Multiple sequence alignment - TraesCS4B01G379600

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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 TraesCS4B01G379600 chr4B 100.000 2719 0 0 1 2719 660591149 660588431 0 5022
1 TraesCS4B01G379600 chrUn 90.187 2680 156 43 84 2705 110522793 110520163 0 3393
2 TraesCS4B01G379600 chr5A 87.662 2626 180 65 84 2641 700445409 700442860 0 2922


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 TraesCS4B01G379600 chr4B 660588431 660591149 2718 True 5022 5022 100.000 1 2719 1 chr4B.!!$R1 2718
1 TraesCS4B01G379600 chrUn 110520163 110522793 2630 True 3393 3393 90.187 84 2705 1 chrUn.!!$R1 2621
2 TraesCS4B01G379600 chr5A 700442860 700445409 2549 True 2922 2922 87.662 84 2641 1 chr5A.!!$R1 2557

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
35 36 0.03601 AGATCAAACCCACCGCAGAG 60.036 55.0 0.0 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2091 1.202964 TCTGGGCATGCTAATCCATGG 60.203 52.381 18.92 4.97 42.18 3.66 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
17 18 4.449638 TCTGACCTGAGGCCTGAG 57.550 61.111 12.00 12.61 0.00 3.35
18 19 1.776969 TCTGACCTGAGGCCTGAGA 59.223 57.895 22.21 0.00 0.00 3.27
19 20 0.337773 TCTGACCTGAGGCCTGAGAT 59.662 55.000 22.21 1.86 0.00 2.75
20 21 0.752054 CTGACCTGAGGCCTGAGATC 59.248 60.000 22.21 14.73 0.00 2.75
21 22 0.041684 TGACCTGAGGCCTGAGATCA 59.958 55.000 22.21 17.75 0.00 2.92
22 23 1.198713 GACCTGAGGCCTGAGATCAA 58.801 55.000 22.21 0.00 0.00 2.57
23 24 1.556911 GACCTGAGGCCTGAGATCAAA 59.443 52.381 22.21 0.00 0.00 2.69
24 25 1.280421 ACCTGAGGCCTGAGATCAAAC 59.720 52.381 22.21 0.00 0.00 2.93
25 26 1.407989 CCTGAGGCCTGAGATCAAACC 60.408 57.143 22.21 0.00 0.00 3.27
26 27 0.620556 TGAGGCCTGAGATCAAACCC 59.379 55.000 12.00 0.00 0.00 4.11
27 28 0.620556 GAGGCCTGAGATCAAACCCA 59.379 55.000 12.00 0.00 0.00 4.51
28 29 0.329596 AGGCCTGAGATCAAACCCAC 59.670 55.000 3.11 0.00 0.00 4.61
29 30 0.681243 GGCCTGAGATCAAACCCACC 60.681 60.000 0.00 0.00 0.00 4.61
30 31 1.026718 GCCTGAGATCAAACCCACCG 61.027 60.000 0.00 0.00 0.00 4.94
31 32 1.026718 CCTGAGATCAAACCCACCGC 61.027 60.000 0.00 0.00 0.00 5.68
32 33 0.321564 CTGAGATCAAACCCACCGCA 60.322 55.000 0.00 0.00 0.00 5.69
33 34 0.321564 TGAGATCAAACCCACCGCAG 60.322 55.000 0.00 0.00 0.00 5.18
34 35 0.036388 GAGATCAAACCCACCGCAGA 60.036 55.000 0.00 0.00 0.00 4.26
35 36 0.036010 AGATCAAACCCACCGCAGAG 60.036 55.000 0.00 0.00 0.00 3.35
36 37 1.648467 GATCAAACCCACCGCAGAGC 61.648 60.000 0.00 0.00 0.00 4.09
37 38 3.365265 CAAACCCACCGCAGAGCC 61.365 66.667 0.00 0.00 0.00 4.70
38 39 4.660938 AAACCCACCGCAGAGCCC 62.661 66.667 0.00 0.00 0.00 5.19
41 42 4.659172 CCCACCGCAGAGCCCAAA 62.659 66.667 0.00 0.00 0.00 3.28
42 43 2.361610 CCACCGCAGAGCCCAAAT 60.362 61.111 0.00 0.00 0.00 2.32
43 44 1.077787 CCACCGCAGAGCCCAAATA 60.078 57.895 0.00 0.00 0.00 1.40
44 45 1.097547 CCACCGCAGAGCCCAAATAG 61.098 60.000 0.00 0.00 0.00 1.73
45 46 1.452108 ACCGCAGAGCCCAAATAGC 60.452 57.895 0.00 0.00 0.00 2.97
46 47 2.189499 CCGCAGAGCCCAAATAGCC 61.189 63.158 0.00 0.00 0.00 3.93
47 48 2.189499 CGCAGAGCCCAAATAGCCC 61.189 63.158 0.00 0.00 0.00 5.19
48 49 2.189499 GCAGAGCCCAAATAGCCCG 61.189 63.158 0.00 0.00 0.00 6.13
49 50 1.224592 CAGAGCCCAAATAGCCCGT 59.775 57.895 0.00 0.00 0.00 5.28
50 51 0.815615 CAGAGCCCAAATAGCCCGTC 60.816 60.000 0.00 0.00 0.00 4.79
51 52 1.887707 GAGCCCAAATAGCCCGTCG 60.888 63.158 0.00 0.00 0.00 5.12
52 53 2.124860 GCCCAAATAGCCCGTCGT 60.125 61.111 0.00 0.00 0.00 4.34
53 54 1.747745 GCCCAAATAGCCCGTCGTT 60.748 57.895 0.00 0.00 0.00 3.85
54 55 1.712018 GCCCAAATAGCCCGTCGTTC 61.712 60.000 0.00 0.00 0.00 3.95
55 56 0.107848 CCCAAATAGCCCGTCGTTCT 60.108 55.000 0.00 0.00 0.00 3.01
56 57 1.287425 CCAAATAGCCCGTCGTTCTC 58.713 55.000 0.00 0.00 0.00 2.87
57 58 0.921347 CAAATAGCCCGTCGTTCTCG 59.079 55.000 0.00 0.00 38.55 4.04
58 59 0.804933 AAATAGCCCGTCGTTCTCGC 60.805 55.000 0.00 0.00 36.96 5.03
59 60 1.664321 AATAGCCCGTCGTTCTCGCT 61.664 55.000 0.00 0.00 36.96 4.93
60 61 2.337749 ATAGCCCGTCGTTCTCGCTG 62.338 60.000 0.00 0.00 36.96 5.18
61 62 4.719369 GCCCGTCGTTCTCGCTGT 62.719 66.667 0.00 0.00 36.96 4.40
62 63 2.504244 CCCGTCGTTCTCGCTGTC 60.504 66.667 0.00 0.00 36.96 3.51
63 64 2.254350 CCGTCGTTCTCGCTGTCA 59.746 61.111 0.00 0.00 36.96 3.58
64 65 2.081212 CCGTCGTTCTCGCTGTCAC 61.081 63.158 0.00 0.00 36.96 3.67
65 66 1.082038 CGTCGTTCTCGCTGTCACT 60.082 57.895 0.00 0.00 36.96 3.41
66 67 1.060726 CGTCGTTCTCGCTGTCACTC 61.061 60.000 0.00 0.00 36.96 3.51
67 68 0.238817 GTCGTTCTCGCTGTCACTCT 59.761 55.000 0.00 0.00 36.96 3.24
68 69 0.238553 TCGTTCTCGCTGTCACTCTG 59.761 55.000 0.00 0.00 36.96 3.35
69 70 0.039978 CGTTCTCGCTGTCACTCTGT 60.040 55.000 0.00 0.00 0.00 3.41
70 71 1.692296 GTTCTCGCTGTCACTCTGTC 58.308 55.000 0.00 0.00 0.00 3.51
71 72 1.268352 GTTCTCGCTGTCACTCTGTCT 59.732 52.381 0.00 0.00 0.00 3.41
72 73 1.160989 TCTCGCTGTCACTCTGTCTC 58.839 55.000 0.00 0.00 0.00 3.36
73 74 0.179202 CTCGCTGTCACTCTGTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
74 75 1.799519 CGCTGTCACTCTGTCTCGC 60.800 63.158 0.00 0.00 0.00 5.03
75 76 1.445238 GCTGTCACTCTGTCTCGCC 60.445 63.158 0.00 0.00 0.00 5.54
76 77 1.872197 GCTGTCACTCTGTCTCGCCT 61.872 60.000 0.00 0.00 0.00 5.52
77 78 0.109365 CTGTCACTCTGTCTCGCCTG 60.109 60.000 0.00 0.00 0.00 4.85
78 79 1.445238 GTCACTCTGTCTCGCCTGC 60.445 63.158 0.00 0.00 0.00 4.85
79 80 1.604879 TCACTCTGTCTCGCCTGCT 60.605 57.895 0.00 0.00 0.00 4.24
80 81 1.153862 CACTCTGTCTCGCCTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
81 82 2.347322 ACTCTGTCTCGCCTGCTCC 61.347 63.158 0.00 0.00 0.00 4.70
82 83 2.036414 TCTGTCTCGCCTGCTCCT 59.964 61.111 0.00 0.00 0.00 3.69
106 107 3.912907 GGATGGATCCGTCGGCGT 61.913 66.667 24.57 0.00 37.19 5.68
486 499 1.276989 TCCACCATCTTCGGTAACCAC 59.723 52.381 0.00 0.00 37.07 4.16
493 506 3.672767 TCTTCGGTAACCACTTTCTCC 57.327 47.619 0.00 0.00 0.00 3.71
528 579 5.469373 TGATGCGCTCAATTTGTAGTTAG 57.531 39.130 9.73 0.00 0.00 2.34
537 588 6.578919 GCTCAATTTGTAGTTAGTTTGCTCAC 59.421 38.462 0.00 0.00 0.00 3.51
541 592 7.582667 ATTTGTAGTTAGTTTGCTCACCTTT 57.417 32.000 0.00 0.00 0.00 3.11
548 599 2.887152 AGTTTGCTCACCTTTCATCCAC 59.113 45.455 0.00 0.00 0.00 4.02
751 821 0.320374 TTGGTGATCACTGACGACCC 59.680 55.000 24.50 6.78 0.00 4.46
763 833 2.813474 CGACCCGCTCGCATCAAA 60.813 61.111 0.00 0.00 35.06 2.69
764 834 2.387445 CGACCCGCTCGCATCAAAA 61.387 57.895 0.00 0.00 35.06 2.44
770 840 1.131126 CCGCTCGCATCAAAATTCAGT 59.869 47.619 0.00 0.00 0.00 3.41
781 851 3.509575 TCAAAATTCAGTTCCATTCCCCG 59.490 43.478 0.00 0.00 0.00 5.73
786 856 2.822701 GTTCCATTCCCCGCCGTC 60.823 66.667 0.00 0.00 0.00 4.79
812 882 7.096763 CGCGACGATTTTTCTGTAACTATGATA 60.097 37.037 0.00 0.00 0.00 2.15
831 901 7.767250 ATGATAGTAGCTGATAGTGCAGTAA 57.233 36.000 5.12 0.00 38.17 2.24
844 914 4.392940 AGTGCAGTAATGCTGTTCTTCTT 58.607 39.130 17.03 0.00 46.64 2.52
845 915 4.453819 AGTGCAGTAATGCTGTTCTTCTTC 59.546 41.667 17.03 0.00 46.64 2.87
846 916 4.453819 GTGCAGTAATGCTGTTCTTCTTCT 59.546 41.667 17.03 0.00 46.64 2.85
893 963 9.691362 TTCTGTTAAAGAAATATTTGCCTTGTC 57.309 29.630 5.17 0.38 42.09 3.18
894 964 9.077885 TCTGTTAAAGAAATATTTGCCTTGTCT 57.922 29.630 5.17 0.00 29.54 3.41
895 965 9.696917 CTGTTAAAGAAATATTTGCCTTGTCTT 57.303 29.630 5.17 0.00 0.00 3.01
911 981 7.764443 TGCCTTGTCTTAGTATACTGTGATTTC 59.236 37.037 15.90 3.20 0.00 2.17
942 1012 5.530543 AGAAAGTTCTTGAGCTTCTTCTTGG 59.469 40.000 0.48 0.00 32.55 3.61
984 1054 5.421693 TGGTGGATAAATGAATTGGTCCAAG 59.578 40.000 10.72 0.00 38.25 3.61
1003 1074 6.752285 CCAAGAATGGGGATTGGAAAATAT 57.248 37.500 0.00 0.00 43.51 1.28
1004 1075 7.140522 CCAAGAATGGGGATTGGAAAATATT 57.859 36.000 0.00 0.00 43.51 1.28
1008 1079 8.496534 AGAATGGGGATTGGAAAATATTAAGG 57.503 34.615 0.00 0.00 0.00 2.69
1009 1080 8.073735 AGAATGGGGATTGGAAAATATTAAGGT 58.926 33.333 0.00 0.00 0.00 3.50
1010 1081 7.616528 ATGGGGATTGGAAAATATTAAGGTG 57.383 36.000 0.00 0.00 0.00 4.00
1011 1082 5.365314 TGGGGATTGGAAAATATTAAGGTGC 59.635 40.000 0.00 0.00 0.00 5.01
1012 1083 5.221641 GGGGATTGGAAAATATTAAGGTGCC 60.222 44.000 0.00 0.00 0.00 5.01
1013 1084 5.365314 GGGATTGGAAAATATTAAGGTGCCA 59.635 40.000 0.00 0.00 0.00 4.92
1014 1085 6.043127 GGGATTGGAAAATATTAAGGTGCCAT 59.957 38.462 0.00 0.00 0.00 4.40
1098 1169 5.136105 CCAGCCTCATCCTTATTTAGCTTT 58.864 41.667 0.00 0.00 0.00 3.51
1100 1171 4.582240 AGCCTCATCCTTATTTAGCTTTGC 59.418 41.667 0.00 0.00 0.00 3.68
1101 1172 4.582240 GCCTCATCCTTATTTAGCTTTGCT 59.418 41.667 0.00 0.00 43.41 3.91
1150 1221 8.330302 CAAGTTATTTTTGGCAAACAAGAAGAG 58.670 33.333 13.10 0.00 40.82 2.85
1170 1241 7.605691 AGAAGAGTTTCGAATCAATGAAGACAT 59.394 33.333 8.83 0.00 38.38 3.06
1194 1265 4.103103 CGACGACGCCTGCTCTCA 62.103 66.667 0.00 0.00 0.00 3.27
1325 1396 0.952497 ACCTGTGCATGTCGAAGCTG 60.952 55.000 7.20 0.00 0.00 4.24
1514 1585 2.034066 AAGGACGTGGGCATGTGG 59.966 61.111 0.00 0.00 0.00 4.17
1540 1611 3.250323 CGCGCACGACCAGATCAG 61.250 66.667 8.75 0.00 43.93 2.90
1719 1790 3.126001 TCACCAACCTCATCAAGTGAC 57.874 47.619 0.00 0.00 32.22 3.67
1720 1791 2.705658 TCACCAACCTCATCAAGTGACT 59.294 45.455 0.00 0.00 32.22 3.41
1724 1795 3.999663 CCAACCTCATCAAGTGACTTCTC 59.000 47.826 0.00 0.00 32.22 2.87
1726 1797 3.515562 ACCTCATCAAGTGACTTCTCCT 58.484 45.455 0.00 0.00 32.22 3.69
1737 1808 4.102367 AGTGACTTCTCCTTTTCTTCAGCT 59.898 41.667 0.00 0.00 0.00 4.24
1762 1842 9.619316 CTAAGTACAGTAGCATCTAAATAGCTG 57.381 37.037 0.00 0.00 39.30 4.24
1769 1849 3.629398 AGCATCTAAATAGCTGTTGGCAC 59.371 43.478 0.00 0.00 44.79 5.01
1771 1851 2.627945 TCTAAATAGCTGTTGGCACGG 58.372 47.619 0.00 0.00 44.79 4.94
1830 1910 1.225908 CGTTGTTGTAATCGCGCCC 60.226 57.895 0.00 0.00 0.00 6.13
1975 2078 5.406175 GTGTATGTGTGCAATGCAAAGAAAT 59.594 36.000 10.44 1.36 41.47 2.17
1986 2089 6.089954 GCAATGCAAAGAAATAGGAACAAGAC 59.910 38.462 0.00 0.00 0.00 3.01
1988 2091 4.159120 GCAAAGAAATAGGAACAAGACGC 58.841 43.478 0.00 0.00 0.00 5.19
2095 2208 4.790962 CGCTCAGCCCACCTGCAT 62.791 66.667 0.00 0.00 41.50 3.96
2096 2209 2.591753 GCTCAGCCCACCTGCATA 59.408 61.111 0.00 0.00 41.50 3.14
2116 2244 8.020861 TGCATAAAATTTCAGTTCAATTCAGC 57.979 30.769 0.00 0.00 0.00 4.26
2117 2245 7.874016 TGCATAAAATTTCAGTTCAATTCAGCT 59.126 29.630 0.00 0.00 0.00 4.24
2118 2246 8.378421 GCATAAAATTTCAGTTCAATTCAGCTC 58.622 33.333 0.00 0.00 0.00 4.09
2119 2247 9.414295 CATAAAATTTCAGTTCAATTCAGCTCA 57.586 29.630 0.00 0.00 0.00 4.26
2120 2248 7.941795 AAAATTTCAGTTCAATTCAGCTCAG 57.058 32.000 0.00 0.00 0.00 3.35
2162 2290 0.767375 ATGGAGAAGCACACCACAGT 59.233 50.000 2.76 0.00 41.62 3.55
2163 2291 0.546122 TGGAGAAGCACACCACAGTT 59.454 50.000 0.00 0.00 34.50 3.16
2164 2292 1.230324 GGAGAAGCACACCACAGTTC 58.770 55.000 0.00 0.00 0.00 3.01
2165 2293 1.475034 GGAGAAGCACACCACAGTTCA 60.475 52.381 0.00 0.00 0.00 3.18
2167 2295 2.880890 GAGAAGCACACCACAGTTCATT 59.119 45.455 0.00 0.00 0.00 2.57
2168 2296 2.620115 AGAAGCACACCACAGTTCATTG 59.380 45.455 0.00 0.00 0.00 2.82
2170 2298 1.677576 AGCACACCACAGTTCATTGTG 59.322 47.619 0.00 0.00 46.24 3.33
2177 2305 1.181098 ACAGTTCATTGTGGCAGGGC 61.181 55.000 0.00 0.00 0.00 5.19
2178 2306 1.153524 AGTTCATTGTGGCAGGGCA 59.846 52.632 0.00 0.00 0.00 5.36
2179 2307 0.896940 AGTTCATTGTGGCAGGGCAG 60.897 55.000 0.00 0.00 0.00 4.85
2180 2308 0.895100 GTTCATTGTGGCAGGGCAGA 60.895 55.000 0.00 0.00 0.00 4.26
2199 2327 3.511146 CAGAAGCAGAAGAGAGAAGAGGT 59.489 47.826 0.00 0.00 0.00 3.85
2202 2330 5.777732 AGAAGCAGAAGAGAGAAGAGGTTAA 59.222 40.000 0.00 0.00 0.00 2.01
2203 2331 5.400066 AGCAGAAGAGAGAAGAGGTTAAC 57.600 43.478 0.00 0.00 0.00 2.01
2205 2333 4.170256 CAGAAGAGAGAAGAGGTTAACGC 58.830 47.826 0.00 0.00 0.00 4.84
2206 2334 3.193903 AGAAGAGAGAAGAGGTTAACGCC 59.806 47.826 0.00 0.00 0.00 5.68
2207 2335 1.473278 AGAGAGAAGAGGTTAACGCCG 59.527 52.381 0.00 0.00 0.00 6.46
2236 2364 4.385405 GAGGGCGTGCAGAGCTGT 62.385 66.667 13.01 0.00 34.52 4.40
2256 2384 2.672996 CCTGACTTGGTTGGGCGG 60.673 66.667 0.00 0.00 0.00 6.13
2263 2391 4.697756 TGGTTGGGCGGCTCGAAG 62.698 66.667 9.56 0.00 0.00 3.79
2264 2392 4.388499 GGTTGGGCGGCTCGAAGA 62.388 66.667 9.56 0.00 0.00 2.87
2407 2535 3.009115 TTGCCGGGGAAGAGGAGG 61.009 66.667 2.18 0.00 0.00 4.30
2641 2769 3.134127 GCCATCGCCACCACCTTC 61.134 66.667 0.00 0.00 0.00 3.46
2643 2771 2.671070 CATCGCCACCACCTTCCT 59.329 61.111 0.00 0.00 0.00 3.36
2644 2772 1.746615 CATCGCCACCACCTTCCTG 60.747 63.158 0.00 0.00 0.00 3.86
2645 2773 3.628646 ATCGCCACCACCTTCCTGC 62.629 63.158 0.00 0.00 0.00 4.85
2656 2784 3.965539 CTTCCTGCTGCTCCGGTGG 62.966 68.421 0.00 0.00 0.00 4.61
2693 2821 1.003233 GTGGTGGTGAAGAGGAGGC 60.003 63.158 0.00 0.00 0.00 4.70
2695 2823 0.768221 TGGTGGTGAAGAGGAGGCTT 60.768 55.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.337773 ATCTCAGGCCTCAGGTCAGA 59.662 55.000 2.83 0.00 0.00 3.27
1 2 0.752054 GATCTCAGGCCTCAGGTCAG 59.248 60.000 12.82 0.00 0.00 3.51
2 3 0.041684 TGATCTCAGGCCTCAGGTCA 59.958 55.000 16.79 16.79 0.00 4.02
3 4 1.198713 TTGATCTCAGGCCTCAGGTC 58.801 55.000 10.55 10.55 0.00 3.85
4 5 1.280421 GTTTGATCTCAGGCCTCAGGT 59.720 52.381 2.83 0.00 0.00 4.00
5 6 1.407989 GGTTTGATCTCAGGCCTCAGG 60.408 57.143 2.83 0.00 0.00 3.86
6 7 1.407989 GGGTTTGATCTCAGGCCTCAG 60.408 57.143 0.00 0.00 0.00 3.35
7 8 0.620556 GGGTTTGATCTCAGGCCTCA 59.379 55.000 0.00 0.00 0.00 3.86
8 9 0.620556 TGGGTTTGATCTCAGGCCTC 59.379 55.000 0.00 0.00 0.00 4.70
9 10 0.329596 GTGGGTTTGATCTCAGGCCT 59.670 55.000 0.00 0.00 0.00 5.19
10 11 0.681243 GGTGGGTTTGATCTCAGGCC 60.681 60.000 0.00 0.00 0.00 5.19
11 12 1.026718 CGGTGGGTTTGATCTCAGGC 61.027 60.000 0.00 0.00 0.00 4.85
12 13 1.026718 GCGGTGGGTTTGATCTCAGG 61.027 60.000 0.00 0.00 0.00 3.86
13 14 0.321564 TGCGGTGGGTTTGATCTCAG 60.322 55.000 0.00 0.00 0.00 3.35
14 15 0.321564 CTGCGGTGGGTTTGATCTCA 60.322 55.000 0.00 0.00 0.00 3.27
15 16 0.036388 TCTGCGGTGGGTTTGATCTC 60.036 55.000 0.00 0.00 0.00 2.75
16 17 0.036010 CTCTGCGGTGGGTTTGATCT 60.036 55.000 0.00 0.00 0.00 2.75
17 18 1.648467 GCTCTGCGGTGGGTTTGATC 61.648 60.000 0.00 0.00 0.00 2.92
18 19 1.675641 GCTCTGCGGTGGGTTTGAT 60.676 57.895 0.00 0.00 0.00 2.57
19 20 2.281484 GCTCTGCGGTGGGTTTGA 60.281 61.111 0.00 0.00 0.00 2.69
20 21 3.365265 GGCTCTGCGGTGGGTTTG 61.365 66.667 0.00 0.00 0.00 2.93
21 22 4.660938 GGGCTCTGCGGTGGGTTT 62.661 66.667 0.00 0.00 0.00 3.27
24 25 2.550699 TATTTGGGCTCTGCGGTGGG 62.551 60.000 0.00 0.00 0.00 4.61
25 26 1.077787 TATTTGGGCTCTGCGGTGG 60.078 57.895 0.00 0.00 0.00 4.61
26 27 1.718757 GCTATTTGGGCTCTGCGGTG 61.719 60.000 0.00 0.00 0.00 4.94
27 28 1.452108 GCTATTTGGGCTCTGCGGT 60.452 57.895 0.00 0.00 0.00 5.68
28 29 2.189499 GGCTATTTGGGCTCTGCGG 61.189 63.158 0.00 0.00 0.00 5.69
29 30 2.189499 GGGCTATTTGGGCTCTGCG 61.189 63.158 0.00 0.00 0.00 5.18
30 31 2.189499 CGGGCTATTTGGGCTCTGC 61.189 63.158 0.00 0.00 0.00 4.26
31 32 0.815615 GACGGGCTATTTGGGCTCTG 60.816 60.000 0.00 0.00 0.00 3.35
32 33 1.527370 GACGGGCTATTTGGGCTCT 59.473 57.895 0.00 0.00 0.00 4.09
33 34 1.887707 CGACGGGCTATTTGGGCTC 60.888 63.158 0.00 0.00 0.00 4.70
34 35 2.189521 CGACGGGCTATTTGGGCT 59.810 61.111 0.00 0.00 0.00 5.19
35 36 1.712018 GAACGACGGGCTATTTGGGC 61.712 60.000 0.00 0.00 0.00 5.36
36 37 0.107848 AGAACGACGGGCTATTTGGG 60.108 55.000 0.00 0.00 0.00 4.12
37 38 1.287425 GAGAACGACGGGCTATTTGG 58.713 55.000 0.00 0.00 0.00 3.28
38 39 0.921347 CGAGAACGACGGGCTATTTG 59.079 55.000 0.00 0.00 42.66 2.32
39 40 0.804933 GCGAGAACGACGGGCTATTT 60.805 55.000 0.00 0.00 42.66 1.40
40 41 1.226888 GCGAGAACGACGGGCTATT 60.227 57.895 0.00 0.00 42.66 1.73
41 42 2.119655 AGCGAGAACGACGGGCTAT 61.120 57.895 0.00 0.00 42.66 2.97
42 43 2.749044 AGCGAGAACGACGGGCTA 60.749 61.111 0.00 0.00 42.66 3.93
43 44 4.421479 CAGCGAGAACGACGGGCT 62.421 66.667 0.00 0.00 42.66 5.19
44 45 4.719369 ACAGCGAGAACGACGGGC 62.719 66.667 0.00 0.00 42.66 6.13
45 46 2.504244 GACAGCGAGAACGACGGG 60.504 66.667 0.00 0.00 42.66 5.28
46 47 2.081212 GTGACAGCGAGAACGACGG 61.081 63.158 0.00 0.00 42.66 4.79
47 48 1.060726 GAGTGACAGCGAGAACGACG 61.061 60.000 0.00 0.00 42.66 5.12
48 49 0.238817 AGAGTGACAGCGAGAACGAC 59.761 55.000 0.00 0.00 42.66 4.34
49 50 0.238553 CAGAGTGACAGCGAGAACGA 59.761 55.000 0.00 0.00 42.66 3.85
50 51 0.039978 ACAGAGTGACAGCGAGAACG 60.040 55.000 0.00 0.00 42.93 3.95
51 52 1.268352 AGACAGAGTGACAGCGAGAAC 59.732 52.381 0.00 0.00 0.00 3.01
52 53 1.537638 GAGACAGAGTGACAGCGAGAA 59.462 52.381 0.00 0.00 0.00 2.87
53 54 1.160989 GAGACAGAGTGACAGCGAGA 58.839 55.000 0.00 0.00 0.00 4.04
54 55 0.179202 CGAGACAGAGTGACAGCGAG 60.179 60.000 0.00 0.00 0.00 5.03
55 56 1.869690 CGAGACAGAGTGACAGCGA 59.130 57.895 0.00 0.00 0.00 4.93
56 57 1.799519 GCGAGACAGAGTGACAGCG 60.800 63.158 0.00 0.00 0.00 5.18
57 58 1.445238 GGCGAGACAGAGTGACAGC 60.445 63.158 0.00 0.00 0.00 4.40
58 59 0.109365 CAGGCGAGACAGAGTGACAG 60.109 60.000 0.00 0.00 0.00 3.51
59 60 1.959848 CAGGCGAGACAGAGTGACA 59.040 57.895 0.00 0.00 0.00 3.58
60 61 1.445238 GCAGGCGAGACAGAGTGAC 60.445 63.158 0.00 0.00 0.00 3.67
61 62 1.590610 GAGCAGGCGAGACAGAGTGA 61.591 60.000 0.00 0.00 0.00 3.41
62 63 1.153862 GAGCAGGCGAGACAGAGTG 60.154 63.158 0.00 0.00 0.00 3.51
63 64 2.347322 GGAGCAGGCGAGACAGAGT 61.347 63.158 0.00 0.00 0.00 3.24
64 65 2.003658 GAGGAGCAGGCGAGACAGAG 62.004 65.000 0.00 0.00 0.00 3.35
65 66 2.036414 AGGAGCAGGCGAGACAGA 59.964 61.111 0.00 0.00 0.00 3.41
66 67 2.282147 CTGAGGAGCAGGCGAGACAG 62.282 65.000 0.00 0.00 41.07 3.51
67 68 2.283173 TGAGGAGCAGGCGAGACA 60.283 61.111 0.00 0.00 0.00 3.41
68 69 1.391157 ATCTGAGGAGCAGGCGAGAC 61.391 60.000 0.00 0.00 44.98 3.36
69 70 1.076412 ATCTGAGGAGCAGGCGAGA 60.076 57.895 0.00 0.00 44.98 4.04
70 71 1.363443 GATCTGAGGAGCAGGCGAG 59.637 63.158 0.00 0.00 44.98 5.03
71 72 2.484928 CGATCTGAGGAGCAGGCGA 61.485 63.158 0.00 0.00 44.98 5.54
72 73 2.027314 CGATCTGAGGAGCAGGCG 59.973 66.667 0.00 0.00 44.98 5.52
73 74 1.470996 ATCCGATCTGAGGAGCAGGC 61.471 60.000 0.00 0.00 44.98 4.85
74 75 0.317799 CATCCGATCTGAGGAGCAGG 59.682 60.000 0.00 0.00 44.98 4.85
75 76 0.317799 CCATCCGATCTGAGGAGCAG 59.682 60.000 0.00 0.00 46.31 4.24
76 77 0.106015 TCCATCCGATCTGAGGAGCA 60.106 55.000 0.00 0.00 41.66 4.26
77 78 1.204467 GATCCATCCGATCTGAGGAGC 59.796 57.143 0.00 3.36 43.65 4.70
78 79 1.824230 GGATCCATCCGATCTGAGGAG 59.176 57.143 6.95 0.00 45.90 3.69
79 80 1.930251 GGATCCATCCGATCTGAGGA 58.070 55.000 6.95 4.45 45.90 3.71
405 418 1.529713 GTAGGCGAGGAGGGAGAGG 60.530 68.421 0.00 0.00 0.00 3.69
486 499 1.656652 ATCAATGTCGCCGGAGAAAG 58.343 50.000 10.32 0.02 0.00 2.62
493 506 0.655337 CGCATCAATCAATGTCGCCG 60.655 55.000 0.00 0.00 0.00 6.46
522 572 5.938125 GGATGAAAGGTGAGCAAACTAACTA 59.062 40.000 0.00 0.00 0.00 2.24
523 573 4.762251 GGATGAAAGGTGAGCAAACTAACT 59.238 41.667 0.00 0.00 0.00 2.24
528 579 2.887152 AGTGGATGAAAGGTGAGCAAAC 59.113 45.455 0.00 0.00 0.00 2.93
537 588 3.068590 AGCAACAACAAGTGGATGAAAGG 59.931 43.478 0.00 0.00 0.00 3.11
541 592 2.929641 TGAGCAACAACAAGTGGATGA 58.070 42.857 0.00 0.00 0.00 2.92
548 599 7.416154 AAATGATCAAATGAGCAACAACAAG 57.584 32.000 5.37 0.00 44.14 3.16
618 688 3.101209 CATCCACATGAACCGCGG 58.899 61.111 26.86 26.86 30.57 6.46
619 689 2.404789 GCATCCACATGAACCGCG 59.595 61.111 0.00 0.00 30.57 6.46
620 690 2.800736 GGCATCCACATGAACCGC 59.199 61.111 0.00 0.00 30.57 5.68
623 693 2.106074 TCGCGGCATCCACATGAAC 61.106 57.895 6.13 0.00 30.57 3.18
624 694 2.106074 GTCGCGGCATCCACATGAA 61.106 57.895 5.47 0.00 30.57 2.57
625 695 2.511373 GTCGCGGCATCCACATGA 60.511 61.111 5.47 0.00 30.57 3.07
626 696 3.928769 CGTCGCGGCATCCACATG 61.929 66.667 12.89 0.00 0.00 3.21
651 721 3.490761 CGCTTCTTCTTCCTCCTCATCTC 60.491 52.174 0.00 0.00 0.00 2.75
751 821 2.532531 ACTGAATTTTGATGCGAGCG 57.467 45.000 0.00 0.00 0.00 5.03
763 833 1.474330 GCGGGGAATGGAACTGAATT 58.526 50.000 0.00 0.00 0.00 2.17
764 834 0.395724 GGCGGGGAATGGAACTGAAT 60.396 55.000 0.00 0.00 0.00 2.57
770 840 4.460683 CGACGGCGGGGAATGGAA 62.461 66.667 13.24 0.00 0.00 3.53
786 856 3.700130 AGTTACAGAAAAATCGTCGCG 57.300 42.857 0.00 0.00 0.00 5.87
803 873 7.450014 ACTGCACTATCAGCTACTATCATAGTT 59.550 37.037 1.69 0.00 37.62 2.24
831 901 4.453819 GCACTGTAAGAAGAAGAACAGCAT 59.546 41.667 1.43 0.00 42.44 3.79
844 914 0.670546 GGCGAGCAAGCACTGTAAGA 60.671 55.000 5.80 0.00 39.27 2.10
845 915 0.950555 TGGCGAGCAAGCACTGTAAG 60.951 55.000 5.80 0.00 39.27 2.34
846 916 0.533978 TTGGCGAGCAAGCACTGTAA 60.534 50.000 5.80 0.00 39.27 2.41
887 957 9.522804 GAGAAATCACAGTATACTAAGACAAGG 57.477 37.037 4.74 0.00 0.00 3.61
893 963 8.932945 TTGCTGAGAAATCACAGTATACTAAG 57.067 34.615 4.74 1.22 37.00 2.18
894 964 8.749354 TCTTGCTGAGAAATCACAGTATACTAA 58.251 33.333 4.74 0.00 37.00 2.24
895 965 8.293699 TCTTGCTGAGAAATCACAGTATACTA 57.706 34.615 4.74 0.00 37.00 1.82
977 1047 1.287739 TCCAATCCCCATTCTTGGACC 59.712 52.381 0.00 0.00 46.92 4.46
984 1054 8.150296 CACCTTAATATTTTCCAATCCCCATTC 58.850 37.037 0.00 0.00 0.00 2.67
1098 1169 5.743636 AAATTATGAGGGAAGCAAAAGCA 57.256 34.783 0.00 0.00 0.00 3.91
1100 1171 9.487790 TTGTTAAAATTATGAGGGAAGCAAAAG 57.512 29.630 0.00 0.00 0.00 2.27
1101 1172 9.487790 CTTGTTAAAATTATGAGGGAAGCAAAA 57.512 29.630 0.00 0.00 0.00 2.44
1150 1221 5.954349 GTCGATGTCTTCATTGATTCGAAAC 59.046 40.000 0.00 0.00 43.67 2.78
1421 1492 3.316573 CTCCTGGGCCTTGACGTCC 62.317 68.421 14.12 0.00 0.00 4.79
1719 1790 7.155328 TGTACTTAGCTGAAGAAAAGGAGAAG 58.845 38.462 0.00 0.00 38.65 2.85
1720 1791 7.062749 TGTACTTAGCTGAAGAAAAGGAGAA 57.937 36.000 0.00 0.00 38.65 2.87
1724 1795 6.311690 GCTACTGTACTTAGCTGAAGAAAAGG 59.688 42.308 15.82 0.00 39.17 3.11
1726 1797 6.755206 TGCTACTGTACTTAGCTGAAGAAAA 58.245 36.000 20.81 3.38 42.21 2.29
1737 1808 9.132923 ACAGCTATTTAGATGCTACTGTACTTA 57.867 33.333 2.88 0.00 43.12 2.24
1771 1851 2.668550 AAGAAACGAGGCCACCGC 60.669 61.111 16.07 2.23 0.00 5.68
1812 1892 1.225908 GGGCGCGATTACAACAACG 60.226 57.895 12.10 0.00 0.00 4.10
1975 2078 1.271856 TCCATGGCGTCTTGTTCCTA 58.728 50.000 6.96 0.00 0.00 2.94
1988 2091 1.202964 TCTGGGCATGCTAATCCATGG 60.203 52.381 18.92 4.97 42.18 3.66
2095 2208 8.632679 ACTGAGCTGAATTGAACTGAAATTTTA 58.367 29.630 0.00 0.00 0.00 1.52
2096 2209 7.495055 ACTGAGCTGAATTGAACTGAAATTTT 58.505 30.769 0.00 0.00 0.00 1.82
2116 2244 3.251479 TGGATTCATCGGTGAACTGAG 57.749 47.619 14.50 0.00 46.43 3.35
2117 2245 3.797039 GATGGATTCATCGGTGAACTGA 58.203 45.455 14.50 0.07 46.43 3.41
2139 2267 1.537202 GTGGTGTGCTTCTCCATGAAC 59.463 52.381 0.00 0.00 41.00 3.18
2141 2269 0.764271 TGTGGTGTGCTTCTCCATGA 59.236 50.000 0.00 0.00 41.00 3.07
2162 2290 0.178967 TTCTGCCCTGCCACAATGAA 60.179 50.000 0.00 0.00 0.00 2.57
2163 2291 0.609957 CTTCTGCCCTGCCACAATGA 60.610 55.000 0.00 0.00 0.00 2.57
2164 2292 1.888018 CTTCTGCCCTGCCACAATG 59.112 57.895 0.00 0.00 0.00 2.82
2165 2293 1.980772 GCTTCTGCCCTGCCACAAT 60.981 57.895 0.00 0.00 0.00 2.71
2167 2295 3.855503 CTGCTTCTGCCCTGCCACA 62.856 63.158 0.00 0.00 38.71 4.17
2168 2296 3.060615 CTGCTTCTGCCCTGCCAC 61.061 66.667 0.00 0.00 38.71 5.01
2170 2298 2.034687 TTCTGCTTCTGCCCTGCC 59.965 61.111 0.00 0.00 38.71 4.85
2173 2301 0.903942 CTCTCTTCTGCTTCTGCCCT 59.096 55.000 0.00 0.00 38.71 5.19
2175 2303 2.233431 TCTTCTCTCTTCTGCTTCTGCC 59.767 50.000 0.00 0.00 38.71 4.85
2177 2305 3.511146 ACCTCTTCTCTCTTCTGCTTCTG 59.489 47.826 0.00 0.00 0.00 3.02
2178 2306 3.778265 ACCTCTTCTCTCTTCTGCTTCT 58.222 45.455 0.00 0.00 0.00 2.85
2179 2307 4.535526 AACCTCTTCTCTCTTCTGCTTC 57.464 45.455 0.00 0.00 0.00 3.86
2180 2308 5.565834 CGTTAACCTCTTCTCTCTTCTGCTT 60.566 44.000 0.00 0.00 0.00 3.91
2199 2327 0.168788 CGTAGGTCAGTCGGCGTTAA 59.831 55.000 6.85 0.00 0.00 2.01
2236 2364 2.520458 CCCAACCAAGTCAGGGCA 59.480 61.111 0.00 0.00 33.91 5.36
2306 2434 2.356793 GCTCATCGCCAGGATCGG 60.357 66.667 0.00 0.00 31.28 4.18
2307 2435 1.372748 GAGCTCATCGCCAGGATCG 60.373 63.158 9.40 0.00 40.39 3.69
2407 2535 4.814294 AAGGTCGTCGGATGGCGC 62.814 66.667 0.00 0.00 0.00 6.53
2419 2547 1.304509 GCAGGCTGCTCTTCAAGGTC 61.305 60.000 31.37 0.00 40.96 3.85
2611 2739 3.492353 ATGGCGGACATCCTGGGG 61.492 66.667 0.00 0.00 33.53 4.96
2670 2798 1.669115 CTCTTCACCACCACCAGCG 60.669 63.158 0.00 0.00 0.00 5.18
2672 2800 0.322975 CTCCTCTTCACCACCACCAG 59.677 60.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.