Multiple sequence alignment - TraesCS2D01G526900

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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 TraesCS2D01G526900 chr2D 100.000 3116 0 0 1 3116 614855395 614852280 0.000000e+00 5755.0
1 TraesCS2D01G526900 chr2D 91.071 560 48 2 1 560 241929842 241930399 0.000000e+00 756.0
2 TraesCS2D01G526900 chr2D 89.492 571 47 7 2 560 508975376 508975945 0.000000e+00 710.0
3 TraesCS2D01G526900 chr2D 85.828 628 83 4 1488 2115 614844335 614844956 0.000000e+00 662.0
4 TraesCS2D01G526900 chr2D 87.762 572 54 5 1 560 221403429 221403996 0.000000e+00 654.0
5 TraesCS2D01G526900 chr2D 77.886 823 152 20 1478 2292 649677308 649678108 4.670000e-133 484.0
6 TraesCS2D01G526900 chr2B 96.528 2160 32 12 600 2743 749239436 749237304 0.000000e+00 3533.0
7 TraesCS2D01G526900 chr2B 86.465 628 79 4 1488 2115 749231300 749231921 0.000000e+00 684.0
8 TraesCS2D01G526900 chr2B 92.988 328 3 2 2791 3116 749237300 749236991 7.870000e-126 460.0
9 TraesCS2D01G526900 chr2B 81.726 394 62 8 1715 2107 785348743 785349127 1.390000e-83 320.0
10 TraesCS2D01G526900 chr2B 93.651 63 3 1 2522 2584 749236667 749236606 3.310000e-15 93.5
11 TraesCS2D01G526900 chr6D 93.706 572 22 4 1 560 372183741 372184310 0.000000e+00 845.0
12 TraesCS2D01G526900 chr6A 92.133 572 16 8 1 560 29564052 29563498 0.000000e+00 780.0
13 TraesCS2D01G526900 chr6A 89.267 559 55 4 6 560 91531400 91530843 0.000000e+00 695.0
14 TraesCS2D01G526900 chr6A 75.625 640 125 14 1478 2115 609091874 609092484 3.930000e-74 289.0
15 TraesCS2D01G526900 chr4A 91.608 572 35 2 1 560 440580561 440579991 0.000000e+00 778.0
16 TraesCS2D01G526900 chr2A 91.971 548 30 3 25 560 758505888 758506433 0.000000e+00 756.0
17 TraesCS2D01G526900 chr2A 80.794 630 105 12 1481 2107 775186664 775186048 2.170000e-131 479.0
18 TraesCS2D01G526900 chr2A 79.730 592 110 6 1516 2107 775215875 775216456 1.340000e-113 420.0
19 TraesCS2D01G526900 chr2A 87.931 58 7 0 503 560 712335519 712335576 5.580000e-08 69.4
20 TraesCS2D01G526900 chr5A 92.218 514 27 2 59 560 521741454 521741966 0.000000e+00 715.0
21 TraesCS2D01G526900 chr5A 89.168 517 51 4 6 518 651936147 651936662 9.420000e-180 640.0
22 TraesCS2D01G526900 chr1A 88.193 559 46 10 6 560 569382328 569381786 0.000000e+00 649.0
23 TraesCS2D01G526900 chr1A 83.203 637 94 9 1481 2115 551813265 551812640 3.490000e-159 571.0
24 TraesCS2D01G526900 chr1D 83.014 730 105 12 1394 2115 460655919 460655201 0.000000e+00 643.0
25 TraesCS2D01G526900 chr7D 84.579 629 88 8 1488 2115 511213692 511214312 1.590000e-172 616.0
26 TraesCS2D01G526900 chr4D 90.426 282 27 0 279 560 362511017 362510736 3.800000e-99 372.0
27 TraesCS2D01G526900 chr4D 91.418 268 22 1 1 268 362597709 362597443 1.770000e-97 366.0
28 TraesCS2D01G526900 chr7B 89.825 285 13 8 2399 2670 6239159 6238878 4.940000e-93 351.0
29 TraesCS2D01G526900 chr7B 79.167 264 12 11 659 900 6257172 6256930 3.240000e-30 143.0
30 TraesCS2D01G526900 chr7B 95.652 69 3 0 1389 1457 6242008 6241940 9.130000e-21 111.0
31 TraesCS2D01G526900 chr4B 89.493 276 19 5 823 1090 673194610 673194883 1.070000e-89 340.0
32 TraesCS2D01G526900 chr4B 80.052 381 50 15 1570 1932 673170772 673170400 3.080000e-65 259.0
33 TraesCS2D01G526900 chr4B 88.889 144 12 3 1130 1270 673194886 673195028 1.150000e-39 174.0
34 TraesCS2D01G526900 chr4B 81.215 181 6 12 2443 2595 673195138 673195318 1.520000e-23 121.0
35 TraesCS2D01G526900 chr5D 76.138 549 103 18 1575 2115 494657883 494658411 2.380000e-66 263.0
36 TraesCS2D01G526900 chrUn 80.000 205 26 10 1483 1672 99840001 99840205 1.510000e-28 137.0


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 TraesCS2D01G526900 chr2D 614852280 614855395 3115 True 5755.000000 5755 100.000000 1 3116 1 chr2D.!!$R1 3115
1 TraesCS2D01G526900 chr2D 241929842 241930399 557 False 756.000000 756 91.071000 1 560 1 chr2D.!!$F2 559
2 TraesCS2D01G526900 chr2D 508975376 508975945 569 False 710.000000 710 89.492000 2 560 1 chr2D.!!$F3 558
3 TraesCS2D01G526900 chr2D 614844335 614844956 621 False 662.000000 662 85.828000 1488 2115 1 chr2D.!!$F4 627
4 TraesCS2D01G526900 chr2D 221403429 221403996 567 False 654.000000 654 87.762000 1 560 1 chr2D.!!$F1 559
5 TraesCS2D01G526900 chr2D 649677308 649678108 800 False 484.000000 484 77.886000 1478 2292 1 chr2D.!!$F5 814
6 TraesCS2D01G526900 chr2B 749236606 749239436 2830 True 1362.166667 3533 94.389000 600 3116 3 chr2B.!!$R1 2516
7 TraesCS2D01G526900 chr2B 749231300 749231921 621 False 684.000000 684 86.465000 1488 2115 1 chr2B.!!$F1 627
8 TraesCS2D01G526900 chr6D 372183741 372184310 569 False 845.000000 845 93.706000 1 560 1 chr6D.!!$F1 559
9 TraesCS2D01G526900 chr6A 29563498 29564052 554 True 780.000000 780 92.133000 1 560 1 chr6A.!!$R1 559
10 TraesCS2D01G526900 chr6A 91530843 91531400 557 True 695.000000 695 89.267000 6 560 1 chr6A.!!$R2 554
11 TraesCS2D01G526900 chr6A 609091874 609092484 610 False 289.000000 289 75.625000 1478 2115 1 chr6A.!!$F1 637
12 TraesCS2D01G526900 chr4A 440579991 440580561 570 True 778.000000 778 91.608000 1 560 1 chr4A.!!$R1 559
13 TraesCS2D01G526900 chr2A 758505888 758506433 545 False 756.000000 756 91.971000 25 560 1 chr2A.!!$F2 535
14 TraesCS2D01G526900 chr2A 775186048 775186664 616 True 479.000000 479 80.794000 1481 2107 1 chr2A.!!$R1 626
15 TraesCS2D01G526900 chr2A 775215875 775216456 581 False 420.000000 420 79.730000 1516 2107 1 chr2A.!!$F3 591
16 TraesCS2D01G526900 chr5A 521741454 521741966 512 False 715.000000 715 92.218000 59 560 1 chr5A.!!$F1 501
17 TraesCS2D01G526900 chr5A 651936147 651936662 515 False 640.000000 640 89.168000 6 518 1 chr5A.!!$F2 512
18 TraesCS2D01G526900 chr1A 569381786 569382328 542 True 649.000000 649 88.193000 6 560 1 chr1A.!!$R2 554
19 TraesCS2D01G526900 chr1A 551812640 551813265 625 True 571.000000 571 83.203000 1481 2115 1 chr1A.!!$R1 634
20 TraesCS2D01G526900 chr1D 460655201 460655919 718 True 643.000000 643 83.014000 1394 2115 1 chr1D.!!$R1 721
21 TraesCS2D01G526900 chr7D 511213692 511214312 620 False 616.000000 616 84.579000 1488 2115 1 chr7D.!!$F1 627
22 TraesCS2D01G526900 chr7B 6238878 6242008 3130 True 231.000000 351 92.738500 1389 2670 2 chr7B.!!$R2 1281
23 TraesCS2D01G526900 chr4B 673194610 673195318 708 False 211.666667 340 86.532333 823 2595 3 chr4B.!!$F1 1772
24 TraesCS2D01G526900 chr5D 494657883 494658411 528 False 263.000000 263 76.138000 1575 2115 1 chr5D.!!$F1 540

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
582 615 0.326264 CCAGTAAAGTCAGGGCTGCT 59.674 55.0 0.0 0.00 0.00 4.24 F
751 791 0.740164 CTGCTCTGCTACAGTGCCAG 60.740 60.0 16.4 11.01 46.35 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3071 0.036010 CACCACACCTCCTCCATGTC 60.036 60.0 0.0 0.0 0.00 3.06 R
2714 5438 0.815734 GGTGAGAGACCGATCCGAAA 59.184 55.0 0.0 0.0 34.02 3.46 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
78 79 8.770828 TGGTTTCTAAAACTCTAAATCAAGTCG 58.229 33.333 2.90 0.00 0.00 4.18
411 444 5.867330 TCAGGGGTAAAGTCGTATTTTCAA 58.133 37.500 0.00 0.00 0.00 2.69
518 551 9.623687 GAAGAAAAAGTTTTTCATTGTCGAATG 57.376 29.630 32.23 0.00 40.47 2.67
564 597 9.682465 AGTGTTAAATAAGGAATTCTCTAACCC 57.318 33.333 5.23 0.00 0.00 4.11
565 598 9.457436 GTGTTAAATAAGGAATTCTCTAACCCA 57.543 33.333 5.23 0.00 0.00 4.51
566 599 9.681062 TGTTAAATAAGGAATTCTCTAACCCAG 57.319 33.333 5.23 0.00 0.00 4.45
567 600 9.682465 GTTAAATAAGGAATTCTCTAACCCAGT 57.318 33.333 5.23 0.00 0.00 4.00
571 604 9.907229 AATAAGGAATTCTCTAACCCAGTAAAG 57.093 33.333 5.23 0.00 0.00 1.85
572 605 6.954352 AGGAATTCTCTAACCCAGTAAAGT 57.046 37.500 5.23 0.00 0.00 2.66
573 606 6.948589 AGGAATTCTCTAACCCAGTAAAGTC 58.051 40.000 5.23 0.00 0.00 3.01
574 607 6.500751 AGGAATTCTCTAACCCAGTAAAGTCA 59.499 38.462 5.23 0.00 0.00 3.41
575 608 6.819146 GGAATTCTCTAACCCAGTAAAGTCAG 59.181 42.308 5.23 0.00 0.00 3.51
576 609 5.740290 TTCTCTAACCCAGTAAAGTCAGG 57.260 43.478 0.00 0.00 0.00 3.86
577 610 4.094476 TCTCTAACCCAGTAAAGTCAGGG 58.906 47.826 0.00 0.00 46.96 4.45
578 611 2.570302 TCTAACCCAGTAAAGTCAGGGC 59.430 50.000 0.00 0.00 45.45 5.19
579 612 1.446016 AACCCAGTAAAGTCAGGGCT 58.554 50.000 0.00 0.00 45.45 5.19
580 613 0.693049 ACCCAGTAAAGTCAGGGCTG 59.307 55.000 0.00 0.00 45.45 4.85
581 614 0.678048 CCCAGTAAAGTCAGGGCTGC 60.678 60.000 0.00 0.00 33.91 5.25
582 615 0.326264 CCAGTAAAGTCAGGGCTGCT 59.674 55.000 0.00 0.00 0.00 4.24
583 616 1.271597 CCAGTAAAGTCAGGGCTGCTT 60.272 52.381 0.00 0.00 0.00 3.91
584 617 2.508526 CAGTAAAGTCAGGGCTGCTTT 58.491 47.619 0.00 0.98 38.96 3.51
585 618 3.559171 CCAGTAAAGTCAGGGCTGCTTTA 60.559 47.826 0.00 0.00 37.73 1.85
586 619 4.265073 CAGTAAAGTCAGGGCTGCTTTAT 58.735 43.478 0.00 0.00 39.20 1.40
587 620 4.702131 CAGTAAAGTCAGGGCTGCTTTATT 59.298 41.667 0.00 0.00 39.20 1.40
588 621 5.183904 CAGTAAAGTCAGGGCTGCTTTATTT 59.816 40.000 0.00 0.00 39.20 1.40
589 622 5.775195 AGTAAAGTCAGGGCTGCTTTATTTT 59.225 36.000 0.00 0.00 39.20 1.82
590 623 5.551305 AAAGTCAGGGCTGCTTTATTTTT 57.449 34.783 0.00 0.00 36.19 1.94
646 679 2.162338 TTGGTCTCCCACGTAAGCCG 62.162 60.000 0.00 0.00 41.67 5.52
712 752 2.360100 CTGCTGCCTGCTCTGCTT 60.360 61.111 0.00 0.00 43.37 3.91
747 787 1.220206 CCCCTGCTCTGCTACAGTG 59.780 63.158 0.00 0.00 32.61 3.66
748 788 1.449246 CCCTGCTCTGCTACAGTGC 60.449 63.158 13.22 13.22 46.84 4.40
749 789 1.449246 CCTGCTCTGCTACAGTGCC 60.449 63.158 16.40 2.83 46.35 5.01
750 790 1.294459 CTGCTCTGCTACAGTGCCA 59.706 57.895 16.40 6.45 46.35 4.92
751 791 0.740164 CTGCTCTGCTACAGTGCCAG 60.740 60.000 16.40 11.01 46.35 4.85
752 792 1.294780 GCTCTGCTACAGTGCCAGT 59.705 57.895 9.83 0.00 42.75 4.00
851 892 1.484240 CCCTCTTCCACACCTCTCATC 59.516 57.143 0.00 0.00 0.00 2.92
1120 1169 4.600576 TCAAGTGCGGCGAGTGCA 62.601 61.111 12.98 0.00 45.35 4.57
1173 1224 2.365617 CGACTGGGTGCTCAGGTATTAT 59.634 50.000 3.95 0.00 38.98 1.28
1439 1491 6.099845 GGGGACATAATAGAGGACTCTTTCAA 59.900 42.308 7.21 0.00 40.93 2.69
1563 2847 3.179939 GCCGACGTCGCCTTTCTC 61.180 66.667 31.73 10.12 38.18 2.87
1564 2848 2.257371 CCGACGTCGCCTTTCTCA 59.743 61.111 31.73 0.00 38.18 3.27
1778 3071 1.672356 CCAGCGACCAAGGTGAAGG 60.672 63.158 0.00 0.00 41.72 3.46
1790 3083 0.543749 GGTGAAGGACATGGAGGAGG 59.456 60.000 0.00 0.00 0.00 4.30
2202 3495 2.946785 AGTTCTCTAGGTATGGTCGGG 58.053 52.381 0.00 0.00 0.00 5.14
2322 3623 1.605710 GATGCATGAGGGTTGAATCGG 59.394 52.381 2.46 0.00 0.00 4.18
2743 5467 0.321996 GTCTCTCACCTTGTGGTCCC 59.678 60.000 0.00 0.00 46.60 4.46
2744 5468 1.185618 TCTCTCACCTTGTGGTCCCG 61.186 60.000 0.00 0.00 46.60 5.14
2746 5470 1.185618 TCTCACCTTGTGGTCCCGAG 61.186 60.000 0.00 0.00 46.60 4.63
2747 5471 2.358737 CACCTTGTGGTCCCGAGC 60.359 66.667 0.00 0.00 46.60 5.03
2748 5472 2.847234 ACCTTGTGGTCCCGAGCA 60.847 61.111 0.00 0.00 44.78 4.26
2749 5473 2.224159 ACCTTGTGGTCCCGAGCAT 61.224 57.895 0.00 0.00 44.78 3.79
2750 5474 0.907704 ACCTTGTGGTCCCGAGCATA 60.908 55.000 0.00 0.00 44.78 3.14
2751 5475 0.179073 CCTTGTGGTCCCGAGCATAG 60.179 60.000 0.00 1.76 41.20 2.23
2752 5476 0.824109 CTTGTGGTCCCGAGCATAGA 59.176 55.000 0.00 0.00 41.20 1.98
2753 5477 0.824109 TTGTGGTCCCGAGCATAGAG 59.176 55.000 0.00 0.00 41.20 2.43
2754 5478 0.324368 TGTGGTCCCGAGCATAGAGT 60.324 55.000 0.00 0.00 41.20 3.24
2755 5479 0.824759 GTGGTCCCGAGCATAGAGTT 59.175 55.000 0.00 0.00 41.20 3.01
2756 5480 1.112113 TGGTCCCGAGCATAGAGTTC 58.888 55.000 0.00 0.00 33.39 3.01
2757 5481 0.389757 GGTCCCGAGCATAGAGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
2758 5482 1.404843 GTCCCGAGCATAGAGTTCCT 58.595 55.000 0.00 0.00 0.00 3.36
2759 5483 1.067821 GTCCCGAGCATAGAGTTCCTG 59.932 57.143 0.00 0.00 0.00 3.86
2760 5484 1.063942 TCCCGAGCATAGAGTTCCTGA 60.064 52.381 0.00 0.00 0.00 3.86
2761 5485 1.067821 CCCGAGCATAGAGTTCCTGAC 59.932 57.143 0.00 0.00 0.00 3.51
2762 5486 1.751351 CCGAGCATAGAGTTCCTGACA 59.249 52.381 0.00 0.00 0.00 3.58
2763 5487 2.363680 CCGAGCATAGAGTTCCTGACAT 59.636 50.000 0.00 0.00 0.00 3.06
2764 5488 3.379240 CGAGCATAGAGTTCCTGACATG 58.621 50.000 0.00 0.00 0.00 3.21
2765 5489 3.067320 CGAGCATAGAGTTCCTGACATGA 59.933 47.826 0.00 0.00 0.00 3.07
2766 5490 4.261952 CGAGCATAGAGTTCCTGACATGAT 60.262 45.833 0.00 0.00 0.00 2.45
2767 5491 5.609423 GAGCATAGAGTTCCTGACATGATT 58.391 41.667 0.00 0.00 0.00 2.57
2768 5492 6.515696 CGAGCATAGAGTTCCTGACATGATTA 60.516 42.308 0.00 0.00 0.00 1.75
2769 5493 6.520272 AGCATAGAGTTCCTGACATGATTAC 58.480 40.000 0.00 0.00 0.00 1.89
2770 5494 6.326064 AGCATAGAGTTCCTGACATGATTACT 59.674 38.462 0.00 0.00 0.00 2.24
2771 5495 6.423302 GCATAGAGTTCCTGACATGATTACTG 59.577 42.308 0.00 0.00 0.00 2.74
2772 5496 4.764172 AGAGTTCCTGACATGATTACTGC 58.236 43.478 0.00 0.00 0.00 4.40
2773 5497 3.873952 GAGTTCCTGACATGATTACTGCC 59.126 47.826 0.00 0.00 0.00 4.85
2774 5498 3.264193 AGTTCCTGACATGATTACTGCCA 59.736 43.478 0.00 0.00 0.00 4.92
2775 5499 3.548745 TCCTGACATGATTACTGCCAG 57.451 47.619 0.00 0.00 0.00 4.85
2776 5500 1.945394 CCTGACATGATTACTGCCAGC 59.055 52.381 0.00 0.00 0.00 4.85
2777 5501 1.596260 CTGACATGATTACTGCCAGCG 59.404 52.381 0.00 0.00 0.00 5.18
2778 5502 1.066215 TGACATGATTACTGCCAGCGT 60.066 47.619 0.00 0.00 0.00 5.07
2779 5503 1.328680 GACATGATTACTGCCAGCGTG 59.671 52.381 0.00 0.00 0.00 5.34
2780 5504 0.028505 CATGATTACTGCCAGCGTGC 59.971 55.000 0.00 0.00 0.00 5.34
2781 5505 0.107508 ATGATTACTGCCAGCGTGCT 60.108 50.000 0.00 0.00 0.00 4.40
2782 5506 1.020861 TGATTACTGCCAGCGTGCTG 61.021 55.000 14.82 14.82 43.26 4.41
2783 5507 2.315038 GATTACTGCCAGCGTGCTGC 62.315 60.000 16.26 11.92 42.35 5.25
2967 5691 1.997311 CCTCTGCACCTGGGGATGA 60.997 63.158 0.00 0.00 0.00 2.92
2975 5699 0.779997 ACCTGGGGATGAACAAAGCT 59.220 50.000 0.00 0.00 0.00 3.74
2987 5711 7.414540 GGGATGAACAAAGCTAAGTGTAGAATG 60.415 40.741 0.00 0.00 0.00 2.67
3041 5767 4.997905 CACTGAAGTGGAATACTGTGTG 57.002 45.455 2.35 0.00 42.10 3.82
3042 5768 4.380531 CACTGAAGTGGAATACTGTGTGT 58.619 43.478 2.35 0.00 42.10 3.72
3043 5769 4.449068 CACTGAAGTGGAATACTGTGTGTC 59.551 45.833 2.35 0.00 42.10 3.67
3044 5770 4.345257 ACTGAAGTGGAATACTGTGTGTCT 59.655 41.667 0.00 0.00 40.26 3.41
3045 5771 4.631131 TGAAGTGGAATACTGTGTGTCTG 58.369 43.478 0.00 0.00 40.26 3.51
3046 5772 3.045601 AGTGGAATACTGTGTGTCTGC 57.954 47.619 0.00 0.00 38.49 4.26
3047 5773 2.368548 AGTGGAATACTGTGTGTCTGCA 59.631 45.455 0.00 0.00 38.49 4.41
3048 5774 3.008375 AGTGGAATACTGTGTGTCTGCAT 59.992 43.478 0.00 0.00 38.49 3.96
3049 5775 3.372206 GTGGAATACTGTGTGTCTGCATC 59.628 47.826 0.00 0.00 0.00 3.91
3050 5776 3.007831 TGGAATACTGTGTGTCTGCATCA 59.992 43.478 0.00 0.00 0.00 3.07
3051 5777 3.372206 GGAATACTGTGTGTCTGCATCAC 59.628 47.826 13.11 13.11 36.48 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.996727 GCACGCACACAATTTCCGAC 60.997 55.000 0.00 0.00 0.00 4.79
411 444 7.874016 TGACTATTAACGGTGTTAAATGACACT 59.126 33.333 8.16 0.00 47.00 3.55
431 464 7.448161 TGTGACACTTTCATCCATTTTGACTAT 59.552 33.333 7.20 0.00 36.32 2.12
489 522 7.700656 TCGACAATGAAAAACTTTTTCTTCCTC 59.299 33.333 21.95 14.17 0.00 3.71
509 542 1.988293 TTTCTTGCCCCATTCGACAA 58.012 45.000 0.00 0.00 0.00 3.18
518 551 5.221441 ACACTGTCTTAAATTTTCTTGCCCC 60.221 40.000 0.00 0.00 0.00 5.80
560 593 1.073923 CAGCCCTGACTTTACTGGGTT 59.926 52.381 0.00 0.00 46.34 4.11
561 594 0.693049 CAGCCCTGACTTTACTGGGT 59.307 55.000 0.00 0.00 46.34 4.51
563 596 0.326264 AGCAGCCCTGACTTTACTGG 59.674 55.000 0.00 0.00 0.00 4.00
564 597 2.191128 AAGCAGCCCTGACTTTACTG 57.809 50.000 0.00 0.00 0.00 2.74
565 598 2.959465 AAAGCAGCCCTGACTTTACT 57.041 45.000 12.65 0.00 36.19 2.24
566 599 5.644977 AAATAAAGCAGCCCTGACTTTAC 57.355 39.130 18.28 0.00 39.49 2.01
567 600 6.664428 AAAAATAAAGCAGCCCTGACTTTA 57.336 33.333 18.24 18.24 40.16 1.85
568 601 5.551305 AAAAATAAAGCAGCCCTGACTTT 57.449 34.783 16.19 16.19 38.96 2.66
587 620 1.408702 GCCCTGACTGTTGCTCAAAAA 59.591 47.619 0.00 0.00 0.00 1.94
588 621 1.032014 GCCCTGACTGTTGCTCAAAA 58.968 50.000 0.00 0.00 0.00 2.44
589 622 0.183492 AGCCCTGACTGTTGCTCAAA 59.817 50.000 0.00 0.00 0.00 2.69
590 623 0.535780 CAGCCCTGACTGTTGCTCAA 60.536 55.000 0.00 0.00 32.78 3.02
591 624 1.071987 CAGCCCTGACTGTTGCTCA 59.928 57.895 0.00 0.00 32.78 4.26
592 625 2.331132 GCAGCCCTGACTGTTGCTC 61.331 63.158 0.00 0.00 39.96 4.26
593 626 1.483595 TAGCAGCCCTGACTGTTGCT 61.484 55.000 7.47 7.47 46.03 3.91
594 627 1.003355 TAGCAGCCCTGACTGTTGC 60.003 57.895 0.00 0.00 39.96 4.17
595 628 0.322975 ACTAGCAGCCCTGACTGTTG 59.677 55.000 0.00 0.00 39.96 3.33
596 629 1.938585 TACTAGCAGCCCTGACTGTT 58.061 50.000 0.00 0.00 39.96 3.16
597 630 2.166907 ATACTAGCAGCCCTGACTGT 57.833 50.000 0.00 0.00 39.96 3.55
598 631 2.959030 TGTATACTAGCAGCCCTGACTG 59.041 50.000 4.17 0.00 40.80 3.51
646 679 1.302271 GGTCCACGTCAAGGAACCC 60.302 63.158 0.00 0.00 36.86 4.11
685 725 0.038526 CAGGCAGCAGCAAAAGAAGG 60.039 55.000 2.65 0.00 44.61 3.46
712 752 2.343758 GGGCGTGAGTGAGAGCAA 59.656 61.111 0.00 0.00 0.00 3.91
747 787 4.962836 ACTGGCACTGGCACTGGC 62.963 66.667 12.65 12.65 43.71 4.85
748 788 2.981909 CACTGGCACTGGCACTGG 60.982 66.667 0.07 0.00 43.71 4.00
749 789 3.667282 GCACTGGCACTGGCACTG 61.667 66.667 0.07 4.64 43.71 3.66
750 790 4.962836 GGCACTGGCACTGGCACT 62.963 66.667 14.26 0.00 43.71 4.40
833 874 1.484240 GGGATGAGAGGTGTGGAAGAG 59.516 57.143 0.00 0.00 0.00 2.85
1120 1169 3.782443 GAACGGGGGCGAGGTGAT 61.782 66.667 0.00 0.00 0.00 3.06
1563 2847 3.447025 GAACCTCTCCCCGCCGATG 62.447 68.421 0.00 0.00 0.00 3.84
1564 2848 3.155167 GAACCTCTCCCCGCCGAT 61.155 66.667 0.00 0.00 0.00 4.18
1778 3071 0.036010 CACCACACCTCCTCCATGTC 60.036 60.000 0.00 0.00 0.00 3.06
1790 3083 1.299648 TGGCTAGCCATCACCACAC 59.700 57.895 32.88 2.62 41.89 3.82
2322 3623 1.831580 ACTGCATCAAGAGGAAAGCC 58.168 50.000 0.00 0.00 31.69 4.35
2494 5182 2.018324 GCTCAACCAAAAGCAGCGC 61.018 57.895 0.00 0.00 38.42 5.92
2709 5433 3.117046 GAGAGACCGATCCGAAATTCAC 58.883 50.000 0.00 0.00 0.00 3.18
2710 5434 2.758423 TGAGAGACCGATCCGAAATTCA 59.242 45.455 0.00 0.00 0.00 2.57
2711 5435 3.117046 GTGAGAGACCGATCCGAAATTC 58.883 50.000 0.00 0.00 0.00 2.17
2712 5436 2.159085 GGTGAGAGACCGATCCGAAATT 60.159 50.000 0.00 0.00 34.02 1.82
2713 5437 1.409427 GGTGAGAGACCGATCCGAAAT 59.591 52.381 0.00 0.00 34.02 2.17
2714 5438 0.815734 GGTGAGAGACCGATCCGAAA 59.184 55.000 0.00 0.00 34.02 3.46
2715 5439 2.490165 GGTGAGAGACCGATCCGAA 58.510 57.895 0.00 0.00 34.02 4.30
2716 5440 4.237445 GGTGAGAGACCGATCCGA 57.763 61.111 0.00 0.00 34.02 4.55
2743 5467 3.067320 TCATGTCAGGAACTCTATGCTCG 59.933 47.826 0.00 0.00 34.60 5.03
2744 5468 4.662468 TCATGTCAGGAACTCTATGCTC 57.338 45.455 0.00 0.00 34.60 4.26
2746 5470 6.423302 CAGTAATCATGTCAGGAACTCTATGC 59.577 42.308 0.00 0.00 34.60 3.14
2747 5471 6.423302 GCAGTAATCATGTCAGGAACTCTATG 59.577 42.308 0.00 0.00 34.60 2.23
2748 5472 6.463614 GGCAGTAATCATGTCAGGAACTCTAT 60.464 42.308 0.00 0.00 34.60 1.98
2749 5473 5.163405 GGCAGTAATCATGTCAGGAACTCTA 60.163 44.000 0.00 0.00 34.60 2.43
2750 5474 4.383552 GGCAGTAATCATGTCAGGAACTCT 60.384 45.833 0.00 0.00 34.60 3.24
2751 5475 3.873952 GGCAGTAATCATGTCAGGAACTC 59.126 47.826 0.00 0.00 34.60 3.01
2752 5476 3.264193 TGGCAGTAATCATGTCAGGAACT 59.736 43.478 0.00 0.00 43.88 3.01
2753 5477 3.609853 TGGCAGTAATCATGTCAGGAAC 58.390 45.455 0.00 0.00 0.00 3.62
2754 5478 3.877559 CTGGCAGTAATCATGTCAGGAA 58.122 45.455 6.28 0.00 44.76 3.36
2755 5479 3.548745 CTGGCAGTAATCATGTCAGGA 57.451 47.619 6.28 0.00 44.76 3.86
2758 5482 1.066215 ACGCTGGCAGTAATCATGTCA 60.066 47.619 17.16 0.00 0.00 3.58
2759 5483 1.328680 CACGCTGGCAGTAATCATGTC 59.671 52.381 17.16 0.00 0.00 3.06
2760 5484 1.372582 CACGCTGGCAGTAATCATGT 58.627 50.000 17.16 1.12 0.00 3.21
2761 5485 0.028505 GCACGCTGGCAGTAATCATG 59.971 55.000 17.16 6.86 0.00 3.07
2762 5486 0.107508 AGCACGCTGGCAGTAATCAT 60.108 50.000 17.16 0.00 35.83 2.45
2763 5487 1.020861 CAGCACGCTGGCAGTAATCA 61.021 55.000 17.16 0.00 40.17 2.57
2764 5488 1.717937 CAGCACGCTGGCAGTAATC 59.282 57.895 17.16 3.74 40.17 1.75
2765 5489 2.401766 GCAGCACGCTGGCAGTAAT 61.402 57.895 20.00 0.00 43.77 1.89
2766 5490 3.049674 GCAGCACGCTGGCAGTAA 61.050 61.111 20.00 0.00 43.77 2.24
2779 5503 4.704833 TTCGGACAGGCAGGCAGC 62.705 66.667 0.00 0.00 44.65 5.25
2780 5504 2.743928 GTTCGGACAGGCAGGCAG 60.744 66.667 0.00 0.00 0.00 4.85
2781 5505 3.241530 AGTTCGGACAGGCAGGCA 61.242 61.111 0.00 0.00 0.00 4.75
2782 5506 2.731691 TTCAGTTCGGACAGGCAGGC 62.732 60.000 0.00 0.00 0.00 4.85
2783 5507 0.036010 ATTCAGTTCGGACAGGCAGG 60.036 55.000 0.00 0.00 0.00 4.85
2784 5508 1.066573 AGATTCAGTTCGGACAGGCAG 60.067 52.381 0.00 0.00 0.00 4.85
2785 5509 0.976641 AGATTCAGTTCGGACAGGCA 59.023 50.000 0.00 0.00 0.00 4.75
2786 5510 2.961526 TAGATTCAGTTCGGACAGGC 57.038 50.000 0.00 0.00 0.00 4.85
2787 5511 4.098654 ACAGATAGATTCAGTTCGGACAGG 59.901 45.833 0.00 0.00 0.00 4.00
2788 5512 5.255710 ACAGATAGATTCAGTTCGGACAG 57.744 43.478 0.00 0.00 0.00 3.51
2789 5513 5.661056 AACAGATAGATTCAGTTCGGACA 57.339 39.130 0.00 0.00 28.75 4.02
2967 5691 7.639945 GTGTTCATTCTACACTTAGCTTTGTT 58.360 34.615 0.00 0.00 41.99 2.83
2987 5711 2.919228 AGGTGTTCCACTTCAGTGTTC 58.081 47.619 6.22 0.00 44.21 3.18
3038 5764 2.158914 AGAACAGTGTGATGCAGACACA 60.159 45.455 25.63 23.16 45.19 3.72
3039 5765 2.487934 AGAACAGTGTGATGCAGACAC 58.512 47.619 19.45 19.45 43.45 3.67
3040 5766 2.916702 AGAACAGTGTGATGCAGACA 57.083 45.000 0.00 0.00 29.61 3.41
3041 5767 5.174395 AGAATAGAACAGTGTGATGCAGAC 58.826 41.667 0.00 0.00 0.00 3.51
3042 5768 5.411831 AGAATAGAACAGTGTGATGCAGA 57.588 39.130 0.00 0.00 0.00 4.26
3043 5769 6.035435 GTGTAGAATAGAACAGTGTGATGCAG 59.965 42.308 0.00 0.00 0.00 4.41
3044 5770 5.869344 GTGTAGAATAGAACAGTGTGATGCA 59.131 40.000 0.00 0.00 0.00 3.96
3045 5771 5.292101 GGTGTAGAATAGAACAGTGTGATGC 59.708 44.000 0.00 0.00 0.00 3.91
3046 5772 5.516696 CGGTGTAGAATAGAACAGTGTGATG 59.483 44.000 0.00 0.00 0.00 3.07
3047 5773 5.185249 ACGGTGTAGAATAGAACAGTGTGAT 59.815 40.000 0.00 0.00 0.00 3.06
3048 5774 4.521639 ACGGTGTAGAATAGAACAGTGTGA 59.478 41.667 0.00 0.00 0.00 3.58
3049 5775 4.621460 CACGGTGTAGAATAGAACAGTGTG 59.379 45.833 0.00 0.00 33.16 3.82
3050 5776 4.280174 ACACGGTGTAGAATAGAACAGTGT 59.720 41.667 12.96 5.02 40.39 3.55
3051 5777 4.806330 ACACGGTGTAGAATAGAACAGTG 58.194 43.478 12.96 3.88 39.09 3.66


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

AutoCloner maintained by Alex Coulton.