Multiple sequence alignment - TraesCS2D01G245400

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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 TraesCS2D01G245400 chr2D 100.000 2740 0 0 1 2740 280064705 280067444 0.000000e+00 5060
1 TraesCS2D01G245400 chr6B 89.241 2779 223 42 1 2740 47737676 47734935 0.000000e+00 3406
2 TraesCS2D01G245400 chr6B 89.097 2779 227 46 1 2740 47698586 47695845 0.000000e+00 3384
3 TraesCS2D01G245400 chr6B 88.989 2779 230 42 1 2740 47658625 47655884 0.000000e+00 3367
4 TraesCS2D01G245400 chr7B 91.044 2155 164 15 1 2137 535642064 535644207 0.000000e+00 2883
5 TraesCS2D01G245400 chr7B 87.023 524 44 18 2225 2740 535644326 535644833 1.100000e-158 569
6 TraesCS2D01G245400 chr6A 90.863 2156 163 14 1 2137 584410276 584412416 0.000000e+00 2859
7 TraesCS2D01G245400 chr6A 90.255 2155 159 17 1 2137 570353059 570355180 0.000000e+00 2769
8 TraesCS2D01G245400 chr6A 89.444 881 77 10 1 869 584418570 584419446 0.000000e+00 1098
9 TraesCS2D01G245400 chr6A 89.241 883 79 10 1 871 570361336 570362214 0.000000e+00 1090
10 TraesCS2D01G245400 chr6A 86.476 525 45 17 2225 2740 570355299 570355806 1.110000e-153 553
11 TraesCS2D01G245400 chr6A 86.450 524 46 19 2225 2740 584412535 584413041 3.990000e-153 551
12 TraesCS2D01G245400 chr1B 90.487 2155 155 19 1 2137 610379384 610381506 0.000000e+00 2798
13 TraesCS2D01G245400 chr1B 86.857 525 43 17 2225 2740 610381625 610382132 5.120000e-157 564
14 TraesCS2D01G245400 chr4A 90.255 2155 160 20 1 2137 739023697 739021575 0.000000e+00 2771
15 TraesCS2D01G245400 chr4A 90.019 2154 166 13 1 2137 611655210 611657331 0.000000e+00 2741
16 TraesCS2D01G245400 chr4A 87.238 525 41 17 2225 2740 739021456 739020949 2.370000e-160 575
17 TraesCS2D01G245400 chr4A 86.857 525 43 17 2225 2740 611657450 611657957 5.120000e-157 564
18 TraesCS2D01G245400 chr2B 90.087 1725 131 18 421 2137 626032647 626034339 0.000000e+00 2202
19 TraesCS2D01G245400 chr2B 89.683 882 75 10 1 870 626040496 626041373 0.000000e+00 1110
20 TraesCS2D01G245400 chr2B 86.857 525 43 17 2225 2740 626034458 626034965 5.120000e-157 564
21 TraesCS2D01G245400 chr2A 91.950 882 60 2 1 871 342135495 342134614 0.000000e+00 1225
22 TraesCS2D01G245400 chr1A 88.889 882 82 10 1 870 533311616 533312493 0.000000e+00 1072


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 TraesCS2D01G245400 chr2D 280064705 280067444 2739 False 5060.0 5060 100.0000 1 2740 1 chr2D.!!$F1 2739
1 TraesCS2D01G245400 chr6B 47734935 47737676 2741 True 3406.0 3406 89.2410 1 2740 1 chr6B.!!$R3 2739
2 TraesCS2D01G245400 chr6B 47695845 47698586 2741 True 3384.0 3384 89.0970 1 2740 1 chr6B.!!$R2 2739
3 TraesCS2D01G245400 chr6B 47655884 47658625 2741 True 3367.0 3367 88.9890 1 2740 1 chr6B.!!$R1 2739
4 TraesCS2D01G245400 chr7B 535642064 535644833 2769 False 1726.0 2883 89.0335 1 2740 2 chr7B.!!$F1 2739
5 TraesCS2D01G245400 chr6A 584410276 584413041 2765 False 1705.0 2859 88.6565 1 2740 2 chr6A.!!$F4 2739
6 TraesCS2D01G245400 chr6A 570353059 570355806 2747 False 1661.0 2769 88.3655 1 2740 2 chr6A.!!$F3 2739
7 TraesCS2D01G245400 chr6A 584418570 584419446 876 False 1098.0 1098 89.4440 1 869 1 chr6A.!!$F2 868
8 TraesCS2D01G245400 chr6A 570361336 570362214 878 False 1090.0 1090 89.2410 1 871 1 chr6A.!!$F1 870
9 TraesCS2D01G245400 chr1B 610379384 610382132 2748 False 1681.0 2798 88.6720 1 2740 2 chr1B.!!$F1 2739
10 TraesCS2D01G245400 chr4A 739020949 739023697 2748 True 1673.0 2771 88.7465 1 2740 2 chr4A.!!$R1 2739
11 TraesCS2D01G245400 chr4A 611655210 611657957 2747 False 1652.5 2741 88.4380 1 2740 2 chr4A.!!$F1 2739
12 TraesCS2D01G245400 chr2B 626032647 626034965 2318 False 1383.0 2202 88.4720 421 2740 2 chr2B.!!$F2 2319
13 TraesCS2D01G245400 chr2B 626040496 626041373 877 False 1110.0 1110 89.6830 1 870 1 chr2B.!!$F1 869
14 TraesCS2D01G245400 chr2A 342134614 342135495 881 True 1225.0 1225 91.9500 1 871 1 chr2A.!!$R1 870
15 TraesCS2D01G245400 chr1A 533311616 533312493 877 False 1072.0 1072 88.8890 1 870 1 chr1A.!!$F1 869

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
272 283 1.064296 CGTCGTGATTCCCGGAGAG 59.936 63.158 0.73 0.0 0.0 3.20 F
651 667 1.135915 AGAGGAAGTGCTATCAGTGCG 59.864 52.381 0.00 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1248 1.002033 CAGACAACTGGTTGAGCAAGC 60.002 52.381 18.63 5.52 42.93 4.01 R
2531 2618 0.395586 TTGGCCAGCACACTCTTGTT 60.396 50.000 5.11 0.00 31.66 2.83 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
251 262 1.276421 CCTCACACAAGTAGGGGACTG 59.724 57.143 0.00 0.00 43.88 3.51
272 283 1.064296 CGTCGTGATTCCCGGAGAG 59.936 63.158 0.73 0.00 0.00 3.20
488 503 8.023128 CCCAACATACTCACTATTGTTTTTCTG 58.977 37.037 0.00 0.00 0.00 3.02
489 504 7.538678 CCAACATACTCACTATTGTTTTTCTGC 59.461 37.037 0.00 0.00 0.00 4.26
490 505 7.986085 ACATACTCACTATTGTTTTTCTGCT 57.014 32.000 0.00 0.00 0.00 4.24
496 511 6.299141 TCACTATTGTTTTTCTGCTCTTCCT 58.701 36.000 0.00 0.00 0.00 3.36
552 567 3.567397 GGTGAGGAGTTAGAGGAGCATA 58.433 50.000 0.00 0.00 0.00 3.14
651 667 1.135915 AGAGGAAGTGCTATCAGTGCG 59.864 52.381 0.00 0.00 0.00 5.34
710 726 8.999431 CACTAGCTTGTCTTTGGTTATTAAAGA 58.001 33.333 0.00 0.00 40.71 2.52
733 749 6.814146 AGAGTGTAAGCTGCTATGTAAAGAAC 59.186 38.462 0.90 0.00 0.00 3.01
774 790 2.023673 CTTGTGCCCTGTTGTTCTGAA 58.976 47.619 0.00 0.00 0.00 3.02
795 811 5.887598 TGAAATATGCTACTCATGCCTTGTT 59.112 36.000 0.00 0.00 36.63 2.83
809 826 6.208402 TCATGCCTTGTTTGCTTATGAGTTTA 59.792 34.615 0.00 0.00 0.00 2.01
810 827 6.398234 TGCCTTGTTTGCTTATGAGTTTAA 57.602 33.333 0.00 0.00 0.00 1.52
811 828 6.446318 TGCCTTGTTTGCTTATGAGTTTAAG 58.554 36.000 0.00 0.00 33.24 1.85
842 859 1.548973 GACACGGCGACTGTCACTTG 61.549 60.000 21.31 6.33 37.97 3.16
889 906 4.286032 ACAGTTTTAGTGGTATCAGAGCCA 59.714 41.667 0.00 0.00 0.00 4.75
890 907 4.872691 CAGTTTTAGTGGTATCAGAGCCAG 59.127 45.833 0.00 0.00 35.14 4.85
905 923 7.034685 TCAGAGCCAGGTTTAAAAACTAAAC 57.965 36.000 5.62 0.00 38.89 2.01
993 1011 5.184892 AGAGGGTTCATGAGCAAACTAAT 57.815 39.130 11.93 0.00 0.00 1.73
1072 1090 4.864726 AGGGACGTACTAGAATAGGTTGT 58.135 43.478 0.00 0.00 44.97 3.32
1095 1113 7.752638 TGTATAGTAAGGCTATGGAGTAGTCA 58.247 38.462 0.00 0.00 40.41 3.41
1120 1138 3.702045 GGATAGGGTAGTAGCTATGCTGG 59.298 52.174 0.00 0.00 40.10 4.85
1125 1143 3.243907 GGGTAGTAGCTATGCTGGTTCTG 60.244 52.174 0.00 0.00 40.10 3.02
1129 1147 4.508662 AGTAGCTATGCTGGTTCTGTTTC 58.491 43.478 0.00 0.00 40.10 2.78
1168 1186 3.454719 TGGATGTGTTGTCCAATCCAT 57.545 42.857 0.00 0.00 42.56 3.41
1230 1248 3.283684 TTTGTGGCGCTGTTCGGG 61.284 61.111 7.64 0.00 38.94 5.14
1238 1257 2.669569 GCTGTTCGGGCTTGCTCA 60.670 61.111 0.00 0.00 0.00 4.26
1260 1279 2.743928 GTTGTCTGCTGGAGGCCG 60.744 66.667 0.00 0.00 40.92 6.13
1344 1363 1.522676 CACGTGTATTATGAGGCTGCG 59.477 52.381 7.58 0.00 0.00 5.18
1403 1422 2.890371 GGTGATCCACGCCGTAGT 59.110 61.111 0.00 0.00 39.46 2.73
1492 1511 1.062206 GATCTGCGCAAGAAGCTGC 59.938 57.895 13.05 0.00 45.29 5.25
1531 1550 3.941573 TGTGCTGAGCTGATGAACATTA 58.058 40.909 5.83 0.00 0.00 1.90
1578 1597 1.260538 TTCTGGAGCGCCTCACTCAT 61.261 55.000 8.34 0.00 35.79 2.90
1598 1617 4.277423 TCATAGGTTCTATCGTCGCATTCA 59.723 41.667 0.00 0.00 0.00 2.57
1602 1621 3.179830 GTTCTATCGTCGCATTCACTGT 58.820 45.455 0.00 0.00 0.00 3.55
1659 1678 3.435186 GGAAGTTCCAGCGGCAGC 61.435 66.667 17.44 0.00 45.58 5.25
1678 1697 1.376466 GTGTGAGCAGTGGATGGGT 59.624 57.895 0.00 0.00 0.00 4.51
1772 1791 0.692756 TGAGTGTGGGTGGTTCAGGA 60.693 55.000 0.00 0.00 0.00 3.86
1862 1883 5.511545 GGGAGCCTCTAGTTATGGTGTTATG 60.512 48.000 0.00 0.00 0.00 1.90
1865 1886 5.839063 AGCCTCTAGTTATGGTGTTATGCTA 59.161 40.000 0.00 0.00 0.00 3.49
1885 1911 7.119709 TGCTATGCTTGTAATGTAAGGACTA 57.880 36.000 0.00 0.00 0.00 2.59
1982 2013 2.912956 AGTTGGATCCTGGTGAAGCTAA 59.087 45.455 14.23 0.00 0.00 3.09
1983 2014 3.330701 AGTTGGATCCTGGTGAAGCTAAA 59.669 43.478 14.23 0.00 0.00 1.85
1984 2015 3.634397 TGGATCCTGGTGAAGCTAAAG 57.366 47.619 14.23 0.00 0.00 1.85
2029 2060 7.209471 TGTTTGTTTTGCCGATTACTATCTT 57.791 32.000 0.00 0.00 0.00 2.40
2061 2092 7.155328 AGAACATCTCGTGACTAATTTGTTCT 58.845 34.615 18.85 18.85 44.18 3.01
2063 2094 7.730364 ACATCTCGTGACTAATTTGTTCTTT 57.270 32.000 0.00 0.00 0.00 2.52
2064 2095 8.154649 ACATCTCGTGACTAATTTGTTCTTTT 57.845 30.769 0.00 0.00 0.00 2.27
2065 2096 8.283291 ACATCTCGTGACTAATTTGTTCTTTTC 58.717 33.333 0.00 0.00 0.00 2.29
2066 2097 6.873656 TCTCGTGACTAATTTGTTCTTTTCG 58.126 36.000 0.00 0.00 0.00 3.46
2071 2102 8.433126 CGTGACTAATTTGTTCTTTTCGATAGT 58.567 33.333 0.00 0.00 37.40 2.12
2082 2117 9.999009 TGTTCTTTTCGATAGTAGTAGTATGTG 57.001 33.333 2.07 0.00 37.40 3.21
2084 2119 9.999009 TTCTTTTCGATAGTAGTAGTATGTGTG 57.001 33.333 2.07 0.00 37.40 3.82
2085 2120 9.170734 TCTTTTCGATAGTAGTAGTATGTGTGT 57.829 33.333 2.07 0.00 37.40 3.72
2095 2130 9.902684 AGTAGTAGTATGTGTGTATAGTTCTGT 57.097 33.333 0.00 0.00 0.00 3.41
2103 2138 6.578944 TGTGTGTATAGTTCTGTTGAAGTGT 58.421 36.000 0.00 0.00 36.59 3.55
2105 2140 6.924060 GTGTGTATAGTTCTGTTGAAGTGTCT 59.076 38.462 0.00 0.00 36.59 3.41
2117 2152 4.871933 TGAAGTGTCTTGATGAGTGCTA 57.128 40.909 0.00 0.00 0.00 3.49
2121 2156 5.070770 AGTGTCTTGATGAGTGCTAAGAG 57.929 43.478 0.00 0.00 30.51 2.85
2123 2158 5.011533 AGTGTCTTGATGAGTGCTAAGAGTT 59.988 40.000 0.00 0.00 30.51 3.01
2124 2159 5.698545 GTGTCTTGATGAGTGCTAAGAGTTT 59.301 40.000 0.00 0.00 30.51 2.66
2127 2162 6.090628 GTCTTGATGAGTGCTAAGAGTTTGAG 59.909 42.308 0.00 0.00 30.51 3.02
2137 2172 4.757149 GCTAAGAGTTTGAGCTTTCTGGAA 59.243 41.667 0.00 0.00 33.28 3.53
2138 2173 5.239525 GCTAAGAGTTTGAGCTTTCTGGAAA 59.760 40.000 0.00 0.00 33.28 3.13
2141 2176 6.141560 AGAGTTTGAGCTTTCTGGAAAAAG 57.858 37.500 0.00 0.00 38.91 2.27
2142 2177 5.888161 AGAGTTTGAGCTTTCTGGAAAAAGA 59.112 36.000 0.00 0.00 38.30 2.52
2143 2178 6.039159 AGAGTTTGAGCTTTCTGGAAAAAGAG 59.961 38.462 0.00 0.00 38.30 2.85
2147 2182 6.773976 TGAGCTTTCTGGAAAAAGAGAAAA 57.226 33.333 0.00 0.00 37.66 2.29
2148 2183 7.352079 TGAGCTTTCTGGAAAAAGAGAAAAT 57.648 32.000 0.00 0.00 37.66 1.82
2149 2184 7.785033 TGAGCTTTCTGGAAAAAGAGAAAATT 58.215 30.769 0.00 0.00 37.66 1.82
2150 2185 8.260114 TGAGCTTTCTGGAAAAAGAGAAAATTT 58.740 29.630 0.00 0.00 37.66 1.82
2151 2186 8.429493 AGCTTTCTGGAAAAAGAGAAAATTTG 57.571 30.769 0.00 0.00 37.66 2.32
2152 2187 7.496920 AGCTTTCTGGAAAAAGAGAAAATTTGG 59.503 33.333 0.00 0.00 37.66 3.28
2155 2190 7.181569 TCTGGAAAAAGAGAAAATTTGGTGT 57.818 32.000 0.00 0.00 0.00 4.16
2157 2192 7.548780 TCTGGAAAAAGAGAAAATTTGGTGTTG 59.451 33.333 0.00 0.00 0.00 3.33
2158 2193 6.093357 TGGAAAAAGAGAAAATTTGGTGTTGC 59.907 34.615 0.00 0.00 0.00 4.17
2159 2194 6.435430 AAAAAGAGAAAATTTGGTGTTGCC 57.565 33.333 0.00 0.00 37.90 4.52
2160 2195 3.751479 AGAGAAAATTTGGTGTTGCCC 57.249 42.857 0.00 0.00 36.04 5.36
2161 2196 3.037549 AGAGAAAATTTGGTGTTGCCCA 58.962 40.909 0.00 0.00 36.04 5.36
2163 2198 1.872952 GAAAATTTGGTGTTGCCCAGC 59.127 47.619 0.00 0.00 42.03 4.85
2164 2199 0.249826 AAATTTGGTGTTGCCCAGCG 60.250 50.000 0.00 0.00 44.68 5.18
2165 2200 1.398958 AATTTGGTGTTGCCCAGCGT 61.399 50.000 0.00 0.00 44.68 5.07
2167 2202 2.290122 TTTGGTGTTGCCCAGCGTTG 62.290 55.000 0.00 0.00 44.68 4.10
2168 2203 3.977244 GGTGTTGCCCAGCGTTGG 61.977 66.667 11.98 11.98 44.60 3.77
2190 2232 6.978338 TGGGATGAACGAATCAGTATAGTAC 58.022 40.000 0.00 0.00 42.53 2.73
2215 2257 1.480954 ACACCCTGTACTATTGGCGAG 59.519 52.381 0.00 0.00 0.00 5.03
2218 2260 1.134521 CCCTGTACTATTGGCGAGCAA 60.135 52.381 0.00 0.00 0.00 3.91
2219 2261 1.933853 CCTGTACTATTGGCGAGCAAC 59.066 52.381 0.00 0.00 0.00 4.17
2241 2320 3.801594 CACGTACTATGCATGCATGTGTA 59.198 43.478 37.43 32.25 37.82 2.90
2247 2328 4.753610 ACTATGCATGCATGTGTAAGCTAG 59.246 41.667 37.43 26.00 37.82 3.42
2249 2330 2.093021 TGCATGCATGTGTAAGCTAGGA 60.093 45.455 26.79 0.00 0.00 2.94
2252 2333 3.251479 TGCATGTGTAAGCTAGGAGTG 57.749 47.619 0.00 0.00 0.00 3.51
2256 2337 4.442052 GCATGTGTAAGCTAGGAGTGATGA 60.442 45.833 0.00 0.00 0.00 2.92
2261 2342 5.357314 GTGTAAGCTAGGAGTGATGAGTGTA 59.643 44.000 0.00 0.00 0.00 2.90
2289 2370 3.478540 GTGGCCTACACCATTCTCC 57.521 57.895 3.32 0.00 44.49 3.71
2290 2371 0.107165 GTGGCCTACACCATTCTCCC 60.107 60.000 3.32 0.00 44.49 4.30
2291 2372 1.279025 TGGCCTACACCATTCTCCCC 61.279 60.000 3.32 0.00 33.75 4.81
2296 2377 2.700897 CCTACACCATTCTCCCCTAGTG 59.299 54.545 0.00 0.00 0.00 2.74
2316 2397 5.570320 AGTGGGCATGTACTGTTTTATCTT 58.430 37.500 0.00 0.00 0.00 2.40
2355 2436 4.204799 TGTCTATACTACGGTGCATGTCT 58.795 43.478 0.00 0.00 0.00 3.41
2356 2437 4.643334 TGTCTATACTACGGTGCATGTCTT 59.357 41.667 0.00 0.00 0.00 3.01
2386 2467 9.269453 ACCTCTTAACAAAACTACTATGTGTTC 57.731 33.333 0.00 0.00 34.43 3.18
2404 2485 8.877864 ATGTGTTCTATGACTAATTTTTCCCA 57.122 30.769 0.00 0.00 0.00 4.37
2408 2495 9.527157 TGTTCTATGACTAATTTTTCCCATTGA 57.473 29.630 0.00 0.00 0.00 2.57
2440 2527 7.041167 TGGCTAATTTGATAAGTTCATCATCGG 60.041 37.037 0.00 0.00 34.95 4.18
2499 2586 5.242838 TGATGGAAATAATTCGGGCAATACC 59.757 40.000 0.00 0.00 36.36 2.73
2502 2589 5.163499 TGGAAATAATTCGGGCAATACCAAC 60.163 40.000 0.00 0.00 35.83 3.77
2512 2599 1.671845 GCAATACCAACGCCGGATTAA 59.328 47.619 5.05 0.00 0.00 1.40
2565 2652 2.025981 TGGCCAATCTGCTCACTAACAT 60.026 45.455 0.61 0.00 0.00 2.71
2573 2660 4.469657 TCTGCTCACTAACATTTTTGGGT 58.530 39.130 0.00 0.00 0.00 4.51
2621 2708 0.032130 TGGATATTCTGGAGCGCGTC 59.968 55.000 8.43 3.87 0.00 5.19
2626 2714 0.108992 ATTCTGGAGCGCGTCGTAAA 60.109 50.000 8.43 0.00 0.00 2.01
2725 2813 1.205893 GAAGCGGAAGACTGGATCACT 59.794 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.243907 ACGGATGGTTCTCACAGTCG 59.756 55.000 0.00 0.00 0.00 4.18
107 108 9.528018 ACGTTCTTAAATTGTTCAAACATCATT 57.472 25.926 0.00 0.00 38.95 2.57
184 185 1.322338 CGCGTACCGTTATTTCAGGTG 59.678 52.381 0.00 0.00 38.90 4.00
332 343 4.634184 TTAAACAAGCGCAAACCTACAA 57.366 36.364 11.47 0.00 0.00 2.41
334 345 5.688176 TGAAATTAAACAAGCGCAAACCTAC 59.312 36.000 11.47 0.00 0.00 3.18
425 436 9.125906 CAAGAATATAAGAATGCAAGCATTAGC 57.874 33.333 19.21 8.96 45.50 3.09
488 503 1.797635 GCGCATATCAGAAGGAAGAGC 59.202 52.381 0.30 0.00 0.00 4.09
489 504 3.058450 CTGCGCATATCAGAAGGAAGAG 58.942 50.000 12.24 0.00 33.54 2.85
490 505 2.695147 TCTGCGCATATCAGAAGGAAGA 59.305 45.455 12.24 0.00 37.61 2.87
496 511 2.543641 CACACTCTGCGCATATCAGAA 58.456 47.619 12.24 0.00 39.77 3.02
552 567 3.821033 GCCTAGGCGTTGATTTATTCCAT 59.179 43.478 20.16 0.00 0.00 3.41
629 645 3.604582 GCACTGATAGCACTTCCTCTTT 58.395 45.455 0.00 0.00 0.00 2.52
684 700 8.999431 TCTTTAATAACCAAAGACAAGCTAGTG 58.001 33.333 0.00 0.00 37.15 2.74
710 726 6.464222 TGTTCTTTACATAGCAGCTTACACT 58.536 36.000 0.00 0.00 0.00 3.55
733 749 8.230486 CACAAGTAATACTTTAGTTCCAGCTTG 58.770 37.037 2.41 0.00 36.03 4.01
774 790 5.450965 GCAAACAAGGCATGAGTAGCATATT 60.451 40.000 0.00 0.00 34.82 1.28
809 826 3.335579 GCCGTGTCCTTATGAGTTTCTT 58.664 45.455 0.00 0.00 0.00 2.52
810 827 2.674177 CGCCGTGTCCTTATGAGTTTCT 60.674 50.000 0.00 0.00 0.00 2.52
811 828 1.659098 CGCCGTGTCCTTATGAGTTTC 59.341 52.381 0.00 0.00 0.00 2.78
993 1011 2.889522 AGGCCAGGGTTATCTCCTAA 57.110 50.000 5.01 0.00 32.49 2.69
1072 1090 7.834681 CCATGACTACTCCATAGCCTTACTATA 59.165 40.741 0.00 0.00 39.71 1.31
1095 1113 4.016105 AGCATAGCTACTACCCTATCCCAT 60.016 45.833 0.00 0.00 36.99 4.00
1120 1138 8.926715 ACATTAGAAAACCAAAGAAACAGAAC 57.073 30.769 0.00 0.00 0.00 3.01
1125 1143 9.974980 TCCATTACATTAGAAAACCAAAGAAAC 57.025 29.630 0.00 0.00 0.00 2.78
1129 1147 9.357652 CACATCCATTACATTAGAAAACCAAAG 57.642 33.333 0.00 0.00 0.00 2.77
1146 1164 3.777087 TGGATTGGACAACACATCCATT 58.223 40.909 1.95 0.00 45.71 3.16
1168 1186 2.557924 GGATGTCAACAAACTCCATGCA 59.442 45.455 0.00 0.00 0.00 3.96
1230 1248 1.002033 CAGACAACTGGTTGAGCAAGC 60.002 52.381 18.63 5.52 42.93 4.01
1232 1250 1.024271 GCAGACAACTGGTTGAGCAA 58.976 50.000 18.63 0.00 42.93 3.91
1352 1371 1.126488 CTGCTCTGCCTCAGGGATAA 58.874 55.000 0.00 0.00 32.95 1.75
1403 1422 5.398603 AATTTCCACATTATGTTCCGCAA 57.601 34.783 0.00 0.00 0.00 4.85
1407 1426 7.839680 ATCCCTAATTTCCACATTATGTTCC 57.160 36.000 0.00 0.00 0.00 3.62
1443 1462 1.918293 CTGCAGGTACCCCAGGTGA 60.918 63.158 18.14 0.00 36.19 4.02
1449 1468 1.153086 CTGATGCTGCAGGTACCCC 60.153 63.158 17.12 0.05 32.26 4.95
1492 1511 1.094073 CAAAGATGCTCGGCCTCCAG 61.094 60.000 0.00 0.00 0.00 3.86
1578 1597 3.630769 AGTGAATGCGACGATAGAACCTA 59.369 43.478 0.00 0.00 41.38 3.08
1602 1621 1.152247 AGCCACAGTGTCCCTCAGA 60.152 57.895 0.00 0.00 0.00 3.27
1659 1678 1.742880 CCCATCCACTGCTCACACG 60.743 63.158 0.00 0.00 0.00 4.49
1678 1697 2.296190 CGGTACTGCTATGGTGCTGATA 59.704 50.000 0.00 0.00 36.10 2.15
1772 1791 3.026694 GTCTATCTTGCAGCCCCAAAAT 58.973 45.455 0.00 0.00 0.00 1.82
1862 1883 7.711339 ACTTAGTCCTTACATTACAAGCATAGC 59.289 37.037 0.00 0.00 0.00 2.97
1865 1886 8.322091 AGAACTTAGTCCTTACATTACAAGCAT 58.678 33.333 0.00 0.00 0.00 3.79
1885 1911 2.443255 ACCATCCCAACACAGAGAACTT 59.557 45.455 0.00 0.00 0.00 2.66
1922 1948 6.884295 AGAACCATATAAGCTAAACAGCAACA 59.116 34.615 0.00 0.00 37.25 3.33
1965 1996 3.914426 TCTTTAGCTTCACCAGGATCC 57.086 47.619 2.48 2.48 0.00 3.36
1982 2013 6.825721 ACATCAACAGAAAGACACTTCTTCTT 59.174 34.615 0.00 0.00 41.56 2.52
1983 2014 6.352516 ACATCAACAGAAAGACACTTCTTCT 58.647 36.000 0.00 0.00 41.56 2.85
1984 2015 6.610741 ACATCAACAGAAAGACACTTCTTC 57.389 37.500 0.00 0.00 41.56 2.87
2045 2076 8.433126 ACTATCGAAAAGAACAAATTAGTCACG 58.567 33.333 5.25 0.00 0.00 4.35
2082 2117 7.652105 TCAAGACACTTCAACAGAACTATACAC 59.348 37.037 0.00 0.00 0.00 2.90
2084 2119 8.651588 CATCAAGACACTTCAACAGAACTATAC 58.348 37.037 0.00 0.00 0.00 1.47
2085 2120 8.585018 TCATCAAGACACTTCAACAGAACTATA 58.415 33.333 0.00 0.00 0.00 1.31
2086 2121 7.445121 TCATCAAGACACTTCAACAGAACTAT 58.555 34.615 0.00 0.00 0.00 2.12
2088 2123 5.674525 TCATCAAGACACTTCAACAGAACT 58.325 37.500 0.00 0.00 0.00 3.01
2089 2124 5.525378 ACTCATCAAGACACTTCAACAGAAC 59.475 40.000 0.00 0.00 0.00 3.01
2090 2125 5.525012 CACTCATCAAGACACTTCAACAGAA 59.475 40.000 0.00 0.00 0.00 3.02
2091 2126 5.052481 CACTCATCAAGACACTTCAACAGA 58.948 41.667 0.00 0.00 0.00 3.41
2092 2127 4.319333 GCACTCATCAAGACACTTCAACAG 60.319 45.833 0.00 0.00 0.00 3.16
2093 2128 3.561310 GCACTCATCAAGACACTTCAACA 59.439 43.478 0.00 0.00 0.00 3.33
2094 2129 3.812053 AGCACTCATCAAGACACTTCAAC 59.188 43.478 0.00 0.00 0.00 3.18
2095 2130 4.077300 AGCACTCATCAAGACACTTCAA 57.923 40.909 0.00 0.00 0.00 2.69
2103 2138 6.101650 TCAAACTCTTAGCACTCATCAAGA 57.898 37.500 0.00 0.00 0.00 3.02
2105 2140 4.692625 GCTCAAACTCTTAGCACTCATCAA 59.307 41.667 0.00 0.00 36.26 2.57
2117 2152 6.378280 TCTTTTTCCAGAAAGCTCAAACTCTT 59.622 34.615 0.00 0.00 36.73 2.85
2121 2156 6.136541 TCTCTTTTTCCAGAAAGCTCAAAC 57.863 37.500 0.00 0.00 36.73 2.93
2123 2158 6.773976 TTTCTCTTTTTCCAGAAAGCTCAA 57.226 33.333 0.00 0.00 34.39 3.02
2124 2159 6.773976 TTTTCTCTTTTTCCAGAAAGCTCA 57.226 33.333 0.00 0.00 39.28 4.26
2127 2162 7.280876 ACCAAATTTTCTCTTTTTCCAGAAAGC 59.719 33.333 0.00 0.00 39.28 3.51
2137 2172 4.881273 GGGCAACACCAAATTTTCTCTTTT 59.119 37.500 0.00 0.00 42.05 2.27
2138 2173 4.080638 TGGGCAACACCAAATTTTCTCTTT 60.081 37.500 0.00 0.00 42.05 2.52
2141 2176 3.392882 CTGGGCAACACCAAATTTTCTC 58.607 45.455 0.00 0.00 40.68 2.87
2142 2177 2.485302 GCTGGGCAACACCAAATTTTCT 60.485 45.455 0.00 0.00 40.68 2.52
2143 2178 1.872952 GCTGGGCAACACCAAATTTTC 59.127 47.619 0.00 0.00 40.68 2.29
2147 2182 1.398958 AACGCTGGGCAACACCAAAT 61.399 50.000 0.00 0.00 40.68 2.32
2148 2183 2.055042 AACGCTGGGCAACACCAAA 61.055 52.632 0.00 0.00 40.68 3.28
2149 2184 2.441164 AACGCTGGGCAACACCAA 60.441 55.556 0.00 0.00 40.68 3.67
2150 2185 3.215568 CAACGCTGGGCAACACCA 61.216 61.111 0.00 0.00 42.05 4.17
2151 2186 3.977244 CCAACGCTGGGCAACACC 61.977 66.667 0.00 0.00 39.30 4.16
2159 2194 3.177600 CGTTCATCCCAACGCTGG 58.822 61.111 0.00 0.00 42.45 4.85
2164 2199 6.281405 ACTATACTGATTCGTTCATCCCAAC 58.719 40.000 0.00 0.00 32.72 3.77
2165 2200 6.479972 ACTATACTGATTCGTTCATCCCAA 57.520 37.500 0.00 0.00 32.72 4.12
2167 2202 7.216973 AGTACTATACTGATTCGTTCATCCC 57.783 40.000 0.00 0.00 37.69 3.85
2168 2203 9.001542 ACTAGTACTATACTGATTCGTTCATCC 57.998 37.037 2.33 0.00 39.81 3.51
2171 2206 9.822185 TGTACTAGTACTATACTGATTCGTTCA 57.178 33.333 28.56 4.54 39.81 3.18
2175 2210 7.877097 AGGGTGTACTAGTACTATACTGATTCG 59.123 40.741 28.56 0.00 39.81 3.34
2212 2254 1.624487 TGCATAGTACGTGTTGCTCG 58.376 50.000 0.00 0.00 36.10 5.03
2215 2257 1.396648 TGCATGCATAGTACGTGTTGC 59.603 47.619 18.46 16.52 35.67 4.17
2218 2260 2.609002 CACATGCATGCATAGTACGTGT 59.391 45.455 31.73 22.05 34.91 4.49
2219 2261 2.609002 ACACATGCATGCATAGTACGTG 59.391 45.455 31.12 31.12 34.91 4.49
2241 2320 5.204292 TCATACACTCATCACTCCTAGCTT 58.796 41.667 0.00 0.00 0.00 3.74
2247 2328 5.335269 CGTCCTATCATACACTCATCACTCC 60.335 48.000 0.00 0.00 0.00 3.85
2249 2330 5.009110 CACGTCCTATCATACACTCATCACT 59.991 44.000 0.00 0.00 0.00 3.41
2252 2333 4.799678 CCACGTCCTATCATACACTCATC 58.200 47.826 0.00 0.00 0.00 2.92
2256 2337 1.687123 GGCCACGTCCTATCATACACT 59.313 52.381 0.00 0.00 0.00 3.55
2261 2342 1.687123 GTGTAGGCCACGTCCTATCAT 59.313 52.381 5.01 0.00 40.54 2.45
2290 2371 3.350219 AAACAGTACATGCCCACTAGG 57.650 47.619 0.00 0.00 39.47 3.02
2291 2372 6.349300 AGATAAAACAGTACATGCCCACTAG 58.651 40.000 0.00 0.00 0.00 2.57
2296 2377 5.163652 GGTCAAGATAAAACAGTACATGCCC 60.164 44.000 0.00 0.00 0.00 5.36
2325 2406 6.823182 TGCACCGTAGTATAGACAAGTACTAA 59.177 38.462 0.00 0.00 35.74 2.24
2328 2409 5.490139 TGCACCGTAGTATAGACAAGTAC 57.510 43.478 0.00 0.00 0.00 2.73
2330 2411 4.401519 ACATGCACCGTAGTATAGACAAGT 59.598 41.667 0.00 0.00 0.00 3.16
2331 2412 4.933330 ACATGCACCGTAGTATAGACAAG 58.067 43.478 0.00 0.00 0.00 3.16
2333 2414 4.204799 AGACATGCACCGTAGTATAGACA 58.795 43.478 0.00 0.00 0.00 3.41
2334 2415 4.832590 AGACATGCACCGTAGTATAGAC 57.167 45.455 0.00 0.00 0.00 2.59
2335 2416 5.183014 CAAGACATGCACCGTAGTATAGA 57.817 43.478 0.00 0.00 0.00 1.98
2355 2436 9.431887 CATAGTAGTTTTGTTAAGAGGTAGCAA 57.568 33.333 0.00 0.00 31.71 3.91
2356 2437 8.591072 ACATAGTAGTTTTGTTAAGAGGTAGCA 58.409 33.333 0.00 0.00 0.00 3.49
2392 2473 8.260114 AGCCAAGTTATCAATGGGAAAAATTAG 58.740 33.333 0.00 0.00 34.71 1.73
2395 2476 6.625532 AGCCAAGTTATCAATGGGAAAAAT 57.374 33.333 0.00 0.00 34.71 1.82
2397 2478 7.732222 ATTAGCCAAGTTATCAATGGGAAAA 57.268 32.000 0.00 0.00 34.71 2.29
2400 2481 6.894654 TCAAATTAGCCAAGTTATCAATGGGA 59.105 34.615 0.00 0.00 34.71 4.37
2401 2482 7.111247 TCAAATTAGCCAAGTTATCAATGGG 57.889 36.000 0.00 0.00 34.71 4.00
2411 2498 8.579850 TGATGAACTTATCAAATTAGCCAAGT 57.420 30.769 0.00 0.00 42.54 3.16
2413 2500 8.344831 CGATGATGAACTTATCAAATTAGCCAA 58.655 33.333 0.00 0.00 42.54 4.52
2435 2522 3.931468 GCCATTATCAGTCATCTCCGATG 59.069 47.826 0.00 0.00 0.00 3.84
2440 2527 3.736720 TGCTGCCATTATCAGTCATCTC 58.263 45.455 0.00 0.00 34.21 2.75
2499 2586 0.661020 GGACCATTAATCCGGCGTTG 59.339 55.000 6.01 0.00 0.00 4.10
2502 2589 0.944386 CTTGGACCATTAATCCGGCG 59.056 55.000 0.00 0.00 39.30 6.46
2512 2599 3.222603 GTTCACCAAGTTCTTGGACCAT 58.777 45.455 30.54 11.46 44.82 3.55
2531 2618 0.395586 TTGGCCAGCACACTCTTGTT 60.396 50.000 5.11 0.00 31.66 2.83
2534 2621 0.403271 AGATTGGCCAGCACACTCTT 59.597 50.000 5.11 0.00 0.00 2.85
2565 2652 4.134563 GTCTCTTGCTGTCTACCCAAAAA 58.865 43.478 0.00 0.00 0.00 1.94
2573 2660 4.621991 GTTGTTGAGTCTCTTGCTGTCTA 58.378 43.478 0.65 0.00 0.00 2.59
2621 2708 3.199677 TCCGGTGGCTATCATTTTTACG 58.800 45.455 0.00 0.00 0.00 3.18
2626 2714 2.332063 CACTCCGGTGGCTATCATTT 57.668 50.000 8.63 0.00 39.59 2.32
2648 2736 5.764686 GCTTGAGTTTTTGAAATTCCCCAAT 59.235 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.