Multiple sequence alignment - TraesCS7D01G424300

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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 TraesCS7D01G424300 chr7D 100.000 2291 0 0 1 2291 544853052 544850762 0.000000e+00 4231.0
1 TraesCS7D01G424300 chr7D 89.855 69 6 1 1862 1929 75551052 75550984 1.130000e-13 87.9
2 TraesCS7D01G424300 chr7A 92.366 917 39 11 620 1513 626615774 626614866 0.000000e+00 1277.0
3 TraesCS7D01G424300 chr7A 89.831 531 31 10 1 517 626616432 626615911 0.000000e+00 660.0
4 TraesCS7D01G424300 chr7A 89.919 248 17 4 2050 2290 626614259 626614013 1.710000e-81 313.0
5 TraesCS7D01G424300 chr7A 90.446 157 11 4 1679 1833 626614649 626614495 1.070000e-48 204.0
6 TraesCS7D01G424300 chr7A 90.909 77 6 1 717 792 626615819 626615743 4.030000e-18 102.0
7 TraesCS7D01G424300 chr7B 92.397 605 22 11 925 1513 588288723 588288127 0.000000e+00 841.0
8 TraesCS7D01G424300 chr7B 89.773 528 38 8 1 517 588289722 588289200 0.000000e+00 662.0
9 TraesCS7D01G424300 chr7B 95.122 328 10 4 620 942 588289063 588288737 1.570000e-141 512.0
10 TraesCS7D01G424300 chr7B 90.816 294 14 7 2001 2287 588287637 588287350 4.620000e-102 381.0
11 TraesCS7D01G424300 chr7B 94.444 72 4 0 555 626 588289192 588289121 6.690000e-21 111.0
12 TraesCS7D01G424300 chr7B 90.909 77 6 1 717 792 588289108 588289032 4.030000e-18 102.0
13 TraesCS7D01G424300 chr7B 88.462 52 6 0 648 699 388902609 388902558 1.900000e-06 63.9
14 TraesCS7D01G424300 chr6D 92.754 69 5 0 1862 1930 330111479 330111411 1.450000e-17 100.0
15 TraesCS7D01G424300 chr1B 90.667 75 5 2 1859 1931 22328148 22328222 5.210000e-17 99.0
16 TraesCS7D01G424300 chr1A 91.549 71 6 0 1862 1932 574636997 574637067 5.210000e-17 99.0
17 TraesCS7D01G424300 chr1A 89.474 76 6 2 1859 1932 350017170 350017095 6.740000e-16 95.3
18 TraesCS7D01G424300 chr1D 89.474 76 6 2 1859 1932 277362594 277362519 6.740000e-16 95.3
19 TraesCS7D01G424300 chr1D 86.022 93 6 5 1842 1929 22943481 22943571 2.420000e-15 93.5
20 TraesCS7D01G424300 chr5D 85.870 92 8 4 1842 1929 184479186 184479276 2.420000e-15 93.5
21 TraesCS7D01G424300 chr6A 84.946 93 7 6 1842 1929 29544860 29544950 1.130000e-13 87.9


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 TraesCS7D01G424300 chr7D 544850762 544853052 2290 True 4231.000000 4231 100.0000 1 2291 1 chr7D.!!$R2 2290
1 TraesCS7D01G424300 chr7A 626614013 626616432 2419 True 511.200000 1277 90.6942 1 2290 5 chr7A.!!$R1 2289
2 TraesCS7D01G424300 chr7B 588287350 588289722 2372 True 434.833333 841 92.2435 1 2287 6 chr7B.!!$R2 2286

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
888 973 0.179045 AGTATTGCCCTCGTGGATGC 60.179 55.0 4.76 1.22 35.39 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2193 0.039035 CCCCTTTCATTCCCGTTCCA 59.961 55.0 0.0 0.0 0.0 3.53 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
76 78 2.325484 GTTGTTGGGGGTCAAAATCCT 58.675 47.619 0.00 0.00 37.08 3.24
90 92 6.201615 GGTCAAAATCCTTTTTCTGCTTCTTG 59.798 38.462 0.00 0.00 32.72 3.02
123 125 5.450688 CGCTTCTCAGTAGCATAAGGTAAGT 60.451 44.000 3.97 0.00 38.55 2.24
207 211 1.961277 CTGCGCGGGAAAGACAGTT 60.961 57.895 8.83 0.00 0.00 3.16
209 213 3.011760 GCGCGGGAAAGACAGTTCG 62.012 63.158 8.83 0.00 0.00 3.95
211 215 1.301479 GCGGGAAAGACAGTTCGGT 60.301 57.895 0.00 0.00 0.00 4.69
293 305 2.097038 GCTGCACGTGCTAGTGAGG 61.097 63.158 37.59 19.76 44.43 3.86
294 306 1.446792 CTGCACGTGCTAGTGAGGG 60.447 63.158 37.59 15.18 44.43 4.30
295 307 2.125512 GCACGTGCTAGTGAGGGG 60.126 66.667 32.55 0.00 44.43 4.79
296 308 2.579201 CACGTGCTAGTGAGGGGG 59.421 66.667 0.82 0.00 44.43 5.40
297 309 1.982395 CACGTGCTAGTGAGGGGGA 60.982 63.158 0.82 0.00 44.43 4.81
349 361 3.376078 GTCGACCGCCCCACTACA 61.376 66.667 3.51 0.00 0.00 2.74
350 362 3.066190 TCGACCGCCCCACTACAG 61.066 66.667 0.00 0.00 0.00 2.74
351 363 4.143333 CGACCGCCCCACTACAGG 62.143 72.222 0.00 0.00 0.00 4.00
377 392 2.373540 TACCACCGCACTATCAACAC 57.626 50.000 0.00 0.00 0.00 3.32
393 408 0.730265 ACACGTTTGTTGATGCACGT 59.270 45.000 0.00 0.00 46.45 4.49
401 416 2.421619 TGTTGATGCACGTGCTAATGA 58.578 42.857 37.59 20.41 42.66 2.57
405 420 3.392882 TGATGCACGTGCTAATGATAGG 58.607 45.455 37.59 0.00 42.66 2.57
415 430 5.392057 CGTGCTAATGATAGGAGCTATCGAA 60.392 44.000 0.00 0.00 43.98 3.71
436 451 2.713863 AACCCGTTGTCCAAGTTACA 57.286 45.000 0.00 0.00 0.00 2.41
437 452 1.957668 ACCCGTTGTCCAAGTTACAC 58.042 50.000 0.00 0.00 0.00 2.90
438 453 1.232119 CCCGTTGTCCAAGTTACACC 58.768 55.000 0.00 0.00 0.00 4.16
489 508 7.069331 TGTGCGAAAATCCTATGGGAAAATAAT 59.931 33.333 0.22 0.00 45.78 1.28
542 561 8.986477 ATTATATGGCAGACAAAGAAAACAAC 57.014 30.769 0.00 0.00 0.00 3.32
543 562 3.518634 TGGCAGACAAAGAAAACAACC 57.481 42.857 0.00 0.00 0.00 3.77
544 563 3.096092 TGGCAGACAAAGAAAACAACCT 58.904 40.909 0.00 0.00 0.00 3.50
545 564 3.130340 TGGCAGACAAAGAAAACAACCTC 59.870 43.478 0.00 0.00 0.00 3.85
546 565 3.130340 GGCAGACAAAGAAAACAACCTCA 59.870 43.478 0.00 0.00 0.00 3.86
547 566 4.354587 GCAGACAAAGAAAACAACCTCAG 58.645 43.478 0.00 0.00 0.00 3.35
548 567 4.096382 GCAGACAAAGAAAACAACCTCAGA 59.904 41.667 0.00 0.00 0.00 3.27
549 568 5.221126 GCAGACAAAGAAAACAACCTCAGAT 60.221 40.000 0.00 0.00 0.00 2.90
550 569 6.017109 GCAGACAAAGAAAACAACCTCAGATA 60.017 38.462 0.00 0.00 0.00 1.98
551 570 7.468631 GCAGACAAAGAAAACAACCTCAGATAA 60.469 37.037 0.00 0.00 0.00 1.75
552 571 8.405531 CAGACAAAGAAAACAACCTCAGATAAA 58.594 33.333 0.00 0.00 0.00 1.40
553 572 8.624776 AGACAAAGAAAACAACCTCAGATAAAG 58.375 33.333 0.00 0.00 0.00 1.85
888 973 0.179045 AGTATTGCCCTCGTGGATGC 60.179 55.000 4.76 1.22 35.39 3.91
895 980 4.794439 CTCGTGGATGCGGCGTCA 62.794 66.667 22.56 7.70 0.00 4.35
913 1001 6.555315 GGCGTCATTTCTTCTTCATAAACAT 58.445 36.000 0.00 0.00 0.00 2.71
917 1005 9.430838 CGTCATTTCTTCTTCATAAACATGATC 57.569 33.333 0.00 0.00 0.00 2.92
989 1108 7.039714 GGATTCACATTTTTCAGGTAGGAAAGT 60.040 37.037 0.00 0.00 37.98 2.66
997 1116 4.669866 TCAGGTAGGAAAGTGAGTCCTA 57.330 45.455 0.00 0.00 43.99 2.94
1206 1325 2.662866 TCAACGATCCGGATACCTTCT 58.337 47.619 19.15 0.00 0.00 2.85
1221 1340 0.689623 CTTCTGACCCTCCTGTTGCT 59.310 55.000 0.00 0.00 0.00 3.91
1293 1427 4.281947 GGCGGTAGCGAGTAGGCC 62.282 72.222 20.16 4.35 46.35 5.19
1309 1443 2.949106 CCGCTGGCTGTTCAAGTG 59.051 61.111 0.00 0.00 0.00 3.16
1310 1444 1.893808 CCGCTGGCTGTTCAAGTGT 60.894 57.895 0.00 0.00 0.00 3.55
1341 1478 5.220548 CACTGTGTGATAGCTTATGCTTGAC 60.221 44.000 8.59 4.32 40.48 3.18
1468 1607 7.467267 GCAGTTCAGACTTGTTTTATTGTCAGA 60.467 37.037 0.00 0.00 32.54 3.27
1473 1612 9.950680 TCAGACTTGTTTTATTGTCAGAAAATC 57.049 29.630 0.00 0.00 32.41 2.17
1474 1613 9.734620 CAGACTTGTTTTATTGTCAGAAAATCA 57.265 29.630 0.00 0.00 32.41 2.57
1475 1614 9.956720 AGACTTGTTTTATTGTCAGAAAATCAG 57.043 29.630 0.00 2.21 32.41 2.90
1476 1615 9.950680 GACTTGTTTTATTGTCAGAAAATCAGA 57.049 29.630 0.00 0.00 0.00 3.27
1479 1618 8.463930 TGTTTTATTGTCAGAAAATCAGAGGT 57.536 30.769 0.00 0.00 0.00 3.85
1481 1620 9.399403 GTTTTATTGTCAGAAAATCAGAGGTTC 57.601 33.333 0.00 0.00 0.00 3.62
1482 1621 5.869753 ATTGTCAGAAAATCAGAGGTTCG 57.130 39.130 0.00 0.00 0.00 3.95
1486 1625 3.997021 TCAGAAAATCAGAGGTTCGAAGC 59.003 43.478 19.40 19.40 0.00 3.86
1487 1626 3.748048 CAGAAAATCAGAGGTTCGAAGCA 59.252 43.478 27.46 8.77 0.00 3.91
1488 1627 4.394300 CAGAAAATCAGAGGTTCGAAGCAT 59.606 41.667 27.46 13.92 0.00 3.79
1504 1643 6.398095 TCGAAGCATATCATGGTACTAATGG 58.602 40.000 8.58 0.00 40.65 3.16
1515 1654 8.934023 TCATGGTACTAATGGTTTCTTTTCTT 57.066 30.769 8.58 0.00 0.00 2.52
1516 1655 9.362151 TCATGGTACTAATGGTTTCTTTTCTTT 57.638 29.630 8.58 0.00 0.00 2.52
1517 1656 9.981114 CATGGTACTAATGGTTTCTTTTCTTTT 57.019 29.630 0.00 0.00 0.00 2.27
1543 1682 6.067263 TGAACACCTAATGGTTTCTTTTCG 57.933 37.500 0.00 0.00 46.05 3.46
1545 1684 6.488683 TGAACACCTAATGGTTTCTTTTCGAT 59.511 34.615 0.00 0.00 46.05 3.59
1546 1685 7.662258 TGAACACCTAATGGTTTCTTTTCGATA 59.338 33.333 0.00 0.00 46.05 2.92
1548 1687 8.040716 ACACCTAATGGTTTCTTTTCGATAAG 57.959 34.615 9.11 9.11 46.05 1.73
1550 1689 6.095021 ACCTAATGGTTTCTTTTCGATAAGCC 59.905 38.462 10.40 7.15 46.05 4.35
1551 1690 6.318900 CCTAATGGTTTCTTTTCGATAAGCCT 59.681 38.462 10.40 0.00 0.00 4.58
1552 1691 6.590234 AATGGTTTCTTTTCGATAAGCCTT 57.410 33.333 10.40 2.95 0.00 4.35
1553 1692 5.371115 TGGTTTCTTTTCGATAAGCCTTG 57.629 39.130 10.40 0.00 0.00 3.61
1554 1693 5.067273 TGGTTTCTTTTCGATAAGCCTTGA 58.933 37.500 10.40 0.00 0.00 3.02
1556 1695 6.039941 TGGTTTCTTTTCGATAAGCCTTGAAA 59.960 34.615 10.40 3.91 0.00 2.69
1557 1696 7.090808 GGTTTCTTTTCGATAAGCCTTGAAAT 58.909 34.615 10.40 0.00 30.51 2.17
1558 1697 7.598869 GGTTTCTTTTCGATAAGCCTTGAAATT 59.401 33.333 10.40 0.00 30.51 1.82
1559 1698 8.427774 GTTTCTTTTCGATAAGCCTTGAAATTG 58.572 33.333 10.40 0.00 30.51 2.32
1568 1707 2.749280 CCTTGAAATTGGCAGGTTCC 57.251 50.000 9.05 0.00 0.00 3.62
1569 1708 1.067635 CCTTGAAATTGGCAGGTTCCG 60.068 52.381 9.05 2.36 0.00 4.30
1571 1710 0.539438 TGAAATTGGCAGGTTCCGCT 60.539 50.000 9.05 0.00 0.00 5.52
1573 1712 2.024414 GAAATTGGCAGGTTCCGCTAT 58.976 47.619 1.82 0.00 0.00 2.97
1574 1713 1.680338 AATTGGCAGGTTCCGCTATC 58.320 50.000 0.00 0.00 0.00 2.08
1575 1714 0.546122 ATTGGCAGGTTCCGCTATCA 59.454 50.000 0.00 0.00 0.00 2.15
1576 1715 0.546122 TTGGCAGGTTCCGCTATCAT 59.454 50.000 0.00 0.00 0.00 2.45
1577 1716 0.546122 TGGCAGGTTCCGCTATCATT 59.454 50.000 0.00 0.00 0.00 2.57
1578 1717 0.947244 GGCAGGTTCCGCTATCATTG 59.053 55.000 0.00 0.00 0.00 2.82
1579 1718 0.947244 GCAGGTTCCGCTATCATTGG 59.053 55.000 0.00 0.00 0.00 3.16
1580 1719 1.475034 GCAGGTTCCGCTATCATTGGA 60.475 52.381 0.00 0.00 0.00 3.53
1581 1720 2.811873 GCAGGTTCCGCTATCATTGGAT 60.812 50.000 0.00 0.00 37.55 3.41
1582 1721 3.557054 GCAGGTTCCGCTATCATTGGATA 60.557 47.826 0.00 0.00 34.89 2.59
1595 1734 8.954950 CTATCATTGGATAGTTCAACAAGAGT 57.045 34.615 4.03 0.00 45.26 3.24
1607 1746 8.099364 AGTTCAACAAGAGTACCAAATGTATG 57.901 34.615 0.00 0.00 0.00 2.39
1615 1754 6.644347 AGAGTACCAAATGTATGAGGTTCAG 58.356 40.000 0.00 0.00 35.62 3.02
1640 1796 1.269936 GCACCAAATTTGCTGACAGCT 60.270 47.619 26.94 5.39 42.97 4.24
1657 1813 3.136763 CAGCTGAATGTAGCCATACCAG 58.863 50.000 8.42 0.00 44.76 4.00
1664 1820 2.118679 TGTAGCCATACCAGCAGTGAT 58.881 47.619 0.00 0.00 0.00 3.06
1672 1828 0.606401 ACCAGCAGTGATCAAACCGG 60.606 55.000 0.00 0.00 0.00 5.28
1674 1830 0.321564 CAGCAGTGATCAAACCGGGA 60.322 55.000 6.32 0.00 0.00 5.14
1676 1832 1.305930 GCAGTGATCAAACCGGGACC 61.306 60.000 6.32 0.00 0.00 4.46
1717 1934 9.615295 TTTGTTCTGAACTACAGTTAAAAACAC 57.385 29.630 20.18 0.00 45.86 3.32
1730 1947 7.013274 ACAGTTAAAAACACACAGCTGATACAT 59.987 33.333 23.35 0.00 0.00 2.29
1757 1974 0.884704 AACACGGATGCTCGCAGTTT 60.885 50.000 0.00 0.00 31.12 2.66
1760 1977 1.448540 CGGATGCTCGCAGTTTCCT 60.449 57.895 8.03 0.00 0.00 3.36
1785 2002 1.866237 GACGCAAGCACGGATTCAA 59.134 52.632 0.00 0.00 45.62 2.69
1819 2037 6.142817 ACATTCGAAAATTGTGAAGCTGTAC 58.857 36.000 0.00 0.00 0.00 2.90
1858 2112 9.715121 ACGAGGATAAACAAAATACTAACTTCA 57.285 29.630 0.00 0.00 0.00 3.02
1924 2178 9.886132 AAATGTCTTATATTTTGAGACGTAGGT 57.114 29.630 0.00 0.00 42.02 3.08
1944 2198 8.842942 GTAGGTAGTACTACGTAAATTGGAAC 57.157 38.462 28.16 16.81 37.90 3.62
1946 2200 5.743872 GGTAGTACTACGTAAATTGGAACGG 59.256 44.000 23.40 0.29 43.25 4.44
1947 2201 4.747810 AGTACTACGTAAATTGGAACGGG 58.252 43.478 11.47 7.25 43.25 5.28
1948 2202 3.959535 ACTACGTAAATTGGAACGGGA 57.040 42.857 11.47 1.14 43.25 5.14
1949 2203 4.270245 ACTACGTAAATTGGAACGGGAA 57.730 40.909 11.47 0.00 43.25 3.97
1950 2204 4.835678 ACTACGTAAATTGGAACGGGAAT 58.164 39.130 11.47 0.00 43.25 3.01
1951 2205 4.632688 ACTACGTAAATTGGAACGGGAATG 59.367 41.667 11.47 2.17 43.25 2.67
1952 2206 3.677190 ACGTAAATTGGAACGGGAATGA 58.323 40.909 11.47 0.00 43.25 2.57
1988 2244 6.760770 CCAGTTTTTGTCAATTTCAAAGCCTA 59.239 34.615 5.93 0.00 36.40 3.93
2015 2271 4.316205 AGTACAAGACGACACAACATCA 57.684 40.909 0.00 0.00 0.00 3.07
2019 2275 2.051879 AGACGACACAACATCAGACG 57.948 50.000 0.00 0.00 0.00 4.18
2033 2289 2.511600 GACGCCGGGGATGAGTTG 60.512 66.667 27.23 0.00 0.00 3.16
2063 2319 4.825085 AGCCCACTTGAAATTCGAAACTTA 59.175 37.500 0.00 0.00 0.00 2.24
2082 2382 8.677148 AAACTTAGAAAGCAATTACACAGAGA 57.323 30.769 0.00 0.00 0.00 3.10
2084 2384 6.366332 ACTTAGAAAGCAATTACACAGAGACG 59.634 38.462 0.00 0.00 0.00 4.18
2086 2386 4.926238 AGAAAGCAATTACACAGAGACGAG 59.074 41.667 0.00 0.00 0.00 4.18
2131 2437 4.734917 CCACTACTACAAGACTAGCACAC 58.265 47.826 0.00 0.00 0.00 3.82
2162 2468 0.329261 TGGCAACTTCTCCCTCCATG 59.671 55.000 0.00 0.00 37.61 3.66
2163 2469 0.620556 GGCAACTTCTCCCTCCATGA 59.379 55.000 0.00 0.00 0.00 3.07
2164 2470 1.004745 GGCAACTTCTCCCTCCATGAA 59.995 52.381 0.00 0.00 0.00 2.57
2239 2549 1.545651 GGGCTTAATCCTATTGCGCCT 60.546 52.381 4.18 0.00 36.37 5.52
2290 2600 7.307694 CAGTGTGAAGAGCAATTAATTAGCAA 58.692 34.615 18.49 3.47 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 1.938585 TTTGACCCCCAACAACAACA 58.061 45.000 0.00 0.00 33.85 3.33
76 78 5.640732 GAGTGTTCACAAGAAGCAGAAAAA 58.359 37.500 5.74 0.00 33.63 1.94
90 92 2.141535 ACTGAGAAGCGAGTGTTCAC 57.858 50.000 0.00 0.00 0.00 3.18
123 125 4.020218 GCCTGATAGCTCATACCATTACCA 60.020 45.833 0.00 0.00 0.00 3.25
207 211 6.924612 GGTTTCTTGCCTTTTAAAAATACCGA 59.075 34.615 1.66 0.00 0.00 4.69
209 213 6.428771 GGGGTTTCTTGCCTTTTAAAAATACC 59.571 38.462 1.66 1.44 0.00 2.73
211 215 7.138054 TGGGGTTTCTTGCCTTTTAAAAATA 57.862 32.000 1.66 0.00 0.00 1.40
280 292 0.617820 AATCCCCCTCACTAGCACGT 60.618 55.000 0.00 0.00 0.00 4.49
305 317 0.962356 CAAAGCCTGGGTCTCGCATT 60.962 55.000 0.00 0.00 0.00 3.56
377 392 0.316937 AGCACGTGCATCAACAAACG 60.317 50.000 39.21 0.00 45.16 3.60
389 404 3.377346 AGCTCCTATCATTAGCACGTG 57.623 47.619 12.28 12.28 38.75 4.49
391 406 4.095036 TCGATAGCTCCTATCATTAGCACG 59.905 45.833 11.52 0.00 41.91 5.34
393 408 6.782082 ATTCGATAGCTCCTATCATTAGCA 57.218 37.500 11.52 0.00 41.91 3.49
401 416 4.342359 ACGGGTTATTCGATAGCTCCTAT 58.658 43.478 0.00 0.00 0.00 2.57
405 420 3.714391 ACAACGGGTTATTCGATAGCTC 58.286 45.455 0.00 0.00 0.00 4.09
415 430 4.067192 GTGTAACTTGGACAACGGGTTAT 58.933 43.478 0.00 0.00 0.00 1.89
436 451 2.831685 TGCAGAGTATTTGTGACGGT 57.168 45.000 0.00 0.00 0.00 4.83
437 452 3.242091 CGATTGCAGAGTATTTGTGACGG 60.242 47.826 0.00 0.00 0.00 4.79
438 453 3.782250 GCGATTGCAGAGTATTTGTGACG 60.782 47.826 0.00 0.00 42.15 4.35
517 536 8.034804 GGTTGTTTTCTTTGTCTGCCATATAAT 58.965 33.333 0.00 0.00 0.00 1.28
519 538 6.719370 AGGTTGTTTTCTTTGTCTGCCATATA 59.281 34.615 0.00 0.00 0.00 0.86
520 539 5.539955 AGGTTGTTTTCTTTGTCTGCCATAT 59.460 36.000 0.00 0.00 0.00 1.78
521 540 4.892934 AGGTTGTTTTCTTTGTCTGCCATA 59.107 37.500 0.00 0.00 0.00 2.74
522 541 3.706086 AGGTTGTTTTCTTTGTCTGCCAT 59.294 39.130 0.00 0.00 0.00 4.40
524 543 3.130340 TGAGGTTGTTTTCTTTGTCTGCC 59.870 43.478 0.00 0.00 0.00 4.85
525 544 4.096382 TCTGAGGTTGTTTTCTTTGTCTGC 59.904 41.667 0.00 0.00 0.00 4.26
526 545 5.818136 TCTGAGGTTGTTTTCTTTGTCTG 57.182 39.130 0.00 0.00 0.00 3.51
527 546 8.519799 TTTATCTGAGGTTGTTTTCTTTGTCT 57.480 30.769 0.00 0.00 0.00 3.41
528 547 8.621286 TCTTTATCTGAGGTTGTTTTCTTTGTC 58.379 33.333 0.00 0.00 0.00 3.18
529 548 8.519799 TCTTTATCTGAGGTTGTTTTCTTTGT 57.480 30.769 0.00 0.00 0.00 2.83
530 549 9.971922 ATTCTTTATCTGAGGTTGTTTTCTTTG 57.028 29.630 0.00 0.00 0.00 2.77
531 550 9.971922 CATTCTTTATCTGAGGTTGTTTTCTTT 57.028 29.630 0.00 0.00 0.00 2.52
532 551 9.136323 ACATTCTTTATCTGAGGTTGTTTTCTT 57.864 29.630 0.00 0.00 0.00 2.52
533 552 8.697507 ACATTCTTTATCTGAGGTTGTTTTCT 57.302 30.769 0.00 0.00 0.00 2.52
537 556 8.462016 GCATTACATTCTTTATCTGAGGTTGTT 58.538 33.333 0.00 0.00 0.00 2.83
538 557 7.831193 AGCATTACATTCTTTATCTGAGGTTGT 59.169 33.333 0.00 0.00 0.00 3.32
539 558 8.127327 CAGCATTACATTCTTTATCTGAGGTTG 58.873 37.037 0.00 0.00 0.00 3.77
540 559 8.049117 TCAGCATTACATTCTTTATCTGAGGTT 58.951 33.333 0.00 0.00 0.00 3.50
541 560 7.568349 TCAGCATTACATTCTTTATCTGAGGT 58.432 34.615 0.00 0.00 0.00 3.85
542 561 8.442632 TTCAGCATTACATTCTTTATCTGAGG 57.557 34.615 0.00 0.00 30.95 3.86
550 569 9.023962 TGGTAGAAATTCAGCATTACATTCTTT 57.976 29.630 0.00 0.00 0.00 2.52
551 570 8.579850 TGGTAGAAATTCAGCATTACATTCTT 57.420 30.769 0.00 0.00 0.00 2.52
552 571 8.757982 ATGGTAGAAATTCAGCATTACATTCT 57.242 30.769 0.00 0.00 28.81 2.40
553 572 9.455847 GAATGGTAGAAATTCAGCATTACATTC 57.544 33.333 16.55 11.87 41.55 2.67
888 973 4.857871 TTATGAAGAAGAAATGACGCCG 57.142 40.909 0.00 0.00 0.00 6.46
913 1001 6.998074 AGGAACACAACAAATTAGTCAGATCA 59.002 34.615 0.00 0.00 0.00 2.92
917 1005 8.783093 TCAATAGGAACACAACAAATTAGTCAG 58.217 33.333 0.00 0.00 0.00 3.51
989 1108 1.339631 CGTGGCCCATTTTAGGACTCA 60.340 52.381 0.00 0.00 31.51 3.41
1014 1133 1.492993 GGGCAGAGACCAACCTCCTT 61.493 60.000 0.00 0.00 33.76 3.36
1206 1325 0.116342 TCCTAGCAACAGGAGGGTCA 59.884 55.000 0.00 0.00 39.89 4.02
1221 1340 2.029290 GCGAGTGTCTGGTCTTTTCCTA 60.029 50.000 0.00 0.00 0.00 2.94
1293 1427 0.381801 AAACACTTGAACAGCCAGCG 59.618 50.000 0.00 0.00 0.00 5.18
1301 1435 5.512788 CACACAGTGAATGAAACACTTGAAC 59.487 40.000 7.81 0.00 44.69 3.18
1302 1436 5.414144 TCACACAGTGAATGAAACACTTGAA 59.586 36.000 7.81 0.00 44.69 2.69
1303 1437 4.940654 TCACACAGTGAATGAAACACTTGA 59.059 37.500 7.81 0.00 44.69 3.02
1304 1438 5.233957 TCACACAGTGAATGAAACACTTG 57.766 39.130 7.81 0.00 44.69 3.16
1305 1439 6.293626 GCTATCACACAGTGAATGAAACACTT 60.294 38.462 7.81 0.00 45.96 3.16
1306 1440 5.180117 GCTATCACACAGTGAATGAAACACT 59.820 40.000 7.81 0.00 45.96 3.55
1307 1441 5.180117 AGCTATCACACAGTGAATGAAACAC 59.820 40.000 7.81 0.00 45.96 3.32
1309 1443 5.869753 AGCTATCACACAGTGAATGAAAC 57.130 39.130 7.81 0.00 45.96 2.78
1310 1444 7.414429 GCATAAGCTATCACACAGTGAATGAAA 60.414 37.037 7.81 0.00 41.02 2.69
1341 1478 7.228706 ACTTCTTTTCCAACTTACACATACAGG 59.771 37.037 0.00 0.00 0.00 4.00
1347 1484 7.696992 AAAGACTTCTTTTCCAACTTACACA 57.303 32.000 0.00 0.00 43.07 3.72
1381 1518 3.275999 CATCACAGCATCTGTCCATGAA 58.724 45.455 0.00 0.00 43.43 2.57
1382 1519 2.237893 ACATCACAGCATCTGTCCATGA 59.762 45.455 16.44 5.36 43.43 3.07
1383 1520 2.354821 CACATCACAGCATCTGTCCATG 59.645 50.000 11.22 11.22 43.43 3.66
1468 1607 6.115446 TGATATGCTTCGAACCTCTGATTTT 58.885 36.000 0.00 0.00 0.00 1.82
1472 1611 4.502087 CCATGATATGCTTCGAACCTCTGA 60.502 45.833 0.00 0.00 0.00 3.27
1473 1612 3.744942 CCATGATATGCTTCGAACCTCTG 59.255 47.826 0.00 0.00 0.00 3.35
1474 1613 3.389329 ACCATGATATGCTTCGAACCTCT 59.611 43.478 0.00 0.00 0.00 3.69
1475 1614 3.733337 ACCATGATATGCTTCGAACCTC 58.267 45.455 0.00 0.00 0.00 3.85
1476 1615 3.845781 ACCATGATATGCTTCGAACCT 57.154 42.857 0.00 0.00 0.00 3.50
1479 1618 6.873605 CCATTAGTACCATGATATGCTTCGAA 59.126 38.462 0.00 0.00 0.00 3.71
1481 1620 6.166279 ACCATTAGTACCATGATATGCTTCG 58.834 40.000 0.00 0.00 0.00 3.79
1482 1621 7.986085 AACCATTAGTACCATGATATGCTTC 57.014 36.000 0.00 0.00 0.00 3.86
1526 1665 6.318900 AGGCTTATCGAAAAGAAACCATTAGG 59.681 38.462 0.00 0.00 42.21 2.69
1527 1666 7.321745 AGGCTTATCGAAAAGAAACCATTAG 57.678 36.000 0.00 0.00 0.00 1.73
1529 1668 6.208599 TCAAGGCTTATCGAAAAGAAACCATT 59.791 34.615 0.00 0.00 0.00 3.16
1531 1670 5.067273 TCAAGGCTTATCGAAAAGAAACCA 58.933 37.500 0.00 0.00 0.00 3.67
1532 1671 5.622770 TCAAGGCTTATCGAAAAGAAACC 57.377 39.130 0.00 0.00 0.00 3.27
1533 1672 8.427774 CAATTTCAAGGCTTATCGAAAAGAAAC 58.572 33.333 13.21 0.00 31.64 2.78
1534 1673 7.598493 CCAATTTCAAGGCTTATCGAAAAGAAA 59.402 33.333 13.21 10.26 31.64 2.52
1535 1674 7.090173 CCAATTTCAAGGCTTATCGAAAAGAA 58.910 34.615 13.21 2.59 31.64 2.52
1537 1676 6.875926 CCAATTTCAAGGCTTATCGAAAAG 57.124 37.500 13.21 9.78 31.64 2.27
1550 1689 1.669795 GCGGAACCTGCCAATTTCAAG 60.670 52.381 0.00 0.00 0.00 3.02
1551 1690 0.316841 GCGGAACCTGCCAATTTCAA 59.683 50.000 0.00 0.00 0.00 2.69
1552 1691 0.539438 AGCGGAACCTGCCAATTTCA 60.539 50.000 0.00 0.00 0.00 2.69
1553 1692 1.459450 TAGCGGAACCTGCCAATTTC 58.541 50.000 0.00 0.00 0.00 2.17
1554 1693 2.024414 GATAGCGGAACCTGCCAATTT 58.976 47.619 0.00 0.00 0.00 1.82
1556 1695 0.546122 TGATAGCGGAACCTGCCAAT 59.454 50.000 0.00 0.00 0.00 3.16
1557 1696 0.546122 ATGATAGCGGAACCTGCCAA 59.454 50.000 0.00 0.00 0.00 4.52
1558 1697 0.546122 AATGATAGCGGAACCTGCCA 59.454 50.000 0.00 0.00 0.00 4.92
1559 1698 0.947244 CAATGATAGCGGAACCTGCC 59.053 55.000 0.00 0.00 0.00 4.85
1561 1700 2.620251 TCCAATGATAGCGGAACCTG 57.380 50.000 0.00 0.00 0.00 4.00
1562 1701 4.543590 CTATCCAATGATAGCGGAACCT 57.456 45.455 0.00 0.00 42.91 3.50
1571 1710 9.817809 GTACTCTTGTTGAACTATCCAATGATA 57.182 33.333 0.00 0.00 32.18 2.15
1573 1712 7.103641 GGTACTCTTGTTGAACTATCCAATGA 58.896 38.462 0.00 0.00 0.00 2.57
1574 1713 6.878923 TGGTACTCTTGTTGAACTATCCAATG 59.121 38.462 0.00 0.00 0.00 2.82
1575 1714 7.016153 TGGTACTCTTGTTGAACTATCCAAT 57.984 36.000 0.00 0.00 0.00 3.16
1576 1715 6.428083 TGGTACTCTTGTTGAACTATCCAA 57.572 37.500 0.00 0.00 0.00 3.53
1577 1716 6.428083 TTGGTACTCTTGTTGAACTATCCA 57.572 37.500 0.00 0.00 0.00 3.41
1578 1717 7.390718 ACATTTGGTACTCTTGTTGAACTATCC 59.609 37.037 0.00 0.00 0.00 2.59
1579 1718 8.324163 ACATTTGGTACTCTTGTTGAACTATC 57.676 34.615 0.00 0.00 0.00 2.08
1580 1719 9.959721 ATACATTTGGTACTCTTGTTGAACTAT 57.040 29.630 0.00 0.00 34.07 2.12
1581 1720 9.214957 CATACATTTGGTACTCTTGTTGAACTA 57.785 33.333 0.00 0.00 34.07 2.24
1582 1721 7.936847 TCATACATTTGGTACTCTTGTTGAACT 59.063 33.333 0.00 0.00 34.07 3.01
1583 1722 8.094798 TCATACATTTGGTACTCTTGTTGAAC 57.905 34.615 0.00 0.00 34.07 3.18
1584 1723 7.390440 CCTCATACATTTGGTACTCTTGTTGAA 59.610 37.037 0.00 0.00 34.07 2.69
1585 1724 6.878923 CCTCATACATTTGGTACTCTTGTTGA 59.121 38.462 0.00 0.21 34.07 3.18
1586 1725 6.655003 ACCTCATACATTTGGTACTCTTGTTG 59.345 38.462 0.00 0.00 34.07 3.33
1587 1726 6.779860 ACCTCATACATTTGGTACTCTTGTT 58.220 36.000 0.00 0.00 34.07 2.83
1588 1727 6.374417 ACCTCATACATTTGGTACTCTTGT 57.626 37.500 0.00 0.00 34.07 3.16
1589 1728 6.878923 TGAACCTCATACATTTGGTACTCTTG 59.121 38.462 0.00 0.00 34.07 3.02
1590 1729 7.016153 TGAACCTCATACATTTGGTACTCTT 57.984 36.000 0.00 0.00 34.07 2.85
1591 1730 6.213600 ACTGAACCTCATACATTTGGTACTCT 59.786 38.462 0.00 0.00 34.07 3.24
1592 1731 6.407202 ACTGAACCTCATACATTTGGTACTC 58.593 40.000 0.00 0.00 34.07 2.59
1593 1732 6.374417 ACTGAACCTCATACATTTGGTACT 57.626 37.500 0.00 0.00 34.07 2.73
1594 1733 6.653320 TCAACTGAACCTCATACATTTGGTAC 59.347 38.462 0.00 0.00 34.07 3.34
1595 1734 6.774673 TCAACTGAACCTCATACATTTGGTA 58.225 36.000 0.00 0.00 36.16 3.25
1607 1746 1.967319 TTGGTGCTCAACTGAACCTC 58.033 50.000 2.99 0.00 33.65 3.85
1640 1796 2.505407 ACTGCTGGTATGGCTACATTCA 59.495 45.455 0.00 0.00 38.53 2.57
1657 1813 1.305930 GGTCCCGGTTTGATCACTGC 61.306 60.000 0.00 0.00 0.00 4.40
1664 1820 0.466543 CCATATCGGTCCCGGTTTGA 59.533 55.000 10.46 0.00 40.25 2.69
1672 1828 4.285260 ACAAATACTACCCCATATCGGTCC 59.715 45.833 0.00 0.00 34.66 4.46
1674 1830 5.605488 AGAACAAATACTACCCCATATCGGT 59.395 40.000 0.00 0.00 37.40 4.69
1676 1832 6.755206 TCAGAACAAATACTACCCCATATCG 58.245 40.000 0.00 0.00 0.00 2.92
1715 1932 3.801050 GCAGACTATGTATCAGCTGTGTG 59.199 47.826 14.67 1.44 0.00 3.82
1717 1934 4.050852 TGCAGACTATGTATCAGCTGTG 57.949 45.455 14.67 1.21 30.45 3.66
1730 1947 0.608130 AGCATCCGTGTTGCAGACTA 59.392 50.000 8.86 0.00 42.62 2.59
1765 1982 3.702334 GAATCCGTGCTTGCGTCGC 62.702 63.158 11.10 11.10 0.00 5.19
1768 1985 0.665835 TTTTGAATCCGTGCTTGCGT 59.334 45.000 0.00 0.00 0.00 5.24
1866 2120 8.943002 GCTAAACTAGCCTACAAAAATGTCTTA 58.057 33.333 0.00 0.00 45.95 2.10
1867 2121 7.817641 GCTAAACTAGCCTACAAAAATGTCTT 58.182 34.615 0.00 0.00 45.95 3.01
1868 2122 7.379098 GCTAAACTAGCCTACAAAAATGTCT 57.621 36.000 0.00 0.00 45.95 3.41
1919 2173 7.640240 CGTTCCAATTTACGTAGTACTACCTAC 59.360 40.741 24.06 5.51 45.76 3.18
1920 2174 7.201696 CCGTTCCAATTTACGTAGTACTACCTA 60.202 40.741 24.06 15.52 45.76 3.08
1922 2176 5.743872 CCGTTCCAATTTACGTAGTACTACC 59.256 44.000 24.06 9.34 45.76 3.18
1924 2178 5.650266 TCCCGTTCCAATTTACGTAGTACTA 59.350 40.000 0.00 0.00 45.76 1.82
1930 2184 4.829968 TCATTCCCGTTCCAATTTACGTA 58.170 39.130 0.00 0.00 36.09 3.57
1931 2185 3.677190 TCATTCCCGTTCCAATTTACGT 58.323 40.909 0.00 0.00 36.09 3.57
1932 2186 4.688511 TTCATTCCCGTTCCAATTTACG 57.311 40.909 0.00 0.00 37.50 3.18
1937 2191 2.456577 CCCTTTCATTCCCGTTCCAAT 58.543 47.619 0.00 0.00 0.00 3.16
1938 2192 1.549037 CCCCTTTCATTCCCGTTCCAA 60.549 52.381 0.00 0.00 0.00 3.53
1939 2193 0.039035 CCCCTTTCATTCCCGTTCCA 59.961 55.000 0.00 0.00 0.00 3.53
1941 2195 1.173913 CACCCCTTTCATTCCCGTTC 58.826 55.000 0.00 0.00 0.00 3.95
1943 2197 1.304134 GCACCCCTTTCATTCCCGT 60.304 57.895 0.00 0.00 0.00 5.28
1944 2198 2.052104 GGCACCCCTTTCATTCCCG 61.052 63.158 0.00 0.00 0.00 5.14
1967 2221 8.691797 ACTACTAGGCTTTGAAATTGACAAAAA 58.308 29.630 0.00 0.00 36.91 1.94
1970 2224 8.154856 ACTACTACTAGGCTTTGAAATTGACAA 58.845 33.333 0.00 0.00 0.00 3.18
1988 2244 5.528690 TGTTGTGTCGTCTTGTACTACTACT 59.471 40.000 0.00 0.00 0.00 2.57
2015 2271 2.683933 AACTCATCCCCGGCGTCT 60.684 61.111 6.01 0.00 0.00 4.18
2019 2275 1.153349 GAGTCAACTCATCCCCGGC 60.153 63.158 0.00 0.00 42.42 6.13
2033 2289 4.034510 CGAATTTCAAGTGGGCTATGAGTC 59.965 45.833 0.00 0.00 0.00 3.36
2063 2319 4.883083 TCGTCTCTGTGTAATTGCTTTCT 58.117 39.130 0.00 0.00 0.00 2.52
2082 2382 5.947228 TTTTCTTTGATGATGAAGCTCGT 57.053 34.783 0.00 0.00 0.00 4.18
2131 2437 1.080569 GTTGCCAATGGACTTGCCG 60.081 57.895 2.05 0.00 40.66 5.69
2150 2456 1.910580 GCCGGTTCATGGAGGGAGAA 61.911 60.000 1.90 0.00 0.00 2.87
2239 2549 6.301486 CAGGATTTCCAGATGATAATGGTGA 58.699 40.000 0.00 0.00 37.84 4.02


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

AutoCloner maintained by Alex Coulton.