Multiple sequence alignment - TraesCS3B01G294900

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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 TraesCS3B01G294900 chr3B 100.000 4351 0 0 1 4351 473695543 473691193 0.000000e+00 8035.0
1 TraesCS3B01G294900 chr3B 73.742 815 169 30 1131 1930 431040213 431040997 1.190000e-70 278.0
2 TraesCS3B01G294900 chr3A 93.665 4357 218 29 1 4313 484638126 484633784 0.000000e+00 6464.0
3 TraesCS3B01G294900 chr3A 74.233 815 165 30 1131 1930 448701984 448702768 2.540000e-77 300.0
4 TraesCS3B01G294900 chr3A 71.744 814 167 48 1132 1915 598553492 598554272 2.080000e-38 171.0
5 TraesCS3B01G294900 chr3A 71.820 802 162 49 1146 1915 625210518 625209749 2.080000e-38 171.0
6 TraesCS3B01G294900 chr3D 94.219 2197 103 16 1 2184 363598802 363596617 0.000000e+00 3332.0
7 TraesCS3B01G294900 chr3D 90.767 1343 104 13 2181 3520 363595635 363594310 0.000000e+00 1775.0
8 TraesCS3B01G294900 chr3D 89.921 635 36 11 3597 4220 363594077 363593460 0.000000e+00 793.0
9 TraesCS3B01G294900 chr3D 74.356 815 164 30 1131 1930 331657185 331657969 5.470000e-79 305.0
10 TraesCS3B01G294900 chr3D 71.569 816 165 51 1132 1915 455869728 455870508 4.500000e-35 159.0
11 TraesCS3B01G294900 chr3D 92.500 80 6 0 3520 3599 363594204 363594125 9.890000e-22 115.0
12 TraesCS3B01G294900 chr6D 90.366 820 75 2 1 820 14169284 14170099 0.000000e+00 1074.0
13 TraesCS3B01G294900 chr5A 87.080 774 98 2 2 774 46423084 46422312 0.000000e+00 874.0
14 TraesCS3B01G294900 chr5A 75.062 810 142 34 1139 1921 41373873 41374649 5.430000e-84 322.0
15 TraesCS3B01G294900 chr2D 73.984 246 47 9 1470 1707 560399494 560399730 2.790000e-12 84.2
16 TraesCS3B01G294900 chr7B 90.741 54 3 2 2085 2137 642034596 642034544 2.170000e-08 71.3
17 TraesCS3B01G294900 chrUn 87.097 62 4 4 2085 2144 183181606 183181665 2.810000e-07 67.6
18 TraesCS3B01G294900 chrUn 87.097 62 4 4 2085 2144 339675848 339675789 2.810000e-07 67.6
19 TraesCS3B01G294900 chrUn 87.097 62 4 4 2085 2144 391943014 391942955 2.810000e-07 67.6
20 TraesCS3B01G294900 chrUn 87.097 62 4 4 2085 2144 391960193 391960252 2.810000e-07 67.6


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 TraesCS3B01G294900 chr3B 473691193 473695543 4350 True 8035.00 8035 100.00000 1 4351 1 chr3B.!!$R1 4350
1 TraesCS3B01G294900 chr3B 431040213 431040997 784 False 278.00 278 73.74200 1131 1930 1 chr3B.!!$F1 799
2 TraesCS3B01G294900 chr3A 484633784 484638126 4342 True 6464.00 6464 93.66500 1 4313 1 chr3A.!!$R1 4312
3 TraesCS3B01G294900 chr3A 448701984 448702768 784 False 300.00 300 74.23300 1131 1930 1 chr3A.!!$F1 799
4 TraesCS3B01G294900 chr3D 363593460 363598802 5342 True 1503.75 3332 91.85175 1 4220 4 chr3D.!!$R1 4219
5 TraesCS3B01G294900 chr3D 331657185 331657969 784 False 305.00 305 74.35600 1131 1930 1 chr3D.!!$F1 799
6 TraesCS3B01G294900 chr6D 14169284 14170099 815 False 1074.00 1074 90.36600 1 820 1 chr6D.!!$F1 819
7 TraesCS3B01G294900 chr5A 46422312 46423084 772 True 874.00 874 87.08000 2 774 1 chr5A.!!$R1 772
8 TraesCS3B01G294900 chr5A 41373873 41374649 776 False 322.00 322 75.06200 1139 1921 1 chr5A.!!$F1 782

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
949 952 1.471119 CTGTCATTTGCAGCATCCCT 58.529 50.0 0.00 0.00 0.00 4.2 F
2516 3551 0.036022 AGACCTTTGCTCACAGGCTC 59.964 55.0 2.18 0.79 32.79 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2880 3915 0.452987 CGGGGTTTGATGCTGATGTG 59.547 55.0 0.0 0.0 0.00 3.21 R
3935 5139 0.872021 GTTCCTCGTAGCCATGCTCG 60.872 60.0 0.0 0.0 40.44 5.03 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
174 175 4.036144 GGTATGCTTTCAAAGATGGCTCTC 59.964 45.833 0.00 0.00 0.00 3.20
227 228 9.822185 AAATTATTTGAAATAGCAGTGGGAATC 57.178 29.630 0.00 0.00 0.00 2.52
305 306 1.619654 TCAAGCCCCACAACATTCTG 58.380 50.000 0.00 0.00 0.00 3.02
407 408 1.541588 GGTGGTGCAAGAGGAACAATC 59.458 52.381 0.00 0.00 33.28 2.67
584 585 5.807011 GCAATGGATTTATGAACACTTGGAC 59.193 40.000 0.00 0.00 0.00 4.02
681 682 4.275689 TGTGGTGCATTCAGTTAAGTTCTG 59.724 41.667 0.00 0.00 0.00 3.02
799 801 6.128391 GGTTTATATTGTTCTCGCACACTTGA 60.128 38.462 0.00 0.00 0.00 3.02
820 823 5.988287 TGATCCAGTGTTGCATAATCTGTA 58.012 37.500 0.00 0.00 0.00 2.74
901 904 1.689273 GTCCGCTGGTCTCCTGATTAT 59.311 52.381 0.00 0.00 0.00 1.28
949 952 1.471119 CTGTCATTTGCAGCATCCCT 58.529 50.000 0.00 0.00 0.00 4.20
1002 1007 0.659427 CCACGTATGCTTGCTGGATG 59.341 55.000 0.00 0.00 0.00 3.51
1047 1059 2.508867 CACAAAAGACATTCGCCATCG 58.491 47.619 0.00 0.00 0.00 3.84
1272 1292 3.382832 CCGGTCCTCAACCTCGCT 61.383 66.667 0.00 0.00 46.87 4.93
1533 1556 1.828660 CGACATAGAGGCCCCGTCT 60.829 63.158 0.00 0.00 0.00 4.18
2022 2064 1.003118 TGCTTTCAGGCTTACACCGAT 59.997 47.619 0.00 0.00 33.69 4.18
2080 2128 8.829514 TGCCGTCGTTTATTCTAAATTTTATG 57.170 30.769 0.00 0.00 0.00 1.90
2123 2171 3.709880 TACAGGGAACGGCGCATCG 62.710 63.158 10.83 7.21 0.00 3.84
2137 2185 3.345714 GCGCATCGTCAGATTACAAAAG 58.654 45.455 0.30 0.00 34.23 2.27
2217 3252 7.054751 AGTGACAGTACATACATAGACTAGCA 58.945 38.462 0.00 0.00 0.00 3.49
2218 3253 7.556635 AGTGACAGTACATACATAGACTAGCAA 59.443 37.037 0.00 0.00 0.00 3.91
2283 3318 3.009026 GCATTGCATTTTAAACCCCCTG 58.991 45.455 3.15 0.00 0.00 4.45
2378 3413 5.290493 TCATCTGCCATAAGAAATACCGT 57.710 39.130 0.00 0.00 0.00 4.83
2514 3549 1.000938 CAAAGACCTTTGCTCACAGGC 60.001 52.381 9.25 0.00 42.66 4.85
2516 3551 0.036022 AGACCTTTGCTCACAGGCTC 59.964 55.000 2.18 0.79 32.79 4.70
2675 3710 1.506718 CAACGTCGCTCCTCTGCTA 59.493 57.895 0.00 0.00 0.00 3.49
2693 3728 0.187361 TAGGGTTTTGCTTGCAGGGT 59.813 50.000 0.00 0.00 0.00 4.34
2694 3729 0.690744 AGGGTTTTGCTTGCAGGGTT 60.691 50.000 0.00 0.00 0.00 4.11
2705 3740 2.359975 CAGGGTTCAACGAGGGCC 60.360 66.667 0.00 0.00 0.00 5.80
2820 3855 2.367241 TGGGAGAAACTGTTCGACATCA 59.633 45.455 0.00 0.00 38.90 3.07
2847 3882 4.373116 TGGCGCGAGGTCTTGACC 62.373 66.667 12.10 11.59 0.00 4.02
2864 3899 1.300465 CCATCTCCACGGCGATGAG 60.300 63.158 16.62 18.35 39.04 2.90
2865 3900 1.735973 CATCTCCACGGCGATGAGA 59.264 57.895 26.07 26.07 39.04 3.27
2930 3965 1.130054 TGGATCAGGAGCTATGCCCC 61.130 60.000 0.00 0.00 0.00 5.80
2951 3986 4.577693 CCCAAGATATCTGATGTTGGTGTG 59.422 45.833 15.95 3.91 36.68 3.82
2983 4018 2.925306 GCGAAACATCTACTCGTGGTGT 60.925 50.000 0.00 0.00 35.06 4.16
2998 4033 1.359130 TGGTGTGAGGGAGAGAGATGA 59.641 52.381 0.00 0.00 0.00 2.92
3185 4220 1.467734 CTGGATGAGTTCTGCAACAGC 59.532 52.381 0.00 0.00 34.60 4.40
3254 4289 4.008933 GTCGGGCTGTGGTGCTCT 62.009 66.667 0.00 0.00 0.00 4.09
3309 4344 0.393132 AGTCGTCGAGATGCTGGAGA 60.393 55.000 0.00 0.00 0.00 3.71
3311 4346 0.107654 TCGTCGAGATGCTGGAGAGA 60.108 55.000 0.00 0.00 0.00 3.10
3347 4382 2.615493 GGAATTGCCGAGAAGAACCTCA 60.615 50.000 0.00 0.00 32.86 3.86
3357 4392 4.495422 GAGAAGAACCTCATGAAGCGTAA 58.505 43.478 0.00 0.00 33.50 3.18
3358 4393 4.894784 AGAAGAACCTCATGAAGCGTAAA 58.105 39.130 0.00 0.00 0.00 2.01
3362 4397 4.691216 AGAACCTCATGAAGCGTAAAAGAC 59.309 41.667 0.00 0.00 0.00 3.01
3363 4398 4.002906 ACCTCATGAAGCGTAAAAGACA 57.997 40.909 0.00 0.00 0.00 3.41
3364 4399 4.579869 ACCTCATGAAGCGTAAAAGACAT 58.420 39.130 0.00 0.00 0.00 3.06
3365 4400 5.730550 ACCTCATGAAGCGTAAAAGACATA 58.269 37.500 0.00 0.00 0.00 2.29
3366 4401 5.812642 ACCTCATGAAGCGTAAAAGACATAG 59.187 40.000 0.00 0.00 0.00 2.23
3367 4402 5.235186 CCTCATGAAGCGTAAAAGACATAGG 59.765 44.000 0.00 0.00 0.00 2.57
3368 4403 5.730550 TCATGAAGCGTAAAAGACATAGGT 58.269 37.500 0.00 0.00 0.00 3.08
3370 4405 4.890088 TGAAGCGTAAAAGACATAGGTGT 58.110 39.130 0.00 0.00 42.49 4.16
3371 4406 6.028146 TGAAGCGTAAAAGACATAGGTGTA 57.972 37.500 0.00 0.00 39.09 2.90
3372 4407 5.865552 TGAAGCGTAAAAGACATAGGTGTAC 59.134 40.000 0.00 0.00 39.09 2.90
3382 4417 7.611213 AAGACATAGGTGTACTTGTAAATGC 57.389 36.000 0.00 0.00 39.09 3.56
3392 4427 3.157087 ACTTGTAAATGCTGTTCAGGGG 58.843 45.455 1.97 0.00 0.00 4.79
3394 4429 2.790433 TGTAAATGCTGTTCAGGGGAC 58.210 47.619 1.97 0.00 0.00 4.46
3414 4449 0.895100 TGCGGCTGCTTCTGGATTTT 60.895 50.000 20.27 0.00 43.34 1.82
3418 4453 2.669391 CGGCTGCTTCTGGATTTTTGTC 60.669 50.000 0.00 0.00 0.00 3.18
3423 4458 4.130857 TGCTTCTGGATTTTTGTCGTGTA 58.869 39.130 0.00 0.00 0.00 2.90
3424 4459 4.576873 TGCTTCTGGATTTTTGTCGTGTAA 59.423 37.500 0.00 0.00 0.00 2.41
3425 4460 5.240623 TGCTTCTGGATTTTTGTCGTGTAAT 59.759 36.000 0.00 0.00 0.00 1.89
3426 4461 6.428465 TGCTTCTGGATTTTTGTCGTGTAATA 59.572 34.615 0.00 0.00 0.00 0.98
3427 4462 7.041030 TGCTTCTGGATTTTTGTCGTGTAATAA 60.041 33.333 0.00 0.00 0.00 1.40
3450 4486 1.201424 TCAGGAGAGCACATGAGCAT 58.799 50.000 17.61 5.25 36.85 3.79
3454 4490 1.329906 GGAGAGCACATGAGCATTTCG 59.670 52.381 17.61 0.00 36.85 3.46
3455 4491 0.731417 AGAGCACATGAGCATTTCGC 59.269 50.000 17.61 0.00 42.91 4.70
3470 4507 1.929230 TTCGCTTCGTTGTTGTCAGA 58.071 45.000 0.00 0.00 0.00 3.27
3479 4516 5.209818 TCGTTGTTGTCAGAATAGGACTT 57.790 39.130 0.00 0.00 36.26 3.01
3484 4521 6.861065 TGTTGTCAGAATAGGACTTGTTTC 57.139 37.500 0.00 0.00 36.26 2.78
3489 4526 5.992217 GTCAGAATAGGACTTGTTTCAGTGT 59.008 40.000 0.00 0.00 32.54 3.55
3501 4538 7.047891 ACTTGTTTCAGTGTCAGATAACTTGA 58.952 34.615 0.00 0.00 0.00 3.02
3504 4541 7.445121 TGTTTCAGTGTCAGATAACTTGATCT 58.555 34.615 0.00 0.00 36.58 2.75
3510 4547 6.148480 AGTGTCAGATAACTTGATCTTGCAAC 59.852 38.462 0.00 0.00 33.75 4.17
3761 4965 4.523083 GAGTTGATGTATTTGCCCAGGTA 58.477 43.478 0.00 0.00 0.00 3.08
3998 5212 2.533266 TCTTTGCAGTGGACTCTGTC 57.467 50.000 3.68 0.00 37.70 3.51
4087 5301 1.875576 CGCCATGCTCTATCTGGAACC 60.876 57.143 0.00 0.00 31.38 3.62
4092 5306 0.461961 GCTCTATCTGGAACCGTGCT 59.538 55.000 0.00 0.00 0.00 4.40
4103 5317 2.809696 GGAACCGTGCTGCTAAAACTTA 59.190 45.455 0.00 0.00 0.00 2.24
4104 5318 3.364664 GGAACCGTGCTGCTAAAACTTAC 60.365 47.826 0.00 0.00 0.00 2.34
4106 5320 4.261578 ACCGTGCTGCTAAAACTTACTA 57.738 40.909 0.00 0.00 0.00 1.82
4184 5399 4.459089 GGGACTCCGGCACTGCTC 62.459 72.222 0.00 0.00 0.00 4.26
4265 5480 1.069296 TGCTGTGCAGATTACGTTTGC 60.069 47.619 3.02 0.00 38.30 3.68
4310 5525 3.067106 AGCACACCGATAAAAGTGTCTG 58.933 45.455 0.00 0.00 45.20 3.51
4313 5528 3.432252 CACACCGATAAAAGTGTCTGGTC 59.568 47.826 0.00 0.00 45.20 4.02
4314 5529 3.323979 ACACCGATAAAAGTGTCTGGTCT 59.676 43.478 0.00 0.00 43.62 3.85
4315 5530 4.525487 ACACCGATAAAAGTGTCTGGTCTA 59.475 41.667 0.00 0.00 43.62 2.59
4316 5531 5.187186 ACACCGATAAAAGTGTCTGGTCTAT 59.813 40.000 0.00 0.00 43.62 1.98
4317 5532 6.379133 ACACCGATAAAAGTGTCTGGTCTATA 59.621 38.462 0.00 0.00 43.62 1.31
4318 5533 7.093640 ACACCGATAAAAGTGTCTGGTCTATAA 60.094 37.037 0.00 0.00 43.62 0.98
4319 5534 7.762615 CACCGATAAAAGTGTCTGGTCTATAAA 59.237 37.037 0.00 0.00 0.00 1.40
4320 5535 7.763071 ACCGATAAAAGTGTCTGGTCTATAAAC 59.237 37.037 0.00 0.00 0.00 2.01
4321 5536 7.762615 CCGATAAAAGTGTCTGGTCTATAAACA 59.237 37.037 0.00 0.00 0.00 2.83
4322 5537 8.592998 CGATAAAAGTGTCTGGTCTATAAACAC 58.407 37.037 0.00 0.00 40.33 3.32
4326 5541 6.665992 AGTGTCTGGTCTATAAACACTCAA 57.334 37.500 0.84 0.00 45.44 3.02
4327 5542 6.456501 AGTGTCTGGTCTATAAACACTCAAC 58.543 40.000 0.84 0.00 45.44 3.18
4328 5543 5.638234 GTGTCTGGTCTATAAACACTCAACC 59.362 44.000 0.00 0.00 37.75 3.77
4329 5544 5.305902 TGTCTGGTCTATAAACACTCAACCA 59.694 40.000 0.00 0.00 34.36 3.67
4330 5545 6.183361 TGTCTGGTCTATAAACACTCAACCAA 60.183 38.462 0.00 0.00 35.08 3.67
4331 5546 6.369065 GTCTGGTCTATAAACACTCAACCAAG 59.631 42.308 0.00 0.00 35.08 3.61
4332 5547 5.001232 TGGTCTATAAACACTCAACCAAGC 58.999 41.667 0.00 0.00 32.65 4.01
4333 5548 4.092968 GGTCTATAAACACTCAACCAAGCG 59.907 45.833 0.00 0.00 0.00 4.68
4334 5549 4.689345 GTCTATAAACACTCAACCAAGCGT 59.311 41.667 0.00 0.00 0.00 5.07
4335 5550 5.178809 GTCTATAAACACTCAACCAAGCGTT 59.821 40.000 0.00 0.00 33.90 4.84
4345 5560 3.896648 AACCAAGCGTTGATAACACAG 57.103 42.857 0.15 0.00 31.79 3.66
4346 5561 2.151202 ACCAAGCGTTGATAACACAGG 58.849 47.619 0.15 0.00 0.00 4.00
4347 5562 2.151202 CCAAGCGTTGATAACACAGGT 58.849 47.619 0.15 0.00 0.00 4.00
4348 5563 2.095768 CCAAGCGTTGATAACACAGGTG 60.096 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 5.185056 CCCAACCTAAAGTATTTCCACCTTG 59.815 44.000 0.00 0.00 40.09 3.61
305 306 5.514274 TTGGACAGAAGTTTTGATCCAAC 57.486 39.130 18.21 0.00 40.44 3.77
584 585 8.803201 TCTCAGAAGCACTAATACAATATTCG 57.197 34.615 0.00 0.00 0.00 3.34
681 682 2.350522 AGTCATTGTTGGACGATCTGC 58.649 47.619 0.00 0.00 40.20 4.26
799 801 7.176515 TGTTTTACAGATTATGCAACACTGGAT 59.823 33.333 14.54 0.00 37.40 3.41
901 904 3.609853 GTGTTATCTCCTGTGCATGGAA 58.390 45.455 11.67 5.02 32.61 3.53
1002 1007 6.195983 GGCGTGTGCTTATATATACGACATAC 59.804 42.308 7.47 8.25 39.23 2.39
1047 1059 0.172578 GCTTCCCGGGCATTGTTAAC 59.827 55.000 18.49 0.00 0.00 2.01
1306 1326 2.801421 GATGTCAGCGGCGAGAGA 59.199 61.111 12.98 6.58 0.00 3.10
1422 1442 3.522343 GGAAGTTGTCCCATAGGTAGGTT 59.478 47.826 0.00 0.00 41.10 3.50
1533 1556 1.633561 CGAGGTCGTCGTAGTACAGA 58.366 55.000 6.77 0.00 44.20 3.41
1644 1679 4.778415 GCGAGCGCGGTCTTGAGA 62.778 66.667 32.55 0.00 38.16 3.27
1825 1863 4.719369 GTCGACGAACCCGCTGCT 62.719 66.667 0.00 0.00 39.95 4.24
1971 2009 2.563620 ACCTGTGTTTTTGTTCCGGTTT 59.436 40.909 0.00 0.00 0.00 3.27
2185 3220 6.656632 ATGTATGTACTGTCACTCTATGGG 57.343 41.667 0.00 0.00 0.00 4.00
2217 3252 4.799564 TCACCAACTTGCAAACTCTTTT 57.200 36.364 0.00 0.00 0.00 2.27
2218 3253 5.343307 AATCACCAACTTGCAAACTCTTT 57.657 34.783 0.00 0.00 0.00 2.52
2477 3512 4.821805 GTCTTTGTCATCCTTTCCACTTCA 59.178 41.667 0.00 0.00 0.00 3.02
2561 3596 4.377708 ACTGTGATCTGCCGCGCA 62.378 61.111 8.75 1.04 36.92 6.09
2607 3642 1.001406 CTCCTTCACGAAGTCCTTGCT 59.999 52.381 6.08 0.00 41.61 3.91
2608 3643 1.433534 CTCCTTCACGAAGTCCTTGC 58.566 55.000 6.08 0.00 41.61 4.01
2656 3691 1.934220 TAGCAGAGGAGCGACGTTGG 61.934 60.000 4.64 0.00 40.15 3.77
2675 3710 0.690744 AACCCTGCAAGCAAAACCCT 60.691 50.000 0.00 0.00 0.00 4.34
2693 3728 1.507140 ATATCAGGGCCCTCGTTGAA 58.493 50.000 25.77 8.58 0.00 2.69
2694 3729 1.968493 GTATATCAGGGCCCTCGTTGA 59.032 52.381 25.77 18.62 0.00 3.18
2705 3740 3.509967 TGGGCATGTACTCGTATATCAGG 59.490 47.826 0.00 0.00 0.00 3.86
2774 3809 2.359214 CAGCCATAGCGAGTAGTTCTCA 59.641 50.000 0.00 0.00 46.67 3.27
2843 3878 2.058001 ATCGCCGTGGAGATGGTCA 61.058 57.895 4.22 0.00 33.55 4.02
2880 3915 0.452987 CGGGGTTTGATGCTGATGTG 59.547 55.000 0.00 0.00 0.00 3.21
2930 3965 4.036027 GCCACACCAACATCAGATATCTTG 59.964 45.833 1.33 2.51 0.00 3.02
2951 3986 2.423538 AGATGTTTCGCATAGGTTTGCC 59.576 45.455 0.00 0.00 39.52 4.52
2983 4018 2.772515 TCGTAGTCATCTCTCTCCCTCA 59.227 50.000 0.00 0.00 0.00 3.86
2998 4033 1.602888 ACCTCAGGTGCGTCGTAGT 60.603 57.895 0.00 0.00 32.98 2.73
3200 4235 3.288308 AAGCTCTCTGGTGTCGCCG 62.288 63.158 0.00 0.00 41.21 6.46
3289 4324 0.248417 CTCCAGCATCTCGACGACTG 60.248 60.000 6.29 6.29 0.00 3.51
3335 4370 2.966050 ACGCTTCATGAGGTTCTTCTC 58.034 47.619 6.70 0.00 0.00 2.87
3347 4382 5.488341 ACACCTATGTCTTTTACGCTTCAT 58.512 37.500 0.00 0.00 31.55 2.57
3357 4392 7.883311 AGCATTTACAAGTACACCTATGTCTTT 59.117 33.333 0.00 0.00 40.48 2.52
3358 4393 7.334421 CAGCATTTACAAGTACACCTATGTCTT 59.666 37.037 0.00 0.00 40.48 3.01
3362 4397 6.985188 ACAGCATTTACAAGTACACCTATG 57.015 37.500 0.00 0.00 0.00 2.23
3363 4398 7.165485 TGAACAGCATTTACAAGTACACCTAT 58.835 34.615 0.00 0.00 0.00 2.57
3364 4399 6.526526 TGAACAGCATTTACAAGTACACCTA 58.473 36.000 0.00 0.00 0.00 3.08
3365 4400 5.373222 TGAACAGCATTTACAAGTACACCT 58.627 37.500 0.00 0.00 0.00 4.00
3366 4401 5.334879 CCTGAACAGCATTTACAAGTACACC 60.335 44.000 0.00 0.00 0.00 4.16
3367 4402 5.334879 CCCTGAACAGCATTTACAAGTACAC 60.335 44.000 0.00 0.00 0.00 2.90
3368 4403 4.759693 CCCTGAACAGCATTTACAAGTACA 59.240 41.667 0.00 0.00 0.00 2.90
3370 4405 4.042311 TCCCCTGAACAGCATTTACAAGTA 59.958 41.667 0.00 0.00 0.00 2.24
3371 4406 3.157087 CCCCTGAACAGCATTTACAAGT 58.843 45.455 0.00 0.00 0.00 3.16
3372 4407 3.191371 GTCCCCTGAACAGCATTTACAAG 59.809 47.826 0.00 0.00 0.00 3.16
3380 4415 2.431683 GCAGTCCCCTGAACAGCA 59.568 61.111 0.00 0.00 41.50 4.41
3381 4416 2.743928 CGCAGTCCCCTGAACAGC 60.744 66.667 0.00 0.00 41.50 4.40
3382 4417 2.046892 CCGCAGTCCCCTGAACAG 60.047 66.667 0.00 0.00 41.50 3.16
3392 4427 2.866085 ATCCAGAAGCAGCCGCAGTC 62.866 60.000 0.00 0.00 42.27 3.51
3394 4429 1.310933 AAATCCAGAAGCAGCCGCAG 61.311 55.000 0.00 0.00 42.27 5.18
3398 4433 2.669391 CGACAAAAATCCAGAAGCAGCC 60.669 50.000 0.00 0.00 0.00 4.85
3399 4434 2.030805 ACGACAAAAATCCAGAAGCAGC 60.031 45.455 0.00 0.00 0.00 5.25
3414 4449 7.148474 GCTCTCCTGAAATTTATTACACGACAA 60.148 37.037 0.00 0.00 0.00 3.18
3418 4453 6.092122 TGTGCTCTCCTGAAATTTATTACACG 59.908 38.462 0.00 0.00 0.00 4.49
3423 4458 6.183360 GCTCATGTGCTCTCCTGAAATTTATT 60.183 38.462 12.42 0.00 0.00 1.40
3424 4459 5.298777 GCTCATGTGCTCTCCTGAAATTTAT 59.701 40.000 12.42 0.00 0.00 1.40
3425 4460 4.637534 GCTCATGTGCTCTCCTGAAATTTA 59.362 41.667 12.42 0.00 0.00 1.40
3426 4461 3.442977 GCTCATGTGCTCTCCTGAAATTT 59.557 43.478 12.42 0.00 0.00 1.82
3427 4462 3.015327 GCTCATGTGCTCTCCTGAAATT 58.985 45.455 12.42 0.00 0.00 1.82
3450 4486 2.272678 TCTGACAACAACGAAGCGAAA 58.727 42.857 0.00 0.00 0.00 3.46
3454 4490 3.994392 TCCTATTCTGACAACAACGAAGC 59.006 43.478 0.00 0.00 0.00 3.86
3455 4491 5.230942 AGTCCTATTCTGACAACAACGAAG 58.769 41.667 0.00 0.00 35.15 3.79
3462 4498 6.483640 ACTGAAACAAGTCCTATTCTGACAAC 59.516 38.462 0.00 0.00 35.15 3.32
3470 4507 6.174720 TCTGACACTGAAACAAGTCCTATT 57.825 37.500 0.00 0.00 0.00 1.73
3479 4516 7.445121 AGATCAAGTTATCTGACACTGAAACA 58.555 34.615 0.00 0.00 34.87 2.83
3484 4521 5.640783 TGCAAGATCAAGTTATCTGACACTG 59.359 40.000 0.00 0.00 36.34 3.66
3489 4526 5.559770 TGGTTGCAAGATCAAGTTATCTGA 58.440 37.500 0.00 0.00 36.34 3.27
3510 4547 8.195617 ACTGTTTGTTTGTTTTCAACATATGG 57.804 30.769 7.80 0.00 41.79 2.74
3534 4682 1.983605 CGTGTGGTGATCGTGTCTTAC 59.016 52.381 0.00 0.00 0.00 2.34
3733 4937 3.378427 GGCAAATACATCAACTCCCAGAC 59.622 47.826 0.00 0.00 0.00 3.51
3767 4971 4.673298 TGTGCACGTACGCCAGGG 62.673 66.667 16.72 1.06 0.00 4.45
3935 5139 0.872021 GTTCCTCGTAGCCATGCTCG 60.872 60.000 0.00 0.00 40.44 5.03
3941 5145 1.292223 GTGCTGTTCCTCGTAGCCA 59.708 57.895 0.00 0.00 36.64 4.75
3998 5212 1.610522 CTCTTGTGCTCCCAAAACCAG 59.389 52.381 0.00 0.00 0.00 4.00
4087 5301 5.564127 GCTTTTAGTAAGTTTTAGCAGCACG 59.436 40.000 0.00 0.00 0.00 5.34
4092 5306 7.976734 TGCAAAAGCTTTTAGTAAGTTTTAGCA 59.023 29.630 23.44 19.35 31.85 3.49
4103 5317 3.490526 CGTGCAATGCAAAAGCTTTTAGT 59.509 39.130 23.44 6.48 41.47 2.24
4104 5318 3.120923 CCGTGCAATGCAAAAGCTTTTAG 60.121 43.478 23.44 17.71 41.47 1.85
4106 5320 1.598601 CCGTGCAATGCAAAAGCTTTT 59.401 42.857 18.74 18.74 41.47 2.27
4223 5438 3.059352 ACCTTGGACATGTCTTGCTAC 57.941 47.619 24.50 8.09 0.00 3.58
4228 5443 2.624838 CAGCAAACCTTGGACATGTCTT 59.375 45.455 24.50 8.54 0.00 3.01
4265 5480 2.356135 CGGTCACCCCACTTCAATTAG 58.644 52.381 0.00 0.00 0.00 1.73
4307 5522 6.428083 TTGGTTGAGTGTTTATAGACCAGA 57.572 37.500 0.00 0.00 37.06 3.86
4310 5525 4.092968 CGCTTGGTTGAGTGTTTATAGACC 59.907 45.833 0.00 0.00 0.00 3.85
4313 5528 5.607119 AACGCTTGGTTGAGTGTTTATAG 57.393 39.130 0.00 0.00 45.33 1.31
4325 5540 2.552315 CCTGTGTTATCAACGCTTGGTT 59.448 45.455 4.44 0.00 42.27 3.67
4326 5541 2.151202 CCTGTGTTATCAACGCTTGGT 58.849 47.619 4.44 0.00 42.27 3.67
4327 5542 2.095768 CACCTGTGTTATCAACGCTTGG 60.096 50.000 4.44 8.29 42.27 3.61
4328 5543 2.548057 ACACCTGTGTTATCAACGCTTG 59.452 45.455 0.00 2.38 41.83 4.01
4329 5544 2.846193 ACACCTGTGTTATCAACGCTT 58.154 42.857 0.00 0.00 41.83 4.68
4330 5545 2.543777 ACACCTGTGTTATCAACGCT 57.456 45.000 0.00 0.00 41.83 5.07


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

AutoCloner maintained by Alex Coulton.