Multiple sequence alignment - TraesCS6D01G244900

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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 TraesCS6D01G244900 chr6D 100.000 4541 0 0 1 4541 346958547 346954007 0.000000e+00 8386.0
1 TraesCS6D01G244900 chr6A 95.798 3284 86 21 709 3977 496471528 496474774 0.000000e+00 5252.0
2 TraesCS6D01G244900 chr6A 91.213 569 31 9 3986 4541 496474838 496475400 0.000000e+00 756.0
3 TraesCS6D01G244900 chr6A 86.553 409 37 8 1 396 496470036 496470439 6.980000e-118 435.0
4 TraesCS6D01G244900 chr6A 98.182 55 1 0 670 724 496470836 496470890 3.740000e-16 97.1
5 TraesCS6D01G244900 chr6A 94.545 55 2 1 670 723 496470920 496470974 2.910000e-12 84.2
6 TraesCS6D01G244900 chr6B 96.024 3194 86 14 894 4072 534091960 534095127 0.000000e+00 5156.0
7 TraesCS6D01G244900 chr6B 95.604 455 15 3 4089 4541 534095570 534096021 0.000000e+00 725.0
8 TraesCS6D01G244900 chr6B 82.927 574 59 17 1 571 534091096 534091633 8.840000e-132 481.0
9 TraesCS6D01G244900 chr6B 90.734 259 23 1 588 845 534091700 534091958 1.210000e-90 344.0


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 TraesCS6D01G244900 chr6D 346954007 346958547 4540 True 8386.00 8386 100.00000 1 4541 1 chr6D.!!$R1 4540
1 TraesCS6D01G244900 chr6A 496470036 496475400 5364 False 1324.86 5252 93.25820 1 4541 5 chr6A.!!$F1 4540
2 TraesCS6D01G244900 chr6B 534091096 534096021 4925 False 1676.50 5156 91.32225 1 4541 4 chr6B.!!$F1 4540

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
430 443 0.036732 GGATGTCTGGGTTGCTGTGA 59.963 55.0 0.00 0.0 0.00 3.58 F
592 611 0.460284 GGTCGCTAGGTGTGGATGTG 60.460 60.0 0.00 0.0 0.00 3.21 F
1625 2560 0.744414 ACGAATTGCCGTAGCTGCAT 60.744 50.0 1.02 0.0 41.44 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 3161 0.244721 GCCATGTTGCCTCTGTTTCC 59.755 55.000 0.00 0.00 0.00 3.13 R
2326 3261 9.788815 TCTGAATATATCCAGGGATTTCATAGA 57.211 33.333 6.07 3.35 32.15 1.98 R
3568 4503 1.676635 TTGATGCAGTGCCTCCAGC 60.677 57.895 13.72 0.00 44.14 4.85 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
91 99 2.027007 CCCGGTTGTACTTTGGGATACA 60.027 50.000 0.00 0.00 42.77 2.29
260 268 7.133483 ACTAGGTAGAGGAACAAATATGGACT 58.867 38.462 0.00 0.00 0.00 3.85
389 402 1.689984 TTGCTTGATGTCTGTGCCAA 58.310 45.000 0.00 0.00 0.00 4.52
391 404 2.241160 TGCTTGATGTCTGTGCCAAAT 58.759 42.857 0.00 0.00 0.00 2.32
392 405 2.629137 TGCTTGATGTCTGTGCCAAATT 59.371 40.909 0.00 0.00 0.00 1.82
393 406 3.069872 TGCTTGATGTCTGTGCCAAATTT 59.930 39.130 0.00 0.00 0.00 1.82
394 407 3.676646 GCTTGATGTCTGTGCCAAATTTC 59.323 43.478 0.00 0.00 0.00 2.17
395 408 4.796946 GCTTGATGTCTGTGCCAAATTTCA 60.797 41.667 0.00 0.00 0.00 2.69
396 409 4.933505 TGATGTCTGTGCCAAATTTCAA 57.066 36.364 0.00 0.00 0.00 2.69
397 410 4.873817 TGATGTCTGTGCCAAATTTCAAG 58.126 39.130 0.00 0.00 0.00 3.02
415 428 5.381174 TCAAGTTTCAGAGCATTTGGATG 57.619 39.130 0.00 0.00 36.32 3.51
420 433 2.995283 TCAGAGCATTTGGATGTCTGG 58.005 47.619 13.68 0.00 39.38 3.86
427 440 1.619654 TTTGGATGTCTGGGTTGCTG 58.380 50.000 0.00 0.00 0.00 4.41
429 442 0.250858 TGGATGTCTGGGTTGCTGTG 60.251 55.000 0.00 0.00 0.00 3.66
430 443 0.036732 GGATGTCTGGGTTGCTGTGA 59.963 55.000 0.00 0.00 0.00 3.58
448 464 5.501252 GCTGTGAGCACAAAAGTCAAATTTG 60.501 40.000 12.15 12.15 41.89 2.32
460 476 6.933514 AAGTCAAATTTGGGGTATGTGAAT 57.066 33.333 17.90 0.00 0.00 2.57
481 497 9.030301 GTGAATAAGTTTAATGTTTGTGCACTT 57.970 29.630 19.41 5.94 0.00 3.16
486 502 6.630071 AGTTTAATGTTTGTGCACTTTCTGT 58.370 32.000 19.41 2.21 0.00 3.41
487 503 7.096551 AGTTTAATGTTTGTGCACTTTCTGTT 58.903 30.769 19.41 8.53 0.00 3.16
489 505 7.897575 TTAATGTTTGTGCACTTTCTGTTTT 57.102 28.000 19.41 4.51 0.00 2.43
533 552 3.950397 ACTCCGATGTCCAAATGCTTTA 58.050 40.909 0.00 0.00 0.00 1.85
539 558 6.811170 TCCGATGTCCAAATGCTTTAAAATTC 59.189 34.615 0.00 0.00 0.00 2.17
545 564 4.450419 CCAAATGCTTTAAAATTCGGCACA 59.550 37.500 1.61 0.00 35.72 4.57
555 574 0.531974 ATTCGGCACACACTTCACGT 60.532 50.000 0.00 0.00 0.00 4.49
561 580 1.787155 GCACACACTTCACGTACTCAG 59.213 52.381 0.00 0.00 0.00 3.35
574 593 5.037385 CACGTACTCAGACATCTTACATGG 58.963 45.833 0.00 0.00 0.00 3.66
575 594 4.705507 ACGTACTCAGACATCTTACATGGT 59.294 41.667 0.00 0.00 0.00 3.55
576 595 5.163642 ACGTACTCAGACATCTTACATGGTC 60.164 44.000 0.00 0.00 0.00 4.02
577 596 4.377839 ACTCAGACATCTTACATGGTCG 57.622 45.455 0.00 0.00 35.49 4.79
578 597 3.119291 CTCAGACATCTTACATGGTCGC 58.881 50.000 0.00 0.00 35.49 5.19
579 598 2.760650 TCAGACATCTTACATGGTCGCT 59.239 45.455 0.00 0.00 35.49 4.93
581 600 4.036852 TCAGACATCTTACATGGTCGCTAG 59.963 45.833 0.00 0.00 35.49 3.42
582 601 3.319405 AGACATCTTACATGGTCGCTAGG 59.681 47.826 0.00 0.00 35.49 3.02
584 603 3.181475 ACATCTTACATGGTCGCTAGGTG 60.181 47.826 0.00 0.00 0.00 4.00
585 604 2.453521 TCTTACATGGTCGCTAGGTGT 58.546 47.619 0.00 0.00 0.00 4.16
588 607 0.902984 ACATGGTCGCTAGGTGTGGA 60.903 55.000 0.00 0.00 0.00 4.02
590 609 0.465705 ATGGTCGCTAGGTGTGGATG 59.534 55.000 0.00 0.00 0.00 3.51
592 611 0.460284 GGTCGCTAGGTGTGGATGTG 60.460 60.000 0.00 0.00 0.00 3.21
593 612 1.084370 GTCGCTAGGTGTGGATGTGC 61.084 60.000 0.00 0.00 0.00 4.57
594 613 1.815421 CGCTAGGTGTGGATGTGCC 60.815 63.158 0.00 0.00 37.10 5.01
622 695 6.016777 GGCTCAGAATTGGATATTCGAACAAT 60.017 38.462 0.00 2.73 35.24 2.71
738 1636 2.933906 TCCACAGTTTCGTCTGTTTGAC 59.066 45.455 7.62 0.00 44.92 3.18
768 1666 7.469594 GCAAAATCCATGATATCTGAAGCTTCA 60.470 37.037 26.87 26.87 35.57 3.02
793 1691 3.575399 GCAGAAGTTTTGCTGTGGG 57.425 52.632 10.98 0.00 38.51 4.61
799 1697 0.818040 AGTTTTGCTGTGGGTCGTCC 60.818 55.000 0.00 0.00 0.00 4.79
819 1717 2.544267 CCAAATAAAGATCGACGGAGGC 59.456 50.000 0.00 0.00 0.00 4.70
868 1766 4.677151 GGGGGTCCCAGTCCCAGT 62.677 72.222 10.98 0.00 46.26 4.00
869 1767 3.009714 GGGGTCCCAGTCCCAGTC 61.010 72.222 10.98 0.00 46.26 3.51
870 1768 3.009714 GGGTCCCAGTCCCAGTCC 61.010 72.222 1.78 0.00 44.05 3.85
923 1821 0.750546 TCCTCGGAGATGTACACGGG 60.751 60.000 6.58 0.00 33.89 5.28
924 1822 1.065928 CTCGGAGATGTACACGGGC 59.934 63.158 0.00 0.00 33.89 6.13
926 1824 1.216977 CGGAGATGTACACGGGCAA 59.783 57.895 0.00 0.00 0.00 4.52
927 1825 1.082117 CGGAGATGTACACGGGCAAC 61.082 60.000 0.00 0.00 0.00 4.17
1067 1973 3.984193 CTGCCGCCTTCTTCCCCAG 62.984 68.421 0.00 0.00 0.00 4.45
1143 2049 1.841556 TCTCGCCATATCCCCACCC 60.842 63.158 0.00 0.00 0.00 4.61
1151 2057 1.421646 CATATCCCCACCCAGAGTTCC 59.578 57.143 0.00 0.00 0.00 3.62
1209 2115 1.818785 GGAGTCCGACGACGAGGAT 60.819 63.158 16.89 8.60 44.28 3.24
1212 2118 1.062206 GTCCGACGACGAGGATGAC 59.938 63.158 16.89 3.41 42.66 3.06
1594 2506 0.962356 ATCTGGTTTCTTGCTGCCCG 60.962 55.000 0.00 0.00 0.00 6.13
1623 2558 1.348594 GACGAATTGCCGTAGCTGC 59.651 57.895 0.00 0.00 43.49 5.25
1624 2559 1.358725 GACGAATTGCCGTAGCTGCA 61.359 55.000 1.02 0.00 43.49 4.41
1625 2560 0.744414 ACGAATTGCCGTAGCTGCAT 60.744 50.000 1.02 0.00 41.44 3.96
1626 2561 1.217001 CGAATTGCCGTAGCTGCATA 58.783 50.000 1.02 0.00 38.76 3.14
1627 2562 1.800586 CGAATTGCCGTAGCTGCATAT 59.199 47.619 1.02 0.00 38.76 1.78
1628 2563 2.993220 CGAATTGCCGTAGCTGCATATA 59.007 45.455 1.02 0.00 38.76 0.86
1629 2564 3.181530 CGAATTGCCGTAGCTGCATATAC 60.182 47.826 1.02 0.00 38.76 1.47
1630 2565 2.900716 TTGCCGTAGCTGCATATACA 57.099 45.000 1.02 0.00 38.76 2.29
1631 2566 2.148916 TGCCGTAGCTGCATATACAC 57.851 50.000 1.02 2.03 40.80 2.90
1632 2567 1.060713 GCCGTAGCTGCATATACACG 58.939 55.000 1.02 0.00 35.50 4.49
1633 2568 1.335597 GCCGTAGCTGCATATACACGA 60.336 52.381 1.02 0.00 35.50 4.35
1634 2569 2.671351 GCCGTAGCTGCATATACACGAT 60.671 50.000 1.02 0.00 35.50 3.73
1635 2570 2.917343 CCGTAGCTGCATATACACGATG 59.083 50.000 1.02 0.00 0.00 3.84
1636 2571 2.917343 CGTAGCTGCATATACACGATGG 59.083 50.000 1.02 0.00 0.00 3.51
1637 2572 2.462456 AGCTGCATATACACGATGGG 57.538 50.000 1.02 0.00 0.00 4.00
1638 2573 1.694150 AGCTGCATATACACGATGGGT 59.306 47.619 1.02 0.00 0.00 4.51
1639 2574 2.069273 GCTGCATATACACGATGGGTC 58.931 52.381 0.00 0.00 0.00 4.46
1845 2780 2.567615 GTCCACCTTCCACATACTGACT 59.432 50.000 0.00 0.00 0.00 3.41
2022 2957 1.078567 CCTCAGGCAGGCTGAGTTC 60.079 63.158 38.42 4.08 44.88 3.01
2226 3161 1.705186 TCCAAAGAAGGGAGGGTTCAG 59.295 52.381 0.00 0.00 0.00 3.02
2326 3261 3.326747 GTTTATGCTCGAACTGGTGAGT 58.673 45.455 0.00 0.00 34.67 3.41
2910 3845 3.925379 TCAAGAGCAGCGTGAGATTTTA 58.075 40.909 0.00 0.00 31.27 1.52
3213 4148 3.119245 GGTTATCTCCACGTGTTCTAGCA 60.119 47.826 15.65 0.00 0.00 3.49
3327 4262 0.952497 ACTCCTTGCATGCACAGTCG 60.952 55.000 22.58 14.61 0.00 4.18
3523 4458 6.879458 TGATTCTGATGATGATGCTCATAAGG 59.121 38.462 0.00 0.00 37.20 2.69
3568 4503 2.035632 GGAGTAGGAGATGTCTGGTGG 58.964 57.143 0.00 0.00 0.00 4.61
3668 4603 0.250338 AGTCTCCAAGTGGCGGTTTC 60.250 55.000 0.00 0.00 34.44 2.78
3710 4645 1.138859 GCCAAACTTGCTCACCCTTTT 59.861 47.619 0.00 0.00 0.00 2.27
3876 4814 3.485463 TCGGAAGGAACACAACTTCAT 57.515 42.857 6.73 0.00 43.70 2.57
3877 4815 3.399330 TCGGAAGGAACACAACTTCATC 58.601 45.455 6.73 0.00 43.70 2.92
3878 4816 3.138304 CGGAAGGAACACAACTTCATCA 58.862 45.455 6.73 0.00 43.70 3.07
3879 4817 3.187227 CGGAAGGAACACAACTTCATCAG 59.813 47.826 6.73 0.00 43.70 2.90
3938 4876 7.563888 ACTTTTACTTAGTTGTTCACCTTCC 57.436 36.000 0.00 0.00 0.00 3.46
3941 4879 8.667076 TTTTACTTAGTTGTTCACCTTCCTAC 57.333 34.615 0.00 0.00 0.00 3.18
3943 4881 6.496144 ACTTAGTTGTTCACCTTCCTACTT 57.504 37.500 0.00 0.00 0.00 2.24
3977 4915 4.521256 ACTAACAACATGTTGCCCGTATTT 59.479 37.500 33.23 21.54 41.30 1.40
3978 4916 4.329462 AACAACATGTTGCCCGTATTTT 57.671 36.364 33.23 17.38 44.03 1.82
3979 4917 3.648009 ACAACATGTTGCCCGTATTTTG 58.352 40.909 33.23 10.90 44.03 2.44
3980 4918 3.319405 ACAACATGTTGCCCGTATTTTGA 59.681 39.130 33.23 0.00 44.03 2.69
3982 4920 4.370364 ACATGTTGCCCGTATTTTGATC 57.630 40.909 0.00 0.00 0.00 2.92
3983 4921 4.016444 ACATGTTGCCCGTATTTTGATCT 58.984 39.130 0.00 0.00 0.00 2.75
3984 4922 4.142403 ACATGTTGCCCGTATTTTGATCTG 60.142 41.667 0.00 0.00 0.00 2.90
4027 5020 7.881775 TGATAGATTTGCACACTAGAGACTA 57.118 36.000 0.00 0.00 0.00 2.59
4072 5066 4.151798 GTCGACCACTTACAGTACGTTAC 58.848 47.826 3.51 0.00 0.00 2.50
4345 5777 8.333984 TCCTACGGATTAATCTATGATCAGGTA 58.666 37.037 14.95 0.00 0.00 3.08
4371 5803 6.034898 ACGACAAAGCAAACAAAGAATTTCTG 59.965 34.615 0.00 0.00 35.03 3.02
4399 5833 2.118679 ACAGCCATGACCTATGCTACA 58.881 47.619 0.00 0.00 35.37 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 49 2.619931 TCAGTCCAGGGACAAGAATGA 58.380 47.619 19.92 11.42 46.76 2.57
46 54 2.867109 ACATTCAGTCCAGGGACAAG 57.133 50.000 19.92 11.98 46.76 3.16
49 57 4.020128 GGGATATACATTCAGTCCAGGGAC 60.020 50.000 10.52 10.52 44.86 4.46
119 127 6.704289 ACAACGTGCTAAGTATATCTGGTA 57.296 37.500 0.00 0.00 0.00 3.25
160 168 5.700832 CAGGCAAAAGGGGATTTTTAACTTC 59.299 40.000 0.00 0.00 39.11 3.01
224 232 9.021807 TGTTCCTCTACCTAGTACATATATTGC 57.978 37.037 0.00 0.00 0.00 3.56
260 268 2.046700 CGGGAGCCAAAACGCCTA 60.047 61.111 0.00 0.00 0.00 3.93
370 383 1.689984 TTGGCACAGACATCAAGCAA 58.310 45.000 0.00 0.00 42.39 3.91
389 402 6.819284 TCCAAATGCTCTGAAACTTGAAATT 58.181 32.000 0.00 0.00 0.00 1.82
391 404 5.850557 TCCAAATGCTCTGAAACTTGAAA 57.149 34.783 0.00 0.00 0.00 2.69
392 405 5.302568 ACATCCAAATGCTCTGAAACTTGAA 59.697 36.000 0.00 0.00 36.26 2.69
393 406 4.828939 ACATCCAAATGCTCTGAAACTTGA 59.171 37.500 0.00 0.00 36.26 3.02
394 407 5.048224 AGACATCCAAATGCTCTGAAACTTG 60.048 40.000 0.00 0.00 36.26 3.16
395 408 5.048224 CAGACATCCAAATGCTCTGAAACTT 60.048 40.000 10.09 0.00 40.11 2.66
396 409 4.458295 CAGACATCCAAATGCTCTGAAACT 59.542 41.667 10.09 0.00 40.11 2.66
397 410 4.380233 CCAGACATCCAAATGCTCTGAAAC 60.380 45.833 14.23 0.00 40.11 2.78
415 428 3.660621 GCTCACAGCAACCCAGAC 58.339 61.111 0.00 0.00 41.89 3.51
427 440 4.270808 CCCAAATTTGACTTTTGTGCTCAC 59.729 41.667 19.86 0.00 33.23 3.51
429 442 3.809279 CCCCAAATTTGACTTTTGTGCTC 59.191 43.478 19.86 0.00 33.23 4.26
430 443 3.199727 ACCCCAAATTTGACTTTTGTGCT 59.800 39.130 19.86 0.00 33.23 4.40
434 447 6.520272 TCACATACCCCAAATTTGACTTTTG 58.480 36.000 19.86 12.76 34.55 2.44
436 449 6.739331 TTCACATACCCCAAATTTGACTTT 57.261 33.333 19.86 3.61 0.00 2.66
439 452 7.836842 ACTTATTCACATACCCCAAATTTGAC 58.163 34.615 19.86 0.00 0.00 3.18
448 464 9.581099 CAAACATTAAACTTATTCACATACCCC 57.419 33.333 0.00 0.00 0.00 4.95
460 476 8.247562 ACAGAAAGTGCACAAACATTAAACTTA 58.752 29.630 21.04 0.00 0.00 2.24
502 521 1.001815 GACATCGGAGTAGCTCTCAGC 60.002 57.143 13.06 0.00 44.40 4.26
516 535 6.237542 CCGAATTTTAAAGCATTTGGACATCG 60.238 38.462 11.36 0.00 39.63 3.84
533 552 2.540769 CGTGAAGTGTGTGCCGAATTTT 60.541 45.455 0.00 0.00 0.00 1.82
539 558 0.596600 AGTACGTGAAGTGTGTGCCG 60.597 55.000 0.00 0.00 0.00 5.69
545 564 3.821600 AGATGTCTGAGTACGTGAAGTGT 59.178 43.478 0.00 0.00 0.00 3.55
555 574 4.202020 GCGACCATGTAAGATGTCTGAGTA 60.202 45.833 0.00 0.00 0.00 2.59
561 580 3.068307 ACCTAGCGACCATGTAAGATGTC 59.932 47.826 0.00 0.00 0.00 3.06
574 593 1.084370 GCACATCCACACCTAGCGAC 61.084 60.000 0.00 0.00 0.00 5.19
575 594 1.218047 GCACATCCACACCTAGCGA 59.782 57.895 0.00 0.00 0.00 4.93
576 595 1.815421 GGCACATCCACACCTAGCG 60.815 63.158 0.00 0.00 34.01 4.26
577 596 0.745845 CAGGCACATCCACACCTAGC 60.746 60.000 0.00 0.00 37.29 3.42
578 597 0.107508 CCAGGCACATCCACACCTAG 60.108 60.000 0.00 0.00 37.29 3.02
579 598 1.561769 CCCAGGCACATCCACACCTA 61.562 60.000 0.00 0.00 37.29 3.08
581 600 2.361610 CCCAGGCACATCCACACC 60.362 66.667 0.00 0.00 37.29 4.16
582 601 3.064324 GCCCAGGCACATCCACAC 61.064 66.667 3.12 0.00 41.49 3.82
584 603 2.439156 GAGCCCAGGCACATCCAC 60.439 66.667 12.03 0.00 44.88 4.02
585 604 2.934932 TGAGCCCAGGCACATCCA 60.935 61.111 12.03 0.00 44.88 3.41
588 607 0.333993 AATTCTGAGCCCAGGCACAT 59.666 50.000 12.03 0.00 44.88 3.21
590 609 1.318158 CCAATTCTGAGCCCAGGCAC 61.318 60.000 12.03 5.16 44.88 5.01
592 611 0.106318 ATCCAATTCTGAGCCCAGGC 60.106 55.000 0.00 0.00 40.76 4.85
593 612 3.803186 ATATCCAATTCTGAGCCCAGG 57.197 47.619 0.00 0.00 40.76 4.45
594 613 3.750130 CGAATATCCAATTCTGAGCCCAG 59.250 47.826 0.00 0.00 41.74 4.45
638 711 6.373216 CCCAAACGTCTTACATTTAGGAATGA 59.627 38.462 6.17 0.00 44.37 2.57
650 723 6.673154 ATATAAACTGCCCAAACGTCTTAC 57.327 37.500 0.00 0.00 0.00 2.34
738 1636 4.999311 TCAGATATCATGGATTTTGCCTCG 59.001 41.667 5.32 0.00 0.00 4.63
799 1697 2.218759 CGCCTCCGTCGATCTTTATTTG 59.781 50.000 0.00 0.00 0.00 2.32
819 1717 1.450312 GGGGCAGTCCAAGTGATCG 60.450 63.158 0.00 0.00 37.22 3.69
923 1821 4.814294 ATCGTCTCCGCGGGTTGC 62.814 66.667 27.83 12.33 41.47 4.17
924 1822 2.885644 CATCGTCTCCGCGGGTTG 60.886 66.667 27.83 16.03 0.00 3.77
926 1824 3.518998 CTCATCGTCTCCGCGGGT 61.519 66.667 27.83 1.53 0.00 5.28
927 1825 4.271816 CCTCATCGTCTCCGCGGG 62.272 72.222 27.83 16.54 0.00 6.13
1143 2049 1.089920 CCGCTGGAATTGGAACTCTG 58.910 55.000 0.00 0.00 0.00 3.35
1151 2057 3.039202 GACGCCACCGCTGGAATTG 62.039 63.158 0.00 0.00 40.55 2.32
1209 2115 1.005275 AGACTCGTCGTCCTCGTCA 60.005 57.895 0.00 0.00 43.91 4.35
1212 2118 2.751913 CCCAGACTCGTCGTCCTCG 61.752 68.421 0.00 0.00 43.91 4.63
1594 2506 2.560896 GCAATTCGTCGAACAGTTCAC 58.439 47.619 10.39 9.35 0.00 3.18
1632 2567 4.161189 ACATCTATGATCCATCGACCCATC 59.839 45.833 0.00 0.00 0.00 3.51
1633 2568 4.099633 ACATCTATGATCCATCGACCCAT 58.900 43.478 0.00 0.00 0.00 4.00
1634 2569 3.510459 ACATCTATGATCCATCGACCCA 58.490 45.455 0.00 0.00 0.00 4.51
1635 2570 4.707448 AGTACATCTATGATCCATCGACCC 59.293 45.833 0.00 0.00 0.00 4.46
1636 2571 5.447954 CGAGTACATCTATGATCCATCGACC 60.448 48.000 0.00 0.00 0.00 4.79
1637 2572 5.122554 ACGAGTACATCTATGATCCATCGAC 59.877 44.000 0.00 0.00 0.00 4.20
1638 2573 5.246307 ACGAGTACATCTATGATCCATCGA 58.754 41.667 0.00 0.00 0.00 3.59
1639 2574 5.553290 ACGAGTACATCTATGATCCATCG 57.447 43.478 0.00 0.00 0.00 3.84
1640 2575 6.096036 CCAACGAGTACATCTATGATCCATC 58.904 44.000 0.00 0.00 0.00 3.51
1935 2870 1.598130 GTTGTGAAGGCTGAGGCGT 60.598 57.895 0.00 0.00 39.81 5.68
1998 2933 2.113986 GCCTGCCTGAGGTTGTGT 59.886 61.111 0.00 0.00 44.97 3.72
2226 3161 0.244721 GCCATGTTGCCTCTGTTTCC 59.755 55.000 0.00 0.00 0.00 3.13
2326 3261 9.788815 TCTGAATATATCCAGGGATTTCATAGA 57.211 33.333 6.07 3.35 32.15 1.98
2910 3845 2.250924 CCTCCCAGAAGCAAACCAATT 58.749 47.619 0.00 0.00 0.00 2.32
3213 4148 4.613437 AGCCTCCAAACATGAACCAATAT 58.387 39.130 0.00 0.00 0.00 1.28
3327 4262 7.818446 CCTTTCCTCTTCACTTTACTAGGTAAC 59.182 40.741 0.00 0.00 0.00 2.50
3523 4458 5.734720 TGGTATTCACTCTTCACTTCCATC 58.265 41.667 0.00 0.00 0.00 3.51
3568 4503 1.676635 TTGATGCAGTGCCTCCAGC 60.677 57.895 13.72 0.00 44.14 4.85
3612 4547 6.722129 ACCACCAAACCACTAAAATATAGCAA 59.278 34.615 0.00 0.00 0.00 3.91
3668 4603 4.857037 GCAGAAAATAACCTTTACAAGCGG 59.143 41.667 0.00 0.00 0.00 5.52
3848 4786 2.076863 GTGTTCCTTCCGATGTTCAGG 58.923 52.381 0.00 0.00 0.00 3.86
3876 4814 4.100653 CCTGATCAATCTGTAGGCTTCTGA 59.899 45.833 0.00 0.00 0.00 3.27
3877 4815 4.378774 CCTGATCAATCTGTAGGCTTCTG 58.621 47.826 0.00 0.00 0.00 3.02
3878 4816 3.390639 CCCTGATCAATCTGTAGGCTTCT 59.609 47.826 0.00 0.00 0.00 2.85
3879 4817 3.135530 ACCCTGATCAATCTGTAGGCTTC 59.864 47.826 0.00 0.00 0.00 3.86
3924 4862 3.974642 AGGAAGTAGGAAGGTGAACAACT 59.025 43.478 0.00 0.00 0.00 3.16
3941 4879 9.924650 AACATGTTGTTAGTACTTACTAGGAAG 57.075 33.333 13.52 13.52 39.09 3.46
3943 4881 7.816031 GCAACATGTTGTTAGTACTTACTAGGA 59.184 37.037 33.01 0.00 38.77 2.94
4072 5066 5.472148 ACAGGTGATTAAATGCACAACATG 58.528 37.500 0.00 0.00 39.60 3.21
4231 5657 2.990967 AAATGCCCGGTGTGCCTG 60.991 61.111 0.00 0.00 0.00 4.85
4345 5777 6.589907 AGAAATTCTTTGTTTGCTTTGTCGTT 59.410 30.769 0.00 0.00 0.00 3.85
4387 5821 9.341899 CAAAATTTGTTACTTGTAGCATAGGTC 57.658 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.