Multiple sequence alignment - TraesCS1D01G381900

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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 TraesCS1D01G381900 chr1D 100.000 2831 0 0 1 2831 457071167 457073997 0.000000e+00 5228.0
1 TraesCS1D01G381900 chr1A 88.041 1455 126 16 561 1999 549709519 549710941 0.000000e+00 1679.0
2 TraesCS1D01G381900 chr1A 96.782 839 24 2 1993 2829 549711201 549712038 0.000000e+00 1397.0
3 TraesCS1D01G381900 chr1A 84.921 126 16 2 2049 2172 13489089 13489213 1.060000e-24 124.0
4 TraesCS1D01G381900 chr1A 73.469 343 51 19 1525 1853 293199082 293199398 3.000000e-15 93.5
5 TraesCS1D01G381900 chr1B 87.869 1187 105 17 561 1743 626685421 626686572 0.000000e+00 1358.0
6 TraesCS1D01G381900 chr1B 93.093 637 38 4 2195 2829 626687242 626687874 0.000000e+00 928.0
7 TraesCS1D01G381900 chr1B 88.933 253 17 5 1949 2190 626686702 626686954 4.580000e-78 302.0
8 TraesCS1D01G381900 chr6D 95.543 516 20 2 1 513 468777633 468777118 0.000000e+00 822.0
9 TraesCS1D01G381900 chr6D 92.233 515 38 1 1 513 50734864 50735378 0.000000e+00 728.0
10 TraesCS1D01G381900 chr6D 91.860 516 39 1 1 513 456323089 456322574 0.000000e+00 717.0
11 TraesCS1D01G381900 chr3D 92.427 515 37 1 1 513 1348499 1349013 0.000000e+00 734.0
12 TraesCS1D01G381900 chr3D 76.327 245 38 11 2514 2745 363867123 363867360 2.310000e-21 113.0
13 TraesCS1D01G381900 chr4D 92.233 515 36 2 1 513 62735626 62736138 0.000000e+00 726.0
14 TraesCS1D01G381900 chr4D 76.094 297 50 11 1591 1869 170625532 170625239 4.920000e-28 135.0
15 TraesCS1D01G381900 chr4D 73.864 352 54 14 1532 1869 170692678 170692351 3.860000e-19 106.0
16 TraesCS1D01G381900 chr2D 91.908 519 42 0 1 519 592034267 592033749 0.000000e+00 726.0
17 TraesCS1D01G381900 chr3A 92.023 514 39 1 1 512 130847300 130847813 0.000000e+00 721.0
18 TraesCS1D01G381900 chr3A 91.845 515 40 1 1 513 57209195 57209709 0.000000e+00 717.0
19 TraesCS1D01G381900 chr3A 84.375 128 17 2 2049 2174 639632616 639632490 3.830000e-24 122.0
20 TraesCS1D01G381900 chr3A 76.000 275 41 16 1531 1784 639643364 639643094 4.950000e-23 119.0
21 TraesCS1D01G381900 chr3A 76.000 250 39 11 2509 2745 485010234 485010475 2.980000e-20 110.0
22 TraesCS1D01G381900 chr7A 91.473 516 39 4 1 513 707978716 707978203 0.000000e+00 704.0
23 TraesCS1D01G381900 chr7A 77.778 315 39 18 1531 1817 42736609 42736920 6.270000e-37 165.0
24 TraesCS1D01G381900 chr7A 77.592 299 45 10 1592 1869 139137036 139136739 8.120000e-36 161.0
25 TraesCS1D01G381900 chr7A 85.156 128 16 2 2049 2174 42737254 42737380 8.230000e-26 128.0
26 TraesCS1D01G381900 chr7B 78.475 223 29 7 1954 2174 572508742 572508947 8.230000e-26 128.0
27 TraesCS1D01G381900 chr6B 82.031 128 20 2 2049 2174 45731640 45731766 3.860000e-19 106.0
28 TraesCS1D01G381900 chr5B 82.031 128 20 2 2049 2174 141161358 141161484 3.860000e-19 106.0
29 TraesCS1D01G381900 chr4B 82.031 128 20 2 2049 2174 167385246 167385372 3.860000e-19 106.0
30 TraesCS1D01G381900 chr2A 97.826 46 1 0 1589 1634 148841760 148841805 2.340000e-11 80.5


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 TraesCS1D01G381900 chr1D 457071167 457073997 2830 False 5228.000000 5228 100.0000 1 2831 1 chr1D.!!$F1 2830
1 TraesCS1D01G381900 chr1A 549709519 549712038 2519 False 1538.000000 1679 92.4115 561 2829 2 chr1A.!!$F3 2268
2 TraesCS1D01G381900 chr1B 626685421 626687874 2453 False 862.666667 1358 89.9650 561 2829 3 chr1B.!!$F1 2268
3 TraesCS1D01G381900 chr6D 468777118 468777633 515 True 822.000000 822 95.5430 1 513 1 chr6D.!!$R2 512
4 TraesCS1D01G381900 chr6D 50734864 50735378 514 False 728.000000 728 92.2330 1 513 1 chr6D.!!$F1 512
5 TraesCS1D01G381900 chr6D 456322574 456323089 515 True 717.000000 717 91.8600 1 513 1 chr6D.!!$R1 512
6 TraesCS1D01G381900 chr3D 1348499 1349013 514 False 734.000000 734 92.4270 1 513 1 chr3D.!!$F1 512
7 TraesCS1D01G381900 chr4D 62735626 62736138 512 False 726.000000 726 92.2330 1 513 1 chr4D.!!$F1 512
8 TraesCS1D01G381900 chr2D 592033749 592034267 518 True 726.000000 726 91.9080 1 519 1 chr2D.!!$R1 518
9 TraesCS1D01G381900 chr3A 130847300 130847813 513 False 721.000000 721 92.0230 1 512 1 chr3A.!!$F2 511
10 TraesCS1D01G381900 chr3A 57209195 57209709 514 False 717.000000 717 91.8450 1 513 1 chr3A.!!$F1 512
11 TraesCS1D01G381900 chr7A 707978203 707978716 513 True 704.000000 704 91.4730 1 513 1 chr7A.!!$R2 512

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
556 563 0.039256 GGTGCACGTACGTAAGGTGA 60.039 55.0 22.34 11.67 44.95 4.02 F
1249 1279 0.650512 CGCCAATAACACTACGCTGG 59.349 55.0 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1421 0.039437 CCTGTCTGTGTACGCGAACT 60.039 55.0 15.93 0.0 0.00 3.01 R
2772 3367 0.666274 TGTTGTAGAGCCGCTTCACG 60.666 55.0 0.00 0.0 43.15 4.35 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
51 52 2.035940 AACTCGTCGCCTCCTCCT 59.964 61.111 0.00 0.00 0.00 3.69
391 397 1.084289 GCGATCAAACGGGCTAAACT 58.916 50.000 0.00 0.00 0.00 2.66
434 440 4.091453 ACGACTTAAATGATTTTGCGGG 57.909 40.909 0.00 0.00 0.00 6.13
471 478 5.702209 GGATTAACGAGTTGGTGGTTTTCTA 59.298 40.000 0.00 0.00 0.00 2.10
512 519 3.068024 TGGTGGTTTCTTGCAATTGACTC 59.932 43.478 10.34 0.00 0.00 3.36
513 520 3.300009 GTGGTTTCTTGCAATTGACTCG 58.700 45.455 10.34 0.00 0.00 4.18
514 521 3.003275 GTGGTTTCTTGCAATTGACTCGA 59.997 43.478 10.34 0.00 0.00 4.04
515 522 3.003275 TGGTTTCTTGCAATTGACTCGAC 59.997 43.478 10.34 0.00 0.00 4.20
516 523 3.555518 GTTTCTTGCAATTGACTCGACC 58.444 45.455 10.34 0.00 0.00 4.79
517 524 1.808411 TCTTGCAATTGACTCGACCC 58.192 50.000 10.34 0.00 0.00 4.46
518 525 0.804989 CTTGCAATTGACTCGACCCC 59.195 55.000 10.34 0.00 0.00 4.95
519 526 0.608035 TTGCAATTGACTCGACCCCC 60.608 55.000 10.34 0.00 0.00 5.40
520 527 2.106683 GCAATTGACTCGACCCCCG 61.107 63.158 10.34 0.00 40.25 5.73
521 528 1.449601 CAATTGACTCGACCCCCGG 60.450 63.158 0.00 0.00 39.14 5.73
522 529 1.916777 AATTGACTCGACCCCCGGT 60.917 57.895 0.00 0.00 39.44 5.28
531 538 2.438795 ACCCCCGGTCATTGTTGG 59.561 61.111 0.00 0.00 0.00 3.77
532 539 2.438795 CCCCCGGTCATTGTTGGT 59.561 61.111 0.00 0.00 0.00 3.67
533 540 1.976474 CCCCCGGTCATTGTTGGTG 60.976 63.158 0.00 0.00 0.00 4.17
534 541 1.976474 CCCCGGTCATTGTTGGTGG 60.976 63.158 0.00 0.00 0.00 4.61
535 542 1.976474 CCCGGTCATTGTTGGTGGG 60.976 63.158 0.00 0.00 0.00 4.61
536 543 2.635443 CCGGTCATTGTTGGTGGGC 61.635 63.158 0.00 0.00 0.00 5.36
537 544 2.961768 GGTCATTGTTGGTGGGCG 59.038 61.111 0.00 0.00 0.00 6.13
538 545 2.635443 GGTCATTGTTGGTGGGCGG 61.635 63.158 0.00 0.00 0.00 6.13
539 546 1.901464 GTCATTGTTGGTGGGCGGT 60.901 57.895 0.00 0.00 0.00 5.68
540 547 1.900981 TCATTGTTGGTGGGCGGTG 60.901 57.895 0.00 0.00 0.00 4.94
541 548 3.302344 ATTGTTGGTGGGCGGTGC 61.302 61.111 0.00 0.00 0.00 5.01
542 549 4.822628 TTGTTGGTGGGCGGTGCA 62.823 61.111 0.00 0.00 0.00 4.57
550 557 4.418401 GGGCGGTGCACGTACGTA 62.418 66.667 22.34 3.16 46.52 3.57
551 558 2.430582 GGCGGTGCACGTACGTAA 60.431 61.111 22.34 9.85 46.52 3.18
552 559 2.438954 GGCGGTGCACGTACGTAAG 61.439 63.158 22.34 11.14 46.52 2.34
553 560 2.438954 GCGGTGCACGTACGTAAGG 61.439 63.158 22.34 10.34 46.52 2.69
554 561 1.081242 CGGTGCACGTACGTAAGGT 60.081 57.895 22.34 4.19 39.07 3.50
555 562 1.339235 CGGTGCACGTACGTAAGGTG 61.339 60.000 22.34 18.72 44.94 4.00
556 563 0.039256 GGTGCACGTACGTAAGGTGA 60.039 55.000 22.34 11.67 44.95 4.02
557 564 1.602668 GGTGCACGTACGTAAGGTGAA 60.603 52.381 22.34 15.61 44.95 3.18
558 565 1.453148 GTGCACGTACGTAAGGTGAAC 59.547 52.381 22.34 21.34 44.95 3.18
559 566 1.337703 TGCACGTACGTAAGGTGAACT 59.662 47.619 22.34 0.00 44.95 3.01
572 579 3.041940 GAACTGTGGCCGTCACCG 61.042 66.667 0.00 0.00 45.48 4.94
590 597 2.977580 ACCGGTTTCTTTCCCTTCTAGT 59.022 45.455 0.00 0.00 0.00 2.57
591 598 3.007723 ACCGGTTTCTTTCCCTTCTAGTC 59.992 47.826 0.00 0.00 0.00 2.59
592 599 3.261137 CCGGTTTCTTTCCCTTCTAGTCT 59.739 47.826 0.00 0.00 0.00 3.24
593 600 4.465305 CCGGTTTCTTTCCCTTCTAGTCTA 59.535 45.833 0.00 0.00 0.00 2.59
594 601 5.394333 CCGGTTTCTTTCCCTTCTAGTCTAG 60.394 48.000 0.00 0.00 0.00 2.43
617 632 2.964925 GTCTTGTCGCGTGCCACA 60.965 61.111 5.77 0.00 0.00 4.17
622 637 4.664677 GTCGCGTGCCACAGGACT 62.665 66.667 5.77 0.00 0.00 3.85
706 721 3.062909 CGAAACGTTTGACTTCAACCTCA 59.937 43.478 20.10 0.00 35.28 3.86
777 792 1.888638 CCGGGCCCGTAAAATACCG 60.889 63.158 40.52 19.70 40.89 4.02
800 815 2.203640 AGCTGACTCCCGACACCA 60.204 61.111 0.00 0.00 0.00 4.17
834 849 5.305902 TGTTTCCAGAACACCAGTCACTATA 59.694 40.000 0.00 0.00 0.00 1.31
838 853 4.462834 CCAGAACACCAGTCACTATACTCA 59.537 45.833 0.00 0.00 0.00 3.41
858 873 2.266055 CGTCCTCCCTTGACCTGC 59.734 66.667 0.00 0.00 0.00 4.85
885 900 1.639298 GACCATGACCGTTGCAGAGC 61.639 60.000 0.00 0.00 0.00 4.09
938 954 2.224621 ACAAACTCTGCTGGCACATACT 60.225 45.455 0.00 0.00 38.20 2.12
941 957 2.430465 ACTCTGCTGGCACATACTTTG 58.570 47.619 0.00 0.00 38.20 2.77
972 1002 2.682856 ACACACATTGCTCGTCTTGTTT 59.317 40.909 0.00 0.00 0.00 2.83
988 1018 1.444895 TTTCGTCTAGCGCGGGAAC 60.445 57.895 8.83 0.00 41.07 3.62
1003 1033 1.892209 GGAACCACTCGACCAAATGT 58.108 50.000 0.00 0.00 0.00 2.71
1010 1040 1.346395 ACTCGACCAAATGTGTAGCCA 59.654 47.619 0.00 0.00 0.00 4.75
1041 1071 3.764466 CTCCTCGTCGCCCTGCTT 61.764 66.667 0.00 0.00 0.00 3.91
1141 1171 3.849951 CGCCCTATCAGTGCGGGT 61.850 66.667 11.92 0.00 44.29 5.28
1167 1197 1.670674 GCGTTCGATGTCAACTACCCA 60.671 52.381 0.00 0.00 0.00 4.51
1212 1242 1.762858 GGACTACTGCTCCTCCCCC 60.763 68.421 0.00 0.00 0.00 5.40
1215 1245 4.475444 TACTGCTCCTCCCCCGGG 62.475 72.222 15.80 15.80 0.00 5.73
1249 1279 0.650512 CGCCAATAACACTACGCTGG 59.349 55.000 0.00 0.00 0.00 4.85
1250 1280 1.737696 CGCCAATAACACTACGCTGGA 60.738 52.381 0.00 0.00 0.00 3.86
1251 1281 2.352388 GCCAATAACACTACGCTGGAA 58.648 47.619 0.00 0.00 0.00 3.53
1261 1291 3.804325 CACTACGCTGGAAATCTACATGG 59.196 47.826 0.00 0.00 0.00 3.66
1263 1293 3.845781 ACGCTGGAAATCTACATGGAT 57.154 42.857 0.00 0.00 0.00 3.41
1275 1305 3.873812 ATGGATTCCGGCGGGTCC 61.874 66.667 31.35 31.35 33.83 4.46
1291 1321 2.742372 CCTTCCAAGTCACGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
1404 1434 2.429571 GCCGAGTTCGCGTACACA 60.430 61.111 18.30 0.00 38.18 3.72
1408 1438 0.385098 CGAGTTCGCGTACACAGACA 60.385 55.000 18.30 0.00 0.00 3.41
1425 1455 2.995574 AGGGACCGGTTCCTGACG 60.996 66.667 34.84 0.00 45.09 4.35
1449 1479 3.279116 GTGAACTGCACCAGCGCA 61.279 61.111 11.47 0.00 46.23 6.09
1464 1494 4.430423 GCAAGCTCGTCGTTGCCG 62.430 66.667 7.60 2.89 42.73 5.69
1495 1525 4.680237 CCTTCGCCTGTGTCGCCA 62.680 66.667 0.00 0.00 0.00 5.69
1745 1775 2.126463 GCACGACAGTAGAGCGCA 60.126 61.111 11.47 0.00 0.00 6.09
1761 1791 1.372997 GCAGGACGATCACACGTGT 60.373 57.895 17.22 17.22 46.52 4.49
1823 1853 1.491754 AGTTTCAGGTACCCCGTGTTT 59.508 47.619 8.74 0.00 35.12 2.83
1824 1854 1.605232 GTTTCAGGTACCCCGTGTTTG 59.395 52.381 8.74 0.00 35.12 2.93
1825 1855 1.129917 TTCAGGTACCCCGTGTTTGA 58.870 50.000 8.74 0.38 35.12 2.69
1826 1856 1.354101 TCAGGTACCCCGTGTTTGAT 58.646 50.000 8.74 0.00 35.12 2.57
1827 1857 1.276989 TCAGGTACCCCGTGTTTGATC 59.723 52.381 8.74 0.00 35.12 2.92
1828 1858 1.278127 CAGGTACCCCGTGTTTGATCT 59.722 52.381 8.74 0.00 35.12 2.75
1830 1860 1.276989 GGTACCCCGTGTTTGATCTGA 59.723 52.381 0.00 0.00 0.00 3.27
1840 1870 5.230942 CGTGTTTGATCTGAGGAGTAACTT 58.769 41.667 0.00 0.00 0.00 2.66
1854 1884 4.151867 GGAGTAACTTGTTGGTCAACGATC 59.848 45.833 8.98 2.33 43.94 3.69
1858 1888 4.073293 ACTTGTTGGTCAACGATCTTCT 57.927 40.909 8.98 0.00 43.94 2.85
1943 1976 3.120477 TGGTTTACGATTACTTGCGCAAG 60.120 43.478 40.80 40.80 43.79 4.01
1958 1991 1.606668 CGCAAGTCCAAAGCAACCTTA 59.393 47.619 0.00 0.00 0.00 2.69
1984 2017 7.961351 AGATGTCCTAATTCCTGACTAATCTG 58.039 38.462 0.00 0.00 0.00 2.90
2032 2339 0.109272 TCGACGCTGACACTTCATCC 60.109 55.000 0.00 0.00 0.00 3.51
2318 2911 4.279169 TCTTGATTTTGCAGGACCAAAGAG 59.721 41.667 0.00 0.00 36.21 2.85
2626 3221 3.695606 GCAGCGACCTGGAGTCCA 61.696 66.667 12.40 12.40 43.08 4.02
2798 3393 1.626654 CGGCTCTACAACAACGGCTG 61.627 60.000 0.00 0.00 0.00 4.85
2829 3424 2.035442 GCAGTTCCTGAACGAGGCC 61.035 63.158 0.00 0.00 45.50 5.19
2830 3425 1.738099 CAGTTCCTGAACGAGGCCG 60.738 63.158 0.00 0.00 45.50 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.035940 AAGGAGGAGGCGACGAGT 59.964 61.111 0.00 0.00 0.00 4.18
51 52 2.646175 CGGCGAAGAGGGTGGAGAA 61.646 63.158 0.00 0.00 0.00 2.87
111 115 2.126071 CGATGTGGAGGACGCGTT 60.126 61.111 15.53 0.00 0.00 4.84
154 158 2.913765 CGGGGTGTGCGCATTTTCA 61.914 57.895 15.91 3.18 0.00 2.69
391 397 1.810151 GCAAAAAGCACTGATCGGGTA 59.190 47.619 6.47 0.00 44.79 3.69
514 521 2.438795 CCAACAATGACCGGGGGT 59.561 61.111 6.32 0.00 39.44 4.95
515 522 1.976474 CACCAACAATGACCGGGGG 60.976 63.158 6.32 0.00 0.00 5.40
516 523 1.976474 CCACCAACAATGACCGGGG 60.976 63.158 6.32 0.00 0.00 5.73
517 524 1.976474 CCCACCAACAATGACCGGG 60.976 63.158 6.32 0.00 0.00 5.73
518 525 2.635443 GCCCACCAACAATGACCGG 61.635 63.158 0.00 0.00 0.00 5.28
519 526 2.961768 GCCCACCAACAATGACCG 59.038 61.111 0.00 0.00 0.00 4.79
520 527 2.635443 CCGCCCACCAACAATGACC 61.635 63.158 0.00 0.00 0.00 4.02
521 528 1.901464 ACCGCCCACCAACAATGAC 60.901 57.895 0.00 0.00 0.00 3.06
522 529 1.900981 CACCGCCCACCAACAATGA 60.901 57.895 0.00 0.00 0.00 2.57
523 530 2.650196 CACCGCCCACCAACAATG 59.350 61.111 0.00 0.00 0.00 2.82
524 531 3.302344 GCACCGCCCACCAACAAT 61.302 61.111 0.00 0.00 0.00 2.71
525 532 4.822628 TGCACCGCCCACCAACAA 62.823 61.111 0.00 0.00 0.00 2.83
533 540 3.912820 TTACGTACGTGCACCGCCC 62.913 63.158 30.25 0.00 41.42 6.13
534 541 2.430582 TTACGTACGTGCACCGCC 60.431 61.111 30.25 0.00 41.42 6.13
535 542 2.438954 CCTTACGTACGTGCACCGC 61.439 63.158 30.25 0.32 41.42 5.68
536 543 1.081242 ACCTTACGTACGTGCACCG 60.081 57.895 30.25 11.88 44.03 4.94
537 544 0.039256 TCACCTTACGTACGTGCACC 60.039 55.000 30.25 0.00 0.00 5.01
538 545 1.453148 GTTCACCTTACGTACGTGCAC 59.547 52.381 30.25 6.82 0.00 4.57
539 546 1.337703 AGTTCACCTTACGTACGTGCA 59.662 47.619 30.25 15.70 0.00 4.57
540 547 1.717645 CAGTTCACCTTACGTACGTGC 59.282 52.381 30.25 9.84 0.00 5.34
541 548 2.722629 CACAGTTCACCTTACGTACGTG 59.277 50.000 30.25 16.37 0.00 4.49
542 549 2.287788 CCACAGTTCACCTTACGTACGT 60.288 50.000 25.98 25.98 0.00 3.57
543 550 2.322161 CCACAGTTCACCTTACGTACG 58.678 52.381 15.01 15.01 0.00 3.67
544 551 2.064014 GCCACAGTTCACCTTACGTAC 58.936 52.381 0.00 0.00 0.00 3.67
545 552 1.001181 GGCCACAGTTCACCTTACGTA 59.999 52.381 0.00 0.00 0.00 3.57
546 553 0.250166 GGCCACAGTTCACCTTACGT 60.250 55.000 0.00 0.00 0.00 3.57
547 554 1.289109 CGGCCACAGTTCACCTTACG 61.289 60.000 2.24 0.00 0.00 3.18
548 555 0.250166 ACGGCCACAGTTCACCTTAC 60.250 55.000 2.24 0.00 0.00 2.34
549 556 0.034337 GACGGCCACAGTTCACCTTA 59.966 55.000 2.24 0.00 0.00 2.69
550 557 1.227853 GACGGCCACAGTTCACCTT 60.228 57.895 2.24 0.00 0.00 3.50
551 558 2.426023 GACGGCCACAGTTCACCT 59.574 61.111 2.24 0.00 0.00 4.00
552 559 2.110213 TGACGGCCACAGTTCACC 59.890 61.111 2.24 0.00 0.00 4.02
553 560 3.330275 GTGACGGCCACAGTTCAC 58.670 61.111 2.24 3.06 45.03 3.18
572 579 6.351202 GGTCTAGACTAGAAGGGAAAGAAACC 60.351 46.154 21.88 3.66 36.40 3.27
590 597 1.174783 GCGACAAGACTGGGTCTAGA 58.825 55.000 0.41 0.00 42.59 2.43
591 598 0.179161 CGCGACAAGACTGGGTCTAG 60.179 60.000 0.00 0.00 42.59 2.43
592 599 0.892358 ACGCGACAAGACTGGGTCTA 60.892 55.000 15.93 0.00 42.59 2.59
593 600 2.201022 ACGCGACAAGACTGGGTCT 61.201 57.895 15.93 0.00 45.64 3.85
594 601 2.022129 CACGCGACAAGACTGGGTC 61.022 63.158 15.93 0.00 0.00 4.46
617 632 3.427233 CGTCGGAATCGAGTTTTAGTCCT 60.427 47.826 0.00 0.00 46.91 3.85
622 637 1.545582 ACCCGTCGGAATCGAGTTTTA 59.454 47.619 14.39 0.00 46.91 1.52
675 690 2.973316 AAACGTTTCGGGCGCATCC 61.973 57.895 10.83 0.00 0.00 3.51
706 721 2.579860 AGAGGAAATTCATGGTGGAGCT 59.420 45.455 0.00 0.00 0.00 4.09
800 815 0.834612 TCTGGAAACAAGGACGTGGT 59.165 50.000 0.00 0.00 42.06 4.16
834 849 2.120718 AAGGGAGGACGGCTGAGT 59.879 61.111 0.00 0.00 0.00 3.41
838 853 3.003763 GGTCAAGGGAGGACGGCT 61.004 66.667 0.00 0.00 36.12 5.52
858 873 1.451927 CGGTCATGGTCCATGGTGG 60.452 63.158 28.01 15.05 41.66 4.61
885 900 2.164827 TGCTTAAGACAGGCATGCATTG 59.835 45.455 21.36 18.82 0.00 2.82
938 954 2.730626 GTGTGTGCACAAACGCAAA 58.269 47.368 23.83 0.00 45.14 3.68
988 1018 1.732259 GCTACACATTTGGTCGAGTGG 59.268 52.381 5.38 0.00 36.35 4.00
1003 1033 4.615901 CACGGAATGCTGGCTACA 57.384 55.556 0.00 0.00 0.00 2.74
1036 1066 1.153939 CCGACGAGAGGACAAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
1232 1262 4.876107 AGATTTCCAGCGTAGTGTTATTGG 59.124 41.667 0.00 0.00 0.00 3.16
1233 1263 6.533723 TGTAGATTTCCAGCGTAGTGTTATTG 59.466 38.462 0.00 0.00 0.00 1.90
1234 1264 6.636705 TGTAGATTTCCAGCGTAGTGTTATT 58.363 36.000 0.00 0.00 0.00 1.40
1235 1265 6.216801 TGTAGATTTCCAGCGTAGTGTTAT 57.783 37.500 0.00 0.00 0.00 1.89
1236 1266 5.648178 TGTAGATTTCCAGCGTAGTGTTA 57.352 39.130 0.00 0.00 0.00 2.41
1242 1272 4.955811 ATCCATGTAGATTTCCAGCGTA 57.044 40.909 0.00 0.00 0.00 4.42
1249 1279 2.480419 CGCCGGAATCCATGTAGATTTC 59.520 50.000 5.05 0.00 36.60 2.17
1250 1280 2.494059 CGCCGGAATCCATGTAGATTT 58.506 47.619 5.05 0.00 36.60 2.17
1251 1281 1.270839 CCGCCGGAATCCATGTAGATT 60.271 52.381 5.05 0.00 39.19 2.40
1261 1291 2.203029 GAAGGACCCGCCGGAATC 60.203 66.667 5.05 0.93 43.43 2.52
1275 1305 2.027625 GACGCCCGTGACTTGGAAG 61.028 63.158 0.00 0.00 0.00 3.46
1281 1311 2.359107 TAGTCGACGCCCGTGACT 60.359 61.111 20.70 20.70 44.63 3.41
1291 1321 1.445582 CCTGGTTGCCGTAGTCGAC 60.446 63.158 7.70 7.70 39.71 4.20
1391 1421 0.039437 CCTGTCTGTGTACGCGAACT 60.039 55.000 15.93 0.00 0.00 3.01
1425 1455 2.033194 GGTGCAGTTCACGTAGGCC 61.033 63.158 0.00 0.00 46.56 5.19
1466 1496 2.872925 CGAAGGCGTCGTACACCG 60.873 66.667 14.73 0.00 45.09 4.94
1495 1525 3.553363 GTAATACGCCCGCCCCCT 61.553 66.667 0.00 0.00 0.00 4.79
1504 1534 1.664151 GTTGTCCAGCCTGTAATACGC 59.336 52.381 0.00 0.00 0.00 4.42
1509 1539 1.302192 GCCGTTGTCCAGCCTGTAA 60.302 57.895 0.00 0.00 0.00 2.41
1656 1686 1.913762 CCACCTCACCGAGAACCCT 60.914 63.158 0.00 0.00 0.00 4.34
1731 1761 1.226435 GTCCTGCGCTCTACTGTCG 60.226 63.158 9.73 0.00 0.00 4.35
1734 1764 0.317436 GATCGTCCTGCGCTCTACTG 60.317 60.000 9.73 1.11 41.07 2.74
1737 1767 1.029947 TGTGATCGTCCTGCGCTCTA 61.030 55.000 9.73 0.00 41.07 2.43
1745 1775 1.340248 AGAAACACGTGTGATCGTCCT 59.660 47.619 24.16 8.68 42.27 3.85
1823 1853 4.593206 ACCAACAAGTTACTCCTCAGATCA 59.407 41.667 0.00 0.00 0.00 2.92
1824 1854 5.153950 ACCAACAAGTTACTCCTCAGATC 57.846 43.478 0.00 0.00 0.00 2.75
1825 1855 4.593206 TGACCAACAAGTTACTCCTCAGAT 59.407 41.667 0.00 0.00 0.00 2.90
1826 1856 3.964688 TGACCAACAAGTTACTCCTCAGA 59.035 43.478 0.00 0.00 0.00 3.27
1827 1857 4.336889 TGACCAACAAGTTACTCCTCAG 57.663 45.455 0.00 0.00 0.00 3.35
1828 1858 4.448210 GTTGACCAACAAGTTACTCCTCA 58.552 43.478 7.92 0.00 40.84 3.86
1830 1860 3.133362 TCGTTGACCAACAAGTTACTCCT 59.867 43.478 12.64 0.00 41.20 3.69
1840 1870 5.789521 TGAATAGAAGATCGTTGACCAACA 58.210 37.500 12.64 1.64 41.20 3.33
1854 1884 8.059798 ACCAGAACATTTTGGATGAATAGAAG 57.940 34.615 8.12 0.00 37.89 2.85
1858 1888 6.127647 GCTGACCAGAACATTTTGGATGAATA 60.128 38.462 8.12 0.00 37.89 1.75
1943 1976 4.082733 GGACATCTTAAGGTTGCTTTGGAC 60.083 45.833 1.85 0.00 0.00 4.02
1946 1979 6.817765 TTAGGACATCTTAAGGTTGCTTTG 57.182 37.500 1.85 0.00 0.00 2.77
1947 1980 7.122799 GGAATTAGGACATCTTAAGGTTGCTTT 59.877 37.037 1.85 0.00 0.00 3.51
1958 1991 8.428063 CAGATTAGTCAGGAATTAGGACATCTT 58.572 37.037 6.44 0.00 34.04 2.40
1984 2017 5.552178 AGAAGTCTTCCATGACCAGTAAAC 58.448 41.667 9.04 0.00 37.66 2.01
2191 2501 5.638234 AGTCAGACACGGCTTAGATTTAAAC 59.362 40.000 2.66 0.00 0.00 2.01
2287 2880 5.063060 GTCCTGCAAAATCAAGAATCAATGC 59.937 40.000 0.00 0.00 0.00 3.56
2318 2911 6.253298 TGCTATTATTGCATTTTTGCTCGTTC 59.747 34.615 0.00 0.00 35.31 3.95
2622 3217 4.980805 TTGTGGACGCCGCTGGAC 62.981 66.667 10.13 0.00 34.70 4.02
2626 3221 4.988598 CAGGTTGTGGACGCCGCT 62.989 66.667 10.13 0.00 34.70 5.52
2772 3367 0.666274 TGTTGTAGAGCCGCTTCACG 60.666 55.000 0.00 0.00 43.15 4.35
2784 3379 2.677003 CCGGCAGCCGTTGTTGTAG 61.677 63.158 31.68 10.57 46.80 2.74


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

AutoCloner maintained by Alex Coulton.