Multiple sequence alignment - TraesCS7A01G097000

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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 TraesCS7A01G097000 chr7A 100.000 2654 0 0 1 2654 59411704 59414357 0.000000e+00 4902.0
1 TraesCS7A01G097000 chr7D 90.876 1896 119 28 782 2654 55423442 55425306 0.000000e+00 2494.0
2 TraesCS7A01G097000 chr7D 85.144 451 59 6 3 451 55421871 55422315 3.110000e-124 455.0
3 TraesCS7A01G097000 chr7D 80.000 105 17 2 529 630 55422422 55422525 1.020000e-09 75.0
4 TraesCS7A01G097000 chr4A 85.031 2131 194 65 578 2654 671940026 671942085 0.000000e+00 2052.0
5 TraesCS7A01G097000 chr3D 89.201 926 76 19 1739 2654 601383432 601382521 0.000000e+00 1134.0
6 TraesCS7A01G097000 chr1D 89.201 926 77 15 1739 2654 28628654 28629566 0.000000e+00 1134.0
7 TraesCS7A01G097000 chr5B 87.473 926 91 20 1739 2654 611768211 611769121 0.000000e+00 1044.0
8 TraesCS7A01G097000 chr2D 92.708 96 6 1 1753 1848 58370340 58370434 1.280000e-28 137.0
9 TraesCS7A01G097000 chr2A 91.304 69 6 0 709 777 29922278 29922210 7.820000e-16 95.3
10 TraesCS7A01G097000 chr4D 92.308 52 2 2 736 785 7993807 7993756 3.660000e-09 73.1
11 TraesCS7A01G097000 chr3B 97.561 41 1 0 738 778 737400737 737400697 1.320000e-08 71.3


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 TraesCS7A01G097000 chr7A 59411704 59414357 2653 False 4902 4902 100.000 1 2654 1 chr7A.!!$F1 2653
1 TraesCS7A01G097000 chr7D 55421871 55425306 3435 False 1008 2494 85.340 3 2654 3 chr7D.!!$F1 2651
2 TraesCS7A01G097000 chr4A 671940026 671942085 2059 False 2052 2052 85.031 578 2654 1 chr4A.!!$F1 2076
3 TraesCS7A01G097000 chr3D 601382521 601383432 911 True 1134 1134 89.201 1739 2654 1 chr3D.!!$R1 915
4 TraesCS7A01G097000 chr1D 28628654 28629566 912 False 1134 1134 89.201 1739 2654 1 chr1D.!!$F1 915
5 TraesCS7A01G097000 chr5B 611768211 611769121 910 False 1044 1044 87.473 1739 2654 1 chr5B.!!$F1 915

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
521 592 0.249699 CCCAAAAACAAGCCCGAACC 60.25 55.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 2645 0.516877 TGAGCAAATCTTTCGCCGTG 59.483 50.0 0.0 0.0 0.0 4.94 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
208 209 5.047021 TGAATTCAATAAATGTTCGCCCCAA 60.047 36.000 5.45 0.00 0.00 4.12
216 217 3.979101 ATGTTCGCCCCAATTTGAAAT 57.021 38.095 0.00 0.00 0.00 2.17
226 227 7.332182 TCGCCCCAATTTGAAATAATGTTAAAC 59.668 33.333 0.00 0.00 0.00 2.01
228 229 8.233868 GCCCCAATTTGAAATAATGTTAAACAC 58.766 33.333 0.00 0.00 0.00 3.32
318 327 6.415573 GTGTATGTTCTAGAACCTTCCCAAT 58.584 40.000 28.43 17.23 40.46 3.16
328 338 0.466189 CCTTCCCAATCCGGACATGG 60.466 60.000 24.89 24.89 36.56 3.66
330 340 1.570857 TTCCCAATCCGGACATGGCT 61.571 55.000 25.96 0.00 36.56 4.75
364 374 4.155733 CATGTACGCAGCGGGGGA 62.156 66.667 21.15 0.00 0.00 4.81
377 387 4.766632 GGGGAGTCGGGGGTACGT 62.767 72.222 0.00 0.00 34.94 3.57
378 388 3.455469 GGGAGTCGGGGGTACGTG 61.455 72.222 0.00 0.00 34.94 4.49
379 389 2.361610 GGAGTCGGGGGTACGTGA 60.362 66.667 0.00 0.00 34.94 4.35
380 390 2.413142 GGAGTCGGGGGTACGTGAG 61.413 68.421 0.00 0.00 34.94 3.51
385 395 2.755469 GGGGGTACGTGAGCGGTA 60.755 66.667 0.00 0.00 43.45 4.02
386 396 2.350458 GGGGGTACGTGAGCGGTAA 61.350 63.158 0.00 0.00 43.45 2.85
403 413 2.654863 GTAACTACCGGGCTACCTACA 58.345 52.381 6.32 0.00 33.28 2.74
404 414 1.772836 AACTACCGGGCTACCTACAG 58.227 55.000 6.32 0.00 33.28 2.74
419 430 1.550976 CTACAGCGGAATAGGATCCCC 59.449 57.143 8.55 0.79 36.00 4.81
421 432 1.913762 AGCGGAATAGGATCCCCGG 60.914 63.158 23.40 10.47 42.02 5.73
452 491 6.990341 ACGTAGGTGACTTAAAACAAAACT 57.010 33.333 0.00 0.00 43.67 2.66
497 568 6.292919 GGTGACAATACCAATATTTCTCGAGC 60.293 42.308 7.81 0.00 40.54 5.03
508 579 4.715523 CTCGAGCCCGGCCCAAAA 62.716 66.667 5.55 0.00 36.24 2.44
509 580 4.272511 TCGAGCCCGGCCCAAAAA 62.273 61.111 5.55 0.00 36.24 1.94
510 581 4.050934 CGAGCCCGGCCCAAAAAC 62.051 66.667 5.55 0.00 0.00 2.43
511 582 2.915137 GAGCCCGGCCCAAAAACA 60.915 61.111 5.55 0.00 0.00 2.83
512 583 2.444895 AGCCCGGCCCAAAAACAA 60.445 55.556 5.55 0.00 0.00 2.83
513 584 2.030412 GCCCGGCCCAAAAACAAG 59.970 61.111 0.00 0.00 0.00 3.16
514 585 2.030412 CCCGGCCCAAAAACAAGC 59.970 61.111 0.00 0.00 0.00 4.01
515 586 2.030412 CCGGCCCAAAAACAAGCC 59.970 61.111 0.00 0.00 42.18 4.35
516 587 2.030412 CGGCCCAAAAACAAGCCC 59.970 61.111 0.00 0.00 42.66 5.19
517 588 2.030412 GGCCCAAAAACAAGCCCG 59.970 61.111 0.00 0.00 39.60 6.13
518 589 2.503382 GGCCCAAAAACAAGCCCGA 61.503 57.895 0.00 0.00 39.60 5.14
519 590 1.443828 GCCCAAAAACAAGCCCGAA 59.556 52.632 0.00 0.00 0.00 4.30
520 591 0.878523 GCCCAAAAACAAGCCCGAAC 60.879 55.000 0.00 0.00 0.00 3.95
521 592 0.249699 CCCAAAAACAAGCCCGAACC 60.250 55.000 0.00 0.00 0.00 3.62
522 593 0.249699 CCAAAAACAAGCCCGAACCC 60.250 55.000 0.00 0.00 0.00 4.11
523 594 0.249699 CAAAAACAAGCCCGAACCCC 60.250 55.000 0.00 0.00 0.00 4.95
524 595 0.688087 AAAAACAAGCCCGAACCCCA 60.688 50.000 0.00 0.00 0.00 4.96
525 596 0.688087 AAAACAAGCCCGAACCCCAA 60.688 50.000 0.00 0.00 0.00 4.12
526 597 0.688087 AAACAAGCCCGAACCCCAAA 60.688 50.000 0.00 0.00 0.00 3.28
527 598 0.688087 AACAAGCCCGAACCCCAAAA 60.688 50.000 0.00 0.00 0.00 2.44
528 599 1.112916 ACAAGCCCGAACCCCAAAAG 61.113 55.000 0.00 0.00 0.00 2.27
529 600 2.207229 AAGCCCGAACCCCAAAAGC 61.207 57.895 0.00 0.00 0.00 3.51
530 601 3.691342 GCCCGAACCCCAAAAGCC 61.691 66.667 0.00 0.00 0.00 4.35
531 602 2.117423 CCCGAACCCCAAAAGCCT 59.883 61.111 0.00 0.00 0.00 4.58
532 603 2.275380 CCCGAACCCCAAAAGCCTG 61.275 63.158 0.00 0.00 0.00 4.85
533 604 2.275380 CCGAACCCCAAAAGCCTGG 61.275 63.158 0.00 0.00 36.10 4.45
534 605 2.931068 CGAACCCCAAAAGCCTGGC 61.931 63.158 11.65 11.65 34.88 4.85
535 606 2.526624 AACCCCAAAAGCCTGGCC 60.527 61.111 16.57 0.00 34.88 5.36
536 607 4.638895 ACCCCAAAAGCCTGGCCC 62.639 66.667 16.57 0.00 34.88 5.80
541 612 2.197324 AAAAGCCTGGCCCGAACA 59.803 55.556 16.57 0.00 0.00 3.18
542 613 1.228862 AAAAGCCTGGCCCGAACAT 60.229 52.632 16.57 0.00 0.00 2.71
550 621 1.969589 GGCCCGAACATTGTTCCGT 60.970 57.895 20.87 0.00 0.00 4.69
551 622 1.209127 GCCCGAACATTGTTCCGTG 59.791 57.895 20.87 11.94 0.00 4.94
552 623 1.873165 CCCGAACATTGTTCCGTGG 59.127 57.895 20.87 16.35 0.00 4.94
554 625 1.448985 CCGAACATTGTTCCGTGGAT 58.551 50.000 20.87 0.00 0.00 3.41
555 626 1.810151 CCGAACATTGTTCCGTGGATT 59.190 47.619 20.87 0.00 0.00 3.01
573 644 3.491447 GGATTATACACGTGTAAGCCCGT 60.491 47.826 30.46 16.28 36.93 5.28
574 645 4.261572 GGATTATACACGTGTAAGCCCGTA 60.262 45.833 30.46 15.27 36.93 4.02
575 646 2.857592 ATACACGTGTAAGCCCGTAG 57.142 50.000 30.46 0.00 35.16 3.51
576 647 1.533625 TACACGTGTAAGCCCGTAGT 58.466 50.000 25.54 0.00 35.16 2.73
605 676 0.329596 AGAAATCAAAGCCCGAGCCT 59.670 50.000 0.00 0.00 41.25 4.58
631 705 3.490078 CCGACACTTTTAGGCTGCAAAAA 60.490 43.478 0.50 6.95 0.00 1.94
632 706 4.298332 CGACACTTTTAGGCTGCAAAAAT 58.702 39.130 0.50 0.00 0.00 1.82
634 708 4.379652 ACACTTTTAGGCTGCAAAAATGG 58.620 39.130 10.13 8.94 0.00 3.16
636 710 4.687483 CACTTTTAGGCTGCAAAAATGGAG 59.313 41.667 0.50 0.00 0.00 3.86
646 720 0.473501 AAAAATGGAGCCCAAGCCCA 60.474 50.000 0.00 0.00 41.63 5.36
649 723 2.097978 AATGGAGCCCAAGCCCAACT 62.098 55.000 0.00 0.00 41.03 3.16
662 736 1.566018 CCCAACTCGAACGTCAAGCC 61.566 60.000 0.00 0.00 0.00 4.35
663 737 0.600255 CCAACTCGAACGTCAAGCCT 60.600 55.000 0.00 0.00 0.00 4.58
668 742 0.671796 TCGAACGTCAAGCCTGAAGA 59.328 50.000 5.20 0.00 35.30 2.87
670 744 1.656095 CGAACGTCAAGCCTGAAGATC 59.344 52.381 5.20 2.11 35.30 2.75
699 773 1.344191 TGGATCGGGTCATCATGCCA 61.344 55.000 1.22 0.00 0.00 4.92
702 776 1.348008 ATCGGGTCATCATGCCAGGT 61.348 55.000 1.22 0.00 0.00 4.00
727 801 9.308318 GTTGTCCATGTAATTTTTGTTACTTGT 57.692 29.630 10.04 0.00 37.71 3.16
729 803 8.908903 TGTCCATGTAATTTTTGTTACTTGTCT 58.091 29.630 10.04 0.00 37.71 3.41
734 808 9.816354 ATGTAATTTTTGTTACTTGTCTTGCTT 57.184 25.926 0.00 0.00 35.94 3.91
741 815 8.455598 TTTGTTACTTGTCTTGCTTTTTGTAC 57.544 30.769 0.00 0.00 0.00 2.90
743 817 7.247728 TGTTACTTGTCTTGCTTTTTGTACTG 58.752 34.615 0.00 0.00 0.00 2.74
778 853 9.541724 TTTGATGAATAGATCGAAAGTTTTTCG 57.458 29.630 15.60 15.60 42.74 3.46
898 1773 2.684001 ATGTCCGACCGAGCAAATTA 57.316 45.000 0.00 0.00 0.00 1.40
935 1811 2.436115 CTTCGGCGGTTCCTTCCC 60.436 66.667 7.21 0.00 0.00 3.97
945 1822 1.272704 GGTTCCTTCCCCTGCAATCTT 60.273 52.381 0.00 0.00 0.00 2.40
946 1823 1.821136 GTTCCTTCCCCTGCAATCTTG 59.179 52.381 0.00 0.00 0.00 3.02
959 1836 3.294038 CAATCTTGCAATCCTCCTCCT 57.706 47.619 0.00 0.00 0.00 3.69
1021 1898 4.742201 CGACGGCTCCACCACCAG 62.742 72.222 0.00 0.00 39.03 4.00
1500 2380 4.148825 GCCGACGGCTCTGATGGT 62.149 66.667 31.30 0.00 46.69 3.55
1512 2392 0.916358 CTGATGGTGAGGGGAAGGGT 60.916 60.000 0.00 0.00 0.00 4.34
1518 2398 2.454941 GAGGGGAAGGGTGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
1524 2404 1.609794 GAAGGGTGGAGGAGACGGT 60.610 63.158 0.00 0.00 0.00 4.83
1526 2406 2.283676 GGGTGGAGGAGACGGTGA 60.284 66.667 0.00 0.00 0.00 4.02
1699 2579 0.188342 ACAGGGGTGCCTGATTTTGT 59.812 50.000 0.00 0.00 39.96 2.83
1745 2645 2.072298 GCTAGATGATGATTCACGGCC 58.928 52.381 0.00 0.00 33.85 6.13
1828 2731 4.380233 GGTGAAGATCAGCATTTCAGGTTG 60.380 45.833 4.78 0.00 43.79 3.77
1879 2785 6.953101 TCATGTTAAGCCCATACTTAAGTGA 58.047 36.000 18.56 3.04 41.52 3.41
1947 2856 1.183549 TCTAGGTGTCGGAAGAAGCC 58.816 55.000 0.00 0.00 45.01 4.35
1948 2857 1.187087 CTAGGTGTCGGAAGAAGCCT 58.813 55.000 0.00 0.00 44.92 4.58
1954 2863 1.071567 GTCGGAAGAAGCCTCGTTCG 61.072 60.000 0.00 0.00 45.01 3.95
1961 2870 4.427312 GAAGAAGCCTCGTTCGGTTAATA 58.573 43.478 0.00 0.00 0.00 0.98
1966 2875 3.638160 AGCCTCGTTCGGTTAATATGGTA 59.362 43.478 0.00 0.00 0.00 3.25
2185 3130 3.323691 TGTCTTGTGACCTGCTAGCTTAA 59.676 43.478 17.23 0.00 42.28 1.85
2240 3194 9.233649 TCTTTCTACTCTTCTACTTCCAGTTAG 57.766 37.037 0.00 0.00 0.00 2.34
2270 3224 8.812513 TCAGAATTCAGTTATGATTTGGACAT 57.187 30.769 8.44 0.00 33.35 3.06
2301 3255 6.714810 TGATGTTACTGTTGATACCTTGCTTT 59.285 34.615 0.00 0.00 0.00 3.51
2348 3304 7.864108 ATGCTTCATTATGTTAGTTGCACTA 57.136 32.000 0.00 0.00 0.00 2.74
2354 3310 8.298030 TCATTATGTTAGTTGCACTATCATCG 57.702 34.615 16.42 10.65 39.22 3.84
2359 3315 5.125578 TGTTAGTTGCACTATCATCGTCTCT 59.874 40.000 0.00 0.00 29.64 3.10
2370 3326 2.297315 TCATCGTCTCTGCAACTGTTCT 59.703 45.455 0.00 0.00 0.00 3.01
2372 3328 1.957177 TCGTCTCTGCAACTGTTCTCT 59.043 47.619 0.00 0.00 0.00 3.10
2373 3329 2.030717 TCGTCTCTGCAACTGTTCTCTC 60.031 50.000 0.00 0.00 0.00 3.20
2377 3337 3.056250 TCTCTGCAACTGTTCTCTCCATC 60.056 47.826 0.00 0.00 0.00 3.51
2380 3340 4.070716 CTGCAACTGTTCTCTCCATCTTT 58.929 43.478 0.00 0.00 0.00 2.52
2390 3350 9.092876 CTGTTCTCTCCATCTTTCATAGTTAAC 57.907 37.037 0.00 0.00 0.00 2.01
2398 3358 6.986817 CCATCTTTCATAGTTAACGGATCTGT 59.013 38.462 0.00 0.00 0.00 3.41
2400 3360 6.570692 TCTTTCATAGTTAACGGATCTGTCC 58.429 40.000 7.86 0.00 41.40 4.02
2428 3388 8.746751 GTCTAAAAGAACTGCATTTCACTTTTC 58.253 33.333 17.88 8.08 38.16 2.29
2430 3390 6.892310 AAAGAACTGCATTTCACTTTTCAC 57.108 33.333 17.88 0.00 0.00 3.18
2432 3392 6.942532 AGAACTGCATTTCACTTTTCACTA 57.057 33.333 17.88 0.00 0.00 2.74
2433 3393 6.963796 AGAACTGCATTTCACTTTTCACTAG 58.036 36.000 17.88 0.00 0.00 2.57
2441 3401 7.094634 GCATTTCACTTTTCACTAGAAGGATGA 60.095 37.037 0.00 0.00 34.71 2.92
2482 3442 4.354155 GCATTGCGCCCGTATCTA 57.646 55.556 4.18 0.00 32.94 1.98
2497 3457 6.153067 CCCGTATCTAACTCATGATGAACTC 58.847 44.000 0.00 0.00 0.00 3.01
2499 3459 7.175119 CCCGTATCTAACTCATGATGAACTCTA 59.825 40.741 0.00 0.00 0.00 2.43
2500 3460 8.233868 CCGTATCTAACTCATGATGAACTCTAG 58.766 40.741 0.00 0.00 0.00 2.43
2545 3505 6.919662 AGTTGTTGTTATGTTCAAATCTGCAG 59.080 34.615 7.63 7.63 0.00 4.41
2555 3515 6.671190 TGTTCAAATCTGCAGATACTGTTTG 58.329 36.000 28.92 26.16 33.73 2.93
2573 3533 1.923356 TGACAGATTCCCAAAAGGCC 58.077 50.000 0.00 0.00 34.51 5.19
2581 3541 2.268076 CCCAAAAGGCCGTCCTGTG 61.268 63.158 0.00 0.00 43.40 3.66
2585 3545 1.106944 AAAAGGCCGTCCTGTGGTTG 61.107 55.000 0.00 0.00 43.40 3.77
2594 3554 2.742053 CGTCCTGTGGTTGGTATTTGAG 59.258 50.000 0.00 0.00 0.00 3.02
2595 3555 3.751518 GTCCTGTGGTTGGTATTTGAGT 58.248 45.455 0.00 0.00 0.00 3.41
2606 3566 8.325787 TGGTTGGTATTTGAGTACACTGATTAT 58.674 33.333 0.00 0.00 0.00 1.28
2631 3591 4.082571 ACATCCAACTGATTTTGCTGCTAC 60.083 41.667 0.00 0.00 0.00 3.58
2648 3611 6.878923 TGCTGCTACTTAAACACTATCATGTT 59.121 34.615 0.00 0.00 44.76 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 8.450180 GGGCGAACATTTATTGAATTCAAAATT 58.550 29.630 23.91 11.06 39.55 1.82
185 186 5.004922 TGGGGCGAACATTTATTGAATTC 57.995 39.130 0.00 0.00 0.00 2.17
186 187 5.413309 TTGGGGCGAACATTTATTGAATT 57.587 34.783 0.00 0.00 0.00 2.17
196 197 3.979101 ATTTCAAATTGGGGCGAACAT 57.021 38.095 0.00 0.00 0.00 2.71
202 203 8.233868 GTGTTTAACATTATTTCAAATTGGGGC 58.766 33.333 0.00 0.00 0.00 5.80
252 253 9.996554 TCCTTTTCATTTTCCTTTTCCTTTATC 57.003 29.630 0.00 0.00 0.00 1.75
254 255 9.207868 TCTCCTTTTCATTTTCCTTTTCCTTTA 57.792 29.630 0.00 0.00 0.00 1.85
255 256 8.089625 TCTCCTTTTCATTTTCCTTTTCCTTT 57.910 30.769 0.00 0.00 0.00 3.11
256 257 7.675161 TCTCCTTTTCATTTTCCTTTTCCTT 57.325 32.000 0.00 0.00 0.00 3.36
257 258 7.675161 TTCTCCTTTTCATTTTCCTTTTCCT 57.325 32.000 0.00 0.00 0.00 3.36
258 259 8.731275 TTTTCTCCTTTTCATTTTCCTTTTCC 57.269 30.769 0.00 0.00 0.00 3.13
286 287 5.467735 GGTTCTAGAACATACACGTTTTGGT 59.532 40.000 31.30 0.00 42.85 3.67
293 302 4.081862 TGGGAAGGTTCTAGAACATACACG 60.082 45.833 31.30 0.00 42.85 4.49
302 311 2.116238 CCGGATTGGGAAGGTTCTAGA 58.884 52.381 0.00 0.00 0.00 2.43
318 327 0.251916 CCAACTAAGCCATGTCCGGA 59.748 55.000 0.00 0.00 0.00 5.14
364 374 3.066814 GCTCACGTACCCCCGACT 61.067 66.667 0.00 0.00 0.00 4.18
383 393 2.620585 CTGTAGGTAGCCCGGTAGTTAC 59.379 54.545 0.00 0.00 35.12 2.50
385 395 1.772836 CTGTAGGTAGCCCGGTAGTT 58.227 55.000 0.00 0.00 35.12 2.24
386 396 0.754587 GCTGTAGGTAGCCCGGTAGT 60.755 60.000 0.00 0.00 37.73 2.73
398 408 1.550976 GGGATCCTATTCCGCTGTAGG 59.449 57.143 12.58 0.00 39.06 3.18
403 413 1.913762 CCGGGGATCCTATTCCGCT 60.914 63.158 18.68 0.00 44.38 5.52
404 414 2.663196 CCGGGGATCCTATTCCGC 59.337 66.667 18.68 0.00 43.42 5.54
421 432 4.409218 TCACCTACGTGGACGCGC 62.409 66.667 5.73 0.00 44.43 6.86
451 490 9.935682 GTCACCATGTCAATATTGTAATGTTAG 57.064 33.333 21.18 13.78 0.00 2.34
452 491 9.454859 TGTCACCATGTCAATATTGTAATGTTA 57.545 29.630 21.18 10.71 0.00 2.41
492 563 4.272511 TTTTTGGGCCGGGCTCGA 62.273 61.111 28.80 12.82 39.00 4.04
497 568 2.030412 GCTTGTTTTTGGGCCGGG 59.970 61.111 2.18 0.00 0.00 5.73
505 576 0.688087 TGGGGTTCGGGCTTGTTTTT 60.688 50.000 0.00 0.00 0.00 1.94
506 577 0.688087 TTGGGGTTCGGGCTTGTTTT 60.688 50.000 0.00 0.00 0.00 2.43
507 578 0.688087 TTTGGGGTTCGGGCTTGTTT 60.688 50.000 0.00 0.00 0.00 2.83
508 579 0.688087 TTTTGGGGTTCGGGCTTGTT 60.688 50.000 0.00 0.00 0.00 2.83
509 580 1.075896 TTTTGGGGTTCGGGCTTGT 60.076 52.632 0.00 0.00 0.00 3.16
510 581 1.665442 CTTTTGGGGTTCGGGCTTG 59.335 57.895 0.00 0.00 0.00 4.01
511 582 2.207229 GCTTTTGGGGTTCGGGCTT 61.207 57.895 0.00 0.00 0.00 4.35
512 583 2.600470 GCTTTTGGGGTTCGGGCT 60.600 61.111 0.00 0.00 0.00 5.19
513 584 3.691342 GGCTTTTGGGGTTCGGGC 61.691 66.667 0.00 0.00 0.00 6.13
514 585 2.117423 AGGCTTTTGGGGTTCGGG 59.883 61.111 0.00 0.00 0.00 5.14
515 586 2.275380 CCAGGCTTTTGGGGTTCGG 61.275 63.158 0.00 0.00 34.46 4.30
516 587 2.931068 GCCAGGCTTTTGGGGTTCG 61.931 63.158 3.29 0.00 38.72 3.95
517 588 2.583441 GGCCAGGCTTTTGGGGTTC 61.583 63.158 12.43 0.00 38.72 3.62
518 589 2.526624 GGCCAGGCTTTTGGGGTT 60.527 61.111 12.43 0.00 38.72 4.11
519 590 4.638895 GGGCCAGGCTTTTGGGGT 62.639 66.667 12.43 0.00 38.72 4.95
521 592 4.676951 TCGGGCCAGGCTTTTGGG 62.677 66.667 12.43 0.00 38.72 4.12
522 593 2.600173 TTCGGGCCAGGCTTTTGG 60.600 61.111 12.43 0.00 41.35 3.28
523 594 1.535204 ATGTTCGGGCCAGGCTTTTG 61.535 55.000 12.43 0.00 0.00 2.44
524 595 0.831711 AATGTTCGGGCCAGGCTTTT 60.832 50.000 12.43 0.00 0.00 2.27
525 596 1.228862 AATGTTCGGGCCAGGCTTT 60.229 52.632 12.43 0.00 0.00 3.51
526 597 1.978617 CAATGTTCGGGCCAGGCTT 60.979 57.895 12.43 0.00 0.00 4.35
527 598 2.361610 CAATGTTCGGGCCAGGCT 60.362 61.111 12.43 0.00 0.00 4.58
528 599 2.212900 GAACAATGTTCGGGCCAGGC 62.213 60.000 10.58 1.26 0.00 4.85
529 600 1.595093 GGAACAATGTTCGGGCCAGG 61.595 60.000 18.52 0.00 0.00 4.45
530 601 1.883021 GGAACAATGTTCGGGCCAG 59.117 57.895 18.52 0.00 0.00 4.85
531 602 1.969064 CGGAACAATGTTCGGGCCA 60.969 57.895 21.29 0.00 0.00 5.36
532 603 1.969589 ACGGAACAATGTTCGGGCC 60.970 57.895 28.67 13.34 0.00 5.80
533 604 1.209127 CACGGAACAATGTTCGGGC 59.791 57.895 28.67 12.87 0.00 6.13
534 605 0.604243 TCCACGGAACAATGTTCGGG 60.604 55.000 28.67 23.30 0.00 5.14
535 606 1.448985 ATCCACGGAACAATGTTCGG 58.551 50.000 25.43 25.43 0.00 4.30
536 607 4.875544 ATAATCCACGGAACAATGTTCG 57.124 40.909 18.52 15.67 0.00 3.95
550 621 3.491276 CGGGCTTACACGTGTATAATCCA 60.491 47.826 27.82 11.84 0.00 3.41
551 622 3.054878 CGGGCTTACACGTGTATAATCC 58.945 50.000 27.82 22.64 0.00 3.01
552 623 3.709987 ACGGGCTTACACGTGTATAATC 58.290 45.455 27.82 16.90 42.39 1.75
554 625 3.694072 ACTACGGGCTTACACGTGTATAA 59.306 43.478 27.82 15.73 43.93 0.98
555 626 3.065233 CACTACGGGCTTACACGTGTATA 59.935 47.826 27.82 17.22 43.93 1.47
562 633 2.095372 GCATTTCACTACGGGCTTACAC 59.905 50.000 0.00 0.00 0.00 2.90
564 635 2.351726 CAGCATTTCACTACGGGCTTAC 59.648 50.000 0.00 0.00 0.00 2.34
569 640 2.672961 TCTCAGCATTTCACTACGGG 57.327 50.000 0.00 0.00 0.00 5.28
573 644 6.349611 GGCTTTGATTTCTCAGCATTTCACTA 60.350 38.462 0.00 0.00 31.68 2.74
574 645 5.467705 GCTTTGATTTCTCAGCATTTCACT 58.532 37.500 0.00 0.00 31.68 3.41
575 646 4.624452 GGCTTTGATTTCTCAGCATTTCAC 59.376 41.667 0.00 0.00 31.68 3.18
576 647 4.322198 GGGCTTTGATTTCTCAGCATTTCA 60.322 41.667 0.00 0.00 31.68 2.69
605 676 1.302993 GCCTAAAAGTGTCGGCCCA 60.303 57.895 0.00 0.00 36.56 5.36
631 705 2.037847 GTTGGGCTTGGGCTCCAT 59.962 61.111 0.00 0.00 38.37 3.41
632 706 3.185203 AGTTGGGCTTGGGCTCCA 61.185 61.111 0.00 0.00 38.37 3.86
634 708 2.747855 CGAGTTGGGCTTGGGCTC 60.748 66.667 0.00 0.00 39.89 4.70
636 710 2.282180 TTCGAGTTGGGCTTGGGC 60.282 61.111 0.00 0.00 37.82 5.36
637 711 2.325082 CGTTCGAGTTGGGCTTGGG 61.325 63.158 0.00 0.00 0.00 4.12
646 720 0.387929 TCAGGCTTGACGTTCGAGTT 59.612 50.000 0.00 0.00 30.44 3.01
649 723 0.671796 TCTTCAGGCTTGACGTTCGA 59.328 50.000 0.00 0.00 31.71 3.71
680 754 1.344191 TGGCATGATGACCCGATCCA 61.344 55.000 0.00 0.00 0.00 3.41
683 757 1.348008 ACCTGGCATGATGACCCGAT 61.348 55.000 0.00 0.00 0.00 4.18
691 765 1.006281 ACATGGACAACCTGGCATGAT 59.994 47.619 15.31 1.33 37.04 2.45
699 773 8.245195 AGTAACAAAAATTACATGGACAACCT 57.755 30.769 0.00 0.00 37.49 3.50
702 776 9.522804 GACAAGTAACAAAAATTACATGGACAA 57.477 29.630 0.00 0.00 37.82 3.18
727 801 6.882610 ATCATGACAGTACAAAAAGCAAGA 57.117 33.333 0.00 0.00 0.00 3.02
729 803 9.409312 CAAATATCATGACAGTACAAAAAGCAA 57.591 29.630 0.00 0.00 0.00 3.91
864 1739 7.548427 TCGGTCGGACATTTTACATTTTATACA 59.452 33.333 10.76 0.00 0.00 2.29
865 1740 7.908230 TCGGTCGGACATTTTACATTTTATAC 58.092 34.615 10.76 0.00 0.00 1.47
866 1741 7.254522 GCTCGGTCGGACATTTTACATTTTATA 60.255 37.037 10.76 0.00 0.00 0.98
867 1742 6.457799 GCTCGGTCGGACATTTTACATTTTAT 60.458 38.462 10.76 0.00 0.00 1.40
868 1743 5.163834 GCTCGGTCGGACATTTTACATTTTA 60.164 40.000 10.76 0.00 0.00 1.52
869 1744 4.379082 GCTCGGTCGGACATTTTACATTTT 60.379 41.667 10.76 0.00 0.00 1.82
870 1745 3.126343 GCTCGGTCGGACATTTTACATTT 59.874 43.478 10.76 0.00 0.00 2.32
871 1746 2.676342 GCTCGGTCGGACATTTTACATT 59.324 45.455 10.76 0.00 0.00 2.71
872 1747 2.277084 GCTCGGTCGGACATTTTACAT 58.723 47.619 10.76 0.00 0.00 2.29
886 1761 1.161843 CCACGGTTAATTTGCTCGGT 58.838 50.000 0.00 0.00 0.00 4.69
945 1822 2.398588 ACGAATAGGAGGAGGATTGCA 58.601 47.619 0.00 0.00 0.00 4.08
946 1823 3.394719 GAACGAATAGGAGGAGGATTGC 58.605 50.000 0.00 0.00 0.00 3.56
947 1824 3.553096 CCGAACGAATAGGAGGAGGATTG 60.553 52.174 0.00 0.00 0.00 2.67
948 1825 2.628657 CCGAACGAATAGGAGGAGGATT 59.371 50.000 0.00 0.00 0.00 3.01
949 1826 2.240279 CCGAACGAATAGGAGGAGGAT 58.760 52.381 0.00 0.00 0.00 3.24
950 1827 1.064166 ACCGAACGAATAGGAGGAGGA 60.064 52.381 0.00 0.00 0.00 3.71
951 1828 1.400737 ACCGAACGAATAGGAGGAGG 58.599 55.000 0.00 0.00 0.00 4.30
952 1829 3.622627 GTACCGAACGAATAGGAGGAG 57.377 52.381 0.00 0.00 0.00 3.69
1422 2302 4.221422 GCCGCCAGCAGGTCGATA 62.221 66.667 12.24 0.00 42.97 2.92
1494 2374 1.163309 ACCCTTCCCCTCACCATCA 59.837 57.895 0.00 0.00 0.00 3.07
1500 2380 2.124996 CCTCCACCCTTCCCCTCA 59.875 66.667 0.00 0.00 0.00 3.86
1512 2392 2.675423 CCGTCACCGTCTCCTCCA 60.675 66.667 0.00 0.00 0.00 3.86
1603 2483 3.449227 CTGCGACCTCTGCCCGTA 61.449 66.667 0.00 0.00 0.00 4.02
1699 2579 2.920724 TGGACGGTCTCAAAATGTCA 57.079 45.000 8.23 0.00 0.00 3.58
1745 2645 0.516877 TGAGCAAATCTTTCGCCGTG 59.483 50.000 0.00 0.00 0.00 4.94
1748 2648 2.997485 AACTGAGCAAATCTTTCGCC 57.003 45.000 0.00 0.00 0.00 5.54
1828 2731 3.350219 AACCCATGTATCAGTGACCAC 57.650 47.619 0.00 0.00 0.00 4.16
1879 2785 6.360370 ACACTTGACTACCACTAACATCAT 57.640 37.500 0.00 0.00 0.00 2.45
1947 2856 5.694910 AGCATTACCATATTAACCGAACGAG 59.305 40.000 0.00 0.00 0.00 4.18
1948 2857 5.464057 CAGCATTACCATATTAACCGAACGA 59.536 40.000 0.00 0.00 0.00 3.85
1954 2863 7.504924 TTACAGCAGCATTACCATATTAACC 57.495 36.000 0.00 0.00 0.00 2.85
1961 2870 2.092212 AGGCTTACAGCAGCATTACCAT 60.092 45.455 0.00 0.00 44.75 3.55
1966 2875 2.026822 ACTACAGGCTTACAGCAGCATT 60.027 45.455 0.00 0.00 44.75 3.56
1991 2900 3.691118 TGCTTCATGTTTACTGGCATCTC 59.309 43.478 0.00 0.00 0.00 2.75
2141 3074 6.631016 ACAATCGATGTACATAACACACTCT 58.369 36.000 8.71 0.00 42.09 3.24
2185 3130 4.655963 ACTCTTGCACATGTAAGGTTCAT 58.344 39.130 9.45 0.00 38.14 2.57
2240 3194 9.565213 CCAAATCATAACTGAATTCTGAGAAAC 57.435 33.333 18.13 0.00 34.37 2.78
2270 3224 8.862325 AGGTATCAACAGTAACATCATTCAAA 57.138 30.769 0.00 0.00 0.00 2.69
2292 3246 7.354312 ACAATGATACCCTTATAAAGCAAGGT 58.646 34.615 0.80 0.00 40.92 3.50
2301 3255 8.100791 GCATACAAGGACAATGATACCCTTATA 58.899 37.037 0.00 0.00 36.93 0.98
2309 3263 9.797642 ATAATGAAGCATACAAGGACAATGATA 57.202 29.630 0.00 0.00 0.00 2.15
2348 3304 3.056250 AGAACAGTTGCAGAGACGATGAT 60.056 43.478 0.00 0.00 0.00 2.45
2354 3310 2.036475 TGGAGAGAACAGTTGCAGAGAC 59.964 50.000 0.00 0.00 0.00 3.36
2359 3315 3.777106 AAGATGGAGAGAACAGTTGCA 57.223 42.857 0.00 0.00 0.00 4.08
2370 3326 6.785337 TCCGTTAACTATGAAAGATGGAGA 57.215 37.500 3.71 0.00 0.00 3.71
2372 3328 7.147724 ACAGATCCGTTAACTATGAAAGATGGA 60.148 37.037 3.71 0.00 0.00 3.41
2373 3329 6.986817 ACAGATCCGTTAACTATGAAAGATGG 59.013 38.462 3.71 0.00 0.00 3.51
2377 3337 6.830114 GGACAGATCCGTTAACTATGAAAG 57.170 41.667 3.71 0.00 34.48 2.62
2398 3358 6.017109 GTGAAATGCAGTTCTTTTAGACAGGA 60.017 38.462 25.47 0.02 0.00 3.86
2400 3360 6.963796 AGTGAAATGCAGTTCTTTTAGACAG 58.036 36.000 25.47 0.00 0.00 3.51
2441 3401 8.085296 TGCGGAAAACATTTCTGTAATTATTGT 58.915 29.630 11.97 0.00 33.36 2.71
2482 3442 8.143193 CAGAATAGCTAGAGTTCATCATGAGTT 58.857 37.037 0.09 0.00 0.00 3.01
2499 3459 8.757877 ACAACTAGAAGAAATCTCAGAATAGCT 58.242 33.333 0.00 0.00 39.71 3.32
2500 3460 8.940768 ACAACTAGAAGAAATCTCAGAATAGC 57.059 34.615 0.00 0.00 39.71 2.97
2545 3505 6.817765 TTTGGGAATCTGTCAAACAGTATC 57.182 37.500 6.96 6.65 46.03 2.24
2555 3515 0.811281 CGGCCTTTTGGGAATCTGTC 59.189 55.000 0.00 0.00 40.82 3.51
2564 3524 2.268076 CCACAGGACGGCCTTTTGG 61.268 63.158 18.66 18.66 43.90 3.28
2573 3533 2.742053 CTCAAATACCAACCACAGGACG 59.258 50.000 0.00 0.00 0.00 4.79
2581 3541 8.612619 CATAATCAGTGTACTCAAATACCAACC 58.387 37.037 0.00 0.00 0.00 3.77
2585 3545 8.942338 TGTCATAATCAGTGTACTCAAATACC 57.058 34.615 0.00 0.00 0.00 2.73
2594 3554 7.041721 TCAGTTGGATGTCATAATCAGTGTAC 58.958 38.462 0.00 0.00 0.00 2.90
2595 3555 7.181569 TCAGTTGGATGTCATAATCAGTGTA 57.818 36.000 0.00 0.00 0.00 2.90
2606 3566 3.305539 GCAGCAAAATCAGTTGGATGTCA 60.306 43.478 0.00 0.00 36.02 3.58


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

AutoCloner maintained by Alex Coulton.