Multiple sequence alignment - TraesCS6A01G050700

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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 TraesCS6A01G050700 chr6A 100.000 1669 0 0 893 2561 26270936 26269268 0.000000e+00 3083
1 TraesCS6A01G050700 chr6A 100.000 433 0 0 1 433 26271828 26271396 0.000000e+00 800
2 TraesCS6A01G050700 chr6B 89.276 1091 76 18 896 1959 45516590 45515514 0.000000e+00 1328
3 TraesCS6A01G050700 chr6B 87.032 1041 96 15 938 1945 45206917 45205883 0.000000e+00 1138
4 TraesCS6A01G050700 chr6B 88.402 388 39 6 909 1295 45528088 45527706 1.800000e-126 462
5 TraesCS6A01G050700 chr6B 87.619 210 26 0 1328 1537 45521890 45521681 7.080000e-61 244
6 TraesCS6A01G050700 chrUn 91.493 623 37 8 1355 1968 94950540 94949925 0.000000e+00 843
7 TraesCS6A01G050700 chrUn 87.352 593 71 2 1972 2561 33170866 33170275 0.000000e+00 676
8 TraesCS6A01G050700 chrUn 80.355 901 124 35 920 1786 94919054 94918173 3.590000e-178 634
9 TraesCS6A01G050700 chrUn 88.235 493 36 7 896 1371 94951047 94950560 1.030000e-158 569
10 TraesCS6A01G050700 chrUn 85.977 435 51 4 1306 1737 94973300 94972873 8.350000e-125 457
11 TraesCS6A01G050700 chrUn 82.716 243 33 7 896 1133 95202593 95202355 9.290000e-50 207
12 TraesCS6A01G050700 chr5A 83.732 879 107 18 896 1751 45379533 45378668 0.000000e+00 798
13 TraesCS6A01G050700 chr5B 83.484 884 106 19 893 1749 61211959 61212829 0.000000e+00 787
14 TraesCS6A01G050700 chr4A 87.687 601 71 2 1964 2561 123254828 123254228 0.000000e+00 697
15 TraesCS6A01G050700 chr3D 86.755 604 72 7 1964 2561 90259744 90260345 0.000000e+00 665
16 TraesCS6A01G050700 chr3D 87.329 584 67 5 1982 2561 15024435 15025015 0.000000e+00 662
17 TraesCS6A01G050700 chr3D 86.446 605 73 4 1965 2561 609130264 609129661 0.000000e+00 654
18 TraesCS6A01G050700 chr7A 86.477 599 76 4 1966 2561 518573611 518573015 0.000000e+00 652
19 TraesCS6A01G050700 chr7A 86.213 602 79 4 1963 2561 69551514 69552114 0.000000e+00 649
20 TraesCS6A01G050700 chr6D 86.555 595 73 5 1970 2561 141140514 141141104 0.000000e+00 649
21 TraesCS6A01G050700 chr7D 86.387 595 78 3 1970 2561 637302140 637301546 0.000000e+00 647
22 TraesCS6A01G050700 chr5D 84.676 509 54 8 931 1421 57069156 57068654 1.070000e-133 486


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 TraesCS6A01G050700 chr6A 26269268 26271828 2560 True 1941.5 3083 100.000 1 2561 2 chr6A.!!$R1 2560
1 TraesCS6A01G050700 chr6B 45515514 45516590 1076 True 1328.0 1328 89.276 896 1959 1 chr6B.!!$R2 1063
2 TraesCS6A01G050700 chr6B 45205883 45206917 1034 True 1138.0 1138 87.032 938 1945 1 chr6B.!!$R1 1007
3 TraesCS6A01G050700 chrUn 94949925 94951047 1122 True 706.0 843 89.864 896 1968 2 chrUn.!!$R5 1072
4 TraesCS6A01G050700 chrUn 33170275 33170866 591 True 676.0 676 87.352 1972 2561 1 chrUn.!!$R1 589
5 TraesCS6A01G050700 chrUn 94918173 94919054 881 True 634.0 634 80.355 920 1786 1 chrUn.!!$R2 866
6 TraesCS6A01G050700 chr5A 45378668 45379533 865 True 798.0 798 83.732 896 1751 1 chr5A.!!$R1 855
7 TraesCS6A01G050700 chr5B 61211959 61212829 870 False 787.0 787 83.484 893 1749 1 chr5B.!!$F1 856
8 TraesCS6A01G050700 chr4A 123254228 123254828 600 True 697.0 697 87.687 1964 2561 1 chr4A.!!$R1 597
9 TraesCS6A01G050700 chr3D 90259744 90260345 601 False 665.0 665 86.755 1964 2561 1 chr3D.!!$F2 597
10 TraesCS6A01G050700 chr3D 15024435 15025015 580 False 662.0 662 87.329 1982 2561 1 chr3D.!!$F1 579
11 TraesCS6A01G050700 chr3D 609129661 609130264 603 True 654.0 654 86.446 1965 2561 1 chr3D.!!$R1 596
12 TraesCS6A01G050700 chr7A 518573015 518573611 596 True 652.0 652 86.477 1966 2561 1 chr7A.!!$R1 595
13 TraesCS6A01G050700 chr7A 69551514 69552114 600 False 649.0 649 86.213 1963 2561 1 chr7A.!!$F1 598
14 TraesCS6A01G050700 chr6D 141140514 141141104 590 False 649.0 649 86.555 1970 2561 1 chr6D.!!$F1 591
15 TraesCS6A01G050700 chr7D 637301546 637302140 594 True 647.0 647 86.387 1970 2561 1 chr7D.!!$R1 591
16 TraesCS6A01G050700 chr5D 57068654 57069156 502 True 486.0 486 84.676 931 1421 1 chr5D.!!$R1 490

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
87 88 0.096976 ATCGAGCGGCAAACAAATCG 59.903 50.0 1.45 0.49 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1729 1.442769 CGTGATCACTTGGAACTGGG 58.557 55.0 22.95 0.16 0.0 4.45 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
17 18 2.042741 TAGTGGGATCGCCGGGAA 60.043 61.111 2.18 0.00 33.83 3.97
18 19 1.686455 TAGTGGGATCGCCGGGAAA 60.686 57.895 2.18 0.00 33.83 3.13
19 20 1.052124 TAGTGGGATCGCCGGGAAAT 61.052 55.000 2.18 0.00 33.83 2.17
20 21 1.892391 GTGGGATCGCCGGGAAATC 60.892 63.158 2.18 0.00 33.83 2.17
21 22 2.281553 GGGATCGCCGGGAAATCC 60.282 66.667 16.00 16.00 38.60 3.01
30 31 4.363034 GGGAAATCCGGAGATCGC 57.637 61.111 11.34 14.91 37.59 4.58
31 32 1.445942 GGGAAATCCGGAGATCGCA 59.554 57.895 23.33 0.00 37.59 5.10
32 33 0.601311 GGGAAATCCGGAGATCGCAG 60.601 60.000 23.33 0.00 37.59 5.18
33 34 0.601311 GGAAATCCGGAGATCGCAGG 60.601 60.000 11.34 9.32 37.59 4.85
34 35 0.389391 GAAATCCGGAGATCGCAGGA 59.611 55.000 19.53 19.53 37.59 3.86
35 36 1.001406 GAAATCCGGAGATCGCAGGAT 59.999 52.381 22.04 22.04 44.64 3.24
36 37 1.051812 AATCCGGAGATCGCAGGATT 58.948 50.000 28.98 28.98 45.57 3.01
37 38 1.051812 ATCCGGAGATCGCAGGATTT 58.948 50.000 22.04 5.71 40.29 2.17
38 39 1.699730 TCCGGAGATCGCAGGATTTA 58.300 50.000 13.99 0.00 37.59 1.40
39 40 1.613925 TCCGGAGATCGCAGGATTTAG 59.386 52.381 13.99 0.00 37.59 1.85
40 41 1.337260 CCGGAGATCGCAGGATTTAGG 60.337 57.143 10.02 0.00 37.59 2.69
41 42 1.337260 CGGAGATCGCAGGATTTAGGG 60.337 57.143 0.00 0.00 31.51 3.53
42 43 1.609320 GGAGATCGCAGGATTTAGGGC 60.609 57.143 0.00 0.00 31.51 5.19
45 46 3.640000 CGCAGGATTTAGGGCGCG 61.640 66.667 0.00 0.00 43.14 6.86
46 47 3.279875 GCAGGATTTAGGGCGCGG 61.280 66.667 8.83 0.00 0.00 6.46
47 48 3.279875 CAGGATTTAGGGCGCGGC 61.280 66.667 26.39 26.39 0.00 6.53
48 49 4.910585 AGGATTTAGGGCGCGGCG 62.911 66.667 27.12 19.62 0.00 6.46
60 61 4.591317 GCGGCGGCGCAATAGTTC 62.591 66.667 45.39 18.12 34.62 3.01
61 62 4.279535 CGGCGGCGCAATAGTTCG 62.280 66.667 34.36 21.39 0.00 3.95
62 63 2.888534 GGCGGCGCAATAGTTCGA 60.889 61.111 34.36 0.00 0.00 3.71
63 64 2.244651 GGCGGCGCAATAGTTCGAT 61.245 57.895 34.36 0.00 0.00 3.59
64 65 1.201825 GCGGCGCAATAGTTCGATC 59.798 57.895 29.21 0.00 0.00 3.69
65 66 1.215655 GCGGCGCAATAGTTCGATCT 61.216 55.000 29.21 0.97 0.00 2.75
66 67 0.504384 CGGCGCAATAGTTCGATCTG 59.496 55.000 10.83 0.00 0.00 2.90
67 68 0.861837 GGCGCAATAGTTCGATCTGG 59.138 55.000 10.83 0.00 0.00 3.86
68 69 1.538204 GGCGCAATAGTTCGATCTGGA 60.538 52.381 10.83 0.00 0.00 3.86
69 70 2.408050 GCGCAATAGTTCGATCTGGAT 58.592 47.619 0.30 0.00 0.00 3.41
70 71 2.410053 GCGCAATAGTTCGATCTGGATC 59.590 50.000 0.30 0.83 34.56 3.36
78 79 2.730733 GATCTGGATCGAGCGGCA 59.269 61.111 1.45 0.00 0.00 5.69
79 80 1.068083 GATCTGGATCGAGCGGCAA 59.932 57.895 1.45 0.00 0.00 4.52
80 81 0.530650 GATCTGGATCGAGCGGCAAA 60.531 55.000 1.45 0.00 0.00 3.68
81 82 0.811616 ATCTGGATCGAGCGGCAAAC 60.812 55.000 1.45 0.00 0.00 2.93
82 83 1.741401 CTGGATCGAGCGGCAAACA 60.741 57.895 1.45 0.00 0.00 2.83
83 84 1.298157 CTGGATCGAGCGGCAAACAA 61.298 55.000 1.45 0.00 0.00 2.83
84 85 0.886938 TGGATCGAGCGGCAAACAAA 60.887 50.000 1.45 0.00 0.00 2.83
85 86 0.451783 GGATCGAGCGGCAAACAAAT 59.548 50.000 1.45 0.00 0.00 2.32
86 87 1.531883 GGATCGAGCGGCAAACAAATC 60.532 52.381 1.45 0.00 0.00 2.17
87 88 0.096976 ATCGAGCGGCAAACAAATCG 59.903 50.000 1.45 0.49 0.00 3.34
88 89 1.206578 CGAGCGGCAAACAAATCGT 59.793 52.632 1.45 0.00 0.00 3.73
89 90 0.385473 CGAGCGGCAAACAAATCGTT 60.385 50.000 1.45 0.00 40.50 3.85
109 110 8.746052 ATCGTTTGGATCTATTAACAAATCCA 57.254 30.769 9.40 9.40 44.51 3.41
134 135 9.928236 CAAATGTTTGGAAAATACAAATTTCGT 57.072 25.926 0.00 0.00 39.68 3.85
135 136 9.928236 AAATGTTTGGAAAATACAAATTTCGTG 57.072 25.926 0.00 0.00 39.68 4.35
136 137 8.879342 ATGTTTGGAAAATACAAATTTCGTGA 57.121 26.923 0.00 0.00 39.68 4.35
137 138 8.879342 TGTTTGGAAAATACAAATTTCGTGAT 57.121 26.923 0.00 0.00 39.68 3.06
138 139 8.759641 TGTTTGGAAAATACAAATTTCGTGATG 58.240 29.630 0.00 0.00 39.68 3.07
139 140 8.760569 GTTTGGAAAATACAAATTTCGTGATGT 58.239 29.630 0.00 0.00 39.68 3.06
140 141 9.967346 TTTGGAAAATACAAATTTCGTGATGTA 57.033 25.926 0.00 0.00 37.60 2.29
427 428 9.722184 ATCATAGACATATTCTTGGAAGTCATG 57.278 33.333 0.00 0.00 35.55 3.07
428 429 8.708378 TCATAGACATATTCTTGGAAGTCATGT 58.292 33.333 0.00 0.00 35.55 3.21
429 430 9.987272 CATAGACATATTCTTGGAAGTCATGTA 57.013 33.333 0.00 0.00 35.55 2.29
432 433 9.334947 AGACATATTCTTGGAAGTCATGTATTG 57.665 33.333 0.00 0.00 0.00 1.90
916 921 5.730296 ACAAACAGTGTGTAGATAGAGCT 57.270 39.130 0.00 0.00 39.72 4.09
960 965 6.456853 CCCATCAGAAAACATACATACACACG 60.457 42.308 0.00 0.00 0.00 4.49
962 967 4.090786 TCAGAAAACATACATACACACGCG 59.909 41.667 3.53 3.53 0.00 6.01
980 985 1.468054 GCGCCAAGGAAGTATTTGCAG 60.468 52.381 0.00 0.00 0.00 4.41
1068 1073 2.667724 GCTGCTTCTCATGTGCTTTGTC 60.668 50.000 0.00 0.00 0.00 3.18
1069 1074 2.812591 CTGCTTCTCATGTGCTTTGTCT 59.187 45.455 0.00 0.00 0.00 3.41
1077 1082 3.253921 TCATGTGCTTTGTCTTCCATGTG 59.746 43.478 0.00 0.00 33.27 3.21
1088 1093 5.555966 TGTCTTCCATGTGCATTGTAAGTA 58.444 37.500 0.00 0.00 0.00 2.24
1127 1133 8.038944 ACTAGTAATTCTCCTTTGTCGCATAAA 58.961 33.333 0.00 0.00 0.00 1.40
1128 1134 7.865706 AGTAATTCTCCTTTGTCGCATAAAT 57.134 32.000 0.00 0.00 0.00 1.40
1180 1191 8.980610 TGCATCAAAATGATACAAAGTGAAAAG 58.019 29.630 0.00 0.00 34.28 2.27
1191 1202 8.762481 ATACAAAGTGAAAAGGAGTTTAACCT 57.238 30.769 0.00 0.00 39.69 3.50
1230 1242 5.773575 AGTATGTCCTACTCGTGCATATTG 58.226 41.667 0.00 0.00 35.73 1.90
1238 1251 6.046593 CCTACTCGTGCATATTGGTCTTTAA 58.953 40.000 0.00 0.00 0.00 1.52
1245 1258 9.781834 TCGTGCATATTGGTCTTTAAAAATAAG 57.218 29.630 0.00 0.00 0.00 1.73
1316 1350 8.444715 TCCATTTTATGTTTGTATACACGTGTC 58.555 33.333 27.16 11.96 0.00 3.67
1376 1446 9.935682 CAACATATATTGATGGATATTAACGGC 57.064 33.333 0.00 0.00 0.00 5.68
1543 1617 6.156519 TGCTATACTACAATGGACTTATGCG 58.843 40.000 0.00 0.00 0.00 4.73
1550 1624 2.332063 ATGGACTTATGCGTGGAAGG 57.668 50.000 0.00 0.00 0.00 3.46
1560 1634 0.451783 GCGTGGAAGGGTGCAAATAG 59.548 55.000 0.00 0.00 0.00 1.73
1566 1640 4.035208 GTGGAAGGGTGCAAATAGAATACG 59.965 45.833 0.00 0.00 0.00 3.06
1610 1693 1.000866 GCTGGCCCATCCTCCTTTT 59.999 57.895 0.00 0.00 35.26 2.27
1611 1694 0.258774 GCTGGCCCATCCTCCTTTTA 59.741 55.000 0.00 0.00 35.26 1.52
1622 1705 6.011274 CCCATCCTCCTTTTATCTTCCCATAT 60.011 42.308 0.00 0.00 0.00 1.78
1623 1706 7.184570 CCCATCCTCCTTTTATCTTCCCATATA 59.815 40.741 0.00 0.00 0.00 0.86
1624 1707 8.049721 CCATCCTCCTTTTATCTTCCCATATAC 58.950 40.741 0.00 0.00 0.00 1.47
1625 1708 7.569599 TCCTCCTTTTATCTTCCCATATACC 57.430 40.000 0.00 0.00 0.00 2.73
1646 1729 3.119708 CCTACACTTTGATCAGCTTTGGC 60.120 47.826 0.00 0.00 39.06 4.52
1761 1862 7.276438 TCGCTGTTATCATCATATGAATAGTGC 59.724 37.037 9.99 8.32 43.50 4.40
1852 1953 3.957497 AGATCGTCTTCAGAGGCATTACT 59.043 43.478 0.00 0.00 0.00 2.24
1868 1969 4.035675 GCATTACTAGTTTGGCATCTGACC 59.964 45.833 0.00 0.00 0.00 4.02
1878 1979 0.107312 GCATCTGACCATCAGCAGGT 60.107 55.000 0.74 0.00 43.95 4.00
1891 1992 3.797039 TCAGCAGGTGTCTATATGCAAC 58.203 45.455 0.00 0.00 41.14 4.17
1936 2038 0.260230 TTGCCAGTTTTGAGGGGTCA 59.740 50.000 0.00 0.00 0.00 4.02
1939 2041 0.771127 CCAGTTTTGAGGGGTCAGGA 59.229 55.000 0.00 0.00 0.00 3.86
1961 2063 5.538813 GGATTTAAGGTTCTGTTTGGTTCCT 59.461 40.000 0.00 0.00 0.00 3.36
1968 2070 4.254492 GTTCTGTTTGGTTCCTAGCCTAG 58.746 47.826 0.00 0.00 0.00 3.02
1986 2088 4.020543 CCTAGGAGCAACTCTAACAGACT 58.979 47.826 1.05 0.00 0.00 3.24
2001 2103 0.109412 AGACTCCGTAAAAGTCGCGG 60.109 55.000 6.13 0.00 46.23 6.46
2049 2151 3.460103 GGCTCGACATAATTTTCCGGTA 58.540 45.455 0.00 0.00 0.00 4.02
2060 2162 3.764237 TTTTCCGGTAAGAACAGAGCT 57.236 42.857 0.00 0.00 0.00 4.09
2069 2171 3.601443 AAGAACAGAGCTCGCATACTT 57.399 42.857 8.37 8.91 0.00 2.24
2073 2175 0.460811 CAGAGCTCGCATACTTGCCA 60.461 55.000 8.37 0.00 46.57 4.92
2084 2186 3.233507 CATACTTGCCAGGCCCATAAAT 58.766 45.455 9.64 0.00 0.00 1.40
2085 2187 2.252535 ACTTGCCAGGCCCATAAATT 57.747 45.000 9.64 0.00 0.00 1.82
2128 2232 0.391597 CACGCCCCGACCACTATATT 59.608 55.000 0.00 0.00 0.00 1.28
2138 2242 5.350633 CCGACCACTATATTTACGGTTTCA 58.649 41.667 0.00 0.00 35.21 2.69
2150 2254 2.023601 GTTTCACGGCGCGTTTGT 59.976 55.556 6.90 0.27 38.32 2.83
2159 2263 2.961669 GCGCGTTTGTGGGTCGAAT 61.962 57.895 8.43 0.00 0.00 3.34
2174 2279 1.846124 GAATCCCTATCCCCCGCCA 60.846 63.158 0.00 0.00 0.00 5.69
2203 2314 4.374584 CGCAATTCCCCACCCCCA 62.375 66.667 0.00 0.00 0.00 4.96
2221 2332 3.012518 CCCATTCTTCACATTTCTCGCT 58.987 45.455 0.00 0.00 0.00 4.93
2301 2412 2.336809 CTCCGGTAGCAGATCCGC 59.663 66.667 0.00 0.00 44.63 5.54
2303 2414 3.227276 CCGGTAGCAGATCCGCCT 61.227 66.667 0.00 0.00 44.63 5.52
2431 2542 0.745486 TCCGCGAGATGGACGAGTAA 60.745 55.000 8.23 0.00 0.00 2.24
2435 2546 1.671845 GCGAGATGGACGAGTAAGACT 59.328 52.381 0.00 0.00 0.00 3.24
2476 2587 2.676822 TCTGCCGCGTCCTTCTCT 60.677 61.111 4.92 0.00 0.00 3.10
2479 2593 4.443266 GCCGCGTCCTTCTCTGCT 62.443 66.667 4.92 0.00 0.00 4.24
2493 2607 3.439154 TCTCTGCTGTGAGATCTTCCTT 58.561 45.455 0.00 0.00 38.08 3.36
2497 2611 1.404717 GCTGTGAGATCTTCCTTCGCA 60.405 52.381 0.00 0.00 0.00 5.10
2509 2623 2.038007 TTCGCAGGGAGCTCCTCT 59.962 61.111 31.36 22.89 46.12 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.052124 ATTTCCCGGCGATCCCACTA 61.052 55.000 9.30 0.00 0.00 2.74
3 4 2.508928 GATTTCCCGGCGATCCCA 59.491 61.111 9.30 0.00 0.00 4.37
4 5 2.281553 GGATTTCCCGGCGATCCC 60.282 66.667 9.30 0.00 34.55 3.85
13 14 0.601311 CTGCGATCTCCGGATTTCCC 60.601 60.000 3.57 0.00 38.13 3.97
14 15 0.601311 CCTGCGATCTCCGGATTTCC 60.601 60.000 3.57 0.36 38.13 3.13
15 16 0.389391 TCCTGCGATCTCCGGATTTC 59.611 55.000 3.57 3.93 38.13 2.17
16 17 1.051812 ATCCTGCGATCTCCGGATTT 58.948 50.000 3.57 0.00 38.13 2.17
17 18 1.051812 AATCCTGCGATCTCCGGATT 58.948 50.000 13.78 13.78 40.46 3.01
18 19 1.051812 AAATCCTGCGATCTCCGGAT 58.948 50.000 3.57 3.03 38.13 4.18
19 20 1.613925 CTAAATCCTGCGATCTCCGGA 59.386 52.381 2.93 2.93 39.04 5.14
20 21 1.337260 CCTAAATCCTGCGATCTCCGG 60.337 57.143 0.00 0.00 39.04 5.14
21 22 1.337260 CCCTAAATCCTGCGATCTCCG 60.337 57.143 0.00 0.00 42.21 4.63
22 23 1.609320 GCCCTAAATCCTGCGATCTCC 60.609 57.143 0.00 0.00 0.00 3.71
23 24 1.802069 GCCCTAAATCCTGCGATCTC 58.198 55.000 0.00 0.00 0.00 2.75
29 30 3.279875 CCGCGCCCTAAATCCTGC 61.280 66.667 0.00 0.00 0.00 4.85
30 31 3.279875 GCCGCGCCCTAAATCCTG 61.280 66.667 0.00 0.00 0.00 3.86
31 32 4.910585 CGCCGCGCCCTAAATCCT 62.911 66.667 0.00 0.00 0.00 3.24
44 45 4.279535 CGAACTATTGCGCCGCCG 62.280 66.667 6.63 0.00 37.57 6.46
45 46 2.159272 GATCGAACTATTGCGCCGCC 62.159 60.000 6.63 0.00 0.00 6.13
46 47 1.201825 GATCGAACTATTGCGCCGC 59.798 57.895 4.18 0.00 0.00 6.53
47 48 0.504384 CAGATCGAACTATTGCGCCG 59.496 55.000 4.18 0.00 0.00 6.46
48 49 0.861837 CCAGATCGAACTATTGCGCC 59.138 55.000 4.18 0.00 0.00 6.53
49 50 1.852942 TCCAGATCGAACTATTGCGC 58.147 50.000 0.00 0.00 0.00 6.09
61 62 0.530650 TTTGCCGCTCGATCCAGATC 60.531 55.000 0.00 0.00 34.56 2.75
62 63 0.811616 GTTTGCCGCTCGATCCAGAT 60.812 55.000 0.00 0.00 0.00 2.90
63 64 1.447838 GTTTGCCGCTCGATCCAGA 60.448 57.895 0.00 0.00 0.00 3.86
64 65 1.298157 TTGTTTGCCGCTCGATCCAG 61.298 55.000 0.00 0.00 0.00 3.86
65 66 0.886938 TTTGTTTGCCGCTCGATCCA 60.887 50.000 0.00 0.00 0.00 3.41
66 67 0.451783 ATTTGTTTGCCGCTCGATCC 59.548 50.000 0.00 0.00 0.00 3.36
67 68 1.815132 GATTTGTTTGCCGCTCGATC 58.185 50.000 0.00 0.00 0.00 3.69
68 69 0.096976 CGATTTGTTTGCCGCTCGAT 59.903 50.000 0.00 0.00 0.00 3.59
69 70 1.225376 ACGATTTGTTTGCCGCTCGA 61.225 50.000 3.30 0.00 0.00 4.04
70 71 0.385473 AACGATTTGTTTGCCGCTCG 60.385 50.000 0.00 0.00 37.59 5.03
71 72 3.472263 AACGATTTGTTTGCCGCTC 57.528 47.368 0.00 0.00 37.59 5.03
83 84 9.184523 TGGATTTGTTAATAGATCCAAACGATT 57.815 29.630 18.51 0.00 43.65 3.34
84 85 8.746052 TGGATTTGTTAATAGATCCAAACGAT 57.254 30.769 18.51 0.00 43.65 3.73
107 108 9.379811 CGAAATTTGTATTTTCCAAACATTTGG 57.620 29.630 15.98 15.98 44.52 3.28
108 109 9.928236 ACGAAATTTGTATTTTCCAAACATTTG 57.072 25.926 0.00 0.00 34.85 2.32
109 110 9.928236 CACGAAATTTGTATTTTCCAAACATTT 57.072 25.926 0.00 0.00 34.85 2.32
110 111 9.319143 TCACGAAATTTGTATTTTCCAAACATT 57.681 25.926 0.00 0.00 34.85 2.71
111 112 8.879342 TCACGAAATTTGTATTTTCCAAACAT 57.121 26.923 0.00 0.00 34.85 2.71
112 113 8.759641 CATCACGAAATTTGTATTTTCCAAACA 58.240 29.630 0.00 0.00 34.85 2.83
113 114 8.760569 ACATCACGAAATTTGTATTTTCCAAAC 58.239 29.630 0.00 0.00 34.85 2.93
114 115 8.879342 ACATCACGAAATTTGTATTTTCCAAA 57.121 26.923 0.00 0.00 34.16 3.28
401 402 9.722184 CATGACTTCCAAGAATATGTCTATGAT 57.278 33.333 0.00 0.00 34.56 2.45
402 403 8.708378 ACATGACTTCCAAGAATATGTCTATGA 58.292 33.333 0.00 0.00 34.56 2.15
403 404 8.899427 ACATGACTTCCAAGAATATGTCTATG 57.101 34.615 0.00 0.00 34.56 2.23
406 407 9.334947 CAATACATGACTTCCAAGAATATGTCT 57.665 33.333 0.00 0.00 38.69 3.41
892 893 7.411486 AGCTCTATCTACACACTGTTTGTAT 57.589 36.000 7.21 0.00 35.67 2.29
893 894 6.835819 AGCTCTATCTACACACTGTTTGTA 57.164 37.500 6.63 6.63 35.67 2.41
894 895 5.730296 AGCTCTATCTACACACTGTTTGT 57.270 39.130 4.85 4.85 39.97 2.83
960 965 0.525761 TGCAAATACTTCCTTGGCGC 59.474 50.000 0.00 0.00 0.00 6.53
962 967 3.942130 AACTGCAAATACTTCCTTGGC 57.058 42.857 0.00 0.00 0.00 4.52
980 985 5.004726 GCCATTAAGACGATGCAATTGAAAC 59.995 40.000 10.34 0.00 0.00 2.78
1068 1073 4.494690 CGCTACTTACAATGCACATGGAAG 60.495 45.833 19.82 19.82 43.14 3.46
1069 1074 3.373748 CGCTACTTACAATGCACATGGAA 59.626 43.478 0.00 2.94 0.00 3.53
1077 1082 2.018542 TGGGACGCTACTTACAATGC 57.981 50.000 0.00 0.00 0.00 3.56
1088 1093 5.421374 AGAATTACTAGTAACTTGGGACGCT 59.579 40.000 17.45 0.00 0.00 5.07
1154 1165 8.883954 TTTTCACTTTGTATCATTTTGATGCA 57.116 26.923 4.46 4.46 45.43 3.96
1172 1183 5.434408 ACGAAGGTTAAACTCCTTTTCACT 58.566 37.500 0.00 0.00 44.19 3.41
1173 1184 5.526479 AGACGAAGGTTAAACTCCTTTTCAC 59.474 40.000 0.00 0.00 44.19 3.18
1180 1191 2.994578 GCAGAGACGAAGGTTAAACTCC 59.005 50.000 0.00 0.00 0.00 3.85
1191 1202 5.386958 ACATACTAGTTTGCAGAGACGAA 57.613 39.130 12.62 0.00 0.00 3.85
1245 1258 7.044798 ACAATCAACTAGAGAACAAGCTATCC 58.955 38.462 0.00 0.00 0.00 2.59
1247 1260 8.531982 TGTACAATCAACTAGAGAACAAGCTAT 58.468 33.333 0.00 0.00 0.00 2.97
1316 1350 6.255950 TCGAATAACGATTATGGATCTAGCG 58.744 40.000 0.00 0.00 46.45 4.26
1543 1617 4.035208 CGTATTCTATTTGCACCCTTCCAC 59.965 45.833 0.00 0.00 0.00 4.02
1560 1634 5.957796 CGTGGCTGAAAAAGAATACGTATTC 59.042 40.000 31.91 31.91 41.78 1.75
1566 1640 4.226761 CCAACGTGGCTGAAAAAGAATAC 58.773 43.478 0.00 0.00 0.00 1.89
1594 1677 2.502745 AGATAAAAGGAGGATGGGCCA 58.497 47.619 9.61 9.61 40.02 5.36
1610 1693 9.615660 ATCAAAGTGTAGGTATATGGGAAGATA 57.384 33.333 0.00 0.00 0.00 1.98
1611 1694 7.931015 TCAAAGTGTAGGTATATGGGAAGAT 57.069 36.000 0.00 0.00 0.00 2.40
1622 1705 5.245531 CCAAAGCTGATCAAAGTGTAGGTA 58.754 41.667 0.00 0.00 0.00 3.08
1623 1706 4.074970 CCAAAGCTGATCAAAGTGTAGGT 58.925 43.478 0.00 0.00 0.00 3.08
1624 1707 3.119708 GCCAAAGCTGATCAAAGTGTAGG 60.120 47.826 0.00 0.00 35.50 3.18
1625 1708 3.119708 GGCCAAAGCTGATCAAAGTGTAG 60.120 47.826 0.00 0.00 39.73 2.74
1646 1729 1.442769 CGTGATCACTTGGAACTGGG 58.557 55.000 22.95 0.16 0.00 4.45
1761 1862 4.159506 TGAAAAGGACTCCAACAAAACCAG 59.840 41.667 0.00 0.00 0.00 4.00
1852 1953 3.998913 TGATGGTCAGATGCCAAACTA 57.001 42.857 0.00 0.00 39.72 2.24
1868 1969 3.999046 TGCATATAGACACCTGCTGATG 58.001 45.455 0.00 0.00 35.66 3.07
1878 1979 9.409312 CAAAATGAAAACTGTTGCATATAGACA 57.591 29.630 8.86 0.00 31.07 3.41
1891 1992 5.234972 GCCTCTGGAAACAAAATGAAAACTG 59.765 40.000 0.00 0.00 42.06 3.16
1927 2028 2.929301 ACCTTAAATCCTGACCCCTCA 58.071 47.619 0.00 0.00 0.00 3.86
1936 2038 5.538813 GGAACCAAACAGAACCTTAAATCCT 59.461 40.000 0.00 0.00 0.00 3.24
1939 2041 6.208797 GCTAGGAACCAAACAGAACCTTAAAT 59.791 38.462 0.00 0.00 0.00 1.40
1961 2063 3.954904 CTGTTAGAGTTGCTCCTAGGCTA 59.045 47.826 2.96 0.00 0.00 3.93
1968 2070 2.416162 CGGAGTCTGTTAGAGTTGCTCC 60.416 54.545 0.00 0.00 38.06 4.70
1980 2082 1.665161 CGCGACTTTTACGGAGTCTGT 60.665 52.381 10.07 10.07 43.93 3.41
2034 2136 6.093633 GCTCTGTTCTTACCGGAAAATTATGT 59.906 38.462 9.46 0.00 0.00 2.29
2036 2138 6.415573 AGCTCTGTTCTTACCGGAAAATTAT 58.584 36.000 9.46 0.00 0.00 1.28
2049 2151 3.257393 CAAGTATGCGAGCTCTGTTCTT 58.743 45.455 12.85 7.12 0.00 2.52
2090 2194 2.361865 GGTTTGCGGGCCATGGTA 60.362 61.111 14.67 0.00 0.00 3.25
2128 2232 3.404707 CGCGCCGTGAAACCGTAA 61.405 61.111 0.00 0.00 0.00 3.18
2159 2263 4.892291 GGTGGCGGGGGATAGGGA 62.892 72.222 0.00 0.00 0.00 4.20
2203 2314 2.421424 GGCAGCGAGAAATGTGAAGAAT 59.579 45.455 0.00 0.00 0.00 2.40
2411 2522 0.534427 TACTCGTCCATCTCGCGGAT 60.534 55.000 6.13 5.14 34.32 4.18
2421 2532 1.162698 CCGACAGTCTTACTCGTCCA 58.837 55.000 0.00 0.00 0.00 4.02
2476 2587 1.404717 GCGAAGGAAGATCTCACAGCA 60.405 52.381 0.00 0.00 0.00 4.41
2479 2593 1.205655 CCTGCGAAGGAAGATCTCACA 59.794 52.381 1.89 0.00 0.00 3.58
2530 2644 1.004918 CCACACCCTCTTCACGGAC 60.005 63.158 0.00 0.00 0.00 4.79
2531 2645 1.458777 ACCACACCCTCTTCACGGA 60.459 57.895 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.