Multiple sequence alignment - TraesCS6D01G030500

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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 TraesCS6D01G030500 chr6D 100.000 2324 0 0 1 2324 11920624 11922947 0.000000e+00 4292.0
1 TraesCS6D01G030500 chr6A 90.896 2054 136 16 283 2324 13433734 13435748 0.000000e+00 2710.0
2 TraesCS6D01G030500 chr6A 78.102 274 44 14 468 734 483544889 483544625 2.390000e-35 159.0
3 TraesCS6D01G030500 chr6B 86.514 1394 134 32 3 1360 21872026 21873401 0.000000e+00 1483.0
4 TraesCS6D01G030500 chr2A 92.035 339 21 5 993 1325 436721337 436720999 2.700000e-129 472.0
5 TraesCS6D01G030500 chr2A 79.562 137 14 7 2129 2253 611726564 611726430 4.110000e-13 86.1
6 TraesCS6D01G030500 chr2D 91.445 339 23 5 993 1325 329861275 329860937 5.850000e-126 460.0
7 TraesCS6D01G030500 chr2B 91.150 339 24 4 993 1325 398395085 398394747 2.720000e-124 455.0
8 TraesCS6D01G030500 chr5A 86.029 136 9 4 2120 2255 646357759 646357884 1.120000e-28 137.0
9 TraesCS6D01G030500 chr5A 97.059 34 1 0 425 458 433935977 433936010 8.970000e-05 58.4
10 TraesCS6D01G030500 chr7B 87.097 93 9 3 2122 2213 88244905 88244815 4.090000e-18 102.0
11 TraesCS6D01G030500 chr7B 85.185 81 11 1 2205 2285 710050411 710050490 5.320000e-12 82.4
12 TraesCS6D01G030500 chr7D 86.000 100 6 8 2122 2218 126664578 126664672 1.470000e-17 100.0
13 TraesCS6D01G030500 chr7A 85.714 98 10 4 2122 2218 127594228 127594322 1.470000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G030500 chr6D 11920624 11922947 2323 False 4292 4292 100.000 1 2324 1 chr6D.!!$F1 2323
1 TraesCS6D01G030500 chr6A 13433734 13435748 2014 False 2710 2710 90.896 283 2324 1 chr6A.!!$F1 2041
2 TraesCS6D01G030500 chr6B 21872026 21873401 1375 False 1483 1483 86.514 3 1360 1 chr6B.!!$F1 1357

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
591 592 0.028505 CGGATGCCAGCGAAGATTTG 59.971 55.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2010 0.037697 TTTCATGACCGTCCGACCTG 60.038 55.0 0.0 0.0 0.0 4.0 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
20 21 1.648116 AGGCCCAATTGCACTTCAAT 58.352 45.000 0.00 0.00 46.82 2.57
24 25 2.288948 GCCCAATTGCACTTCAATGTCA 60.289 45.455 0.00 0.00 44.23 3.58
27 28 4.322123 CCCAATTGCACTTCAATGTCATCA 60.322 41.667 0.00 0.00 44.23 3.07
29 30 5.518847 CCAATTGCACTTCAATGTCATCATC 59.481 40.000 0.00 0.00 44.23 2.92
34 35 2.204237 CTTCAATGTCATCATCGCGGA 58.796 47.619 6.13 0.00 32.56 5.54
39 40 2.106938 TCATCATCGCGGAGGTGC 59.893 61.111 6.13 0.00 0.00 5.01
41 42 2.107750 ATCATCGCGGAGGTGCAG 59.892 61.111 6.13 0.00 34.15 4.41
53 54 3.127533 GTGCAGCCGGTGTCCATC 61.128 66.667 1.90 0.00 0.00 3.51
54 55 4.408821 TGCAGCCGGTGTCCATCC 62.409 66.667 1.90 0.00 0.00 3.51
61 62 3.717294 GGTGTCCATCCGGCTGGT 61.717 66.667 23.26 0.00 37.57 4.00
74 75 2.031012 CTGGTGCAGGACGAGCAA 59.969 61.111 0.00 0.00 44.64 3.91
101 102 2.188161 CCTCGCCTCCTCGTACCTC 61.188 68.421 0.00 0.00 0.00 3.85
103 104 0.820074 CTCGCCTCCTCGTACCTCAT 60.820 60.000 0.00 0.00 0.00 2.90
104 105 0.818445 TCGCCTCCTCGTACCTCATC 60.818 60.000 0.00 0.00 0.00 2.92
111 112 1.681793 CCTCGTACCTCATCGGTTGAT 59.318 52.381 0.00 0.00 46.37 2.57
130 131 2.113860 TGGAGTGCCAAATCTACAGC 57.886 50.000 0.00 0.00 42.49 4.40
134 135 1.276421 AGTGCCAAATCTACAGCGAGT 59.724 47.619 0.00 0.00 0.00 4.18
172 173 4.520846 GCGTTCATGGCCGCGAAG 62.521 66.667 8.23 0.00 40.56 3.79
183 184 1.666872 CCGCGAAGGAACCGAACTT 60.667 57.895 8.23 0.00 45.00 2.66
184 185 1.623973 CCGCGAAGGAACCGAACTTC 61.624 60.000 8.23 0.00 45.00 3.01
188 189 1.058404 GAAGGAACCGAACTTCGTCG 58.942 55.000 10.22 0.00 38.40 5.12
194 195 0.888285 ACCGAACTTCGTCGAGGAGT 60.888 55.000 11.75 2.34 43.86 3.85
198 199 1.467734 GAACTTCGTCGAGGAGTAGCA 59.532 52.381 11.75 0.00 0.00 3.49
215 216 2.037367 AGGTGCTCTACGAGGCCA 59.963 61.111 5.01 0.00 0.00 5.36
219 220 2.202623 GCTCTACGAGGCCACGTG 60.203 66.667 34.20 23.77 46.02 4.49
220 221 2.697761 GCTCTACGAGGCCACGTGA 61.698 63.158 34.20 26.06 46.02 4.35
295 296 1.078848 GGTGCCACAGAAGATCGCT 60.079 57.895 0.00 0.00 0.00 4.93
298 299 0.321346 TGCCACAGAAGATCGCTGAA 59.679 50.000 20.74 5.34 36.86 3.02
299 300 1.005340 GCCACAGAAGATCGCTGAAG 58.995 55.000 20.74 13.56 36.86 3.02
302 303 1.066573 CACAGAAGATCGCTGAAGGGT 60.067 52.381 20.74 0.71 36.86 4.34
305 306 2.166459 CAGAAGATCGCTGAAGGGTACA 59.834 50.000 11.75 0.00 35.39 2.90
310 311 0.968901 TCGCTGAAGGGTACATCGGT 60.969 55.000 0.00 0.00 0.00 4.69
329 330 1.358725 TAGCTCCATGTCGTTTGCGC 61.359 55.000 0.00 0.00 38.14 6.09
416 417 2.593436 CCCCAACTGGCGACGTTT 60.593 61.111 0.00 0.00 0.00 3.60
418 419 1.296056 CCCCAACTGGCGACGTTTAG 61.296 60.000 0.00 0.00 0.00 1.85
437 438 3.812019 CCGTGGACTCCGACGAGG 61.812 72.222 16.87 0.00 40.77 4.63
462 463 3.706594 GAGTTGGACATGGGAGACAGATA 59.293 47.826 0.00 0.00 0.00 1.98
471 472 0.029567 GGAGACAGATACGCCTCGTG 59.970 60.000 1.77 0.00 41.39 4.35
497 498 3.826236 TGTCTTACTCTTTCTCGTCGG 57.174 47.619 0.00 0.00 0.00 4.79
503 504 2.506438 CTTTCTCGTCGGCGACCC 60.506 66.667 31.86 11.00 42.81 4.46
518 519 0.036388 GACCCGCATCTTCACTTCCA 60.036 55.000 0.00 0.00 0.00 3.53
521 522 1.134280 CCCGCATCTTCACTTCCAGAT 60.134 52.381 0.00 0.00 0.00 2.90
532 533 3.664025 TTCCAGATGCTCACGGCCG 62.664 63.158 26.86 26.86 40.92 6.13
538 539 4.830765 TGCTCACGGCCGGCATAC 62.831 66.667 31.76 15.09 40.92 2.39
551 552 1.439353 GGCATACGCAGGACATGTGG 61.439 60.000 1.15 0.00 44.07 4.17
554 555 1.665679 CATACGCAGGACATGTGGAAC 59.334 52.381 1.15 0.00 44.07 3.62
572 573 4.202326 TGGAACACTAAGGACTTGGAAGAC 60.202 45.833 2.29 0.00 0.00 3.01
576 577 3.195825 CACTAAGGACTTGGAAGACGGAT 59.804 47.826 2.29 0.00 0.00 4.18
580 581 0.036388 GACTTGGAAGACGGATGCCA 60.036 55.000 0.00 0.00 0.00 4.92
591 592 0.028505 CGGATGCCAGCGAAGATTTG 59.971 55.000 0.00 0.00 0.00 2.32
605 606 4.689345 CGAAGATTTGGACTCGGTTAACTT 59.311 41.667 5.42 0.00 0.00 2.66
607 608 5.223449 AGATTTGGACTCGGTTAACTTCA 57.777 39.130 5.42 0.00 0.00 3.02
608 609 5.805728 AGATTTGGACTCGGTTAACTTCAT 58.194 37.500 5.42 0.00 0.00 2.57
623 624 9.959749 GGTTAACTTCATGACACTTTTGATTAA 57.040 29.630 5.42 0.00 0.00 1.40
671 672 7.176865 TGAATGTATTCCGGTTTACATGGAAAA 59.823 33.333 23.44 0.00 44.39 2.29
699 700 4.304110 CAGCTTGCAAACAAATCATCTGT 58.696 39.130 0.00 0.00 34.74 3.41
717 720 7.406553 TCATCTGTTTTTGTTCAAACTACGAG 58.593 34.615 0.00 0.00 37.51 4.18
720 723 6.369340 TCTGTTTTTGTTCAAACTACGAGTGA 59.631 34.615 0.00 0.00 37.51 3.41
721 724 6.900189 TGTTTTTGTTCAAACTACGAGTGAA 58.100 32.000 0.00 0.00 37.51 3.18
734 737 2.069273 CGAGTGAAATGTGTCCAGACC 58.931 52.381 0.00 0.00 0.00 3.85
743 746 0.892755 GTGTCCAGACCGATGGTGTA 59.107 55.000 0.00 0.00 41.43 2.90
744 747 1.480954 GTGTCCAGACCGATGGTGTAT 59.519 52.381 0.00 0.00 41.43 2.29
745 748 2.691526 GTGTCCAGACCGATGGTGTATA 59.308 50.000 0.00 0.00 41.43 1.47
746 749 2.691526 TGTCCAGACCGATGGTGTATAC 59.308 50.000 0.00 0.00 41.43 1.47
751 754 6.602406 GTCCAGACCGATGGTGTATACTATAT 59.398 42.308 4.17 0.00 41.43 0.86
761 764 9.770097 GATGGTGTATACTATATGATTGGATGG 57.230 37.037 4.17 0.00 0.00 3.51
764 767 7.365563 GGTGTATACTATATGATTGGATGGCCA 60.366 40.741 8.56 8.56 44.17 5.36
803 806 3.379057 TCCGCAGACGAATAATGTGTCTA 59.621 43.478 0.00 0.00 40.83 2.59
873 876 0.100682 CCGACCGACGTCATCTCATT 59.899 55.000 17.16 0.00 39.11 2.57
910 915 4.605183 TCTATATAAGCTCTGCCCCTCTC 58.395 47.826 0.00 0.00 0.00 3.20
938 950 1.131126 CTTTGCACCATCGATCACCAC 59.869 52.381 0.00 0.00 0.00 4.16
948 960 2.202932 ATCACCACTGCCGATCGC 60.203 61.111 10.32 6.08 38.31 4.58
950 962 2.913054 ATCACCACTGCCGATCGCTG 62.913 60.000 10.32 11.63 41.91 5.18
984 1027 5.248477 TCAAGTGAAGTTGGAATAGCTAGGT 59.752 40.000 0.00 0.00 0.00 3.08
985 1028 6.439375 TCAAGTGAAGTTGGAATAGCTAGGTA 59.561 38.462 3.73 3.73 0.00 3.08
986 1029 6.472686 AGTGAAGTTGGAATAGCTAGGTAG 57.527 41.667 7.83 0.00 0.00 3.18
1331 1374 1.874466 GCGACGCCTGAGTAGCTTC 60.874 63.158 9.14 0.00 39.21 3.86
1373 1421 4.275936 GTGTAATCTACCACCGTACCGTAT 59.724 45.833 0.00 0.00 0.00 3.06
1377 1425 2.682856 TCTACCACCGTACCGTATGTTC 59.317 50.000 0.00 0.00 0.00 3.18
1391 1439 3.605922 CGTATGTTCGTGTTGCATGTGTT 60.606 43.478 0.00 0.00 0.00 3.32
1392 1440 2.466870 TGTTCGTGTTGCATGTGTTC 57.533 45.000 0.00 0.00 0.00 3.18
1452 1500 2.180017 GCTTGCCGTTCTGCATGG 59.820 61.111 0.00 0.00 41.70 3.66
1460 1508 2.810400 GCCGTTCTGCATGGGTGTATAT 60.810 50.000 0.00 0.00 31.00 0.86
1485 1533 1.550130 TAAGGCTCCGTCAACAGGGG 61.550 60.000 0.00 0.00 0.00 4.79
1556 1604 3.507622 GGTTTTGCTATTTCTGAGGTGCT 59.492 43.478 0.00 0.00 0.00 4.40
1572 1620 5.163774 TGAGGTGCTTGAAATTTTGTTTTGC 60.164 36.000 0.00 0.00 0.00 3.68
1573 1621 4.699257 AGGTGCTTGAAATTTTGTTTTGCA 59.301 33.333 0.00 0.00 0.00 4.08
1590 1638 6.928492 TGTTTTGCATCAGTTAATTTTCTCCC 59.072 34.615 0.00 0.00 0.00 4.30
1632 1680 3.878699 GGACCTCGTAGGAGAAGAACTAG 59.121 52.174 13.99 0.00 43.27 2.57
1646 1694 2.054799 GAACTAGCCCCACCATCCATA 58.945 52.381 0.00 0.00 0.00 2.74
1649 1697 3.881871 ACTAGCCCCACCATCCATATAA 58.118 45.455 0.00 0.00 0.00 0.98
1660 1708 5.009010 CACCATCCATATAAAGTGAAGCCAC 59.991 44.000 0.00 0.00 43.50 5.01
1668 1716 2.351276 GTGAAGCCACGGTCCCAT 59.649 61.111 0.00 0.00 33.10 4.00
1669 1717 1.303317 GTGAAGCCACGGTCCCATT 60.303 57.895 0.00 0.00 33.10 3.16
1670 1718 0.035820 GTGAAGCCACGGTCCCATTA 60.036 55.000 0.00 0.00 33.10 1.90
1671 1719 0.916086 TGAAGCCACGGTCCCATTAT 59.084 50.000 0.00 0.00 0.00 1.28
1672 1720 1.134220 TGAAGCCACGGTCCCATTATC 60.134 52.381 0.00 0.00 0.00 1.75
1673 1721 1.141053 GAAGCCACGGTCCCATTATCT 59.859 52.381 0.00 0.00 0.00 1.98
1674 1722 2.097110 AGCCACGGTCCCATTATCTA 57.903 50.000 0.00 0.00 0.00 1.98
1675 1723 2.621070 AGCCACGGTCCCATTATCTAT 58.379 47.619 0.00 0.00 0.00 1.98
1676 1724 3.786553 AGCCACGGTCCCATTATCTATA 58.213 45.455 0.00 0.00 0.00 1.31
1677 1725 4.362677 AGCCACGGTCCCATTATCTATAT 58.637 43.478 0.00 0.00 0.00 0.86
1678 1726 4.783227 AGCCACGGTCCCATTATCTATATT 59.217 41.667 0.00 0.00 0.00 1.28
1679 1727 5.962031 AGCCACGGTCCCATTATCTATATTA 59.038 40.000 0.00 0.00 0.00 0.98
1680 1728 6.098409 AGCCACGGTCCCATTATCTATATTAG 59.902 42.308 0.00 0.00 0.00 1.73
1681 1729 6.685620 GCCACGGTCCCATTATCTATATTAGG 60.686 46.154 0.00 0.00 0.00 2.69
1682 1730 6.183360 CCACGGTCCCATTATCTATATTAGGG 60.183 46.154 0.00 0.00 36.15 3.53
1683 1731 5.903589 ACGGTCCCATTATCTATATTAGGGG 59.096 44.000 0.00 0.00 35.52 4.79
1684 1732 5.307196 CGGTCCCATTATCTATATTAGGGGG 59.693 48.000 0.00 0.00 35.52 5.40
1685 1733 6.458784 GGTCCCATTATCTATATTAGGGGGA 58.541 44.000 0.00 0.00 39.65 4.81
1686 1734 6.912561 GGTCCCATTATCTATATTAGGGGGAA 59.087 42.308 0.00 0.00 43.24 3.97
1687 1735 7.072581 GGTCCCATTATCTATATTAGGGGGAAG 59.927 44.444 0.00 0.00 43.24 3.46
1715 1763 6.370166 GCAACTCCATTATCTATCTTAGTGGC 59.630 42.308 0.00 0.00 0.00 5.01
1724 1772 4.109675 CTTAGTGGCGGGGGTGGG 62.110 72.222 0.00 0.00 0.00 4.61
1742 1790 0.468029 GGGGAATTGCATGGGATCGT 60.468 55.000 0.00 0.00 0.00 3.73
1888 1936 4.408821 GGGTGGATGCTGGCGACA 62.409 66.667 0.00 0.00 39.59 4.35
1905 1953 3.048501 CGACAGTTGATGGATCAGATCG 58.951 50.000 4.23 0.00 38.19 3.69
1921 1969 2.347630 TCGTGGCTCGAGGAAGAAA 58.652 52.632 15.58 0.00 44.01 2.52
1923 1971 0.038159 CGTGGCTCGAGGAAGAAAGT 60.038 55.000 15.58 0.00 42.86 2.66
1954 2002 0.534412 AGAAGATGACCTGTGAGCCG 59.466 55.000 0.00 0.00 0.00 5.52
1961 2009 2.730382 TGACCTGTGAGCCGTTAGATA 58.270 47.619 0.00 0.00 0.00 1.98
1962 2010 2.426024 TGACCTGTGAGCCGTTAGATAC 59.574 50.000 0.00 0.00 0.00 2.24
2001 2049 2.653726 ACAAGGTGACTGATGCAAACA 58.346 42.857 0.00 0.00 42.68 2.83
2048 2096 1.807142 CTCTCCCTTGTTTCTTTCCGC 59.193 52.381 0.00 0.00 0.00 5.54
2094 2142 4.145365 TGTCAAATATTACCCCTCACCG 57.855 45.455 0.00 0.00 0.00 4.94
2112 2160 2.009774 CCGCCAATGGTAAGTGAAGAG 58.990 52.381 0.00 0.00 0.00 2.85
2113 2161 2.354704 CCGCCAATGGTAAGTGAAGAGA 60.355 50.000 0.00 0.00 0.00 3.10
2114 2162 3.535561 CGCCAATGGTAAGTGAAGAGAT 58.464 45.455 0.00 0.00 0.00 2.75
2118 2166 4.080356 CCAATGGTAAGTGAAGAGATGGGA 60.080 45.833 0.00 0.00 0.00 4.37
2162 2210 2.486982 CTCAAATGCTCCTGGTGTGAAG 59.513 50.000 0.00 0.00 0.00 3.02
2166 2214 2.009681 TGCTCCTGGTGTGAAGAGTA 57.990 50.000 0.00 0.00 0.00 2.59
2174 2222 6.361433 TCCTGGTGTGAAGAGTAAAATTCAA 58.639 36.000 0.00 0.00 37.19 2.69
2230 2279 4.142945 TGTTTGTTGTGCATGCAAAGTTTC 60.143 37.500 24.58 9.53 33.50 2.78
2253 2302 3.252215 GTCACGAAATCACATTGGTGGAA 59.748 43.478 0.00 0.00 45.32 3.53
2299 2348 2.361992 TCTAGTGCGCGGGAGGAA 60.362 61.111 8.83 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.300956 TTGAAGTGCAATTGGGCCTA 57.699 45.000 3.09 0.00 0.00 3.93
1 2 1.276989 CATTGAAGTGCAATTGGGCCT 59.723 47.619 3.09 0.00 44.68 5.19
20 21 1.141665 CACCTCCGCGATGATGACA 59.858 57.895 8.23 0.00 0.00 3.58
24 25 2.107750 CTGCACCTCCGCGATGAT 59.892 61.111 8.23 0.00 33.35 2.45
58 59 2.280797 GTTGCTCGTCCTGCACCA 60.281 61.111 0.00 0.00 40.40 4.17
61 62 0.319555 GTAGTGTTGCTCGTCCTGCA 60.320 55.000 0.00 0.00 38.80 4.41
68 69 1.060713 CGAGGTTGTAGTGTTGCTCG 58.939 55.000 0.00 0.00 0.00 5.03
74 75 0.542232 AGGAGGCGAGGTTGTAGTGT 60.542 55.000 0.00 0.00 0.00 3.55
76 77 1.313812 CGAGGAGGCGAGGTTGTAGT 61.314 60.000 0.00 0.00 0.00 2.73
103 104 0.109532 TTTGGCACTCCATCAACCGA 59.890 50.000 0.00 0.00 43.05 4.69
104 105 1.133025 GATTTGGCACTCCATCAACCG 59.867 52.381 0.00 0.00 43.05 4.44
111 112 1.675714 CGCTGTAGATTTGGCACTCCA 60.676 52.381 0.00 0.00 41.55 3.86
183 184 1.025113 CACCTGCTACTCCTCGACGA 61.025 60.000 0.00 0.00 0.00 4.20
184 185 1.429825 CACCTGCTACTCCTCGACG 59.570 63.158 0.00 0.00 0.00 5.12
186 187 3.604629 GCACCTGCTACTCCTCGA 58.395 61.111 0.00 0.00 38.21 4.04
212 213 4.077188 GTGAGCGCTTCACGTGGC 62.077 66.667 13.26 11.30 46.13 5.01
218 219 2.666190 GCCAGTGTGAGCGCTTCA 60.666 61.111 13.26 12.00 32.31 3.02
219 220 3.426568 GGCCAGTGTGAGCGCTTC 61.427 66.667 13.26 9.12 32.31 3.86
277 278 1.078848 AGCGATCTTCTGTGGCACC 60.079 57.895 16.26 0.00 0.00 5.01
279 280 0.321346 TTCAGCGATCTTCTGTGGCA 59.679 50.000 10.41 0.00 33.48 4.92
281 282 1.649664 CCTTCAGCGATCTTCTGTGG 58.350 55.000 10.41 10.09 33.48 4.17
295 296 2.029623 GAGCTACCGATGTACCCTTCA 58.970 52.381 0.00 0.00 0.00 3.02
298 299 0.260816 TGGAGCTACCGATGTACCCT 59.739 55.000 0.00 0.00 42.61 4.34
299 300 1.000955 CATGGAGCTACCGATGTACCC 59.999 57.143 0.00 0.00 42.61 3.69
302 303 1.607148 CGACATGGAGCTACCGATGTA 59.393 52.381 1.98 0.00 39.02 2.29
305 306 1.112113 AACGACATGGAGCTACCGAT 58.888 50.000 0.00 0.00 42.61 4.18
310 311 1.358725 GCGCAAACGACATGGAGCTA 61.359 55.000 0.30 0.00 43.93 3.32
349 350 4.284550 TGGTGCTCCTTGTGGCCC 62.285 66.667 0.00 0.00 34.23 5.80
365 366 4.838152 CGTGGATGGGTCGGCCTG 62.838 72.222 5.77 0.00 34.45 4.85
393 394 2.358737 CGCCAGTTGGGGTGAGAC 60.359 66.667 7.03 0.00 42.54 3.36
394 395 2.525629 TCGCCAGTTGGGGTGAGA 60.526 61.111 14.02 0.00 46.93 3.27
416 417 2.753043 GTCGGAGTCCACGGCCTA 60.753 66.667 10.49 0.00 0.00 3.93
422 423 0.959372 TCTTCCTCGTCGGAGTCCAC 60.959 60.000 10.49 5.87 44.28 4.02
437 438 2.303022 TGTCTCCCATGTCCAACTCTTC 59.697 50.000 0.00 0.00 0.00 2.87
471 472 4.082136 ACGAGAAAGAGTAAGACATGGGAC 60.082 45.833 0.00 0.00 0.00 4.46
521 522 4.830765 GTATGCCGGCCGTGAGCA 62.831 66.667 26.11 26.11 46.50 4.26
532 533 1.439353 CCACATGTCCTGCGTATGCC 61.439 60.000 4.05 0.00 41.78 4.40
536 537 0.682292 TGTTCCACATGTCCTGCGTA 59.318 50.000 0.00 0.00 0.00 4.42
538 539 0.603707 AGTGTTCCACATGTCCTGCG 60.604 55.000 0.00 0.00 36.74 5.18
541 542 3.008049 GTCCTTAGTGTTCCACATGTCCT 59.992 47.826 0.00 0.00 36.74 3.85
547 548 3.042682 TCCAAGTCCTTAGTGTTCCACA 58.957 45.455 0.00 0.00 36.74 4.17
551 552 3.988517 CGTCTTCCAAGTCCTTAGTGTTC 59.011 47.826 0.00 0.00 0.00 3.18
554 555 2.561419 TCCGTCTTCCAAGTCCTTAGTG 59.439 50.000 0.00 0.00 0.00 2.74
556 557 3.786635 CATCCGTCTTCCAAGTCCTTAG 58.213 50.000 0.00 0.00 0.00 2.18
572 573 0.028505 CAAATCTTCGCTGGCATCCG 59.971 55.000 0.00 0.00 0.00 4.18
576 577 0.036732 AGTCCAAATCTTCGCTGGCA 59.963 50.000 0.00 0.00 0.00 4.92
580 581 0.608640 ACCGAGTCCAAATCTTCGCT 59.391 50.000 0.00 0.00 0.00 4.93
591 592 3.678548 GTGTCATGAAGTTAACCGAGTCC 59.321 47.826 0.00 0.00 0.00 3.85
605 606 7.490962 AGTTCGTTAATCAAAAGTGTCATGA 57.509 32.000 0.00 0.00 0.00 3.07
607 608 8.999431 ACATAGTTCGTTAATCAAAAGTGTCAT 58.001 29.630 0.00 0.00 0.00 3.06
608 609 8.373048 ACATAGTTCGTTAATCAAAAGTGTCA 57.627 30.769 0.00 0.00 0.00 3.58
623 624 7.821595 TCATTACATTTTCGACATAGTTCGT 57.178 32.000 0.00 0.00 40.07 3.85
663 664 3.118920 TGCAAGCTGGATGATTTTCCATG 60.119 43.478 0.00 0.00 44.66 3.66
671 672 4.020928 TGATTTGTTTGCAAGCTGGATGAT 60.021 37.500 14.67 0.15 35.82 2.45
678 679 4.595762 ACAGATGATTTGTTTGCAAGCT 57.404 36.364 14.67 0.00 35.82 3.74
680 681 7.465989 ACAAAAACAGATGATTTGTTTGCAAG 58.534 30.769 13.82 7.68 45.28 4.01
699 700 8.024285 ACATTTCACTCGTAGTTTGAACAAAAA 58.976 29.630 1.47 0.00 31.36 1.94
717 720 2.163818 TCGGTCTGGACACATTTCAC 57.836 50.000 3.10 0.00 0.00 3.18
720 723 1.351017 ACCATCGGTCTGGACACATTT 59.649 47.619 6.60 0.00 39.73 2.32
721 724 0.984230 ACCATCGGTCTGGACACATT 59.016 50.000 6.60 0.00 39.73 2.71
734 737 9.468532 CATCCAATCATATAGTATACACCATCG 57.531 37.037 5.50 0.00 0.00 3.84
761 764 0.463654 TGCATGATACGGGACTTGGC 60.464 55.000 0.00 0.00 0.00 4.52
764 767 1.270305 CGGATGCATGATACGGGACTT 60.270 52.381 2.46 0.00 34.38 3.01
803 806 4.855298 TCTCTATCCCCAAAACGGAAAT 57.145 40.909 0.00 0.00 36.56 2.17
839 842 1.471119 GTCGGAGGATGGACACACTA 58.529 55.000 0.00 0.00 33.41 2.74
910 915 2.861271 GATGGTGCAAAGGGGAGGGG 62.861 65.000 0.00 0.00 0.00 4.79
948 960 0.528017 TCACTTGACTAGCGAGCCAG 59.472 55.000 0.00 0.00 0.00 4.85
950 962 1.067495 ACTTCACTTGACTAGCGAGCC 60.067 52.381 0.00 0.00 0.00 4.70
1341 1389 4.438744 GGTGGTAGATTACACAAAGCATGC 60.439 45.833 10.51 10.51 39.31 4.06
1343 1391 3.938963 CGGTGGTAGATTACACAAAGCAT 59.061 43.478 0.00 0.00 39.31 3.79
1373 1421 1.267782 CGAACACATGCAACACGAACA 60.268 47.619 0.00 0.00 0.00 3.18
1377 1425 1.783067 CGATCGAACACATGCAACACG 60.783 52.381 10.26 0.00 0.00 4.49
1443 1491 5.628797 TTGAGATATACACCCATGCAGAA 57.371 39.130 0.00 0.00 0.00 3.02
1452 1500 5.047235 ACGGAGCCTTATTGAGATATACACC 60.047 44.000 0.00 0.00 0.00 4.16
1460 1508 2.565391 TGTTGACGGAGCCTTATTGAGA 59.435 45.455 0.00 0.00 0.00 3.27
1485 1533 0.458025 CAAACGAGTAGGCCGGAGTC 60.458 60.000 5.05 0.76 0.00 3.36
1572 1620 7.066766 CAGGAAGAGGGAGAAAATTAACTGATG 59.933 40.741 0.00 0.00 0.00 3.07
1573 1621 7.115414 CAGGAAGAGGGAGAAAATTAACTGAT 58.885 38.462 0.00 0.00 0.00 2.90
1632 1680 3.157087 CACTTTATATGGATGGTGGGGC 58.843 50.000 0.00 0.00 0.00 5.80
1646 1694 1.339727 GGGACCGTGGCTTCACTTTAT 60.340 52.381 0.00 0.00 39.16 1.40
1649 1697 1.779061 ATGGGACCGTGGCTTCACTT 61.779 55.000 0.00 0.00 39.16 3.16
1660 1708 5.307196 CCCCCTAATATAGATAATGGGACCG 59.693 48.000 0.00 0.00 35.40 4.79
1665 1713 6.464465 CGGCTTCCCCCTAATATAGATAATGG 60.464 46.154 0.00 0.00 0.00 3.16
1666 1714 6.525629 CGGCTTCCCCCTAATATAGATAATG 58.474 44.000 0.00 0.00 0.00 1.90
1667 1715 5.071923 GCGGCTTCCCCCTAATATAGATAAT 59.928 44.000 0.00 0.00 0.00 1.28
1668 1716 4.407945 GCGGCTTCCCCCTAATATAGATAA 59.592 45.833 0.00 0.00 0.00 1.75
1669 1717 3.965347 GCGGCTTCCCCCTAATATAGATA 59.035 47.826 0.00 0.00 0.00 1.98
1670 1718 2.772515 GCGGCTTCCCCCTAATATAGAT 59.227 50.000 0.00 0.00 0.00 1.98
1671 1719 2.185387 GCGGCTTCCCCCTAATATAGA 58.815 52.381 0.00 0.00 0.00 1.98
1672 1720 1.906574 TGCGGCTTCCCCCTAATATAG 59.093 52.381 0.00 0.00 0.00 1.31
1673 1721 2.032965 TGCGGCTTCCCCCTAATATA 57.967 50.000 0.00 0.00 0.00 0.86
1674 1722 1.145571 TTGCGGCTTCCCCCTAATAT 58.854 50.000 0.00 0.00 0.00 1.28
1675 1723 0.181824 GTTGCGGCTTCCCCCTAATA 59.818 55.000 0.00 0.00 0.00 0.98
1676 1724 1.076995 GTTGCGGCTTCCCCCTAAT 60.077 57.895 0.00 0.00 0.00 1.73
1677 1725 2.193087 GAGTTGCGGCTTCCCCCTAA 62.193 60.000 0.00 0.00 0.00 2.69
1678 1726 2.609610 AGTTGCGGCTTCCCCCTA 60.610 61.111 0.00 0.00 0.00 3.53
1679 1727 4.035102 GAGTTGCGGCTTCCCCCT 62.035 66.667 0.00 0.00 0.00 4.79
1681 1729 3.645268 ATGGAGTTGCGGCTTCCCC 62.645 63.158 13.49 5.91 0.00 4.81
1682 1730 0.393808 TAATGGAGTTGCGGCTTCCC 60.394 55.000 13.49 5.62 0.00 3.97
1683 1731 1.604278 GATAATGGAGTTGCGGCTTCC 59.396 52.381 0.00 6.67 0.00 3.46
1684 1732 2.565841 AGATAATGGAGTTGCGGCTTC 58.434 47.619 0.00 0.00 0.00 3.86
1685 1733 2.717639 AGATAATGGAGTTGCGGCTT 57.282 45.000 0.00 0.00 0.00 4.35
1686 1734 3.580458 AGATAGATAATGGAGTTGCGGCT 59.420 43.478 0.00 0.00 0.00 5.52
1687 1735 3.931578 AGATAGATAATGGAGTTGCGGC 58.068 45.455 0.00 0.00 0.00 6.53
1724 1772 1.402787 AACGATCCCATGCAATTCCC 58.597 50.000 0.00 0.00 0.00 3.97
1742 1790 4.441356 GCACCACAGATGAAAACCTTCAAA 60.441 41.667 0.00 0.00 44.64 2.69
1888 1936 2.484417 GCCACGATCTGATCCATCAACT 60.484 50.000 11.84 0.00 36.18 3.16
1905 1953 1.000955 TCACTTTCTTCCTCGAGCCAC 59.999 52.381 6.99 0.00 0.00 5.01
1921 1969 6.671779 AGGTCATCTTCTTCCTCTTAATCACT 59.328 38.462 0.00 0.00 0.00 3.41
1923 1971 6.441924 ACAGGTCATCTTCTTCCTCTTAATCA 59.558 38.462 0.00 0.00 0.00 2.57
1954 2002 2.019984 ACCGTCCGACCTGTATCTAAC 58.980 52.381 0.00 0.00 0.00 2.34
1961 2009 1.183030 TTCATGACCGTCCGACCTGT 61.183 55.000 0.00 0.00 0.00 4.00
1962 2010 0.037697 TTTCATGACCGTCCGACCTG 60.038 55.000 0.00 0.00 0.00 4.00
2009 2057 6.397272 GGAGAGTCTAATCATTAGATGCCTG 58.603 44.000 10.40 0.00 43.59 4.85
2015 2063 7.979786 AACAAGGGAGAGTCTAATCATTAGA 57.020 36.000 2.70 2.70 39.83 2.10
2022 2070 6.477253 GGAAAGAAACAAGGGAGAGTCTAAT 58.523 40.000 0.00 0.00 0.00 1.73
2029 2077 1.544759 GGCGGAAAGAAACAAGGGAGA 60.545 52.381 0.00 0.00 0.00 3.71
2048 2096 3.616219 TGAAGGGTAATTTGATGACGGG 58.384 45.455 0.00 0.00 0.00 5.28
2094 2142 3.629398 CCATCTCTTCACTTACCATTGGC 59.371 47.826 1.54 0.00 0.00 4.52
2112 2160 4.151867 GTGTAGAAACTTCACGTTCCCATC 59.848 45.833 0.00 0.00 33.90 3.51
2113 2161 4.062991 GTGTAGAAACTTCACGTTCCCAT 58.937 43.478 0.00 0.00 33.90 4.00
2114 2162 3.460103 GTGTAGAAACTTCACGTTCCCA 58.540 45.455 0.00 0.00 33.90 4.37
2118 2166 2.476821 CGGGTGTAGAAACTTCACGTT 58.523 47.619 0.00 0.00 33.56 3.99
2208 2257 4.333615 GAAACTTTGCATGCACAACAAAC 58.666 39.130 22.58 6.01 0.00 2.93
2230 2279 2.412716 CCACCAATGTGATTTCGTGACG 60.413 50.000 0.00 0.00 45.76 4.35
2299 2348 2.769095 GGTCAGGCAGAAGATAGGAACT 59.231 50.000 0.00 0.00 46.37 3.01


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

AutoCloner maintained by Alex Coulton.