Multiple sequence alignment - TraesCS6B01G408200

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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 TraesCS6B01G408200 chr6B 100.000 4017 0 0 1 4017 682556479 682560495 0.000000e+00 7419.0
1 TraesCS6B01G408200 chr6A 91.795 2596 155 33 853 3418 595621945 595624512 0.000000e+00 3561.0
2 TraesCS6B01G408200 chr6A 91.089 505 37 6 3516 4014 595624540 595625042 0.000000e+00 676.0
3 TraesCS6B01G408200 chr6A 78.871 691 105 28 77 744 595619186 595619858 2.870000e-116 429.0
4 TraesCS6B01G408200 chr6D 86.579 2444 203 64 6 2410 450106681 450109038 0.000000e+00 2580.0
5 TraesCS6B01G408200 chr6D 96.199 1026 37 2 2420 3444 450109094 450110118 0.000000e+00 1677.0
6 TraesCS6B01G408200 chr6D 91.825 526 33 6 3501 4017 450110100 450110624 0.000000e+00 725.0
7 TraesCS6B01G408200 chr3B 98.246 57 1 0 3445 3501 422559673 422559729 2.550000e-17 100.0
8 TraesCS6B01G408200 chr5A 96.552 58 2 0 3444 3501 539904712 539904655 3.300000e-16 97.1
9 TraesCS6B01G408200 chr3A 98.182 55 1 0 3445 3499 32127569 32127515 3.300000e-16 97.1
10 TraesCS6B01G408200 chr2A 94.737 57 3 0 3445 3501 10724482 10724426 5.530000e-14 89.8
11 TraesCS6B01G408200 chr4A 93.220 59 4 0 3450 3508 733934453 733934395 1.990000e-13 87.9
12 TraesCS6B01G408200 chr7D 94.545 55 2 1 3445 3499 192366903 192366850 2.570000e-12 84.2
13 TraesCS6B01G408200 chr7D 87.719 57 4 3 767 820 139187053 139187109 3.350000e-06 63.9
14 TraesCS6B01G408200 chr2B 91.228 57 3 2 3445 3501 13918089 13918143 4.310000e-10 76.8
15 TraesCS6B01G408200 chr7A 88.889 54 4 2 773 824 65051486 65051433 9.320000e-07 65.8


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 TraesCS6B01G408200 chr6B 682556479 682560495 4016 False 7419.000000 7419 100.000000 1 4017 1 chr6B.!!$F1 4016
1 TraesCS6B01G408200 chr6A 595619186 595625042 5856 False 1555.333333 3561 87.251667 77 4014 3 chr6A.!!$F1 3937
2 TraesCS6B01G408200 chr6D 450106681 450110624 3943 False 1660.666667 2580 91.534333 6 4017 3 chr6D.!!$F1 4011

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
692 714 0.035056 AGCAGCACCCAACAGGATAC 60.035 55.0 0.0 0.0 39.89 2.24 F
1620 3663 0.817654 TGATGACGAAGATGGACGCT 59.182 50.0 0.0 0.0 0.00 5.07 F
2416 4462 0.036164 AGTCGGTGTGCAATAAGCCA 59.964 50.0 0.0 0.0 44.83 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 3783 0.038618 TGTTCCAGGTGACGATGTCG 60.039 55.0 0.11 0.11 46.33 4.35 R
2573 4666 0.114364 GGAGGAAGGCCCCTTTTCAA 59.886 55.0 0.00 0.00 36.49 2.69 R
3645 5744 1.062488 ACCCAGAACAGAACAGGCCT 61.062 55.0 0.00 0.00 0.00 5.19 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
20 21 2.125106 CTGTAGGGTTCGCTGGGC 60.125 66.667 0.00 0.00 0.00 5.36
42 43 2.295909 CCCATTTGTAAGGGTGTGTGTG 59.704 50.000 0.00 0.00 40.34 3.82
43 44 2.295909 CCATTTGTAAGGGTGTGTGTGG 59.704 50.000 0.00 0.00 0.00 4.17
70 71 5.293324 GGTTGAGGGTTCATGTTTGTTTTTC 59.707 40.000 0.00 0.00 32.27 2.29
71 72 5.930837 TGAGGGTTCATGTTTGTTTTTCT 57.069 34.783 0.00 0.00 0.00 2.52
72 73 6.293004 TGAGGGTTCATGTTTGTTTTTCTT 57.707 33.333 0.00 0.00 0.00 2.52
76 77 7.815641 AGGGTTCATGTTTGTTTTTCTTTTTG 58.184 30.769 0.00 0.00 0.00 2.44
450 466 0.819259 AGCAGTGGAGCGAGCAAAAA 60.819 50.000 0.00 0.00 40.15 1.94
485 503 1.000955 GAGTGGAACAGAGAGCCGAAA 59.999 52.381 0.00 0.00 41.80 3.46
489 507 4.000988 GTGGAACAGAGAGCCGAAATAAA 58.999 43.478 0.00 0.00 41.80 1.40
513 532 0.179108 CAGTAGCTTAGTGACCGGCC 60.179 60.000 0.00 0.00 0.00 6.13
514 533 1.143401 GTAGCTTAGTGACCGGCCC 59.857 63.158 0.00 0.00 0.00 5.80
522 541 3.632080 TGACCGGCCCGTGTGAAT 61.632 61.111 0.00 0.00 0.00 2.57
556 575 5.786311 CAGTTCCACAATTTCAACATGGAT 58.214 37.500 0.00 0.00 39.18 3.41
575 597 0.624500 TAAGCTCCCAAGGGGCTCAT 60.625 55.000 8.80 0.00 43.94 2.90
589 611 0.309922 GCTCATGCCATGACCATTCG 59.690 55.000 2.53 0.00 35.06 3.34
592 614 1.140652 TCATGCCATGACCATTCGCTA 59.859 47.619 2.53 0.00 33.59 4.26
598 620 2.355197 CATGACCATTCGCTAACACCA 58.645 47.619 0.00 0.00 0.00 4.17
602 624 3.252215 TGACCATTCGCTAACACCAAAAG 59.748 43.478 0.00 0.00 0.00 2.27
603 625 3.219281 ACCATTCGCTAACACCAAAAGT 58.781 40.909 0.00 0.00 0.00 2.66
643 665 3.421826 CGTAAGCACACATCGAACAACTC 60.422 47.826 0.00 0.00 0.00 3.01
650 672 3.181465 ACACATCGAACAACTCCACTCTT 60.181 43.478 0.00 0.00 0.00 2.85
655 677 3.637229 TCGAACAACTCCACTCTTCTCTT 59.363 43.478 0.00 0.00 0.00 2.85
667 689 7.974504 TCCACTCTTCTCTTAAACAAATACCT 58.025 34.615 0.00 0.00 0.00 3.08
669 691 9.067986 CCACTCTTCTCTTAAACAAATACCTTT 57.932 33.333 0.00 0.00 0.00 3.11
684 706 1.144913 ACCTTTTCTAGCAGCACCCAA 59.855 47.619 0.00 0.00 0.00 4.12
687 709 1.896220 TTTCTAGCAGCACCCAACAG 58.104 50.000 0.00 0.00 0.00 3.16
692 714 0.035056 AGCAGCACCCAACAGGATAC 60.035 55.000 0.00 0.00 39.89 2.24
694 716 1.683011 GCAGCACCCAACAGGATACAT 60.683 52.381 0.00 0.00 39.89 2.29
700 722 3.633525 CACCCAACAGGATACATGAATGG 59.366 47.826 0.00 0.00 39.89 3.16
744 768 6.440328 AGAACATAATTAACACCCAAGCCAAT 59.560 34.615 0.00 0.00 0.00 3.16
745 769 5.976458 ACATAATTAACACCCAAGCCAATG 58.024 37.500 0.00 0.00 0.00 2.82
746 770 5.483583 ACATAATTAACACCCAAGCCAATGT 59.516 36.000 0.00 0.00 0.00 2.71
754 2758 4.949856 ACACCCAAGCCAATGTAGATAAAG 59.050 41.667 0.00 0.00 0.00 1.85
762 2766 4.733523 GCCAATGTAGATAAAGCCAAACGG 60.734 45.833 0.00 0.00 0.00 4.44
838 2873 3.475566 AGCTGTTTGTGAAGTGCTCTA 57.524 42.857 0.00 0.00 0.00 2.43
839 2874 3.397482 AGCTGTTTGTGAAGTGCTCTAG 58.603 45.455 0.00 0.00 0.00 2.43
840 2875 3.134458 GCTGTTTGTGAAGTGCTCTAGT 58.866 45.455 0.00 0.00 0.00 2.57
841 2876 4.039245 AGCTGTTTGTGAAGTGCTCTAGTA 59.961 41.667 0.00 0.00 0.00 1.82
842 2877 4.932200 GCTGTTTGTGAAGTGCTCTAGTAT 59.068 41.667 0.00 0.00 0.00 2.12
843 2878 6.071334 AGCTGTTTGTGAAGTGCTCTAGTATA 60.071 38.462 0.00 0.00 0.00 1.47
844 2879 6.758886 GCTGTTTGTGAAGTGCTCTAGTATAT 59.241 38.462 0.00 0.00 0.00 0.86
845 2880 7.278868 GCTGTTTGTGAAGTGCTCTAGTATATT 59.721 37.037 0.00 0.00 0.00 1.28
846 2881 9.155975 CTGTTTGTGAAGTGCTCTAGTATATTT 57.844 33.333 0.00 0.00 0.00 1.40
847 2882 9.151471 TGTTTGTGAAGTGCTCTAGTATATTTC 57.849 33.333 0.00 0.00 0.00 2.17
850 2885 8.932945 TGTGAAGTGCTCTAGTATATTTCTTG 57.067 34.615 0.00 0.00 0.00 3.02
893 2931 8.417273 TTCTTTTTAGGGGTTTTAGAGAATGG 57.583 34.615 0.00 0.00 0.00 3.16
915 2953 5.134339 TGGGATGGGTATAGAGAATTTTGCT 59.866 40.000 0.00 0.00 0.00 3.91
996 3039 3.876589 TTCACTTCCTCGTGGCGGC 62.877 63.158 0.00 0.00 35.63 6.53
1066 3109 2.636830 CCGTCATCAAATGCTCCTTCT 58.363 47.619 0.00 0.00 0.00 2.85
1067 3110 2.611292 CCGTCATCAAATGCTCCTTCTC 59.389 50.000 0.00 0.00 0.00 2.87
1620 3663 0.817654 TGATGACGAAGATGGACGCT 59.182 50.000 0.00 0.00 0.00 5.07
1934 3977 4.883354 GCGAGGGGCAATGGAGGG 62.883 72.222 0.00 0.00 42.87 4.30
1971 4014 1.434555 GTGTGGCTATGTACAACGCA 58.565 50.000 17.91 10.80 0.00 5.24
2132 4175 2.250939 CGGCGTGCAAGGTCAAGAA 61.251 57.895 0.00 0.00 0.00 2.52
2267 4310 1.818674 GGGTGCAGGTACTCCAAATTG 59.181 52.381 0.00 0.00 34.60 2.32
2268 4311 2.554344 GGGTGCAGGTACTCCAAATTGA 60.554 50.000 0.00 0.00 34.60 2.57
2286 4329 6.869421 AATTGATCTTATTTTGCGGTTTCG 57.131 33.333 0.00 0.00 39.81 3.46
2289 4332 6.912203 TGATCTTATTTTGCGGTTTCGATA 57.088 33.333 0.00 0.00 39.00 2.92
2293 4336 6.539324 TCTTATTTTGCGGTTTCGATAAGTG 58.461 36.000 0.00 0.00 39.00 3.16
2304 4347 5.362263 GTTTCGATAAGTGGTATTAGCCCA 58.638 41.667 0.00 0.00 0.00 5.36
2305 4348 5.818678 TTCGATAAGTGGTATTAGCCCAT 57.181 39.130 0.00 0.00 33.76 4.00
2306 4349 5.818678 TCGATAAGTGGTATTAGCCCATT 57.181 39.130 0.00 0.00 33.76 3.16
2349 4395 8.691661 AATAATATGATGTCTAACCAACCACC 57.308 34.615 0.00 0.00 0.00 4.61
2350 4396 5.708736 ATATGATGTCTAACCAACCACCA 57.291 39.130 0.00 0.00 0.00 4.17
2351 4397 3.866703 TGATGTCTAACCAACCACCAA 57.133 42.857 0.00 0.00 0.00 3.67
2352 4398 3.482436 TGATGTCTAACCAACCACCAAC 58.518 45.455 0.00 0.00 0.00 3.77
2355 4401 2.175931 TGTCTAACCAACCACCAACCAT 59.824 45.455 0.00 0.00 0.00 3.55
2366 4412 5.313280 ACCACCAACCATTACTTTGAGTA 57.687 39.130 0.00 0.00 0.00 2.59
2370 4416 4.250464 CCAACCATTACTTTGAGTAGCGA 58.750 43.478 0.00 0.00 31.47 4.93
2371 4417 4.693566 CCAACCATTACTTTGAGTAGCGAA 59.306 41.667 0.00 0.00 31.47 4.70
2385 4431 6.582636 TGAGTAGCGAATGATCCTTATGTTT 58.417 36.000 0.00 0.00 0.00 2.83
2386 4432 7.047891 TGAGTAGCGAATGATCCTTATGTTTT 58.952 34.615 0.00 0.00 0.00 2.43
2387 4433 7.011389 TGAGTAGCGAATGATCCTTATGTTTTG 59.989 37.037 0.00 0.00 0.00 2.44
2411 4457 3.472652 AGAAAACAGTCGGTGTGCAATA 58.527 40.909 0.00 0.00 40.26 1.90
2414 4460 1.156736 ACAGTCGGTGTGCAATAAGC 58.843 50.000 0.00 0.00 45.96 3.09
2416 4462 0.036164 AGTCGGTGTGCAATAAGCCA 59.964 50.000 0.00 0.00 44.83 4.75
2432 4524 4.853924 AAGCCAAATCACTGGTTACTTG 57.146 40.909 0.00 0.00 38.86 3.16
2433 4525 4.098914 AGCCAAATCACTGGTTACTTGA 57.901 40.909 0.00 0.00 38.86 3.02
2656 4749 2.054453 GGGGCTGGTTGATCTTGCC 61.054 63.158 0.00 0.00 42.56 4.52
2689 4782 0.250424 ACCAAATGCAAGGCAAAGGC 60.250 50.000 0.00 0.00 43.62 4.35
2800 4893 1.181741 TGTCGAAGAGGCAGCTGTCT 61.182 55.000 23.48 23.48 36.95 3.41
3071 5170 4.640771 TCATTACCATATGCTCCCTTCC 57.359 45.455 0.00 0.00 0.00 3.46
3117 5216 4.699637 ACGAAACACACTCTGGTAATTCA 58.300 39.130 0.00 0.00 0.00 2.57
3125 5224 4.080129 ACACTCTGGTAATTCATGGCATCT 60.080 41.667 0.00 0.00 0.00 2.90
3144 5243 4.073293 TCTCTCTGTTCTTTGTTGGTCC 57.927 45.455 0.00 0.00 0.00 4.46
3175 5274 3.380637 ACCGATCTCGTGTATTTACTGCT 59.619 43.478 0.00 0.00 37.74 4.24
3232 5331 1.973281 CCCATCTTGTTGGCGCTGT 60.973 57.895 7.64 0.00 35.29 4.40
3334 5433 0.250467 CAGGACAGTTGAGGTGGTGG 60.250 60.000 0.00 0.00 0.00 4.61
3436 5535 4.647424 TTTTTGGGCAGTTAAGAGTGTG 57.353 40.909 0.00 0.00 0.00 3.82
3437 5536 1.604604 TTGGGCAGTTAAGAGTGTGC 58.395 50.000 0.00 0.00 35.07 4.57
3438 5537 0.764890 TGGGCAGTTAAGAGTGTGCT 59.235 50.000 0.00 0.00 36.15 4.40
3439 5538 1.974957 TGGGCAGTTAAGAGTGTGCTA 59.025 47.619 0.00 0.00 36.15 3.49
3440 5539 2.370519 TGGGCAGTTAAGAGTGTGCTAA 59.629 45.455 0.00 0.00 36.15 3.09
3441 5540 2.742589 GGGCAGTTAAGAGTGTGCTAAC 59.257 50.000 0.00 0.00 36.15 2.34
3442 5541 3.557264 GGGCAGTTAAGAGTGTGCTAACT 60.557 47.826 0.00 0.00 36.15 2.24
3443 5542 3.680458 GGCAGTTAAGAGTGTGCTAACTC 59.320 47.826 10.36 10.36 45.82 3.01
3484 5583 9.485591 TCGAAACTTTATTTCTCAAATAATCGC 57.514 29.630 13.00 0.00 41.51 4.58
3485 5584 9.272901 CGAAACTTTATTTCTCAAATAATCGCA 57.727 29.630 8.43 0.00 41.51 5.10
3488 5587 9.573133 AACTTTATTTCTCAAATAATCGCAAGG 57.427 29.630 2.97 0.00 41.51 3.61
3489 5588 8.739972 ACTTTATTTCTCAAATAATCGCAAGGT 58.260 29.630 2.97 0.00 41.51 3.50
3490 5589 9.226345 CTTTATTTCTCAAATAATCGCAAGGTC 57.774 33.333 2.97 0.00 41.51 3.85
3491 5590 6.757897 ATTTCTCAAATAATCGCAAGGTCA 57.242 33.333 0.00 0.00 38.47 4.02
3492 5591 6.757897 TTTCTCAAATAATCGCAAGGTCAT 57.242 33.333 0.00 0.00 38.47 3.06
3493 5592 6.757897 TTCTCAAATAATCGCAAGGTCATT 57.242 33.333 0.00 0.00 38.47 2.57
3494 5593 6.757897 TCTCAAATAATCGCAAGGTCATTT 57.242 33.333 0.00 0.00 24.57 2.32
3495 5594 7.857734 TCTCAAATAATCGCAAGGTCATTTA 57.142 32.000 0.00 0.00 23.98 1.40
3496 5595 7.693952 TCTCAAATAATCGCAAGGTCATTTAC 58.306 34.615 0.00 0.00 23.98 2.01
3497 5596 7.335673 TCTCAAATAATCGCAAGGTCATTTACA 59.664 33.333 0.00 0.00 23.98 2.41
3498 5597 7.821652 TCAAATAATCGCAAGGTCATTTACAA 58.178 30.769 0.00 0.00 23.98 2.41
3499 5598 7.967854 TCAAATAATCGCAAGGTCATTTACAAG 59.032 33.333 0.00 0.00 23.98 3.16
3639 5738 6.564328 CAAATAAAACCCAGATGCTTAGACC 58.436 40.000 0.00 0.00 0.00 3.85
3645 5744 3.780294 ACCCAGATGCTTAGACCACATTA 59.220 43.478 0.00 0.00 0.00 1.90
3685 5784 4.323715 GGTGGATCCATTCATTTGCCTTTT 60.324 41.667 19.62 0.00 35.97 2.27
3727 5828 4.326826 TGGCTGTTTTTCTGAGTAGATGG 58.673 43.478 0.00 0.00 31.81 3.51
3861 5965 3.668447 AGTGACAGAACTGCAGTATTGG 58.332 45.455 22.01 12.58 0.00 3.16
3869 5973 0.035152 CTGCAGTATTGGCCCACTGA 60.035 55.000 25.43 13.63 43.99 3.41
3871 5975 1.202989 TGCAGTATTGGCCCACTGAAA 60.203 47.619 25.43 13.95 43.99 2.69
3889 5993 7.360438 CCACTGAAATTACTTCTTGAGCTACAC 60.360 40.741 0.00 0.00 34.86 2.90
3957 6066 4.862447 CATGCCGCTGCTAGCCCA 62.862 66.667 13.29 2.00 38.18 5.36
3959 6068 3.643595 ATGCCGCTGCTAGCCCAAA 62.644 57.895 13.29 0.00 38.18 3.28
3961 6070 2.045926 CCGCTGCTAGCCCAAACT 60.046 61.111 13.29 0.00 38.18 2.66
3973 6082 2.109304 AGCCCAAACTGCTAAAACCCTA 59.891 45.455 0.00 0.00 37.28 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.258445 CCCAGCGAACCCTACAGTCT 61.258 60.000 0.00 0.00 0.00 3.24
1 2 1.218316 CCCAGCGAACCCTACAGTC 59.782 63.158 0.00 0.00 0.00 3.51
2 3 2.955881 GCCCAGCGAACCCTACAGT 61.956 63.158 0.00 0.00 0.00 3.55
4 5 3.712907 GGCCCAGCGAACCCTACA 61.713 66.667 0.00 0.00 0.00 2.74
11 12 2.143575 TACAAATGGGGCCCAGCGAA 62.144 55.000 31.98 12.27 36.75 4.70
14 15 1.329913 CCTTACAAATGGGGCCCAGC 61.330 60.000 31.98 7.78 36.75 4.85
24 25 3.306472 ACCACACACACCCTTACAAAT 57.694 42.857 0.00 0.00 0.00 2.32
42 43 1.995376 ACATGAACCCTCAACCAACC 58.005 50.000 0.00 0.00 34.49 3.77
43 44 3.132111 ACAAACATGAACCCTCAACCAAC 59.868 43.478 0.00 0.00 34.49 3.77
407 423 9.434420 GCTATCTCATAAAAAGCTGACTATCAT 57.566 33.333 0.00 0.00 0.00 2.45
414 430 5.819379 CCACTGCTATCTCATAAAAAGCTGA 59.181 40.000 6.53 0.00 36.39 4.26
450 466 3.146066 TCCACTCGCTTGCATAACTTTT 58.854 40.909 0.00 0.00 0.00 2.27
454 470 1.804151 TGTTCCACTCGCTTGCATAAC 59.196 47.619 0.00 0.00 0.00 1.89
461 479 0.037790 GCTCTCTGTTCCACTCGCTT 60.038 55.000 0.00 0.00 0.00 4.68
509 528 0.951525 TGTAACATTCACACGGGCCG 60.952 55.000 27.06 27.06 0.00 6.13
513 532 1.196808 GCCACTGTAACATTCACACGG 59.803 52.381 0.00 0.00 0.00 4.94
514 533 1.870402 TGCCACTGTAACATTCACACG 59.130 47.619 0.00 0.00 0.00 4.49
575 597 1.339535 TGTTAGCGAATGGTCATGGCA 60.340 47.619 0.00 0.00 0.00 4.92
580 602 2.552599 TTGGTGTTAGCGAATGGTCA 57.447 45.000 0.00 0.00 0.00 4.02
588 610 4.440758 CACATTTCACTTTTGGTGTTAGCG 59.559 41.667 0.00 0.00 45.50 4.26
589 611 5.348164 ACACATTTCACTTTTGGTGTTAGC 58.652 37.500 0.00 0.00 45.50 3.09
592 614 6.153680 TCCTTACACATTTCACTTTTGGTGTT 59.846 34.615 0.00 0.00 45.50 3.32
622 644 3.120649 GGAGTTGTTCGATGTGTGCTTAC 60.121 47.826 0.00 0.00 0.00 2.34
623 645 3.064207 GGAGTTGTTCGATGTGTGCTTA 58.936 45.455 0.00 0.00 0.00 3.09
626 648 1.069906 GTGGAGTTGTTCGATGTGTGC 60.070 52.381 0.00 0.00 0.00 4.57
643 665 8.622948 AAGGTATTTGTTTAAGAGAAGAGTGG 57.377 34.615 0.00 0.00 0.00 4.00
650 672 9.787435 TGCTAGAAAAGGTATTTGTTTAAGAGA 57.213 29.630 0.00 0.00 0.00 3.10
655 677 7.308951 GGTGCTGCTAGAAAAGGTATTTGTTTA 60.309 37.037 0.00 0.00 0.00 2.01
667 689 2.229792 CTGTTGGGTGCTGCTAGAAAA 58.770 47.619 0.00 0.00 0.00 2.29
669 691 0.036732 CCTGTTGGGTGCTGCTAGAA 59.963 55.000 0.00 0.00 0.00 2.10
710 734 8.671028 GGGTGTTAATTATGTTCTGATAACGTT 58.329 33.333 5.88 5.88 0.00 3.99
711 735 7.825270 TGGGTGTTAATTATGTTCTGATAACGT 59.175 33.333 0.00 0.00 0.00 3.99
712 736 8.203937 TGGGTGTTAATTATGTTCTGATAACG 57.796 34.615 0.00 0.00 0.00 3.18
732 756 4.202050 GCTTTATCTACATTGGCTTGGGTG 60.202 45.833 0.00 0.00 0.00 4.61
744 768 6.636562 TTTTTCCGTTTGGCTTTATCTACA 57.363 33.333 0.00 0.00 34.14 2.74
772 2807 4.433615 GCCGTTCTTCACTCATGAGATTA 58.566 43.478 29.27 10.67 35.83 1.75
806 2841 4.796231 ACAGCTAAGGCCGACGCG 62.796 66.667 3.53 3.53 39.73 6.01
811 2846 1.197721 CTTCACAAACAGCTAAGGCCG 59.802 52.381 0.00 0.00 39.73 6.13
812 2847 2.030805 CACTTCACAAACAGCTAAGGCC 60.031 50.000 0.00 0.00 39.73 5.19
815 2850 3.812053 AGAGCACTTCACAAACAGCTAAG 59.188 43.478 0.00 0.00 31.61 2.18
870 2905 6.951778 TCCCATTCTCTAAAACCCCTAAAAAG 59.048 38.462 0.00 0.00 0.00 2.27
893 2931 7.454225 ACTAGCAAAATTCTCTATACCCATCC 58.546 38.462 0.00 0.00 0.00 3.51
915 2953 5.453903 GCATATGCCCTTTTCAGAGAGACTA 60.454 44.000 17.26 0.00 34.31 2.59
976 3019 0.882927 CCGCCACGAGGAAGTGAAAA 60.883 55.000 1.86 0.00 44.43 2.29
977 3020 1.301401 CCGCCACGAGGAAGTGAAA 60.301 57.895 1.86 0.00 44.43 2.69
978 3021 2.342279 CCGCCACGAGGAAGTGAA 59.658 61.111 1.86 0.00 44.43 3.18
1300 3343 2.835895 GAGGAGCGAGGGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1671 3714 1.153289 CTGCATCCCCTTCCTGACG 60.153 63.158 0.00 0.00 0.00 4.35
1740 3783 0.038618 TGTTCCAGGTGACGATGTCG 60.039 55.000 0.11 0.11 46.33 4.35
1926 3969 0.254299 ACATCCCCCTTCCCTCCATT 60.254 55.000 0.00 0.00 0.00 3.16
1934 3977 1.276859 ACCCGGTAACATCCCCCTTC 61.277 60.000 0.00 0.00 0.00 3.46
1971 4014 4.718774 TCCTCACAGAGCTTCCTAATGATT 59.281 41.667 0.00 0.00 0.00 2.57
2132 4175 1.293458 ACCCTGACTCCATCATCCTCT 59.707 52.381 0.00 0.00 36.48 3.69
2235 4278 2.024655 ACCTGCACCCATCATCTCAAAT 60.025 45.455 0.00 0.00 0.00 2.32
2267 4310 7.373441 CACTTATCGAAACCGCAAAATAAGATC 59.627 37.037 6.87 0.00 33.20 2.75
2268 4311 7.186804 CACTTATCGAAACCGCAAAATAAGAT 58.813 34.615 6.87 0.00 33.20 2.40
2286 4329 7.390718 CCTTACAATGGGCTAATACCACTTATC 59.609 40.741 0.00 0.00 41.58 1.75
2289 4332 5.192923 TCCTTACAATGGGCTAATACCACTT 59.807 40.000 0.00 0.00 41.58 3.16
2293 4336 5.306114 AGTCCTTACAATGGGCTAATACC 57.694 43.478 0.00 0.00 37.83 2.73
2332 4378 2.817844 GGTTGGTGGTTGGTTAGACATC 59.182 50.000 0.00 0.00 0.00 3.06
2344 4390 4.178956 ACTCAAAGTAATGGTTGGTGGT 57.821 40.909 0.00 0.00 0.00 4.16
2349 4395 5.856126 TTCGCTACTCAAAGTAATGGTTG 57.144 39.130 0.00 0.00 29.00 3.77
2350 4396 6.170506 TCATTCGCTACTCAAAGTAATGGTT 58.829 36.000 0.00 0.00 29.00 3.67
2351 4397 5.730550 TCATTCGCTACTCAAAGTAATGGT 58.269 37.500 0.00 0.00 29.00 3.55
2352 4398 6.073548 GGATCATTCGCTACTCAAAGTAATGG 60.074 42.308 0.00 0.00 29.00 3.16
2355 4401 6.222038 AGGATCATTCGCTACTCAAAGTAA 57.778 37.500 0.00 0.00 29.00 2.24
2366 4412 6.949352 ATCAAAACATAAGGATCATTCGCT 57.051 33.333 0.00 0.00 0.00 4.93
2385 4431 3.496884 GCACACCGACTGTTTTCTATCAA 59.503 43.478 0.00 0.00 0.00 2.57
2386 4432 3.064207 GCACACCGACTGTTTTCTATCA 58.936 45.455 0.00 0.00 0.00 2.15
2387 4433 3.064207 TGCACACCGACTGTTTTCTATC 58.936 45.455 0.00 0.00 0.00 2.08
2411 4457 4.278419 GTCAAGTAACCAGTGATTTGGCTT 59.722 41.667 0.00 0.00 42.18 4.35
2414 4460 5.964958 ATGTCAAGTAACCAGTGATTTGG 57.035 39.130 0.00 0.00 44.09 3.28
2416 4462 9.959721 ACTAATATGTCAAGTAACCAGTGATTT 57.040 29.630 0.00 0.00 0.00 2.17
2537 4630 2.102438 GTAGCACTGCATCTGCGCA 61.102 57.895 10.98 10.98 45.83 6.09
2538 4631 1.760268 GAGTAGCACTGCATCTGCGC 61.760 60.000 0.00 0.00 45.83 6.09
2539 4632 0.459063 TGAGTAGCACTGCATCTGCG 60.459 55.000 3.30 0.00 45.83 5.18
2573 4666 0.114364 GGAGGAAGGCCCCTTTTCAA 59.886 55.000 0.00 0.00 36.49 2.69
2656 4749 5.355596 TGCATTTGGTGAAGTACTTTTTGG 58.644 37.500 10.02 0.00 0.00 3.28
2689 4782 2.094286 CACCAGACAGTCAGCTTCTAGG 60.094 54.545 2.66 0.00 0.00 3.02
2783 4876 1.181741 ACAGACAGCTGCCTCTTCGA 61.182 55.000 15.27 0.00 46.26 3.71
3071 5170 1.466167 CTTGCACGATGGAAGGTTCAG 59.534 52.381 10.05 0.00 41.35 3.02
3117 5216 4.298103 ACAAAGAACAGAGAGATGCCAT 57.702 40.909 0.00 0.00 0.00 4.40
3125 5224 3.199946 AGTGGACCAACAAAGAACAGAGA 59.800 43.478 0.00 0.00 0.00 3.10
3144 5243 4.288670 ACACGAGATCGGTATTACAGTG 57.711 45.455 7.22 0.00 44.95 3.66
3175 5274 7.489574 GGCACCTGAAAACAATTTTTGATAA 57.510 32.000 0.00 0.00 34.94 1.75
3232 5331 1.079819 GAGCACAGCTCGCAACCTA 60.080 57.895 2.96 0.00 45.85 3.08
3259 5358 1.880796 TTCGTGCACGCGATATGGG 60.881 57.895 33.63 5.25 40.76 4.00
3334 5433 2.223745 TCCGGCTAACAAGGTGTTTTC 58.776 47.619 0.00 0.00 41.45 2.29
3420 5519 2.742589 GTTAGCACACTCTTAACTGCCC 59.257 50.000 0.00 0.00 0.00 5.36
3421 5520 3.665190 AGTTAGCACACTCTTAACTGCC 58.335 45.455 0.00 0.00 30.73 4.85
3422 5521 4.912528 GAGTTAGCACACTCTTAACTGC 57.087 45.455 7.82 0.00 40.23 4.40
3458 5557 9.485591 GCGATTATTTGAGAAATAAAGTTTCGA 57.514 29.630 17.99 0.00 44.07 3.71
3459 5558 9.272901 TGCGATTATTTGAGAAATAAAGTTTCG 57.727 29.630 13.28 13.28 44.07 3.46
3462 5561 9.573133 CCTTGCGATTATTTGAGAAATAAAGTT 57.427 29.630 5.78 0.00 44.07 2.66
3463 5562 8.739972 ACCTTGCGATTATTTGAGAAATAAAGT 58.260 29.630 5.78 0.00 44.07 2.66
3464 5563 9.226345 GACCTTGCGATTATTTGAGAAATAAAG 57.774 33.333 5.78 5.08 44.07 1.85
3465 5564 8.735315 TGACCTTGCGATTATTTGAGAAATAAA 58.265 29.630 5.78 0.00 44.07 1.40
3466 5565 8.275015 TGACCTTGCGATTATTTGAGAAATAA 57.725 30.769 4.43 4.43 44.73 1.40
3467 5566 7.857734 TGACCTTGCGATTATTTGAGAAATA 57.142 32.000 0.00 0.00 32.38 1.40
3468 5567 6.757897 TGACCTTGCGATTATTTGAGAAAT 57.242 33.333 0.00 0.00 34.90 2.17
3469 5568 6.757897 ATGACCTTGCGATTATTTGAGAAA 57.242 33.333 0.00 0.00 0.00 2.52
3470 5569 6.757897 AATGACCTTGCGATTATTTGAGAA 57.242 33.333 0.00 0.00 0.00 2.87
3471 5570 6.757897 AAATGACCTTGCGATTATTTGAGA 57.242 33.333 0.00 0.00 0.00 3.27
3472 5571 7.471721 TGTAAATGACCTTGCGATTATTTGAG 58.528 34.615 0.00 0.00 0.00 3.02
3473 5572 7.384439 TGTAAATGACCTTGCGATTATTTGA 57.616 32.000 0.00 0.00 0.00 2.69
3474 5573 7.220683 CCTTGTAAATGACCTTGCGATTATTTG 59.779 37.037 0.00 0.00 0.00 2.32
3475 5574 7.093945 ACCTTGTAAATGACCTTGCGATTATTT 60.094 33.333 0.00 0.00 0.00 1.40
3476 5575 6.377146 ACCTTGTAAATGACCTTGCGATTATT 59.623 34.615 0.00 0.00 0.00 1.40
3477 5576 5.885912 ACCTTGTAAATGACCTTGCGATTAT 59.114 36.000 0.00 0.00 0.00 1.28
3478 5577 5.250200 ACCTTGTAAATGACCTTGCGATTA 58.750 37.500 0.00 0.00 0.00 1.75
3479 5578 4.079253 ACCTTGTAAATGACCTTGCGATT 58.921 39.130 0.00 0.00 0.00 3.34
3480 5579 3.686016 ACCTTGTAAATGACCTTGCGAT 58.314 40.909 0.00 0.00 0.00 4.58
3481 5580 3.134574 ACCTTGTAAATGACCTTGCGA 57.865 42.857 0.00 0.00 0.00 5.10
3482 5581 3.915437 AACCTTGTAAATGACCTTGCG 57.085 42.857 0.00 0.00 0.00 4.85
3483 5582 6.206829 ACTCTTAACCTTGTAAATGACCTTGC 59.793 38.462 0.00 0.00 0.00 4.01
3484 5583 7.228706 ACACTCTTAACCTTGTAAATGACCTTG 59.771 37.037 0.00 0.00 0.00 3.61
3485 5584 7.228706 CACACTCTTAACCTTGTAAATGACCTT 59.771 37.037 0.00 0.00 0.00 3.50
3486 5585 6.710744 CACACTCTTAACCTTGTAAATGACCT 59.289 38.462 0.00 0.00 0.00 3.85
3487 5586 6.567891 GCACACTCTTAACCTTGTAAATGACC 60.568 42.308 0.00 0.00 0.00 4.02
3488 5587 6.204882 AGCACACTCTTAACCTTGTAAATGAC 59.795 38.462 0.00 0.00 0.00 3.06
3489 5588 6.296026 AGCACACTCTTAACCTTGTAAATGA 58.704 36.000 0.00 0.00 0.00 2.57
3490 5589 6.560253 AGCACACTCTTAACCTTGTAAATG 57.440 37.500 0.00 0.00 0.00 2.32
3491 5590 7.937394 AGTTAGCACACTCTTAACCTTGTAAAT 59.063 33.333 0.00 0.00 0.00 1.40
3492 5591 7.277396 AGTTAGCACACTCTTAACCTTGTAAA 58.723 34.615 0.00 0.00 0.00 2.01
3493 5592 6.823497 AGTTAGCACACTCTTAACCTTGTAA 58.177 36.000 0.00 0.00 0.00 2.41
3494 5593 6.041182 TGAGTTAGCACACTCTTAACCTTGTA 59.959 38.462 14.46 0.00 43.32 2.41
3495 5594 5.163343 TGAGTTAGCACACTCTTAACCTTGT 60.163 40.000 14.46 0.00 43.32 3.16
3496 5595 5.297547 TGAGTTAGCACACTCTTAACCTTG 58.702 41.667 14.46 0.00 43.32 3.61
3497 5596 5.546621 TGAGTTAGCACACTCTTAACCTT 57.453 39.130 14.46 0.00 43.32 3.50
3498 5597 5.546621 TTGAGTTAGCACACTCTTAACCT 57.453 39.130 14.46 0.00 43.32 3.50
3499 5598 6.803154 AATTGAGTTAGCACACTCTTAACC 57.197 37.500 14.46 0.00 43.32 2.85
3546 5645 5.741673 GCACATTGCTTCCTTTTCCCTAAAA 60.742 40.000 0.00 0.00 40.96 1.52
3639 5738 3.438087 CAGAACAGAACAGGCCTAATGTG 59.562 47.826 3.98 8.87 0.00 3.21
3645 5744 1.062488 ACCCAGAACAGAACAGGCCT 61.062 55.000 0.00 0.00 0.00 5.19
3704 5805 4.761739 CCATCTACTCAGAAAAACAGCCAA 59.238 41.667 0.00 0.00 33.50 4.52
3708 5809 5.947228 TTGCCATCTACTCAGAAAAACAG 57.053 39.130 0.00 0.00 33.50 3.16
3767 5868 9.262358 GCCACACAAACCAGTTTTTAATTATTA 57.738 29.630 0.00 0.00 0.00 0.98
3770 5871 6.879400 AGCCACACAAACCAGTTTTTAATTA 58.121 32.000 0.00 0.00 0.00 1.40
3772 5873 5.351948 AGCCACACAAACCAGTTTTTAAT 57.648 34.783 0.00 0.00 0.00 1.40
3773 5874 4.810191 AGCCACACAAACCAGTTTTTAA 57.190 36.364 0.00 0.00 0.00 1.52
3781 5885 1.965754 GCCCAAAGCCACACAAACCA 61.966 55.000 0.00 0.00 34.35 3.67
3783 5887 4.436515 GCCCAAAGCCACACAAAC 57.563 55.556 0.00 0.00 34.35 2.93
3861 5965 4.379918 GCTCAAGAAGTAATTTCAGTGGGC 60.380 45.833 0.00 1.43 40.29 5.36
3889 5993 4.184629 CCACCACCTTATCTTCTTCTTCG 58.815 47.826 0.00 0.00 0.00 3.79
3957 6066 6.210784 GGAAAGGAATAGGGTTTTAGCAGTTT 59.789 38.462 0.00 0.00 0.00 2.66
3959 6068 5.262009 GGAAAGGAATAGGGTTTTAGCAGT 58.738 41.667 0.00 0.00 0.00 4.40
3961 6070 4.606210 GGGAAAGGAATAGGGTTTTAGCA 58.394 43.478 0.00 0.00 0.00 3.49
3973 6082 3.007542 GGGAGGCGGGAAAGGAAT 58.992 61.111 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.