0.00 0.86
641 650 2.313041 TCACTCTTCCTCCTCTCCATCA 59.687 50.000 0.00 0.00 0.00 3.07
668 680 3.684788 AGAGCATGTAGTTAAAACGGCAG 59.315 43.478 0.00 0.00 0.00 4.85
706 718 1.133976 GGAGCCAGGCACAACATAGAT 60.134 52.381 15.80 0.00 0.00 1.98
736 748 3.448660 TCATTGCTCTCCTCGATCTTCAA 59.551 43.478 0.00 0.00 0.00 2.69
739 751 3.295093 TCTCATTGCTCTCCTCGATCTT 58.705 45.455 0.00 0.00 0.00 2.40
866 878 3.103911 CGTCGTCGCCAACCTCAC 61.104 66.667 0.00 0.00 0.00 3.51
903 915 2.669569 TTGCGGTGCTTGCTCCTC 60.670 61.111 11.23 4.72 0.00 3.71
906 918 1.227999 TGTAGTTGCGGTGCTTGCTC 61.228 55.000 0.00 0.00 0.00 4.26
925 937 2.305927 CACCCTTCTCATGGTAGTGGTT 59.694 50.000 0.00 0.00 32.32 3.67
940 952 1.655114 AAGTGAGTTGGGCCACCCTT 61.655 55.000 5.23 0.78 45.70 3.95
1041 1053 4.333926 GTGTTGTTCTTGAGCTTGAACTCT 59.666 41.667 20.71 0.00 41.99 3.24
1055 1067 0.536006 GGAGCAGCTGGTGTTGTTCT 60.536 55.000 25.60 4.29 35.61 3.01
1066 1078 1.537397 TCACCTTCCAGGAGCAGCT 60.537 57.895 0.00 0.00 37.67 4.24
1149 1161 3.006217 TCATGTAGCCGATCTTGATCTGG 59.994 47.826 8.70 11.33 0.00 3.86
1171 1183 1.620819 AGTCAGGAGCTTGAACGTCAT 59.379 47.619 0.00 0.00 0.00 3.06
1213 1225 2.602257 TGCCATCATCGTCGAAGATT 57.398 45.000 11.35 0.00 40.67 2.40
1285 1297 3.468140 GAGGTGCCCCGGACCTAC 61.468 72.222 13.07 4.35 44.28 3.18
1316 1328 5.502544 GCATAAACCATAAAGCAGACTCGAC 60.503 44.000 0.00 0.00 0.00 4.20
1374 1386 1.876799 CACTTCGGCACAACCATGTAA 59.123 47.619 0.00 0.00 37.82 2.41
1452 1537 1.004679 CCAAGGCATGGTGTTTGGC 60.005 57.895 0.00 0.00 44.85 4.52
1491 1576 0.324275 ACTGCCAGGTGTTTGGTTGT 60.324 50.000 0.00 0.00 40.49 3.32
1593 1678 0.612744 GCCTTCTCAACTCAGCCTCT 59.387 55.000 0.00 0.00 0.00 3.69
1594 1679 0.612744 AGCCTTCTCAACTCAGCCTC 59.387 55.000 0.00 0.00 0.00 4.70
1622 1707 2.719739 TGCCGTAGTCTACAGTAGCTT 58.280 47.619 10.59 0.00 0.00 3.74
1661 1746 3.506067 CCACCAAATTCTAGTGGGTTGTC 59.494 47.826 11.76 0.00 46.01 3.18
1673 1758 2.497273 CCCCACTTCATCCACCAAATTC 59.503 50.000 0.00 0.00 0.00 2.17
1686 1771 1.903404 CCCACTTGTGCCCCACTTC 60.903 63.158 0.00 0.00 35.11 3.01
1708 1793 7.452880 TCTGTTGTATTCTTTCCTCAAATGG 57.547 36.000 0.00 0.00 0.00 3.16
1710 1795 9.918630 CATTTCTGTTGTATTCTTTCCTCAAAT 57.081 29.630 0.00 0.00 0.00 2.32
1807 1892 2.618709 GCGGGCTAGAAAGTTATGCATT 59.381 45.455 3.54 0.00 0.00 3.56
1808 1893 2.222027 GCGGGCTAGAAAGTTATGCAT 58.778 47.619 3.79 3.79 0.00 3.96
1809 1894 1.065782 TGCGGGCTAGAAAGTTATGCA 60.066 47.619 0.00 0.00 0.00 3.96
1810 1895 1.663695 TGCGGGCTAGAAAGTTATGC 58.336 50.000 0.00 0.00 0.00 3.14
1811 1896 4.695217 TTTTGCGGGCTAGAAAGTTATG 57.305 40.909 0.00 0.00 0.00 1.90
1835 1920 9.899226 GTGAAGTTAAGTTATGCATTTCTTTCT 57.101 29.630 3.54 9.12 0.00 2.52
1836 1921 9.677567 TGTGAAGTTAAGTTATGCATTTCTTTC 57.322 29.630 3.54 5.47 0.00 2.62
1838 1923 9.630098 CATGTGAAGTTAAGTTATGCATTTCTT 57.370 29.630 3.54 12.36 0.00 2.52
1839 1924 9.013229 TCATGTGAAGTTAAGTTATGCATTTCT 57.987 29.630 3.54 0.48 0.00 2.52
1840 1925 9.624697 TTCATGTGAAGTTAAGTTATGCATTTC 57.375 29.630 3.54 0.01 0.00 2.17
1841 1926 9.410556 GTTCATGTGAAGTTAAGTTATGCATTT 57.589 29.630 3.54 0.00 34.27 2.32
1854 1939 7.450074 TCCTAAGTGTATGTTCATGTGAAGTT 58.550 34.615 0.00 0.00 34.27 2.66
1919 2004 0.955919 GTTGCCCCTGTAGACAGCAC 60.956 60.000 4.03 0.00 42.47 4.40
1923 2008 1.057275 TGTGGTTGCCCCTGTAGACA 61.057 55.000 0.00 0.00 0.00 3.41
1925 2010 1.057275 TGTGTGGTTGCCCCTGTAGA 61.057 55.000 0.00 0.00 0.00 2.59
1952 2037 9.897744 GTGATGTTCATGTCTGAAAATTTTCTA 57.102 29.630 26.73 15.07 42.85 2.10
1962 2047 8.620116 TCTTAATTTGTGATGTTCATGTCTGA 57.380 30.769 0.00 0.00 0.00 3.27
1979 2064 5.163754 CGCGGACTGAAAATCCTCTTAATTT 60.164 40.000 0.00 0.00 33.70 1.82
1989 2074 2.033662 GCAGTATCGCGGACTGAAAATC 60.034 50.000 32.63 17.95 46.01 2.17
2001 2086 2.069273 AGTTCAGTGTTGCAGTATCGC 58.931 47.619 0.00 0.00 0.00 4.58
2003 2088 5.424121 ACAAAGTTCAGTGTTGCAGTATC 57.576 39.130 0.00 0.00 0.00 2.24
2014 2099 7.217200 TGTTCTATGAAGCTACAAAGTTCAGT 58.783 34.615 0.00 0.00 33.83 3.41
2090 2175 4.216257 TGCATTCGGAGAAGAAGAAAAAGG 59.784 41.667 0.00 0.00 45.90 3.11
2107 2192 7.189512 ACTAATAAGCATTCTTCGTTGCATTC 58.810 34.615 0.00 0.00 41.35 2.67
2110 2195 7.603963 TTACTAATAAGCATTCTTCGTTGCA 57.396 32.000 0.00 0.00 41.35 4.08
2227 2312 5.333339 CGGTGTTCAATTGTTCAGTACTCAG 60.333 44.000 5.13 0.00 0.00 3.35
2235 2320 0.671251 GCCCGGTGTTCAATTGTTCA 59.329 50.000 5.13 3.47 0.00 3.18
2249 2334 1.097547 AAGCAATTGAGATCGCCCGG 61.098 55.000 10.34 0.00 0.00 5.73
2250 2335 0.734889 AAAGCAATTGAGATCGCCCG 59.265 50.000 10.34 0.00 0.00 6.13
2256 2341 3.022406 GCCCAGAGAAAGCAATTGAGAT 58.978 45.455 10.34 0.00 0.00 2.75
2262 2347 1.481871 CATGGCCCAGAGAAAGCAAT 58.518 50.000 0.00 0.00 0.00 3.56
2266 2351 0.040204 AACCCATGGCCCAGAGAAAG 59.960 55.000 6.09 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.