Multiple sequence alignment - TraesCS5A01G333600

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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 TraesCS5A01G333600 chr5A 100.000 2471 0 0 1 2471 542525914 542528384 0.000000e+00 4564
1 TraesCS5A01G333600 chr5D 89.405 1529 130 9 280 1806 428037252 428038750 0.000000e+00 1897
2 TraesCS5A01G333600 chr5D 91.644 371 27 1 1837 2207 428038748 428039114 6.100000e-141 510
3 TraesCS5A01G333600 chr5D 92.347 196 14 1 2267 2461 428039348 428039543 6.730000e-71 278
4 TraesCS5A01G333600 chr5D 81.073 354 49 10 1298 1646 428307494 428307834 1.460000e-67 267
5 TraesCS5A01G333600 chr5B 84.414 1187 141 21 736 1915 517246539 517247688 0.000000e+00 1127
6 TraesCS5A01G333600 chr5B 84.769 650 68 15 1 633 517245454 517246089 7.500000e-175 623


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 TraesCS5A01G333600 chr5A 542525914 542528384 2470 False 4564 4564 100.0000 1 2471 1 chr5A.!!$F1 2470
1 TraesCS5A01G333600 chr5D 428037252 428039543 2291 False 895 1897 91.1320 280 2461 3 chr5D.!!$F2 2181
2 TraesCS5A01G333600 chr5B 517245454 517247688 2234 False 875 1127 84.5915 1 1915 2 chr5B.!!$F1 1914

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
986 1353 0.179189 GAGTGGAGGCGAAATTTGCG 60.179 55.0 0.0 0.39 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2264 2635 0.395311 CCCAGATGCACATGGAAGCT 60.395 55.0 18.46 0.0 39.02 3.74 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
29 30 9.982651 GAAATACCTTTGTGATATGCTAGTAGA 57.017 33.333 0.00 0.00 0.00 2.59
30 31 9.988815 AAATACCTTTGTGATATGCTAGTAGAG 57.011 33.333 0.00 0.00 0.00 2.43
62 63 1.826385 ATGGACTTCTTTTGAGCCCG 58.174 50.000 0.00 0.00 0.00 6.13
73 74 3.941081 GAGCCCGACTCATCTGGA 58.059 61.111 1.05 0.00 45.49 3.86
83 97 4.180057 CGACTCATCTGGAAAGAAGGAAG 58.820 47.826 0.00 0.00 0.00 3.46
105 119 8.718734 GGAAGTATTACCAAGAACAAGTTACAG 58.281 37.037 0.00 0.00 0.00 2.74
106 120 9.269453 GAAGTATTACCAAGAACAAGTTACAGT 57.731 33.333 0.00 0.00 0.00 3.55
113 127 5.448632 CCAAGAACAAGTTACAGTCCACAAC 60.449 44.000 0.00 0.00 0.00 3.32
114 128 5.099042 AGAACAAGTTACAGTCCACAACT 57.901 39.130 0.00 0.00 39.44 3.16
127 141 5.747342 AGTCCACAACTGTAACCAAAAGTA 58.253 37.500 0.00 0.00 36.65 2.24
129 143 6.831868 AGTCCACAACTGTAACCAAAAGTAAT 59.168 34.615 0.00 0.00 36.65 1.89
130 144 6.915843 GTCCACAACTGTAACCAAAAGTAATG 59.084 38.462 0.00 0.00 0.00 1.90
164 178 7.752239 GGAATATGTAGCGTATACGTACAACAT 59.248 37.037 28.02 26.63 42.22 2.71
165 179 8.443898 AATATGTAGCGTATACGTACAACATG 57.556 34.615 28.02 0.00 42.22 3.21
167 181 5.639757 TGTAGCGTATACGTACAACATGTT 58.360 37.500 25.04 4.92 42.22 2.71
172 186 6.470235 AGCGTATACGTACAACATGTTAGAAC 59.530 38.462 25.04 8.68 42.22 3.01
176 190 4.232221 ACGTACAACATGTTAGAACCTCG 58.768 43.478 11.53 11.24 0.00 4.63
177 191 4.022935 ACGTACAACATGTTAGAACCTCGA 60.023 41.667 11.53 0.00 0.00 4.04
178 192 4.557690 CGTACAACATGTTAGAACCTCGAG 59.442 45.833 11.53 5.13 0.00 4.04
189 203 0.250467 AACCTCGAGTGCAACATGCT 60.250 50.000 12.31 0.00 45.31 3.79
225 239 0.824759 GGAACTGGACATAGCCGACT 59.175 55.000 0.00 0.00 0.00 4.18
229 243 2.299521 ACTGGACATAGCCGACTAGAC 58.700 52.381 0.00 0.00 0.00 2.59
230 244 2.298610 CTGGACATAGCCGACTAGACA 58.701 52.381 0.00 0.00 0.00 3.41
232 246 1.002684 GGACATAGCCGACTAGACACG 60.003 57.143 0.00 0.00 0.00 4.49
236 250 3.003482 ACATAGCCGACTAGACACGATTC 59.997 47.826 0.00 0.00 0.00 2.52
249 263 1.942657 CACGATTCGCCCAAGATTGAT 59.057 47.619 5.86 0.00 0.00 2.57
255 269 1.068588 TCGCCCAAGATTGATAGACGG 59.931 52.381 0.00 0.00 0.00 4.79
256 270 1.230324 GCCCAAGATTGATAGACGGC 58.770 55.000 0.00 0.00 0.00 5.68
259 273 2.487934 CCAAGATTGATAGACGGCCAG 58.512 52.381 2.24 0.00 0.00 4.85
275 289 3.321648 AGGATGTGCCGCAGACCA 61.322 61.111 0.00 0.00 43.43 4.02
276 290 2.359850 GGATGTGCCGCAGACCAA 60.360 61.111 0.00 0.00 0.00 3.67
277 291 2.690778 GGATGTGCCGCAGACCAAC 61.691 63.158 0.00 0.00 0.00 3.77
278 292 1.965930 GATGTGCCGCAGACCAACA 60.966 57.895 0.00 0.00 0.00 3.33
292 306 4.400251 CAGACCAACATTCTACATGGCAAT 59.600 41.667 0.00 0.00 36.37 3.56
312 326 2.756829 TGCGTTCGTGTTGGATTAAGA 58.243 42.857 0.00 0.00 0.00 2.10
344 358 6.017192 GGTAATACACGTGTAAAACCTTGGTT 60.017 38.462 33.96 23.35 36.87 3.67
362 376 4.850680 TGGTTAGGCCAAATCTATTTCGT 58.149 39.130 5.01 0.00 45.94 3.85
365 379 3.004752 AGGCCAAATCTATTTCGTGCT 57.995 42.857 5.01 0.00 0.00 4.40
372 386 7.023575 GCCAAATCTATTTCGTGCTATATTGG 58.976 38.462 0.00 0.00 36.41 3.16
377 391 4.552166 ATTTCGTGCTATATTGGTGTGC 57.448 40.909 0.00 0.00 0.00 4.57
395 409 1.536073 GCCCAAAAGAGCAAGGGGAC 61.536 60.000 0.00 0.00 41.49 4.46
428 442 9.973450 AAATATGCAATTGTAACAACAAGTGTA 57.027 25.926 16.88 13.98 44.48 2.90
511 525 2.425143 ACCTAGCCATGTGAATGTGG 57.575 50.000 0.00 0.00 0.00 4.17
562 576 8.669571 AGGCCTGAAATAAGTTACATACCATAT 58.330 33.333 3.11 0.00 0.00 1.78
634 648 0.825840 ATCTGAGGACCTCTAGCGCC 60.826 60.000 22.14 0.00 0.00 6.53
644 658 2.874780 CTAGCGCCACACGTCGAC 60.875 66.667 2.29 5.18 46.11 4.20
649 663 3.400590 GCCACACGTCGACGGTTC 61.401 66.667 37.89 21.87 44.95 3.62
665 680 1.893137 GGTTCCCTGACCCAACAATTC 59.107 52.381 0.00 0.00 33.41 2.17
692 707 4.453136 GGACAAAGCCAATTAGACGTGTTA 59.547 41.667 0.00 0.00 0.00 2.41
728 743 3.817084 CCAGACAACTCACAATGTGACAT 59.183 43.478 12.63 0.54 37.67 3.06
764 1125 4.274705 TGATGCGTATTTGCGTTGGATTAT 59.725 37.500 0.00 0.00 37.81 1.28
827 1193 5.745312 ATCGATTCCAGGCTATGTCATTA 57.255 39.130 0.00 0.00 0.00 1.90
837 1203 5.829924 CAGGCTATGTCATTAATGGGAAACT 59.170 40.000 15.36 3.50 0.00 2.66
854 1220 7.351166 TGGGAAACTACCTAGGGAAATAATTG 58.649 38.462 14.81 0.00 0.00 2.32
884 1251 9.176460 CATTGCCAAAAATACAAGGGAAAATAT 57.824 29.630 0.00 0.00 35.09 1.28
906 1273 4.331159 AGAAATAAAAGCCAAGCCCCTA 57.669 40.909 0.00 0.00 0.00 3.53
910 1277 2.443958 AAAAGCCAAGCCCCTATCTC 57.556 50.000 0.00 0.00 0.00 2.75
983 1350 2.569404 AGAGAGAGTGGAGGCGAAATTT 59.431 45.455 0.00 0.00 0.00 1.82
986 1353 0.179189 GAGTGGAGGCGAAATTTGCG 60.179 55.000 0.00 0.39 0.00 4.85
990 1357 0.793104 GGAGGCGAAATTTGCGAACG 60.793 55.000 0.00 3.62 0.00 3.95
1018 1385 3.080158 ATGGCAACCCACCCACACA 62.080 57.895 0.00 0.00 45.77 3.72
1035 1402 5.280113 CCCACACAAATCTCCCATGAAAAAT 60.280 40.000 0.00 0.00 0.00 1.82
1036 1403 6.232692 CCACACAAATCTCCCATGAAAAATT 58.767 36.000 0.00 0.00 0.00 1.82
1042 1409 8.650490 ACAAATCTCCCATGAAAAATTTACAGT 58.350 29.630 0.00 0.00 0.00 3.55
1140 1507 2.174319 GGAGGAATTCACGGCGCTC 61.174 63.158 6.90 3.03 0.00 5.03
1189 1556 1.546834 CCTTAGCGAGAGTAACGTGC 58.453 55.000 0.00 0.00 0.00 5.34
1192 1559 0.961857 TAGCGAGAGTAACGTGCCCA 60.962 55.000 0.00 0.00 0.00 5.36
1266 1633 1.077068 CTCCTCTCCTCCGCACTCT 60.077 63.158 0.00 0.00 0.00 3.24
1316 1683 0.380378 GGCGCAATAATTCTTGGCGA 59.620 50.000 10.83 0.00 31.71 5.54
1347 1714 0.467804 GGGAGGAAGATGAGGAGCAC 59.532 60.000 0.00 0.00 0.00 4.40
1436 1803 2.045438 AATTGGCGGGCACATCGA 60.045 55.556 2.73 0.00 0.00 3.59
1442 1809 2.598632 GCGGGCACATCGATAGCAC 61.599 63.158 19.71 16.44 0.00 4.40
1446 1813 0.882042 GGCACATCGATAGCACCCAG 60.882 60.000 19.71 0.00 0.00 4.45
1457 1827 2.849294 AGCACCCAGAAGAAGAAGAC 57.151 50.000 0.00 0.00 0.00 3.01
1459 1829 1.000955 GCACCCAGAAGAAGAAGACGA 59.999 52.381 0.00 0.00 0.00 4.20
1462 1832 3.005897 CACCCAGAAGAAGAAGACGAAGA 59.994 47.826 0.00 0.00 0.00 2.87
1463 1833 3.257127 ACCCAGAAGAAGAAGACGAAGAG 59.743 47.826 0.00 0.00 0.00 2.85
1465 1835 3.367910 CCAGAAGAAGAAGACGAAGAGGG 60.368 52.174 0.00 0.00 0.00 4.30
1466 1836 3.508012 CAGAAGAAGAAGACGAAGAGGGA 59.492 47.826 0.00 0.00 0.00 4.20
1467 1837 4.021894 CAGAAGAAGAAGACGAAGAGGGAA 60.022 45.833 0.00 0.00 0.00 3.97
1468 1838 4.775253 AGAAGAAGAAGACGAAGAGGGAAT 59.225 41.667 0.00 0.00 0.00 3.01
1469 1839 5.952947 AGAAGAAGAAGACGAAGAGGGAATA 59.047 40.000 0.00 0.00 0.00 1.75
1470 1840 5.845391 AGAAGAAGACGAAGAGGGAATAG 57.155 43.478 0.00 0.00 0.00 1.73
1528 1898 4.335735 AATTCATGTGATTTCCAGGGGA 57.664 40.909 0.00 0.00 0.00 4.81
1529 1899 4.547886 ATTCATGTGATTTCCAGGGGAT 57.452 40.909 0.00 0.00 0.00 3.85
1567 1938 4.349365 CTTGTAGTCCTCTCCTTCCTCTT 58.651 47.826 0.00 0.00 0.00 2.85
1572 1943 3.077695 AGTCCTCTCCTTCCTCTTACCAA 59.922 47.826 0.00 0.00 0.00 3.67
1607 1978 5.060323 CGCTATCATTATCTTTCTCGCTGTC 59.940 44.000 0.00 0.00 0.00 3.51
1624 1995 5.181056 TCGCTGTCAAATCTTATCTTTGCAA 59.819 36.000 0.00 0.00 34.36 4.08
1642 2013 9.995003 TCTTTGCAATAAGAATTAATTGTTGGT 57.005 25.926 18.20 6.45 32.17 3.67
1645 2016 8.545229 TGCAATAAGAATTAATTGTTGGTTGG 57.455 30.769 23.72 14.24 32.17 3.77
1646 2017 7.605691 TGCAATAAGAATTAATTGTTGGTTGGG 59.394 33.333 23.72 11.52 32.17 4.12
1647 2018 7.065683 GCAATAAGAATTAATTGTTGGTTGGGG 59.934 37.037 23.72 11.09 32.17 4.96
1648 2019 5.497464 AAGAATTAATTGTTGGTTGGGGG 57.503 39.130 9.61 0.00 0.00 5.40
1649 2020 3.263170 AGAATTAATTGTTGGTTGGGGGC 59.737 43.478 5.17 0.00 0.00 5.80
1654 2025 2.922503 GTTGGTTGGGGGCTTGGG 60.923 66.667 0.00 0.00 0.00 4.12
1658 2029 4.638895 GTTGGGGGCTTGGGGCTT 62.639 66.667 0.00 0.00 41.46 4.35
1709 2080 9.748708 CTCTGAGATGAATTGGTTTTGTTTTTA 57.251 29.630 0.00 0.00 0.00 1.52
1732 2103 0.389817 TACTGTGTTGCTAGCTGGCG 60.390 55.000 17.89 4.19 34.52 5.69
1782 2153 3.421394 TGTAGATGGATGGTCTCCCTT 57.579 47.619 0.00 0.00 44.23 3.95
1805 2176 3.181463 GCAAAGAGGATCAGATCAGCTCT 60.181 47.826 12.66 12.02 37.82 4.09
1807 2178 5.453057 GCAAAGAGGATCAGATCAGCTCTAA 60.453 44.000 15.76 0.00 37.82 2.10
1824 2195 2.107378 TCTAACCATGGTTGTGGCTTCA 59.893 45.455 35.49 15.27 43.27 3.02
1833 2204 1.394917 GTTGTGGCTTCATAGCTCACG 59.605 52.381 0.00 0.00 46.90 4.35
1835 2206 1.482182 TGTGGCTTCATAGCTCACGAT 59.518 47.619 0.00 0.00 46.90 3.73
1836 2207 2.093500 TGTGGCTTCATAGCTCACGATT 60.093 45.455 0.00 0.00 46.90 3.34
1872 2243 1.831106 TGACTGGTCGATGCCTATGTT 59.169 47.619 0.00 0.00 0.00 2.71
1873 2244 2.236146 TGACTGGTCGATGCCTATGTTT 59.764 45.455 0.00 0.00 0.00 2.83
1940 2311 7.326789 TCTGATTCGCAAAAATCTTGATTGAAC 59.673 33.333 0.00 0.00 36.73 3.18
1948 2319 7.411157 GCAAAAATCTTGATTGAACGATTCAGG 60.411 37.037 0.00 0.00 41.38 3.86
1949 2320 6.824305 AAATCTTGATTGAACGATTCAGGT 57.176 33.333 0.00 0.00 41.38 4.00
1958 2329 7.608376 TGATTGAACGATTCAGGTAATTTGGTA 59.392 33.333 0.00 0.00 41.38 3.25
1994 2365 0.391661 CTGGTAACGCTGAGGTGCAT 60.392 55.000 0.00 0.00 42.51 3.96
2004 2375 0.610174 TGAGGTGCATCTCACTGGTC 59.390 55.000 25.84 0.00 44.98 4.02
2013 2384 1.633774 TCTCACTGGTCTGGGAGTTC 58.366 55.000 6.94 0.00 0.00 3.01
2014 2385 1.133167 TCTCACTGGTCTGGGAGTTCA 60.133 52.381 6.94 0.00 0.00 3.18
2024 2395 2.108075 TCTGGGAGTTCAATTTCCTGCA 59.892 45.455 0.00 0.00 33.85 4.41
2025 2396 2.892852 CTGGGAGTTCAATTTCCTGCAA 59.107 45.455 0.00 0.00 33.85 4.08
2030 2401 5.764686 GGGAGTTCAATTTCCTGCAAAAATT 59.235 36.000 11.71 11.71 36.91 1.82
2031 2402 6.073058 GGGAGTTCAATTTCCTGCAAAAATTC 60.073 38.462 13.72 6.37 34.84 2.17
2079 2450 3.445008 TCAGTAGATATGATGGAGGGCC 58.555 50.000 0.00 0.00 0.00 5.80
2084 2455 0.178891 ATATGATGGAGGGCCGGAGT 60.179 55.000 5.05 0.00 36.79 3.85
2101 2472 1.748493 GAGTGCCGAGTCTCTTCATCT 59.252 52.381 0.00 0.00 0.00 2.90
2106 2477 3.954258 TGCCGAGTCTCTTCATCTAATGA 59.046 43.478 0.00 0.00 37.55 2.57
2108 2479 4.202060 GCCGAGTCTCTTCATCTAATGACA 60.202 45.833 0.00 0.00 39.39 3.58
2112 2483 5.347342 AGTCTCTTCATCTAATGACAAGCG 58.653 41.667 0.00 0.00 39.39 4.68
2148 2519 1.623811 ACCTTGCCTCGTCACATTAGT 59.376 47.619 0.00 0.00 0.00 2.24
2149 2520 2.271800 CCTTGCCTCGTCACATTAGTC 58.728 52.381 0.00 0.00 0.00 2.59
2171 2542 1.610624 GGTCGATTCAGGCAAGTCCAA 60.611 52.381 0.00 0.00 37.29 3.53
2172 2543 1.464997 GTCGATTCAGGCAAGTCCAAC 59.535 52.381 0.00 0.00 37.29 3.77
2173 2544 1.347707 TCGATTCAGGCAAGTCCAACT 59.652 47.619 0.00 0.00 37.29 3.16
2174 2545 2.154462 CGATTCAGGCAAGTCCAACTT 58.846 47.619 0.00 0.00 39.39 2.66
2194 2565 1.360931 CTTGCACGCGACATGATGGA 61.361 55.000 15.93 0.00 0.00 3.41
2207 2578 3.956199 ACATGATGGAATGTGGTCAATCC 59.044 43.478 0.00 0.00 42.32 3.01
2211 2582 2.524306 TGGAATGTGGTCAATCCAACC 58.476 47.619 2.97 0.00 46.72 3.77
2212 2583 3.138701 TGGAATGTGGTCAATCCAACCG 61.139 50.000 2.97 0.00 46.72 4.44
2215 2586 4.395519 TGGTCAATCCAACCGCTG 57.604 55.556 0.00 0.00 44.12 5.18
2225 2596 3.840831 CAACCGCTGGATCAGAGAA 57.159 52.632 0.00 0.00 33.20 2.87
2226 2597 2.099141 CAACCGCTGGATCAGAGAAA 57.901 50.000 0.00 0.00 33.20 2.52
2227 2598 2.426522 CAACCGCTGGATCAGAGAAAA 58.573 47.619 0.00 0.00 33.20 2.29
2228 2599 2.393271 ACCGCTGGATCAGAGAAAAG 57.607 50.000 0.00 0.00 33.20 2.27
2229 2600 1.065854 ACCGCTGGATCAGAGAAAAGG 60.066 52.381 0.00 0.00 33.20 3.11
2230 2601 1.661341 CGCTGGATCAGAGAAAAGGG 58.339 55.000 0.00 0.00 33.20 3.95
2231 2602 1.387539 GCTGGATCAGAGAAAAGGGC 58.612 55.000 0.00 0.00 32.44 5.19
2232 2603 1.340405 GCTGGATCAGAGAAAAGGGCA 60.340 52.381 0.00 0.00 32.44 5.36
2233 2604 2.363683 CTGGATCAGAGAAAAGGGCAC 58.636 52.381 0.00 0.00 32.44 5.01
2234 2605 2.943199 CTGGATCAGAGAAAAGGGCACC 60.943 54.545 0.00 0.00 41.38 5.01
2265 2636 6.790232 GGGGGATGATCTAGAAGAAGATAG 57.210 45.833 0.00 0.00 36.33 2.08
2280 2825 4.387598 GAAGATAGCTTCCATGTGCATCT 58.612 43.478 9.66 7.87 43.80 2.90
2303 2848 2.554344 GGGTGGGAGACAATGCAAGTAA 60.554 50.000 0.00 0.00 0.00 2.24
2322 2867 5.682659 AGTAACTAGCCACGAGAGAGATAA 58.317 41.667 0.00 0.00 0.00 1.75
2339 2884 5.594725 AGAGATAAACATCTTGCCTCTACGA 59.405 40.000 0.00 0.00 0.00 3.43
2363 2908 4.556233 GTTCATTCCTTTTACACCAAGCC 58.444 43.478 0.00 0.00 0.00 4.35
2364 2909 2.817258 TCATTCCTTTTACACCAAGCCG 59.183 45.455 0.00 0.00 0.00 5.52
2467 3013 9.476202 TCCTACAAATATGATAGTTCATGTTCG 57.524 33.333 0.00 0.00 41.27 3.95
2468 3014 9.261180 CCTACAAATATGATAGTTCATGTTCGT 57.739 33.333 0.00 0.00 41.27 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.900123 ACCTCTACTAGCATATCACAAAGGT 59.100 40.000 0.00 0.00 0.00 3.50
14 15 6.885952 TCTTGACCTCTACTAGCATATCAC 57.114 41.667 0.00 0.00 0.00 3.06
21 22 6.460953 CCATTCTCTTCTTGACCTCTACTAGC 60.461 46.154 0.00 0.00 0.00 3.42
24 25 5.420739 GTCCATTCTCTTCTTGACCTCTACT 59.579 44.000 0.00 0.00 0.00 2.57
29 30 4.843516 AGAAGTCCATTCTCTTCTTGACCT 59.156 41.667 0.00 0.00 45.50 3.85
30 31 5.159273 AGAAGTCCATTCTCTTCTTGACC 57.841 43.478 0.00 0.00 45.50 4.02
62 63 5.159273 ACTTCCTTCTTTCCAGATGAGTC 57.841 43.478 0.00 0.00 0.00 3.36
67 68 7.510675 TGGTAATACTTCCTTCTTTCCAGAT 57.489 36.000 0.00 0.00 0.00 2.90
71 72 7.664318 TGTTCTTGGTAATACTTCCTTCTTTCC 59.336 37.037 0.00 0.00 0.00 3.13
73 74 8.990163 TTGTTCTTGGTAATACTTCCTTCTTT 57.010 30.769 0.00 0.00 0.00 2.52
83 97 7.658575 TGGACTGTAACTTGTTCTTGGTAATAC 59.341 37.037 0.00 0.00 0.00 1.89
105 119 4.976224 ACTTTTGGTTACAGTTGTGGAC 57.024 40.909 0.00 0.00 0.00 4.02
106 120 6.603997 ACATTACTTTTGGTTACAGTTGTGGA 59.396 34.615 0.00 0.00 0.00 4.02
114 128 9.976776 TCCCATATTACATTACTTTTGGTTACA 57.023 29.630 0.00 0.00 0.00 2.41
125 139 9.595823 ACGCTACATATTCCCATATTACATTAC 57.404 33.333 0.00 0.00 0.00 1.89
130 144 9.390795 CGTATACGCTACATATTCCCATATTAC 57.609 37.037 13.08 0.00 0.00 1.89
139 153 8.572976 CATGTTGTACGTATACGCTACATATTC 58.427 37.037 26.40 20.12 44.43 1.75
164 178 2.101750 TGTTGCACTCGAGGTTCTAACA 59.898 45.455 18.41 16.01 0.00 2.41
165 179 2.750948 TGTTGCACTCGAGGTTCTAAC 58.249 47.619 18.41 13.82 0.00 2.34
167 181 2.930887 GCATGTTGCACTCGAGGTTCTA 60.931 50.000 18.41 0.00 44.26 2.10
189 203 5.397899 CCAGTTCCTCTAAGGATTGCCATTA 60.398 44.000 0.00 0.00 45.34 1.90
201 215 2.693591 CGGCTATGTCCAGTTCCTCTAA 59.306 50.000 0.00 0.00 0.00 2.10
203 217 1.115467 CGGCTATGTCCAGTTCCTCT 58.885 55.000 0.00 0.00 0.00 3.69
205 219 0.824759 GTCGGCTATGTCCAGTTCCT 59.175 55.000 0.00 0.00 0.00 3.36
206 220 0.824759 AGTCGGCTATGTCCAGTTCC 59.175 55.000 0.00 0.00 0.00 3.62
225 239 1.179152 TCTTGGGCGAATCGTGTCTA 58.821 50.000 4.07 0.00 0.00 2.59
229 243 1.368641 TCAATCTTGGGCGAATCGTG 58.631 50.000 4.07 0.00 0.00 4.35
230 244 2.332063 ATCAATCTTGGGCGAATCGT 57.668 45.000 4.07 0.00 0.00 3.73
232 246 3.430218 CGTCTATCAATCTTGGGCGAATC 59.570 47.826 0.00 0.00 0.00 2.52
236 250 1.502231 CCGTCTATCAATCTTGGGCG 58.498 55.000 0.00 0.00 0.00 6.13
249 263 2.731571 GGCACATCCTGGCCGTCTA 61.732 63.158 0.00 0.00 40.93 2.59
255 269 4.783621 TCTGCGGCACATCCTGGC 62.784 66.667 0.00 0.00 42.21 4.85
256 270 2.821366 GTCTGCGGCACATCCTGG 60.821 66.667 0.00 0.00 0.00 4.45
259 273 2.359850 TTGGTCTGCGGCACATCC 60.360 61.111 0.00 2.44 0.00 3.51
268 282 2.098117 GCCATGTAGAATGTTGGTCTGC 59.902 50.000 0.00 0.00 0.00 4.26
270 284 3.719268 TGCCATGTAGAATGTTGGTCT 57.281 42.857 0.00 0.00 0.00 3.85
275 289 2.754552 ACGCATTGCCATGTAGAATGTT 59.245 40.909 2.41 0.00 32.28 2.71
276 290 2.368439 ACGCATTGCCATGTAGAATGT 58.632 42.857 2.41 0.00 32.28 2.71
277 291 3.365832 GAACGCATTGCCATGTAGAATG 58.634 45.455 2.41 0.00 32.28 2.67
278 292 2.032054 CGAACGCATTGCCATGTAGAAT 59.968 45.455 2.41 0.00 32.28 2.40
292 306 2.477375 GTCTTAATCCAACACGAACGCA 59.523 45.455 0.00 0.00 0.00 5.24
312 326 7.095102 GGTTTTACACGTGTATTACCATTGAGT 60.095 37.037 33.22 11.24 35.82 3.41
344 358 4.150897 AGCACGAAATAGATTTGGCCTA 57.849 40.909 3.32 0.00 0.00 3.93
377 391 0.178964 TGTCCCCTTGCTCTTTTGGG 60.179 55.000 0.00 0.00 39.37 4.12
511 525 2.462889 TCACACTCGTTGTAACCGTTC 58.537 47.619 0.00 0.00 35.67 3.95
577 591 9.784376 ATGCTATAGATTTCCCTACCATAGTTA 57.216 33.333 3.21 0.00 0.00 2.24
617 631 1.754621 TGGCGCTAGAGGTCCTCAG 60.755 63.158 21.26 15.80 32.06 3.35
634 648 2.732094 GGGAACCGTCGACGTGTG 60.732 66.667 33.49 21.93 40.86 3.82
649 663 1.616159 AACGAATTGTTGGGTCAGGG 58.384 50.000 0.00 0.00 40.00 4.45
692 707 4.879545 AGTTGTCTGGTTAATCAAACGTGT 59.120 37.500 0.00 0.00 39.13 4.49
728 743 2.356913 CATCACCGTGTGGACGCA 60.357 61.111 0.00 0.00 44.68 5.24
784 1145 1.614996 TGGCATGACAACCGTTTCAT 58.385 45.000 0.00 4.19 32.44 2.57
827 1193 7.533923 TTATTTCCCTAGGTAGTTTCCCATT 57.466 36.000 8.29 0.00 0.00 3.16
837 1203 8.691797 GCAATGTTTCAATTATTTCCCTAGGTA 58.308 33.333 8.29 0.00 0.00 3.08
854 1220 5.994668 TCCCTTGTATTTTTGGCAATGTTTC 59.005 36.000 0.00 0.00 0.00 2.78
884 1251 4.331159 AGGGGCTTGGCTTTTATTTCTA 57.669 40.909 0.00 0.00 0.00 2.10
906 1273 6.714356 CCTTTTCCTCTTGTTTTCTGAGAGAT 59.286 38.462 1.40 0.00 39.36 2.75
910 1277 6.058183 TCTCCTTTTCCTCTTGTTTTCTGAG 58.942 40.000 0.00 0.00 0.00 3.35
995 1362 3.061848 GGTGGGTTGCCATGGACG 61.062 66.667 18.40 0.00 0.00 4.79
1018 1385 7.603784 GCACTGTAAATTTTTCATGGGAGATTT 59.396 33.333 0.00 0.00 0.00 2.17
1056 1423 1.907739 CTCCATCTTCCCCTTCGCA 59.092 57.895 0.00 0.00 0.00 5.10
1058 1425 1.147153 GGCTCCATCTTCCCCTTCG 59.853 63.158 0.00 0.00 0.00 3.79
1108 1475 3.699894 CTCCACCTCTGCTGGCGT 61.700 66.667 0.00 0.00 0.00 5.68
1228 1595 1.954362 GACTGACCTGAGAGCGCCAT 61.954 60.000 2.29 0.00 0.00 4.40
1290 1657 2.936202 AGAATTATTGCGCCAGGACAT 58.064 42.857 4.18 0.00 0.00 3.06
1291 1658 2.418368 AGAATTATTGCGCCAGGACA 57.582 45.000 4.18 0.00 0.00 4.02
1292 1659 2.223572 CCAAGAATTATTGCGCCAGGAC 60.224 50.000 4.18 0.00 0.00 3.85
1316 1683 1.771255 CTTCCTCCCAATCCTCGGAAT 59.229 52.381 0.00 0.00 33.66 3.01
1394 1761 1.352404 GTCGCAGCGTAGATCTCGT 59.648 57.895 15.93 0.00 0.00 4.18
1407 1774 2.745884 CCAATTGGCTCCGTCGCA 60.746 61.111 12.53 0.00 0.00 5.10
1433 1800 2.735151 TCTTCTTCTGGGTGCTATCGA 58.265 47.619 0.00 0.00 0.00 3.59
1436 1803 3.118956 CGTCTTCTTCTTCTGGGTGCTAT 60.119 47.826 0.00 0.00 0.00 2.97
1442 1809 3.367910 CCTCTTCGTCTTCTTCTTCTGGG 60.368 52.174 0.00 0.00 0.00 4.45
1446 1813 4.522722 TTCCCTCTTCGTCTTCTTCTTC 57.477 45.455 0.00 0.00 0.00 2.87
1457 1827 2.550606 CTCCTCGTCTATTCCCTCTTCG 59.449 54.545 0.00 0.00 0.00 3.79
1459 1829 3.460340 TCTCTCCTCGTCTATTCCCTCTT 59.540 47.826 0.00 0.00 0.00 2.85
1462 1832 3.396276 TCATCTCTCCTCGTCTATTCCCT 59.604 47.826 0.00 0.00 0.00 4.20
1463 1833 3.756434 CTCATCTCTCCTCGTCTATTCCC 59.244 52.174 0.00 0.00 0.00 3.97
1465 1835 5.547465 TCTCTCATCTCTCCTCGTCTATTC 58.453 45.833 0.00 0.00 0.00 1.75
1466 1836 5.513094 CCTCTCTCATCTCTCCTCGTCTATT 60.513 48.000 0.00 0.00 0.00 1.73
1467 1837 4.020218 CCTCTCTCATCTCTCCTCGTCTAT 60.020 50.000 0.00 0.00 0.00 1.98
1468 1838 3.323691 CCTCTCTCATCTCTCCTCGTCTA 59.676 52.174 0.00 0.00 0.00 2.59
1469 1839 2.104792 CCTCTCTCATCTCTCCTCGTCT 59.895 54.545 0.00 0.00 0.00 4.18
1470 1840 2.104111 TCCTCTCTCATCTCTCCTCGTC 59.896 54.545 0.00 0.00 0.00 4.20
1528 1898 3.490348 ACAAGCTCAACCTACAAGCAAT 58.510 40.909 0.00 0.00 38.51 3.56
1529 1899 2.930950 ACAAGCTCAACCTACAAGCAA 58.069 42.857 0.00 0.00 38.51 3.91
1567 1938 2.577059 CGCCTTCGCCTCTTGGTA 59.423 61.111 0.00 0.00 35.27 3.25
1579 1950 4.926238 CGAGAAAGATAATGATAGCGCCTT 59.074 41.667 2.29 0.00 0.00 4.35
1582 1953 3.923461 AGCGAGAAAGATAATGATAGCGC 59.077 43.478 0.00 0.00 40.85 5.92
1584 1955 5.923114 TGACAGCGAGAAAGATAATGATAGC 59.077 40.000 0.00 0.00 0.00 2.97
1590 1961 7.856145 AAGATTTGACAGCGAGAAAGATAAT 57.144 32.000 0.00 0.00 0.00 1.28
1624 1995 6.352651 GCCCCCAACCAACAATTAATTCTTAT 60.353 38.462 0.00 0.00 0.00 1.73
1642 2013 4.637102 CAAGCCCCAAGCCCCCAA 62.637 66.667 0.00 0.00 45.47 4.12
1644 2015 4.079961 ATCAAGCCCCAAGCCCCC 62.080 66.667 0.00 0.00 45.47 5.40
1645 2016 2.442830 GATCAAGCCCCAAGCCCC 60.443 66.667 0.00 0.00 45.47 5.80
1646 2017 2.442830 GGATCAAGCCCCAAGCCC 60.443 66.667 0.00 0.00 45.47 5.19
1647 2018 1.075748 ATGGATCAAGCCCCAAGCC 60.076 57.895 0.00 0.00 45.47 4.35
1648 2019 1.111715 GGATGGATCAAGCCCCAAGC 61.112 60.000 0.00 0.00 44.25 4.01
1649 2020 0.259647 TGGATGGATCAAGCCCCAAG 59.740 55.000 0.83 0.00 35.85 3.61
1709 2080 3.801698 CCAGCTAGCAACACAGTATGAT 58.198 45.455 18.83 0.00 39.69 2.45
1732 2103 2.140792 TTAGCTGGGATCCCGCCTC 61.141 63.158 31.30 19.04 39.42 4.70
1745 2116 6.552445 ATCTACAAAGATGACCAGTTAGCT 57.448 37.500 0.00 0.00 41.08 3.32
1782 2153 2.504585 AGCTGATCTGATCCTCTTTGCA 59.495 45.455 14.71 0.00 0.00 4.08
1805 2176 2.666272 TGAAGCCACAACCATGGTTA 57.334 45.000 29.36 9.10 42.28 2.85
1807 2178 2.726821 CTATGAAGCCACAACCATGGT 58.273 47.619 13.00 13.00 42.28 3.55
1824 2195 1.269309 GCGGACAGAATCGTGAGCTAT 60.269 52.381 0.00 0.00 0.00 2.97
1833 2204 3.567797 GCAGCGGCGGACAGAATC 61.568 66.667 9.78 0.00 0.00 2.52
1835 2206 4.393155 ATGCAGCGGCGGACAGAA 62.393 61.111 9.78 0.00 45.35 3.02
1858 2229 6.604735 AGTTGAATAAACATAGGCATCGAC 57.395 37.500 0.00 0.00 41.61 4.20
1958 2329 9.730420 GCGTTACCAGAATCAAATAAACAATAT 57.270 29.630 0.00 0.00 0.00 1.28
1994 2365 1.133167 TGAACTCCCAGACCAGTGAGA 60.133 52.381 0.00 0.00 0.00 3.27
2004 2375 2.517959 TGCAGGAAATTGAACTCCCAG 58.482 47.619 0.00 0.00 31.50 4.45
2084 2455 3.954258 TCATTAGATGAAGAGACTCGGCA 59.046 43.478 0.00 0.00 36.11 5.69
2101 2472 3.644823 TCGAAGAACACGCTTGTCATTA 58.355 40.909 0.00 0.00 33.55 1.90
2106 2477 3.386486 TGTATTCGAAGAACACGCTTGT 58.614 40.909 11.04 0.00 45.90 3.16
2108 2479 3.185797 GGTTGTATTCGAAGAACACGCTT 59.814 43.478 13.90 0.00 45.90 4.68
2112 2483 4.464112 GCAAGGTTGTATTCGAAGAACAC 58.536 43.478 13.90 5.12 45.90 3.32
2148 2519 0.976641 ACTTGCCTGAATCGACCAGA 59.023 50.000 15.82 0.00 33.65 3.86
2149 2520 1.363744 GACTTGCCTGAATCGACCAG 58.636 55.000 9.11 9.11 0.00 4.00
2171 2542 0.599991 TCATGTCGCGTGCAAGAAGT 60.600 50.000 5.77 0.00 0.00 3.01
2172 2543 0.723414 ATCATGTCGCGTGCAAGAAG 59.277 50.000 5.77 0.00 0.00 2.85
2173 2544 0.443478 CATCATGTCGCGTGCAAGAA 59.557 50.000 5.77 0.00 0.00 2.52
2174 2545 1.360931 CCATCATGTCGCGTGCAAGA 61.361 55.000 5.77 9.78 0.00 3.02
2207 2578 2.099141 TTTCTCTGATCCAGCGGTTG 57.901 50.000 0.00 0.00 0.00 3.77
2208 2579 2.616510 CCTTTTCTCTGATCCAGCGGTT 60.617 50.000 0.00 0.00 0.00 4.44
2209 2580 1.065854 CCTTTTCTCTGATCCAGCGGT 60.066 52.381 0.00 0.00 0.00 5.68
2211 2582 1.661341 CCCTTTTCTCTGATCCAGCG 58.339 55.000 0.00 0.00 0.00 5.18
2212 2583 1.340405 TGCCCTTTTCTCTGATCCAGC 60.340 52.381 0.00 0.00 0.00 4.85
2213 2584 2.363683 GTGCCCTTTTCTCTGATCCAG 58.636 52.381 0.00 0.00 0.00 3.86
2214 2585 1.004745 GGTGCCCTTTTCTCTGATCCA 59.995 52.381 0.00 0.00 0.00 3.41
2215 2586 1.283321 AGGTGCCCTTTTCTCTGATCC 59.717 52.381 0.00 0.00 0.00 3.36
2216 2587 2.637947 GAGGTGCCCTTTTCTCTGATC 58.362 52.381 0.00 0.00 31.76 2.92
2217 2588 1.283321 GGAGGTGCCCTTTTCTCTGAT 59.717 52.381 0.00 0.00 31.76 2.90
2218 2589 0.693049 GGAGGTGCCCTTTTCTCTGA 59.307 55.000 0.00 0.00 31.76 3.27
2219 2590 3.256281 GGAGGTGCCCTTTTCTCTG 57.744 57.895 0.00 0.00 31.76 3.35
2242 2613 5.128663 GCTATCTTCTTCTAGATCATCCCCC 59.871 48.000 0.00 0.00 36.34 5.40
2243 2614 5.957774 AGCTATCTTCTTCTAGATCATCCCC 59.042 44.000 0.00 0.00 36.34 4.81
2244 2615 7.363793 GGAAGCTATCTTCTTCTAGATCATCCC 60.364 44.444 6.30 0.00 46.12 3.85
2245 2616 7.178274 TGGAAGCTATCTTCTTCTAGATCATCC 59.822 40.741 6.30 0.00 46.12 3.51
2246 2617 8.121305 TGGAAGCTATCTTCTTCTAGATCATC 57.879 38.462 6.30 0.00 46.12 2.92
2247 2618 8.533657 CATGGAAGCTATCTTCTTCTAGATCAT 58.466 37.037 6.30 0.00 46.12 2.45
2248 2619 7.508636 ACATGGAAGCTATCTTCTTCTAGATCA 59.491 37.037 6.30 0.00 46.12 2.92
2249 2620 7.814107 CACATGGAAGCTATCTTCTTCTAGATC 59.186 40.741 6.30 0.00 46.12 2.75
2250 2621 7.669427 CACATGGAAGCTATCTTCTTCTAGAT 58.331 38.462 6.30 0.00 46.12 1.98
2251 2622 6.462207 GCACATGGAAGCTATCTTCTTCTAGA 60.462 42.308 6.30 0.00 46.12 2.43
2252 2623 5.695816 GCACATGGAAGCTATCTTCTTCTAG 59.304 44.000 6.30 0.00 46.12 2.43
2253 2624 5.129320 TGCACATGGAAGCTATCTTCTTCTA 59.871 40.000 6.30 0.00 46.12 2.10
2254 2625 4.080695 TGCACATGGAAGCTATCTTCTTCT 60.081 41.667 6.30 0.00 46.12 2.85
2255 2626 4.194640 TGCACATGGAAGCTATCTTCTTC 58.805 43.478 6.30 0.00 46.12 2.87
2256 2627 4.226427 TGCACATGGAAGCTATCTTCTT 57.774 40.909 6.30 0.00 46.12 2.52
2257 2628 3.920231 TGCACATGGAAGCTATCTTCT 57.080 42.857 6.30 0.00 46.12 2.85
2258 2629 4.213694 CAGATGCACATGGAAGCTATCTTC 59.786 45.833 0.00 0.00 46.15 2.87
2259 2630 4.135306 CAGATGCACATGGAAGCTATCTT 58.865 43.478 0.00 0.00 31.21 2.40
2260 2631 3.496337 CCAGATGCACATGGAAGCTATCT 60.496 47.826 12.73 6.86 39.02 1.98
2261 2632 2.812591 CCAGATGCACATGGAAGCTATC 59.187 50.000 12.73 4.90 39.02 2.08
2262 2633 2.488528 CCCAGATGCACATGGAAGCTAT 60.489 50.000 18.46 0.00 39.02 2.97
2263 2634 1.134007 CCCAGATGCACATGGAAGCTA 60.134 52.381 18.46 0.00 39.02 3.32
2264 2635 0.395311 CCCAGATGCACATGGAAGCT 60.395 55.000 18.46 0.00 39.02 3.74
2265 2636 1.389609 CCCCAGATGCACATGGAAGC 61.390 60.000 18.46 0.00 39.02 3.86
2274 2819 2.124768 TCTCCCACCCCAGATGCA 59.875 61.111 0.00 0.00 0.00 3.96
2280 2825 1.724148 TTGCATTGTCTCCCACCCCA 61.724 55.000 0.00 0.00 0.00 4.96
2303 2848 4.270834 TGTTTATCTCTCTCGTGGCTAGT 58.729 43.478 0.00 0.00 0.00 2.57
2339 2884 4.280929 GCTTGGTGTAAAAGGAATGAACCT 59.719 41.667 0.00 0.00 42.69 3.50
2349 2894 1.535462 CCTCACGGCTTGGTGTAAAAG 59.465 52.381 0.00 0.00 39.00 2.27
2363 2908 7.033530 ACTTCTCTCAGATTATAACCTCACG 57.966 40.000 0.00 0.00 0.00 4.35
2364 2909 8.079809 GCTACTTCTCTCAGATTATAACCTCAC 58.920 40.741 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.