Multiple sequence alignment - TraesCS2D01G185100

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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 TraesCS2D01G185100 chr2D 100.000 3212 0 0 1 3212 130079745 130076534 0.000000e+00 5932.0
1 TraesCS2D01G185100 chr2D 98.002 2602 44 3 613 3212 617340745 617343340 0.000000e+00 4510.0
2 TraesCS2D01G185100 chr2D 82.143 84 13 1 2727 2808 573424733 573424816 1.600000e-08 71.3
3 TraesCS2D01G185100 chr4D 98.120 2607 40 4 609 3212 491381486 491384086 0.000000e+00 4534.0
4 TraesCS2D01G185100 chr3D 98.040 2602 44 2 613 3212 334133 336729 0.000000e+00 4516.0
5 TraesCS2D01G185100 chr3D 97.654 2600 46 4 613 3212 468955024 468957608 0.000000e+00 4449.0
6 TraesCS2D01G185100 chr1D 97.886 2602 49 2 612 3212 316243969 316241373 0.000000e+00 4495.0
7 TraesCS2D01G185100 chr1D 87.273 165 20 1 445 608 221918425 221918589 1.520000e-43 187.0
8 TraesCS2D01G185100 chr6D 97.425 2602 55 6 613 3212 420171217 420173808 0.000000e+00 4423.0
9 TraesCS2D01G185100 chr5D 97.196 2603 59 5 613 3212 78602934 78600343 0.000000e+00 4390.0
10 TraesCS2D01G185100 chr5D 98.148 2052 32 2 612 2662 555413535 555415581 0.000000e+00 3574.0
11 TraesCS2D01G185100 chr4A 95.636 2612 79 16 613 3212 731637348 731634760 0.000000e+00 4159.0
12 TraesCS2D01G185100 chr7A 95.698 1813 57 8 1403 3212 70256082 70254288 0.000000e+00 2896.0
13 TraesCS2D01G185100 chr7A 79.503 483 82 12 2747 3212 658704101 658703619 8.590000e-86 327.0
14 TraesCS2D01G185100 chr2B 93.252 904 46 2 2310 3212 191887813 191886924 0.000000e+00 1317.0
15 TraesCS2D01G185100 chr2B 96.114 386 11 2 35 420 183513482 183513101 7.560000e-176 627.0
16 TraesCS2D01G185100 chr2B 89.524 210 9 5 414 621 183513044 183512846 1.480000e-63 254.0
17 TraesCS2D01G185100 chr2B 91.667 168 14 0 441 608 214649922 214649755 1.930000e-57 233.0
18 TraesCS2D01G185100 chr2B 100.000 36 0 0 1 36 183513611 183513576 2.070000e-07 67.6
19 TraesCS2D01G185100 chr3B 80.710 451 74 5 2775 3212 389494265 389493815 3.970000e-89 339.0
20 TraesCS2D01G185100 chr3B 87.931 174 14 3 441 608 119419805 119419977 7.030000e-47 198.0
21 TraesCS2D01G185100 chr2A 93.373 166 11 0 445 610 601332315 601332480 2.470000e-61 246.0
22 TraesCS2D01G185100 chr7B 94.175 103 6 0 452 554 216674640 216674538 1.190000e-34 158.0
23 TraesCS2D01G185100 chr1B 93.182 88 4 1 445 530 317791724 317791637 9.350000e-26 128.0


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 TraesCS2D01G185100 chr2D 130076534 130079745 3211 True 5932.0 5932 100.000000 1 3212 1 chr2D.!!$R1 3211
1 TraesCS2D01G185100 chr2D 617340745 617343340 2595 False 4510.0 4510 98.002000 613 3212 1 chr2D.!!$F2 2599
2 TraesCS2D01G185100 chr4D 491381486 491384086 2600 False 4534.0 4534 98.120000 609 3212 1 chr4D.!!$F1 2603
3 TraesCS2D01G185100 chr3D 334133 336729 2596 False 4516.0 4516 98.040000 613 3212 1 chr3D.!!$F1 2599
4 TraesCS2D01G185100 chr3D 468955024 468957608 2584 False 4449.0 4449 97.654000 613 3212 1 chr3D.!!$F2 2599
5 TraesCS2D01G185100 chr1D 316241373 316243969 2596 True 4495.0 4495 97.886000 612 3212 1 chr1D.!!$R1 2600
6 TraesCS2D01G185100 chr6D 420171217 420173808 2591 False 4423.0 4423 97.425000 613 3212 1 chr6D.!!$F1 2599
7 TraesCS2D01G185100 chr5D 78600343 78602934 2591 True 4390.0 4390 97.196000 613 3212 1 chr5D.!!$R1 2599
8 TraesCS2D01G185100 chr5D 555413535 555415581 2046 False 3574.0 3574 98.148000 612 2662 1 chr5D.!!$F1 2050
9 TraesCS2D01G185100 chr4A 731634760 731637348 2588 True 4159.0 4159 95.636000 613 3212 1 chr4A.!!$R1 2599
10 TraesCS2D01G185100 chr7A 70254288 70256082 1794 True 2896.0 2896 95.698000 1403 3212 1 chr7A.!!$R1 1809
11 TraesCS2D01G185100 chr2B 191886924 191887813 889 True 1317.0 1317 93.252000 2310 3212 1 chr2B.!!$R1 902
12 TraesCS2D01G185100 chr2B 183512846 183513611 765 True 316.2 627 95.212667 1 621 3 chr2B.!!$R3 620

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
566 725 0.037590 TTGGCAAAGTAGCGGTGGAT 59.962 50.0 0.00 0.0 34.64 3.41 F
567 726 0.037590 TGGCAAAGTAGCGGTGGATT 59.962 50.0 0.00 0.0 34.64 3.01 F
601 760 0.038343 TGAAAAGGCTGAAATGCGCC 60.038 50.0 4.18 0.0 46.65 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1831 2.038426 CACCACAGTTCACACCATCCTA 59.962 50.000 0.00 0.0 0.0 2.94 R
1771 1945 2.494888 TGAGCCTCATTATCCTGGGA 57.505 50.000 0.00 0.0 0.0 4.37 R
2257 2433 3.782523 AGACTGATCATTCCTAGGCCAAA 59.217 43.478 5.01 0.0 0.0 3.28 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
75 171 5.515797 TCTAGACTTGTACCATTCCATCG 57.484 43.478 0.00 0.00 0.00 3.84
92 188 5.556355 CCATCGTTGGATCATATGGAATG 57.444 43.478 6.68 0.00 46.92 2.67
145 241 0.708918 GTTCAGCACTAACGACGAGC 59.291 55.000 0.00 0.00 0.00 5.03
146 242 0.312729 TTCAGCACTAACGACGAGCA 59.687 50.000 0.00 0.00 0.00 4.26
271 367 3.624861 GCATTGTATCTGTGAGTTGGGAG 59.375 47.826 0.00 0.00 0.00 4.30
301 397 4.778534 TCCTAGTCGTAAACAAGGTGAG 57.221 45.455 0.00 0.00 0.00 3.51
304 400 4.022589 CCTAGTCGTAAACAAGGTGAGTGA 60.023 45.833 0.00 0.00 0.00 3.41
388 484 4.034510 GGAACTCCGCATAATCTGAAACTG 59.965 45.833 0.00 0.00 0.00 3.16
409 505 3.181472 TGCACTATGATACCTCAGTGCTG 60.181 47.826 21.86 0.00 46.18 4.41
427 586 3.265791 GCTGCTACTAACTGAATGCACT 58.734 45.455 0.00 0.00 0.00 4.40
432 591 7.348080 TGCTACTAACTGAATGCACTATAGT 57.652 36.000 0.00 0.00 0.00 2.12
454 613 3.128415 TGATCACATTATGGCCGTGTTTG 59.872 43.478 8.05 4.91 32.42 2.93
479 638 0.179179 GCTTCGGCTTGCACAGAATC 60.179 55.000 0.00 0.00 38.08 2.52
482 641 1.136147 CGGCTTGCACAGAATCAGC 59.864 57.895 0.00 0.00 0.00 4.26
483 642 1.303799 CGGCTTGCACAGAATCAGCT 61.304 55.000 4.44 0.00 0.00 4.24
484 643 0.170561 GGCTTGCACAGAATCAGCTG 59.829 55.000 7.63 7.63 41.63 4.24
496 655 3.341823 GAATCAGCTGTGGATTCACTGT 58.658 45.455 14.67 0.00 46.26 3.55
497 656 2.174363 TCAGCTGTGGATTCACTGTG 57.826 50.000 14.67 0.17 43.94 3.66
498 657 1.162698 CAGCTGTGGATTCACTGTGG 58.837 55.000 12.18 2.06 43.94 4.17
499 658 0.767375 AGCTGTGGATTCACTGTGGT 59.233 50.000 12.18 2.68 43.94 4.16
500 659 0.877071 GCTGTGGATTCACTGTGGTG 59.123 55.000 12.18 0.00 43.94 4.17
501 660 1.527034 CTGTGGATTCACTGTGGTGG 58.473 55.000 5.55 0.00 43.94 4.61
502 661 0.537143 TGTGGATTCACTGTGGTGGC 60.537 55.000 5.55 0.00 43.94 5.01
503 662 0.537143 GTGGATTCACTGTGGTGGCA 60.537 55.000 8.11 0.00 43.17 4.92
504 663 0.184692 TGGATTCACTGTGGTGGCAA 59.815 50.000 8.11 0.00 43.17 4.52
505 664 1.327303 GGATTCACTGTGGTGGCAAA 58.673 50.000 8.11 0.00 43.17 3.68
506 665 1.270550 GGATTCACTGTGGTGGCAAAG 59.729 52.381 8.11 0.00 43.17 2.77
507 666 0.675633 ATTCACTGTGGTGGCAAAGC 59.324 50.000 8.11 0.00 43.17 3.51
508 667 0.395586 TTCACTGTGGTGGCAAAGCT 60.396 50.000 8.11 0.00 43.17 3.74
509 668 1.102809 TCACTGTGGTGGCAAAGCTG 61.103 55.000 8.11 0.00 43.17 4.24
510 669 1.102809 CACTGTGGTGGCAAAGCTGA 61.103 55.000 0.00 0.00 39.59 4.26
511 670 0.178981 ACTGTGGTGGCAAAGCTGAT 60.179 50.000 0.00 0.00 0.00 2.90
512 671 0.963962 CTGTGGTGGCAAAGCTGATT 59.036 50.000 0.00 0.00 0.00 2.57
513 672 0.961019 TGTGGTGGCAAAGCTGATTC 59.039 50.000 0.00 0.00 0.00 2.52
514 673 0.109597 GTGGTGGCAAAGCTGATTCG 60.110 55.000 0.00 0.00 0.00 3.34
515 674 1.153958 GGTGGCAAAGCTGATTCGC 60.154 57.895 0.00 0.00 0.00 4.70
516 675 1.589716 GGTGGCAAAGCTGATTCGCT 61.590 55.000 0.00 0.00 43.31 4.93
517 676 1.086696 GTGGCAAAGCTGATTCGCTA 58.913 50.000 0.00 0.00 39.86 4.26
518 677 1.468520 GTGGCAAAGCTGATTCGCTAA 59.531 47.619 0.00 0.00 39.86 3.09
519 678 1.739466 TGGCAAAGCTGATTCGCTAAG 59.261 47.619 0.00 2.27 39.86 2.18
520 679 1.064654 GGCAAAGCTGATTCGCTAAGG 59.935 52.381 0.00 0.08 39.86 2.69
521 680 2.009774 GCAAAGCTGATTCGCTAAGGA 58.990 47.619 0.00 0.00 39.86 3.36
522 681 2.420022 GCAAAGCTGATTCGCTAAGGAA 59.580 45.455 0.00 0.00 39.86 3.36
523 682 3.065925 GCAAAGCTGATTCGCTAAGGAAT 59.934 43.478 0.00 0.00 39.86 3.01
530 689 1.656652 TTCGCTAAGGAATCAGCTGC 58.343 50.000 9.47 0.00 35.57 5.25
531 690 0.536724 TCGCTAAGGAATCAGCTGCA 59.463 50.000 9.47 0.00 35.57 4.41
532 691 0.935898 CGCTAAGGAATCAGCTGCAG 59.064 55.000 10.11 10.11 35.57 4.41
533 692 1.741732 CGCTAAGGAATCAGCTGCAGT 60.742 52.381 16.64 0.00 35.57 4.40
534 693 1.669779 GCTAAGGAATCAGCTGCAGTG 59.330 52.381 16.64 12.33 34.86 3.66
535 694 2.679059 GCTAAGGAATCAGCTGCAGTGA 60.679 50.000 16.64 17.14 34.86 3.41
536 695 2.574006 AAGGAATCAGCTGCAGTGAA 57.426 45.000 16.64 0.72 0.00 3.18
537 696 2.110901 AGGAATCAGCTGCAGTGAAG 57.889 50.000 16.64 0.00 0.00 3.02
538 697 1.093159 GGAATCAGCTGCAGTGAAGG 58.907 55.000 16.64 0.81 0.00 3.46
539 698 1.612726 GGAATCAGCTGCAGTGAAGGT 60.613 52.381 16.64 0.00 0.00 3.50
540 699 2.157738 GAATCAGCTGCAGTGAAGGTT 58.842 47.619 16.64 9.00 0.00 3.50
541 700 3.338249 GAATCAGCTGCAGTGAAGGTTA 58.662 45.455 16.64 0.00 0.00 2.85
542 701 2.462456 TCAGCTGCAGTGAAGGTTAG 57.538 50.000 16.64 0.00 0.00 2.34
543 702 0.801251 CAGCTGCAGTGAAGGTTAGC 59.199 55.000 16.64 0.00 0.00 3.09
544 703 0.322008 AGCTGCAGTGAAGGTTAGCC 60.322 55.000 16.64 0.00 31.82 3.93
545 704 1.639298 GCTGCAGTGAAGGTTAGCCG 61.639 60.000 16.64 0.00 40.50 5.52
546 705 0.320771 CTGCAGTGAAGGTTAGCCGT 60.321 55.000 5.25 0.00 40.50 5.68
547 706 0.107831 TGCAGTGAAGGTTAGCCGTT 59.892 50.000 0.00 0.00 40.50 4.44
548 707 1.235724 GCAGTGAAGGTTAGCCGTTT 58.764 50.000 0.00 0.00 40.50 3.60
549 708 1.069227 GCAGTGAAGGTTAGCCGTTTG 60.069 52.381 0.00 0.00 40.50 2.93
550 709 1.535462 CAGTGAAGGTTAGCCGTTTGG 59.465 52.381 0.00 0.00 40.50 3.28
560 719 4.838959 CCGTTTGGCAAAGTAGCG 57.161 55.556 13.94 12.89 34.64 4.26
561 720 1.209127 CCGTTTGGCAAAGTAGCGG 59.791 57.895 20.55 20.55 34.64 5.52
562 721 1.512156 CCGTTTGGCAAAGTAGCGGT 61.512 55.000 23.76 0.00 33.87 5.68
563 722 0.385473 CGTTTGGCAAAGTAGCGGTG 60.385 55.000 13.94 0.00 34.64 4.94
564 723 0.039527 GTTTGGCAAAGTAGCGGTGG 60.040 55.000 13.94 0.00 34.64 4.61
565 724 0.179015 TTTGGCAAAGTAGCGGTGGA 60.179 50.000 8.93 0.00 34.64 4.02
566 725 0.037590 TTGGCAAAGTAGCGGTGGAT 59.962 50.000 0.00 0.00 34.64 3.41
567 726 0.037590 TGGCAAAGTAGCGGTGGATT 59.962 50.000 0.00 0.00 34.64 3.01
568 727 0.733150 GGCAAAGTAGCGGTGGATTC 59.267 55.000 0.00 0.00 34.64 2.52
569 728 0.373716 GCAAAGTAGCGGTGGATTCG 59.626 55.000 0.00 0.00 0.00 3.34
570 729 1.006832 CAAAGTAGCGGTGGATTCGG 58.993 55.000 0.00 0.00 0.00 4.30
571 730 0.743345 AAAGTAGCGGTGGATTCGGC 60.743 55.000 0.00 0.00 0.00 5.54
572 731 1.614241 AAGTAGCGGTGGATTCGGCT 61.614 55.000 0.00 0.00 44.06 5.52
573 732 1.153429 GTAGCGGTGGATTCGGCTT 60.153 57.895 0.00 0.00 42.38 4.35
574 733 0.743345 GTAGCGGTGGATTCGGCTTT 60.743 55.000 0.00 0.00 42.38 3.51
575 734 0.742990 TAGCGGTGGATTCGGCTTTG 60.743 55.000 0.00 0.00 42.38 2.77
576 735 2.038269 GCGGTGGATTCGGCTTTGA 61.038 57.895 0.00 0.00 0.00 2.69
577 736 1.376609 GCGGTGGATTCGGCTTTGAT 61.377 55.000 0.00 0.00 0.00 2.57
578 737 0.657840 CGGTGGATTCGGCTTTGATC 59.342 55.000 0.00 0.00 0.00 2.92
579 738 1.743772 CGGTGGATTCGGCTTTGATCT 60.744 52.381 0.00 0.00 0.00 2.75
580 739 2.483013 CGGTGGATTCGGCTTTGATCTA 60.483 50.000 0.00 0.00 0.00 1.98
581 740 3.134458 GGTGGATTCGGCTTTGATCTAG 58.866 50.000 0.00 0.00 0.00 2.43
582 741 3.432326 GGTGGATTCGGCTTTGATCTAGT 60.432 47.826 0.00 0.00 0.00 2.57
583 742 3.557595 GTGGATTCGGCTTTGATCTAGTG 59.442 47.826 0.00 0.00 0.00 2.74
584 743 3.450817 TGGATTCGGCTTTGATCTAGTGA 59.549 43.478 0.00 0.00 0.00 3.41
585 744 4.081142 TGGATTCGGCTTTGATCTAGTGAA 60.081 41.667 0.00 1.87 0.00 3.18
586 745 4.876107 GGATTCGGCTTTGATCTAGTGAAA 59.124 41.667 0.00 0.00 0.00 2.69
587 746 5.354234 GGATTCGGCTTTGATCTAGTGAAAA 59.646 40.000 0.00 0.00 0.00 2.29
588 747 5.862924 TTCGGCTTTGATCTAGTGAAAAG 57.137 39.130 0.00 8.49 33.67 2.27
589 748 4.253685 TCGGCTTTGATCTAGTGAAAAGG 58.746 43.478 12.45 2.30 31.67 3.11
590 749 3.181506 CGGCTTTGATCTAGTGAAAAGGC 60.182 47.826 20.10 20.10 46.18 4.35
591 750 4.013050 GGCTTTGATCTAGTGAAAAGGCT 58.987 43.478 21.49 0.00 46.16 4.58
592 751 4.142513 GGCTTTGATCTAGTGAAAAGGCTG 60.143 45.833 21.49 2.22 46.16 4.85
593 752 4.697352 GCTTTGATCTAGTGAAAAGGCTGA 59.303 41.667 12.45 0.00 31.67 4.26
594 753 5.182001 GCTTTGATCTAGTGAAAAGGCTGAA 59.818 40.000 12.45 0.00 31.67 3.02
595 754 6.294176 GCTTTGATCTAGTGAAAAGGCTGAAA 60.294 38.462 12.45 0.00 31.67 2.69
596 755 7.576477 GCTTTGATCTAGTGAAAAGGCTGAAAT 60.576 37.037 12.45 0.00 31.67 2.17
597 756 6.748333 TGATCTAGTGAAAAGGCTGAAATG 57.252 37.500 0.00 0.00 0.00 2.32
598 757 5.124457 TGATCTAGTGAAAAGGCTGAAATGC 59.876 40.000 0.00 0.00 0.00 3.56
599 758 2.712057 AGTGAAAAGGCTGAAATGCG 57.288 45.000 0.00 0.00 0.00 4.73
600 759 1.063031 GTGAAAAGGCTGAAATGCGC 58.937 50.000 0.00 0.00 0.00 6.09
601 760 0.038343 TGAAAAGGCTGAAATGCGCC 60.038 50.000 4.18 0.00 46.65 6.53
606 765 3.629858 GGCTGAAATGCGCCTAAAG 57.370 52.632 4.18 0.00 42.98 1.85
607 766 0.811281 GGCTGAAATGCGCCTAAAGT 59.189 50.000 4.18 0.00 42.98 2.66
945 1112 0.817013 CTCACTCCACTCCTCTCTGC 59.183 60.000 0.00 0.00 0.00 4.26
946 1113 0.407528 TCACTCCACTCCTCTCTGCT 59.592 55.000 0.00 0.00 0.00 4.24
947 1114 0.817013 CACTCCACTCCTCTCTGCTC 59.183 60.000 0.00 0.00 0.00 4.26
948 1115 0.704076 ACTCCACTCCTCTCTGCTCT 59.296 55.000 0.00 0.00 0.00 4.09
949 1116 1.340991 ACTCCACTCCTCTCTGCTCTC 60.341 57.143 0.00 0.00 0.00 3.20
1063 1230 1.202043 ACGAGTACATGAGCGAGTTCG 60.202 52.381 0.00 0.00 43.27 3.95
1284 1458 2.637382 TGTGGGCTTGTGACTGAATCTA 59.363 45.455 0.00 0.00 0.00 1.98
1376 1550 5.011431 CAGGAGATTCATAGGATGTGCTACA 59.989 44.000 0.00 0.00 0.00 2.74
1440 1614 7.446931 TGAATTTCTGCTATGTAGTGGAAACAA 59.553 33.333 0.00 0.00 46.06 2.83
1771 1945 1.668826 TGGGCAGAACCTTGGTAGAT 58.331 50.000 0.00 0.00 39.10 1.98
1890 2064 5.748630 GTCCAAGTTGTTTGATTTTCAGGAC 59.251 40.000 1.45 0.00 39.21 3.85
2989 3187 3.492102 GCTTGTGCTGGAGGGATATAA 57.508 47.619 0.00 0.00 36.03 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 188 2.552743 GCGAAGTAATAGGGGGAAATGC 59.447 50.000 0.00 0.00 0.00 3.56
142 238 7.072397 ACTGGAGAAGTATAAAGCTGTTGCTC 61.072 42.308 0.00 0.00 43.03 4.26
143 239 5.280215 ACTGGAGAAGTATAAAGCTGTTGCT 60.280 40.000 0.00 0.00 44.78 3.91
144 240 4.938226 ACTGGAGAAGTATAAAGCTGTTGC 59.062 41.667 0.00 0.00 37.36 4.17
145 241 6.621596 GCAACTGGAGAAGTATAAAGCTGTTG 60.622 42.308 0.00 0.00 38.56 3.33
146 242 5.412904 GCAACTGGAGAAGTATAAAGCTGTT 59.587 40.000 0.00 0.00 38.56 3.16
271 367 4.159135 TGTTTACGACTAGGATCTGGAACC 59.841 45.833 0.00 0.00 0.00 3.62
301 397 4.808364 TGGTTGCAGCAAAATTAACTTCAC 59.192 37.500 10.11 0.00 0.00 3.18
304 400 5.275067 TCTGGTTGCAGCAAAATTAACTT 57.725 34.783 10.11 0.00 0.00 2.66
356 452 7.604164 CAGATTATGCGGAGTTCCATACTATTT 59.396 37.037 0.00 0.00 37.17 1.40
409 505 7.426410 TCACTATAGTGCATTCAGTTAGTAGC 58.574 38.462 25.31 0.00 45.25 3.58
427 586 5.011635 ACACGGCCATAATGTGATCACTATA 59.988 40.000 25.55 17.93 37.08 1.31
432 591 2.708216 ACACGGCCATAATGTGATCA 57.292 45.000 13.82 0.00 37.08 2.92
433 592 3.128589 ACAAACACGGCCATAATGTGATC 59.871 43.478 13.82 0.00 37.08 2.92
454 613 2.049156 GCAAGCCGAAGCCCAAAC 60.049 61.111 0.00 0.00 41.25 2.93
479 638 1.162698 CCACAGTGAATCCACAGCTG 58.837 55.000 13.48 13.48 45.54 4.24
491 650 1.102809 TCAGCTTTGCCACCACAGTG 61.103 55.000 0.00 0.00 44.12 3.66
492 651 0.178981 ATCAGCTTTGCCACCACAGT 60.179 50.000 0.00 0.00 0.00 3.55
493 652 0.963962 AATCAGCTTTGCCACCACAG 59.036 50.000 0.00 0.00 0.00 3.66
494 653 0.961019 GAATCAGCTTTGCCACCACA 59.039 50.000 0.00 0.00 0.00 4.17
495 654 0.109597 CGAATCAGCTTTGCCACCAC 60.110 55.000 0.00 0.00 0.00 4.16
496 655 1.865788 GCGAATCAGCTTTGCCACCA 61.866 55.000 0.00 0.00 38.18 4.17
497 656 1.153958 GCGAATCAGCTTTGCCACC 60.154 57.895 0.00 0.00 38.18 4.61
498 657 1.086696 TAGCGAATCAGCTTTGCCAC 58.913 50.000 5.10 0.00 46.80 5.01
499 658 1.739466 CTTAGCGAATCAGCTTTGCCA 59.261 47.619 5.10 0.00 46.80 4.92
500 659 1.064654 CCTTAGCGAATCAGCTTTGCC 59.935 52.381 5.10 0.00 46.80 4.52
501 660 2.009774 TCCTTAGCGAATCAGCTTTGC 58.990 47.619 5.10 0.00 46.80 3.68
502 661 4.842029 GATTCCTTAGCGAATCAGCTTTG 58.158 43.478 14.28 0.48 46.80 2.77
509 668 2.222911 GCAGCTGATTCCTTAGCGAATC 59.777 50.000 20.43 13.04 45.59 2.52
510 669 2.216898 GCAGCTGATTCCTTAGCGAAT 58.783 47.619 20.43 0.00 44.43 3.34
511 670 1.066215 TGCAGCTGATTCCTTAGCGAA 60.066 47.619 20.43 0.00 44.43 4.70
512 671 0.536724 TGCAGCTGATTCCTTAGCGA 59.463 50.000 20.43 0.00 44.43 4.93
513 672 0.935898 CTGCAGCTGATTCCTTAGCG 59.064 55.000 20.43 0.00 44.43 4.26
514 673 1.669779 CACTGCAGCTGATTCCTTAGC 59.330 52.381 20.43 0.00 40.18 3.09
515 674 3.257469 TCACTGCAGCTGATTCCTTAG 57.743 47.619 20.43 5.63 0.00 2.18
516 675 3.603532 CTTCACTGCAGCTGATTCCTTA 58.396 45.455 20.43 0.43 0.00 2.69
517 676 2.434428 CTTCACTGCAGCTGATTCCTT 58.566 47.619 20.43 0.00 0.00 3.36
518 677 1.339824 CCTTCACTGCAGCTGATTCCT 60.340 52.381 20.43 0.00 0.00 3.36
519 678 1.093159 CCTTCACTGCAGCTGATTCC 58.907 55.000 20.43 0.00 0.00 3.01
520 679 1.818642 ACCTTCACTGCAGCTGATTC 58.181 50.000 20.43 0.00 0.00 2.52
521 680 2.283145 AACCTTCACTGCAGCTGATT 57.717 45.000 20.43 5.83 0.00 2.57
522 681 2.938756 GCTAACCTTCACTGCAGCTGAT 60.939 50.000 20.43 0.00 0.00 2.90
523 682 1.609061 GCTAACCTTCACTGCAGCTGA 60.609 52.381 20.43 13.85 0.00 4.26
524 683 0.801251 GCTAACCTTCACTGCAGCTG 59.199 55.000 15.27 10.11 0.00 4.24
525 684 0.322008 GGCTAACCTTCACTGCAGCT 60.322 55.000 15.27 0.00 0.00 4.24
526 685 1.639298 CGGCTAACCTTCACTGCAGC 61.639 60.000 15.27 0.00 0.00 5.25
527 686 0.320771 ACGGCTAACCTTCACTGCAG 60.321 55.000 13.48 13.48 0.00 4.41
528 687 0.107831 AACGGCTAACCTTCACTGCA 59.892 50.000 0.00 0.00 0.00 4.41
529 688 1.069227 CAAACGGCTAACCTTCACTGC 60.069 52.381 0.00 0.00 0.00 4.40
530 689 1.535462 CCAAACGGCTAACCTTCACTG 59.465 52.381 0.00 0.00 0.00 3.66
531 690 1.892209 CCAAACGGCTAACCTTCACT 58.108 50.000 0.00 0.00 0.00 3.41
532 691 0.240145 GCCAAACGGCTAACCTTCAC 59.760 55.000 0.00 0.00 46.85 3.18
533 692 2.636299 GCCAAACGGCTAACCTTCA 58.364 52.632 0.00 0.00 46.85 3.02
543 702 1.209127 CCGCTACTTTGCCAAACGG 59.791 57.895 3.04 3.04 0.00 4.44
544 703 0.385473 CACCGCTACTTTGCCAAACG 60.385 55.000 0.00 0.00 0.00 3.60
545 704 0.039527 CCACCGCTACTTTGCCAAAC 60.040 55.000 0.00 0.00 0.00 2.93
546 705 0.179015 TCCACCGCTACTTTGCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
547 706 0.037590 ATCCACCGCTACTTTGCCAA 59.962 50.000 0.00 0.00 0.00 4.52
548 707 0.037590 AATCCACCGCTACTTTGCCA 59.962 50.000 0.00 0.00 0.00 4.92
549 708 0.733150 GAATCCACCGCTACTTTGCC 59.267 55.000 0.00 0.00 0.00 4.52
550 709 0.373716 CGAATCCACCGCTACTTTGC 59.626 55.000 0.00 0.00 0.00 3.68
551 710 1.006832 CCGAATCCACCGCTACTTTG 58.993 55.000 0.00 0.00 0.00 2.77
552 711 0.743345 GCCGAATCCACCGCTACTTT 60.743 55.000 0.00 0.00 0.00 2.66
553 712 1.153429 GCCGAATCCACCGCTACTT 60.153 57.895 0.00 0.00 0.00 2.24
554 713 1.614241 AAGCCGAATCCACCGCTACT 61.614 55.000 0.00 0.00 0.00 2.57
555 714 0.743345 AAAGCCGAATCCACCGCTAC 60.743 55.000 0.00 0.00 0.00 3.58
556 715 0.742990 CAAAGCCGAATCCACCGCTA 60.743 55.000 0.00 0.00 0.00 4.26
557 716 2.040544 CAAAGCCGAATCCACCGCT 61.041 57.895 0.00 0.00 0.00 5.52
558 717 1.376609 ATCAAAGCCGAATCCACCGC 61.377 55.000 0.00 0.00 0.00 5.68
559 718 0.657840 GATCAAAGCCGAATCCACCG 59.342 55.000 0.00 0.00 0.00 4.94
560 719 2.044123 AGATCAAAGCCGAATCCACC 57.956 50.000 0.00 0.00 0.00 4.61
561 720 3.557595 CACTAGATCAAAGCCGAATCCAC 59.442 47.826 0.00 0.00 0.00 4.02
562 721 3.450817 TCACTAGATCAAAGCCGAATCCA 59.549 43.478 0.00 0.00 0.00 3.41
563 722 4.060038 TCACTAGATCAAAGCCGAATCC 57.940 45.455 0.00 0.00 0.00 3.01
564 723 6.422776 TTTTCACTAGATCAAAGCCGAATC 57.577 37.500 0.00 0.00 0.00 2.52
565 724 5.355350 CCTTTTCACTAGATCAAAGCCGAAT 59.645 40.000 0.00 0.00 0.00 3.34
566 725 4.695455 CCTTTTCACTAGATCAAAGCCGAA 59.305 41.667 0.00 0.00 0.00 4.30
567 726 4.253685 CCTTTTCACTAGATCAAAGCCGA 58.746 43.478 0.00 0.00 0.00 5.54
568 727 3.181506 GCCTTTTCACTAGATCAAAGCCG 60.182 47.826 0.00 0.00 0.00 5.52
569 728 4.013050 AGCCTTTTCACTAGATCAAAGCC 58.987 43.478 0.00 0.00 0.00 4.35
570 729 4.697352 TCAGCCTTTTCACTAGATCAAAGC 59.303 41.667 0.00 0.00 0.00 3.51
571 730 6.808008 TTCAGCCTTTTCACTAGATCAAAG 57.192 37.500 0.00 1.27 0.00 2.77
572 731 7.596494 CATTTCAGCCTTTTCACTAGATCAAA 58.404 34.615 0.00 0.00 0.00 2.69
573 732 6.349611 GCATTTCAGCCTTTTCACTAGATCAA 60.350 38.462 0.00 0.00 0.00 2.57
574 733 5.124457 GCATTTCAGCCTTTTCACTAGATCA 59.876 40.000 0.00 0.00 0.00 2.92
575 734 5.576895 GCATTTCAGCCTTTTCACTAGATC 58.423 41.667 0.00 0.00 0.00 2.75
576 735 4.095483 CGCATTTCAGCCTTTTCACTAGAT 59.905 41.667 0.00 0.00 0.00 1.98
577 736 3.436704 CGCATTTCAGCCTTTTCACTAGA 59.563 43.478 0.00 0.00 0.00 2.43
578 737 3.751621 CGCATTTCAGCCTTTTCACTAG 58.248 45.455 0.00 0.00 0.00 2.57
579 738 2.095263 GCGCATTTCAGCCTTTTCACTA 60.095 45.455 0.30 0.00 0.00 2.74
580 739 1.336240 GCGCATTTCAGCCTTTTCACT 60.336 47.619 0.30 0.00 0.00 3.41
581 740 1.063031 GCGCATTTCAGCCTTTTCAC 58.937 50.000 0.30 0.00 0.00 3.18
582 741 3.495124 GCGCATTTCAGCCTTTTCA 57.505 47.368 0.30 0.00 0.00 2.69
589 748 1.202188 GGACTTTAGGCGCATTTCAGC 60.202 52.381 10.83 0.00 0.00 4.26
590 749 2.096496 CAGGACTTTAGGCGCATTTCAG 59.904 50.000 10.83 1.03 0.00 3.02
591 750 2.083774 CAGGACTTTAGGCGCATTTCA 58.916 47.619 10.83 0.00 0.00 2.69
592 751 1.401905 CCAGGACTTTAGGCGCATTTC 59.598 52.381 10.83 0.00 0.00 2.17
593 752 1.004277 TCCAGGACTTTAGGCGCATTT 59.996 47.619 10.83 0.00 0.00 2.32
594 753 0.618458 TCCAGGACTTTAGGCGCATT 59.382 50.000 10.83 0.00 0.00 3.56
595 754 0.179000 CTCCAGGACTTTAGGCGCAT 59.821 55.000 10.83 3.98 0.00 4.73
596 755 1.192146 ACTCCAGGACTTTAGGCGCA 61.192 55.000 10.83 0.00 0.00 6.09
597 756 0.741221 CACTCCAGGACTTTAGGCGC 60.741 60.000 0.00 0.00 0.00 6.53
598 757 0.608640 ACACTCCAGGACTTTAGGCG 59.391 55.000 0.00 0.00 0.00 5.52
599 758 2.814336 CAAACACTCCAGGACTTTAGGC 59.186 50.000 0.00 0.00 0.00 3.93
600 759 4.065789 GTCAAACACTCCAGGACTTTAGG 58.934 47.826 0.00 0.00 0.00 2.69
601 760 4.703897 TGTCAAACACTCCAGGACTTTAG 58.296 43.478 0.00 0.00 0.00 1.85
602 761 4.764050 TGTCAAACACTCCAGGACTTTA 57.236 40.909 0.00 0.00 0.00 1.85
603 762 3.644966 TGTCAAACACTCCAGGACTTT 57.355 42.857 0.00 0.00 0.00 2.66
604 763 3.644966 TTGTCAAACACTCCAGGACTT 57.355 42.857 0.00 0.00 0.00 3.01
605 764 3.644966 TTTGTCAAACACTCCAGGACT 57.355 42.857 0.00 0.00 0.00 3.85
606 765 4.712122 TTTTTGTCAAACACTCCAGGAC 57.288 40.909 0.00 0.00 0.00 3.85
945 1112 2.026641 CAGAAGCAGAGGAGAGGAGAG 58.973 57.143 0.00 0.00 0.00 3.20
946 1113 1.357420 ACAGAAGCAGAGGAGAGGAGA 59.643 52.381 0.00 0.00 0.00 3.71
947 1114 1.851304 ACAGAAGCAGAGGAGAGGAG 58.149 55.000 0.00 0.00 0.00 3.69
948 1115 2.317371 AACAGAAGCAGAGGAGAGGA 57.683 50.000 0.00 0.00 0.00 3.71
949 1116 2.566724 AGAAACAGAAGCAGAGGAGAGG 59.433 50.000 0.00 0.00 0.00 3.69
1063 1230 0.179037 TACTCCATCTGCATGCTGCC 60.179 55.000 20.33 0.00 44.23 4.85
1657 1831 2.038426 CACCACAGTTCACACCATCCTA 59.962 50.000 0.00 0.00 0.00 2.94
1771 1945 2.494888 TGAGCCTCATTATCCTGGGA 57.505 50.000 0.00 0.00 0.00 4.37
1890 2064 4.818005 TCCATGTCATGAGATTTGATTCCG 59.182 41.667 14.67 0.00 0.00 4.30
2257 2433 3.782523 AGACTGATCATTCCTAGGCCAAA 59.217 43.478 5.01 0.00 0.00 3.28
2532 2709 6.360618 ACTTCTCTGAATTTGTCTGAACCTT 58.639 36.000 0.00 0.00 34.16 3.50


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

AutoCloner maintained by Alex Coulton.