Multiple sequence alignment - TraesCS6A01G308700

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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 TraesCS6A01G308700 chr6A 100.000 2720 0 0 1 2720 543930034 543932753 0.000000e+00 5024.0
1 TraesCS6A01G308700 chr6D 88.173 1226 45 28 801 1986 397629294 397630459 0.000000e+00 1369.0
2 TraesCS6A01G308700 chr6D 84.769 801 74 27 33 821 397628515 397629279 0.000000e+00 760.0
3 TraesCS6A01G308700 chr6D 91.770 243 16 2 2298 2536 397630752 397630994 4.340000e-88 335.0
4 TraesCS6A01G308700 chr6D 90.991 222 7 4 2014 2234 397630517 397630726 1.230000e-73 287.0
5 TraesCS6A01G308700 chr6D 88.136 177 15 3 2549 2720 397635991 397636166 3.550000e-49 206.0
6 TraesCS6A01G308700 chr6D 97.500 40 1 0 1460 1499 102261455 102261494 4.860000e-08 69.4
7 TraesCS6A01G308700 chr6B 86.430 1098 46 40 880 1935 594439196 594440232 0.000000e+00 1107.0
8 TraesCS6A01G308700 chr6B 83.777 752 70 29 1989 2720 594440312 594441031 0.000000e+00 665.0
9 TraesCS6A01G308700 chr6B 79.273 550 59 20 309 812 594438557 594439097 1.560000e-87 333.0
10 TraesCS6A01G308700 chr6B 97.500 40 1 0 1460 1499 188138142 188138181 4.860000e-08 69.4
11 TraesCS6A01G308700 chr7A 84.118 340 39 12 1313 1640 148832512 148832176 5.650000e-82 315.0
12 TraesCS6A01G308700 chr7D 83.383 337 44 10 1313 1640 147579643 147579310 4.400000e-78 302.0
13 TraesCS6A01G308700 chr7D 81.579 228 30 11 1345 1563 634158823 634159047 7.740000e-41 178.0
14 TraesCS6A01G308700 chr7B 83.436 326 43 9 1313 1631 110353074 110352753 2.650000e-75 292.0
15 TraesCS6A01G308700 chr7B 77.686 121 20 6 1460 1575 693200135 693200017 1.750000e-07 67.6


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 TraesCS6A01G308700 chr6A 543930034 543932753 2719 False 5024.000000 5024 100.00000 1 2720 1 chr6A.!!$F1 2719
1 TraesCS6A01G308700 chr6D 397628515 397630994 2479 False 687.750000 1369 88.92575 33 2536 4 chr6D.!!$F3 2503
2 TraesCS6A01G308700 chr6B 594438557 594441031 2474 False 701.666667 1107 83.16000 309 2720 3 chr6B.!!$F2 2411

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
673 711 0.179004 ATGTTTCTCCAACGCCACCA 60.179 50.0 0.0 0.0 38.36 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2446 0.110486 GTCCCAAGAGGCCAAGAACA 59.89 55.0 5.01 0.0 34.51 3.18 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 4.552365 TATGCCTGGAGCTGCGGC 62.552 66.667 25.93 25.93 44.23 6.53
25 26 4.704833 GAGCTGCGGCCACAAGGA 62.705 66.667 15.55 0.00 39.73 3.36
26 27 4.269523 AGCTGCGGCCACAAGGAA 62.270 61.111 15.55 0.00 39.73 3.36
27 28 3.064324 GCTGCGGCCACAAGGAAT 61.064 61.111 6.12 0.00 36.89 3.01
28 29 3.056313 GCTGCGGCCACAAGGAATC 62.056 63.158 6.12 0.00 36.89 2.52
29 30 2.361104 TGCGGCCACAAGGAATCC 60.361 61.111 2.24 0.00 36.89 3.01
30 31 2.361104 GCGGCCACAAGGAATCCA 60.361 61.111 2.24 0.00 36.89 3.41
31 32 2.409870 GCGGCCACAAGGAATCCAG 61.410 63.158 2.24 0.00 36.89 3.86
48 49 1.077644 AGATCCAGGCTGCTGCTTG 60.078 57.895 18.99 18.99 44.57 4.01
57 58 3.564345 CTGCTGCTTGGCCTGGACT 62.564 63.158 3.32 0.00 0.00 3.85
59 60 2.435586 CTGCTTGGCCTGGACTCG 60.436 66.667 3.32 0.00 0.00 4.18
100 101 5.332355 CGCTGGTCTACATAATTAAGCGTTC 60.332 44.000 13.21 0.00 45.21 3.95
101 102 5.050295 GCTGGTCTACATAATTAAGCGTTCC 60.050 44.000 0.00 0.00 0.00 3.62
102 103 5.362263 TGGTCTACATAATTAAGCGTTCCC 58.638 41.667 0.00 0.00 0.00 3.97
103 104 5.129815 TGGTCTACATAATTAAGCGTTCCCT 59.870 40.000 0.00 0.00 0.00 4.20
106 107 7.712205 GGTCTACATAATTAAGCGTTCCCTTAA 59.288 37.037 0.00 0.00 40.44 1.85
107 108 8.762426 GTCTACATAATTAAGCGTTCCCTTAAG 58.238 37.037 0.00 0.00 39.76 1.85
109 110 5.007332 ACATAATTAAGCGTTCCCTTAAGCG 59.993 40.000 0.00 0.00 39.76 4.68
110 111 2.460757 TTAAGCGTTCCCTTAAGCGT 57.539 45.000 0.00 0.00 33.59 5.07
111 112 3.591196 TTAAGCGTTCCCTTAAGCGTA 57.409 42.857 0.00 0.00 33.59 4.42
112 113 2.685850 AAGCGTTCCCTTAAGCGTAT 57.314 45.000 0.00 0.00 34.34 3.06
113 114 2.685850 AGCGTTCCCTTAAGCGTATT 57.314 45.000 0.00 0.00 34.34 1.89
114 115 3.806625 AGCGTTCCCTTAAGCGTATTA 57.193 42.857 0.00 0.00 34.34 0.98
115 116 4.332428 AGCGTTCCCTTAAGCGTATTAT 57.668 40.909 0.00 0.00 34.34 1.28
116 117 5.458041 AGCGTTCCCTTAAGCGTATTATA 57.542 39.130 0.00 0.00 34.34 0.98
117 118 5.225642 AGCGTTCCCTTAAGCGTATTATAC 58.774 41.667 0.00 0.00 34.34 1.47
118 119 4.984161 GCGTTCCCTTAAGCGTATTATACA 59.016 41.667 3.16 0.00 0.00 2.29
119 120 5.463061 GCGTTCCCTTAAGCGTATTATACAA 59.537 40.000 3.16 0.00 0.00 2.41
120 121 6.562825 GCGTTCCCTTAAGCGTATTATACAAC 60.563 42.308 3.16 0.00 0.00 3.32
121 122 6.345250 CGTTCCCTTAAGCGTATTATACAACG 60.345 42.308 3.16 4.30 41.92 4.10
126 127 7.306399 CCCTTAAGCGTATTATACAACGAACTG 60.306 40.741 9.60 0.00 41.55 3.16
130 131 5.742453 AGCGTATTATACAACGAACTGACAG 59.258 40.000 9.60 0.00 41.55 3.51
133 134 6.291112 CGTATTATACAACGAACTGACAGCAG 60.291 42.308 1.25 0.00 43.46 4.24
161 162 2.040278 AGACAGCTATTTGGCCTGAACA 59.960 45.455 3.32 0.00 0.00 3.18
169 170 1.021202 TTGGCCTGAACACGAACAAG 58.979 50.000 3.32 0.00 0.00 3.16
180 181 0.650512 ACGAACAAGCGCCATTATCG 59.349 50.000 2.29 11.22 35.16 2.92
182 183 1.332028 CGAACAAGCGCCATTATCGTC 60.332 52.381 2.29 0.00 0.00 4.20
187 188 2.022129 GCGCCATTATCGTCTCCCG 61.022 63.158 0.00 0.00 38.13 5.14
225 226 1.081892 CAGTACATGCACAGTCAGCC 58.918 55.000 0.00 0.00 0.00 4.85
240 241 4.789075 GCCGCCAGCAGTGCAATG 62.789 66.667 19.20 10.38 42.97 2.82
253 254 0.744281 TGCAATGATCATGCTGCCTG 59.256 50.000 23.31 12.58 44.14 4.85
275 276 7.325694 CCTGTCAGCAAAATCAATTCCTTAAT 58.674 34.615 0.00 0.00 0.00 1.40
276 277 7.490402 CCTGTCAGCAAAATCAATTCCTTAATC 59.510 37.037 0.00 0.00 0.00 1.75
291 293 4.716784 TCCTTAATCATACAGTGCCAGAGT 59.283 41.667 0.00 0.00 0.00 3.24
407 427 2.178890 CAGCAGCAAGATCTCCCGC 61.179 63.158 0.00 0.00 0.00 6.13
411 431 2.110006 GCAAGATCTCCCGCTCCC 59.890 66.667 0.00 0.00 0.00 4.30
502 539 1.687297 GATCCCTTCCGACTCCACCC 61.687 65.000 0.00 0.00 0.00 4.61
519 556 1.353103 CCGGCGCACTTCATCATTC 59.647 57.895 10.83 0.00 0.00 2.67
521 558 0.247814 CGGCGCACTTCATCATTCAC 60.248 55.000 10.83 0.00 0.00 3.18
551 588 3.482156 AGGCGCAGATAAATGTGATCT 57.518 42.857 10.83 0.00 33.82 2.75
596 634 7.172875 GGGATGAAATGAATCTCATGTGACTAG 59.827 40.741 0.00 0.00 37.15 2.57
619 657 1.337817 CGCACTACTATGCCGATCGC 61.338 60.000 10.32 6.08 42.99 4.58
634 672 0.250124 ATCGCCGTCAGAAACAACCA 60.250 50.000 0.00 0.00 0.00 3.67
667 705 3.250762 TGAAGCTGAATGTTTCTCCAACG 59.749 43.478 0.00 0.00 38.36 4.10
669 707 1.401539 GCTGAATGTTTCTCCAACGCC 60.402 52.381 0.00 0.00 38.36 5.68
673 711 0.179004 ATGTTTCTCCAACGCCACCA 60.179 50.000 0.00 0.00 38.36 4.17
674 712 1.098712 TGTTTCTCCAACGCCACCAC 61.099 55.000 0.00 0.00 38.36 4.16
687 725 2.767505 GCCACCACCGGAGAATAATAG 58.232 52.381 9.46 0.00 0.00 1.73
690 728 4.202284 GCCACCACCGGAGAATAATAGTAA 60.202 45.833 9.46 0.00 0.00 2.24
696 734 8.148999 ACCACCGGAGAATAATAGTAAAAGATC 58.851 37.037 9.46 0.00 0.00 2.75
729 784 2.068837 TCGGACCGTGTCATGTTTAC 57.931 50.000 14.79 0.00 33.68 2.01
750 805 0.389391 ACGACTCCAAGTGGACAGTG 59.611 55.000 0.00 0.00 39.78 3.66
759 817 2.280797 TGGACAGTGCCAACGAGC 60.281 61.111 4.08 0.00 34.31 5.03
779 837 0.901124 AACCTCTTCGCTGATCTGCT 59.099 50.000 20.58 0.00 0.00 4.24
799 857 1.079317 GCGAGACGAGGGAGAAAAGC 61.079 60.000 0.00 0.00 0.00 3.51
1055 1196 2.224159 AGACCCAACCACATCGGCT 61.224 57.895 0.00 0.00 39.03 5.52
1083 1224 2.361230 CGCAGGGGTTTCCTTCCC 60.361 66.667 0.00 0.00 45.47 3.97
1091 1232 1.073098 GGTTTCCTTCCCTCCTTCCA 58.927 55.000 0.00 0.00 0.00 3.53
1253 1403 4.244802 CTCGTCCTCCGCGCTCTC 62.245 72.222 5.56 0.00 36.19 3.20
1323 1473 3.958860 GAGCACTGGTGGCAGGGT 61.959 66.667 2.84 0.00 0.00 4.34
1716 1878 1.005450 ACACAACACCACAGGGAAAGT 59.995 47.619 0.00 0.00 38.05 2.66
1727 1889 4.189231 CACAGGGAAAGTAAAGGTATCGG 58.811 47.826 0.00 0.00 0.00 4.18
1807 1969 0.391130 TTTCTCGGATGGTTCGGCTG 60.391 55.000 0.00 0.00 0.00 4.85
1848 2025 4.746466 TCTTCCAGTTCTTTCTCTCCTCT 58.254 43.478 0.00 0.00 0.00 3.69
1855 2032 2.733956 TCTTTCTCTCCTCTCCTGCTC 58.266 52.381 0.00 0.00 0.00 4.26
1857 2034 0.032615 TTCTCTCCTCTCCTGCTCCC 60.033 60.000 0.00 0.00 0.00 4.30
1858 2035 1.217747 TCTCTCCTCTCCTGCTCCCA 61.218 60.000 0.00 0.00 0.00 4.37
1859 2036 0.105555 CTCTCCTCTCCTGCTCCCAT 60.106 60.000 0.00 0.00 0.00 4.00
1860 2037 0.398239 TCTCCTCTCCTGCTCCCATG 60.398 60.000 0.00 0.00 0.00 3.66
1862 2039 0.267054 TCCTCTCCTGCTCCCATGAT 59.733 55.000 0.00 0.00 0.00 2.45
1871 2048 4.351704 TCCTGCTCCCATGATTGATTGATA 59.648 41.667 0.00 0.00 0.00 2.15
1872 2049 5.014860 TCCTGCTCCCATGATTGATTGATAT 59.985 40.000 0.00 0.00 0.00 1.63
1907 2087 8.889717 TGTACAAAGAAAAACGAAGAAGAGAAT 58.110 29.630 0.00 0.00 0.00 2.40
1909 2089 7.418408 ACAAAGAAAAACGAAGAAGAGAATCC 58.582 34.615 0.00 0.00 33.66 3.01
1914 2094 6.884280 AAAACGAAGAAGAGAATCCATTGT 57.116 33.333 0.00 0.00 33.66 2.71
1942 2122 8.761497 ACATTCGTTGTCATACTTATTAATCCG 58.239 33.333 0.00 0.00 30.89 4.18
1943 2123 8.761497 CATTCGTTGTCATACTTATTAATCCGT 58.239 33.333 0.00 0.00 0.00 4.69
1944 2124 7.919313 TCGTTGTCATACTTATTAATCCGTC 57.081 36.000 0.00 0.00 0.00 4.79
1945 2125 7.709947 TCGTTGTCATACTTATTAATCCGTCT 58.290 34.615 0.00 0.00 0.00 4.18
1946 2126 8.192774 TCGTTGTCATACTTATTAATCCGTCTT 58.807 33.333 0.00 0.00 0.00 3.01
1986 2166 4.566759 CGATTACGGCTGAGAAATTCTTCA 59.433 41.667 0.00 0.00 33.28 3.02
1987 2167 5.500931 CGATTACGGCTGAGAAATTCTTCAC 60.501 44.000 0.00 0.00 33.28 3.18
1992 2211 2.222685 GCTGAGAAATTCTTCACTCGCG 60.223 50.000 0.00 0.00 33.64 5.87
1994 2213 2.987149 TGAGAAATTCTTCACTCGCGTC 59.013 45.455 5.77 0.00 33.64 5.19
2007 2226 2.560861 GCGTCAGCAATTTCGCCA 59.439 55.556 0.00 0.00 44.35 5.69
2012 2231 2.676076 GTCAGCAATTTCGCCATTGTT 58.324 42.857 7.85 0.50 36.63 2.83
2013 2232 3.059166 GTCAGCAATTTCGCCATTGTTT 58.941 40.909 7.85 0.00 36.63 2.83
2014 2233 3.494251 GTCAGCAATTTCGCCATTGTTTT 59.506 39.130 7.85 0.00 36.63 2.43
2015 2234 3.493877 TCAGCAATTTCGCCATTGTTTTG 59.506 39.130 7.85 5.42 36.63 2.44
2016 2235 2.223845 AGCAATTTCGCCATTGTTTTGC 59.776 40.909 7.85 0.00 36.63 3.68
2088 2307 4.486125 AGAAGAAGAGGAATTCTGAGCC 57.514 45.455 5.23 0.00 39.47 4.70
2230 2450 3.103911 CACGAGACGGCGGTGTTC 61.104 66.667 13.24 0.00 35.12 3.18
2231 2451 3.292936 ACGAGACGGCGGTGTTCT 61.293 61.111 13.24 4.32 35.12 3.01
2232 2452 2.049433 CGAGACGGCGGTGTTCTT 60.049 61.111 13.24 0.00 0.00 2.52
2233 2453 2.372690 CGAGACGGCGGTGTTCTTG 61.373 63.158 13.24 4.89 0.00 3.02
2234 2454 2.027625 GAGACGGCGGTGTTCTTGG 61.028 63.158 13.24 0.00 0.00 3.61
2235 2455 3.723348 GACGGCGGTGTTCTTGGC 61.723 66.667 13.24 0.00 0.00 4.52
2242 2462 1.237285 CGGTGTTCTTGGCCTCTTGG 61.237 60.000 3.32 0.00 0.00 3.61
2262 2482 0.521735 GACGCATGTCCCCACTTTTC 59.478 55.000 0.00 0.00 39.30 2.29
2263 2483 0.110486 ACGCATGTCCCCACTTTTCT 59.890 50.000 0.00 0.00 0.00 2.52
2264 2484 0.804989 CGCATGTCCCCACTTTTCTC 59.195 55.000 0.00 0.00 0.00 2.87
2265 2485 1.881925 CGCATGTCCCCACTTTTCTCA 60.882 52.381 0.00 0.00 0.00 3.27
2266 2486 2.238521 GCATGTCCCCACTTTTCTCAA 58.761 47.619 0.00 0.00 0.00 3.02
2269 2498 1.214175 TGTCCCCACTTTTCTCAAGCA 59.786 47.619 0.00 0.00 0.00 3.91
2274 2503 4.018506 TCCCCACTTTTCTCAAGCATGATA 60.019 41.667 0.00 0.00 34.37 2.15
2325 2554 1.399440 CTCGCTGTGAATTGGATGGTG 59.601 52.381 0.00 0.00 0.00 4.17
2352 2584 3.614159 ATTGATGTGAATTCATCGCGG 57.386 42.857 12.12 0.00 44.82 6.46
2355 2587 1.528586 GATGTGAATTCATCGCGGGAG 59.471 52.381 12.12 0.52 41.64 4.30
2376 2608 2.856720 GCCGTGATCTCGAGAGAATCAC 60.857 54.545 26.88 26.88 45.03 3.06
2401 2635 1.129326 GCGGTATCGAATTCCAGACG 58.871 55.000 0.00 0.22 39.00 4.18
2460 2694 2.760374 CCGGACCAGAATAGAATGCTC 58.240 52.381 0.00 0.00 0.00 4.26
2536 2784 5.021033 ACTTTGAATGGTTTGTGCAATGA 57.979 34.783 0.00 0.00 0.00 2.57
2537 2785 5.426504 ACTTTGAATGGTTTGTGCAATGAA 58.573 33.333 0.00 0.00 0.00 2.57
2538 2786 5.524646 ACTTTGAATGGTTTGTGCAATGAAG 59.475 36.000 0.00 0.00 0.00 3.02
2539 2787 3.391965 TGAATGGTTTGTGCAATGAAGC 58.608 40.909 0.00 0.00 0.00 3.86
2540 2788 2.460757 ATGGTTTGTGCAATGAAGCC 57.539 45.000 0.00 0.00 0.00 4.35
2541 2789 1.117994 TGGTTTGTGCAATGAAGCCA 58.882 45.000 6.01 6.01 30.75 4.75
2542 2790 1.693062 TGGTTTGTGCAATGAAGCCAT 59.307 42.857 6.01 0.00 28.47 4.40
2543 2791 2.288948 TGGTTTGTGCAATGAAGCCATC 60.289 45.455 6.01 0.00 28.47 3.51
2544 2792 2.288948 GGTTTGTGCAATGAAGCCATCA 60.289 45.455 0.00 0.00 43.67 3.07
2551 2799 3.434053 ATGAAGCCATCATCAGCCC 57.566 52.632 0.00 0.00 45.91 5.19
2559 2807 1.701292 CCATCATCAGCCCATAGTGGA 59.299 52.381 0.00 0.00 40.96 4.02
2565 2813 2.050144 TCAGCCCATAGTGGATTCCTC 58.950 52.381 3.95 0.00 40.96 3.71
2575 2823 8.929671 CCATAGTGGATTCCTCCCTGGAGTAT 62.930 50.000 12.09 5.30 42.81 2.12
2584 2832 3.438668 CCTCCCTGGAGTATGTAGACCAT 60.439 52.174 12.09 0.00 40.44 3.55
2592 2840 5.719563 TGGAGTATGTAGACCATCTTTGACA 59.280 40.000 0.00 0.00 34.86 3.58
2610 2858 7.753132 TCTTTGACAAATATGAAAACCATACGC 59.247 33.333 0.05 0.00 40.29 4.42
2614 2862 6.272318 ACAAATATGAAAACCATACGCCATG 58.728 36.000 0.00 0.00 40.29 3.66
2645 2901 8.879227 TCAATCATGGTCAGGTGTATGAATATA 58.121 33.333 0.00 0.00 33.71 0.86
2649 2905 9.320295 TCATGGTCAGGTGTATGAATATATGTA 57.680 33.333 0.00 0.00 0.00 2.29
2650 2906 9.591792 CATGGTCAGGTGTATGAATATATGTAG 57.408 37.037 0.00 0.00 0.00 2.74
2655 2911 9.034800 TCAGGTGTATGAATATATGTAGCATCA 57.965 33.333 0.00 0.00 0.00 3.07
2656 2912 9.828039 CAGGTGTATGAATATATGTAGCATCAT 57.172 33.333 1.95 1.95 0.00 2.45
2670 2926 7.364522 TGTAGCATCATCTTAACTTTGTCAC 57.635 36.000 0.00 0.00 0.00 3.67
2698 2954 1.694018 GCTGTGACGAGCTCATGCAG 61.694 60.000 15.40 15.62 42.74 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.704833 TCCTTGTGGCCGCAGCTC 62.705 66.667 20.15 0.00 39.73 4.09
9 10 3.574074 ATTCCTTGTGGCCGCAGCT 62.574 57.895 20.15 0.74 39.73 4.24
10 11 3.056313 GATTCCTTGTGGCCGCAGC 62.056 63.158 20.15 0.00 38.76 5.25
11 12 2.409870 GGATTCCTTGTGGCCGCAG 61.410 63.158 20.15 13.31 0.00 5.18
12 13 2.361104 GGATTCCTTGTGGCCGCA 60.361 61.111 16.89 16.89 0.00 5.69
13 14 2.361104 TGGATTCCTTGTGGCCGC 60.361 61.111 10.11 10.11 0.00 6.53
14 15 0.107017 ATCTGGATTCCTTGTGGCCG 60.107 55.000 3.95 0.00 0.00 6.13
15 16 1.685148 GATCTGGATTCCTTGTGGCC 58.315 55.000 3.95 0.00 0.00 5.36
16 17 1.064463 TGGATCTGGATTCCTTGTGGC 60.064 52.381 3.95 0.00 0.00 5.01
17 18 2.422519 CCTGGATCTGGATTCCTTGTGG 60.423 54.545 3.95 0.00 0.00 4.17
18 19 2.928334 CCTGGATCTGGATTCCTTGTG 58.072 52.381 3.95 0.00 0.00 3.33
19 20 1.213926 GCCTGGATCTGGATTCCTTGT 59.786 52.381 3.95 0.00 0.00 3.16
20 21 1.493871 AGCCTGGATCTGGATTCCTTG 59.506 52.381 3.95 0.00 0.00 3.61
21 22 1.493871 CAGCCTGGATCTGGATTCCTT 59.506 52.381 3.95 0.00 0.00 3.36
22 23 1.138568 CAGCCTGGATCTGGATTCCT 58.861 55.000 3.95 0.00 0.00 3.36
23 24 0.536915 GCAGCCTGGATCTGGATTCC 60.537 60.000 0.00 0.00 32.41 3.01
24 25 0.473326 AGCAGCCTGGATCTGGATTC 59.527 55.000 0.00 0.00 32.41 2.52
25 26 0.183014 CAGCAGCCTGGATCTGGATT 59.817 55.000 0.00 0.00 35.38 3.01
26 27 1.837789 CAGCAGCCTGGATCTGGAT 59.162 57.895 0.00 0.48 35.38 3.41
27 28 3.040206 GCAGCAGCCTGGATCTGGA 62.040 63.158 0.00 0.00 39.54 3.86
28 29 2.516460 GCAGCAGCCTGGATCTGG 60.516 66.667 0.00 0.00 39.54 3.86
29 30 1.077644 AAGCAGCAGCCTGGATCTG 60.078 57.895 0.00 2.39 43.56 2.90
30 31 1.077644 CAAGCAGCAGCCTGGATCT 60.078 57.895 0.00 0.00 43.56 2.75
31 32 3.510846 CAAGCAGCAGCCTGGATC 58.489 61.111 0.00 0.00 43.56 3.36
74 75 4.085055 CGCTTAATTATGTAGACCAGCGTG 60.085 45.833 13.21 0.00 42.98 5.34
75 76 4.049186 CGCTTAATTATGTAGACCAGCGT 58.951 43.478 13.21 0.00 42.98 5.07
77 78 5.050295 GGAACGCTTAATTATGTAGACCAGC 60.050 44.000 0.84 0.00 0.00 4.85
100 101 6.698766 AGTTCGTTGTATAATACGCTTAAGGG 59.301 38.462 17.33 17.33 37.66 3.95
101 102 7.433131 TCAGTTCGTTGTATAATACGCTTAAGG 59.567 37.037 4.29 0.00 37.66 2.69
102 103 8.257841 GTCAGTTCGTTGTATAATACGCTTAAG 58.742 37.037 0.00 0.00 37.66 1.85
103 104 7.754475 TGTCAGTTCGTTGTATAATACGCTTAA 59.246 33.333 3.65 0.00 37.66 1.85
106 107 5.643664 TGTCAGTTCGTTGTATAATACGCT 58.356 37.500 3.65 0.00 37.66 5.07
107 108 5.553952 GCTGTCAGTTCGTTGTATAATACGC 60.554 44.000 0.93 0.00 37.66 4.42
109 110 6.750501 TCTGCTGTCAGTTCGTTGTATAATAC 59.249 38.462 0.93 0.00 41.10 1.89
110 111 6.859017 TCTGCTGTCAGTTCGTTGTATAATA 58.141 36.000 0.93 0.00 41.10 0.98
111 112 5.720202 TCTGCTGTCAGTTCGTTGTATAAT 58.280 37.500 0.93 0.00 41.10 1.28
112 113 5.128992 TCTGCTGTCAGTTCGTTGTATAA 57.871 39.130 0.93 0.00 41.10 0.98
113 114 4.776795 TCTGCTGTCAGTTCGTTGTATA 57.223 40.909 0.93 0.00 41.10 1.47
114 115 3.660501 TCTGCTGTCAGTTCGTTGTAT 57.339 42.857 0.93 0.00 41.10 2.29
115 116 3.446310 TTCTGCTGTCAGTTCGTTGTA 57.554 42.857 0.93 0.00 41.10 2.41
116 117 2.309528 TTCTGCTGTCAGTTCGTTGT 57.690 45.000 0.93 0.00 41.10 3.32
117 118 2.866156 TCTTTCTGCTGTCAGTTCGTTG 59.134 45.455 0.93 0.00 41.10 4.10
118 119 3.179443 TCTTTCTGCTGTCAGTTCGTT 57.821 42.857 0.93 0.00 41.10 3.85
119 120 2.890808 TCTTTCTGCTGTCAGTTCGT 57.109 45.000 0.93 0.00 41.10 3.85
120 121 4.560819 GTCTATCTTTCTGCTGTCAGTTCG 59.439 45.833 0.93 0.00 41.10 3.95
121 122 5.473931 TGTCTATCTTTCTGCTGTCAGTTC 58.526 41.667 0.93 0.00 41.10 3.01
126 127 4.122143 AGCTGTCTATCTTTCTGCTGTC 57.878 45.455 0.00 0.00 35.66 3.51
130 131 5.277731 GCCAAATAGCTGTCTATCTTTCTGC 60.278 44.000 0.00 0.00 34.53 4.26
133 134 5.238214 CAGGCCAAATAGCTGTCTATCTTTC 59.762 44.000 5.01 0.00 34.53 2.62
161 162 0.650512 CGATAATGGCGCTTGTTCGT 59.349 50.000 7.64 0.00 0.00 3.85
169 170 3.952811 GGGAGACGATAATGGCGC 58.047 61.111 0.00 0.00 0.00 6.53
180 181 0.250338 AGCAGGTTTTGACGGGAGAC 60.250 55.000 0.00 0.00 0.00 3.36
182 183 0.250295 TGAGCAGGTTTTGACGGGAG 60.250 55.000 0.00 0.00 0.00 4.30
187 188 2.206750 TGTACGTGAGCAGGTTTTGAC 58.793 47.619 0.00 0.00 0.00 3.18
225 226 1.063649 GATCATTGCACTGCTGGCG 59.936 57.895 1.98 0.00 0.00 5.69
253 254 8.937634 ATGATTAAGGAATTGATTTTGCTGAC 57.062 30.769 0.00 0.00 0.00 3.51
259 260 9.807649 GCACTGTATGATTAAGGAATTGATTTT 57.192 29.630 0.00 0.00 0.00 1.82
275 276 1.937191 TGGACTCTGGCACTGTATGA 58.063 50.000 0.00 0.00 0.00 2.15
276 277 2.558378 CATGGACTCTGGCACTGTATG 58.442 52.381 0.00 0.00 0.00 2.39
291 293 0.460811 CTTACTCGCAGCTGCATGGA 60.461 55.000 36.03 24.15 42.21 3.41
411 431 4.742201 CTGTCCTGCGGGTGACGG 62.742 72.222 12.43 4.50 44.51 4.79
479 516 0.386113 GGAGTCGGAAGGGATCGAAG 59.614 60.000 0.00 0.00 37.14 3.79
481 518 1.035932 GTGGAGTCGGAAGGGATCGA 61.036 60.000 0.00 0.00 0.00 3.59
502 539 0.247814 GTGAATGATGAAGTGCGCCG 60.248 55.000 4.18 0.00 0.00 6.46
519 556 1.266718 TCTGCGCCTTTTGCTTTAGTG 59.733 47.619 4.18 0.00 38.05 2.74
521 558 2.927553 ATCTGCGCCTTTTGCTTTAG 57.072 45.000 4.18 0.00 38.05 1.85
562 599 4.463891 AGATTCATTTCATCCCGTGCTTTT 59.536 37.500 0.00 0.00 0.00 2.27
578 615 5.980116 GCGTTACTAGTCACATGAGATTCAT 59.020 40.000 0.00 0.00 37.65 2.57
596 634 2.480224 TCGGCATAGTAGTGCGTTAC 57.520 50.000 0.00 0.00 45.97 2.50
619 657 2.350772 GCTTCATGGTTGTTTCTGACGG 60.351 50.000 0.00 0.00 0.00 4.79
667 705 2.104281 ACTATTATTCTCCGGTGGTGGC 59.896 50.000 0.00 0.00 0.00 5.01
669 707 7.270047 TCTTTTACTATTATTCTCCGGTGGTG 58.730 38.462 0.00 0.00 0.00 4.17
673 711 8.148999 GTGGATCTTTTACTATTATTCTCCGGT 58.851 37.037 0.00 0.00 0.00 5.28
674 712 8.148351 TGTGGATCTTTTACTATTATTCTCCGG 58.852 37.037 0.00 0.00 0.00 5.14
678 716 8.718656 AGGCTGTGGATCTTTTACTATTATTCT 58.281 33.333 0.00 0.00 0.00 2.40
679 717 8.778358 CAGGCTGTGGATCTTTTACTATTATTC 58.222 37.037 6.28 0.00 0.00 1.75
687 725 4.072131 TCAACAGGCTGTGGATCTTTTAC 58.928 43.478 22.83 0.00 0.00 2.01
690 728 2.957402 TCAACAGGCTGTGGATCTTT 57.043 45.000 22.83 0.00 0.00 2.52
696 734 1.021390 GTCCGATCAACAGGCTGTGG 61.021 60.000 22.83 19.40 0.00 4.17
750 805 1.869690 GAAGAGGTTGCTCGTTGGC 59.130 57.895 0.00 0.00 0.00 4.52
759 817 1.005340 GCAGATCAGCGAAGAGGTTG 58.995 55.000 0.00 0.00 0.00 3.77
779 837 0.243907 CTTTTCTCCCTCGTCTCGCA 59.756 55.000 0.00 0.00 0.00 5.10
825 920 3.003480 GCTGACACGCTTCCTAATTCTT 58.997 45.455 0.00 0.00 0.00 2.52
834 930 1.194772 GTTACCAAGCTGACACGCTTC 59.805 52.381 8.58 0.00 46.68 3.86
848 944 5.488341 GCCAGAGTAGATCTTTTGTTACCA 58.512 41.667 0.00 0.00 35.47 3.25
859 955 2.186076 CAACGTTCGCCAGAGTAGATC 58.814 52.381 0.00 0.00 0.00 2.75
865 964 3.423154 GCCCAACGTTCGCCAGAG 61.423 66.667 0.00 0.00 0.00 3.35
967 1090 2.905373 GCGGGCCTTTTATCGGGG 60.905 66.667 0.84 0.00 0.00 5.73
1025 1148 1.827399 TTGGGTCTGGTCTCTTCGGC 61.827 60.000 0.00 0.00 0.00 5.54
1028 1169 1.056660 TGGTTGGGTCTGGTCTCTTC 58.943 55.000 0.00 0.00 0.00 2.87
1075 1216 1.203557 TGGATGGAAGGAGGGAAGGAA 60.204 52.381 0.00 0.00 0.00 3.36
1076 1217 0.421495 TGGATGGAAGGAGGGAAGGA 59.579 55.000 0.00 0.00 0.00 3.36
1077 1218 0.548510 GTGGATGGAAGGAGGGAAGG 59.451 60.000 0.00 0.00 0.00 3.46
1078 1219 0.179000 CGTGGATGGAAGGAGGGAAG 59.821 60.000 0.00 0.00 0.00 3.46
1083 1224 1.123077 TGGATCGTGGATGGAAGGAG 58.877 55.000 0.00 0.00 0.00 3.69
1091 1232 4.221422 CGGCCGTGGATCGTGGAT 62.221 66.667 19.50 0.00 37.94 3.41
1152 1293 3.138798 GCCTCCGCCTCGTCTACA 61.139 66.667 0.00 0.00 0.00 2.74
1374 1524 4.394712 AAGGTCTTCCAGCGCGGG 62.395 66.667 21.57 21.57 35.89 6.13
1445 1607 1.080093 TCGTAGTTGAGCTTGCGGG 60.080 57.895 0.00 0.00 0.00 6.13
1696 1858 1.005450 ACTTTCCCTGTGGTGTTGTGT 59.995 47.619 0.00 0.00 0.00 3.72
1697 1859 1.762708 ACTTTCCCTGTGGTGTTGTG 58.237 50.000 0.00 0.00 0.00 3.33
1698 1860 3.655615 TTACTTTCCCTGTGGTGTTGT 57.344 42.857 0.00 0.00 0.00 3.32
1699 1861 3.317993 CCTTTACTTTCCCTGTGGTGTTG 59.682 47.826 0.00 0.00 0.00 3.33
1700 1862 3.053170 ACCTTTACTTTCCCTGTGGTGTT 60.053 43.478 0.00 0.00 0.00 3.32
1716 1878 4.146564 TCATCCATCGACCGATACCTTTA 58.853 43.478 4.48 0.00 32.93 1.85
1727 1889 1.138859 TGACCACCATCATCCATCGAC 59.861 52.381 0.00 0.00 0.00 4.20
1848 2025 2.510800 TCAATCAATCATGGGAGCAGGA 59.489 45.455 0.00 0.00 0.00 3.86
1855 2032 6.309436 CGACGAAATATCAATCAATCATGGG 58.691 40.000 0.00 0.00 0.00 4.00
1857 2034 6.518736 CAGCGACGAAATATCAATCAATCATG 59.481 38.462 0.00 0.00 0.00 3.07
1858 2035 6.203530 ACAGCGACGAAATATCAATCAATCAT 59.796 34.615 0.00 0.00 0.00 2.45
1859 2036 5.523552 ACAGCGACGAAATATCAATCAATCA 59.476 36.000 0.00 0.00 0.00 2.57
1860 2037 5.978878 ACAGCGACGAAATATCAATCAATC 58.021 37.500 0.00 0.00 0.00 2.67
1862 2039 5.808030 TGTACAGCGACGAAATATCAATCAA 59.192 36.000 0.00 0.00 0.00 2.57
1871 2048 5.412526 TTTTCTTTGTACAGCGACGAAAT 57.587 34.783 0.00 0.00 31.46 2.17
1872 2049 4.861389 TTTTCTTTGTACAGCGACGAAA 57.139 36.364 0.00 0.00 29.95 3.46
1907 2087 6.876789 AGTATGACAACGAATGTAACAATGGA 59.123 34.615 0.00 0.00 44.12 3.41
1938 2118 5.414765 GGGACAAAACTTTGATAAGACGGAT 59.585 40.000 9.12 0.00 40.55 4.18
1939 2119 4.758165 GGGACAAAACTTTGATAAGACGGA 59.242 41.667 9.12 0.00 40.55 4.69
1940 2120 4.082949 GGGGACAAAACTTTGATAAGACGG 60.083 45.833 9.12 0.00 40.55 4.79
1941 2121 4.378046 CGGGGACAAAACTTTGATAAGACG 60.378 45.833 9.12 2.82 40.55 4.18
1942 2122 4.758165 TCGGGGACAAAACTTTGATAAGAC 59.242 41.667 9.12 0.00 40.55 3.01
1943 2123 4.975631 TCGGGGACAAAACTTTGATAAGA 58.024 39.130 9.12 0.16 40.55 2.10
1944 2124 5.897377 ATCGGGGACAAAACTTTGATAAG 57.103 39.130 9.12 0.00 40.55 1.73
1945 2125 6.128227 CGTAATCGGGGACAAAACTTTGATAA 60.128 38.462 9.12 0.00 40.55 1.75
1946 2126 5.352016 CGTAATCGGGGACAAAACTTTGATA 59.648 40.000 9.12 0.00 40.55 2.15
1987 2167 1.578618 GCGAAATTGCTGACGCGAG 60.579 57.895 15.93 0.36 41.49 5.03
1992 2211 2.352503 ACAATGGCGAAATTGCTGAC 57.647 45.000 9.63 0.00 40.54 3.51
1994 2213 3.801293 CAAAACAATGGCGAAATTGCTG 58.199 40.909 9.63 3.24 40.54 4.41
2007 2226 8.242739 ACTTTTGTTTATGCAAAGCAAAACAAT 58.757 25.926 26.17 17.78 45.75 2.71
2012 2231 7.118971 ACTCAACTTTTGTTTATGCAAAGCAAA 59.881 29.630 14.65 14.65 40.78 3.68
2013 2232 6.593382 ACTCAACTTTTGTTTATGCAAAGCAA 59.407 30.769 0.00 0.00 40.78 3.91
2014 2233 6.035866 CACTCAACTTTTGTTTATGCAAAGCA 59.964 34.615 0.00 0.00 41.35 3.91
2015 2234 6.035975 ACACTCAACTTTTGTTTATGCAAAGC 59.964 34.615 0.00 0.00 41.35 3.51
2016 2235 7.254084 GGACACTCAACTTTTGTTTATGCAAAG 60.254 37.037 0.00 0.00 41.35 2.77
2056 2275 2.860735 CCTCTTCTTCTTACCAATCGCG 59.139 50.000 0.00 0.00 0.00 5.87
2088 2307 3.516263 GCCAAGCGCTTAGAATTCG 57.484 52.632 24.55 8.45 0.00 3.34
2110 2329 0.747283 GCAATCAGTCCCAGCTGGAG 60.747 60.000 34.91 23.01 46.38 3.86
2226 2446 0.110486 GTCCCAAGAGGCCAAGAACA 59.890 55.000 5.01 0.00 34.51 3.18
2227 2447 0.955919 CGTCCCAAGAGGCCAAGAAC 60.956 60.000 5.01 0.00 34.51 3.01
2228 2448 1.374947 CGTCCCAAGAGGCCAAGAA 59.625 57.895 5.01 0.00 34.51 2.52
2230 2450 2.747855 GCGTCCCAAGAGGCCAAG 60.748 66.667 5.01 0.00 45.99 3.61
2235 2455 4.208632 GACATGCGTCCCAAGAGG 57.791 61.111 0.00 0.00 36.02 3.69
2262 2482 4.567959 TCGTTCACATGTATCATGCTTGAG 59.432 41.667 8.40 0.00 34.73 3.02
2263 2483 4.502962 TCGTTCACATGTATCATGCTTGA 58.497 39.130 4.57 4.57 36.00 3.02
2264 2484 4.863152 TCGTTCACATGTATCATGCTTG 57.137 40.909 0.00 0.00 0.00 4.01
2265 2485 5.118286 TGATCGTTCACATGTATCATGCTT 58.882 37.500 0.00 0.00 0.00 3.91
2266 2486 4.696455 TGATCGTTCACATGTATCATGCT 58.304 39.130 0.00 0.00 0.00 3.79
2269 2498 7.974482 ATTGATGATCGTTCACATGTATCAT 57.026 32.000 17.14 17.14 39.39 2.45
2295 2524 0.243907 TCACAGCGAGGAGTAACAGC 59.756 55.000 0.00 0.00 0.00 4.40
2325 2554 5.278169 CGATGAATTCACATCAATTCCCTCC 60.278 44.000 11.07 0.00 44.57 4.30
2352 2584 0.816018 TCTCTCGAGATCACGGCTCC 60.816 60.000 17.03 0.00 31.41 4.70
2355 2587 1.335182 TGATTCTCTCGAGATCACGGC 59.665 52.381 17.03 4.55 37.29 5.68
2365 2597 1.586564 GCGGTCCGTGATTCTCTCG 60.587 63.158 13.94 0.00 33.67 4.04
2376 2608 1.273455 GAATTCGATACCGCGGTCCG 61.273 60.000 38.01 35.17 35.37 4.79
2401 2635 1.251251 AACATCAAGCAAGGCTGTCC 58.749 50.000 0.00 0.00 39.62 4.02
2460 2694 0.611200 TATCCACACGACAACCCAGG 59.389 55.000 0.00 0.00 0.00 4.45
2536 2784 1.779092 ACTATGGGCTGATGATGGCTT 59.221 47.619 0.00 0.00 0.00 4.35
2537 2785 1.073444 CACTATGGGCTGATGATGGCT 59.927 52.381 0.00 0.00 0.00 4.75
2538 2786 1.531423 CACTATGGGCTGATGATGGC 58.469 55.000 0.00 0.00 0.00 4.40
2539 2787 1.701292 TCCACTATGGGCTGATGATGG 59.299 52.381 0.00 0.00 38.32 3.51
2540 2788 3.715638 ATCCACTATGGGCTGATGATG 57.284 47.619 0.00 0.00 38.32 3.07
2541 2789 3.009916 GGAATCCACTATGGGCTGATGAT 59.990 47.826 0.00 0.00 38.32 2.45
2542 2790 2.373169 GGAATCCACTATGGGCTGATGA 59.627 50.000 0.00 0.00 38.32 2.92
2543 2791 2.374504 AGGAATCCACTATGGGCTGATG 59.625 50.000 0.61 0.00 38.32 3.07
2544 2792 2.641815 GAGGAATCCACTATGGGCTGAT 59.358 50.000 0.61 0.00 38.32 2.90
2545 2793 2.050144 GAGGAATCCACTATGGGCTGA 58.950 52.381 0.61 0.00 38.32 4.26
2546 2794 1.072965 GGAGGAATCCACTATGGGCTG 59.927 57.143 0.61 0.00 38.32 4.85
2547 2795 1.439543 GGAGGAATCCACTATGGGCT 58.560 55.000 0.61 0.00 38.32 5.19
2548 2796 0.402121 GGGAGGAATCCACTATGGGC 59.598 60.000 0.61 0.00 38.32 5.36
2549 2797 1.701847 CAGGGAGGAATCCACTATGGG 59.298 57.143 0.61 0.00 38.32 4.00
2550 2798 1.701847 CCAGGGAGGAATCCACTATGG 59.298 57.143 0.61 4.32 41.22 2.74
2551 2799 2.694397 TCCAGGGAGGAATCCACTATG 58.306 52.381 0.61 0.00 45.65 2.23
2559 2807 8.374068 ATGGTCTACATACTCCAGGGAGGAAT 62.374 46.154 19.02 9.47 41.72 3.01
2565 2813 3.850752 AGATGGTCTACATACTCCAGGG 58.149 50.000 0.00 0.00 40.72 4.45
2575 2823 9.513906 TTTCATATTTGTCAAAGATGGTCTACA 57.486 29.630 25.25 8.70 39.80 2.74
2584 2832 7.753132 GCGTATGGTTTTCATATTTGTCAAAGA 59.247 33.333 4.03 0.00 40.15 2.52
2592 2840 5.068987 AGCATGGCGTATGGTTTTCATATTT 59.931 36.000 0.00 0.00 44.75 1.40
2614 2862 2.617308 CACCTGACCATGATTGATGAGC 59.383 50.000 0.00 0.00 33.31 4.26
2628 2876 9.307121 GATGCTACATATATTCATACACCTGAC 57.693 37.037 0.00 0.00 0.00 3.51
2645 2901 7.201556 CGTGACAAAGTTAAGATGATGCTACAT 60.202 37.037 0.00 0.00 0.00 2.29
2649 2905 5.120830 GTCGTGACAAAGTTAAGATGATGCT 59.879 40.000 0.00 0.00 0.00 3.79
2650 2906 5.316770 GTCGTGACAAAGTTAAGATGATGC 58.683 41.667 0.00 0.00 0.00 3.91
2655 2911 4.062991 GTGGGTCGTGACAAAGTTAAGAT 58.937 43.478 2.00 0.00 0.00 2.40
2656 2912 3.460103 GTGGGTCGTGACAAAGTTAAGA 58.540 45.455 2.00 0.00 0.00 2.10
2657 2913 2.220133 CGTGGGTCGTGACAAAGTTAAG 59.780 50.000 2.00 0.00 34.52 1.85
2679 2935 1.694018 CTGCATGAGCTCGTCACAGC 61.694 60.000 18.07 13.70 42.74 4.40
2698 2954 2.083774 TGATTGAAATGGACGGAGCAC 58.916 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.