Multiple sequence alignment - TraesCS2B01G417200

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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 TraesCS2B01G417200 chr2B 100.000 5418 0 0 1 5418 596657254 596651837 0.000000e+00 10006.0
1 TraesCS2B01G417200 chr2A 95.761 2123 73 8 1379 3494 652336275 652334163 0.000000e+00 3406.0
2 TraesCS2B01G417200 chr2A 89.818 1925 84 38 3512 5400 652334117 652332269 0.000000e+00 2366.0
3 TraesCS2B01G417200 chr2A 91.853 1387 67 16 1 1357 652337633 652336263 0.000000e+00 1893.0
4 TraesCS2B01G417200 chr2D 95.370 1987 79 4 1073 3054 507832330 507830352 0.000000e+00 3147.0
5 TraesCS2B01G417200 chr2D 90.776 1507 58 26 3944 5418 507828958 507827501 0.000000e+00 1938.0
6 TraesCS2B01G417200 chr2D 92.843 1020 49 7 60 1074 507833984 507832984 0.000000e+00 1458.0
7 TraesCS2B01G417200 chr2D 88.549 751 42 18 3078 3785 507830359 507829610 0.000000e+00 870.0
8 TraesCS2B01G417200 chr2D 96.552 58 2 0 1 58 507834068 507834011 4.470000e-16 97.1
9 TraesCS2B01G417200 chr6B 84.000 275 40 3 2614 2886 481402465 481402193 1.500000e-65 261.0
10 TraesCS2B01G417200 chr6D 83.273 275 42 3 2614 2886 338899706 338899978 3.240000e-62 250.0


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 TraesCS2B01G417200 chr2B 596651837 596657254 5417 True 10006.00 10006 100.000000 1 5418 1 chr2B.!!$R1 5417
1 TraesCS2B01G417200 chr2A 652332269 652337633 5364 True 2555.00 3406 92.477333 1 5400 3 chr2A.!!$R1 5399
2 TraesCS2B01G417200 chr2D 507827501 507834068 6567 True 1502.02 3147 92.818000 1 5418 5 chr2D.!!$R1 5417

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
137 163 1.036707 GGTTTTGTTGCTACCTGGCA 58.963 50.000 0.00 0.0 40.74 4.92 F
649 681 1.188863 TAAACAGGGAGACGGGTAGC 58.811 55.000 0.00 0.0 0.00 3.58 F
2266 2964 1.078567 CTCAGTGAGCCTTGGAGCC 60.079 63.158 7.33 0.0 0.00 4.70 F
3261 3968 0.681887 CCCATGAGCCAGCAACATCA 60.682 55.000 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2639 0.679505 TGAAAGAGAGTGGACCCGTG 59.320 55.000 0.00 0.0 0.00 4.94 R
2537 3241 3.667497 GACATGTGGTCTGAAGTCTGA 57.333 47.619 1.15 0.0 43.46 3.27 R
3736 4488 0.449388 AGTTCGTAACGTAGCTCCCG 59.551 55.000 0.00 0.0 36.23 5.14 R
5088 6386 1.006571 GACTCAACGACCGGAGCAA 60.007 57.895 9.46 0.0 34.48 3.91 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
44 45 6.761714 TGAAAGAGAAGTTGTTGAAGTACTCC 59.238 38.462 0.00 0.00 0.00 3.85
137 163 1.036707 GGTTTTGTTGCTACCTGGCA 58.963 50.000 0.00 0.00 40.74 4.92
287 313 7.096147 GCGCTCTGTTAATACTTAATACTGGTC 60.096 40.741 0.00 0.00 0.00 4.02
321 351 4.212847 GCAATCAGTGATAAGTCATGCGAT 59.787 41.667 5.94 0.00 36.60 4.58
322 352 5.406477 GCAATCAGTGATAAGTCATGCGATA 59.594 40.000 5.94 0.00 36.60 2.92
323 353 6.400834 GCAATCAGTGATAAGTCATGCGATAG 60.401 42.308 5.94 0.00 36.60 2.08
324 354 6.581171 ATCAGTGATAAGTCATGCGATAGA 57.419 37.500 3.05 0.00 36.60 1.98
343 373 7.306632 GCGATAGACAGATATTTAGCACGTTTT 60.307 37.037 0.00 0.00 39.76 2.43
376 406 5.420409 GCTACAGCAGACTAACATTTACCT 58.580 41.667 0.00 0.00 41.59 3.08
507 538 5.517904 CAAAAGCTTTGTTCTCCTTGAGAG 58.482 41.667 13.54 0.00 39.98 3.20
621 653 3.268330 GAGTGGACGGTTCCCTAAATTC 58.732 50.000 0.00 0.00 42.01 2.17
649 681 1.188863 TAAACAGGGAGACGGGTAGC 58.811 55.000 0.00 0.00 0.00 3.58
698 732 6.395426 TTTTGTTTGACTGATGCTGAATCT 57.605 33.333 0.00 0.00 36.15 2.40
705 739 4.453478 TGACTGATGCTGAATCTTGTGAAC 59.547 41.667 0.00 0.00 36.15 3.18
788 822 5.599999 AGTTGTACATCGCTATCTTTCCT 57.400 39.130 0.00 0.00 0.00 3.36
789 823 5.352284 AGTTGTACATCGCTATCTTTCCTG 58.648 41.667 0.00 0.00 0.00 3.86
811 845 3.933332 GCTTTCCTACGTTAGACTGCAAT 59.067 43.478 0.00 0.00 0.00 3.56
814 848 4.119442 TCCTACGTTAGACTGCAATTCC 57.881 45.455 0.00 0.00 0.00 3.01
831 865 6.778559 TGCAATTCCATGATCCATTTGATAGA 59.221 34.615 0.00 0.00 32.41 1.98
1059 1099 7.272144 AGTAGAAGAATGGAAAGGGTATGTT 57.728 36.000 0.00 0.00 0.00 2.71
1099 1797 7.479980 TCACAAGTCTAACAAATTTCCTGTTG 58.520 34.615 4.58 0.00 37.56 3.33
1100 1798 7.122055 TCACAAGTCTAACAAATTTCCTGTTGT 59.878 33.333 4.58 0.00 39.63 3.32
1101 1799 7.759433 CACAAGTCTAACAAATTTCCTGTTGTT 59.241 33.333 6.95 6.95 46.73 2.83
1352 2050 1.816835 TCCTACACCACGAGCTTAGTG 59.183 52.381 14.16 14.16 39.19 2.74
1362 2060 5.168569 CCACGAGCTTAGTGTCTTGAAATA 58.831 41.667 18.03 0.00 37.88 1.40
1737 2435 4.321899 GCAAGTGGTAATTTTCTGGCATCA 60.322 41.667 0.00 0.00 0.00 3.07
1741 2439 5.296780 AGTGGTAATTTTCTGGCATCATACG 59.703 40.000 0.00 0.00 0.00 3.06
1922 2620 8.102676 TCCATATATGATAACCCATCTGTTGTG 58.897 37.037 14.54 0.00 34.46 3.33
1941 2639 3.694072 TGTGCTGCAGGTAATGTATTTCC 59.306 43.478 17.12 0.00 0.00 3.13
1946 2644 2.616842 GCAGGTAATGTATTTCCACGGG 59.383 50.000 3.58 0.00 30.50 5.28
1971 2669 6.931840 GTCCACTCTCTTTCAGTTCTATTTGT 59.068 38.462 0.00 0.00 0.00 2.83
1992 2690 6.251655 TGTTGTACGGTTTTAAAAGTGTGT 57.748 33.333 12.84 7.17 0.00 3.72
1995 2693 6.251655 TGTACGGTTTTAAAAGTGTGTTGT 57.748 33.333 12.84 3.37 0.00 3.32
2000 2698 7.536855 ACGGTTTTAAAAGTGTGTTGTGATTA 58.463 30.769 0.00 0.00 0.00 1.75
2266 2964 1.078567 CTCAGTGAGCCTTGGAGCC 60.079 63.158 7.33 0.00 0.00 4.70
2438 3136 2.481441 TGGCATATGACCTGAACTCCT 58.519 47.619 5.99 0.00 0.00 3.69
2485 3183 6.979238 GGATACTATGCGGGTATGTAGATTTC 59.021 42.308 1.69 0.00 31.03 2.17
2509 3210 7.039882 TCTTTTCTCACTTCGACAAACTTACT 58.960 34.615 0.00 0.00 0.00 2.24
2521 3222 7.726079 TCGACAAACTTACTGTTATGAATTCG 58.274 34.615 0.04 0.00 38.03 3.34
2539 3243 8.078959 TGAATTCGTTTTTAGTTTCTCGATCA 57.921 30.769 0.04 0.00 0.00 2.92
2540 3244 8.221100 TGAATTCGTTTTTAGTTTCTCGATCAG 58.779 33.333 0.04 0.00 0.00 2.90
2541 3245 7.884816 ATTCGTTTTTAGTTTCTCGATCAGA 57.115 32.000 0.00 0.00 0.00 3.27
2542 3246 6.686130 TCGTTTTTAGTTTCTCGATCAGAC 57.314 37.500 0.00 0.00 0.00 3.51
2543 3247 6.444633 TCGTTTTTAGTTTCTCGATCAGACT 58.555 36.000 0.00 0.00 0.00 3.24
2821 3525 1.146930 CCTGGATGGGTCATGTCCG 59.853 63.158 2.78 0.00 34.72 4.79
3031 3738 5.992729 TGAAAACATAAACTACGCTGGAAC 58.007 37.500 0.00 0.00 0.00 3.62
3062 3769 1.343142 ACGATAACAGTGTGTGCTCCA 59.657 47.619 0.00 0.00 0.00 3.86
3067 3774 1.153188 CAGTGTGTGCTCCACCACA 60.153 57.895 14.69 3.50 43.85 4.17
3091 3798 5.755375 AGGCATTATGTAACATCGTCAGAAG 59.245 40.000 0.00 0.00 0.00 2.85
3206 3913 4.749820 TCAGAAGAGAGGCTGGATGATAT 58.250 43.478 0.00 0.00 33.05 1.63
3233 3940 6.438425 TCGGAGGATAATGATGATGAAGATGA 59.562 38.462 0.00 0.00 0.00 2.92
3261 3968 0.681887 CCCATGAGCCAGCAACATCA 60.682 55.000 0.00 0.00 0.00 3.07
3324 4031 2.846193 TGTTTTTCGCCTAACTGCTCT 58.154 42.857 0.00 0.00 0.00 4.09
3481 4204 3.482436 AGGTAAGTTGGCATCGACAAAA 58.518 40.909 0.00 0.00 29.78 2.44
3510 4233 7.755582 AAAAAGACTGTCTTGTGTATTTTGC 57.244 32.000 22.67 0.00 37.56 3.68
3664 4416 8.038944 AGTGTCGTCACCACATACTATTTTAAT 58.961 33.333 9.22 0.00 44.83 1.40
3706 4458 4.096382 GCCATCTTTTTAGCGATTCTTGGA 59.904 41.667 0.00 0.00 0.00 3.53
3736 4488 5.048083 TGTTCTTCCAGTAAATGCCATTGTC 60.048 40.000 0.00 0.00 0.00 3.18
3754 4506 0.447801 TCGGGAGCTACGTTACGAAC 59.552 55.000 13.03 0.00 0.00 3.95
4016 5281 1.990799 TCATGAGCTTCCGTTACACG 58.009 50.000 0.00 0.00 42.11 4.49
4028 5293 1.789410 CGTTACACGCCTCACTACTCG 60.789 57.143 0.00 0.00 33.65 4.18
4064 5329 1.272490 TCTTCGGCTCTCATCACGTTT 59.728 47.619 0.00 0.00 0.00 3.60
4147 5433 7.225931 ACGCAATATATCTGAAACAACCGTAAT 59.774 33.333 0.00 0.00 0.00 1.89
4148 5434 8.705134 CGCAATATATCTGAAACAACCGTAATA 58.295 33.333 0.00 0.00 0.00 0.98
4164 5450 4.273480 CCGTAATAAACCTCTCCATTGCTG 59.727 45.833 0.00 0.00 0.00 4.41
4189 5475 5.116180 CGATCAAATGCAGGAGTAAACCTA 58.884 41.667 0.00 0.00 38.32 3.08
4434 5720 3.731652 CTGAGGAGGCTGATCAGTAAG 57.268 52.381 23.38 2.56 36.52 2.34
4464 5750 8.637196 TTTCTACTCTCTGAAGAATGTACAGA 57.363 34.615 0.33 0.00 38.16 3.41
4535 5822 5.935206 TGGCGATATTTGTTTGTAGACTTCA 59.065 36.000 0.00 0.00 0.00 3.02
4536 5823 6.597672 TGGCGATATTTGTTTGTAGACTTCAT 59.402 34.615 0.00 0.00 0.00 2.57
4537 5824 7.126398 GGCGATATTTGTTTGTAGACTTCATC 58.874 38.462 0.00 0.00 0.00 2.92
4538 5825 7.201609 GGCGATATTTGTTTGTAGACTTCATCA 60.202 37.037 0.00 0.00 0.00 3.07
4568 5855 9.528018 AACTTCAATAAACTGTGTAAATGTTGG 57.472 29.630 0.00 0.00 0.00 3.77
4600 5887 3.058501 CGTCCATGTAAGAAAAAGGCGTT 60.059 43.478 0.00 0.00 0.00 4.84
4609 5896 2.685897 AGAAAAAGGCGTTGTAGTGCAA 59.314 40.909 0.00 0.00 34.16 4.08
4703 5991 6.641169 TGCATTTAGTGTGTGTTGGAAATA 57.359 33.333 0.00 0.00 0.00 1.40
4735 6023 1.089920 GATTTCTGGCGCACACTGAT 58.910 50.000 10.83 0.00 0.00 2.90
4742 6030 3.119884 TCTGGCGCACACTGATAAATTTG 60.120 43.478 10.83 0.00 0.00 2.32
4762 6050 7.823745 ATTTGAAGTGACAAGGTATTTCTGT 57.176 32.000 0.00 0.00 0.00 3.41
4763 6051 8.918202 ATTTGAAGTGACAAGGTATTTCTGTA 57.082 30.769 0.00 0.00 0.00 2.74
4764 6052 7.724305 TTGAAGTGACAAGGTATTTCTGTAC 57.276 36.000 0.00 0.00 0.00 2.90
4765 6053 7.062749 TGAAGTGACAAGGTATTTCTGTACT 57.937 36.000 0.00 0.00 0.00 2.73
4766 6054 7.152645 TGAAGTGACAAGGTATTTCTGTACTC 58.847 38.462 0.00 0.00 0.00 2.59
4767 6055 6.038997 AGTGACAAGGTATTTCTGTACTCC 57.961 41.667 0.00 0.00 0.00 3.85
4808 6106 0.107654 AATACTGAGCTCCCAACGCC 60.108 55.000 12.15 0.00 0.00 5.68
4809 6107 1.972660 ATACTGAGCTCCCAACGCCC 61.973 60.000 12.15 0.00 0.00 6.13
4810 6108 4.785453 CTGAGCTCCCAACGCCCC 62.785 72.222 12.15 0.00 0.00 5.80
4815 6113 4.101448 CTCCCAACGCCCCCTGAG 62.101 72.222 0.00 0.00 0.00 3.35
4818 6116 4.785453 CCAACGCCCCCTGAGCTC 62.785 72.222 6.82 6.82 0.00 4.09
4819 6117 4.785453 CAACGCCCCCTGAGCTCC 62.785 72.222 12.15 0.00 0.00 4.70
4823 6121 4.432741 GCCCCCTGAGCTCCCAAC 62.433 72.222 12.15 0.00 0.00 3.77
4824 6122 4.101448 CCCCCTGAGCTCCCAACG 62.101 72.222 12.15 0.00 0.00 4.10
4825 6123 4.785453 CCCCTGAGCTCCCAACGC 62.785 72.222 12.15 0.00 0.00 4.84
4898 6196 0.945813 TGGGGCGTGTTAAAGAAACG 59.054 50.000 0.00 0.00 41.30 3.60
4932 6230 2.885644 TTTCGAGCGCGCCAGATC 60.886 61.111 30.33 18.08 37.46 2.75
5083 6381 1.277557 GGAGATGAGCTCACTGGTTGT 59.722 52.381 20.97 0.05 45.81 3.32
5084 6382 2.615869 GAGATGAGCTCACTGGTTGTC 58.384 52.381 20.97 10.93 43.38 3.18
5085 6383 2.233431 GAGATGAGCTCACTGGTTGTCT 59.767 50.000 20.97 15.94 43.38 3.41
5086 6384 2.028294 AGATGAGCTCACTGGTTGTCTG 60.028 50.000 20.97 0.00 0.00 3.51
5087 6385 0.394192 TGAGCTCACTGGTTGTCTGG 59.606 55.000 13.74 0.00 0.00 3.86
5088 6386 0.394565 GAGCTCACTGGTTGTCTGGT 59.605 55.000 9.40 0.00 0.00 4.00
5089 6387 0.839946 AGCTCACTGGTTGTCTGGTT 59.160 50.000 0.00 0.00 0.00 3.67
5090 6388 0.947244 GCTCACTGGTTGTCTGGTTG 59.053 55.000 0.00 0.00 0.00 3.77
5098 6396 1.070786 TTGTCTGGTTGCTCCGGTC 59.929 57.895 0.00 0.00 42.90 4.79
5148 6446 3.503363 GCTCATGGCGTGCTCACC 61.503 66.667 0.65 0.00 0.00 4.02
5173 6471 3.067011 TGCTGTACCCTAGCACACT 57.933 52.632 2.41 0.00 45.52 3.55
5174 6472 0.608130 TGCTGTACCCTAGCACACTG 59.392 55.000 2.41 0.00 45.52 3.66
5175 6473 0.741221 GCTGTACCCTAGCACACTGC 60.741 60.000 0.00 0.00 45.46 4.40
5184 6482 2.935955 GCACACTGCACACGTACC 59.064 61.111 0.00 0.00 44.26 3.34
5185 6483 2.938823 GCACACTGCACACGTACCG 61.939 63.158 0.00 0.00 44.26 4.02
5186 6484 1.590525 CACACTGCACACGTACCGT 60.591 57.895 0.00 0.00 42.36 4.83
5203 6501 2.438254 TGGGATGTGGTCGCATGC 60.438 61.111 7.91 7.91 43.96 4.06
5333 6636 2.022129 CAGTCCAACCTCGTCACGC 61.022 63.158 0.00 0.00 0.00 5.34
5337 6640 2.254350 CAACCTCGTCACGCTCGA 59.746 61.111 0.00 0.00 35.96 4.04
5348 6663 1.442184 ACGCTCGACTTGCACGTAG 60.442 57.895 0.00 0.00 34.79 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.920569 TCTCTTTCACCTTGTCTTTGTAAC 57.079 37.500 0.00 0.00 0.00 2.50
137 163 9.620259 GAGAAAACTAATCTCCAAGGTTGATAT 57.380 33.333 0.00 0.00 37.86 1.63
188 214 8.723365 AGGGATAATATTAACACCTCAACATCA 58.277 33.333 0.00 0.00 0.00 3.07
287 313 3.865446 TCACTGATTGCACCTACATCAG 58.135 45.455 19.25 19.25 43.04 2.90
321 351 8.653338 GTCAAAAACGTGCTAAATATCTGTCTA 58.347 33.333 0.00 0.00 0.00 2.59
322 352 7.387948 AGTCAAAAACGTGCTAAATATCTGTCT 59.612 33.333 0.00 0.00 0.00 3.41
323 353 7.478667 CAGTCAAAAACGTGCTAAATATCTGTC 59.521 37.037 0.00 0.00 0.00 3.51
324 354 7.172532 TCAGTCAAAAACGTGCTAAATATCTGT 59.827 33.333 0.00 0.00 0.00 3.41
376 406 3.092301 ACGATTGATGAGTCACTGGAGA 58.908 45.455 0.00 0.00 33.11 3.71
409 439 3.709653 AGGAGGATCGCACAGGTTAATTA 59.290 43.478 0.00 0.00 34.37 1.40
507 538 7.903431 CACACAGTGAGTACTTTTTAACAGTTC 59.097 37.037 7.81 0.00 35.23 3.01
508 539 7.625606 GCACACAGTGAGTACTTTTTAACAGTT 60.626 37.037 7.81 0.00 35.23 3.16
577 609 8.735315 ACTCCATAAGAGATACTACATCATTCG 58.265 37.037 0.00 0.00 46.50 3.34
621 653 5.065988 CCCGTCTCCCTGTTTATACAAAATG 59.934 44.000 0.00 0.00 32.92 2.32
685 717 3.727079 GCGTTCACAAGATTCAGCATCAG 60.727 47.826 0.00 0.00 33.75 2.90
687 719 2.160219 TGCGTTCACAAGATTCAGCATC 59.840 45.455 0.00 0.00 0.00 3.91
705 739 3.822594 TTAGCCAATAAACAGTGTGCG 57.177 42.857 0.00 0.00 0.00 5.34
788 822 2.297880 TGCAGTCTAACGTAGGAAAGCA 59.702 45.455 11.41 11.41 0.00 3.91
789 823 2.955614 TGCAGTCTAACGTAGGAAAGC 58.044 47.619 0.00 0.00 0.00 3.51
811 845 8.592529 TTGTTTCTATCAAATGGATCATGGAA 57.407 30.769 0.00 0.00 37.44 3.53
814 848 8.680001 TCACTTGTTTCTATCAAATGGATCATG 58.320 33.333 0.00 0.00 37.44 3.07
860 894 9.603921 ACGTCTAGGGAATTATTTTCGAAATTA 57.396 29.630 12.12 9.81 0.00 1.40
1011 1051 1.089920 CTGCCATCAACTTCTTCCCG 58.910 55.000 0.00 0.00 0.00 5.14
1303 2001 7.491372 CGATAGACCAAATGAACAAGTAGCTTA 59.509 37.037 0.00 0.00 39.76 3.09
1371 2069 6.040391 ACACCAAAGAACTTTAGCTAATTGCA 59.960 34.615 7.08 0.00 45.94 4.08
1373 2071 9.394477 GTAACACCAAAGAACTTTAGCTAATTG 57.606 33.333 7.08 7.55 0.00 2.32
1374 2072 9.350951 AGTAACACCAAAGAACTTTAGCTAATT 57.649 29.630 7.08 0.00 0.00 1.40
1492 2190 5.239963 TGATGTATCAACCTGCTGCATAATG 59.760 40.000 1.31 2.53 33.08 1.90
1501 2199 5.886960 AAACTCTTGATGTATCAACCTGC 57.113 39.130 3.28 0.00 41.51 4.85
1737 2435 3.634910 AGAAAAACCTGTTGCCAACGTAT 59.365 39.130 2.68 0.00 0.00 3.06
1741 2439 4.123497 AGAAGAAAAACCTGTTGCCAAC 57.877 40.909 0.00 0.00 0.00 3.77
1916 2614 1.979855 ACATTACCTGCAGCACAACA 58.020 45.000 8.66 0.00 0.00 3.33
1922 2620 3.242739 CGTGGAAATACATTACCTGCAGC 60.243 47.826 8.66 0.00 0.00 5.25
1941 2639 0.679505 TGAAAGAGAGTGGACCCGTG 59.320 55.000 0.00 0.00 0.00 4.94
1946 2644 6.931840 ACAAATAGAACTGAAAGAGAGTGGAC 59.068 38.462 0.00 0.00 37.43 4.02
1971 2669 6.581542 CACAACACACTTTTAAAACCGTACAA 59.418 34.615 0.00 0.00 0.00 2.41
2000 2698 9.190317 GATAGGGTCCTGAACATAAAAGAAAAT 57.810 33.333 0.00 0.00 0.00 1.82
2007 2705 7.016268 GGTCTATGATAGGGTCCTGAACATAAA 59.984 40.741 0.00 0.00 0.00 1.40
2008 2706 6.497259 GGTCTATGATAGGGTCCTGAACATAA 59.503 42.308 0.00 0.00 0.00 1.90
2009 2707 6.017192 GGTCTATGATAGGGTCCTGAACATA 58.983 44.000 0.00 6.23 0.00 2.29
2012 2710 4.223953 TGGTCTATGATAGGGTCCTGAAC 58.776 47.826 0.00 0.00 0.00 3.18
2206 2904 7.320399 GGACGATGATATATGTGTTCACCATA 58.680 38.462 0.00 0.00 0.00 2.74
2266 2964 4.368808 CCACAAACTGTCGCGGCG 62.369 66.667 17.70 17.70 0.00 6.46
2392 3090 4.746089 GCATACAGCAGATTCCCAGAGAAT 60.746 45.833 0.00 0.00 45.19 2.40
2478 3176 8.548721 GTTTGTCGAAGTGAGAAAAGAAATCTA 58.451 33.333 0.00 0.00 41.03 1.98
2485 3183 7.119997 CAGTAAGTTTGTCGAAGTGAGAAAAG 58.880 38.462 0.00 0.00 41.03 2.27
2509 3210 9.588774 CGAGAAACTAAAAACGAATTCATAACA 57.411 29.630 6.22 0.00 0.00 2.41
2521 3222 8.073355 TGAAGTCTGATCGAGAAACTAAAAAC 57.927 34.615 0.00 0.00 30.26 2.43
2537 3241 3.667497 GACATGTGGTCTGAAGTCTGA 57.333 47.619 1.15 0.00 43.46 3.27
2821 3525 3.068165 ACCAAGTAAAGAAGCCAAGCAAC 59.932 43.478 0.00 0.00 0.00 4.17
3031 3738 5.516696 CACACTGTTATCGTACAAGGATGAG 59.483 44.000 0.00 0.00 0.00 2.90
3062 3769 3.876914 CGATGTTACATAATGCCTGTGGT 59.123 43.478 0.00 0.00 0.00 4.16
3067 3774 5.276461 TCTGACGATGTTACATAATGCCT 57.724 39.130 0.00 0.00 0.00 4.75
3119 3826 6.944862 AGCACTTTCTTGATGACCTATTTTCT 59.055 34.615 0.00 0.00 0.00 2.52
3206 3913 7.066307 TCTTCATCATCATTATCCTCCGAAA 57.934 36.000 0.00 0.00 0.00 3.46
3233 3940 3.026694 GCTGGCTCATGGGAACTTTTAT 58.973 45.455 0.00 0.00 0.00 1.40
3324 4031 5.175127 GCTTGAGTTCAGGGAAAACAAAAA 58.825 37.500 0.00 0.00 0.00 1.94
3494 4217 8.935844 CAGTAGATAAGCAAAATACACAAGACA 58.064 33.333 0.00 0.00 0.00 3.41
3495 4218 9.151471 TCAGTAGATAAGCAAAATACACAAGAC 57.849 33.333 0.00 0.00 0.00 3.01
3496 4219 9.719355 TTCAGTAGATAAGCAAAATACACAAGA 57.281 29.630 0.00 0.00 0.00 3.02
3499 4222 9.502091 AGTTTCAGTAGATAAGCAAAATACACA 57.498 29.630 0.00 0.00 0.00 3.72
3505 4228 9.204570 GACAGTAGTTTCAGTAGATAAGCAAAA 57.795 33.333 0.00 0.00 0.00 2.44
3507 4230 8.123639 AGACAGTAGTTTCAGTAGATAAGCAA 57.876 34.615 0.00 0.00 0.00 3.91
3508 4231 7.704578 AGACAGTAGTTTCAGTAGATAAGCA 57.295 36.000 0.00 0.00 0.00 3.91
3509 4232 8.030106 ACAAGACAGTAGTTTCAGTAGATAAGC 58.970 37.037 0.00 0.00 0.00 3.09
3510 4233 9.347934 CACAAGACAGTAGTTTCAGTAGATAAG 57.652 37.037 0.00 0.00 0.00 1.73
3664 4416 1.886222 GCCACAGCACTTGTATCCCAA 60.886 52.381 0.00 0.00 38.16 4.12
3736 4488 0.449388 AGTTCGTAACGTAGCTCCCG 59.551 55.000 0.00 0.00 36.23 5.14
3754 4506 3.771577 AGTTACCTGTCCTCAAACCAG 57.228 47.619 0.00 0.00 0.00 4.00
3825 4578 9.601217 AGAACAACAATATGACCAGTAGAATAC 57.399 33.333 0.00 0.00 43.47 1.89
3826 4579 9.817809 GAGAACAACAATATGACCAGTAGAATA 57.182 33.333 0.00 0.00 0.00 1.75
3827 4580 7.492669 CGAGAACAACAATATGACCAGTAGAAT 59.507 37.037 0.00 0.00 0.00 2.40
3829 4582 6.330278 CGAGAACAACAATATGACCAGTAGA 58.670 40.000 0.00 0.00 0.00 2.59
3830 4583 5.005779 GCGAGAACAACAATATGACCAGTAG 59.994 44.000 0.00 0.00 0.00 2.57
3845 4600 2.616842 GGTTCAAAGAAGGCGAGAACAA 59.383 45.455 0.00 0.00 40.11 2.83
3938 4737 4.037923 AGAATTTGCCTGCGAAAGAAAGAA 59.962 37.500 0.00 0.00 0.00 2.52
3964 5229 2.947652 AGAACCATGATTTCAGATGCCG 59.052 45.455 0.00 0.00 0.00 5.69
4016 5281 1.476891 TGTGGAATCGAGTAGTGAGGC 59.523 52.381 0.00 0.00 0.00 4.70
4028 5293 3.427243 CGAAGAGACGTACTGTGGAATC 58.573 50.000 0.00 0.00 0.00 2.52
4082 5347 5.362105 TGGTTATGGTGTACATACCTTCC 57.638 43.478 0.00 0.00 41.61 3.46
4147 5433 2.565391 TCGTCAGCAATGGAGAGGTTTA 59.435 45.455 0.00 0.00 0.00 2.01
4148 5434 1.347707 TCGTCAGCAATGGAGAGGTTT 59.652 47.619 0.00 0.00 0.00 3.27
4164 5450 4.201822 GGTTTACTCCTGCATTTGATCGTC 60.202 45.833 0.00 0.00 0.00 4.20
4309 5595 1.757340 GTCCGTGCCTAGGTAGCCT 60.757 63.158 11.31 0.00 37.71 4.58
4433 5719 7.234577 ACATTCTTCAGAGAGTAGAAAAGGTCT 59.765 37.037 0.00 0.00 37.22 3.85
4434 5720 7.382898 ACATTCTTCAGAGAGTAGAAAAGGTC 58.617 38.462 0.00 0.00 37.22 3.85
4568 5855 1.790755 TACATGGACGTGCAACAGAC 58.209 50.000 15.51 0.00 35.74 3.51
4703 5991 4.276678 CGCCAGAAATCATATCCATGTTGT 59.723 41.667 0.00 0.00 33.57 3.32
4706 5994 2.816087 GCGCCAGAAATCATATCCATGT 59.184 45.455 0.00 0.00 33.57 3.21
4742 6030 6.590677 GGAGTACAGAAATACCTTGTCACTTC 59.409 42.308 0.00 0.00 0.00 3.01
4758 6046 4.646945 CAGGATTGCTTAGAGGAGTACAGA 59.353 45.833 0.00 0.00 0.00 3.41
4759 6047 4.646945 TCAGGATTGCTTAGAGGAGTACAG 59.353 45.833 0.00 0.00 0.00 2.74
4760 6048 4.610333 TCAGGATTGCTTAGAGGAGTACA 58.390 43.478 0.00 0.00 0.00 2.90
4761 6049 4.038642 CCTCAGGATTGCTTAGAGGAGTAC 59.961 50.000 5.85 0.00 46.89 2.73
4762 6050 4.219115 CCTCAGGATTGCTTAGAGGAGTA 58.781 47.826 5.85 0.00 46.89 2.59
4763 6051 3.037549 CCTCAGGATTGCTTAGAGGAGT 58.962 50.000 5.85 0.00 46.89 3.85
4764 6052 2.224257 GCCTCAGGATTGCTTAGAGGAG 60.224 54.545 13.67 0.32 46.89 3.69
4765 6053 1.765314 GCCTCAGGATTGCTTAGAGGA 59.235 52.381 13.67 0.00 46.89 3.71
4766 6054 1.767681 AGCCTCAGGATTGCTTAGAGG 59.232 52.381 0.00 7.08 46.71 3.69
4767 6055 3.557228 AAGCCTCAGGATTGCTTAGAG 57.443 47.619 0.00 0.00 43.14 2.43
4808 6106 4.785453 GCGTTGGGAGCTCAGGGG 62.785 72.222 17.19 1.31 0.00 4.79
4809 6107 4.785453 GGCGTTGGGAGCTCAGGG 62.785 72.222 17.19 0.55 34.52 4.45
4810 6108 4.785453 GGGCGTTGGGAGCTCAGG 62.785 72.222 17.19 1.77 34.67 3.86
5083 6381 2.504274 AACGACCGGAGCAACCAGA 61.504 57.895 9.46 0.00 38.90 3.86
5084 6382 2.030562 AACGACCGGAGCAACCAG 59.969 61.111 9.46 0.00 38.90 4.00
5085 6383 2.280524 CAACGACCGGAGCAACCA 60.281 61.111 9.46 0.00 38.90 3.67
5086 6384 2.027625 CTCAACGACCGGAGCAACC 61.028 63.158 9.46 0.00 0.00 3.77
5087 6385 1.282930 GACTCAACGACCGGAGCAAC 61.283 60.000 9.46 0.00 34.48 4.17
5088 6386 1.006571 GACTCAACGACCGGAGCAA 60.007 57.895 9.46 0.00 34.48 3.91
5089 6387 2.649034 GACTCAACGACCGGAGCA 59.351 61.111 9.46 0.00 34.48 4.26
5090 6388 2.126031 GGACTCAACGACCGGAGC 60.126 66.667 9.46 0.00 34.48 4.70
5098 6396 2.334838 CGGTAGGAAAAGGACTCAACG 58.665 52.381 0.00 0.00 0.00 4.10
5180 6478 1.153706 CGACCACATCCCACGGTAC 60.154 63.158 0.00 0.00 31.63 3.34
5181 6479 3.009192 GCGACCACATCCCACGGTA 62.009 63.158 0.00 0.00 31.63 4.02
5182 6480 4.388499 GCGACCACATCCCACGGT 62.388 66.667 0.00 0.00 35.12 4.83
5183 6481 3.680620 ATGCGACCACATCCCACGG 62.681 63.158 0.00 0.00 0.00 4.94
5184 6482 2.125147 ATGCGACCACATCCCACG 60.125 61.111 0.00 0.00 0.00 4.94
5185 6483 2.764314 GCATGCGACCACATCCCAC 61.764 63.158 0.00 0.00 0.00 4.61
5186 6484 2.438254 GCATGCGACCACATCCCA 60.438 61.111 0.00 0.00 0.00 4.37
5187 6485 3.576356 CGCATGCGACCACATCCC 61.576 66.667 35.82 0.00 42.83 3.85
5188 6486 2.819595 ACGCATGCGACCACATCC 60.820 61.111 43.72 0.00 42.83 3.51
5189 6487 2.400798 CACGCATGCGACCACATC 59.599 61.111 43.72 0.00 42.83 3.06
5190 6488 3.803082 GCACGCATGCGACCACAT 61.803 61.111 43.72 20.03 43.33 3.21
5203 6501 1.542272 GCATGCACACTTGTTGCACG 61.542 55.000 14.21 0.00 41.61 5.34
5310 6613 0.109039 GACGAGGTTGGACTGAGAGC 60.109 60.000 0.00 0.00 0.00 4.09
5337 6640 1.014044 CATGGCGACTACGTGCAAGT 61.014 55.000 10.83 10.83 41.98 3.16


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

AutoCloner maintained by Alex Coulton.