Multiple sequence alignment - TraesCS4B01G022700

Loading Multiple Alignment...

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 TraesCS4B01G022700 chr4B 100.000 2411 0 0 1 2411 16784018 16786428 0.000000e+00 4453.0
1 TraesCS4B01G022700 chr4B 99.180 244 2 0 596 839 16784369 16784612 7.910000e-120 440.0
2 TraesCS4B01G022700 chr4B 99.180 244 2 0 352 595 16784613 16784856 7.910000e-120 440.0
3 TraesCS4B01G022700 chr4B 86.646 322 35 7 631 947 167919372 167919054 1.370000e-92 350.0
4 TraesCS4B01G022700 chr3B 99.394 1816 9 2 596 2411 555553186 555551373 0.000000e+00 3291.0
5 TraesCS4B01G022700 chr3B 88.560 1215 84 23 1224 2409 685078796 685077608 0.000000e+00 1423.0
6 TraesCS4B01G022700 chr3B 98.992 595 3 1 1 595 555553534 555552943 0.000000e+00 1062.0
7 TraesCS4B01G022700 chr3D 93.994 1848 69 17 596 2411 16447166 16449003 0.000000e+00 2760.0
8 TraesCS4B01G022700 chr3D 88.550 1214 81 23 1221 2409 32171969 32173149 0.000000e+00 1419.0
9 TraesCS4B01G022700 chr3D 96.796 593 17 2 1 591 16446814 16447406 0.000000e+00 989.0
10 TraesCS4B01G022700 chr5A 94.779 1743 44 16 596 2302 606396731 606395000 0.000000e+00 2671.0
11 TraesCS4B01G022700 chr5A 97.639 593 12 2 4 595 606397079 606396488 0.000000e+00 1016.0
12 TraesCS4B01G022700 chr5A 87.918 389 43 2 1 388 135038098 135037713 2.830000e-124 455.0
13 TraesCS4B01G022700 chr5A 86.301 219 24 6 381 594 475381175 475381392 1.440000e-57 233.0
14 TraesCS4B01G022700 chr5A 97.297 37 1 0 596 632 135037749 135037713 2.000000e-06 63.9
15 TraesCS4B01G022700 chr7D 93.179 1730 57 16 706 2411 446553579 446551887 0.000000e+00 2484.0
16 TraesCS4B01G022700 chr7D 96.269 134 5 0 462 595 446553579 446553446 1.120000e-53 220.0
17 TraesCS4B01G022700 chr4A 97.451 1373 14 5 596 1965 729647302 729645948 0.000000e+00 2322.0
18 TraesCS4B01G022700 chr4A 97.148 596 7 3 1 595 729647654 729647068 0.000000e+00 998.0
19 TraesCS4B01G022700 chr4A 97.418 581 12 3 1832 2411 729645949 729645371 0.000000e+00 987.0
20 TraesCS4B01G022700 chr2A 93.271 1397 54 13 1039 2411 46334480 46335860 0.000000e+00 2023.0
21 TraesCS4B01G022700 chr2A 96.154 598 20 3 1 595 46333721 46334318 0.000000e+00 974.0
22 TraesCS4B01G022700 chr2A 88.966 716 58 9 1495 2204 363365172 363365872 0.000000e+00 865.0
23 TraesCS4B01G022700 chr2A 96.806 407 12 1 596 1001 46334074 46334480 0.000000e+00 678.0
24 TraesCS4B01G022700 chr2A 87.267 322 34 6 631 947 648745695 648745376 6.340000e-96 361.0
25 TraesCS4B01G022700 chr6B 97.467 829 14 3 1142 1965 247037488 247036662 0.000000e+00 1408.0
26 TraesCS4B01G022700 chr6B 97.246 581 12 3 1832 2411 247036663 247036086 0.000000e+00 981.0
27 TraesCS4B01G022700 chr6B 91.608 715 38 9 1495 2204 247042266 247041569 0.000000e+00 968.0
28 TraesCS4B01G022700 chr3A 90.722 388 28 3 1 386 640035464 640035083 5.950000e-141 510.0
29 TraesCS4B01G022700 chr1A 88.626 422 33 6 1224 1634 505878737 505878320 1.290000e-137 499.0
30 TraesCS4B01G022700 chr1A 97.297 37 1 0 596 632 226565826 226565862 2.000000e-06 63.9
31 TraesCS4B01G022700 chr1D 86.842 456 39 8 942 1379 210228969 210228517 7.750000e-135 490.0
32 TraesCS4B01G022700 chr1D 88.489 139 15 1 941 1079 298144710 298144573 1.480000e-37 167.0
33 TraesCS4B01G022700 chr5B 86.475 451 40 7 944 1376 199657515 199657962 2.170000e-130 475.0
34 TraesCS4B01G022700 chr5B 86.301 219 24 6 381 594 640418401 640418618 1.440000e-57 233.0
35 TraesCS4B01G022700 chr6D 85.435 460 39 11 942 1378 472510517 472510063 1.020000e-123 453.0
36 TraesCS4B01G022700 chr6D 88.923 325 32 2 65 388 43959996 43960317 4.830000e-107 398.0
37 TraesCS4B01G022700 chr6D 97.297 37 1 0 596 632 43960281 43960317 2.000000e-06 63.9
38 TraesCS4B01G022700 chr2B 87.500 392 45 2 1 391 31912948 31913336 1.310000e-122 449.0
39 TraesCS4B01G022700 chrUn 86.301 219 24 6 381 594 62072307 62072524 1.440000e-57 233.0


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 TraesCS4B01G022700 chr4B 16784018 16786428 2410 False 1777.666667 4453 99.453333 1 2411 3 chr4B.!!$F1 2410
1 TraesCS4B01G022700 chr3B 555551373 555553534 2161 True 2176.500000 3291 99.193000 1 2411 2 chr3B.!!$R2 2410
2 TraesCS4B01G022700 chr3B 685077608 685078796 1188 True 1423.000000 1423 88.560000 1224 2409 1 chr3B.!!$R1 1185
3 TraesCS4B01G022700 chr3D 16446814 16449003 2189 False 1874.500000 2760 95.395000 1 2411 2 chr3D.!!$F2 2410
4 TraesCS4B01G022700 chr3D 32171969 32173149 1180 False 1419.000000 1419 88.550000 1221 2409 1 chr3D.!!$F1 1188
5 TraesCS4B01G022700 chr5A 606395000 606397079 2079 True 1843.500000 2671 96.209000 4 2302 2 chr5A.!!$R2 2298
6 TraesCS4B01G022700 chr7D 446551887 446553579 1692 True 1352.000000 2484 94.724000 462 2411 2 chr7D.!!$R1 1949
7 TraesCS4B01G022700 chr4A 729645371 729647654 2283 True 1435.666667 2322 97.339000 1 2411 3 chr4A.!!$R1 2410
8 TraesCS4B01G022700 chr2A 46333721 46335860 2139 False 1225.000000 2023 95.410333 1 2411 3 chr2A.!!$F2 2410
9 TraesCS4B01G022700 chr2A 363365172 363365872 700 False 865.000000 865 88.966000 1495 2204 1 chr2A.!!$F1 709
10 TraesCS4B01G022700 chr6B 247036086 247037488 1402 True 1194.500000 1408 97.356500 1142 2411 2 chr6B.!!$R2 1269
11 TraesCS4B01G022700 chr6B 247041569 247042266 697 True 968.000000 968 91.608000 1495 2204 1 chr6B.!!$R1 709

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
670 674 0.034756 TGAACTAGCCGCAAGAAGCA 59.965 50.0 0.0 0.0 46.13 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1755 1.067425 GTGTCTATGTGTGTGCCCGTA 60.067 52.381 0.0 0.0 0.0 4.02 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
444 448 3.412386 AGCACGGTTAAAATTCAGCTCT 58.588 40.909 0.00 0.00 0.00 4.09
471 475 9.745880 ATTTGATTTACATTCAGATCATCTTGC 57.254 29.630 0.00 0.00 0.00 4.01
472 476 8.515695 TTGATTTACATTCAGATCATCTTGCT 57.484 30.769 0.00 0.00 0.00 3.91
473 477 7.927048 TGATTTACATTCAGATCATCTTGCTG 58.073 34.615 0.00 0.00 0.00 4.41
474 478 5.746307 TTACATTCAGATCATCTTGCTGC 57.254 39.130 0.00 0.00 0.00 5.25
475 479 3.617284 ACATTCAGATCATCTTGCTGCA 58.383 40.909 0.00 0.00 0.00 4.41
476 480 4.014406 ACATTCAGATCATCTTGCTGCAA 58.986 39.130 15.16 15.16 0.00 4.08
477 481 4.142447 ACATTCAGATCATCTTGCTGCAAC 60.142 41.667 11.69 0.34 0.00 4.17
478 482 3.062122 TCAGATCATCTTGCTGCAACA 57.938 42.857 11.69 1.01 0.00 3.33
479 483 2.745821 TCAGATCATCTTGCTGCAACAC 59.254 45.455 11.69 0.03 0.00 3.32
480 484 2.089980 AGATCATCTTGCTGCAACACC 58.910 47.619 11.69 0.00 0.00 4.16
481 485 1.814394 GATCATCTTGCTGCAACACCA 59.186 47.619 11.69 0.00 0.00 4.17
482 486 0.953727 TCATCTTGCTGCAACACCAC 59.046 50.000 11.69 0.00 0.00 4.16
483 487 0.956633 CATCTTGCTGCAACACCACT 59.043 50.000 11.69 0.00 0.00 4.00
484 488 2.153645 CATCTTGCTGCAACACCACTA 58.846 47.619 11.69 0.00 0.00 2.74
485 489 1.593196 TCTTGCTGCAACACCACTAC 58.407 50.000 11.69 0.00 0.00 2.73
486 490 1.140852 TCTTGCTGCAACACCACTACT 59.859 47.619 11.69 0.00 0.00 2.57
487 491 1.949525 CTTGCTGCAACACCACTACTT 59.050 47.619 11.69 0.00 0.00 2.24
488 492 2.051334 TGCTGCAACACCACTACTTT 57.949 45.000 0.00 0.00 0.00 2.66
489 493 2.374184 TGCTGCAACACCACTACTTTT 58.626 42.857 0.00 0.00 0.00 2.27
490 494 2.357637 TGCTGCAACACCACTACTTTTC 59.642 45.455 0.00 0.00 0.00 2.29
491 495 2.618709 GCTGCAACACCACTACTTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
492 496 3.066760 GCTGCAACACCACTACTTTTCTT 59.933 43.478 0.00 0.00 0.00 2.52
493 497 4.601019 CTGCAACACCACTACTTTTCTTG 58.399 43.478 0.00 0.00 0.00 3.02
494 498 4.265893 TGCAACACCACTACTTTTCTTGA 58.734 39.130 0.00 0.00 0.00 3.02
495 499 4.887071 TGCAACACCACTACTTTTCTTGAT 59.113 37.500 0.00 0.00 0.00 2.57
496 500 6.058833 TGCAACACCACTACTTTTCTTGATA 58.941 36.000 0.00 0.00 0.00 2.15
497 501 6.204688 TGCAACACCACTACTTTTCTTGATAG 59.795 38.462 0.00 0.00 0.00 2.08
498 502 6.603095 CAACACCACTACTTTTCTTGATAGC 58.397 40.000 0.00 0.00 0.00 2.97
499 503 5.865085 ACACCACTACTTTTCTTGATAGCA 58.135 37.500 0.00 0.00 0.00 3.49
500 504 6.296026 ACACCACTACTTTTCTTGATAGCAA 58.704 36.000 0.00 0.00 0.00 3.91
501 505 6.770785 ACACCACTACTTTTCTTGATAGCAAA 59.229 34.615 0.00 0.00 32.73 3.68
502 506 7.078228 CACCACTACTTTTCTTGATAGCAAAC 58.922 38.462 0.00 0.00 32.73 2.93
503 507 6.770785 ACCACTACTTTTCTTGATAGCAAACA 59.229 34.615 0.00 0.00 32.73 2.83
504 508 7.284489 ACCACTACTTTTCTTGATAGCAAACAA 59.716 33.333 0.00 0.00 32.73 2.83
505 509 7.591426 CCACTACTTTTCTTGATAGCAAACAAC 59.409 37.037 0.00 0.00 32.73 3.32
506 510 7.591426 CACTACTTTTCTTGATAGCAAACAACC 59.409 37.037 0.00 0.00 32.73 3.77
507 511 6.463995 ACTTTTCTTGATAGCAAACAACCA 57.536 33.333 0.00 0.00 32.73 3.67
508 512 6.507023 ACTTTTCTTGATAGCAAACAACCAG 58.493 36.000 0.00 0.00 32.73 4.00
509 513 6.096846 ACTTTTCTTGATAGCAAACAACCAGT 59.903 34.615 0.00 0.00 32.73 4.00
510 514 6.463995 TTTCTTGATAGCAAACAACCAGTT 57.536 33.333 0.00 0.00 43.89 3.16
526 530 9.466497 AACAACCAGTTTCAGTCATCATATATT 57.534 29.630 0.00 0.00 37.03 1.28
527 531 8.896744 ACAACCAGTTTCAGTCATCATATATTG 58.103 33.333 0.00 0.00 0.00 1.90
528 532 7.502120 ACCAGTTTCAGTCATCATATATTGC 57.498 36.000 0.00 0.00 0.00 3.56
529 533 7.285566 ACCAGTTTCAGTCATCATATATTGCT 58.714 34.615 0.00 0.00 0.00 3.91
530 534 7.776969 ACCAGTTTCAGTCATCATATATTGCTT 59.223 33.333 0.00 0.00 0.00 3.91
531 535 8.627403 CCAGTTTCAGTCATCATATATTGCTTT 58.373 33.333 0.00 0.00 0.00 3.51
536 540 9.617523 TTCAGTCATCATATATTGCTTTTCTGA 57.382 29.630 0.00 0.00 0.00 3.27
537 541 9.788889 TCAGTCATCATATATTGCTTTTCTGAT 57.211 29.630 0.00 0.00 0.00 2.90
595 599 8.519526 AGAGATAGTTAATCGCTTAATGAGAGG 58.480 37.037 0.00 0.00 41.45 3.69
596 600 8.410673 AGATAGTTAATCGCTTAATGAGAGGA 57.589 34.615 0.00 0.00 39.79 3.71
597 601 8.861086 AGATAGTTAATCGCTTAATGAGAGGAA 58.139 33.333 0.00 0.00 39.79 3.36
598 602 8.819643 ATAGTTAATCGCTTAATGAGAGGAAC 57.180 34.615 0.00 0.00 0.00 3.62
599 603 6.049790 AGTTAATCGCTTAATGAGAGGAACC 58.950 40.000 0.00 0.00 0.00 3.62
600 604 4.762289 AATCGCTTAATGAGAGGAACCT 57.238 40.909 0.00 0.00 0.00 3.50
601 605 5.871396 AATCGCTTAATGAGAGGAACCTA 57.129 39.130 0.00 0.00 0.00 3.08
602 606 6.426646 AATCGCTTAATGAGAGGAACCTAT 57.573 37.500 0.00 0.00 0.00 2.57
603 607 5.871396 TCGCTTAATGAGAGGAACCTATT 57.129 39.130 0.00 0.00 0.00 1.73
604 608 6.971726 TCGCTTAATGAGAGGAACCTATTA 57.028 37.500 0.00 0.00 0.00 0.98
605 609 7.356089 TCGCTTAATGAGAGGAACCTATTAA 57.644 36.000 0.00 1.10 0.00 1.40
606 610 7.788026 TCGCTTAATGAGAGGAACCTATTAAA 58.212 34.615 0.00 0.00 0.00 1.52
607 611 8.429641 TCGCTTAATGAGAGGAACCTATTAAAT 58.570 33.333 0.00 0.00 0.00 1.40
608 612 9.706691 CGCTTAATGAGAGGAACCTATTAAATA 57.293 33.333 0.00 0.00 0.00 1.40
634 638 9.819267 AGTTATGTTAAGCTAGATGGTTTACTC 57.181 33.333 0.00 0.00 36.84 2.59
635 639 9.595823 GTTATGTTAAGCTAGATGGTTTACTCA 57.404 33.333 0.00 0.00 36.84 3.41
641 645 9.998106 TTAAGCTAGATGGTTTACTCATATTCC 57.002 33.333 0.00 0.00 37.56 3.01
642 646 7.618019 AGCTAGATGGTTTACTCATATTCCA 57.382 36.000 0.00 0.00 0.00 3.53
643 647 8.212259 AGCTAGATGGTTTACTCATATTCCAT 57.788 34.615 0.00 0.00 38.21 3.41
644 648 8.317679 AGCTAGATGGTTTACTCATATTCCATC 58.682 37.037 12.32 12.32 46.51 3.51
646 650 6.170675 GATGGTTTACTCATATTCCATCGC 57.829 41.667 0.00 0.00 40.79 4.58
647 651 5.290493 TGGTTTACTCATATTCCATCGCT 57.710 39.130 0.00 0.00 0.00 4.93
648 652 6.413783 TGGTTTACTCATATTCCATCGCTA 57.586 37.500 0.00 0.00 0.00 4.26
649 653 6.455647 TGGTTTACTCATATTCCATCGCTAG 58.544 40.000 0.00 0.00 0.00 3.42
650 654 6.266786 TGGTTTACTCATATTCCATCGCTAGA 59.733 38.462 0.00 0.00 0.00 2.43
651 655 7.039011 TGGTTTACTCATATTCCATCGCTAGAT 60.039 37.037 0.00 0.00 37.65 1.98
666 670 3.717400 CTAGATGAACTAGCCGCAAGA 57.283 47.619 0.00 0.00 41.45 3.02
667 671 4.046938 CTAGATGAACTAGCCGCAAGAA 57.953 45.455 0.00 0.00 41.45 2.52
668 672 2.898705 AGATGAACTAGCCGCAAGAAG 58.101 47.619 0.00 0.00 43.02 2.85
669 673 1.328986 GATGAACTAGCCGCAAGAAGC 59.671 52.381 0.00 0.00 43.02 3.86
670 674 0.034756 TGAACTAGCCGCAAGAAGCA 59.965 50.000 0.00 0.00 46.13 3.91
671 675 0.444260 GAACTAGCCGCAAGAAGCAC 59.556 55.000 0.00 0.00 46.13 4.40
672 676 1.291877 AACTAGCCGCAAGAAGCACG 61.292 55.000 0.00 0.00 46.13 5.34
676 680 3.960237 CCGCAAGAAGCACGGTTA 58.040 55.556 0.00 0.00 46.13 2.85
677 681 2.240230 CCGCAAGAAGCACGGTTAA 58.760 52.632 0.00 0.00 46.13 2.01
678 682 0.589223 CCGCAAGAAGCACGGTTAAA 59.411 50.000 0.00 0.00 46.13 1.52
679 683 1.002251 CCGCAAGAAGCACGGTTAAAA 60.002 47.619 0.00 0.00 46.13 1.52
680 684 2.351350 CCGCAAGAAGCACGGTTAAAAT 60.351 45.455 0.00 0.00 46.13 1.82
681 685 3.305110 CGCAAGAAGCACGGTTAAAATT 58.695 40.909 0.00 0.00 46.13 1.82
682 686 3.360758 CGCAAGAAGCACGGTTAAAATTC 59.639 43.478 0.00 0.00 46.13 2.17
683 687 4.295051 GCAAGAAGCACGGTTAAAATTCA 58.705 39.130 0.00 0.00 44.79 2.57
684 688 4.382754 GCAAGAAGCACGGTTAAAATTCAG 59.617 41.667 0.00 0.00 44.79 3.02
685 689 4.160736 AGAAGCACGGTTAAAATTCAGC 57.839 40.909 0.00 0.00 0.00 4.26
686 690 3.821033 AGAAGCACGGTTAAAATTCAGCT 59.179 39.130 0.00 0.00 0.00 4.24
687 691 3.831715 AGCACGGTTAAAATTCAGCTC 57.168 42.857 0.00 0.00 0.00 4.09
688 692 2.488153 AGCACGGTTAAAATTCAGCTCC 59.512 45.455 0.00 0.00 0.00 4.70
689 693 2.227865 GCACGGTTAAAATTCAGCTCCA 59.772 45.455 0.00 0.00 0.00 3.86
690 694 3.119495 GCACGGTTAAAATTCAGCTCCAT 60.119 43.478 0.00 0.00 0.00 3.41
691 695 4.618227 GCACGGTTAAAATTCAGCTCCATT 60.618 41.667 0.00 0.00 0.00 3.16
692 696 5.469479 CACGGTTAAAATTCAGCTCCATTT 58.531 37.500 0.00 0.00 0.00 2.32
693 697 5.345741 CACGGTTAAAATTCAGCTCCATTTG 59.654 40.000 1.20 0.00 0.00 2.32
694 698 5.242838 ACGGTTAAAATTCAGCTCCATTTGA 59.757 36.000 1.20 0.00 0.00 2.69
695 699 6.071391 ACGGTTAAAATTCAGCTCCATTTGAT 60.071 34.615 1.20 0.00 0.00 2.57
696 700 6.813152 CGGTTAAAATTCAGCTCCATTTGATT 59.187 34.615 1.20 0.00 0.00 2.57
697 701 7.331687 CGGTTAAAATTCAGCTCCATTTGATTT 59.668 33.333 1.20 0.00 0.00 2.17
698 702 9.651913 GGTTAAAATTCAGCTCCATTTGATTTA 57.348 29.630 1.20 0.00 0.00 1.40
702 706 9.729281 AAAATTCAGCTCCATTTGATTTACATT 57.271 25.926 1.20 0.00 0.00 2.71
703 707 8.937634 AATTCAGCTCCATTTGATTTACATTC 57.062 30.769 0.00 0.00 0.00 2.67
704 708 7.465353 TTCAGCTCCATTTGATTTACATTCA 57.535 32.000 0.00 0.00 0.00 2.57
705 709 7.092137 TCAGCTCCATTTGATTTACATTCAG 57.908 36.000 0.00 0.00 0.00 3.02
706 710 6.885918 TCAGCTCCATTTGATTTACATTCAGA 59.114 34.615 0.00 0.00 0.00 3.27
707 711 7.558807 TCAGCTCCATTTGATTTACATTCAGAT 59.441 33.333 0.00 0.00 0.00 2.90
708 712 7.861372 CAGCTCCATTTGATTTACATTCAGATC 59.139 37.037 0.00 0.00 0.00 2.75
709 713 7.558807 AGCTCCATTTGATTTACATTCAGATCA 59.441 33.333 0.00 0.00 0.00 2.92
1575 1592 8.425703 AGAAGCAGAGTAGGATAATAAAGGTTC 58.574 37.037 0.00 0.00 0.00 3.62
1576 1593 7.676683 AGCAGAGTAGGATAATAAAGGTTCA 57.323 36.000 0.00 0.00 0.00 3.18
1731 1755 7.123247 AGTTTCATTTGCAAATAGACCAGCTAT 59.877 33.333 23.69 4.32 41.59 2.97
1904 2091 5.023533 TGTACTCCAAGGCATTGATAGTC 57.976 43.478 13.66 9.82 38.83 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
466 470 1.140852 AGTAGTGGTGTTGCAGCAAGA 59.859 47.619 8.49 3.94 43.50 3.02
467 471 1.597742 AGTAGTGGTGTTGCAGCAAG 58.402 50.000 8.49 0.00 43.50 4.01
468 472 2.051334 AAGTAGTGGTGTTGCAGCAA 57.949 45.000 4.25 2.83 43.50 3.91
469 473 2.051334 AAAGTAGTGGTGTTGCAGCA 57.949 45.000 0.00 0.00 39.63 4.41
470 474 2.618709 AGAAAAGTAGTGGTGTTGCAGC 59.381 45.455 0.00 0.00 0.00 5.25
471 475 4.335315 TCAAGAAAAGTAGTGGTGTTGCAG 59.665 41.667 0.00 0.00 0.00 4.41
472 476 4.265893 TCAAGAAAAGTAGTGGTGTTGCA 58.734 39.130 0.00 0.00 0.00 4.08
473 477 4.893424 TCAAGAAAAGTAGTGGTGTTGC 57.107 40.909 0.00 0.00 0.00 4.17
474 478 6.204688 TGCTATCAAGAAAAGTAGTGGTGTTG 59.795 38.462 0.00 0.00 0.00 3.33
475 479 6.296026 TGCTATCAAGAAAAGTAGTGGTGTT 58.704 36.000 0.00 0.00 0.00 3.32
476 480 5.865085 TGCTATCAAGAAAAGTAGTGGTGT 58.135 37.500 0.00 0.00 0.00 4.16
477 481 6.801539 TTGCTATCAAGAAAAGTAGTGGTG 57.198 37.500 0.00 0.00 0.00 4.17
478 482 6.770785 TGTTTGCTATCAAGAAAAGTAGTGGT 59.229 34.615 0.00 0.00 30.44 4.16
479 483 7.202016 TGTTTGCTATCAAGAAAAGTAGTGG 57.798 36.000 0.00 0.00 30.44 4.00
480 484 7.591426 GGTTGTTTGCTATCAAGAAAAGTAGTG 59.409 37.037 0.00 0.00 30.44 2.74
481 485 7.284489 TGGTTGTTTGCTATCAAGAAAAGTAGT 59.716 33.333 0.00 0.00 30.44 2.73
482 486 7.648142 TGGTTGTTTGCTATCAAGAAAAGTAG 58.352 34.615 0.00 0.00 30.44 2.57
483 487 7.284489 ACTGGTTGTTTGCTATCAAGAAAAGTA 59.716 33.333 0.00 0.00 30.44 2.24
484 488 6.096846 ACTGGTTGTTTGCTATCAAGAAAAGT 59.903 34.615 0.00 0.00 30.44 2.66
485 489 6.507023 ACTGGTTGTTTGCTATCAAGAAAAG 58.493 36.000 0.00 0.00 30.44 2.27
486 490 6.463995 ACTGGTTGTTTGCTATCAAGAAAA 57.536 33.333 0.00 0.00 33.12 2.29
487 491 6.463995 AACTGGTTGTTTGCTATCAAGAAA 57.536 33.333 0.00 0.00 34.84 2.52
488 492 6.463995 AAACTGGTTGTTTGCTATCAAGAA 57.536 33.333 0.00 0.00 46.08 2.52
500 504 9.466497 AATATATGATGACTGAAACTGGTTGTT 57.534 29.630 0.00 0.00 41.29 2.83
501 505 8.896744 CAATATATGATGACTGAAACTGGTTGT 58.103 33.333 0.00 0.00 0.00 3.32
502 506 7.859377 GCAATATATGATGACTGAAACTGGTTG 59.141 37.037 0.00 0.00 0.00 3.77
503 507 7.776969 AGCAATATATGATGACTGAAACTGGTT 59.223 33.333 0.00 0.00 0.00 3.67
504 508 7.285566 AGCAATATATGATGACTGAAACTGGT 58.714 34.615 0.00 0.00 0.00 4.00
505 509 7.741027 AGCAATATATGATGACTGAAACTGG 57.259 36.000 0.00 0.00 0.00 4.00
510 514 9.617523 TCAGAAAAGCAATATATGATGACTGAA 57.382 29.630 0.00 0.00 32.77 3.02
511 515 9.788889 ATCAGAAAAGCAATATATGATGACTGA 57.211 29.630 0.00 0.00 36.70 3.41
568 572 9.906660 CTCTCATTAAGCGATTAACTATCTCTT 57.093 33.333 8.21 0.00 40.47 2.85
569 573 8.519526 CCTCTCATTAAGCGATTAACTATCTCT 58.480 37.037 8.21 0.00 29.58 3.10
570 574 8.516234 TCCTCTCATTAAGCGATTAACTATCTC 58.484 37.037 8.21 0.00 0.00 2.75
571 575 8.410673 TCCTCTCATTAAGCGATTAACTATCT 57.589 34.615 8.21 0.00 0.00 1.98
572 576 8.917655 GTTCCTCTCATTAAGCGATTAACTATC 58.082 37.037 8.21 0.00 0.00 2.08
573 577 7.873505 GGTTCCTCTCATTAAGCGATTAACTAT 59.126 37.037 8.21 0.00 0.00 2.12
574 578 7.069578 AGGTTCCTCTCATTAAGCGATTAACTA 59.930 37.037 8.21 0.00 0.00 2.24
575 579 6.049790 GGTTCCTCTCATTAAGCGATTAACT 58.950 40.000 8.21 0.00 0.00 2.24
576 580 6.049790 AGGTTCCTCTCATTAAGCGATTAAC 58.950 40.000 8.21 0.00 0.00 2.01
577 581 6.235231 AGGTTCCTCTCATTAAGCGATTAA 57.765 37.500 8.50 8.50 0.00 1.40
578 582 5.871396 AGGTTCCTCTCATTAAGCGATTA 57.129 39.130 0.00 0.00 0.00 1.75
579 583 4.762289 AGGTTCCTCTCATTAAGCGATT 57.238 40.909 0.00 0.00 0.00 3.34
580 584 6.426646 AATAGGTTCCTCTCATTAAGCGAT 57.573 37.500 0.00 0.00 0.00 4.58
581 585 5.871396 AATAGGTTCCTCTCATTAAGCGA 57.129 39.130 0.00 0.00 0.00 4.93
582 586 8.608844 ATTTAATAGGTTCCTCTCATTAAGCG 57.391 34.615 0.00 0.00 0.00 4.68
608 612 9.819267 GAGTAAACCATCTAGCTTAACATAACT 57.181 33.333 0.00 0.00 0.00 2.24
609 613 9.595823 TGAGTAAACCATCTAGCTTAACATAAC 57.404 33.333 0.00 0.00 0.00 1.89
615 619 9.998106 GGAATATGAGTAAACCATCTAGCTTAA 57.002 33.333 0.00 0.00 0.00 1.85
616 620 9.154632 TGGAATATGAGTAAACCATCTAGCTTA 57.845 33.333 0.00 0.00 0.00 3.09
617 621 8.034313 TGGAATATGAGTAAACCATCTAGCTT 57.966 34.615 0.00 0.00 0.00 3.74
618 622 7.618019 TGGAATATGAGTAAACCATCTAGCT 57.382 36.000 0.00 0.00 0.00 3.32
619 623 7.276658 CGATGGAATATGAGTAAACCATCTAGC 59.723 40.741 17.69 0.00 46.37 3.42
620 624 7.276658 GCGATGGAATATGAGTAAACCATCTAG 59.723 40.741 17.69 7.93 46.37 2.43
621 625 7.039011 AGCGATGGAATATGAGTAAACCATCTA 60.039 37.037 17.69 0.00 46.37 1.98
622 626 5.934625 GCGATGGAATATGAGTAAACCATCT 59.065 40.000 17.69 0.00 46.37 2.90
623 627 5.934625 AGCGATGGAATATGAGTAAACCATC 59.065 40.000 0.00 0.00 45.62 3.51
624 628 5.869579 AGCGATGGAATATGAGTAAACCAT 58.130 37.500 0.00 0.00 40.21 3.55
625 629 5.290493 AGCGATGGAATATGAGTAAACCA 57.710 39.130 0.00 0.00 0.00 3.67
626 630 6.688578 TCTAGCGATGGAATATGAGTAAACC 58.311 40.000 0.00 0.00 0.00 3.27
627 631 8.029522 TCATCTAGCGATGGAATATGAGTAAAC 58.970 37.037 0.00 0.00 45.66 2.01
628 632 8.122472 TCATCTAGCGATGGAATATGAGTAAA 57.878 34.615 0.00 0.00 45.66 2.01
629 633 7.703058 TCATCTAGCGATGGAATATGAGTAA 57.297 36.000 0.00 0.00 45.66 2.24
630 634 7.394641 AGTTCATCTAGCGATGGAATATGAGTA 59.605 37.037 0.00 0.00 45.66 2.59
631 635 6.210385 AGTTCATCTAGCGATGGAATATGAGT 59.790 38.462 0.00 0.00 45.66 3.41
632 636 6.629128 AGTTCATCTAGCGATGGAATATGAG 58.371 40.000 0.00 0.00 45.66 2.90
633 637 6.596309 AGTTCATCTAGCGATGGAATATGA 57.404 37.500 0.00 0.00 45.66 2.15
634 638 7.984002 CTAGTTCATCTAGCGATGGAATATG 57.016 40.000 0.00 0.00 45.66 1.78
646 650 3.717400 TCTTGCGGCTAGTTCATCTAG 57.283 47.619 11.06 0.00 46.39 2.43
647 651 3.738281 GCTTCTTGCGGCTAGTTCATCTA 60.738 47.826 11.06 0.00 0.00 1.98
648 652 2.898705 CTTCTTGCGGCTAGTTCATCT 58.101 47.619 11.06 0.00 0.00 2.90
649 653 1.328986 GCTTCTTGCGGCTAGTTCATC 59.671 52.381 11.06 0.00 0.00 2.92
650 654 1.339055 TGCTTCTTGCGGCTAGTTCAT 60.339 47.619 11.06 0.00 46.63 2.57
651 655 0.034756 TGCTTCTTGCGGCTAGTTCA 59.965 50.000 11.06 5.42 46.63 3.18
652 656 0.444260 GTGCTTCTTGCGGCTAGTTC 59.556 55.000 11.06 3.15 46.63 3.01
653 657 1.291877 CGTGCTTCTTGCGGCTAGTT 61.292 55.000 11.06 0.00 46.63 2.24
654 658 1.738099 CGTGCTTCTTGCGGCTAGT 60.738 57.895 11.06 0.00 46.63 2.57
655 659 2.456119 CCGTGCTTCTTGCGGCTAG 61.456 63.158 5.02 5.02 46.63 3.42
656 660 2.434185 CCGTGCTTCTTGCGGCTA 60.434 61.111 0.00 0.00 46.63 3.93
660 664 2.392933 TTTTAACCGTGCTTCTTGCG 57.607 45.000 0.00 0.00 46.63 4.85
661 665 4.295051 TGAATTTTAACCGTGCTTCTTGC 58.705 39.130 0.00 0.00 43.25 4.01
662 666 4.382754 GCTGAATTTTAACCGTGCTTCTTG 59.617 41.667 0.00 0.00 0.00 3.02
663 667 4.278419 AGCTGAATTTTAACCGTGCTTCTT 59.722 37.500 0.00 0.00 0.00 2.52
664 668 3.821033 AGCTGAATTTTAACCGTGCTTCT 59.179 39.130 0.00 0.00 0.00 2.85
665 669 4.159120 GAGCTGAATTTTAACCGTGCTTC 58.841 43.478 0.00 0.00 0.00 3.86
666 670 3.057526 GGAGCTGAATTTTAACCGTGCTT 60.058 43.478 0.00 0.00 0.00 3.91
667 671 2.488153 GGAGCTGAATTTTAACCGTGCT 59.512 45.455 0.00 0.00 0.00 4.40
668 672 2.227865 TGGAGCTGAATTTTAACCGTGC 59.772 45.455 0.00 0.00 0.00 5.34
669 673 4.701956 ATGGAGCTGAATTTTAACCGTG 57.298 40.909 0.00 0.00 0.00 4.94
670 674 5.242838 TCAAATGGAGCTGAATTTTAACCGT 59.757 36.000 0.00 0.00 0.00 4.83
671 675 5.708948 TCAAATGGAGCTGAATTTTAACCG 58.291 37.500 0.00 0.00 0.00 4.44
672 676 8.552083 AAATCAAATGGAGCTGAATTTTAACC 57.448 30.769 0.00 0.00 0.00 2.85
676 680 9.729281 AATGTAAATCAAATGGAGCTGAATTTT 57.271 25.926 0.00 0.00 0.00 1.82
677 681 9.374838 GAATGTAAATCAAATGGAGCTGAATTT 57.625 29.630 0.00 0.00 0.00 1.82
678 682 8.533657 TGAATGTAAATCAAATGGAGCTGAATT 58.466 29.630 0.00 0.00 0.00 2.17
679 683 8.070034 TGAATGTAAATCAAATGGAGCTGAAT 57.930 30.769 0.00 0.00 0.00 2.57
680 684 7.394077 TCTGAATGTAAATCAAATGGAGCTGAA 59.606 33.333 0.00 0.00 0.00 3.02
681 685 6.885918 TCTGAATGTAAATCAAATGGAGCTGA 59.114 34.615 0.00 0.00 0.00 4.26
682 686 7.092137 TCTGAATGTAAATCAAATGGAGCTG 57.908 36.000 0.00 0.00 0.00 4.24
683 687 7.558807 TGATCTGAATGTAAATCAAATGGAGCT 59.441 33.333 0.00 0.00 0.00 4.09
684 688 7.709947 TGATCTGAATGTAAATCAAATGGAGC 58.290 34.615 0.00 0.00 0.00 4.70
685 689 9.894783 GATGATCTGAATGTAAATCAAATGGAG 57.105 33.333 0.00 0.00 32.31 3.86
686 690 9.636789 AGATGATCTGAATGTAAATCAAATGGA 57.363 29.630 0.00 0.00 32.31 3.41
689 693 9.745880 GCAAGATGATCTGAATGTAAATCAAAT 57.254 29.630 0.00 0.00 32.31 2.32
690 694 8.963725 AGCAAGATGATCTGAATGTAAATCAAA 58.036 29.630 0.00 0.00 32.31 2.69
691 695 8.403236 CAGCAAGATGATCTGAATGTAAATCAA 58.597 33.333 0.00 0.00 32.31 2.57
692 696 7.468220 GCAGCAAGATGATCTGAATGTAAATCA 60.468 37.037 0.00 0.00 33.04 2.57
693 697 6.856938 GCAGCAAGATGATCTGAATGTAAATC 59.143 38.462 0.00 0.00 0.00 2.17
694 698 6.320418 TGCAGCAAGATGATCTGAATGTAAAT 59.680 34.615 0.00 0.00 0.00 1.40
695 699 5.648960 TGCAGCAAGATGATCTGAATGTAAA 59.351 36.000 0.00 0.00 0.00 2.01
696 700 5.187687 TGCAGCAAGATGATCTGAATGTAA 58.812 37.500 0.00 0.00 0.00 2.41
697 701 4.773013 TGCAGCAAGATGATCTGAATGTA 58.227 39.130 0.00 0.00 0.00 2.29
698 702 3.617284 TGCAGCAAGATGATCTGAATGT 58.383 40.909 0.00 0.00 0.00 2.71
699 703 4.142469 TGTTGCAGCAAGATGATCTGAATG 60.142 41.667 8.49 0.00 0.00 2.67
700 704 4.014406 TGTTGCAGCAAGATGATCTGAAT 58.986 39.130 8.49 0.00 0.00 2.57
701 705 3.189910 GTGTTGCAGCAAGATGATCTGAA 59.810 43.478 8.49 0.00 0.00 3.02
702 706 2.745821 GTGTTGCAGCAAGATGATCTGA 59.254 45.455 8.49 0.00 0.00 3.27
703 707 2.159421 GGTGTTGCAGCAAGATGATCTG 60.159 50.000 8.49 0.00 0.00 2.90
704 708 2.089980 GGTGTTGCAGCAAGATGATCT 58.910 47.619 8.49 0.00 0.00 2.75
705 709 1.814394 TGGTGTTGCAGCAAGATGATC 59.186 47.619 8.49 0.00 38.96 2.92
706 710 1.542915 GTGGTGTTGCAGCAAGATGAT 59.457 47.619 8.49 0.00 43.50 2.45
707 711 0.953727 GTGGTGTTGCAGCAAGATGA 59.046 50.000 8.49 0.00 43.50 2.92
708 712 0.956633 AGTGGTGTTGCAGCAAGATG 59.043 50.000 8.49 0.00 43.50 2.90
709 713 2.154462 GTAGTGGTGTTGCAGCAAGAT 58.846 47.619 8.49 0.00 43.50 2.40
1731 1755 1.067425 GTGTCTATGTGTGTGCCCGTA 60.067 52.381 0.00 0.00 0.00 4.02
1904 2091 5.479306 TCCAAGAACTTGAATTCGGTAGAG 58.521 41.667 14.99 0.00 42.93 2.43
2313 2665 2.786777 ACGTGAGGGGGTCAATAAAAC 58.213 47.619 0.00 0.00 36.74 2.43


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

AutoCloner maintained by Alex Coulton.