Multiple sequence alignment - TraesCS6A01G217700

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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 TraesCS6A01G217700 chr6A 100.000 3282 0 0 1 3282 401221458 401218177 0.000000e+00 6061.0
1 TraesCS6A01G217700 chr6A 94.029 1591 65 6 1014 2593 401201797 401200226 0.000000e+00 2385.0
2 TraesCS6A01G217700 chr6A 87.165 857 87 13 1364 2213 402884689 402885529 0.000000e+00 952.0
3 TraesCS6A01G217700 chr6A 80.081 1235 157 44 1933 3149 401199428 401198265 0.000000e+00 835.0
4 TraesCS6A01G217700 chr6A 97.011 435 11 2 2850 3282 401200042 401199608 0.000000e+00 730.0
5 TraesCS6A01G217700 chr6A 85.193 493 50 13 1364 1849 402271295 402271771 4.920000e-133 484.0
6 TraesCS6A01G217700 chr6A 95.337 193 7 1 2624 2816 401200227 401200037 4.110000e-79 305.0
7 TraesCS6A01G217700 chr6A 93.893 131 7 1 3152 3282 6897677 6897548 2.580000e-46 196.0
8 TraesCS6A01G217700 chr6A 88.235 119 14 0 2095 2213 402888866 402888984 3.410000e-30 143.0
9 TraesCS6A01G217700 chr6D 91.825 2887 154 25 337 3154 277856920 277854047 0.000000e+00 3949.0
10 TraesCS6A01G217700 chr6D 87.607 1638 144 28 959 2563 277849480 277847869 0.000000e+00 1845.0
11 TraesCS6A01G217700 chr6D 88.228 790 85 4 1431 2213 278630882 278631670 0.000000e+00 937.0
12 TraesCS6A01G217700 chr6D 93.269 312 18 3 1 311 277861016 277860707 1.070000e-124 457.0
13 TraesCS6A01G217700 chr6D 81.359 574 78 18 2589 3154 277847873 277847321 1.080000e-119 440.0
14 TraesCS6A01G217700 chr6D 75.610 410 61 22 2610 3007 427314421 427314039 2.030000e-37 167.0
15 TraesCS6A01G217700 chr6B 92.472 2298 122 18 337 2603 439731791 439729514 0.000000e+00 3238.0
16 TraesCS6A01G217700 chr6B 88.154 1511 125 29 974 2456 439678318 439676834 0.000000e+00 1749.0
17 TraesCS6A01G217700 chr6B 89.185 601 43 15 2565 3154 439729525 439728936 0.000000e+00 730.0
18 TraesCS6A01G217700 chr6B 87.862 552 59 4 1431 1975 440757358 440757908 2.760000e-180 641.0
19 TraesCS6A01G217700 chr6B 92.982 342 19 5 1 339 439732164 439731825 8.180000e-136 494.0
20 TraesCS6A01G217700 chr6B 87.814 279 28 6 2881 3154 439676623 439676346 4.090000e-84 322.0
21 TraesCS6A01G217700 chr7A 96.850 127 4 0 3156 3282 716413787 716413913 2.570000e-51 213.0
22 TraesCS6A01G217700 chr7A 85.787 197 27 1 337 532 727467533 727467729 1.190000e-49 207.0
23 TraesCS6A01G217700 chr1D 94.118 136 5 3 3147 3282 433100754 433100886 1.540000e-48 204.0
24 TraesCS6A01G217700 chr5D 95.276 127 6 0 3156 3282 231956074 231956200 5.550000e-48 202.0
25 TraesCS6A01G217700 chr5B 95.238 126 6 0 3157 3282 12313083 12312958 2.000000e-47 200.0
26 TraesCS6A01G217700 chr5A 94.574 129 7 0 3154 3282 564555934 564555806 2.000000e-47 200.0
27 TraesCS6A01G217700 chr5A 79.000 100 17 4 2611 2708 616635839 616635742 7.600000e-07 65.8
28 TraesCS6A01G217700 chr2B 95.238 126 6 0 3157 3282 791135796 791135921 2.000000e-47 200.0
29 TraesCS6A01G217700 chr3A 92.647 136 9 1 3148 3282 32986271 32986136 9.290000e-46 195.0
30 TraesCS6A01G217700 chr3B 77.592 299 63 2 4 302 136452070 136452364 9.360000e-41 178.0
31 TraesCS6A01G217700 chr4D 79.592 196 35 4 337 530 352290143 352290335 5.710000e-28 135.0
32 TraesCS6A01G217700 chr2A 82.000 100 17 1 194 293 712070295 712070197 2.100000e-12 84.2


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 TraesCS6A01G217700 chr6A 401218177 401221458 3281 True 6061.000000 6061 100.000000 1 3282 1 chr6A.!!$R2 3281
1 TraesCS6A01G217700 chr6A 401198265 401201797 3532 True 1063.750000 2385 91.614500 1014 3282 4 chr6A.!!$R3 2268
2 TraesCS6A01G217700 chr6A 402884689 402888984 4295 False 547.500000 952 87.700000 1364 2213 2 chr6A.!!$F2 849
3 TraesCS6A01G217700 chr6D 277854047 277861016 6969 True 2203.000000 3949 92.547000 1 3154 2 chr6D.!!$R3 3153
4 TraesCS6A01G217700 chr6D 277847321 277849480 2159 True 1142.500000 1845 84.483000 959 3154 2 chr6D.!!$R2 2195
5 TraesCS6A01G217700 chr6D 278630882 278631670 788 False 937.000000 937 88.228000 1431 2213 1 chr6D.!!$F1 782
6 TraesCS6A01G217700 chr6B 439728936 439732164 3228 True 1487.333333 3238 91.546333 1 3154 3 chr6B.!!$R2 3153
7 TraesCS6A01G217700 chr6B 439676346 439678318 1972 True 1035.500000 1749 87.984000 974 3154 2 chr6B.!!$R1 2180
8 TraesCS6A01G217700 chr6B 440757358 440757908 550 False 641.000000 641 87.862000 1431 1975 1 chr6B.!!$F1 544

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
921 4711 0.512952 CAGACGCCAGGAACGAAAAG 59.487 55.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 8219 1.857217 CCTCATGAATCTTCGCAGACG 59.143 52.381 0.0 0.0 42.01 4.18 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
55 56 5.877012 TCAAGGCAATAAGAGATCACACTTC 59.123 40.000 0.00 0.00 0.00 3.01
143 145 3.711060 CCATTGTTCATGGCCCTCCCA 62.711 57.143 0.00 0.00 46.59 4.37
150 152 2.860960 TGGCCCTCCCAAGCAATT 59.139 55.556 0.00 0.00 41.82 2.32
151 153 1.610086 TGGCCCTCCCAAGCAATTG 60.610 57.895 0.00 0.00 41.82 2.32
170 172 1.106285 GAACCCACAGATCCAATGGC 58.894 55.000 0.00 0.00 31.66 4.40
223 225 8.228035 TGCATAACATGATCATTGAAGATGAA 57.772 30.769 5.16 0.00 0.00 2.57
247 249 6.235231 AGAGGTGTGACAGAGAACTTTTAA 57.765 37.500 0.00 0.00 0.00 1.52
269 271 0.538057 CATCACCAATGGGGATCCCG 60.538 60.000 24.90 12.77 43.17 5.14
277 279 3.326900 GGGGATCCCGTTAAGCCA 58.673 61.111 24.90 0.00 36.85 4.75
282 284 1.065709 GGATCCCGTTAAGCCAGAACA 60.066 52.381 0.00 0.00 0.00 3.18
313 4039 7.177216 TGCAAAGATGATACACAAATTTCTCCT 59.823 33.333 0.00 0.00 0.00 3.69
326 4052 7.011389 CACAAATTTCTCCTAGCACATCGAATA 59.989 37.037 0.00 0.00 0.00 1.75
328 4054 7.484035 AATTTCTCCTAGCACATCGAATAAC 57.516 36.000 0.00 0.00 0.00 1.89
329 4055 5.592104 TTCTCCTAGCACATCGAATAACA 57.408 39.130 0.00 0.00 0.00 2.41
330 4056 5.188327 TCTCCTAGCACATCGAATAACAG 57.812 43.478 0.00 0.00 0.00 3.16
331 4057 4.038042 TCTCCTAGCACATCGAATAACAGG 59.962 45.833 0.00 0.00 0.00 4.00
332 4058 3.958147 TCCTAGCACATCGAATAACAGGA 59.042 43.478 0.00 0.00 0.00 3.86
334 4060 4.508124 CCTAGCACATCGAATAACAGGAAC 59.492 45.833 0.00 0.00 0.00 3.62
392 4155 6.735130 TGATATGCTTCAATCATGCTCTTTG 58.265 36.000 0.00 0.00 0.00 2.77
474 4237 3.768406 TGCAATATTCGTGAATTGTGCC 58.232 40.909 19.19 8.72 37.99 5.01
484 4247 3.426191 CGTGAATTGTGCCAACTTTGATG 59.574 43.478 0.00 0.00 0.00 3.07
558 4321 5.248870 ACACACAAGCTTAGAAAACTTGG 57.751 39.130 0.00 0.00 44.01 3.61
560 4323 3.699038 ACACAAGCTTAGAAAACTTGGCA 59.301 39.130 0.00 0.00 44.01 4.92
682 4467 6.949463 TGAGGGGTTTAATTTTAAGGAATCGT 59.051 34.615 0.00 0.00 0.00 3.73
693 4478 3.634568 AAGGAATCGTCTAGAGATGCG 57.365 47.619 0.00 0.00 0.00 4.73
819 4604 2.301346 GTCATTGCATTAGGGGTCCTG 58.699 52.381 0.00 0.00 34.61 3.86
834 4619 2.147150 GTCCTGTTTTGAGAGCAGTCC 58.853 52.381 0.00 0.00 0.00 3.85
848 4633 1.669779 GCAGTCCTCATTGCACTGATC 59.330 52.381 7.26 2.21 40.07 2.92
877 4667 8.638685 AAACAAAATATACTACGTAGCGATGT 57.361 30.769 22.40 13.89 0.00 3.06
911 4701 1.821216 AAATAACCACCAGACGCCAG 58.179 50.000 0.00 0.00 0.00 4.85
919 4709 1.301401 CCAGACGCCAGGAACGAAA 60.301 57.895 0.00 0.00 0.00 3.46
921 4711 0.512952 CAGACGCCAGGAACGAAAAG 59.487 55.000 0.00 0.00 0.00 2.27
964 4754 2.280119 GTCATCATGGCGCGGCTA 60.280 61.111 33.23 19.80 0.00 3.93
966 4756 2.588596 CATCATGGCGCGGCTACA 60.589 61.111 33.23 14.45 0.00 2.74
967 4757 2.588877 ATCATGGCGCGGCTACAC 60.589 61.111 33.23 1.82 0.00 2.90
1040 4877 6.013842 AGAAAAAGGAAAGAAACGCATAGG 57.986 37.500 0.00 0.00 0.00 2.57
1105 4943 1.542472 CAGTTGTCATGCAGCCAATCA 59.458 47.619 0.00 0.00 0.00 2.57
1273 5131 1.153449 CCGTCGCCTTATCAGCCAA 60.153 57.895 0.00 0.00 0.00 4.52
1311 5169 2.185494 ATCGACGACTACCTCCGCC 61.185 63.158 0.00 0.00 0.00 6.13
2010 7332 1.219124 CACTACAGATGCCTGCGGT 59.781 57.895 0.00 0.00 44.16 5.68
2051 7373 3.621805 TCGGCGGTCTTTCTGGCA 61.622 61.111 7.21 0.00 46.64 4.92
2079 7401 0.962356 CTTGAACCCAATGGCGAGCT 60.962 55.000 0.00 0.00 33.59 4.09
2174 7496 3.386078 AGTCGCTGTACATGATGAATCCT 59.614 43.478 0.00 0.00 0.00 3.24
2274 7696 4.158949 CCAGTTGCATGATTGAATCCTGAA 59.841 41.667 13.52 1.01 0.00 3.02
2483 7928 4.687483 TGTGCATAGTATGATGATGCTTCG 59.313 41.667 14.52 0.00 45.04 3.79
2519 7965 1.795768 GTCGTCTGATGGCTTGTTGA 58.204 50.000 0.00 0.00 0.00 3.18
2551 7997 3.069300 GCTGCCATGAGAGTGAAGATAGA 59.931 47.826 0.00 0.00 0.00 1.98
2575 8048 7.790314 AGATACCTAGGTAGTAAAATGCTTCCT 59.210 37.037 25.40 4.80 37.48 3.36
2624 8097 2.473457 GCGGAAATGCCTAACGGAA 58.527 52.632 0.00 0.00 0.00 4.30
2708 8187 8.452989 AATCTCTCAAAAACAAAATACGCATC 57.547 30.769 0.00 0.00 0.00 3.91
2715 8194 7.490725 TCAAAAACAAAATACGCATCCATATGG 59.509 33.333 16.25 16.25 33.38 2.74
2754 8242 3.555139 GTCTGCGAAGATTCATGAGGAAG 59.445 47.826 0.00 0.00 39.30 3.46
2807 8296 9.035607 AGAATAACAAGTCACATATTTCTAGCG 57.964 33.333 0.00 0.00 0.00 4.26
2879 8370 5.518487 GGCCACATAAAAACGTATTTCATGG 59.482 40.000 0.00 5.27 30.06 3.66
2967 10220 9.657419 ACTTCAAAAGTTCATTCTTGAATGTTT 57.343 25.926 19.02 11.76 43.49 2.83
2990 10245 6.284891 TGAAAAATTTAGGCTTCATGGAGG 57.715 37.500 2.40 0.00 0.00 4.30
3059 10470 7.596749 AAATAGTGAGAACATAAAGACACCG 57.403 36.000 0.00 0.00 0.00 4.94
3154 11294 6.238953 GCTTCTGAATTTGCATGATAGGTGAT 60.239 38.462 0.00 0.00 0.00 3.06
3155 11295 7.649533 TTCTGAATTTGCATGATAGGTGATT 57.350 32.000 0.00 0.00 0.00 2.57
3157 11297 8.070034 TCTGAATTTGCATGATAGGTGATTTT 57.930 30.769 0.00 0.00 0.00 1.82
3158 11298 8.533657 TCTGAATTTGCATGATAGGTGATTTTT 58.466 29.630 0.00 0.00 0.00 1.94
3187 11327 9.884636 TCGATAAAGGACTTTTCATTGAATAGA 57.115 29.630 19.59 1.38 34.23 1.98
3209 11349 7.867305 AGATATATCGAGGTGATACAATCGT 57.133 36.000 7.08 0.00 42.24 3.73
3210 11350 8.959705 AGATATATCGAGGTGATACAATCGTA 57.040 34.615 7.08 0.00 42.24 3.43
3211 11351 9.562408 AGATATATCGAGGTGATACAATCGTAT 57.438 33.333 7.08 0.00 42.24 3.06
3228 11368 4.278956 TCGAAAGAAAGCTCGGCC 57.721 55.556 0.00 0.00 37.03 6.13
3229 11369 1.671742 TCGAAAGAAAGCTCGGCCT 59.328 52.632 0.00 0.00 37.03 5.19
3230 11370 0.389948 TCGAAAGAAAGCTCGGCCTC 60.390 55.000 0.00 0.00 37.03 4.70
3231 11371 0.390472 CGAAAGAAAGCTCGGCCTCT 60.390 55.000 0.00 0.00 0.00 3.69
3232 11372 1.082690 GAAAGAAAGCTCGGCCTCTG 58.917 55.000 0.00 0.00 0.00 3.35
3233 11373 0.957888 AAAGAAAGCTCGGCCTCTGC 60.958 55.000 0.00 1.79 0.00 4.26
3234 11374 2.046892 GAAAGCTCGGCCTCTGCA 60.047 61.111 0.00 0.00 40.13 4.41
3235 11375 1.451028 GAAAGCTCGGCCTCTGCAT 60.451 57.895 0.00 0.00 40.13 3.96
3236 11376 0.179073 GAAAGCTCGGCCTCTGCATA 60.179 55.000 0.00 0.00 40.13 3.14
3237 11377 0.471617 AAAGCTCGGCCTCTGCATAT 59.528 50.000 0.00 0.00 40.13 1.78
3238 11378 0.034616 AAGCTCGGCCTCTGCATATC 59.965 55.000 0.00 0.00 40.13 1.63
3239 11379 0.831288 AGCTCGGCCTCTGCATATCT 60.831 55.000 0.00 0.00 40.13 1.98
3240 11380 0.891373 GCTCGGCCTCTGCATATCTA 59.109 55.000 0.00 0.00 40.13 1.98
3241 11381 1.135141 GCTCGGCCTCTGCATATCTAG 60.135 57.143 0.00 0.00 40.13 2.43
3242 11382 2.441410 CTCGGCCTCTGCATATCTAGA 58.559 52.381 0.00 0.00 40.13 2.43
3243 11383 3.023119 CTCGGCCTCTGCATATCTAGAT 58.977 50.000 10.73 10.73 40.13 1.98
3244 11384 2.757314 TCGGCCTCTGCATATCTAGATG 59.243 50.000 15.79 2.00 40.13 2.90
3256 11396 6.682423 CATATCTAGATGCACACAACCAAA 57.318 37.500 15.79 0.00 0.00 3.28
3257 11397 7.087409 CATATCTAGATGCACACAACCAAAA 57.913 36.000 15.79 0.00 0.00 2.44
3258 11398 7.537715 CATATCTAGATGCACACAACCAAAAA 58.462 34.615 15.79 0.00 0.00 1.94
3259 11399 5.437289 TCTAGATGCACACAACCAAAAAG 57.563 39.130 0.00 0.00 0.00 2.27
3260 11400 4.887071 TCTAGATGCACACAACCAAAAAGT 59.113 37.500 0.00 0.00 0.00 2.66
3261 11401 4.045636 AGATGCACACAACCAAAAAGTC 57.954 40.909 0.00 0.00 0.00 3.01
3262 11402 2.663826 TGCACACAACCAAAAAGTCC 57.336 45.000 0.00 0.00 0.00 3.85
3263 11403 1.895798 TGCACACAACCAAAAAGTCCA 59.104 42.857 0.00 0.00 0.00 4.02
3264 11404 2.499289 TGCACACAACCAAAAAGTCCAT 59.501 40.909 0.00 0.00 0.00 3.41
3265 11405 3.701542 TGCACACAACCAAAAAGTCCATA 59.298 39.130 0.00 0.00 0.00 2.74
3266 11406 4.202101 TGCACACAACCAAAAAGTCCATAG 60.202 41.667 0.00 0.00 0.00 2.23
3267 11407 4.298332 CACACAACCAAAAAGTCCATAGC 58.702 43.478 0.00 0.00 0.00 2.97
3268 11408 3.957497 ACACAACCAAAAAGTCCATAGCA 59.043 39.130 0.00 0.00 0.00 3.49
3269 11409 4.202111 ACACAACCAAAAAGTCCATAGCAC 60.202 41.667 0.00 0.00 0.00 4.40
3270 11410 3.320826 ACAACCAAAAAGTCCATAGCACC 59.679 43.478 0.00 0.00 0.00 5.01
3271 11411 2.525368 ACCAAAAAGTCCATAGCACCC 58.475 47.619 0.00 0.00 0.00 4.61
3272 11412 2.110011 ACCAAAAAGTCCATAGCACCCT 59.890 45.455 0.00 0.00 0.00 4.34
3273 11413 3.332485 ACCAAAAAGTCCATAGCACCCTA 59.668 43.478 0.00 0.00 0.00 3.53
3274 11414 4.202631 ACCAAAAAGTCCATAGCACCCTAA 60.203 41.667 0.00 0.00 0.00 2.69
3275 11415 4.770010 CCAAAAAGTCCATAGCACCCTAAA 59.230 41.667 0.00 0.00 0.00 1.85
3276 11416 5.245075 CCAAAAAGTCCATAGCACCCTAAAA 59.755 40.000 0.00 0.00 0.00 1.52
3277 11417 6.239458 CCAAAAAGTCCATAGCACCCTAAAAA 60.239 38.462 0.00 0.00 0.00 1.94
3278 11418 7.386059 CAAAAAGTCCATAGCACCCTAAAAAT 58.614 34.615 0.00 0.00 0.00 1.82
3279 11419 8.527810 CAAAAAGTCCATAGCACCCTAAAAATA 58.472 33.333 0.00 0.00 0.00 1.40
3280 11420 8.658840 AAAAGTCCATAGCACCCTAAAAATAA 57.341 30.769 0.00 0.00 0.00 1.40
3281 11421 8.658840 AAAGTCCATAGCACCCTAAAAATAAA 57.341 30.769 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 145 2.827921 GGATCTGTGGGTTCAATTGCTT 59.172 45.455 0.00 0.00 0.00 3.91
148 150 3.368248 CCATTGGATCTGTGGGTTCAAT 58.632 45.455 0.00 0.00 0.00 2.57
150 152 1.616725 GCCATTGGATCTGTGGGTTCA 60.617 52.381 6.95 0.00 33.58 3.18
151 153 1.106285 GCCATTGGATCTGTGGGTTC 58.894 55.000 6.95 0.00 33.58 3.62
170 172 5.989168 AGATGATGCAACATGCCATTATTTG 59.011 36.000 14.87 0.00 44.23 2.32
223 225 4.762289 AAAGTTCTCTGTCACACCTCTT 57.238 40.909 0.00 0.00 0.00 2.85
247 249 2.379907 GGGATCCCCATTGGTGATGTAT 59.620 50.000 21.42 0.00 44.65 2.29
269 271 2.225491 TGCATCGTTGTTCTGGCTTAAC 59.775 45.455 0.00 0.00 0.00 2.01
277 279 5.643348 TGTATCATCTTTGCATCGTTGTTCT 59.357 36.000 0.00 0.00 0.00 3.01
282 284 5.878332 TTGTGTATCATCTTTGCATCGTT 57.122 34.783 0.00 0.00 0.00 3.85
313 4039 4.439057 GGTTCCTGTTATTCGATGTGCTA 58.561 43.478 0.00 0.00 0.00 3.49
326 4052 0.396435 TCACTGATGCGGTTCCTGTT 59.604 50.000 0.00 0.00 0.00 3.16
328 4054 0.036952 AGTCACTGATGCGGTTCCTG 60.037 55.000 0.00 0.00 0.00 3.86
329 4055 1.204941 GTAGTCACTGATGCGGTTCCT 59.795 52.381 0.00 0.00 0.00 3.36
330 4056 1.204941 AGTAGTCACTGATGCGGTTCC 59.795 52.381 0.00 0.00 32.25 3.62
331 4057 2.531206 GAGTAGTCACTGATGCGGTTC 58.469 52.381 0.00 0.00 34.21 3.62
332 4058 1.204941 GGAGTAGTCACTGATGCGGTT 59.795 52.381 0.00 0.00 34.21 4.44
334 4060 0.817654 TGGAGTAGTCACTGATGCGG 59.182 55.000 0.00 0.00 34.21 5.69
392 4155 3.189287 ACACGAAAGAGTCCAAATGATGC 59.811 43.478 0.00 0.00 0.00 3.91
484 4247 9.549509 TGCACACATAATAAATTCGAACTTAAC 57.450 29.630 2.86 0.00 0.00 2.01
612 4376 9.495754 CACTTCTTATATTTGCTCAGCTAAAAC 57.504 33.333 0.00 0.00 0.00 2.43
682 4467 3.876274 AAAAGTCAGCGCATCTCTAGA 57.124 42.857 11.47 0.00 0.00 2.43
786 4571 3.599343 TGCAATGACATCGGCTATATCC 58.401 45.455 11.83 0.00 0.00 2.59
819 4604 3.365767 GCAATGAGGACTGCTCTCAAAAC 60.366 47.826 0.00 0.00 43.43 2.43
834 4619 4.786507 TGTTTTTCGATCAGTGCAATGAG 58.213 39.130 22.45 9.91 31.44 2.90
848 4633 8.313227 TCGCTACGTAGTATATTTTGTTTTTCG 58.687 33.333 22.98 11.99 44.56 3.46
877 4667 1.231296 TATTTTGCCGTGCACAGCGA 61.231 50.000 19.61 15.58 38.71 4.93
921 4711 7.229506 CCTGGTTGAAATTAAGAGGACATATCC 59.770 40.741 0.00 0.00 46.69 2.59
963 4753 8.579006 TCTTTCCTTCTTAACAAGATACGTGTA 58.421 33.333 0.00 0.00 37.38 2.90
964 4754 7.439381 TCTTTCCTTCTTAACAAGATACGTGT 58.561 34.615 0.00 0.00 37.38 4.49
966 4756 8.771766 GTTTCTTTCCTTCTTAACAAGATACGT 58.228 33.333 0.00 0.00 37.38 3.57
967 4757 8.770828 TGTTTCTTTCCTTCTTAACAAGATACG 58.229 33.333 0.00 0.00 37.38 3.06
1040 4877 3.431346 GGGTCCAGTAATCCGACTTTACC 60.431 52.174 0.00 0.00 33.57 2.85
1287 5145 1.298190 GGTAGTCGTCGATGTCCGC 60.298 63.158 4.21 0.00 38.37 5.54
1311 5169 1.030457 GCAGGAAGAGCATTGATGGG 58.970 55.000 0.00 0.00 0.00 4.00
1453 5311 2.462782 GCGTCGTAGTCGGAGAGCT 61.463 63.158 0.00 0.00 39.83 4.09
1992 5856 4.115279 CCGCAGGCATCTGTAGTG 57.885 61.111 0.00 0.00 46.14 2.74
2051 7373 2.978156 TTGGGTTCAAGATCAGCCTT 57.022 45.000 0.00 0.00 0.00 4.35
2079 7401 2.038033 CCCTGTTCCACTTTCGAACCTA 59.962 50.000 0.00 0.00 39.10 3.08
2301 7727 3.168035 TCAAAGGGAGCTTGCCAATTA 57.832 42.857 0.00 0.00 0.00 1.40
2483 7928 2.360165 ACGACGACTCCATACATAACCC 59.640 50.000 0.00 0.00 0.00 4.11
2519 7965 3.693807 TCTCATGGCAGCTCTCAAAATT 58.306 40.909 0.00 0.00 0.00 1.82
2551 7997 7.347485 ACAGGAAGCATTTTACTACCTAGGTAT 59.653 37.037 22.02 14.06 0.00 2.73
2575 8048 7.094933 GGAAGCCTTTTACTTTTCTCGAATACA 60.095 37.037 0.00 0.00 0.00 2.29
2624 8097 1.916181 AGGGTTCCATGGAGTTCGAAT 59.084 47.619 15.53 0.00 0.00 3.34
2708 8187 8.226819 ACGAGTAGTATACATCATCCATATGG 57.773 38.462 16.25 16.25 46.26 2.74
2715 8194 5.120363 TCGCAGACGAGTAGTATACATCATC 59.880 44.000 5.50 0.00 45.12 2.92
2716 8195 4.995487 TCGCAGACGAGTAGTATACATCAT 59.005 41.667 5.50 0.00 45.12 2.45
2717 8196 4.374399 TCGCAGACGAGTAGTATACATCA 58.626 43.478 5.50 0.00 45.12 3.07
2731 8219 1.857217 CCTCATGAATCTTCGCAGACG 59.143 52.381 0.00 0.00 42.01 4.18
2742 8230 7.611467 TGCATAAAACAGTACTTCCTCATGAAT 59.389 33.333 0.00 0.00 31.06 2.57
2754 8242 9.834628 TTTTATGTAGCTTGCATAAAACAGTAC 57.165 29.630 27.08 5.90 45.74 2.73
2782 8271 7.794349 GCGCTAGAAATATGTGACTTGTTATTC 59.206 37.037 0.00 0.00 0.00 1.75
2783 8272 7.279981 TGCGCTAGAAATATGTGACTTGTTATT 59.720 33.333 9.73 0.00 0.00 1.40
2854 8345 5.707242 TGAAATACGTTTTTATGTGGCCA 57.293 34.783 0.00 0.00 0.00 5.36
2879 8370 3.149196 ACTGGATGTGTGTGGATTTCAC 58.851 45.455 0.00 0.00 46.23 3.18
2967 10220 5.337491 GCCTCCATGAAGCCTAAATTTTTCA 60.337 40.000 0.00 0.43 34.42 2.69
3059 10470 2.990066 ATCCCACCTCACTTCGATTC 57.010 50.000 0.00 0.00 0.00 2.52
3161 11301 9.884636 TCTATTCAATGAAAAGTCCTTTATCGA 57.115 29.630 0.00 0.00 31.63 3.59
3183 11323 9.562408 ACGATTGTATCACCTCGATATATCTAT 57.438 33.333 10.93 0.00 38.85 1.98
3184 11324 8.959705 ACGATTGTATCACCTCGATATATCTA 57.040 34.615 10.93 0.00 38.85 1.98
3185 11325 7.867305 ACGATTGTATCACCTCGATATATCT 57.133 36.000 10.93 0.00 38.85 1.98
3200 11340 6.142480 CGAGCTTTCTTTCGATACGATTGTAT 59.858 38.462 5.22 5.22 43.97 2.29
3201 11341 5.454554 CGAGCTTTCTTTCGATACGATTGTA 59.545 40.000 0.00 0.00 39.06 2.41
3203 11343 4.317418 CCGAGCTTTCTTTCGATACGATTG 60.317 45.833 0.00 0.00 39.06 2.67
3205 11345 3.372954 CCGAGCTTTCTTTCGATACGAT 58.627 45.455 0.00 0.00 39.06 3.73
3206 11346 2.793933 CCGAGCTTTCTTTCGATACGA 58.206 47.619 0.00 0.00 39.06 3.43
3207 11347 1.255600 GCCGAGCTTTCTTTCGATACG 59.744 52.381 0.00 0.00 39.06 3.06
3208 11348 1.593469 GGCCGAGCTTTCTTTCGATAC 59.407 52.381 0.00 0.00 39.06 2.24
3209 11349 1.480954 AGGCCGAGCTTTCTTTCGATA 59.519 47.619 0.00 0.00 39.06 2.92
3210 11350 0.250513 AGGCCGAGCTTTCTTTCGAT 59.749 50.000 0.00 0.00 39.06 3.59
3211 11351 0.389948 GAGGCCGAGCTTTCTTTCGA 60.390 55.000 0.00 0.00 39.06 3.71
3212 11352 0.390472 AGAGGCCGAGCTTTCTTTCG 60.390 55.000 0.00 0.00 36.62 3.46
3213 11353 1.082690 CAGAGGCCGAGCTTTCTTTC 58.917 55.000 0.00 0.00 0.00 2.62
3214 11354 0.957888 GCAGAGGCCGAGCTTTCTTT 60.958 55.000 9.45 0.00 0.00 2.52
3215 11355 1.376553 GCAGAGGCCGAGCTTTCTT 60.377 57.895 9.45 0.00 0.00 2.52
3216 11356 1.908340 ATGCAGAGGCCGAGCTTTCT 61.908 55.000 16.18 1.59 40.13 2.52
3217 11357 0.179073 TATGCAGAGGCCGAGCTTTC 60.179 55.000 16.18 0.00 40.13 2.62
3218 11358 0.471617 ATATGCAGAGGCCGAGCTTT 59.528 50.000 16.18 8.03 40.13 3.51
3219 11359 0.034616 GATATGCAGAGGCCGAGCTT 59.965 55.000 16.18 12.79 40.13 3.74
3220 11360 0.831288 AGATATGCAGAGGCCGAGCT 60.831 55.000 16.18 4.53 40.13 4.09
3221 11361 0.891373 TAGATATGCAGAGGCCGAGC 59.109 55.000 9.75 9.75 40.13 5.03
3222 11362 2.441410 TCTAGATATGCAGAGGCCGAG 58.559 52.381 0.00 0.00 40.13 4.63
3223 11363 2.586648 TCTAGATATGCAGAGGCCGA 57.413 50.000 0.00 0.00 40.13 5.54
3224 11364 3.162202 CATCTAGATATGCAGAGGCCG 57.838 52.381 4.54 0.00 40.13 6.13
3233 11373 6.682423 TTTGGTTGTGTGCATCTAGATATG 57.318 37.500 4.54 0.00 0.00 1.78
3234 11374 7.394359 ACTTTTTGGTTGTGTGCATCTAGATAT 59.606 33.333 4.54 0.00 0.00 1.63
3235 11375 6.714810 ACTTTTTGGTTGTGTGCATCTAGATA 59.285 34.615 4.54 0.00 0.00 1.98
3236 11376 5.536161 ACTTTTTGGTTGTGTGCATCTAGAT 59.464 36.000 0.00 0.00 0.00 1.98
3237 11377 4.887071 ACTTTTTGGTTGTGTGCATCTAGA 59.113 37.500 0.00 0.00 0.00 2.43
3238 11378 5.186996 ACTTTTTGGTTGTGTGCATCTAG 57.813 39.130 0.00 0.00 0.00 2.43
3239 11379 4.037446 GGACTTTTTGGTTGTGTGCATCTA 59.963 41.667 0.00 0.00 0.00 1.98
3240 11380 3.181476 GGACTTTTTGGTTGTGTGCATCT 60.181 43.478 0.00 0.00 0.00 2.90
3241 11381 3.123050 GGACTTTTTGGTTGTGTGCATC 58.877 45.455 0.00 0.00 0.00 3.91
3242 11382 2.499289 TGGACTTTTTGGTTGTGTGCAT 59.501 40.909 0.00 0.00 0.00 3.96
3243 11383 1.895798 TGGACTTTTTGGTTGTGTGCA 59.104 42.857 0.00 0.00 0.00 4.57
3244 11384 2.663826 TGGACTTTTTGGTTGTGTGC 57.336 45.000 0.00 0.00 0.00 4.57
3245 11385 4.202101 TGCTATGGACTTTTTGGTTGTGTG 60.202 41.667 0.00 0.00 0.00 3.82
3246 11386 3.957497 TGCTATGGACTTTTTGGTTGTGT 59.043 39.130 0.00 0.00 0.00 3.72
3247 11387 4.298332 GTGCTATGGACTTTTTGGTTGTG 58.702 43.478 0.00 0.00 0.00 3.33
3248 11388 3.320826 GGTGCTATGGACTTTTTGGTTGT 59.679 43.478 0.00 0.00 0.00 3.32
3249 11389 3.306019 GGGTGCTATGGACTTTTTGGTTG 60.306 47.826 0.00 0.00 0.00 3.77
3250 11390 2.897326 GGGTGCTATGGACTTTTTGGTT 59.103 45.455 0.00 0.00 0.00 3.67
3251 11391 2.110011 AGGGTGCTATGGACTTTTTGGT 59.890 45.455 0.00 0.00 0.00 3.67
3252 11392 2.807676 AGGGTGCTATGGACTTTTTGG 58.192 47.619 0.00 0.00 0.00 3.28
3253 11393 5.975693 TTTAGGGTGCTATGGACTTTTTG 57.024 39.130 0.00 0.00 0.00 2.44
3254 11394 6.987403 TTTTTAGGGTGCTATGGACTTTTT 57.013 33.333 0.00 0.00 0.00 1.94
3255 11395 8.658840 TTATTTTTAGGGTGCTATGGACTTTT 57.341 30.769 0.00 0.00 0.00 2.27
3256 11396 8.658840 TTTATTTTTAGGGTGCTATGGACTTT 57.341 30.769 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.