Multiple sequence alignment - TraesCS5D01G508800

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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 TraesCS5D01G508800 chr5D 100.000 2017 0 0 680 2696 533912774 533914790 0.000000e+00 3725.0
1 TraesCS5D01G508800 chr5D 100.000 315 0 0 1 315 533912095 533912409 1.390000e-162 582.0
2 TraesCS5D01G508800 chr5B 89.267 1528 70 31 680 2158 673988527 673990009 0.000000e+00 1827.0
3 TraesCS5D01G508800 chr5B 86.444 568 27 16 2111 2649 673990056 673990602 6.470000e-161 577.0
4 TraesCS5D01G508800 chr5B 81.230 309 30 17 20 315 673988221 673988514 9.710000e-55 224.0
5 TraesCS5D01G508800 chr4A 92.985 784 34 10 900 1670 637966852 637966077 0.000000e+00 1123.0
6 TraesCS5D01G508800 chr4A 91.429 350 15 6 1817 2158 637966070 637965728 1.460000e-127 466.0
7 TraesCS5D01G508800 chr4A 82.927 328 17 15 2 315 637967613 637967311 2.660000e-65 259.0
8 TraesCS5D01G508800 chr4A 82.845 239 11 19 2467 2696 637965512 637965295 1.270000e-43 187.0
9 TraesCS5D01G508800 chr3D 84.848 99 12 2 1138 1236 613747841 613747936 2.210000e-16 97.1
10 TraesCS5D01G508800 chr3B 92.308 65 5 0 1172 1236 822984291 822984355 2.860000e-15 93.5
11 TraesCS5D01G508800 chr3A 92.308 65 5 0 1172 1236 749415195 749415259 2.860000e-15 93.5


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 TraesCS5D01G508800 chr5D 533912095 533914790 2695 False 2153.50 3725 100.0000 1 2696 2 chr5D.!!$F1 2695
1 TraesCS5D01G508800 chr5B 673988221 673990602 2381 False 876.00 1827 85.6470 20 2649 3 chr5B.!!$F1 2629
2 TraesCS5D01G508800 chr4A 637965295 637967613 2318 True 508.75 1123 87.5465 2 2696 4 chr4A.!!$R1 2694


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
828 1133 0.031917 TATAGCCCGTGGGTTCCTCA 60.032 55.0 6.82 0.0 37.65 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 2905 0.322975 GAGCAGCAGAGGGTGAAAGA 59.677 55.0 0.0 0.0 45.29 2.52 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
73 74 3.067601 CACCATCATCCATCCATGTGTTG 59.932 47.826 0.00 0.00 0.00 3.33
85 86 4.798882 TCCATGTGTTGTAAAACCTTCCT 58.201 39.130 0.00 0.00 0.00 3.36
96 97 6.718294 TGTAAAACCTTCCTAAATCCTCCTC 58.282 40.000 0.00 0.00 0.00 3.71
97 98 4.864483 AAACCTTCCTAAATCCTCCTCC 57.136 45.455 0.00 0.00 0.00 4.30
98 99 3.805360 ACCTTCCTAAATCCTCCTCCT 57.195 47.619 0.00 0.00 0.00 3.69
99 100 4.920781 ACCTTCCTAAATCCTCCTCCTA 57.079 45.455 0.00 0.00 0.00 2.94
100 101 4.558715 ACCTTCCTAAATCCTCCTCCTAC 58.441 47.826 0.00 0.00 0.00 3.18
101 102 4.015541 ACCTTCCTAAATCCTCCTCCTACA 60.016 45.833 0.00 0.00 0.00 2.74
107 109 2.238319 ATCCTCCTCCTACACGGCCA 62.238 60.000 2.24 0.00 0.00 5.36
124 126 2.034221 AGCCGAAAAGCCCCAGAC 59.966 61.111 0.00 0.00 0.00 3.51
125 127 3.062466 GCCGAAAAGCCCCAGACC 61.062 66.667 0.00 0.00 0.00 3.85
127 129 1.228429 CCGAAAAGCCCCAGACCAA 60.228 57.895 0.00 0.00 0.00 3.67
129 131 1.524008 CGAAAAGCCCCAGACCAACC 61.524 60.000 0.00 0.00 0.00 3.77
130 132 1.524008 GAAAAGCCCCAGACCAACCG 61.524 60.000 0.00 0.00 0.00 4.44
131 133 2.292785 AAAAGCCCCAGACCAACCGT 62.293 55.000 0.00 0.00 0.00 4.83
132 134 1.420532 AAAGCCCCAGACCAACCGTA 61.421 55.000 0.00 0.00 0.00 4.02
134 136 2.267961 CCCCAGACCAACCGTAGC 59.732 66.667 0.00 0.00 0.00 3.58
135 137 2.125673 CCCAGACCAACCGTAGCG 60.126 66.667 0.00 0.00 0.00 4.26
145 147 2.338984 CCGTAGCGGCTATCACCC 59.661 66.667 13.60 0.00 41.17 4.61
146 148 2.338984 CGTAGCGGCTATCACCCC 59.661 66.667 13.60 0.00 0.00 4.95
147 149 2.495409 CGTAGCGGCTATCACCCCA 61.495 63.158 13.60 0.00 0.00 4.96
148 150 1.827394 GTAGCGGCTATCACCCCAA 59.173 57.895 13.60 0.00 0.00 4.12
149 151 0.179468 GTAGCGGCTATCACCCCAAA 59.821 55.000 13.60 0.00 0.00 3.28
150 152 0.913205 TAGCGGCTATCACCCCAAAA 59.087 50.000 5.42 0.00 0.00 2.44
153 155 0.808755 CGGCTATCACCCCAAAACAC 59.191 55.000 0.00 0.00 0.00 3.32
250 281 4.735358 GTTTCCCTCCACGGCCCC 62.735 72.222 0.00 0.00 0.00 5.80
755 803 0.044244 CCTCCTCCTCCAAACCCCTA 59.956 60.000 0.00 0.00 0.00 3.53
757 805 0.797579 TCCTCCTCCAAACCCCTACT 59.202 55.000 0.00 0.00 0.00 2.57
758 806 1.205055 CCTCCTCCAAACCCCTACTC 58.795 60.000 0.00 0.00 0.00 2.59
759 807 1.205055 CTCCTCCAAACCCCTACTCC 58.795 60.000 0.00 0.00 0.00 3.85
760 808 0.253020 TCCTCCAAACCCCTACTCCC 60.253 60.000 0.00 0.00 0.00 4.30
762 810 2.253403 CTCCAAACCCCTACTCCCGC 62.253 65.000 0.00 0.00 0.00 6.13
764 812 3.396570 AAACCCCTACTCCCGCCG 61.397 66.667 0.00 0.00 0.00 6.46
809 1114 1.827399 CTCTGGTGGTTGGCCGTAGT 61.827 60.000 0.00 0.00 37.67 2.73
811 1116 0.539986 CTGGTGGTTGGCCGTAGTAT 59.460 55.000 0.00 0.00 37.67 2.12
812 1117 1.758280 CTGGTGGTTGGCCGTAGTATA 59.242 52.381 0.00 0.00 37.67 1.47
813 1118 1.758280 TGGTGGTTGGCCGTAGTATAG 59.242 52.381 0.00 0.00 37.67 1.31
814 1119 1.539712 GGTGGTTGGCCGTAGTATAGC 60.540 57.143 0.00 0.00 37.67 2.97
816 1121 0.034476 GGTTGGCCGTAGTATAGCCC 59.966 60.000 10.09 0.00 46.55 5.19
817 1122 0.319297 GTTGGCCGTAGTATAGCCCG 60.319 60.000 10.09 0.00 46.55 6.13
818 1123 0.756442 TTGGCCGTAGTATAGCCCGT 60.756 55.000 10.09 0.00 46.55 5.28
819 1124 1.288127 GGCCGTAGTATAGCCCGTG 59.712 63.158 0.00 0.00 41.00 4.94
820 1125 1.288127 GCCGTAGTATAGCCCGTGG 59.712 63.158 0.00 0.00 0.00 4.94
821 1126 1.962144 CCGTAGTATAGCCCGTGGG 59.038 63.158 0.00 0.00 38.57 4.61
822 1127 0.825010 CCGTAGTATAGCCCGTGGGT 60.825 60.000 6.82 0.00 37.65 4.51
828 1133 0.031917 TATAGCCCGTGGGTTCCTCA 60.032 55.000 6.82 0.00 37.65 3.86
830 1135 4.717313 GCCCGTGGGTTCCTCACC 62.717 72.222 6.82 0.00 46.46 4.02
884 1189 1.529152 CCGGCACCAAACCCCTAAAC 61.529 60.000 0.00 0.00 0.00 2.01
885 1190 1.529152 CGGCACCAAACCCCTAAACC 61.529 60.000 0.00 0.00 0.00 3.27
886 1191 1.189524 GGCACCAAACCCCTAAACCC 61.190 60.000 0.00 0.00 0.00 4.11
887 1192 0.470268 GCACCAAACCCCTAAACCCA 60.470 55.000 0.00 0.00 0.00 4.51
888 1193 1.334160 CACCAAACCCCTAAACCCAC 58.666 55.000 0.00 0.00 0.00 4.61
889 1194 0.178984 ACCAAACCCCTAAACCCACG 60.179 55.000 0.00 0.00 0.00 4.94
890 1195 1.529152 CCAAACCCCTAAACCCACGC 61.529 60.000 0.00 0.00 0.00 5.34
1027 1332 2.182030 CGGTCGAGAAGGTGAGCC 59.818 66.667 0.00 0.00 0.00 4.70
1070 1375 0.941463 CGTGCCCGATCTGTAGATGC 60.941 60.000 0.00 0.00 34.37 3.91
1073 1378 0.387878 GCCCGATCTGTAGATGCGAG 60.388 60.000 0.00 0.00 34.37 5.03
1111 1416 0.878523 TCTGACGTGTTTTGCCTCGG 60.879 55.000 0.00 0.00 0.00 4.63
1127 1432 2.747686 GGTCTGTTCGCAGGGGAA 59.252 61.111 0.00 0.00 45.04 3.97
1281 1586 2.236395 CCGATCTGTTGTCTAACCCCTT 59.764 50.000 0.00 0.00 35.92 3.95
1572 1911 3.112709 GTGGAGCTCCGCGTTGTC 61.113 66.667 29.54 9.04 39.43 3.18
1726 2065 1.764054 CAGCCCCACCTAGCTAGCT 60.764 63.158 23.12 23.12 37.18 3.32
1752 2091 1.405105 CAAGCGGAGAGAGGAGAAGAG 59.595 57.143 0.00 0.00 0.00 2.85
1753 2092 0.916086 AGCGGAGAGAGGAGAAGAGA 59.084 55.000 0.00 0.00 0.00 3.10
1754 2093 1.283613 AGCGGAGAGAGGAGAAGAGAA 59.716 52.381 0.00 0.00 0.00 2.87
1755 2094 1.676006 GCGGAGAGAGGAGAAGAGAAG 59.324 57.143 0.00 0.00 0.00 2.85
1756 2095 2.682563 GCGGAGAGAGGAGAAGAGAAGA 60.683 54.545 0.00 0.00 0.00 2.87
1757 2096 3.206150 CGGAGAGAGGAGAAGAGAAGAG 58.794 54.545 0.00 0.00 0.00 2.85
1758 2097 3.118408 CGGAGAGAGGAGAAGAGAAGAGA 60.118 52.174 0.00 0.00 0.00 3.10
1759 2098 4.625324 CGGAGAGAGGAGAAGAGAAGAGAA 60.625 50.000 0.00 0.00 0.00 2.87
1760 2099 4.884164 GGAGAGAGGAGAAGAGAAGAGAAG 59.116 50.000 0.00 0.00 0.00 2.85
1761 2100 5.339200 GGAGAGAGGAGAAGAGAAGAGAAGA 60.339 48.000 0.00 0.00 0.00 2.87
1930 2276 8.635983 CAATAATGAATGAATGAACGATGATGC 58.364 33.333 0.00 0.00 0.00 3.91
1931 2277 5.761165 ATGAATGAATGAACGATGATGCA 57.239 34.783 0.00 0.00 0.00 3.96
1934 2286 2.635714 TGAATGAACGATGATGCAGCT 58.364 42.857 2.53 0.00 0.00 4.24
1958 2310 3.647824 GCTGCTGCTGTTCTTCGT 58.352 55.556 8.53 0.00 36.03 3.85
1986 2339 2.781945 AGCGGCTTTGTTCTTTCTTG 57.218 45.000 0.00 0.00 0.00 3.02
2012 2365 4.363999 CCTAGTAGCAGCTGTGATGTTAC 58.636 47.826 16.64 8.64 35.35 2.50
2050 2404 8.144862 AGTAGCGGTTATCCTAGTAGTAGTAT 57.855 38.462 3.91 0.00 0.00 2.12
2136 2493 0.035725 TGGCTCCAGATCTGTGCAAG 60.036 55.000 27.69 18.04 32.45 4.01
2166 2620 1.172180 TTCACCTGAAAGCGGGCTTG 61.172 55.000 6.69 0.00 44.98 4.01
2170 2624 1.303309 CCTGAAAGCGGGCTTGATAG 58.697 55.000 6.69 5.88 36.26 2.08
2192 2646 0.675837 GCTCCAGATCTGTGCAAGCA 60.676 55.000 24.20 0.00 0.00 3.91
2206 2660 0.039165 CAAGCACCCGCCTTTTCTTC 60.039 55.000 0.00 0.00 39.83 2.87
2207 2661 1.179174 AAGCACCCGCCTTTTCTTCC 61.179 55.000 0.00 0.00 39.83 3.46
2209 2663 1.074951 CACCCGCCTTTTCTTCCCT 59.925 57.895 0.00 0.00 0.00 4.20
2211 2665 1.745489 CCCGCCTTTTCTTCCCTCG 60.745 63.158 0.00 0.00 0.00 4.63
2238 2705 3.199727 TGAAATTCATCCCAGGTGATCGA 59.800 43.478 0.00 0.00 0.00 3.59
2239 2706 4.141413 TGAAATTCATCCCAGGTGATCGAT 60.141 41.667 0.00 0.00 0.00 3.59
2240 2707 3.692257 ATTCATCCCAGGTGATCGATC 57.308 47.619 18.72 18.72 0.00 3.69
2241 2708 2.388526 TCATCCCAGGTGATCGATCT 57.611 50.000 25.02 3.30 0.00 2.75
2242 2709 1.966354 TCATCCCAGGTGATCGATCTG 59.034 52.381 25.02 15.25 0.00 2.90
2243 2710 0.683973 ATCCCAGGTGATCGATCTGC 59.316 55.000 25.02 17.16 0.00 4.26
2244 2711 1.070445 CCCAGGTGATCGATCTGCC 59.930 63.158 25.02 23.96 0.00 4.85
2245 2712 1.689243 CCCAGGTGATCGATCTGCCA 61.689 60.000 28.39 10.46 0.00 4.92
2280 2747 0.391528 TCTGATGTGATGGTGCACGG 60.392 55.000 11.45 0.00 41.63 4.94
2282 2749 1.377202 GATGTGATGGTGCACGGGT 60.377 57.895 11.45 0.00 41.63 5.28
2304 2771 1.452108 GTTTCCGCCTGGGATCTGG 60.452 63.158 0.00 0.00 46.62 3.86
2305 2772 2.679342 TTTCCGCCTGGGATCTGGG 61.679 63.158 0.00 0.00 46.62 4.45
2308 2775 3.411517 CGCCTGGGATCTGGGGTT 61.412 66.667 0.00 0.00 39.16 4.11
2431 2903 0.250338 GAAAAGTCAGCACCCGGTCT 60.250 55.000 0.00 0.00 0.00 3.85
2433 2905 0.182775 AAAGTCAGCACCCGGTCTTT 59.817 50.000 0.00 0.00 0.00 2.52
2434 2906 0.250338 AAGTCAGCACCCGGTCTTTC 60.250 55.000 0.00 0.00 0.00 2.62
2437 2909 0.472471 TCAGCACCCGGTCTTTCTTT 59.528 50.000 0.00 0.00 0.00 2.52
2452 2926 0.322975 TCTTTCACCCTCTGCTGCTC 59.677 55.000 0.00 0.00 0.00 4.26
2457 2931 2.268280 CCCTCTGCTGCTCCACTG 59.732 66.667 0.00 0.00 0.00 3.66
2462 2936 2.031616 TGCTGCTCCACTGCACTC 59.968 61.111 0.00 0.00 46.94 3.51
2494 2972 2.674380 CCAGCTTTCAGCCCGCTT 60.674 61.111 0.00 0.00 43.77 4.68
2542 3024 0.477597 AGTGGGGTGGAGGAATCCAA 60.478 55.000 0.61 0.00 42.10 3.53
2555 3037 5.221742 GGAGGAATCCAAACCCTATCTACTG 60.222 48.000 0.61 0.00 0.00 2.74
2556 3038 4.660771 AGGAATCCAAACCCTATCTACTGG 59.339 45.833 0.61 0.00 0.00 4.00
2557 3039 4.658901 GGAATCCAAACCCTATCTACTGGA 59.341 45.833 0.00 0.00 37.37 3.86
2558 3040 5.221742 GGAATCCAAACCCTATCTACTGGAG 60.222 48.000 0.00 0.00 36.45 3.86
2559 3041 4.348020 TCCAAACCCTATCTACTGGAGT 57.652 45.455 0.00 0.00 0.00 3.85
2582 3067 1.120530 AGTATCCCGATGTGTGACCC 58.879 55.000 0.00 0.00 0.00 4.46
2584 3069 1.119684 TATCCCGATGTGTGACCCAG 58.880 55.000 0.00 0.00 0.00 4.45
2585 3070 2.257409 ATCCCGATGTGTGACCCAGC 62.257 60.000 0.00 0.00 0.00 4.85
2586 3071 2.815211 CCGATGTGTGACCCAGCG 60.815 66.667 0.00 0.00 41.08 5.18
2587 3072 2.815211 CGATGTGTGACCCAGCGG 60.815 66.667 0.00 0.00 38.01 5.52
2649 3139 2.359975 CTTGTTCGGGAGGGTGCC 60.360 66.667 0.00 0.00 0.00 5.01
2650 3140 3.920093 CTTGTTCGGGAGGGTGCCC 62.920 68.421 0.00 0.00 45.10 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.940046 TCTTTGTGGTTTGTGTTAACGGTA 59.060 37.500 0.26 0.00 0.00 4.02
73 74 6.069556 AGGAGGAGGATTTAGGAAGGTTTTAC 60.070 42.308 0.00 0.00 0.00 2.01
85 86 2.037144 GCCGTGTAGGAGGAGGATTTA 58.963 52.381 0.00 0.00 45.00 1.40
107 109 2.034221 GTCTGGGGCTTTTCGGCT 59.966 61.111 0.00 0.00 38.46 5.52
129 131 2.023414 TTGGGGTGATAGCCGCTACG 62.023 60.000 1.14 0.00 41.45 3.51
130 132 0.179468 TTTGGGGTGATAGCCGCTAC 59.821 55.000 1.14 0.00 41.45 3.58
131 133 0.913205 TTTTGGGGTGATAGCCGCTA 59.087 50.000 1.73 1.73 41.45 4.26
132 134 0.679960 GTTTTGGGGTGATAGCCGCT 60.680 55.000 0.00 0.00 41.45 5.52
134 136 0.808755 GTGTTTTGGGGTGATAGCCG 59.191 55.000 0.00 0.00 36.39 5.52
135 137 2.092323 GAGTGTTTTGGGGTGATAGCC 58.908 52.381 0.00 0.00 34.31 3.93
136 138 2.790433 TGAGTGTTTTGGGGTGATAGC 58.210 47.619 0.00 0.00 0.00 2.97
137 139 4.396166 GTGATGAGTGTTTTGGGGTGATAG 59.604 45.833 0.00 0.00 0.00 2.08
138 140 4.042809 AGTGATGAGTGTTTTGGGGTGATA 59.957 41.667 0.00 0.00 0.00 2.15
139 141 3.157087 GTGATGAGTGTTTTGGGGTGAT 58.843 45.455 0.00 0.00 0.00 3.06
140 142 2.174639 AGTGATGAGTGTTTTGGGGTGA 59.825 45.455 0.00 0.00 0.00 4.02
141 143 2.554032 GAGTGATGAGTGTTTTGGGGTG 59.446 50.000 0.00 0.00 0.00 4.61
142 144 2.810400 CGAGTGATGAGTGTTTTGGGGT 60.810 50.000 0.00 0.00 0.00 4.95
143 145 1.806542 CGAGTGATGAGTGTTTTGGGG 59.193 52.381 0.00 0.00 0.00 4.96
144 146 2.480419 GTCGAGTGATGAGTGTTTTGGG 59.520 50.000 0.00 0.00 0.00 4.12
145 147 3.130633 TGTCGAGTGATGAGTGTTTTGG 58.869 45.455 0.00 0.00 0.00 3.28
146 148 4.794248 TTGTCGAGTGATGAGTGTTTTG 57.206 40.909 0.00 0.00 0.00 2.44
147 149 4.260784 GCTTTGTCGAGTGATGAGTGTTTT 60.261 41.667 0.00 0.00 0.00 2.43
148 150 3.248602 GCTTTGTCGAGTGATGAGTGTTT 59.751 43.478 0.00 0.00 0.00 2.83
149 151 2.802816 GCTTTGTCGAGTGATGAGTGTT 59.197 45.455 0.00 0.00 0.00 3.32
150 152 2.224042 TGCTTTGTCGAGTGATGAGTGT 60.224 45.455 0.00 0.00 0.00 3.55
153 155 1.388093 CGTGCTTTGTCGAGTGATGAG 59.612 52.381 0.00 0.00 0.00 2.90
207 238 1.173913 GGGTGGAGGGAAATGAAACG 58.826 55.000 0.00 0.00 0.00 3.60
208 239 2.604912 AGGGTGGAGGGAAATGAAAC 57.395 50.000 0.00 0.00 0.00 2.78
209 240 3.628832 AAAGGGTGGAGGGAAATGAAA 57.371 42.857 0.00 0.00 0.00 2.69
210 241 3.506398 GAAAAGGGTGGAGGGAAATGAA 58.494 45.455 0.00 0.00 0.00 2.57
211 242 2.225267 GGAAAAGGGTGGAGGGAAATGA 60.225 50.000 0.00 0.00 0.00 2.57
250 281 4.845307 GGGGGAGGGAAGAGGGGG 62.845 77.778 0.00 0.00 0.00 5.40
755 803 4.143333 CGATTGGTCGGCGGGAGT 62.143 66.667 7.21 0.00 44.00 3.85
764 812 0.103208 ACTGGCTCGATCGATTGGTC 59.897 55.000 19.78 9.46 0.00 4.02
768 816 4.427394 GCACTGGCTCGATCGATT 57.573 55.556 19.78 0.00 36.96 3.34
809 1114 0.031917 TGAGGAACCCACGGGCTATA 60.032 55.000 0.69 0.00 39.32 1.31
811 1116 2.120940 TGAGGAACCCACGGGCTA 59.879 61.111 0.69 0.00 39.32 3.93
812 1117 3.637273 GTGAGGAACCCACGGGCT 61.637 66.667 0.69 0.00 39.32 5.19
813 1118 4.717313 GGTGAGGAACCCACGGGC 62.717 72.222 0.69 0.00 44.02 6.13
820 1125 0.173708 CTCTGCTACGGTGAGGAACC 59.826 60.000 0.00 0.00 46.60 3.62
821 1126 1.174783 TCTCTGCTACGGTGAGGAAC 58.825 55.000 0.00 0.00 0.00 3.62
822 1127 2.025155 GATCTCTGCTACGGTGAGGAA 58.975 52.381 0.00 0.00 0.00 3.36
864 1169 3.871850 TTAGGGGTTTGGTGCCGGC 62.872 63.158 22.73 22.73 0.00 6.13
865 1170 1.228613 TTTAGGGGTTTGGTGCCGG 60.229 57.895 0.00 0.00 0.00 6.13
866 1171 1.529152 GGTTTAGGGGTTTGGTGCCG 61.529 60.000 0.00 0.00 0.00 5.69
1070 1375 0.609131 AACACCAAATCCCTGCCTCG 60.609 55.000 0.00 0.00 0.00 4.63
1073 1378 1.478105 GATCAACACCAAATCCCTGCC 59.522 52.381 0.00 0.00 0.00 4.85
1281 1586 3.762407 TCACAGATCGGGAAAGAACAA 57.238 42.857 0.00 0.00 0.00 2.83
1362 1680 0.337082 TCTTCCTGTACCGGATCCCA 59.663 55.000 9.46 0.00 32.02 4.37
1509 1848 1.059098 TCTTCTTCTTGGGCTGCTGA 58.941 50.000 0.00 0.00 0.00 4.26
1569 1908 1.228124 CTCCTTGCCAAACCCGACA 60.228 57.895 0.00 0.00 0.00 4.35
1572 1911 2.115266 ACCTCCTTGCCAAACCCG 59.885 61.111 0.00 0.00 0.00 5.28
1578 1917 3.177884 AGCACCACCTCCTTGCCA 61.178 61.111 0.00 0.00 36.91 4.92
1726 2065 1.670949 CCTCTCTCCGCTTGCTGCTA 61.671 60.000 0.00 0.00 40.11 3.49
1744 2083 6.122277 TCATCTCTCTTCTCTTCTCTTCTCC 58.878 44.000 0.00 0.00 0.00 3.71
1752 2091 5.684704 TCTCCTCTCATCTCTCTTCTCTTC 58.315 45.833 0.00 0.00 0.00 2.87
1753 2092 5.715439 TCTCCTCTCATCTCTCTTCTCTT 57.285 43.478 0.00 0.00 0.00 2.85
1754 2093 5.222007 GGATCTCCTCTCATCTCTCTTCTCT 60.222 48.000 0.00 0.00 0.00 3.10
1755 2094 5.006386 GGATCTCCTCTCATCTCTCTTCTC 58.994 50.000 0.00 0.00 0.00 2.87
1756 2095 4.416513 TGGATCTCCTCTCATCTCTCTTCT 59.583 45.833 0.00 0.00 36.82 2.85
1757 2096 4.728772 TGGATCTCCTCTCATCTCTCTTC 58.271 47.826 0.00 0.00 36.82 2.87
1758 2097 4.416513 TCTGGATCTCCTCTCATCTCTCTT 59.583 45.833 0.00 0.00 36.82 2.85
1759 2098 3.982730 TCTGGATCTCCTCTCATCTCTCT 59.017 47.826 0.00 0.00 36.82 3.10
1760 2099 4.202503 ACTCTGGATCTCCTCTCATCTCTC 60.203 50.000 0.00 0.00 36.82 3.20
1761 2100 3.723681 ACTCTGGATCTCCTCTCATCTCT 59.276 47.826 0.00 0.00 36.82 3.10
1943 2295 2.253758 GGCACGAAGAACAGCAGCA 61.254 57.895 0.00 0.00 0.00 4.41
1958 2310 2.034066 AAAGCCGCTAAGCTGGCA 59.966 55.556 14.66 0.00 45.36 4.92
1986 2339 1.066858 TCACAGCTGCTACTAGGCAAC 60.067 52.381 15.27 0.00 41.94 4.17
2012 2365 3.549794 ACCGCTACTACTACTACTTGGG 58.450 50.000 0.00 0.00 0.00 4.12
2050 2404 4.062293 GCAATGTTACACACTACCACTGA 58.938 43.478 0.00 0.00 0.00 3.41
2136 2493 4.791088 GCTTTCAGGTGAAAAAGAGAGTGC 60.791 45.833 6.61 1.01 42.72 4.40
2192 2646 1.379146 GAGGGAAGAAAAGGCGGGT 59.621 57.895 0.00 0.00 0.00 5.28
2206 2660 1.332997 GATGAATTTCAGCTGCGAGGG 59.667 52.381 9.47 0.00 28.67 4.30
2207 2661 1.332997 GGATGAATTTCAGCTGCGAGG 59.667 52.381 9.47 0.00 32.54 4.63
2209 2663 1.339920 TGGGATGAATTTCAGCTGCGA 60.340 47.619 9.47 0.00 32.54 5.10
2211 2665 1.407979 CCTGGGATGAATTTCAGCTGC 59.592 52.381 9.47 0.00 32.54 5.25
2244 2711 6.918022 CACATCAGATCAAACATCCATCAATG 59.082 38.462 0.00 0.00 0.00 2.82
2245 2712 6.831868 TCACATCAGATCAAACATCCATCAAT 59.168 34.615 0.00 0.00 0.00 2.57
2280 2747 2.983592 CCAGGCGGAAACACCACC 60.984 66.667 0.00 0.00 40.94 4.61
2282 2749 2.478335 GATCCCAGGCGGAAACACCA 62.478 60.000 0.00 0.00 46.47 4.17
2291 2758 3.411517 AACCCCAGATCCCAGGCG 61.412 66.667 0.00 0.00 0.00 5.52
2295 2762 3.727258 CGCCAACCCCAGATCCCA 61.727 66.667 0.00 0.00 0.00 4.37
2308 2775 3.536917 CTACTCATCCGGCCGCCA 61.537 66.667 22.85 8.89 0.00 5.69
2431 2903 1.143684 AGCAGCAGAGGGTGAAAGAAA 59.856 47.619 0.00 0.00 45.29 2.52
2433 2905 0.322975 GAGCAGCAGAGGGTGAAAGA 59.677 55.000 0.00 0.00 45.29 2.52
2434 2906 0.676151 GGAGCAGCAGAGGGTGAAAG 60.676 60.000 0.00 0.00 45.29 2.62
2437 2909 2.203832 TGGAGCAGCAGAGGGTGA 60.204 61.111 0.00 0.00 45.29 4.02
2452 2926 1.964891 CAGCAGTGGAGTGCAGTGG 60.965 63.158 19.69 1.85 46.60 4.00
2457 2931 2.281345 ACAGCAGCAGTGGAGTGC 60.281 61.111 0.00 0.00 44.35 4.40
2462 2936 2.111669 TGGTGACAGCAGCAGTGG 59.888 61.111 2.50 0.00 46.66 4.00
2483 2961 2.669569 GTGAGCAAGCGGGCTGAA 60.670 61.111 9.95 0.00 45.99 3.02
2484 2962 3.596066 GAGTGAGCAAGCGGGCTGA 62.596 63.158 9.95 0.00 45.99 4.26
2494 2972 0.390492 CCAGTGTCAGTGAGTGAGCA 59.610 55.000 9.36 0.00 35.13 4.26
2555 3037 4.215827 CACACATCGGGATACTACTACTCC 59.784 50.000 0.00 0.00 0.00 3.85
2556 3038 5.049543 GTCACACATCGGGATACTACTACTC 60.050 48.000 0.00 0.00 0.00 2.59
2557 3039 4.820716 GTCACACATCGGGATACTACTACT 59.179 45.833 0.00 0.00 0.00 2.57
2558 3040 4.023365 GGTCACACATCGGGATACTACTAC 60.023 50.000 0.00 0.00 0.00 2.73
2559 3041 4.139786 GGTCACACATCGGGATACTACTA 58.860 47.826 0.00 0.00 0.00 1.82



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

AutoCloner maintained by Alex Coulton.