Multiple sequence alignment - TraesCS1D01G216800

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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 TraesCS1D01G216800 chr1D 100.000 3448 0 0 1 3448 302412141 302415588 0.000000e+00 6368
1 TraesCS1D01G216800 chr1D 97.267 3147 78 5 307 3448 311907519 311904376 0.000000e+00 5328
2 TraesCS1D01G216800 chr1D 97.039 304 8 1 1 304 302397843 302398145 8.540000e-141 510
3 TraesCS1D01G216800 chr1D 96.711 304 9 1 1 304 346668062 346668364 3.970000e-139 505
4 TraesCS1D01G216800 chr2D 96.975 3140 88 5 314 3448 515619698 515616561 0.000000e+00 5265
5 TraesCS1D01G216800 chr2D 96.662 3146 87 11 314 3448 571229642 571226504 0.000000e+00 5212
6 TraesCS1D01G216800 chr2D 96.417 307 10 1 1 307 154228856 154228551 3.970000e-139 505
7 TraesCS1D01G216800 chrUn 96.823 3148 83 6 307 3448 27172508 27169372 0.000000e+00 5243
8 TraesCS1D01G216800 chrUn 96.792 3148 84 8 307 3448 27177973 27174837 0.000000e+00 5238
9 TraesCS1D01G216800 chr7D 96.816 3141 90 7 314 3448 133217247 133220383 0.000000e+00 5238
10 TraesCS1D01G216800 chr5D 96.665 3148 93 6 307 3448 236162351 236159210 0.000000e+00 5221
11 TraesCS1D01G216800 chr6D 96.694 3146 89 5 307 3448 100513153 100516287 0.000000e+00 5219
12 TraesCS1D01G216800 chr3D 96.535 3146 101 5 309 3448 167360500 167363643 0.000000e+00 5199
13 TraesCS1D01G216800 chr3D 97.368 304 7 1 1 304 40699533 40699231 1.830000e-142 516
14 TraesCS1D01G216800 chr3D 97.039 304 9 0 1 304 170720615 170720312 2.370000e-141 512
15 TraesCS1D01G216800 chr3D 96.711 304 9 1 1 304 411400698 411400396 3.970000e-139 505
16 TraesCS1D01G216800 chr3D 96.104 308 11 1 1 308 345927295 345927601 5.140000e-138 501
17 TraesCS1D01G216800 chr4D 97.368 304 8 0 1 304 97408038 97408341 5.100000e-143 518
18 TraesCS1D01G216800 chr4D 96.711 304 9 1 1 304 317519056 317519358 3.970000e-139 505


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 TraesCS1D01G216800 chr1D 302412141 302415588 3447 False 6368.0 6368 100.0000 1 3448 1 chr1D.!!$F2 3447
1 TraesCS1D01G216800 chr1D 311904376 311907519 3143 True 5328.0 5328 97.2670 307 3448 1 chr1D.!!$R1 3141
2 TraesCS1D01G216800 chr2D 515616561 515619698 3137 True 5265.0 5265 96.9750 314 3448 1 chr2D.!!$R2 3134
3 TraesCS1D01G216800 chr2D 571226504 571229642 3138 True 5212.0 5212 96.6620 314 3448 1 chr2D.!!$R3 3134
4 TraesCS1D01G216800 chrUn 27169372 27177973 8601 True 5240.5 5243 96.8075 307 3448 2 chrUn.!!$R1 3141
5 TraesCS1D01G216800 chr7D 133217247 133220383 3136 False 5238.0 5238 96.8160 314 3448 1 chr7D.!!$F1 3134
6 TraesCS1D01G216800 chr5D 236159210 236162351 3141 True 5221.0 5221 96.6650 307 3448 1 chr5D.!!$R1 3141
7 TraesCS1D01G216800 chr6D 100513153 100516287 3134 False 5219.0 5219 96.6940 307 3448 1 chr6D.!!$F1 3141
8 TraesCS1D01G216800 chr3D 167360500 167363643 3143 False 5199.0 5199 96.5350 309 3448 1 chr3D.!!$F1 3139

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
137 138 0.166814 CTTGCGCTAGTTGTTGAGGC 59.833 55.0 9.73 0.00 0.0 4.70 F
228 229 0.454285 CCAAACGCGTGCCAGTATTG 60.454 55.0 14.98 11.79 0.0 1.90 F
775 795 0.460284 CTAGCCGCCACGAACAGATT 60.460 55.0 0.00 0.00 0.0 2.40 F
1912 1936 0.618458 AAGGGCAAAGGACTCGCATA 59.382 50.0 0.00 0.00 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 1347 0.447801 CCACTTGCCGAGAAATTCCG 59.552 55.000 0.0 0.0 0.00 4.30 R
1912 1936 1.850755 TCCCTTCGGCCCCTTTTCT 60.851 57.895 0.0 0.0 0.00 2.52 R
2312 2336 2.106511 CCATTCCCCATCAATACGGACT 59.893 50.000 0.0 0.0 0.00 3.85 R
3295 8787 2.359975 AGCCCCAAGTACGCAAGC 60.360 61.111 0.0 0.0 45.62 4.01 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
18 19 2.728397 TCTCGTCCCCATCATACGG 58.272 57.895 0.00 0.00 37.24 4.02
19 20 1.006102 CTCGTCCCCATCATACGGC 60.006 63.158 0.00 0.00 37.24 5.68
20 21 2.030562 CGTCCCCATCATACGGCC 59.969 66.667 0.00 0.00 33.13 6.13
21 22 2.507854 CGTCCCCATCATACGGCCT 61.508 63.158 0.00 0.00 33.13 5.19
22 23 1.071471 GTCCCCATCATACGGCCTG 59.929 63.158 0.00 0.00 0.00 4.85
23 24 2.146724 TCCCCATCATACGGCCTGG 61.147 63.158 0.00 0.00 0.00 4.45
24 25 2.146724 CCCCATCATACGGCCTGGA 61.147 63.158 8.01 0.00 0.00 3.86
25 26 1.492133 CCCCATCATACGGCCTGGAT 61.492 60.000 8.01 0.00 0.00 3.41
26 27 0.321919 CCCATCATACGGCCTGGATG 60.322 60.000 12.11 12.11 37.48 3.51
27 28 3.238232 CATCATACGGCCTGGATGG 57.762 57.895 16.57 2.11 34.84 3.51
28 29 0.321919 CATCATACGGCCTGGATGGG 60.322 60.000 16.57 8.29 34.84 4.00
29 30 0.473694 ATCATACGGCCTGGATGGGA 60.474 55.000 16.57 2.80 36.00 4.37
30 31 1.071471 CATACGGCCTGGATGGGAC 59.929 63.158 10.85 0.00 36.00 4.46
35 36 3.866582 GCCTGGATGGGACGGGAG 61.867 72.222 0.00 0.00 36.43 4.30
52 53 4.778143 GTTGACCCGCGGCTGGAT 62.778 66.667 22.85 0.95 0.00 3.41
53 54 4.028490 TTGACCCGCGGCTGGATT 62.028 61.111 22.85 0.00 0.00 3.01
54 55 4.776322 TGACCCGCGGCTGGATTG 62.776 66.667 22.85 6.71 0.00 2.67
59 60 3.630148 CGCGGCTGGATTGCGTAG 61.630 66.667 0.00 0.00 46.29 3.51
72 73 3.195002 CGTAGCACGCCATGGGTG 61.195 66.667 22.21 22.21 46.85 4.61
90 91 4.742201 GCGCTGGCTTGTCGAGGA 62.742 66.667 0.00 0.00 35.83 3.71
91 92 2.507992 CGCTGGCTTGTCGAGGAG 60.508 66.667 0.00 0.00 0.00 3.69
92 93 2.125350 GCTGGCTTGTCGAGGAGG 60.125 66.667 0.00 0.00 0.00 4.30
93 94 2.125350 CTGGCTTGTCGAGGAGGC 60.125 66.667 12.90 12.90 38.78 4.70
94 95 2.604686 TGGCTTGTCGAGGAGGCT 60.605 61.111 18.42 0.00 39.05 4.58
95 96 2.177594 CTGGCTTGTCGAGGAGGCTT 62.178 60.000 18.42 0.00 39.05 4.35
96 97 1.003233 GGCTTGTCGAGGAGGCTTT 60.003 57.895 12.61 0.00 35.73 3.51
97 98 1.301677 GGCTTGTCGAGGAGGCTTTG 61.302 60.000 12.61 0.00 35.73 2.77
98 99 1.301677 GCTTGTCGAGGAGGCTTTGG 61.302 60.000 0.00 0.00 0.00 3.28
99 100 1.301677 CTTGTCGAGGAGGCTTTGGC 61.302 60.000 0.00 0.00 37.82 4.52
122 123 3.423154 CGGGTTCGGCTGTCTTGC 61.423 66.667 0.00 0.00 0.00 4.01
123 124 3.423154 GGGTTCGGCTGTCTTGCG 61.423 66.667 0.00 0.00 0.00 4.85
124 125 4.090057 GGTTCGGCTGTCTTGCGC 62.090 66.667 0.00 0.00 0.00 6.09
125 126 3.044305 GTTCGGCTGTCTTGCGCT 61.044 61.111 9.73 0.00 0.00 5.92
126 127 1.736645 GTTCGGCTGTCTTGCGCTA 60.737 57.895 9.73 0.00 0.00 4.26
127 128 1.446099 TTCGGCTGTCTTGCGCTAG 60.446 57.895 12.92 12.92 0.00 3.42
128 129 2.125912 CGGCTGTCTTGCGCTAGT 60.126 61.111 18.20 0.00 0.00 2.57
129 130 1.738099 CGGCTGTCTTGCGCTAGTT 60.738 57.895 18.20 0.00 0.00 2.24
130 131 1.790387 GGCTGTCTTGCGCTAGTTG 59.210 57.895 18.20 10.55 0.00 3.16
131 132 0.951040 GGCTGTCTTGCGCTAGTTGT 60.951 55.000 18.20 0.00 0.00 3.32
132 133 0.868406 GCTGTCTTGCGCTAGTTGTT 59.132 50.000 18.20 0.00 0.00 2.83
133 134 1.398960 GCTGTCTTGCGCTAGTTGTTG 60.399 52.381 18.20 7.12 0.00 3.33
134 135 2.135139 CTGTCTTGCGCTAGTTGTTGA 58.865 47.619 18.20 0.00 0.00 3.18
135 136 2.135139 TGTCTTGCGCTAGTTGTTGAG 58.865 47.619 18.20 0.00 0.00 3.02
136 137 1.461127 GTCTTGCGCTAGTTGTTGAGG 59.539 52.381 18.20 0.00 0.00 3.86
137 138 0.166814 CTTGCGCTAGTTGTTGAGGC 59.833 55.000 9.73 0.00 0.00 4.70
138 139 1.234615 TTGCGCTAGTTGTTGAGGCC 61.235 55.000 9.73 0.00 0.00 5.19
139 140 2.740714 GCGCTAGTTGTTGAGGCCG 61.741 63.158 0.00 0.00 0.00 6.13
140 141 1.080093 CGCTAGTTGTTGAGGCCGA 60.080 57.895 0.00 0.00 0.00 5.54
141 142 1.078759 CGCTAGTTGTTGAGGCCGAG 61.079 60.000 0.00 0.00 0.00 4.63
142 143 1.362406 GCTAGTTGTTGAGGCCGAGC 61.362 60.000 0.00 0.00 0.00 5.03
153 154 4.719369 GCCGAGCCGACGTGTCTT 62.719 66.667 0.00 0.00 0.00 3.01
154 155 2.805353 CCGAGCCGACGTGTCTTG 60.805 66.667 0.00 0.00 0.00 3.02
155 156 3.470567 CGAGCCGACGTGTCTTGC 61.471 66.667 0.00 1.31 0.00 4.01
156 157 3.112709 GAGCCGACGTGTCTTGCC 61.113 66.667 0.00 0.00 0.00 4.52
160 161 4.657824 CGACGTGTCTTGCCGGGT 62.658 66.667 2.18 0.00 0.00 5.28
161 162 2.737376 GACGTGTCTTGCCGGGTC 60.737 66.667 2.18 0.00 0.00 4.46
162 163 4.657824 ACGTGTCTTGCCGGGTCG 62.658 66.667 2.18 0.00 0.00 4.79
172 173 4.208686 CCGGGTCGGCTAGTCTGC 62.209 72.222 0.00 0.00 41.17 4.26
179 180 3.787001 GGCTAGTCTGCCCGGCTT 61.787 66.667 11.61 0.00 46.82 4.35
180 181 2.512515 GCTAGTCTGCCCGGCTTG 60.513 66.667 11.61 3.78 0.00 4.01
181 182 2.512515 CTAGTCTGCCCGGCTTGC 60.513 66.667 11.61 0.00 0.00 4.01
182 183 4.451150 TAGTCTGCCCGGCTTGCG 62.451 66.667 11.61 0.00 0.00 4.85
225 226 3.350612 GCCAAACGCGTGCCAGTA 61.351 61.111 14.98 0.00 0.00 2.74
226 227 2.686816 GCCAAACGCGTGCCAGTAT 61.687 57.895 14.98 0.00 0.00 2.12
227 228 1.873165 CCAAACGCGTGCCAGTATT 59.127 52.632 14.98 0.00 0.00 1.89
228 229 0.454285 CCAAACGCGTGCCAGTATTG 60.454 55.000 14.98 11.79 0.00 1.90
229 230 0.515127 CAAACGCGTGCCAGTATTGA 59.485 50.000 14.98 0.00 0.00 2.57
230 231 0.796312 AAACGCGTGCCAGTATTGAG 59.204 50.000 14.98 0.00 0.00 3.02
231 232 1.019278 AACGCGTGCCAGTATTGAGG 61.019 55.000 14.98 0.00 0.00 3.86
232 233 2.173669 CGCGTGCCAGTATTGAGGG 61.174 63.158 0.00 0.00 0.00 4.30
233 234 1.819632 GCGTGCCAGTATTGAGGGG 60.820 63.158 0.00 0.00 0.00 4.79
234 235 1.819632 CGTGCCAGTATTGAGGGGC 60.820 63.158 0.00 0.00 46.58 5.80
236 237 2.203209 GCCAGTATTGAGGGGCGG 60.203 66.667 0.00 0.00 36.58 6.13
237 238 3.043999 GCCAGTATTGAGGGGCGGT 62.044 63.158 0.00 0.00 36.58 5.68
238 239 1.153168 CCAGTATTGAGGGGCGGTG 60.153 63.158 0.00 0.00 0.00 4.94
239 240 1.819632 CAGTATTGAGGGGCGGTGC 60.820 63.158 0.00 0.00 0.00 5.01
253 254 3.223589 GTGCCAGCCCCGTTGTTT 61.224 61.111 0.00 0.00 0.00 2.83
254 255 2.443016 TGCCAGCCCCGTTGTTTT 60.443 55.556 0.00 0.00 0.00 2.43
255 256 2.060980 TGCCAGCCCCGTTGTTTTT 61.061 52.632 0.00 0.00 0.00 1.94
273 274 3.518992 TTTTTGAAGAGGATCCGGGTT 57.481 42.857 5.98 0.64 33.66 4.11
274 275 2.781681 TTTGAAGAGGATCCGGGTTC 57.218 50.000 5.98 10.99 33.66 3.62
275 276 0.909623 TTGAAGAGGATCCGGGTTCC 59.090 55.000 15.13 15.13 33.66 3.62
277 278 1.305887 AAGAGGATCCGGGTTCCGT 60.306 57.895 16.57 7.23 46.80 4.69
278 279 0.908180 AAGAGGATCCGGGTTCCGTT 60.908 55.000 16.57 12.09 46.80 4.44
279 280 1.153429 GAGGATCCGGGTTCCGTTG 60.153 63.158 16.57 0.00 46.80 4.10
280 281 2.822701 GGATCCGGGTTCCGTTGC 60.823 66.667 8.35 0.00 46.80 4.17
281 282 2.822701 GATCCGGGTTCCGTTGCC 60.823 66.667 0.00 0.00 46.80 4.52
282 283 3.325201 GATCCGGGTTCCGTTGCCT 62.325 63.158 0.00 0.00 46.80 4.75
283 284 3.622060 ATCCGGGTTCCGTTGCCTG 62.622 63.158 0.00 0.00 46.80 4.85
401 403 5.012768 GTGGGTTATATGGCACTAGGTGTAT 59.987 44.000 0.00 0.00 35.75 2.29
775 795 0.460284 CTAGCCGCCACGAACAGATT 60.460 55.000 0.00 0.00 0.00 2.40
821 844 2.670934 CGTTCCCTTGCTGCTGCT 60.671 61.111 17.00 0.00 40.48 4.24
1014 1037 3.311110 ACCATGTCCACCGACGCT 61.311 61.111 0.00 0.00 42.37 5.07
1121 1144 3.311103 TGGCCTACTGGAGGGTATAACTT 60.311 47.826 8.30 0.00 46.81 2.66
1122 1145 4.078454 TGGCCTACTGGAGGGTATAACTTA 60.078 45.833 8.30 0.00 46.81 2.24
1153 1176 5.411669 CCGCTCCTACTGTTTTCTGTTTTAT 59.588 40.000 0.00 0.00 34.05 1.40
1324 1347 9.139174 CAACAATCCAAAAACCTATTATGTGTC 57.861 33.333 0.00 0.00 0.00 3.67
1332 1355 9.072294 CAAAAACCTATTATGTGTCGGAATTTC 57.928 33.333 0.00 0.00 0.00 2.17
1366 1389 2.664851 CCGCTGCACTGAAACCGA 60.665 61.111 0.00 0.00 0.00 4.69
1376 1399 6.236017 TGCACTGAAACCGAATAAGTTTAG 57.764 37.500 0.00 0.00 37.55 1.85
1427 1450 3.551259 CCACTTTATGGCTCACGGT 57.449 52.632 0.00 0.00 43.24 4.83
1656 1680 7.201830 GGGAGCGAGATGTATATTATAGAGCAA 60.202 40.741 0.00 0.00 0.00 3.91
1912 1936 0.618458 AAGGGCAAAGGACTCGCATA 59.382 50.000 0.00 0.00 0.00 3.14
2064 2088 1.718280 AGAACAAGAAGGACGAGGGT 58.282 50.000 0.00 0.00 0.00 4.34
2312 2336 3.625897 CCAGGTCACAGGCCACGA 61.626 66.667 5.01 0.00 0.00 4.35
2459 2483 0.175989 CTCGTTAGTGGCTCCCTTCC 59.824 60.000 0.00 0.00 0.00 3.46
2567 8056 0.544697 GGAGGGATGTTCCGCCTTTA 59.455 55.000 0.00 0.00 42.52 1.85
2822 8311 8.708378 ACCATTAGAACTCATACATTCTGATCA 58.292 33.333 0.00 0.00 35.91 2.92
3097 8586 1.003051 ACGCCTCCCTATTCACCCT 59.997 57.895 0.00 0.00 0.00 4.34
3119 8608 4.572571 AAACGGGGTTGCCGAGCA 62.573 61.111 0.00 0.00 36.47 4.26
3137 8626 4.863131 CGAGCAGAAAAACCGTACTCTAAT 59.137 41.667 0.00 0.00 0.00 1.73
3295 8787 2.294791 AGAGAAGGACAACACTCTCGTG 59.705 50.000 0.00 0.00 46.63 4.35
3376 8868 1.843851 TGGACCAAAGACTGTGGACTT 59.156 47.619 19.18 0.00 39.62 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.461091 GCCGTATGATGGGGACGAGA 61.461 60.000 0.00 0.00 38.88 4.04
1 2 1.006102 GCCGTATGATGGGGACGAG 60.006 63.158 0.00 0.00 38.88 4.18
2 3 2.504274 GGCCGTATGATGGGGACGA 61.504 63.158 0.00 0.00 38.88 4.20
3 4 2.030562 GGCCGTATGATGGGGACG 59.969 66.667 0.00 0.00 36.36 4.79
4 5 1.071471 CAGGCCGTATGATGGGGAC 59.929 63.158 0.00 0.00 0.00 4.46
5 6 2.146724 CCAGGCCGTATGATGGGGA 61.147 63.158 0.00 0.00 0.00 4.81
6 7 1.492133 ATCCAGGCCGTATGATGGGG 61.492 60.000 6.61 0.00 33.45 4.96
7 8 0.321919 CATCCAGGCCGTATGATGGG 60.322 60.000 15.03 2.43 32.79 4.00
8 9 0.321919 CCATCCAGGCCGTATGATGG 60.322 60.000 22.72 22.72 45.86 3.51
9 10 0.321919 CCCATCCAGGCCGTATGATG 60.322 60.000 14.39 15.03 35.49 3.07
10 11 0.473694 TCCCATCCAGGCCGTATGAT 60.474 55.000 14.39 5.31 35.39 2.45
11 12 1.074850 TCCCATCCAGGCCGTATGA 60.075 57.895 14.39 3.27 35.39 2.15
12 13 1.071471 GTCCCATCCAGGCCGTATG 59.929 63.158 0.00 2.31 35.39 2.39
13 14 2.507854 CGTCCCATCCAGGCCGTAT 61.508 63.158 0.00 0.00 35.39 3.06
14 15 3.151710 CGTCCCATCCAGGCCGTA 61.152 66.667 0.00 0.00 35.39 4.02
18 19 3.866582 CTCCCGTCCCATCCAGGC 61.867 72.222 0.00 0.00 35.39 4.85
19 20 1.995626 AACTCCCGTCCCATCCAGG 60.996 63.158 0.00 0.00 37.03 4.45
20 21 1.221840 CAACTCCCGTCCCATCCAG 59.778 63.158 0.00 0.00 0.00 3.86
21 22 1.229368 TCAACTCCCGTCCCATCCA 60.229 57.895 0.00 0.00 0.00 3.41
22 23 1.221021 GTCAACTCCCGTCCCATCC 59.779 63.158 0.00 0.00 0.00 3.51
23 24 1.221021 GGTCAACTCCCGTCCCATC 59.779 63.158 0.00 0.00 0.00 3.51
24 25 2.298661 GGGTCAACTCCCGTCCCAT 61.299 63.158 0.00 0.00 37.93 4.00
25 26 2.926242 GGGTCAACTCCCGTCCCA 60.926 66.667 0.00 0.00 37.93 4.37
35 36 4.778143 ATCCAGCCGCGGGTCAAC 62.778 66.667 30.00 9.63 0.00 3.18
36 37 4.028490 AATCCAGCCGCGGGTCAA 62.028 61.111 30.00 19.00 0.00 3.18
37 38 4.776322 CAATCCAGCCGCGGGTCA 62.776 66.667 30.00 17.93 0.00 4.02
43 44 3.941836 GCTACGCAATCCAGCCGC 61.942 66.667 0.00 0.00 0.00 6.53
44 45 2.511373 TGCTACGCAATCCAGCCG 60.511 61.111 0.00 0.00 34.76 5.52
45 46 2.813179 CGTGCTACGCAATCCAGCC 61.813 63.158 0.00 0.00 41.47 4.85
46 47 2.703409 CGTGCTACGCAATCCAGC 59.297 61.111 0.00 0.00 41.47 4.85
55 56 3.195002 CACCCATGGCGTGCTACG 61.195 66.667 17.10 4.61 45.88 3.51
56 57 2.824041 CCACCCATGGCGTGCTAC 60.824 66.667 21.52 0.00 39.82 3.58
73 74 4.742201 TCCTCGACAAGCCAGCGC 62.742 66.667 0.00 0.00 0.00 5.92
74 75 2.507992 CTCCTCGACAAGCCAGCG 60.508 66.667 0.00 0.00 0.00 5.18
75 76 2.125350 CCTCCTCGACAAGCCAGC 60.125 66.667 0.00 0.00 0.00 4.85
76 77 2.125350 GCCTCCTCGACAAGCCAG 60.125 66.667 0.00 0.00 0.00 4.85
77 78 1.768684 AAAGCCTCCTCGACAAGCCA 61.769 55.000 0.00 0.00 0.00 4.75
78 79 1.003233 AAAGCCTCCTCGACAAGCC 60.003 57.895 0.00 0.00 0.00 4.35
79 80 1.301677 CCAAAGCCTCCTCGACAAGC 61.302 60.000 0.00 0.00 0.00 4.01
80 81 1.301677 GCCAAAGCCTCCTCGACAAG 61.302 60.000 0.00 0.00 0.00 3.16
81 82 1.302511 GCCAAAGCCTCCTCGACAA 60.303 57.895 0.00 0.00 0.00 3.18
82 83 2.347490 GCCAAAGCCTCCTCGACA 59.653 61.111 0.00 0.00 0.00 4.35
105 106 3.423154 GCAAGACAGCCGAACCCG 61.423 66.667 0.00 0.00 0.00 5.28
106 107 3.423154 CGCAAGACAGCCGAACCC 61.423 66.667 0.00 0.00 43.02 4.11
107 108 4.090057 GCGCAAGACAGCCGAACC 62.090 66.667 0.30 0.00 43.02 3.62
108 109 1.687494 CTAGCGCAAGACAGCCGAAC 61.687 60.000 11.47 0.00 43.02 3.95
109 110 1.446099 CTAGCGCAAGACAGCCGAA 60.446 57.895 11.47 0.00 43.02 4.30
110 111 2.154798 AACTAGCGCAAGACAGCCGA 62.155 55.000 11.47 0.00 43.02 5.54
111 112 1.738099 AACTAGCGCAAGACAGCCG 60.738 57.895 11.47 0.00 43.02 5.52
112 113 0.951040 ACAACTAGCGCAAGACAGCC 60.951 55.000 11.47 0.00 43.02 4.85
113 114 0.868406 AACAACTAGCGCAAGACAGC 59.132 50.000 11.47 0.00 43.02 4.40
114 115 2.135139 TCAACAACTAGCGCAAGACAG 58.865 47.619 11.47 0.39 43.02 3.51
115 116 2.135139 CTCAACAACTAGCGCAAGACA 58.865 47.619 11.47 0.00 43.02 3.41
116 117 1.461127 CCTCAACAACTAGCGCAAGAC 59.539 52.381 11.47 0.00 43.02 3.01
117 118 1.795768 CCTCAACAACTAGCGCAAGA 58.204 50.000 11.47 0.00 43.02 3.02
118 119 0.166814 GCCTCAACAACTAGCGCAAG 59.833 55.000 11.47 0.00 43.44 4.01
119 120 1.234615 GGCCTCAACAACTAGCGCAA 61.235 55.000 11.47 0.00 0.00 4.85
120 121 1.671054 GGCCTCAACAACTAGCGCA 60.671 57.895 11.47 0.00 0.00 6.09
121 122 2.740714 CGGCCTCAACAACTAGCGC 61.741 63.158 0.00 0.00 0.00 5.92
122 123 1.078759 CTCGGCCTCAACAACTAGCG 61.079 60.000 0.00 0.00 0.00 4.26
123 124 1.362406 GCTCGGCCTCAACAACTAGC 61.362 60.000 0.00 0.00 0.00 3.42
124 125 0.741221 GGCTCGGCCTCAACAACTAG 60.741 60.000 0.00 0.00 46.69 2.57
125 126 1.295423 GGCTCGGCCTCAACAACTA 59.705 57.895 0.00 0.00 46.69 2.24
126 127 2.032681 GGCTCGGCCTCAACAACT 59.967 61.111 0.00 0.00 46.69 3.16
136 137 4.719369 AAGACACGTCGGCTCGGC 62.719 66.667 0.00 0.00 34.94 5.54
137 138 2.805353 CAAGACACGTCGGCTCGG 60.805 66.667 0.00 0.00 34.94 4.63
138 139 3.470567 GCAAGACACGTCGGCTCG 61.471 66.667 0.00 0.00 33.87 5.03
139 140 3.112709 GGCAAGACACGTCGGCTC 61.113 66.667 13.84 0.00 35.88 4.70
143 144 4.657824 ACCCGGCAAGACACGTCG 62.658 66.667 0.00 0.00 34.09 5.12
144 145 2.737376 GACCCGGCAAGACACGTC 60.737 66.667 0.00 0.00 0.00 4.34
145 146 4.657824 CGACCCGGCAAGACACGT 62.658 66.667 0.00 0.00 0.00 4.49
156 157 4.208686 GGCAGACTAGCCGACCCG 62.209 72.222 0.00 0.00 46.12 5.28
163 164 2.512515 CAAGCCGGGCAGACTAGC 60.513 66.667 23.09 0.00 0.00 3.42
164 165 2.512515 GCAAGCCGGGCAGACTAG 60.513 66.667 23.09 4.97 0.00 2.57
165 166 4.451150 CGCAAGCCGGGCAGACTA 62.451 66.667 23.09 0.00 0.00 2.59
208 209 2.195123 AATACTGGCACGCGTTTGGC 62.195 55.000 10.22 13.34 42.37 4.52
209 210 0.454285 CAATACTGGCACGCGTTTGG 60.454 55.000 10.22 0.00 0.00 3.28
210 211 0.515127 TCAATACTGGCACGCGTTTG 59.485 50.000 10.22 10.40 0.00 2.93
211 212 0.796312 CTCAATACTGGCACGCGTTT 59.204 50.000 10.22 0.00 0.00 3.60
212 213 1.019278 CCTCAATACTGGCACGCGTT 61.019 55.000 10.22 0.00 0.00 4.84
213 214 1.447838 CCTCAATACTGGCACGCGT 60.448 57.895 5.58 5.58 0.00 6.01
214 215 2.173669 CCCTCAATACTGGCACGCG 61.174 63.158 3.53 3.53 0.00 6.01
215 216 1.819632 CCCCTCAATACTGGCACGC 60.820 63.158 0.00 0.00 0.00 5.34
216 217 1.819632 GCCCCTCAATACTGGCACG 60.820 63.158 0.00 0.00 43.46 5.34
217 218 1.819632 CGCCCCTCAATACTGGCAC 60.820 63.158 0.00 0.00 44.22 5.01
218 219 2.589540 CGCCCCTCAATACTGGCA 59.410 61.111 0.00 0.00 44.22 4.92
219 220 2.203209 CCGCCCCTCAATACTGGC 60.203 66.667 0.00 0.00 40.54 4.85
220 221 1.153168 CACCGCCCCTCAATACTGG 60.153 63.158 0.00 0.00 0.00 4.00
221 222 1.819632 GCACCGCCCCTCAATACTG 60.820 63.158 0.00 0.00 0.00 2.74
222 223 2.590092 GCACCGCCCCTCAATACT 59.410 61.111 0.00 0.00 0.00 2.12
223 224 2.516225 GGCACCGCCCCTCAATAC 60.516 66.667 0.00 0.00 44.06 1.89
236 237 2.304901 AAAAACAACGGGGCTGGCAC 62.305 55.000 2.88 0.00 0.00 5.01
237 238 2.060980 AAAAACAACGGGGCTGGCA 61.061 52.632 2.88 0.00 0.00 4.92
238 239 2.818841 AAAAACAACGGGGCTGGC 59.181 55.556 0.00 0.00 0.00 4.85
253 254 3.418047 GAACCCGGATCCTCTTCAAAAA 58.582 45.455 10.75 0.00 0.00 1.94
254 255 2.290705 GGAACCCGGATCCTCTTCAAAA 60.291 50.000 16.53 0.00 33.98 2.44
255 256 1.280998 GGAACCCGGATCCTCTTCAAA 59.719 52.381 16.53 0.00 33.98 2.69
256 257 0.909623 GGAACCCGGATCCTCTTCAA 59.090 55.000 16.53 0.00 33.98 2.69
257 258 1.327690 CGGAACCCGGATCCTCTTCA 61.328 60.000 20.00 0.00 44.15 3.02
258 259 1.442148 CGGAACCCGGATCCTCTTC 59.558 63.158 20.00 7.22 44.15 2.87
259 260 3.630289 CGGAACCCGGATCCTCTT 58.370 61.111 20.00 0.00 44.15 2.85
300 301 0.764890 TTCAGCAATCCCCCTATCGG 59.235 55.000 0.00 0.00 0.00 4.18
301 302 2.638480 TTTCAGCAATCCCCCTATCG 57.362 50.000 0.00 0.00 0.00 2.92
302 303 4.895297 TCAAATTTCAGCAATCCCCCTATC 59.105 41.667 0.00 0.00 0.00 2.08
303 304 4.882559 TCAAATTTCAGCAATCCCCCTAT 58.117 39.130 0.00 0.00 0.00 2.57
304 305 4.017591 TCTCAAATTTCAGCAATCCCCCTA 60.018 41.667 0.00 0.00 0.00 3.53
305 306 3.102204 CTCAAATTTCAGCAATCCCCCT 58.898 45.455 0.00 0.00 0.00 4.79
732 750 1.267121 AGGAGACACCGCACACTTAT 58.733 50.000 0.00 0.00 44.74 1.73
733 751 1.913778 TAGGAGACACCGCACACTTA 58.086 50.000 0.00 0.00 44.74 2.24
821 844 3.399181 GGGATGGAGTCACCGGCA 61.399 66.667 0.00 0.00 42.61 5.69
911 934 1.847328 CCCAAAAACCTATTCGCCCT 58.153 50.000 0.00 0.00 0.00 5.19
1121 1144 5.881923 AAACAGTAGGAGCGGGATAAATA 57.118 39.130 0.00 0.00 0.00 1.40
1122 1145 4.772886 AAACAGTAGGAGCGGGATAAAT 57.227 40.909 0.00 0.00 0.00 1.40
1196 1219 5.756833 TGATATTCAGTCAAGCTAGCACATG 59.243 40.000 18.83 12.78 0.00 3.21
1229 1252 4.380841 AGCATGGCATTGACACAAATAG 57.619 40.909 0.00 0.00 0.00 1.73
1288 1311 9.362151 AGGTTTTTGGATTGTTGAGTAAATAGA 57.638 29.630 0.00 0.00 0.00 1.98
1324 1347 0.447801 CCACTTGCCGAGAAATTCCG 59.552 55.000 0.00 0.00 0.00 4.30
1332 1355 2.256461 GCAAAGCCACTTGCCGAG 59.744 61.111 4.79 0.00 44.88 4.63
1366 1389 9.977762 CTTAAAATACGAACCGCTAAACTTATT 57.022 29.630 0.00 0.00 0.00 1.40
1376 1399 2.793268 ACGCTTAAAATACGAACCGC 57.207 45.000 0.00 0.00 0.00 5.68
1427 1450 3.395639 GTGACCCAGAACACGTTCATAA 58.604 45.455 12.21 0.00 41.84 1.90
1656 1680 5.496556 TCAACCATCTTGTAATCGTGGAAT 58.503 37.500 0.00 0.00 34.13 3.01
1690 1714 2.977580 TCTCATGAGCCTGCTCCAATAT 59.022 45.455 18.36 0.60 42.09 1.28
1912 1936 1.850755 TCCCTTCGGCCCCTTTTCT 60.851 57.895 0.00 0.00 0.00 2.52
2064 2088 2.645802 ACCGAACCACAAGTAAAGCAA 58.354 42.857 0.00 0.00 0.00 3.91
2312 2336 2.106511 CCATTCCCCATCAATACGGACT 59.893 50.000 0.00 0.00 0.00 3.85
2459 2483 6.238648 ACCAACTTAAACCCTTCTCTACATG 58.761 40.000 0.00 0.00 0.00 3.21
2521 8010 7.309438 GCTCTCATAACCTTTTCCAACAAAGAT 60.309 37.037 0.00 0.00 36.03 2.40
2567 8056 7.174253 TGACTTTATTACAAAAATCTGCGAGGT 59.826 33.333 0.00 0.00 0.00 3.85
2822 8311 5.048504 GTCAACACACCATTCATCTCACAAT 60.049 40.000 0.00 0.00 0.00 2.71
3097 8586 4.804806 GGCAACCCCGTTTGACTA 57.195 55.556 0.00 0.00 31.08 2.59
3119 8608 8.512138 CCAAATCAATTAGAGTACGGTTTTTCT 58.488 33.333 0.00 0.00 0.00 2.52
3137 8626 4.592485 AACATGGCGTTAACCAAATCAA 57.408 36.364 0.00 0.00 44.65 2.57
3295 8787 2.359975 AGCCCCAAGTACGCAAGC 60.360 61.111 0.00 0.00 45.62 4.01


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

AutoCloner maintained by Alex Coulton.