Multiple sequence alignment - TraesCS6A01G307600

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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 TraesCS6A01G307600 chr6A 100.000 2523 0 0 1 2523 542197830 542200352 0.000000e+00 4660.0
1 TraesCS6A01G307600 chr6D 90.476 1701 125 17 3 1679 395501625 395503312 0.000000e+00 2209.0
2 TraesCS6A01G307600 chr6D 84.094 1490 194 23 4 1462 395527019 395528496 0.000000e+00 1399.0
3 TraesCS6A01G307600 chr6D 83.382 686 59 34 1843 2517 395503313 395503954 3.620000e-163 584.0
4 TraesCS6A01G307600 chr6D 86.463 229 26 5 1970 2194 380505117 380505344 1.940000e-61 246.0
5 TraesCS6A01G307600 chr6D 82.772 267 37 7 1938 2199 80600119 80600381 1.950000e-56 230.0
6 TraesCS6A01G307600 chr6B 84.600 1000 109 14 589 1547 591505139 591506134 0.000000e+00 952.0
7 TraesCS6A01G307600 chr6B 92.929 594 40 2 2 595 591461544 591462135 0.000000e+00 863.0
8 TraesCS6A01G307600 chr6B 90.556 180 16 1 1680 1858 536817881 536817702 1.170000e-58 237.0
9 TraesCS6A01G307600 chr6B 89.617 183 18 1 1676 1857 292817264 292817446 5.430000e-57 231.0
10 TraesCS6A01G307600 chr5B 91.477 176 14 1 1674 1849 575061151 575061325 9.020000e-60 241.0
11 TraesCS6A01G307600 chr5B 83.019 265 37 5 1933 2192 121249762 121249501 1.510000e-57 233.0
12 TraesCS6A01G307600 chr5B 78.512 121 17 8 195 312 610023415 610023529 1.250000e-08 71.3
13 TraesCS6A01G307600 chr2B 91.525 177 11 3 1680 1853 139490795 139490620 9.020000e-60 241.0
14 TraesCS6A01G307600 chr2B 91.765 170 14 0 1680 1849 594834040 594833871 1.170000e-58 237.0
15 TraesCS6A01G307600 chr2B 78.146 151 23 9 189 333 373040114 373040260 1.240000e-13 87.9
16 TraesCS6A01G307600 chr2B 77.600 125 21 6 189 310 373087817 373087937 4.500000e-08 69.4
17 TraesCS6A01G307600 chr5D 91.813 171 14 0 1675 1845 368995353 368995523 3.240000e-59 239.0
18 TraesCS6A01G307600 chr5D 82.264 265 37 6 1933 2192 61793578 61793837 1.170000e-53 220.0
19 TraesCS6A01G307600 chr5D 94.444 36 1 1 1899 1934 525731713 525731679 1.000000e-03 54.7
20 TraesCS6A01G307600 chr3D 91.860 172 13 1 1674 1845 74794932 74795102 3.240000e-59 239.0
21 TraesCS6A01G307600 chr3D 83.146 89 14 1 218 306 572227110 572227197 2.080000e-11 80.5
22 TraesCS6A01G307600 chr3B 91.813 171 14 0 1679 1849 495839439 495839609 3.240000e-59 239.0
23 TraesCS6A01G307600 chr3B 88.235 85 10 0 1850 1934 115399039 115399123 4.440000e-18 102.0
24 TraesCS6A01G307600 chr3B 83.146 89 14 1 218 306 761707431 761707344 2.080000e-11 80.5
25 TraesCS6A01G307600 chr1D 91.765 170 14 0 1676 1845 288702856 288702687 1.170000e-58 237.0
26 TraesCS6A01G307600 chr4A 83.077 260 34 9 1938 2192 437487877 437488131 7.020000e-56 228.0
27 TraesCS6A01G307600 chr5A 82.331 266 38 6 1933 2192 115095386 115095124 3.270000e-54 222.0
28 TraesCS6A01G307600 chr4D 82.129 263 38 8 1938 2196 120352400 120352143 1.520000e-52 217.0
29 TraesCS6A01G307600 chr3A 81.439 264 40 7 1934 2192 91026495 91026754 9.150000e-50 207.0
30 TraesCS6A01G307600 chr7A 80.374 107 18 2 198 304 222232680 222232577 7.480000e-11 78.7


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 TraesCS6A01G307600 chr6A 542197830 542200352 2522 False 4660.0 4660 100.000 1 2523 1 chr6A.!!$F1 2522
1 TraesCS6A01G307600 chr6D 395527019 395528496 1477 False 1399.0 1399 84.094 4 1462 1 chr6D.!!$F3 1458
2 TraesCS6A01G307600 chr6D 395501625 395503954 2329 False 1396.5 2209 86.929 3 2517 2 chr6D.!!$F4 2514
3 TraesCS6A01G307600 chr6B 591505139 591506134 995 False 952.0 952 84.600 589 1547 1 chr6B.!!$F3 958
4 TraesCS6A01G307600 chr6B 591461544 591462135 591 False 863.0 863 92.929 2 595 1 chr6B.!!$F2 593

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
876 884 1.418264 TCTCATTGGACGTTTGACCCA 59.582 47.619 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1883 1.622312 GTTGTTACTCCCTCCGTTCCT 59.378 52.381 0.0 0.0 0.0 3.36 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
37 38 6.300354 ACAGTTCTAAGGTGACAAAATTCG 57.700 37.500 0.00 0.00 0.00 3.34
78 79 6.238211 CGACCCACATGAAAGACATAAAGATC 60.238 42.308 0.00 0.00 37.46 2.75
150 151 1.802636 CGCTTGGTGTAATGGCCAG 59.197 57.895 13.05 0.00 36.00 4.85
184 185 3.838244 TGCTTAAAGTGGCCGAGATAT 57.162 42.857 0.00 0.00 0.00 1.63
194 195 3.006967 GTGGCCGAGATATCCAACTACAT 59.993 47.826 0.00 0.00 0.00 2.29
297 298 6.295745 CCATTCTCTACATGACTAGGATGCAT 60.296 42.308 0.00 0.00 0.00 3.96
321 322 9.214957 CATACAACCAAGACAATTAGAAGTACA 57.785 33.333 0.00 0.00 0.00 2.90
365 366 5.180492 TCAACAATAAAGTCGTTCATGACCC 59.820 40.000 0.00 0.00 39.77 4.46
384 385 2.166254 CCCAAACCATGCCTATGACAAC 59.834 50.000 0.00 0.00 36.36 3.32
425 426 1.704641 AGACTATGCCGCCACTCATA 58.295 50.000 0.00 0.00 0.00 2.15
435 436 3.140325 CGCCACTCATATGGGGTAAAT 57.860 47.619 7.68 0.00 45.37 1.40
470 471 2.027745 CCTGCTCCAAGAGTGTACACAT 60.028 50.000 27.06 12.95 31.39 3.21
474 475 4.256920 GCTCCAAGAGTGTACACATCATT 58.743 43.478 27.06 12.85 31.39 2.57
616 617 2.770164 ATAGCTGGCGTTCAGACTTT 57.230 45.000 11.18 2.46 46.18 2.66
617 618 1.795768 TAGCTGGCGTTCAGACTTTG 58.204 50.000 11.18 0.00 46.18 2.77
800 808 9.444600 GGTCAAACTTAGTTCTTGGAATATGTA 57.555 33.333 0.00 0.00 0.00 2.29
876 884 1.418264 TCTCATTGGACGTTTGACCCA 59.582 47.619 0.00 0.00 0.00 4.51
926 942 2.159085 AGTAATTCCTAGTGCCTCGTGC 60.159 50.000 0.00 0.00 41.77 5.34
1077 1108 0.242825 CGCTCACCTTCGAGTTGGTA 59.757 55.000 6.53 0.00 35.33 3.25
1217 1248 3.129638 AGAAGTCTACAGAAGGTCATCGC 59.870 47.826 0.00 0.00 0.00 4.58
1239 1270 2.237143 TGATGTTAAGGTGCTCTCCCTG 59.763 50.000 0.00 0.00 30.99 4.45
1254 1305 5.047235 GCTCTCCCTGTTACAACTCTTCTAA 60.047 44.000 0.00 0.00 0.00 2.10
1260 1311 5.927115 CCTGTTACAACTCTTCTAACACTCC 59.073 44.000 0.00 0.00 0.00 3.85
1262 1313 6.513180 TGTTACAACTCTTCTAACACTCCTG 58.487 40.000 0.00 0.00 0.00 3.86
1263 1314 6.322969 TGTTACAACTCTTCTAACACTCCTGA 59.677 38.462 0.00 0.00 0.00 3.86
1264 1315 7.015292 TGTTACAACTCTTCTAACACTCCTGAT 59.985 37.037 0.00 0.00 0.00 2.90
1267 1318 6.931840 ACAACTCTTCTAACACTCCTGATTTC 59.068 38.462 0.00 0.00 0.00 2.17
1306 1360 4.473477 AATCTGCAAGGTAGGTGAGTAC 57.527 45.455 0.00 0.00 0.00 2.73
1347 1401 1.915078 CTCGGGAATGAAGGCACCCT 61.915 60.000 0.00 0.00 40.12 4.34
1420 1474 3.648067 TGAAACTGATTGTGGAGAGACCT 59.352 43.478 0.00 0.00 39.86 3.85
1427 1481 3.685139 TTGTGGAGAGACCTGATGTTC 57.315 47.619 0.00 0.00 39.86 3.18
1481 1535 6.183360 GCAAGCATGTTACAAGGAGATGTATT 60.183 38.462 0.00 0.00 35.80 1.89
1482 1536 6.932356 AGCATGTTACAAGGAGATGTATTG 57.068 37.500 0.00 0.00 35.80 1.90
1574 1628 3.553828 TGTCCGTCTTGAAAAGGTTCT 57.446 42.857 0.00 0.00 46.24 3.01
1603 1657 6.480320 GCACTTCGAAATAACATACTCCATCT 59.520 38.462 0.00 0.00 0.00 2.90
1609 1663 0.179045 AACATACTCCATCTGCCCGC 60.179 55.000 0.00 0.00 0.00 6.13
1639 1693 6.072342 ACGTTTTGTTTACTCAAGTTCAAGGT 60.072 34.615 0.00 0.00 0.00 3.50
1670 1724 6.418057 AGCCCTCTAGATGAGAATTAACTG 57.582 41.667 0.00 0.00 45.39 3.16
1671 1725 5.306678 AGCCCTCTAGATGAGAATTAACTGG 59.693 44.000 0.00 0.00 45.39 4.00
1679 1733 6.352516 AGATGAGAATTAACTGGGTCACATC 58.647 40.000 0.00 0.00 37.96 3.06
1680 1734 5.762179 TGAGAATTAACTGGGTCACATCT 57.238 39.130 0.00 0.00 0.00 2.90
1681 1735 6.867519 TGAGAATTAACTGGGTCACATCTA 57.132 37.500 0.00 0.00 0.00 1.98
1682 1736 6.640518 TGAGAATTAACTGGGTCACATCTAC 58.359 40.000 0.00 0.00 0.00 2.59
1683 1737 6.440647 TGAGAATTAACTGGGTCACATCTACT 59.559 38.462 0.00 0.00 0.00 2.57
1684 1738 6.879400 AGAATTAACTGGGTCACATCTACTC 58.121 40.000 0.00 0.00 0.00 2.59
1685 1739 5.615925 ATTAACTGGGTCACATCTACTCC 57.384 43.478 0.00 0.00 0.00 3.85
1686 1740 2.930109 ACTGGGTCACATCTACTCCT 57.070 50.000 0.00 0.00 0.00 3.69
1687 1741 3.191888 ACTGGGTCACATCTACTCCTT 57.808 47.619 0.00 0.00 0.00 3.36
1688 1742 3.100671 ACTGGGTCACATCTACTCCTTC 58.899 50.000 0.00 0.00 0.00 3.46
1689 1743 2.432510 CTGGGTCACATCTACTCCTTCC 59.567 54.545 0.00 0.00 0.00 3.46
1690 1744 1.409427 GGGTCACATCTACTCCTTCCG 59.591 57.143 0.00 0.00 0.00 4.30
1691 1745 2.100989 GGTCACATCTACTCCTTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
1692 1746 2.496470 GGTCACATCTACTCCTTCCGTT 59.504 50.000 0.00 0.00 0.00 4.44
1693 1747 3.429135 GGTCACATCTACTCCTTCCGTTC 60.429 52.174 0.00 0.00 0.00 3.95
1694 1748 2.758979 TCACATCTACTCCTTCCGTTCC 59.241 50.000 0.00 0.00 0.00 3.62
1695 1749 2.761208 CACATCTACTCCTTCCGTTCCT 59.239 50.000 0.00 0.00 0.00 3.36
1696 1750 3.952323 CACATCTACTCCTTCCGTTCCTA 59.048 47.826 0.00 0.00 0.00 2.94
1697 1751 4.401519 CACATCTACTCCTTCCGTTCCTAA 59.598 45.833 0.00 0.00 0.00 2.69
1698 1752 5.021458 ACATCTACTCCTTCCGTTCCTAAA 58.979 41.667 0.00 0.00 0.00 1.85
1699 1753 5.661759 ACATCTACTCCTTCCGTTCCTAAAT 59.338 40.000 0.00 0.00 0.00 1.40
1700 1754 6.837568 ACATCTACTCCTTCCGTTCCTAAATA 59.162 38.462 0.00 0.00 0.00 1.40
1701 1755 7.509659 ACATCTACTCCTTCCGTTCCTAAATAT 59.490 37.037 0.00 0.00 0.00 1.28
1702 1756 7.909485 TCTACTCCTTCCGTTCCTAAATATT 57.091 36.000 0.00 0.00 0.00 1.28
1703 1757 8.315220 TCTACTCCTTCCGTTCCTAAATATTT 57.685 34.615 5.89 5.89 0.00 1.40
1704 1758 9.425248 TCTACTCCTTCCGTTCCTAAATATTTA 57.575 33.333 7.66 7.66 0.00 1.40
1707 1761 8.935741 ACTCCTTCCGTTCCTAAATATTTATCT 58.064 33.333 8.34 0.00 0.00 1.98
1708 1762 9.780186 CTCCTTCCGTTCCTAAATATTTATCTT 57.220 33.333 8.34 0.00 0.00 2.40
1743 1797 9.791820 TTTCAAATGAAATACTGCATACAGATG 57.208 29.630 0.00 0.00 41.39 2.90
1786 1840 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
1787 1841 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
1788 1842 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
1789 1843 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
1790 1844 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
1791 1845 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
1792 1846 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
1793 1847 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
1794 1848 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
1795 1849 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
1796 1850 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
1797 1851 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
1798 1852 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
1799 1853 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
1800 1854 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
1801 1855 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
1802 1856 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
1803 1857 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
1804 1858 6.016213 TGCTTCGTATGTAGTCACTTGTTA 57.984 37.500 0.00 0.00 0.00 2.41
1805 1859 6.448852 TGCTTCGTATGTAGTCACTTGTTAA 58.551 36.000 0.00 0.00 0.00 2.01
1806 1860 6.924612 TGCTTCGTATGTAGTCACTTGTTAAA 59.075 34.615 0.00 0.00 0.00 1.52
1807 1861 7.438757 TGCTTCGTATGTAGTCACTTGTTAAAA 59.561 33.333 0.00 0.00 0.00 1.52
1808 1862 8.440833 GCTTCGTATGTAGTCACTTGTTAAAAT 58.559 33.333 0.00 0.00 0.00 1.82
1839 1893 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
1840 1894 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1841 1895 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1854 1908 2.560105 ACGGAGGGAGTAACAACTACAC 59.440 50.000 0.00 0.00 32.37 2.90
1869 1929 8.865590 AACAACTACACCATTTGATTTTACAC 57.134 30.769 0.00 0.00 0.00 2.90
1870 1930 7.430441 ACAACTACACCATTTGATTTTACACC 58.570 34.615 0.00 0.00 0.00 4.16
1884 1944 2.106477 TACACCAAGATGCATGCGAA 57.894 45.000 14.09 0.00 0.00 4.70
1940 2000 7.556844 TCAAATGATGTAGGAGTTACTTCCTC 58.443 38.462 6.63 0.00 44.33 3.71
1948 2008 3.999046 GGAGTTACTTCCTCCGTTTCAA 58.001 45.455 0.00 0.00 39.22 2.69
1956 2016 6.679327 ACTTCCTCCGTTTCAAAATATAGC 57.321 37.500 0.00 0.00 0.00 2.97
1957 2017 5.293569 ACTTCCTCCGTTTCAAAATATAGCG 59.706 40.000 0.00 0.00 0.00 4.26
1963 2023 7.383029 CCTCCGTTTCAAAATATAGCGTGTATA 59.617 37.037 0.00 0.00 0.00 1.47
2147 2207 8.050778 ACTTAGTCAAAGTTTGTGTGAATTGA 57.949 30.769 15.08 0.00 46.61 2.57
2148 2208 7.968405 ACTTAGTCAAAGTTTGTGTGAATTGAC 59.032 33.333 15.08 8.06 46.61 3.18
2151 2211 7.581011 GTCAAAGTTTGTGTGAATTGACTTT 57.419 32.000 15.08 0.00 41.92 2.66
2152 2212 8.017587 GTCAAAGTTTGTGTGAATTGACTTTT 57.982 30.769 15.08 0.00 41.92 2.27
2153 2213 8.162245 GTCAAAGTTTGTGTGAATTGACTTTTC 58.838 33.333 15.08 0.00 41.92 2.29
2158 2218 9.050601 AGTTTGTGTGAATTGACTTTTCAAAAA 57.949 25.926 0.00 0.00 45.01 1.94
2159 2219 9.316859 GTTTGTGTGAATTGACTTTTCAAAAAG 57.683 29.630 12.51 12.51 45.01 2.27
2200 2260 8.798975 ATAAAATGGAGGGAGTAGATAAGACA 57.201 34.615 0.00 0.00 0.00 3.41
2214 2274 9.953697 AGTAGATAAGACATCGTTATTTCTCAC 57.046 33.333 0.00 0.00 0.00 3.51
2216 2276 7.782049 AGATAAGACATCGTTATTTCTCACCA 58.218 34.615 0.00 0.00 0.00 4.17
2280 2340 6.183359 CCATAAATTTCGTGTACGCTGTTTTG 60.183 38.462 4.67 0.00 39.60 2.44
2281 2341 3.955771 ATTTCGTGTACGCTGTTTTGT 57.044 38.095 4.67 0.00 39.60 2.83
2298 2358 8.905702 GCTGTTTTGTCAATAGTTAACAATCAG 58.094 33.333 8.61 6.57 37.75 2.90
2305 2365 9.371136 TGTCAATAGTTAACAATCAGAGTCATC 57.629 33.333 8.61 0.00 0.00 2.92
2324 2384 4.037446 TCATCTTCGGTTTTGGTTTTCTGG 59.963 41.667 0.00 0.00 0.00 3.86
2325 2385 3.622630 TCTTCGGTTTTGGTTTTCTGGA 58.377 40.909 0.00 0.00 0.00 3.86
2399 2459 7.981142 TCAAATTAATAGTGGGTTAAAGCTCG 58.019 34.615 0.00 0.00 0.00 5.03
2428 2488 5.549347 TGGCAAACAAAATACATCTTGCAT 58.451 33.333 6.89 0.00 40.66 3.96
2429 2489 6.695429 TGGCAAACAAAATACATCTTGCATA 58.305 32.000 6.89 0.00 40.66 3.14
2430 2490 7.329499 TGGCAAACAAAATACATCTTGCATAT 58.671 30.769 6.89 0.00 40.66 1.78
2488 2548 4.817318 AAACACCAAACATTTGTGAGGT 57.183 36.364 3.79 2.47 36.74 3.85
2492 2552 6.084326 ACACCAAACATTTGTGAGGTAATC 57.916 37.500 6.92 0.00 35.22 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.317893 ACAACGAATTTTGTCACCTTAGAACT 59.682 34.615 0.00 0.00 34.48 3.01
27 28 9.750882 GGTACTTATCTTACAACGAATTTTGTC 57.249 33.333 0.00 0.00 40.29 3.18
37 38 5.105063 GTGGGTCGGTACTTATCTTACAAC 58.895 45.833 0.00 0.00 0.00 3.32
51 52 0.762418 TGTCTTTCATGTGGGTCGGT 59.238 50.000 0.00 0.00 0.00 4.69
78 79 4.036971 CCGTCTCTTTGAGATAGTACCCAG 59.963 50.000 0.40 0.00 40.98 4.45
297 298 9.616156 TTTGTACTTCTAATTGTCTTGGTTGTA 57.384 29.630 0.00 0.00 0.00 2.41
348 349 3.816523 GGTTTGGGTCATGAACGACTTTA 59.183 43.478 4.29 0.00 36.12 1.85
365 366 2.746904 TCGTTGTCATAGGCATGGTTTG 59.253 45.455 0.00 0.00 32.61 2.93
384 385 1.813513 GGATATGCCTCCCACATTCG 58.186 55.000 0.00 0.00 0.00 3.34
425 426 6.240468 GGTGGTGAAGGATATATTTACCCCAT 60.240 42.308 10.08 0.00 35.90 4.00
435 436 2.972713 GGAGCAGGTGGTGAAGGATATA 59.027 50.000 0.00 0.00 0.00 0.86
470 471 5.712004 CAGCACCAATCAATGTTACAATGA 58.288 37.500 5.53 5.53 0.00 2.57
474 475 2.889678 TGCAGCACCAATCAATGTTACA 59.110 40.909 0.00 0.00 0.00 2.41
876 884 6.183360 CGCCTTGGTAATTGTATTGACTCATT 60.183 38.462 0.00 0.00 0.00 2.57
926 942 4.641396 TCCTTATAGTGCCGATGGATTTG 58.359 43.478 0.00 0.00 0.00 2.32
930 946 2.891580 GACTCCTTATAGTGCCGATGGA 59.108 50.000 0.00 0.00 0.00 3.41
963 979 3.622630 CTGCTGACCTGTAGTACCTAGT 58.377 50.000 0.00 0.00 0.00 2.57
1123 1154 1.745489 GAAGCGTCATCCCCACACC 60.745 63.158 0.00 0.00 0.00 4.16
1124 1155 1.021390 CAGAAGCGTCATCCCCACAC 61.021 60.000 1.61 0.00 0.00 3.82
1217 1248 2.503356 AGGGAGAGCACCTTAACATCAG 59.497 50.000 0.00 0.00 33.64 2.90
1239 1270 6.746120 TCAGGAGTGTTAGAAGAGTTGTAAC 58.254 40.000 0.90 0.90 39.19 2.50
1262 1313 8.895932 ATTTGTAAACGTATGCTGAAGAAATC 57.104 30.769 0.00 0.00 0.00 2.17
1263 1314 8.730680 AGATTTGTAAACGTATGCTGAAGAAAT 58.269 29.630 0.00 0.00 0.00 2.17
1264 1315 8.015087 CAGATTTGTAAACGTATGCTGAAGAAA 58.985 33.333 0.00 0.00 0.00 2.52
1267 1318 5.734498 GCAGATTTGTAAACGTATGCTGAAG 59.266 40.000 0.00 0.00 0.00 3.02
1282 1335 3.073062 ACTCACCTACCTTGCAGATTTGT 59.927 43.478 0.00 0.00 0.00 2.83
1306 1360 1.100510 CCTGCAGGACATGACATTGG 58.899 55.000 29.88 0.00 37.39 3.16
1347 1401 1.836604 GTTTGCCCTGCCCTTTCCA 60.837 57.895 0.00 0.00 0.00 3.53
1420 1474 3.516700 TCTTCTCATCCAGCTGAACATCA 59.483 43.478 17.39 0.00 0.00 3.07
1427 1481 2.538437 CTTCGTCTTCTCATCCAGCTG 58.462 52.381 6.78 6.78 0.00 4.24
1481 1535 2.047274 CCTCTTTCTTCGGCGGCA 60.047 61.111 10.53 0.00 0.00 5.69
1482 1536 0.953960 TTTCCTCTTTCTTCGGCGGC 60.954 55.000 7.21 0.00 0.00 6.53
1574 1628 6.755141 GGAGTATGTTATTTCGAAGTGCACTA 59.245 38.462 22.01 3.84 0.00 2.74
1603 1657 1.167155 ACAAAACGTGTATGCGGGCA 61.167 50.000 0.00 0.00 39.29 5.36
1609 1663 7.906010 TGAACTTGAGTAAACAAAACGTGTATG 59.094 33.333 0.00 0.00 40.60 2.39
1639 1693 6.455690 TCTCATCTAGAGGGCTAGTCATAA 57.544 41.667 4.28 0.00 44.81 1.90
1670 1724 1.409427 CGGAAGGAGTAGATGTGACCC 59.591 57.143 0.00 0.00 0.00 4.46
1671 1725 2.100989 ACGGAAGGAGTAGATGTGACC 58.899 52.381 0.00 0.00 0.00 4.02
1681 1735 8.935741 AGATAAATATTTAGGAACGGAAGGAGT 58.064 33.333 13.15 0.00 0.00 3.85
1682 1736 9.780186 AAGATAAATATTTAGGAACGGAAGGAG 57.220 33.333 13.15 0.00 0.00 3.69
1717 1771 9.791820 CATCTGTATGCAGTATTTCATTTGAAA 57.208 29.630 10.80 8.09 43.74 2.69
1718 1772 8.959548 ACATCTGTATGCAGTATTTCATTTGAA 58.040 29.630 10.80 0.00 43.05 2.69
1719 1773 8.510243 ACATCTGTATGCAGTATTTCATTTGA 57.490 30.769 10.80 0.00 43.05 2.69
1763 1817 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
1764 1818 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
1765 1819 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
1766 1820 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
1767 1821 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
1768 1822 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
1769 1823 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
1770 1824 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
1771 1825 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
1772 1826 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
1773 1827 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
1774 1828 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
1775 1829 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
1776 1830 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
1777 1831 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
1778 1832 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
1779 1833 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
1780 1834 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
1781 1835 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
1782 1836 6.939551 TTAACAAGTGACTACATACGAAGC 57.060 37.500 0.00 0.00 0.00 3.86
1813 1867 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
1814 1868 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
1815 1869 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1816 1870 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1817 1871 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1818 1872 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1819 1873 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1820 1874 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1821 1875 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1822 1876 6.384886 TGTTACTCCCTCCGTTCCTAAATATT 59.615 38.462 0.00 0.00 0.00 1.28
1823 1877 5.901276 TGTTACTCCCTCCGTTCCTAAATAT 59.099 40.000 0.00 0.00 0.00 1.28
1824 1878 5.271598 TGTTACTCCCTCCGTTCCTAAATA 58.728 41.667 0.00 0.00 0.00 1.40
1825 1879 4.098894 TGTTACTCCCTCCGTTCCTAAAT 58.901 43.478 0.00 0.00 0.00 1.40
1826 1880 3.509442 TGTTACTCCCTCCGTTCCTAAA 58.491 45.455 0.00 0.00 0.00 1.85
1827 1881 3.173953 TGTTACTCCCTCCGTTCCTAA 57.826 47.619 0.00 0.00 0.00 2.69
1828 1882 2.827921 GTTGTTACTCCCTCCGTTCCTA 59.172 50.000 0.00 0.00 0.00 2.94
1829 1883 1.622312 GTTGTTACTCCCTCCGTTCCT 59.378 52.381 0.00 0.00 0.00 3.36
1830 1884 1.622312 AGTTGTTACTCCCTCCGTTCC 59.378 52.381 0.00 0.00 0.00 3.62
1831 1885 3.256631 TGTAGTTGTTACTCCCTCCGTTC 59.743 47.826 0.00 0.00 35.78 3.95
1832 1886 3.006217 GTGTAGTTGTTACTCCCTCCGTT 59.994 47.826 0.00 0.00 35.78 4.44
1833 1887 2.560105 GTGTAGTTGTTACTCCCTCCGT 59.440 50.000 0.00 0.00 35.78 4.69
1834 1888 2.094338 GGTGTAGTTGTTACTCCCTCCG 60.094 54.545 0.00 0.00 39.13 4.63
1835 1889 2.901839 TGGTGTAGTTGTTACTCCCTCC 59.098 50.000 3.73 0.00 42.63 4.30
1836 1890 4.820894 ATGGTGTAGTTGTTACTCCCTC 57.179 45.455 3.73 0.00 42.63 4.30
1837 1891 5.072600 TCAAATGGTGTAGTTGTTACTCCCT 59.927 40.000 3.73 0.00 42.63 4.20
1838 1892 5.310451 TCAAATGGTGTAGTTGTTACTCCC 58.690 41.667 3.73 0.00 42.63 4.30
1839 1893 7.448748 AATCAAATGGTGTAGTTGTTACTCC 57.551 36.000 0.00 0.00 43.27 3.85
1854 1908 6.164876 TGCATCTTGGTGTAAAATCAAATGG 58.835 36.000 0.00 0.00 0.00 3.16
1935 1995 5.064198 CACGCTATATTTTGAAACGGAGGAA 59.936 40.000 0.00 0.00 0.00 3.36
1936 1996 4.569162 CACGCTATATTTTGAAACGGAGGA 59.431 41.667 0.00 0.00 0.00 3.71
1940 2000 8.289440 TCTATACACGCTATATTTTGAAACGG 57.711 34.615 0.00 0.00 0.00 4.44
1986 2046 9.706691 TCTATAAACTTGGTCAAACTCTACAAG 57.293 33.333 0.00 0.00 43.01 3.16
2123 2183 8.184192 AGTCAATTCACACAAACTTTGACTAAG 58.816 33.333 12.87 0.00 46.76 2.18
2124 2184 8.050778 AGTCAATTCACACAAACTTTGACTAA 57.949 30.769 12.87 0.00 46.76 2.24
2125 2185 7.624360 AGTCAATTCACACAAACTTTGACTA 57.376 32.000 12.87 0.00 46.76 2.59
2126 2186 6.515272 AGTCAATTCACACAAACTTTGACT 57.485 33.333 8.55 9.62 44.97 3.41
2127 2187 7.581011 AAAGTCAATTCACACAAACTTTGAC 57.419 32.000 8.55 5.67 41.88 3.18
2128 2188 7.869937 TGAAAAGTCAATTCACACAAACTTTGA 59.130 29.630 8.55 0.00 37.12 2.69
2129 2189 8.016497 TGAAAAGTCAATTCACACAAACTTTG 57.984 30.769 0.00 0.00 37.12 2.77
2130 2190 8.600449 TTGAAAAGTCAATTCACACAAACTTT 57.400 26.923 0.00 0.00 38.88 2.66
2131 2191 8.600449 TTTGAAAAGTCAATTCACACAAACTT 57.400 26.923 0.00 0.00 43.29 2.66
2132 2192 8.600449 TTTTGAAAAGTCAATTCACACAAACT 57.400 26.923 0.00 0.00 43.29 2.66
2133 2193 9.316859 CTTTTTGAAAAGTCAATTCACACAAAC 57.683 29.630 7.82 0.00 43.29 2.93
2177 2237 7.472100 CGATGTCTTATCTACTCCCTCCATTTT 60.472 40.741 0.00 0.00 0.00 1.82
2182 2242 4.400120 ACGATGTCTTATCTACTCCCTCC 58.600 47.826 0.00 0.00 0.00 4.30
2183 2243 7.690952 ATAACGATGTCTTATCTACTCCCTC 57.309 40.000 0.00 0.00 0.00 4.30
2184 2244 8.480133 AAATAACGATGTCTTATCTACTCCCT 57.520 34.615 0.00 0.00 0.00 4.20
2186 2246 9.615295 GAGAAATAACGATGTCTTATCTACTCC 57.385 37.037 0.00 0.00 28.90 3.85
2191 2251 7.782049 TGGTGAGAAATAACGATGTCTTATCT 58.218 34.615 0.00 0.00 28.90 1.98
2195 2255 6.934645 TCTTTGGTGAGAAATAACGATGTCTT 59.065 34.615 0.00 0.00 28.90 3.01
2200 2260 7.331026 TCTCATCTTTGGTGAGAAATAACGAT 58.669 34.615 7.94 0.00 46.58 3.73
2214 2274 6.696148 GCAGATTTGCTAATTCTCATCTTTGG 59.304 38.462 0.00 0.00 46.95 3.28
2245 2305 6.212955 ACACGAAATTTATGGTCAAAGGTTG 58.787 36.000 6.82 0.00 0.00 3.77
2265 2325 2.722936 TTGACAAAACAGCGTACACG 57.277 45.000 0.00 0.00 43.27 4.49
2280 2340 9.593134 AGATGACTCTGATTGTTAACTATTGAC 57.407 33.333 7.22 0.00 0.00 3.18
2298 2358 4.830826 AAACCAAAACCGAAGATGACTC 57.169 40.909 0.00 0.00 0.00 3.36
2305 2365 4.379339 TTCCAGAAAACCAAAACCGAAG 57.621 40.909 0.00 0.00 0.00 3.79
2377 2437 7.608761 TGTTCGAGCTTTAACCCACTATTAATT 59.391 33.333 0.00 0.00 0.00 1.40
2391 2451 3.316588 TGTTTGCCAATGTTCGAGCTTTA 59.683 39.130 0.00 0.00 0.00 1.85
2399 2459 7.656707 AGATGTATTTTGTTTGCCAATGTTC 57.343 32.000 0.00 0.00 31.81 3.18
2458 2518 4.806342 ATGTTTGGTGTTTACTCGTGAC 57.194 40.909 0.00 0.00 0.00 3.67
2468 2528 5.923733 TTACCTCACAAATGTTTGGTGTT 57.076 34.783 14.07 0.00 42.34 3.32


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

AutoCloner maintained by Alex Coulton.