Multiple sequence alignment - TraesCS6D01G244800

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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 TraesCS6D01G244800 chr6D 100.000 2489 0 0 1 2489 346952600 346955088 0 4597
1 TraesCS6D01G244800 chr6A 92.187 1843 83 33 148 1963 496476646 496474838 0 2549
2 TraesCS6D01G244800 chr6A 94.615 520 21 5 1972 2489 496474774 496474260 0 798
3 TraesCS6D01G244800 chr6B 93.469 1669 60 22 218 1860 534097215 534095570 0 2433
4 TraesCS6D01G244800 chr6B 93.160 614 17 9 1877 2488 534095127 534094537 0 878


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 TraesCS6D01G244800 chr6D 346952600 346955088 2488 False 4597.0 4597 100.0000 1 2489 1 chr6D.!!$F1 2488
1 TraesCS6D01G244800 chr6A 496474260 496476646 2386 True 1673.5 2549 93.4010 148 2489 2 chr6A.!!$R1 2341
2 TraesCS6D01G244800 chr6B 534094537 534097215 2678 True 1655.5 2433 93.3145 218 2488 2 chr6B.!!$R1 2270

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
34 35 0.032952 CGAGTGAGGTTGGAACGGAA 59.967 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1748 0.178992 CCCTTCCAGAAACAGGCACA 60.179 55.0 0.0 0.0 0.0 4.57 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
28 29 4.373116 GCGGCGAGTGAGGTTGGA 62.373 66.667 12.98 0.00 0.00 3.53
29 30 2.342279 CGGCGAGTGAGGTTGGAA 59.658 61.111 0.00 0.00 0.00 3.53
30 31 2.027625 CGGCGAGTGAGGTTGGAAC 61.028 63.158 0.00 0.00 0.00 3.62
31 32 2.027625 GGCGAGTGAGGTTGGAACG 61.028 63.158 0.00 0.00 0.00 3.95
32 33 2.027625 GCGAGTGAGGTTGGAACGG 61.028 63.158 0.00 0.00 0.00 4.44
33 34 1.663739 CGAGTGAGGTTGGAACGGA 59.336 57.895 0.00 0.00 0.00 4.69
34 35 0.032952 CGAGTGAGGTTGGAACGGAA 59.967 55.000 0.00 0.00 0.00 4.30
35 36 1.797025 GAGTGAGGTTGGAACGGAAG 58.203 55.000 0.00 0.00 0.00 3.46
36 37 0.396811 AGTGAGGTTGGAACGGAAGG 59.603 55.000 0.00 0.00 0.00 3.46
37 38 0.605589 GTGAGGTTGGAACGGAAGGG 60.606 60.000 0.00 0.00 0.00 3.95
38 39 1.002502 GAGGTTGGAACGGAAGGGG 60.003 63.158 0.00 0.00 0.00 4.79
39 40 2.675423 GGTTGGAACGGAAGGGGC 60.675 66.667 0.00 0.00 0.00 5.80
40 41 3.053896 GTTGGAACGGAAGGGGCG 61.054 66.667 0.00 0.00 0.00 6.13
41 42 4.338710 TTGGAACGGAAGGGGCGG 62.339 66.667 0.00 0.00 0.00 6.13
43 44 4.024545 GGAACGGAAGGGGCGGAA 62.025 66.667 0.00 0.00 0.00 4.30
44 45 2.436115 GAACGGAAGGGGCGGAAG 60.436 66.667 0.00 0.00 0.00 3.46
45 46 3.246880 AACGGAAGGGGCGGAAGT 61.247 61.111 0.00 0.00 0.00 3.01
46 47 2.743126 GAACGGAAGGGGCGGAAGTT 62.743 60.000 0.00 0.00 0.00 2.66
47 48 2.033602 CGGAAGGGGCGGAAGTTT 59.966 61.111 0.00 0.00 0.00 2.66
48 49 2.038837 CGGAAGGGGCGGAAGTTTC 61.039 63.158 0.00 0.00 0.00 2.78
49 50 1.677966 GGAAGGGGCGGAAGTTTCC 60.678 63.158 0.63 0.63 44.05 3.13
50 51 1.379146 GAAGGGGCGGAAGTTTCCT 59.621 57.895 9.11 0.00 45.33 3.36
51 52 0.251209 GAAGGGGCGGAAGTTTCCTT 60.251 55.000 9.11 0.00 45.33 3.36
52 53 0.251209 AAGGGGCGGAAGTTTCCTTC 60.251 55.000 9.11 0.00 45.33 3.46
53 54 2.038837 GGGGCGGAAGTTTCCTTCG 61.039 63.158 9.11 0.00 46.72 3.79
54 55 2.687805 GGGCGGAAGTTTCCTTCGC 61.688 63.158 9.11 7.26 46.72 4.70
55 56 2.474712 GCGGAAGTTTCCTTCGCG 59.525 61.111 0.00 0.00 46.72 5.87
56 57 2.474712 CGGAAGTTTCCTTCGCGC 59.525 61.111 0.00 0.00 46.72 6.86
57 58 2.868196 GGAAGTTTCCTTCGCGCC 59.132 61.111 0.00 0.00 46.72 6.53
58 59 1.964373 GGAAGTTTCCTTCGCGCCA 60.964 57.895 0.00 0.00 46.72 5.69
59 60 1.512156 GGAAGTTTCCTTCGCGCCAA 61.512 55.000 0.00 0.00 46.72 4.52
60 61 0.110192 GAAGTTTCCTTCGCGCCAAG 60.110 55.000 7.89 7.89 37.92 3.61
61 62 1.515521 AAGTTTCCTTCGCGCCAAGG 61.516 55.000 25.93 25.93 44.09 3.61
64 65 4.760047 TCCTTCGCGCCAAGGAGC 62.760 66.667 29.59 4.63 46.00 4.70
72 73 3.081409 GCCAAGGAGCGGGAGGTA 61.081 66.667 0.00 0.00 43.00 3.08
73 74 2.444256 GCCAAGGAGCGGGAGGTAT 61.444 63.158 0.00 0.00 43.00 2.73
74 75 1.749033 CCAAGGAGCGGGAGGTATC 59.251 63.158 0.00 0.00 43.00 2.24
75 76 1.364171 CAAGGAGCGGGAGGTATCG 59.636 63.158 0.00 0.00 43.00 2.92
76 77 1.833049 AAGGAGCGGGAGGTATCGG 60.833 63.158 0.00 0.00 43.00 4.18
77 78 3.303928 GGAGCGGGAGGTATCGGG 61.304 72.222 0.00 0.00 43.00 5.14
78 79 2.203451 GAGCGGGAGGTATCGGGA 60.203 66.667 0.00 0.00 43.00 5.14
79 80 1.831286 GAGCGGGAGGTATCGGGAA 60.831 63.158 0.00 0.00 43.00 3.97
80 81 1.382146 AGCGGGAGGTATCGGGAAA 60.382 57.895 0.00 0.00 39.85 3.13
81 82 1.227468 GCGGGAGGTATCGGGAAAC 60.227 63.158 0.00 0.00 0.00 2.78
94 95 1.830279 GGGAAACCGGTAAAAGGAGG 58.170 55.000 8.00 0.00 43.64 4.30
95 96 1.352017 GGGAAACCGGTAAAAGGAGGA 59.648 52.381 8.00 0.00 43.64 3.71
96 97 2.224843 GGGAAACCGGTAAAAGGAGGAA 60.225 50.000 8.00 0.00 43.64 3.36
97 98 3.079578 GGAAACCGGTAAAAGGAGGAAG 58.920 50.000 8.00 0.00 0.00 3.46
98 99 2.873094 AACCGGTAAAAGGAGGAAGG 57.127 50.000 8.00 0.00 0.00 3.46
99 100 0.989602 ACCGGTAAAAGGAGGAAGGG 59.010 55.000 4.49 0.00 0.00 3.95
100 101 1.282382 CCGGTAAAAGGAGGAAGGGA 58.718 55.000 0.00 0.00 0.00 4.20
101 102 1.631898 CCGGTAAAAGGAGGAAGGGAA 59.368 52.381 0.00 0.00 0.00 3.97
102 103 2.040679 CCGGTAAAAGGAGGAAGGGAAA 59.959 50.000 0.00 0.00 0.00 3.13
103 104 3.079578 CGGTAAAAGGAGGAAGGGAAAC 58.920 50.000 0.00 0.00 0.00 2.78
116 117 1.792006 GGGAAACCGTAGATATGGCG 58.208 55.000 0.00 0.00 43.64 5.69
122 123 3.677960 CGTAGATATGGCGGACTCG 57.322 57.895 0.00 0.00 39.81 4.18
123 124 0.168348 CGTAGATATGGCGGACTCGG 59.832 60.000 0.00 0.00 36.79 4.63
131 132 4.208686 GCGGACTCGGCTCGGAAT 62.209 66.667 1.42 0.00 36.79 3.01
132 133 2.494918 CGGACTCGGCTCGGAATT 59.505 61.111 0.00 0.00 0.00 2.17
133 134 1.153628 CGGACTCGGCTCGGAATTT 60.154 57.895 0.00 0.00 0.00 1.82
134 135 0.101759 CGGACTCGGCTCGGAATTTA 59.898 55.000 0.00 0.00 0.00 1.40
135 136 1.568606 GGACTCGGCTCGGAATTTAC 58.431 55.000 0.00 0.00 0.00 2.01
136 137 1.134907 GGACTCGGCTCGGAATTTACA 60.135 52.381 0.00 0.00 0.00 2.41
137 138 2.483188 GGACTCGGCTCGGAATTTACAT 60.483 50.000 0.00 0.00 0.00 2.29
138 139 2.795470 GACTCGGCTCGGAATTTACATC 59.205 50.000 0.00 0.00 0.00 3.06
139 140 2.135933 CTCGGCTCGGAATTTACATCC 58.864 52.381 0.00 0.00 0.00 3.51
140 141 1.760613 TCGGCTCGGAATTTACATCCT 59.239 47.619 0.00 0.00 34.66 3.24
141 142 1.867233 CGGCTCGGAATTTACATCCTG 59.133 52.381 0.00 0.00 34.66 3.86
142 143 1.604278 GGCTCGGAATTTACATCCTGC 59.396 52.381 0.00 0.00 34.66 4.85
143 144 2.288666 GCTCGGAATTTACATCCTGCA 58.711 47.619 0.00 0.00 35.53 4.41
144 145 2.682856 GCTCGGAATTTACATCCTGCAA 59.317 45.455 0.00 0.00 35.53 4.08
145 146 3.128589 GCTCGGAATTTACATCCTGCAAA 59.871 43.478 0.00 0.00 35.53 3.68
146 147 4.380444 GCTCGGAATTTACATCCTGCAAAA 60.380 41.667 0.00 0.00 35.53 2.44
175 176 2.973694 ACAGCCGGTTGAATATACGT 57.026 45.000 26.33 0.00 0.00 3.57
178 179 4.553323 ACAGCCGGTTGAATATACGTATC 58.447 43.478 26.33 0.00 0.00 2.24
206 207 3.739300 TGGACAGAAAAATCGTTCTCGTC 59.261 43.478 0.00 0.00 35.63 4.20
207 208 3.123116 GGACAGAAAAATCGTTCTCGTCC 59.877 47.826 14.81 14.81 42.20 4.79
320 322 2.387445 CGCGAATGAAACCAGCGGA 61.387 57.895 0.00 0.00 46.06 5.54
429 439 9.710900 GAAAATCAATCAAACAAATCCTAAGGT 57.289 29.630 0.00 0.00 0.00 3.50
433 443 6.775142 TCAATCAAACAAATCCTAAGGTGACA 59.225 34.615 0.00 0.00 0.00 3.58
462 473 5.451908 CAACACCAGAATGTATGTCAACAC 58.548 41.667 0.00 0.00 33.00 3.32
464 475 4.756642 ACACCAGAATGTATGTCAACACTG 59.243 41.667 0.00 0.00 28.48 3.66
493 504 1.507141 CGCGGGCAAGTCTTGTCTTT 61.507 55.000 16.47 0.00 35.12 2.52
677 700 2.125952 CAGAGCATGACGTGGCGA 60.126 61.111 0.00 0.00 34.54 5.54
892 916 0.394352 CCCTTTATCAACCCGCAGCT 60.394 55.000 0.00 0.00 0.00 4.24
893 917 1.017387 CCTTTATCAACCCGCAGCTC 58.983 55.000 0.00 0.00 0.00 4.09
894 918 0.652592 CTTTATCAACCCGCAGCTCG 59.347 55.000 0.00 0.00 38.08 5.03
973 999 3.365264 GCACAATCACAATCACATCACGT 60.365 43.478 0.00 0.00 0.00 4.49
1560 1592 9.341899 CAAAATTTGTTACTTGTAGCATAGGTC 57.658 33.333 0.00 0.00 0.00 3.85
1602 1636 6.589907 AGAAATTCTTTGTTTGCTTTGTCGTT 59.410 30.769 0.00 0.00 0.00 3.85
1707 1746 1.952102 AAGATGCTGCCAAATGCCCG 61.952 55.000 0.00 0.00 40.16 6.13
1709 1748 4.992740 TGCTGCCAAATGCCCGGT 62.993 61.111 0.00 0.00 40.16 5.28
1716 1755 2.990967 AAATGCCCGGTGTGCCTG 60.991 61.111 0.00 0.00 0.00 4.85
1825 1869 6.346439 CGACAATCCATGAAAATTTCGCAAAA 60.346 34.615 0.00 0.00 0.00 2.44
1875 2347 5.472148 ACAGGTGATTAAATGCACAACATG 58.528 37.500 0.00 0.00 39.60 3.21
2003 2531 7.064253 GGCAACATGTTGTTAGTACTTACTAGG 59.936 40.741 33.01 8.09 38.77 3.02
2004 2532 7.816031 GCAACATGTTGTTAGTACTTACTAGGA 59.184 37.037 33.01 0.00 38.77 2.94
2005 2533 9.701098 CAACATGTTGTTAGTACTTACTAGGAA 57.299 33.333 27.08 0.00 38.77 3.36
2006 2534 9.924650 AACATGTTGTTAGTACTTACTAGGAAG 57.075 33.333 13.52 13.52 39.09 3.46
2023 2551 3.974642 AGGAAGTAGGAAGGTGAACAACT 59.025 43.478 0.00 0.00 0.00 3.16
2068 2596 3.135530 ACCCTGATCAATCTGTAGGCTTC 59.864 47.826 0.00 0.00 0.00 3.86
2069 2597 3.390639 CCCTGATCAATCTGTAGGCTTCT 59.609 47.826 0.00 0.00 0.00 2.85
2070 2598 4.378774 CCTGATCAATCTGTAGGCTTCTG 58.621 47.826 0.00 0.00 0.00 3.02
2071 2599 4.100653 CCTGATCAATCTGTAGGCTTCTGA 59.899 45.833 0.00 0.00 0.00 3.27
2099 2627 2.076863 GTGTTCCTTCCGATGTTCAGG 58.923 52.381 0.00 0.00 0.00 3.86
2279 2810 4.857037 GCAGAAAATAACCTTTACAAGCGG 59.143 41.667 0.00 0.00 0.00 5.52
2335 2866 6.722129 ACCACCAAACCACTAAAATATAGCAA 59.278 34.615 0.00 0.00 0.00 3.91
2379 2910 1.676635 TTGATGCAGTGCCTCCAGC 60.677 57.895 13.72 0.00 44.14 4.85
2424 2955 5.734720 TGGTATTCACTCTTCACTTCCATC 58.265 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.876589 TTCCAACCTCACTCGCCGC 62.877 63.158 0.00 0.00 0.00 6.53
12 13 2.027625 GTTCCAACCTCACTCGCCG 61.028 63.158 0.00 0.00 0.00 6.46
13 14 2.027625 CGTTCCAACCTCACTCGCC 61.028 63.158 0.00 0.00 0.00 5.54
14 15 2.027625 CCGTTCCAACCTCACTCGC 61.028 63.158 0.00 0.00 0.00 5.03
15 16 0.032952 TTCCGTTCCAACCTCACTCG 59.967 55.000 0.00 0.00 0.00 4.18
16 17 1.608283 CCTTCCGTTCCAACCTCACTC 60.608 57.143 0.00 0.00 0.00 3.51
17 18 0.396811 CCTTCCGTTCCAACCTCACT 59.603 55.000 0.00 0.00 0.00 3.41
18 19 0.605589 CCCTTCCGTTCCAACCTCAC 60.606 60.000 0.00 0.00 0.00 3.51
19 20 1.758592 CCCTTCCGTTCCAACCTCA 59.241 57.895 0.00 0.00 0.00 3.86
20 21 1.002502 CCCCTTCCGTTCCAACCTC 60.003 63.158 0.00 0.00 0.00 3.85
21 22 3.167414 CCCCTTCCGTTCCAACCT 58.833 61.111 0.00 0.00 0.00 3.50
22 23 2.675423 GCCCCTTCCGTTCCAACC 60.675 66.667 0.00 0.00 0.00 3.77
23 24 3.053896 CGCCCCTTCCGTTCCAAC 61.054 66.667 0.00 0.00 0.00 3.77
24 25 4.338710 CCGCCCCTTCCGTTCCAA 62.339 66.667 0.00 0.00 0.00 3.53
26 27 3.971109 CTTCCGCCCCTTCCGTTCC 62.971 68.421 0.00 0.00 0.00 3.62
27 28 2.436115 CTTCCGCCCCTTCCGTTC 60.436 66.667 0.00 0.00 0.00 3.95
28 29 2.347691 AAACTTCCGCCCCTTCCGTT 62.348 55.000 0.00 0.00 0.00 4.44
29 30 2.743126 GAAACTTCCGCCCCTTCCGT 62.743 60.000 0.00 0.00 0.00 4.69
30 31 2.033602 AAACTTCCGCCCCTTCCG 59.966 61.111 0.00 0.00 0.00 4.30
31 32 1.677966 GGAAACTTCCGCCCCTTCC 60.678 63.158 0.00 0.00 37.65 3.46
32 33 3.998156 GGAAACTTCCGCCCCTTC 58.002 61.111 0.00 0.00 37.65 3.46
43 44 1.966451 CCTTGGCGCGAAGGAAACT 60.966 57.895 38.97 0.00 44.87 2.66
44 45 2.561373 CCTTGGCGCGAAGGAAAC 59.439 61.111 38.97 7.24 44.87 2.78
55 56 2.384653 GATACCTCCCGCTCCTTGGC 62.385 65.000 0.00 0.00 0.00 4.52
56 57 1.749033 GATACCTCCCGCTCCTTGG 59.251 63.158 0.00 0.00 0.00 3.61
57 58 1.364171 CGATACCTCCCGCTCCTTG 59.636 63.158 0.00 0.00 0.00 3.61
58 59 1.833049 CCGATACCTCCCGCTCCTT 60.833 63.158 0.00 0.00 0.00 3.36
59 60 2.203509 CCGATACCTCCCGCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
60 61 3.303928 CCCGATACCTCCCGCTCC 61.304 72.222 0.00 0.00 0.00 4.70
61 62 1.397390 TTTCCCGATACCTCCCGCTC 61.397 60.000 0.00 0.00 0.00 5.03
62 63 1.382146 TTTCCCGATACCTCCCGCT 60.382 57.895 0.00 0.00 0.00 5.52
63 64 1.227468 GTTTCCCGATACCTCCCGC 60.227 63.158 0.00 0.00 0.00 6.13
64 65 1.444672 GGTTTCCCGATACCTCCCG 59.555 63.158 0.00 0.00 30.96 5.14
75 76 1.352017 TCCTCCTTTTACCGGTTTCCC 59.648 52.381 15.04 0.00 0.00 3.97
76 77 2.865119 TCCTCCTTTTACCGGTTTCC 57.135 50.000 15.04 0.00 0.00 3.13
77 78 3.079578 CCTTCCTCCTTTTACCGGTTTC 58.920 50.000 15.04 0.00 0.00 2.78
78 79 2.224942 CCCTTCCTCCTTTTACCGGTTT 60.225 50.000 15.04 0.00 0.00 3.27
79 80 1.353358 CCCTTCCTCCTTTTACCGGTT 59.647 52.381 15.04 0.00 0.00 4.44
80 81 0.989602 CCCTTCCTCCTTTTACCGGT 59.010 55.000 13.98 13.98 0.00 5.28
81 82 1.282382 TCCCTTCCTCCTTTTACCGG 58.718 55.000 0.00 0.00 0.00 5.28
82 83 3.079578 GTTTCCCTTCCTCCTTTTACCG 58.920 50.000 0.00 0.00 0.00 4.02
83 84 3.428532 GGTTTCCCTTCCTCCTTTTACC 58.571 50.000 0.00 0.00 0.00 2.85
84 85 3.079578 CGGTTTCCCTTCCTCCTTTTAC 58.920 50.000 0.00 0.00 0.00 2.01
85 86 2.712627 ACGGTTTCCCTTCCTCCTTTTA 59.287 45.455 0.00 0.00 0.00 1.52
86 87 1.497716 ACGGTTTCCCTTCCTCCTTTT 59.502 47.619 0.00 0.00 0.00 2.27
87 88 1.146452 ACGGTTTCCCTTCCTCCTTT 58.854 50.000 0.00 0.00 0.00 3.11
88 89 1.907255 CTACGGTTTCCCTTCCTCCTT 59.093 52.381 0.00 0.00 0.00 3.36
89 90 1.078324 TCTACGGTTTCCCTTCCTCCT 59.922 52.381 0.00 0.00 0.00 3.69
90 91 1.565067 TCTACGGTTTCCCTTCCTCC 58.435 55.000 0.00 0.00 0.00 4.30
91 92 4.262506 CCATATCTACGGTTTCCCTTCCTC 60.263 50.000 0.00 0.00 0.00 3.71
92 93 3.646637 CCATATCTACGGTTTCCCTTCCT 59.353 47.826 0.00 0.00 0.00 3.36
93 94 3.806157 GCCATATCTACGGTTTCCCTTCC 60.806 52.174 0.00 0.00 0.00 3.46
94 95 3.400255 GCCATATCTACGGTTTCCCTTC 58.600 50.000 0.00 0.00 0.00 3.46
95 96 2.224209 CGCCATATCTACGGTTTCCCTT 60.224 50.000 0.00 0.00 0.00 3.95
96 97 1.343465 CGCCATATCTACGGTTTCCCT 59.657 52.381 0.00 0.00 0.00 4.20
97 98 1.607251 CCGCCATATCTACGGTTTCCC 60.607 57.143 0.00 0.00 42.01 3.97
98 99 1.342174 TCCGCCATATCTACGGTTTCC 59.658 52.381 7.30 0.00 46.92 3.13
99 100 2.035576 AGTCCGCCATATCTACGGTTTC 59.964 50.000 7.30 1.85 46.92 2.78
100 101 2.035576 GAGTCCGCCATATCTACGGTTT 59.964 50.000 7.30 0.00 46.92 3.27
101 102 1.612463 GAGTCCGCCATATCTACGGTT 59.388 52.381 7.30 0.00 46.92 4.44
102 103 1.245732 GAGTCCGCCATATCTACGGT 58.754 55.000 7.30 0.00 46.92 4.83
104 105 0.168348 CCGAGTCCGCCATATCTACG 59.832 60.000 0.00 0.00 0.00 3.51
105 106 0.109226 GCCGAGTCCGCCATATCTAC 60.109 60.000 0.00 0.00 0.00 2.59
106 107 0.251209 AGCCGAGTCCGCCATATCTA 60.251 55.000 0.00 0.00 0.00 1.98
107 108 1.528292 GAGCCGAGTCCGCCATATCT 61.528 60.000 0.00 0.00 0.00 1.98
108 109 1.080434 GAGCCGAGTCCGCCATATC 60.080 63.158 0.00 0.00 0.00 1.63
109 110 2.920645 CGAGCCGAGTCCGCCATAT 61.921 63.158 0.00 0.00 0.00 1.78
110 111 3.592814 CGAGCCGAGTCCGCCATA 61.593 66.667 0.00 0.00 0.00 2.74
114 115 3.718210 AATTCCGAGCCGAGTCCGC 62.718 63.158 0.00 0.00 0.00 5.54
115 116 0.101759 TAAATTCCGAGCCGAGTCCG 59.898 55.000 0.00 0.00 0.00 4.79
116 117 1.134907 TGTAAATTCCGAGCCGAGTCC 60.135 52.381 0.00 0.00 0.00 3.85
117 118 2.288961 TGTAAATTCCGAGCCGAGTC 57.711 50.000 0.00 0.00 0.00 3.36
118 119 2.483188 GGATGTAAATTCCGAGCCGAGT 60.483 50.000 0.00 0.00 0.00 4.18
119 120 2.135933 GGATGTAAATTCCGAGCCGAG 58.864 52.381 0.00 0.00 0.00 4.63
120 121 1.760613 AGGATGTAAATTCCGAGCCGA 59.239 47.619 0.00 0.00 38.36 5.54
121 122 1.867233 CAGGATGTAAATTCCGAGCCG 59.133 52.381 0.00 0.00 38.36 5.52
122 123 1.604278 GCAGGATGTAAATTCCGAGCC 59.396 52.381 0.00 0.00 39.31 4.70
123 124 2.288666 TGCAGGATGTAAATTCCGAGC 58.711 47.619 0.00 0.00 39.31 5.03
124 125 4.963276 TTTGCAGGATGTAAATTCCGAG 57.037 40.909 0.00 0.00 45.65 4.63
153 154 4.757594 ACGTATATTCAACCGGCTGTTAA 58.242 39.130 0.00 0.00 34.69 2.01
158 159 4.280174 ACAGATACGTATATTCAACCGGCT 59.720 41.667 8.34 0.00 0.00 5.52
161 162 6.362551 CCAGAACAGATACGTATATTCAACCG 59.637 42.308 20.38 5.75 0.00 4.44
165 166 7.576861 TGTCCAGAACAGATACGTATATTCA 57.423 36.000 20.38 5.75 32.81 2.57
195 196 2.093941 CGATATAGCGGACGAGAACGAT 59.906 50.000 1.57 0.00 42.66 3.73
206 207 4.902448 CCGTAATAATCGTCGATATAGCGG 59.098 45.833 10.94 14.21 0.00 5.52
207 208 4.375117 GCCGTAATAATCGTCGATATAGCG 59.625 45.833 8.43 3.47 0.00 4.26
344 346 2.109799 CCGGCATGTGCTCTAGGG 59.890 66.667 4.84 0.00 41.70 3.53
444 454 4.393062 GGACAGTGTTGACATACATTCTGG 59.607 45.833 0.00 0.00 0.00 3.86
579 590 1.964223 TCCCTGGATAGCGATGAAGTC 59.036 52.381 0.00 0.00 0.00 3.01
582 593 2.381752 TCTCCCTGGATAGCGATGAA 57.618 50.000 0.00 0.00 0.00 2.57
642 653 0.318360 TGCGAACGGATGCCTATACG 60.318 55.000 0.00 0.00 46.23 3.06
896 920 3.487202 CGTTCACCATCGGCCGTG 61.487 66.667 27.15 21.41 0.00 4.94
1548 1580 2.118679 ACAGCCATGACCTATGCTACA 58.881 47.619 0.00 0.00 35.37 2.74
1576 1610 6.034898 ACGACAAAGCAAACAAAGAATTTCTG 59.965 34.615 0.00 0.00 35.03 3.02
1602 1636 8.333984 TCCTACGGATTAATCTATGATCAGGTA 58.666 37.037 14.95 0.00 0.00 3.08
1707 1746 0.954452 CTTCCAGAAACAGGCACACC 59.046 55.000 0.00 0.00 0.00 4.16
1709 1748 0.178992 CCCTTCCAGAAACAGGCACA 60.179 55.000 0.00 0.00 0.00 4.57
1875 2347 4.151798 GTCGACCACTTACAGTACGTTAC 58.848 47.826 3.51 0.00 0.00 2.50
1919 2392 8.293699 TGATAGATTTGCACACTAGAGACTAA 57.706 34.615 0.00 0.00 0.00 2.24
1963 2436 4.142403 ACATGTTGCCCGTATTTTGATCTG 60.142 41.667 0.00 0.00 0.00 2.90
1965 2438 4.370364 ACATGTTGCCCGTATTTTGATC 57.630 40.909 0.00 0.00 0.00 2.92
1966 2439 4.021544 ACAACATGTTGCCCGTATTTTGAT 60.022 37.500 33.23 10.56 44.03 2.57
1967 2440 3.319405 ACAACATGTTGCCCGTATTTTGA 59.681 39.130 33.23 0.00 44.03 2.69
1969 2442 4.329462 AACAACATGTTGCCCGTATTTT 57.671 36.364 33.23 17.38 44.03 1.82
1970 2443 4.521256 ACTAACAACATGTTGCCCGTATTT 59.479 37.500 33.23 21.54 41.30 1.40
2003 2531 6.522946 ACTTAGTTGTTCACCTTCCTACTTC 58.477 40.000 0.00 0.00 0.00 3.01
2004 2532 6.496144 ACTTAGTTGTTCACCTTCCTACTT 57.504 37.500 0.00 0.00 0.00 2.24
2005 2533 7.607615 TTACTTAGTTGTTCACCTTCCTACT 57.392 36.000 0.00 0.00 0.00 2.57
2006 2534 8.667076 TTTTACTTAGTTGTTCACCTTCCTAC 57.333 34.615 0.00 0.00 0.00 3.18
2009 2537 7.563888 ACTTTTACTTAGTTGTTCACCTTCC 57.436 36.000 0.00 0.00 0.00 3.46
2068 2596 3.187227 CGGAAGGAACACAACTTCATCAG 59.813 47.826 6.73 0.00 43.70 2.90
2069 2597 3.138304 CGGAAGGAACACAACTTCATCA 58.862 45.455 6.73 0.00 43.70 3.07
2070 2598 3.399330 TCGGAAGGAACACAACTTCATC 58.601 45.455 6.73 0.00 43.70 2.92
2071 2599 3.485463 TCGGAAGGAACACAACTTCAT 57.515 42.857 6.73 0.00 43.70 2.57
2237 2768 1.138859 GCCAAACTTGCTCACCCTTTT 59.861 47.619 0.00 0.00 0.00 2.27
2279 2810 0.250338 AGTCTCCAAGTGGCGGTTTC 60.250 55.000 0.00 0.00 34.44 2.78
2379 2910 2.035632 GGAGTAGGAGATGTCTGGTGG 58.964 57.143 0.00 0.00 0.00 4.61
2424 2955 6.879458 TGATTCTGATGATGATGCTCATAAGG 59.121 38.462 0.00 0.00 37.20 2.69


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

AutoCloner maintained by Alex Coulton.