Multiple sequence alignment - TraesCS2D01G519200

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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 TraesCS2D01G519200 chr2D 100.000 2198 0 0 1 2198 608978630 608980827 0.000000e+00 4060
1 TraesCS2D01G519200 chr2A 95.220 1611 53 8 1 1603 740873054 740874648 0.000000e+00 2527
2 TraesCS2D01G519200 chr2A 90.200 500 42 6 1704 2198 740874644 740875141 0.000000e+00 645
3 TraesCS2D01G519200 chr2B 94.172 1287 54 11 327 1603 742892514 742893789 0.000000e+00 1941
4 TraesCS2D01G519200 chr2B 89.600 500 43 7 1704 2198 742893785 742894280 5.150000e-176 627
5 TraesCS2D01G519200 chr2B 97.436 273 7 0 1 273 742892243 742892515 1.190000e-127 466
6 TraesCS2D01G519200 chr4D 95.370 108 5 0 1599 1706 477738758 477738865 2.900000e-39 172
7 TraesCS2D01G519200 chr7B 93.694 111 7 0 1596 1706 683101464 683101574 1.350000e-37 167
8 TraesCS2D01G519200 chr3D 89.922 129 11 2 1586 1713 44007450 44007323 4.850000e-37 165
9 TraesCS2D01G519200 chr3D 92.793 111 8 0 1599 1709 536331138 536331028 6.280000e-36 161
10 TraesCS2D01G519200 chr5D 91.525 118 9 1 1588 1705 365693294 365693410 6.280000e-36 161
11 TraesCS2D01G519200 chr5A 91.525 118 9 1 1588 1705 467377443 467377559 6.280000e-36 161
12 TraesCS2D01G519200 chr5A 92.105 114 8 1 1592 1705 308093344 308093232 2.260000e-35 159
13 TraesCS2D01G519200 chr5A 92.105 114 8 1 1592 1705 308179888 308179776 2.260000e-35 159
14 TraesCS2D01G519200 chr4B 89.831 118 10 2 1592 1708 414860858 414860742 1.360000e-32 150


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 TraesCS2D01G519200 chr2D 608978630 608980827 2197 False 4060.000000 4060 100.000 1 2198 1 chr2D.!!$F1 2197
1 TraesCS2D01G519200 chr2A 740873054 740875141 2087 False 1586.000000 2527 92.710 1 2198 2 chr2A.!!$F1 2197
2 TraesCS2D01G519200 chr2B 742892243 742894280 2037 False 1011.333333 1941 93.736 1 2198 3 chr2B.!!$F1 2197

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
290 293 0.688749 ATTCATGCAAAGCCCCTCCC 60.689 55.0 0.00 0.0 0.0 4.30 F
1074 1086 0.326264 GGGCGGCTGAGGATGATATT 59.674 55.0 9.56 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 1119 1.146544 TCAAAGGGGAAGGGGAAGGG 61.147 60.000 0.00 0.0 0.00 3.95 R
1918 1934 1.219213 TGGTTTCCCATGGACCAAAGT 59.781 47.619 18.98 0.0 40.31 2.66 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
27 28 6.670077 TGCTGTATTGCATTTAATCGTACA 57.330 33.333 0.00 0.00 38.12 2.90
64 65 5.931724 ACCATTTATTTGCCAAAGTGCTAAC 59.068 36.000 0.00 0.00 0.00 2.34
228 231 3.898005 CGATTCTCTCGTCTTTTCAGC 57.102 47.619 0.00 0.00 42.56 4.26
229 232 2.600867 CGATTCTCTCGTCTTTTCAGCC 59.399 50.000 0.00 0.00 42.56 4.85
287 290 2.037144 GATGATTCATGCAAAGCCCCT 58.963 47.619 3.32 0.00 0.00 4.79
290 293 0.688749 ATTCATGCAAAGCCCCTCCC 60.689 55.000 0.00 0.00 0.00 4.30
291 294 2.761213 CATGCAAAGCCCCTCCCC 60.761 66.667 0.00 0.00 0.00 4.81
292 295 4.079961 ATGCAAAGCCCCTCCCCC 62.080 66.667 0.00 0.00 0.00 5.40
322 325 5.579511 ACAAAAATGATTCTTGCATAGCAGC 59.420 36.000 0.00 0.00 40.61 5.25
341 344 2.615447 AGCTGCATACACGAATCATTGG 59.385 45.455 1.02 0.00 0.00 3.16
342 345 2.355756 GCTGCATACACGAATCATTGGT 59.644 45.455 0.00 0.00 0.00 3.67
343 346 3.559655 GCTGCATACACGAATCATTGGTA 59.440 43.478 0.00 0.00 0.00 3.25
344 347 4.552767 GCTGCATACACGAATCATTGGTAC 60.553 45.833 0.00 0.00 0.00 3.34
345 348 4.508662 TGCATACACGAATCATTGGTACA 58.491 39.130 0.00 0.00 0.00 2.90
929 938 4.468689 GGCGGCTGAGGGTGGTAC 62.469 72.222 0.00 0.00 0.00 3.34
932 941 3.702048 GGCTGAGGGTGGTACGCA 61.702 66.667 0.00 0.00 43.02 5.24
986 995 3.958860 GGTGGCTGCTCAGTGGGT 61.959 66.667 0.00 0.00 0.00 4.51
992 1001 2.848679 TGCTCAGTGGGTGGCTGA 60.849 61.111 0.00 0.00 40.28 4.26
1010 1019 2.265467 GATGGTGGTATGCCGGTGGT 62.265 60.000 1.90 0.00 37.67 4.16
1039 1048 1.400530 GGCGGCTGAGGGTAGTATGT 61.401 60.000 0.00 0.00 0.00 2.29
1053 1065 1.153568 TATGTCTGTGGCTGCTCGC 60.154 57.895 0.00 0.00 38.13 5.03
1074 1086 0.326264 GGGCGGCTGAGGATGATATT 59.674 55.000 9.56 0.00 0.00 1.28
1262 1274 3.208594 GCATGATAGCTTGTGTGGATCA 58.791 45.455 0.00 0.00 0.00 2.92
1333 1345 4.582656 CGTCCTAATCCTCTCTTGATCTGT 59.417 45.833 0.00 0.00 0.00 3.41
1344 1356 7.038729 TCCTCTCTTGATCTGTACAAGTCATTT 60.039 37.037 9.81 0.00 43.30 2.32
1350 1362 7.439157 TGATCTGTACAAGTCATTTTCTTGG 57.561 36.000 0.00 0.00 44.29 3.61
1354 1366 7.054124 TCTGTACAAGTCATTTTCTTGGAAGT 58.946 34.615 0.00 0.00 44.29 3.01
1383 1397 7.352739 ACTAGCAAGTAAGAAATTTGTGTTCG 58.647 34.615 0.00 0.00 32.84 3.95
1392 1406 5.901552 AGAAATTTGTGTTCGTGATTGGTT 58.098 33.333 0.00 0.00 0.00 3.67
1394 1408 7.484975 AGAAATTTGTGTTCGTGATTGGTTTA 58.515 30.769 0.00 0.00 0.00 2.01
1408 1422 3.138884 TGGTTTAGCAAGCTCATGTGA 57.861 42.857 0.00 0.00 0.00 3.58
1438 1452 5.250982 TCTTTGTGACTGAGATGCATGAAT 58.749 37.500 2.46 0.00 0.00 2.57
1449 1463 8.155510 ACTGAGATGCATGAATGAACATATAGT 58.844 33.333 2.46 0.00 0.00 2.12
1451 1465 9.649167 TGAGATGCATGAATGAACATATAGTAG 57.351 33.333 2.46 0.00 0.00 2.57
1586 1601 3.535280 TGTGTTGACAGAAGCACAGTA 57.465 42.857 0.00 0.00 37.00 2.74
1613 1628 8.572855 AGTAAATAGTTACTACCTCTGTTCGT 57.427 34.615 13.65 0.00 46.59 3.85
1614 1629 9.018582 AGTAAATAGTTACTACCTCTGTTCGTT 57.981 33.333 13.65 0.00 46.59 3.85
1615 1630 9.631452 GTAAATAGTTACTACCTCTGTTCGTTT 57.369 33.333 5.84 0.00 37.27 3.60
1617 1632 9.551734 AAATAGTTACTACCTCTGTTCGTTTTT 57.448 29.630 0.00 0.00 0.00 1.94
1624 1639 8.754230 ACTACCTCTGTTCGTTTTTATAAGAC 57.246 34.615 0.00 0.00 0.00 3.01
1625 1640 6.701432 ACCTCTGTTCGTTTTTATAAGACG 57.299 37.500 13.97 13.97 38.09 4.18
1626 1641 6.218746 ACCTCTGTTCGTTTTTATAAGACGT 58.781 36.000 17.49 0.00 37.95 4.34
1627 1642 6.703165 ACCTCTGTTCGTTTTTATAAGACGTT 59.297 34.615 17.49 0.00 37.95 3.99
1628 1643 7.225341 ACCTCTGTTCGTTTTTATAAGACGTTT 59.775 33.333 17.49 0.00 37.95 3.60
1629 1644 8.066000 CCTCTGTTCGTTTTTATAAGACGTTTT 58.934 33.333 17.49 0.00 37.95 2.43
1633 1648 9.848172 TGTTCGTTTTTATAAGACGTTTTAGAC 57.152 29.630 17.49 11.04 37.95 2.59
1645 1660 4.283950 CGTTTTAGACGTTAAGACACCG 57.716 45.455 0.00 0.00 46.49 4.94
1646 1661 3.730715 CGTTTTAGACGTTAAGACACCGT 59.269 43.478 0.00 0.00 46.49 4.83
1647 1662 4.207019 CGTTTTAGACGTTAAGACACCGTT 59.793 41.667 0.00 0.00 46.49 4.44
1648 1663 5.608206 CGTTTTAGACGTTAAGACACCGTTC 60.608 44.000 0.00 0.00 46.49 3.95
1649 1664 4.566545 TTAGACGTTAAGACACCGTTCA 57.433 40.909 0.00 0.00 34.51 3.18
1650 1665 3.441496 AGACGTTAAGACACCGTTCAA 57.559 42.857 0.00 0.00 34.51 2.69
1651 1666 3.784338 AGACGTTAAGACACCGTTCAAA 58.216 40.909 0.00 0.00 34.51 2.69
1652 1667 4.183101 AGACGTTAAGACACCGTTCAAAA 58.817 39.130 0.00 0.00 34.51 2.44
1653 1668 4.033243 AGACGTTAAGACACCGTTCAAAAC 59.967 41.667 0.00 0.00 34.51 2.43
1654 1669 3.683822 ACGTTAAGACACCGTTCAAAACA 59.316 39.130 0.00 0.00 0.00 2.83
1655 1670 4.201744 ACGTTAAGACACCGTTCAAAACAG 60.202 41.667 0.00 0.00 0.00 3.16
1656 1671 4.201744 CGTTAAGACACCGTTCAAAACAGT 60.202 41.667 0.00 0.00 0.00 3.55
1657 1672 5.005586 CGTTAAGACACCGTTCAAAACAGTA 59.994 40.000 0.00 0.00 0.00 2.74
1658 1673 4.870221 AAGACACCGTTCAAAACAGTAC 57.130 40.909 0.00 0.00 0.00 2.73
1659 1674 3.864243 AGACACCGTTCAAAACAGTACA 58.136 40.909 0.00 0.00 0.00 2.90
1660 1675 4.255301 AGACACCGTTCAAAACAGTACAA 58.745 39.130 0.00 0.00 0.00 2.41
1661 1676 4.696402 AGACACCGTTCAAAACAGTACAAA 59.304 37.500 0.00 0.00 0.00 2.83
1662 1677 5.181622 AGACACCGTTCAAAACAGTACAAAA 59.818 36.000 0.00 0.00 0.00 2.44
1663 1678 5.155643 ACACCGTTCAAAACAGTACAAAAC 58.844 37.500 0.00 0.00 0.00 2.43
1664 1679 5.154932 CACCGTTCAAAACAGTACAAAACA 58.845 37.500 0.00 0.00 0.00 2.83
1665 1680 5.629849 CACCGTTCAAAACAGTACAAAACAA 59.370 36.000 0.00 0.00 0.00 2.83
1666 1681 5.859648 ACCGTTCAAAACAGTACAAAACAAG 59.140 36.000 0.00 0.00 0.00 3.16
1667 1682 5.220135 CCGTTCAAAACAGTACAAAACAAGC 60.220 40.000 0.00 0.00 0.00 4.01
1668 1683 5.571357 CGTTCAAAACAGTACAAAACAAGCT 59.429 36.000 0.00 0.00 0.00 3.74
1669 1684 6.452350 CGTTCAAAACAGTACAAAACAAGCTG 60.452 38.462 0.00 0.00 0.00 4.24
1670 1685 6.019779 TCAAAACAGTACAAAACAAGCTGT 57.980 33.333 0.00 0.00 41.51 4.40
1671 1686 6.090129 TCAAAACAGTACAAAACAAGCTGTC 58.910 36.000 0.00 0.00 39.19 3.51
1672 1687 5.897377 AAACAGTACAAAACAAGCTGTCT 57.103 34.783 0.00 0.00 39.19 3.41
1673 1688 4.882671 ACAGTACAAAACAAGCTGTCTG 57.117 40.909 0.00 0.00 35.78 3.51
1674 1689 4.513442 ACAGTACAAAACAAGCTGTCTGA 58.487 39.130 0.00 0.00 35.78 3.27
1675 1690 4.941263 ACAGTACAAAACAAGCTGTCTGAA 59.059 37.500 0.00 0.00 35.78 3.02
1676 1691 5.414454 ACAGTACAAAACAAGCTGTCTGAAA 59.586 36.000 0.00 0.00 35.78 2.69
1677 1692 5.739161 CAGTACAAAACAAGCTGTCTGAAAC 59.261 40.000 0.00 0.00 0.00 2.78
1678 1693 3.758300 ACAAAACAAGCTGTCTGAAACG 58.242 40.909 0.00 0.00 0.00 3.60
1679 1694 3.190535 ACAAAACAAGCTGTCTGAAACGT 59.809 39.130 0.00 0.00 0.00 3.99
1680 1695 3.675467 AAACAAGCTGTCTGAAACGTC 57.325 42.857 0.00 0.00 0.00 4.34
1681 1696 2.604046 ACAAGCTGTCTGAAACGTCT 57.396 45.000 0.00 0.00 0.00 4.18
1682 1697 2.906354 ACAAGCTGTCTGAAACGTCTT 58.094 42.857 0.00 0.00 0.00 3.01
1683 1698 4.054780 ACAAGCTGTCTGAAACGTCTTA 57.945 40.909 0.00 0.00 0.00 2.10
1684 1699 4.632153 ACAAGCTGTCTGAAACGTCTTAT 58.368 39.130 0.00 0.00 0.00 1.73
1685 1700 5.779922 ACAAGCTGTCTGAAACGTCTTATA 58.220 37.500 0.00 0.00 0.00 0.98
1686 1701 6.220930 ACAAGCTGTCTGAAACGTCTTATAA 58.779 36.000 0.00 0.00 0.00 0.98
1687 1702 6.704493 ACAAGCTGTCTGAAACGTCTTATAAA 59.296 34.615 0.00 0.00 0.00 1.40
1688 1703 7.225931 ACAAGCTGTCTGAAACGTCTTATAAAA 59.774 33.333 0.00 0.00 0.00 1.52
1689 1704 7.724305 AGCTGTCTGAAACGTCTTATAAAAA 57.276 32.000 0.00 0.00 0.00 1.94
1690 1705 7.573627 AGCTGTCTGAAACGTCTTATAAAAAC 58.426 34.615 0.00 0.00 0.00 2.43
1691 1706 7.225931 AGCTGTCTGAAACGTCTTATAAAAACA 59.774 33.333 0.00 0.00 0.00 2.83
1692 1707 7.853929 GCTGTCTGAAACGTCTTATAAAAACAA 59.146 33.333 0.00 0.00 0.00 2.83
1693 1708 9.710979 CTGTCTGAAACGTCTTATAAAAACAAA 57.289 29.630 0.00 0.00 0.00 2.83
1694 1709 9.493206 TGTCTGAAACGTCTTATAAAAACAAAC 57.507 29.630 0.00 0.00 0.00 2.93
1695 1710 8.667204 GTCTGAAACGTCTTATAAAAACAAACG 58.333 33.333 0.00 0.00 35.00 3.60
1696 1711 7.851963 TCTGAAACGTCTTATAAAAACAAACGG 59.148 33.333 0.00 0.00 33.26 4.44
1697 1712 7.692088 TGAAACGTCTTATAAAAACAAACGGA 58.308 30.769 0.00 0.00 33.26 4.69
1698 1713 7.639461 TGAAACGTCTTATAAAAACAAACGGAC 59.361 33.333 0.00 0.00 33.26 4.79
1699 1714 5.669122 ACGTCTTATAAAAACAAACGGACG 58.331 37.500 13.36 13.36 45.86 4.79
1700 1715 5.074791 CGTCTTATAAAAACAAACGGACGG 58.925 41.667 9.14 0.00 39.80 4.79
1701 1716 5.107530 CGTCTTATAAAAACAAACGGACGGA 60.108 40.000 9.14 0.00 39.80 4.69
1702 1717 6.301861 GTCTTATAAAAACAAACGGACGGAG 58.698 40.000 0.00 0.00 0.00 4.63
1749 1764 6.888632 AGTGCATACTTTCCAATTTCAGAGAT 59.111 34.615 0.00 0.00 31.66 2.75
1791 1806 8.929260 TGGTTATCTTATGAATGAATGCTCAT 57.071 30.769 0.00 0.00 44.54 2.90
1833 1848 6.127479 ACAAAAACTGCAATTCCTTCACTACA 60.127 34.615 0.00 0.00 0.00 2.74
1878 1893 7.394923 TCTTTGGAACTCAGGTTTCTAAAAACA 59.605 33.333 3.71 0.00 45.44 2.83
1917 1933 4.224818 TGTATGGTTGAGATGTCATGACCA 59.775 41.667 22.85 16.38 44.29 4.02
1918 1934 3.786368 TGGTTGAGATGTCATGACCAA 57.214 42.857 22.85 15.83 39.61 3.67
1979 1995 9.713740 CTTTGACTCATTTGATGCTAGTAATTC 57.286 33.333 0.00 0.00 0.00 2.17
1981 1997 7.337938 TGACTCATTTGATGCTAGTAATTCCA 58.662 34.615 0.00 0.00 0.00 3.53
1982 1998 7.994911 TGACTCATTTGATGCTAGTAATTCCAT 59.005 33.333 0.00 0.00 0.00 3.41
1983 1999 9.494271 GACTCATTTGATGCTAGTAATTCCATA 57.506 33.333 0.00 0.00 0.00 2.74
1984 2000 9.499479 ACTCATTTGATGCTAGTAATTCCATAG 57.501 33.333 0.00 0.00 0.00 2.23
2007 2026 6.054295 AGGAATATGAAGTGACAGAAGATGC 58.946 40.000 0.00 0.00 0.00 3.91
2045 2064 9.533831 AAATACAAATTTCCATGAGGTCTAACT 57.466 29.630 0.00 0.00 35.89 2.24
2090 2109 8.267894 TGGTTTATCCTCTTCTTAGAAATCCTG 58.732 37.037 0.00 0.00 37.07 3.86
2111 2130 6.039270 TCCTGTGAAATTGTGGTGTAAGAAAG 59.961 38.462 0.00 0.00 0.00 2.62
2135 2154 6.264744 AGCAATCCATAGAAATTGATGGTCTG 59.735 38.462 11.92 11.17 42.82 3.51
2137 2156 5.715439 TCCATAGAAATTGATGGTCTGGT 57.285 39.130 11.92 0.00 42.82 4.00
2146 2165 8.360390 AGAAATTGATGGTCTGGTTTCTTTTAC 58.640 33.333 0.00 0.00 33.50 2.01
2151 2170 4.611367 TGGTCTGGTTTCTTTTACCCAAA 58.389 39.130 0.00 0.00 34.66 3.28
2153 2172 5.303333 TGGTCTGGTTTCTTTTACCCAAATC 59.697 40.000 0.00 0.00 34.66 2.17
2172 2191 7.719193 CCCAAATCACCCTAAAAACAAATTTCT 59.281 33.333 0.00 0.00 0.00 2.52
2173 2192 8.558700 CCAAATCACCCTAAAAACAAATTTCTG 58.441 33.333 0.00 0.00 0.00 3.02
2176 2195 6.811954 TCACCCTAAAAACAAATTTCTGACC 58.188 36.000 0.00 0.00 0.00 4.02
2178 2197 7.044798 CACCCTAAAAACAAATTTCTGACCAA 58.955 34.615 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 7.173047 GGCAAATAAATGGTGTGTGAGAAATTT 59.827 33.333 0.00 0.00 0.00 1.82
228 231 4.072839 CTCCCATTCACATCAGATCATGG 58.927 47.826 0.00 0.00 0.00 3.66
229 232 4.969484 TCTCCCATTCACATCAGATCATG 58.031 43.478 0.00 0.00 0.00 3.07
292 295 4.222588 TGCAAGAATCATTTTTGTAGGGGG 59.777 41.667 2.81 0.00 0.00 5.40
293 296 5.404466 TGCAAGAATCATTTTTGTAGGGG 57.596 39.130 2.81 0.00 0.00 4.79
294 297 6.698766 GCTATGCAAGAATCATTTTTGTAGGG 59.301 38.462 2.81 0.00 0.00 3.53
295 298 7.259882 TGCTATGCAAGAATCATTTTTGTAGG 58.740 34.615 2.81 0.00 34.76 3.18
296 299 7.043590 GCTGCTATGCAAGAATCATTTTTGTAG 60.044 37.037 2.81 0.00 38.41 2.74
322 325 4.570369 TGTACCAATGATTCGTGTATGCAG 59.430 41.667 0.00 0.00 0.00 4.41
341 344 5.585500 TTTGCGTGTCTTGATTACTGTAC 57.415 39.130 0.00 0.00 0.00 2.90
342 345 5.524281 TGTTTTGCGTGTCTTGATTACTGTA 59.476 36.000 0.00 0.00 0.00 2.74
343 346 4.334203 TGTTTTGCGTGTCTTGATTACTGT 59.666 37.500 0.00 0.00 0.00 3.55
344 347 4.670621 GTGTTTTGCGTGTCTTGATTACTG 59.329 41.667 0.00 0.00 0.00 2.74
345 348 4.334203 TGTGTTTTGCGTGTCTTGATTACT 59.666 37.500 0.00 0.00 0.00 2.24
932 941 4.335647 CCCACCGAGCAGCAACCT 62.336 66.667 0.00 0.00 0.00 3.50
986 995 1.227102 GGCATACCACCATCAGCCA 59.773 57.895 0.00 0.00 41.63 4.75
992 1001 1.858739 AACCACCGGCATACCACCAT 61.859 55.000 0.00 0.00 34.57 3.55
1053 1065 1.475169 TATCATCCTCAGCCGCCCAG 61.475 60.000 0.00 0.00 0.00 4.45
1107 1119 1.146544 TCAAAGGGGAAGGGGAAGGG 61.147 60.000 0.00 0.00 0.00 3.95
1262 1274 1.813753 CATCATCGACGGGCCGTTT 60.814 57.895 34.58 18.29 41.37 3.60
1344 1356 9.871238 CTTACTTGCTAGTATAACTTCCAAGAA 57.129 33.333 8.86 11.20 37.32 2.52
1383 1397 4.082571 ACATGAGCTTGCTAAACCAATCAC 60.083 41.667 0.00 0.00 0.00 3.06
1392 1406 4.277515 ACTCTTCACATGAGCTTGCTAA 57.722 40.909 0.00 0.00 35.12 3.09
1394 1408 2.855209 ACTCTTCACATGAGCTTGCT 57.145 45.000 0.00 0.00 35.12 3.91
1408 1422 5.238214 GCATCTCAGTCACAAAGAAACTCTT 59.762 40.000 0.00 0.00 38.59 2.85
1454 1468 7.307396 GCGTAGAACATATGAATGTACTGCATT 60.307 37.037 10.38 0.00 45.79 3.56
1455 1469 6.146184 GCGTAGAACATATGAATGTACTGCAT 59.854 38.462 10.38 0.00 45.79 3.96
1465 1479 5.079689 TCAAGGTGCGTAGAACATATGAA 57.920 39.130 10.38 0.00 0.00 2.57
1469 1483 3.857052 CCTTCAAGGTGCGTAGAACATA 58.143 45.455 0.00 0.00 0.00 2.29
1586 1601 9.852091 CGAACAGAGGTAGTAACTATTTACTTT 57.148 33.333 10.40 0.00 44.77 2.66
1603 1618 6.701432 ACGTCTTATAAAAACGAACAGAGG 57.299 37.500 20.71 5.58 39.59 3.69
1604 1619 8.982925 AAAACGTCTTATAAAAACGAACAGAG 57.017 30.769 20.71 0.00 39.59 3.35
1607 1622 9.848172 GTCTAAAACGTCTTATAAAAACGAACA 57.152 29.630 20.71 7.27 39.59 3.18
1608 1623 9.019867 CGTCTAAAACGTCTTATAAAAACGAAC 57.980 33.333 20.71 10.74 46.42 3.95
1625 1640 5.231991 TGAACGGTGTCTTAACGTCTAAAAC 59.768 40.000 0.00 0.00 40.31 2.43
1626 1641 5.347342 TGAACGGTGTCTTAACGTCTAAAA 58.653 37.500 0.00 0.00 40.31 1.52
1627 1642 4.930963 TGAACGGTGTCTTAACGTCTAAA 58.069 39.130 0.00 0.00 40.31 1.85
1628 1643 4.566545 TGAACGGTGTCTTAACGTCTAA 57.433 40.909 0.00 0.00 40.31 2.10
1629 1644 4.566545 TTGAACGGTGTCTTAACGTCTA 57.433 40.909 0.00 0.00 40.31 2.59
1630 1645 3.441496 TTGAACGGTGTCTTAACGTCT 57.559 42.857 0.00 0.00 40.31 4.18
1631 1646 4.201705 TGTTTTGAACGGTGTCTTAACGTC 60.202 41.667 0.00 0.00 40.31 4.34
1632 1647 3.683822 TGTTTTGAACGGTGTCTTAACGT 59.316 39.130 0.00 0.00 43.43 3.99
1633 1648 4.261736 TGTTTTGAACGGTGTCTTAACG 57.738 40.909 0.00 0.00 0.00 3.18
1643 1658 5.220135 GCTTGTTTTGTACTGTTTTGAACGG 60.220 40.000 0.00 0.00 43.50 4.44
1644 1659 5.571357 AGCTTGTTTTGTACTGTTTTGAACG 59.429 36.000 0.00 0.00 0.00 3.95
1645 1660 6.364976 ACAGCTTGTTTTGTACTGTTTTGAAC 59.635 34.615 0.00 0.00 38.38 3.18
1646 1661 6.451393 ACAGCTTGTTTTGTACTGTTTTGAA 58.549 32.000 0.00 0.00 38.38 2.69
1647 1662 6.019779 ACAGCTTGTTTTGTACTGTTTTGA 57.980 33.333 0.00 0.00 38.38 2.69
1648 1663 6.033831 CAGACAGCTTGTTTTGTACTGTTTTG 59.966 38.462 0.00 0.00 41.45 2.44
1649 1664 6.072175 TCAGACAGCTTGTTTTGTACTGTTTT 60.072 34.615 0.00 0.00 41.45 2.43
1650 1665 5.414454 TCAGACAGCTTGTTTTGTACTGTTT 59.586 36.000 0.00 0.00 41.45 2.83
1651 1666 4.941263 TCAGACAGCTTGTTTTGTACTGTT 59.059 37.500 0.00 0.00 41.45 3.16
1652 1667 4.513442 TCAGACAGCTTGTTTTGTACTGT 58.487 39.130 0.00 0.00 43.93 3.55
1653 1668 5.484173 TTCAGACAGCTTGTTTTGTACTG 57.516 39.130 0.00 0.00 0.00 2.74
1654 1669 5.447279 CGTTTCAGACAGCTTGTTTTGTACT 60.447 40.000 0.00 0.00 0.00 2.73
1655 1670 4.728608 CGTTTCAGACAGCTTGTTTTGTAC 59.271 41.667 0.00 0.00 0.00 2.90
1656 1671 4.393680 ACGTTTCAGACAGCTTGTTTTGTA 59.606 37.500 0.00 0.00 0.00 2.41
1657 1672 3.190535 ACGTTTCAGACAGCTTGTTTTGT 59.809 39.130 0.00 0.00 0.00 2.83
1658 1673 3.758300 ACGTTTCAGACAGCTTGTTTTG 58.242 40.909 0.00 0.00 0.00 2.44
1659 1674 3.689649 AGACGTTTCAGACAGCTTGTTTT 59.310 39.130 0.00 0.00 0.00 2.43
1660 1675 3.270877 AGACGTTTCAGACAGCTTGTTT 58.729 40.909 0.00 0.00 0.00 2.83
1661 1676 2.906354 AGACGTTTCAGACAGCTTGTT 58.094 42.857 0.00 0.00 0.00 2.83
1662 1677 2.604046 AGACGTTTCAGACAGCTTGT 57.396 45.000 0.00 0.00 0.00 3.16
1663 1678 6.706055 TTATAAGACGTTTCAGACAGCTTG 57.294 37.500 0.00 0.00 0.00 4.01
1664 1679 7.724305 TTTTATAAGACGTTTCAGACAGCTT 57.276 32.000 0.00 0.00 0.00 3.74
1665 1680 7.225931 TGTTTTTATAAGACGTTTCAGACAGCT 59.774 33.333 0.00 0.00 0.00 4.24
1666 1681 7.349711 TGTTTTTATAAGACGTTTCAGACAGC 58.650 34.615 0.00 0.00 0.00 4.40
1667 1682 9.710979 TTTGTTTTTATAAGACGTTTCAGACAG 57.289 29.630 0.00 0.00 0.00 3.51
1668 1683 9.493206 GTTTGTTTTTATAAGACGTTTCAGACA 57.507 29.630 0.00 0.00 0.00 3.41
1669 1684 8.667204 CGTTTGTTTTTATAAGACGTTTCAGAC 58.333 33.333 0.00 0.00 0.00 3.51
1670 1685 7.851963 CCGTTTGTTTTTATAAGACGTTTCAGA 59.148 33.333 0.00 0.00 0.00 3.27
1671 1686 7.851963 TCCGTTTGTTTTTATAAGACGTTTCAG 59.148 33.333 0.00 0.00 0.00 3.02
1672 1687 7.639461 GTCCGTTTGTTTTTATAAGACGTTTCA 59.361 33.333 0.00 0.00 0.00 2.69
1673 1688 7.149462 CGTCCGTTTGTTTTTATAAGACGTTTC 60.149 37.037 8.92 0.00 39.62 2.78
1674 1689 6.628461 CGTCCGTTTGTTTTTATAAGACGTTT 59.372 34.615 8.92 0.00 39.62 3.60
1675 1690 6.128729 CGTCCGTTTGTTTTTATAAGACGTT 58.871 36.000 8.92 0.00 39.62 3.99
1676 1691 5.333263 CCGTCCGTTTGTTTTTATAAGACGT 60.333 40.000 13.55 0.00 42.08 4.34
1677 1692 5.074791 CCGTCCGTTTGTTTTTATAAGACG 58.925 41.667 9.76 9.76 42.98 4.18
1678 1693 6.073602 ACTCCGTCCGTTTGTTTTTATAAGAC 60.074 38.462 0.00 0.00 0.00 3.01
1679 1694 5.990996 ACTCCGTCCGTTTGTTTTTATAAGA 59.009 36.000 0.00 0.00 0.00 2.10
1680 1695 6.232139 ACTCCGTCCGTTTGTTTTTATAAG 57.768 37.500 0.00 0.00 0.00 1.73
1681 1696 6.928492 AGTACTCCGTCCGTTTGTTTTTATAA 59.072 34.615 0.00 0.00 0.00 0.98
1682 1697 6.454795 AGTACTCCGTCCGTTTGTTTTTATA 58.545 36.000 0.00 0.00 0.00 0.98
1683 1698 5.299949 AGTACTCCGTCCGTTTGTTTTTAT 58.700 37.500 0.00 0.00 0.00 1.40
1684 1699 4.692228 AGTACTCCGTCCGTTTGTTTTTA 58.308 39.130 0.00 0.00 0.00 1.52
1685 1700 3.534554 AGTACTCCGTCCGTTTGTTTTT 58.465 40.909 0.00 0.00 0.00 1.94
1686 1701 3.183793 AGTACTCCGTCCGTTTGTTTT 57.816 42.857 0.00 0.00 0.00 2.43
1687 1702 2.896745 AGTACTCCGTCCGTTTGTTT 57.103 45.000 0.00 0.00 0.00 2.83
1688 1703 4.022068 TCATTAGTACTCCGTCCGTTTGTT 60.022 41.667 0.00 0.00 0.00 2.83
1689 1704 3.507233 TCATTAGTACTCCGTCCGTTTGT 59.493 43.478 0.00 0.00 0.00 2.83
1690 1705 4.100707 TCATTAGTACTCCGTCCGTTTG 57.899 45.455 0.00 0.00 0.00 2.93
1691 1706 4.741342 CTTCATTAGTACTCCGTCCGTTT 58.259 43.478 0.00 0.00 0.00 3.60
1692 1707 3.428589 GCTTCATTAGTACTCCGTCCGTT 60.429 47.826 0.00 0.00 0.00 4.44
1693 1708 2.098770 GCTTCATTAGTACTCCGTCCGT 59.901 50.000 0.00 0.00 0.00 4.69
1694 1709 2.543238 GGCTTCATTAGTACTCCGTCCG 60.543 54.545 0.00 0.00 0.00 4.79
1695 1710 2.694109 AGGCTTCATTAGTACTCCGTCC 59.306 50.000 0.00 0.00 0.00 4.79
1696 1711 3.380637 TGAGGCTTCATTAGTACTCCGTC 59.619 47.826 0.00 0.00 32.45 4.79
1697 1712 3.362706 TGAGGCTTCATTAGTACTCCGT 58.637 45.455 0.00 0.00 32.45 4.69
1698 1713 4.386867 TTGAGGCTTCATTAGTACTCCG 57.613 45.455 0.00 0.00 32.45 4.63
1699 1714 6.823689 TGATTTTGAGGCTTCATTAGTACTCC 59.176 38.462 0.00 0.00 32.45 3.85
1700 1715 7.550906 ACTGATTTTGAGGCTTCATTAGTACTC 59.449 37.037 0.00 0.00 32.27 2.59
1701 1716 7.335422 CACTGATTTTGAGGCTTCATTAGTACT 59.665 37.037 0.00 0.00 32.27 2.73
1702 1717 7.467623 CACTGATTTTGAGGCTTCATTAGTAC 58.532 38.462 0.00 0.00 32.27 2.73
1703 1718 6.094048 GCACTGATTTTGAGGCTTCATTAGTA 59.906 38.462 0.00 0.00 32.27 1.82
1704 1719 5.105997 GCACTGATTTTGAGGCTTCATTAGT 60.106 40.000 0.00 0.00 32.27 2.24
1705 1720 5.106038 TGCACTGATTTTGAGGCTTCATTAG 60.106 40.000 0.00 0.00 32.27 1.73
1706 1721 4.766373 TGCACTGATTTTGAGGCTTCATTA 59.234 37.500 0.00 0.00 32.27 1.90
1707 1722 3.575256 TGCACTGATTTTGAGGCTTCATT 59.425 39.130 0.00 0.00 32.27 2.57
1749 1764 2.378038 ACCAAGAACAAAAGCTCAGCA 58.622 42.857 0.00 0.00 0.00 4.41
1791 1806 8.410141 CAGTTTTTGTGTCCCAAAGAACTATTA 58.590 33.333 11.39 0.00 43.63 0.98
1833 1848 7.951806 TCCAAAGATGCCCTTATTATTGATCAT 59.048 33.333 0.00 0.00 34.00 2.45
1888 1903 9.460019 TCATGACATCTCAACCATACATTTTTA 57.540 29.630 0.00 0.00 0.00 1.52
1917 1933 2.325484 GGTTTCCCATGGACCAAAGTT 58.675 47.619 15.22 0.00 33.61 2.66
1918 1934 1.219213 TGGTTTCCCATGGACCAAAGT 59.781 47.619 18.98 0.00 40.31 2.66
1952 1968 8.798859 ATTACTAGCATCAAATGAGTCAAAGT 57.201 30.769 0.00 0.00 0.00 2.66
1953 1969 9.713740 GAATTACTAGCATCAAATGAGTCAAAG 57.286 33.333 0.00 0.00 0.00 2.77
1954 1970 8.677300 GGAATTACTAGCATCAAATGAGTCAAA 58.323 33.333 0.00 0.00 0.00 2.69
1979 1995 7.730084 TCTTCTGTCACTTCATATTCCTATGG 58.270 38.462 0.00 0.00 36.23 2.74
1981 1997 7.877097 GCATCTTCTGTCACTTCATATTCCTAT 59.123 37.037 0.00 0.00 0.00 2.57
1982 1998 7.212976 GCATCTTCTGTCACTTCATATTCCTA 58.787 38.462 0.00 0.00 0.00 2.94
1983 1999 6.054295 GCATCTTCTGTCACTTCATATTCCT 58.946 40.000 0.00 0.00 0.00 3.36
1984 2000 5.238214 GGCATCTTCTGTCACTTCATATTCC 59.762 44.000 0.00 0.00 0.00 3.01
2007 2026 2.214376 TTGTATTTGTGCCTCCCAGG 57.786 50.000 0.00 0.00 38.80 4.45
2064 2083 8.267894 CAGGATTTCTAAGAAGAGGATAAACCA 58.732 37.037 0.00 0.00 42.04 3.67
2071 2090 6.935240 TTCACAGGATTTCTAAGAAGAGGA 57.065 37.500 0.00 0.00 31.96 3.71
2090 2109 5.587289 TGCTTTCTTACACCACAATTTCAC 58.413 37.500 0.00 0.00 0.00 3.18
2111 2130 6.444633 CAGACCATCAATTTCTATGGATTGC 58.555 40.000 15.07 5.00 44.62 3.56
2135 2154 4.591498 AGGGTGATTTGGGTAAAAGAAACC 59.409 41.667 0.00 0.00 36.19 3.27
2137 2156 7.916077 TTTAGGGTGATTTGGGTAAAAGAAA 57.084 32.000 0.00 0.00 0.00 2.52
2146 2165 7.719193 AGAAATTTGTTTTTAGGGTGATTTGGG 59.281 33.333 0.00 0.00 0.00 4.12
2151 2170 7.070571 TGGTCAGAAATTTGTTTTTAGGGTGAT 59.929 33.333 0.00 0.00 0.00 3.06
2153 2172 6.578023 TGGTCAGAAATTTGTTTTTAGGGTG 58.422 36.000 0.00 0.00 0.00 4.61
2172 2191 4.933505 TTTGCATGATTTCTGTTGGTCA 57.066 36.364 0.00 0.00 0.00 4.02
2173 2192 6.790285 ATTTTTGCATGATTTCTGTTGGTC 57.210 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.