Multiple sequence alignment - TraesCS6B01G358500

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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 TraesCS6B01G358500 chr6B 100.000 2666 0 0 1 2666 626807123 626809788 0.000000e+00 4924.0
1 TraesCS6B01G358500 chr6B 92.930 877 47 6 1071 1935 626819201 626820074 0.000000e+00 1262.0
2 TraesCS6B01G358500 chr6B 90.705 893 75 3 790 1679 626593742 626592855 0.000000e+00 1182.0
3 TraesCS6B01G358500 chr6B 89.162 895 65 16 878 1765 626463302 626462433 0.000000e+00 1086.0
4 TraesCS6B01G358500 chr6B 94.165 617 34 2 1 615 577443226 577442610 0.000000e+00 939.0
5 TraesCS6B01G358500 chr6B 93.031 617 39 3 1 615 577452423 577451809 0.000000e+00 898.0
6 TraesCS6B01G358500 chr6B 91.850 638 43 5 1 630 18271373 18272009 0.000000e+00 881.0
7 TraesCS6B01G358500 chr6B 97.581 124 2 1 1934 2056 626820114 626820237 7.480000e-51 211.0
8 TraesCS6B01G358500 chr6B 94.355 124 6 1 1934 2056 626592574 626592451 3.500000e-44 189.0
9 TraesCS6B01G358500 chr6B 92.308 78 5 1 711 787 626594099 626594022 2.810000e-20 110.0
10 TraesCS6B01G358500 chr6A 93.737 958 48 6 829 1779 560133257 560132305 0.000000e+00 1426.0
11 TraesCS6B01G358500 chr6A 92.146 713 52 2 992 1704 560478848 560479556 0.000000e+00 1003.0
12 TraesCS6B01G358500 chr6A 88.249 851 82 12 831 1672 560544185 560545026 0.000000e+00 1002.0
13 TraesCS6B01G358500 chr6A 91.865 713 54 2 992 1704 560407081 560407789 0.000000e+00 992.0
14 TraesCS6B01G358500 chr6A 92.462 597 42 1 992 1588 560359095 560359688 0.000000e+00 850.0
15 TraesCS6B01G358500 chr6A 92.308 52 3 1 1885 1935 560545115 560545166 3.680000e-09 73.1
16 TraesCS6B01G358500 chr6A 97.561 41 1 0 718 758 560133405 560133365 1.320000e-08 71.3
17 TraesCS6B01G358500 chr6D 88.497 965 86 17 831 1779 417888142 417889097 0.000000e+00 1144.0
18 TraesCS6B01G358500 chr6D 95.432 613 25 3 2057 2666 464697138 464696526 0.000000e+00 974.0
19 TraesCS6B01G358500 chr6D 95.269 613 26 2 2057 2666 446133056 446133668 0.000000e+00 968.0
20 TraesCS6B01G358500 chr6D 94.943 613 28 2 2057 2666 313021521 313020909 0.000000e+00 957.0
21 TraesCS6B01G358500 chr6D 92.581 310 17 5 824 1132 417715602 417715298 8.760000e-120 440.0
22 TraesCS6B01G358500 chr6D 82.078 385 31 14 615 975 417761766 417762136 7.220000e-76 294.0
23 TraesCS6B01G358500 chr2D 96.098 615 20 3 2056 2666 276935675 276936289 0.000000e+00 1000.0
24 TraesCS6B01G358500 chr2D 95.153 619 26 4 2052 2666 285350089 285349471 0.000000e+00 974.0
25 TraesCS6B01G358500 chr4B 95.772 615 24 1 1 615 374731893 374731281 0.000000e+00 990.0
26 TraesCS6B01G358500 chr4B 94.797 615 30 2 2053 2666 406325844 406325231 0.000000e+00 957.0
27 TraesCS6B01G358500 chr7D 94.968 616 25 3 2057 2666 145918975 145919590 0.000000e+00 961.0
28 TraesCS6B01G358500 chr2B 94.935 612 28 3 2058 2666 24844343 24843732 0.000000e+00 955.0
29 TraesCS6B01G358500 chr2B 92.869 617 41 2 1 615 712499891 712499276 0.000000e+00 893.0
30 TraesCS6B01G358500 chr3B 94.918 610 30 1 2057 2666 155461341 155460733 0.000000e+00 953.0
31 TraesCS6B01G358500 chr3B 93.053 619 38 4 1 615 431151488 431152105 0.000000e+00 900.0
32 TraesCS6B01G358500 chr3B 92.019 639 41 7 1 633 666212309 666212943 0.000000e+00 889.0
33 TraesCS6B01G358500 chr1B 93.517 617 37 3 1 616 26702133 26701519 0.000000e+00 915.0
34 TraesCS6B01G358500 chr1B 92.175 639 42 5 1 633 681249707 681250343 0.000000e+00 896.0


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 TraesCS6B01G358500 chr6B 626807123 626809788 2665 False 4924.000000 4924 100.0000 1 2666 1 chr6B.!!$F2 2665
1 TraesCS6B01G358500 chr6B 626462433 626463302 869 True 1086.000000 1086 89.1620 878 1765 1 chr6B.!!$R3 887
2 TraesCS6B01G358500 chr6B 577442610 577443226 616 True 939.000000 939 94.1650 1 615 1 chr6B.!!$R1 614
3 TraesCS6B01G358500 chr6B 577451809 577452423 614 True 898.000000 898 93.0310 1 615 1 chr6B.!!$R2 614
4 TraesCS6B01G358500 chr6B 18271373 18272009 636 False 881.000000 881 91.8500 1 630 1 chr6B.!!$F1 629
5 TraesCS6B01G358500 chr6B 626819201 626820237 1036 False 736.500000 1262 95.2555 1071 2056 2 chr6B.!!$F3 985
6 TraesCS6B01G358500 chr6B 626592451 626594099 1648 True 493.666667 1182 92.4560 711 2056 3 chr6B.!!$R4 1345
7 TraesCS6B01G358500 chr6A 560478848 560479556 708 False 1003.000000 1003 92.1460 992 1704 1 chr6A.!!$F3 712
8 TraesCS6B01G358500 chr6A 560407081 560407789 708 False 992.000000 992 91.8650 992 1704 1 chr6A.!!$F2 712
9 TraesCS6B01G358500 chr6A 560359095 560359688 593 False 850.000000 850 92.4620 992 1588 1 chr6A.!!$F1 596
10 TraesCS6B01G358500 chr6A 560132305 560133405 1100 True 748.650000 1426 95.6490 718 1779 2 chr6A.!!$R1 1061
11 TraesCS6B01G358500 chr6A 560544185 560545166 981 False 537.550000 1002 90.2785 831 1935 2 chr6A.!!$F4 1104
12 TraesCS6B01G358500 chr6D 417888142 417889097 955 False 1144.000000 1144 88.4970 831 1779 1 chr6D.!!$F2 948
13 TraesCS6B01G358500 chr6D 464696526 464697138 612 True 974.000000 974 95.4320 2057 2666 1 chr6D.!!$R3 609
14 TraesCS6B01G358500 chr6D 446133056 446133668 612 False 968.000000 968 95.2690 2057 2666 1 chr6D.!!$F3 609
15 TraesCS6B01G358500 chr6D 313020909 313021521 612 True 957.000000 957 94.9430 2057 2666 1 chr6D.!!$R1 609
16 TraesCS6B01G358500 chr2D 276935675 276936289 614 False 1000.000000 1000 96.0980 2056 2666 1 chr2D.!!$F1 610
17 TraesCS6B01G358500 chr2D 285349471 285350089 618 True 974.000000 974 95.1530 2052 2666 1 chr2D.!!$R1 614
18 TraesCS6B01G358500 chr4B 374731281 374731893 612 True 990.000000 990 95.7720 1 615 1 chr4B.!!$R1 614
19 TraesCS6B01G358500 chr4B 406325231 406325844 613 True 957.000000 957 94.7970 2053 2666 1 chr4B.!!$R2 613
20 TraesCS6B01G358500 chr7D 145918975 145919590 615 False 961.000000 961 94.9680 2057 2666 1 chr7D.!!$F1 609
21 TraesCS6B01G358500 chr2B 24843732 24844343 611 True 955.000000 955 94.9350 2058 2666 1 chr2B.!!$R1 608
22 TraesCS6B01G358500 chr2B 712499276 712499891 615 True 893.000000 893 92.8690 1 615 1 chr2B.!!$R2 614
23 TraesCS6B01G358500 chr3B 155460733 155461341 608 True 953.000000 953 94.9180 2057 2666 1 chr3B.!!$R1 609
24 TraesCS6B01G358500 chr3B 431151488 431152105 617 False 900.000000 900 93.0530 1 615 1 chr3B.!!$F1 614
25 TraesCS6B01G358500 chr3B 666212309 666212943 634 False 889.000000 889 92.0190 1 633 1 chr3B.!!$F2 632
26 TraesCS6B01G358500 chr1B 26701519 26702133 614 True 915.000000 915 93.5170 1 616 1 chr1B.!!$R1 615
27 TraesCS6B01G358500 chr1B 681249707 681250343 636 False 896.000000 896 92.1750 1 633 1 chr1B.!!$F1 632

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
656 684 0.096454 GCAAGTCCGATTTGTACGCC 59.904 55.0 5.62 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2701 0.669318 GCGACCGAGTGAATGTCCAA 60.669 55.0 0.0 0.0 0.0 3.53 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
215 216 7.578310 AACTTAATCTATAGTGCACGGTCTA 57.422 36.000 12.01 0.00 0.00 2.59
220 223 0.759436 ATAGTGCACGGTCTAGGGGG 60.759 60.000 12.01 0.00 0.00 5.40
479 507 2.407090 TCGTTGTGTGAGCATTGAGAG 58.593 47.619 0.00 0.00 0.00 3.20
573 601 1.165270 ATTGGGTTAAGAGCGTGTGC 58.835 50.000 0.00 0.00 43.24 4.57
588 616 0.462225 TGTGCGTTTTTCTGTCCCGA 60.462 50.000 0.00 0.00 0.00 5.14
589 617 0.658897 GTGCGTTTTTCTGTCCCGAA 59.341 50.000 0.00 0.00 0.00 4.30
595 623 1.314730 TTTTCTGTCCCGAAGCAACC 58.685 50.000 0.00 0.00 0.00 3.77
619 647 3.501062 ACGGGCTCTTTTGCTAGTAAAAC 59.499 43.478 13.90 5.77 0.00 2.43
624 652 6.929049 GGGCTCTTTTGCTAGTAAAACAAAAT 59.071 34.615 13.90 0.00 41.11 1.82
638 666 8.974408 AGTAAAACAAAATAAAATTGGTCGAGC 58.026 29.630 7.89 7.89 32.02 5.03
639 667 7.778470 AAAACAAAATAAAATTGGTCGAGCA 57.222 28.000 14.39 14.39 32.02 4.26
640 668 7.778470 AAACAAAATAAAATTGGTCGAGCAA 57.222 28.000 30.00 30.00 32.02 3.91
641 669 7.406799 AACAAAATAAAATTGGTCGAGCAAG 57.593 32.000 30.90 18.05 32.02 4.01
642 670 6.512297 ACAAAATAAAATTGGTCGAGCAAGT 58.488 32.000 30.90 27.20 32.02 3.16
643 671 6.640907 ACAAAATAAAATTGGTCGAGCAAGTC 59.359 34.615 30.90 0.00 32.02 3.01
644 672 4.965119 ATAAAATTGGTCGAGCAAGTCC 57.035 40.909 30.90 8.33 0.00 3.85
645 673 1.156736 AAATTGGTCGAGCAAGTCCG 58.843 50.000 30.90 0.00 0.00 4.79
646 674 0.320374 AATTGGTCGAGCAAGTCCGA 59.680 50.000 30.90 11.27 0.00 4.55
647 675 0.537188 ATTGGTCGAGCAAGTCCGAT 59.463 50.000 30.90 13.75 37.14 4.18
648 676 0.320374 TTGGTCGAGCAAGTCCGATT 59.680 50.000 25.16 0.00 37.14 3.34
649 677 0.320374 TGGTCGAGCAAGTCCGATTT 59.680 50.000 16.20 0.00 37.14 2.17
650 678 0.721718 GGTCGAGCAAGTCCGATTTG 59.278 55.000 10.30 0.00 37.14 2.32
651 679 1.429463 GTCGAGCAAGTCCGATTTGT 58.571 50.000 5.62 0.00 37.14 2.83
652 680 2.602878 GTCGAGCAAGTCCGATTTGTA 58.397 47.619 5.62 0.00 37.14 2.41
653 681 2.344741 GTCGAGCAAGTCCGATTTGTAC 59.655 50.000 5.62 0.00 37.14 2.90
654 682 1.320555 CGAGCAAGTCCGATTTGTACG 59.679 52.381 5.62 7.53 0.00 3.67
655 683 1.060698 GAGCAAGTCCGATTTGTACGC 59.939 52.381 5.62 0.00 0.00 4.42
656 684 0.096454 GCAAGTCCGATTTGTACGCC 59.904 55.000 5.62 0.00 0.00 5.68
657 685 1.722011 CAAGTCCGATTTGTACGCCT 58.278 50.000 0.00 0.00 0.00 5.52
658 686 2.883574 CAAGTCCGATTTGTACGCCTA 58.116 47.619 0.00 0.00 0.00 3.93
659 687 3.255725 CAAGTCCGATTTGTACGCCTAA 58.744 45.455 0.00 0.00 0.00 2.69
660 688 3.814005 AGTCCGATTTGTACGCCTAAT 57.186 42.857 0.00 0.00 0.00 1.73
661 689 3.454375 AGTCCGATTTGTACGCCTAATG 58.546 45.455 0.00 0.00 0.00 1.90
662 690 3.118884 AGTCCGATTTGTACGCCTAATGT 60.119 43.478 0.00 0.00 0.00 2.71
663 691 3.000925 GTCCGATTTGTACGCCTAATGTG 59.999 47.826 0.00 0.00 0.00 3.21
664 692 2.933906 CCGATTTGTACGCCTAATGTGT 59.066 45.455 0.00 0.00 41.55 3.72
665 693 4.114073 CCGATTTGTACGCCTAATGTGTA 58.886 43.478 0.00 0.00 38.91 2.90
666 694 4.208460 CCGATTTGTACGCCTAATGTGTAG 59.792 45.833 0.00 0.00 40.48 2.74
667 695 4.317839 CGATTTGTACGCCTAATGTGTAGC 60.318 45.833 0.00 0.00 40.48 3.58
668 696 3.596310 TTGTACGCCTAATGTGTAGCA 57.404 42.857 0.00 0.00 40.48 3.49
669 697 3.596310 TGTACGCCTAATGTGTAGCAA 57.404 42.857 0.00 0.00 40.48 3.91
670 698 4.131649 TGTACGCCTAATGTGTAGCAAT 57.868 40.909 0.00 0.00 40.48 3.56
671 699 3.868661 TGTACGCCTAATGTGTAGCAATG 59.131 43.478 0.00 0.00 40.48 2.82
672 700 3.260475 ACGCCTAATGTGTAGCAATGA 57.740 42.857 0.00 0.00 35.45 2.57
673 701 3.605634 ACGCCTAATGTGTAGCAATGAA 58.394 40.909 0.00 0.00 35.45 2.57
674 702 3.623060 ACGCCTAATGTGTAGCAATGAAG 59.377 43.478 0.00 0.00 35.45 3.02
675 703 3.871006 CGCCTAATGTGTAGCAATGAAGA 59.129 43.478 0.00 0.00 0.00 2.87
676 704 4.332543 CGCCTAATGTGTAGCAATGAAGAA 59.667 41.667 0.00 0.00 0.00 2.52
677 705 5.008019 CGCCTAATGTGTAGCAATGAAGAAT 59.992 40.000 0.00 0.00 0.00 2.40
678 706 6.202762 CGCCTAATGTGTAGCAATGAAGAATA 59.797 38.462 0.00 0.00 0.00 1.75
679 707 7.355778 GCCTAATGTGTAGCAATGAAGAATAC 58.644 38.462 0.00 0.00 0.00 1.89
680 708 7.520614 GCCTAATGTGTAGCAATGAAGAATACC 60.521 40.741 0.00 0.00 0.00 2.73
681 709 7.716998 CCTAATGTGTAGCAATGAAGAATACCT 59.283 37.037 0.00 0.00 0.00 3.08
682 710 6.932356 ATGTGTAGCAATGAAGAATACCTG 57.068 37.500 0.00 0.00 0.00 4.00
683 711 4.635765 TGTGTAGCAATGAAGAATACCTGC 59.364 41.667 0.00 0.00 0.00 4.85
684 712 3.871006 TGTAGCAATGAAGAATACCTGCG 59.129 43.478 0.00 0.00 35.00 5.18
685 713 3.266510 AGCAATGAAGAATACCTGCGA 57.733 42.857 0.00 0.00 35.00 5.10
686 714 3.201290 AGCAATGAAGAATACCTGCGAG 58.799 45.455 0.00 0.00 35.00 5.03
687 715 2.286654 GCAATGAAGAATACCTGCGAGC 60.287 50.000 0.00 0.00 0.00 5.03
688 716 2.938451 CAATGAAGAATACCTGCGAGCA 59.062 45.455 0.00 0.00 0.00 4.26
689 717 2.760634 TGAAGAATACCTGCGAGCAA 57.239 45.000 0.00 0.00 0.00 3.91
690 718 2.621338 TGAAGAATACCTGCGAGCAAG 58.379 47.619 0.00 0.00 0.00 4.01
691 719 1.328986 GAAGAATACCTGCGAGCAAGC 59.671 52.381 0.00 0.00 37.71 4.01
692 720 0.539051 AGAATACCTGCGAGCAAGCT 59.461 50.000 0.00 0.00 38.13 3.74
693 721 1.757118 AGAATACCTGCGAGCAAGCTA 59.243 47.619 0.00 0.00 38.13 3.32
694 722 2.131183 GAATACCTGCGAGCAAGCTAG 58.869 52.381 0.00 0.00 38.13 3.42
695 723 0.249657 ATACCTGCGAGCAAGCTAGC 60.250 55.000 18.37 18.37 43.42 3.42
696 724 2.298158 TACCTGCGAGCAAGCTAGCC 62.298 60.000 21.44 7.07 42.66 3.93
697 725 2.125391 CTGCGAGCAAGCTAGCCA 60.125 61.111 21.44 10.66 42.66 4.75
698 726 1.523258 CTGCGAGCAAGCTAGCCAT 60.523 57.895 21.44 0.00 42.66 4.40
699 727 1.497223 CTGCGAGCAAGCTAGCCATC 61.497 60.000 21.44 3.58 42.66 3.51
700 728 2.250237 GCGAGCAAGCTAGCCATCC 61.250 63.158 12.13 0.00 38.47 3.51
701 729 1.953138 CGAGCAAGCTAGCCATCCG 60.953 63.158 12.13 5.44 34.23 4.18
702 730 1.443407 GAGCAAGCTAGCCATCCGA 59.557 57.895 12.13 0.00 34.23 4.55
703 731 0.599728 GAGCAAGCTAGCCATCCGAG 60.600 60.000 12.13 0.00 34.23 4.63
704 732 1.144936 GCAAGCTAGCCATCCGAGT 59.855 57.895 12.13 0.00 0.00 4.18
705 733 0.878086 GCAAGCTAGCCATCCGAGTC 60.878 60.000 12.13 0.00 0.00 3.36
706 734 0.596083 CAAGCTAGCCATCCGAGTCG 60.596 60.000 12.13 5.29 0.00 4.18
707 735 1.038130 AAGCTAGCCATCCGAGTCGT 61.038 55.000 12.13 0.00 0.00 4.34
708 736 0.179026 AGCTAGCCATCCGAGTCGTA 60.179 55.000 12.13 0.00 0.00 3.43
709 737 0.882474 GCTAGCCATCCGAGTCGTAT 59.118 55.000 12.31 0.00 0.00 3.06
713 741 0.319900 GCCATCCGAGTCGTATGCAT 60.320 55.000 12.24 3.79 0.00 3.96
716 744 0.389025 ATCCGAGTCGTATGCATGCA 59.611 50.000 25.04 25.04 0.00 3.96
720 748 0.999406 GAGTCGTATGCATGCAACGT 59.001 50.000 33.47 24.33 37.83 3.99
787 1093 7.254017 GGCAACGTAGATTACAATTGACTACTC 60.254 40.741 13.59 0.00 32.47 2.59
788 1094 7.274904 GCAACGTAGATTACAATTGACTACTCA 59.725 37.037 13.59 0.00 33.57 3.41
797 1103 9.896645 ATTACAATTGACTACTCATCAACTGAT 57.103 29.630 13.59 0.00 35.78 2.90
801 1107 7.993821 ATTGACTACTCATCAACTGATAACG 57.006 36.000 0.00 0.00 38.84 3.18
806 1112 7.249147 ACTACTCATCAACTGATAACGTACAC 58.751 38.462 0.00 0.00 32.10 2.90
865 1201 0.107214 CCGAATCCAGCCAGCCTTTA 60.107 55.000 0.00 0.00 0.00 1.85
867 1203 1.393603 GAATCCAGCCAGCCTTTACC 58.606 55.000 0.00 0.00 0.00 2.85
979 1322 6.884187 TCACAAAGAAGATTGTTTACGCTAC 58.116 36.000 0.00 0.00 41.44 3.58
983 1326 5.857822 AGAAGATTGTTTACGCTACAACC 57.142 39.130 0.00 0.00 38.23 3.77
986 1329 5.857822 AGATTGTTTACGCTACAACCTTC 57.142 39.130 0.00 0.00 38.23 3.46
1431 1778 3.695606 GGCCAGGAGACGCAGACA 61.696 66.667 0.00 0.00 0.00 3.41
1461 1808 1.245732 GGGCCATGCAAGATGAGATC 58.754 55.000 4.39 0.00 0.00 2.75
2376 2902 4.261530 CCATGTGTTTTGCAGTGTACATGA 60.262 41.667 25.05 7.03 44.85 3.07
2388 2914 3.326588 AGTGTACATGACAACTGCCCTAA 59.673 43.478 0.00 0.00 40.66 2.69
2451 2982 2.937591 CATGTCAGTTGCCATGTGTTC 58.062 47.619 0.00 0.00 34.97 3.18
2608 3142 6.042552 TCCTAAGGTTTTCAAATCATGGCAAA 59.957 34.615 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 8.742554 ACAGCTAAAAGTAACAACATATTTGC 57.257 30.769 0.00 0.00 0.00 3.68
215 216 2.115266 CAGTGCGGAAAACCCCCT 59.885 61.111 0.00 0.00 0.00 4.79
479 507 1.805428 ATTTGTGTTCCCGGCAGTGC 61.805 55.000 6.55 6.55 0.00 4.40
573 601 0.941542 TGCTTCGGGACAGAAAAACG 59.058 50.000 0.00 0.00 0.00 3.60
588 616 2.640581 AAAGAGCCCGTGGGTTGCTT 62.641 55.000 6.82 5.18 34.99 3.91
589 617 2.640581 AAAAGAGCCCGTGGGTTGCT 62.641 55.000 6.82 0.00 38.24 3.91
595 623 0.321653 ACTAGCAAAAGAGCCCGTGG 60.322 55.000 0.00 0.00 34.23 4.94
619 647 6.089417 GGACTTGCTCGACCAATTTTATTTTG 59.911 38.462 0.00 0.00 0.00 2.44
624 652 2.739913 CGGACTTGCTCGACCAATTTTA 59.260 45.455 0.00 0.00 0.00 1.52
633 661 2.602878 GTACAAATCGGACTTGCTCGA 58.397 47.619 0.00 0.00 39.79 4.04
634 662 1.320555 CGTACAAATCGGACTTGCTCG 59.679 52.381 0.00 1.20 0.00 5.03
635 663 1.060698 GCGTACAAATCGGACTTGCTC 59.939 52.381 0.00 0.00 0.00 4.26
636 664 1.076332 GCGTACAAATCGGACTTGCT 58.924 50.000 0.00 0.00 0.00 3.91
637 665 0.096454 GGCGTACAAATCGGACTTGC 59.904 55.000 0.00 0.00 0.00 4.01
638 666 1.722011 AGGCGTACAAATCGGACTTG 58.278 50.000 0.00 0.00 0.00 3.16
639 667 3.598019 TTAGGCGTACAAATCGGACTT 57.402 42.857 0.00 0.00 0.00 3.01
640 668 3.118884 ACATTAGGCGTACAAATCGGACT 60.119 43.478 0.00 0.00 0.00 3.85
641 669 3.000925 CACATTAGGCGTACAAATCGGAC 59.999 47.826 0.00 0.00 0.00 4.79
642 670 3.191669 CACATTAGGCGTACAAATCGGA 58.808 45.455 0.00 0.00 0.00 4.55
643 671 2.933906 ACACATTAGGCGTACAAATCGG 59.066 45.455 0.00 0.00 0.00 4.18
644 672 4.317839 GCTACACATTAGGCGTACAAATCG 60.318 45.833 0.00 0.00 0.00 3.34
645 673 4.569162 TGCTACACATTAGGCGTACAAATC 59.431 41.667 0.00 0.00 0.00 2.17
646 674 4.509616 TGCTACACATTAGGCGTACAAAT 58.490 39.130 0.00 0.00 0.00 2.32
647 675 3.927854 TGCTACACATTAGGCGTACAAA 58.072 40.909 0.00 0.00 0.00 2.83
648 676 3.596310 TGCTACACATTAGGCGTACAA 57.404 42.857 0.00 0.00 0.00 2.41
649 677 3.596310 TTGCTACACATTAGGCGTACA 57.404 42.857 0.00 0.00 0.00 2.90
650 678 4.116961 TCATTGCTACACATTAGGCGTAC 58.883 43.478 0.00 0.00 0.00 3.67
651 679 4.394439 TCATTGCTACACATTAGGCGTA 57.606 40.909 0.00 0.00 0.00 4.42
652 680 3.260475 TCATTGCTACACATTAGGCGT 57.740 42.857 0.00 0.00 0.00 5.68
653 681 3.871006 TCTTCATTGCTACACATTAGGCG 59.129 43.478 0.00 0.00 0.00 5.52
654 682 5.818136 TTCTTCATTGCTACACATTAGGC 57.182 39.130 0.00 0.00 0.00 3.93
655 683 7.716998 AGGTATTCTTCATTGCTACACATTAGG 59.283 37.037 0.00 0.00 0.00 2.69
656 684 8.554528 CAGGTATTCTTCATTGCTACACATTAG 58.445 37.037 0.00 0.00 0.00 1.73
657 685 7.012327 GCAGGTATTCTTCATTGCTACACATTA 59.988 37.037 0.00 0.00 0.00 1.90
658 686 6.183360 GCAGGTATTCTTCATTGCTACACATT 60.183 38.462 0.00 0.00 0.00 2.71
659 687 5.297776 GCAGGTATTCTTCATTGCTACACAT 59.702 40.000 0.00 0.00 0.00 3.21
660 688 4.635765 GCAGGTATTCTTCATTGCTACACA 59.364 41.667 0.00 0.00 0.00 3.72
661 689 4.260375 CGCAGGTATTCTTCATTGCTACAC 60.260 45.833 0.00 0.00 0.00 2.90
662 690 3.871006 CGCAGGTATTCTTCATTGCTACA 59.129 43.478 0.00 0.00 0.00 2.74
663 691 4.119862 TCGCAGGTATTCTTCATTGCTAC 58.880 43.478 0.00 0.00 0.00 3.58
664 692 4.371786 CTCGCAGGTATTCTTCATTGCTA 58.628 43.478 0.00 0.00 0.00 3.49
665 693 3.201290 CTCGCAGGTATTCTTCATTGCT 58.799 45.455 0.00 0.00 0.00 3.91
666 694 2.286654 GCTCGCAGGTATTCTTCATTGC 60.287 50.000 0.00 0.00 0.00 3.56
667 695 2.938451 TGCTCGCAGGTATTCTTCATTG 59.062 45.455 0.00 0.00 0.00 2.82
668 696 3.266510 TGCTCGCAGGTATTCTTCATT 57.733 42.857 0.00 0.00 0.00 2.57
669 697 2.988010 TGCTCGCAGGTATTCTTCAT 57.012 45.000 0.00 0.00 0.00 2.57
670 698 2.621338 CTTGCTCGCAGGTATTCTTCA 58.379 47.619 0.00 0.00 0.00 3.02
671 699 1.328986 GCTTGCTCGCAGGTATTCTTC 59.671 52.381 2.97 0.00 0.00 2.87
672 700 1.065854 AGCTTGCTCGCAGGTATTCTT 60.066 47.619 2.97 0.00 0.00 2.52
673 701 0.539051 AGCTTGCTCGCAGGTATTCT 59.461 50.000 2.97 0.00 0.00 2.40
674 702 2.131183 CTAGCTTGCTCGCAGGTATTC 58.869 52.381 0.00 0.00 0.00 1.75
675 703 1.808133 GCTAGCTTGCTCGCAGGTATT 60.808 52.381 13.17 0.00 0.00 1.89
676 704 0.249657 GCTAGCTTGCTCGCAGGTAT 60.250 55.000 13.17 0.00 0.00 2.73
677 705 1.141881 GCTAGCTTGCTCGCAGGTA 59.858 57.895 13.17 2.52 0.00 3.08
678 706 2.125350 GCTAGCTTGCTCGCAGGT 60.125 61.111 13.17 1.54 0.00 4.00
679 707 2.894387 GGCTAGCTTGCTCGCAGG 60.894 66.667 19.45 0.00 0.00 4.85
680 708 1.497223 GATGGCTAGCTTGCTCGCAG 61.497 60.000 19.45 4.34 0.00 5.18
681 709 1.522355 GATGGCTAGCTTGCTCGCA 60.522 57.895 19.45 9.79 0.00 5.10
682 710 2.250237 GGATGGCTAGCTTGCTCGC 61.250 63.158 19.45 10.14 0.00 5.03
683 711 1.953138 CGGATGGCTAGCTTGCTCG 60.953 63.158 19.45 13.76 0.00 5.03
684 712 0.599728 CTCGGATGGCTAGCTTGCTC 60.600 60.000 19.45 10.13 0.00 4.26
685 713 1.333636 ACTCGGATGGCTAGCTTGCT 61.334 55.000 19.45 0.44 0.00 3.91
686 714 0.878086 GACTCGGATGGCTAGCTTGC 60.878 60.000 15.72 12.01 0.00 4.01
687 715 0.596083 CGACTCGGATGGCTAGCTTG 60.596 60.000 15.72 0.00 0.00 4.01
688 716 1.038130 ACGACTCGGATGGCTAGCTT 61.038 55.000 15.72 2.16 0.00 3.74
689 717 0.179026 TACGACTCGGATGGCTAGCT 60.179 55.000 15.72 0.00 0.00 3.32
690 718 0.882474 ATACGACTCGGATGGCTAGC 59.118 55.000 6.04 6.04 0.00 3.42
691 719 1.401670 GCATACGACTCGGATGGCTAG 60.402 57.143 22.45 0.20 46.96 3.42
692 720 0.596577 GCATACGACTCGGATGGCTA 59.403 55.000 22.45 0.00 46.96 3.93
693 721 1.364171 GCATACGACTCGGATGGCT 59.636 57.895 22.45 0.00 46.96 4.75
694 722 0.319900 ATGCATACGACTCGGATGGC 60.320 55.000 22.45 15.57 46.96 4.40
695 723 1.422388 CATGCATACGACTCGGATGG 58.578 55.000 22.45 5.11 46.96 3.51
697 725 0.389025 TGCATGCATACGACTCGGAT 59.611 50.000 18.46 0.00 0.00 4.18
698 726 0.174617 TTGCATGCATACGACTCGGA 59.825 50.000 23.37 0.00 0.00 4.55
699 727 0.301687 GTTGCATGCATACGACTCGG 59.698 55.000 23.37 0.00 0.00 4.63
700 728 0.043907 CGTTGCATGCATACGACTCG 60.044 55.000 32.76 20.49 34.74 4.18
701 729 0.999406 ACGTTGCATGCATACGACTC 59.001 50.000 37.83 18.80 35.80 3.36
702 730 0.999406 GACGTTGCATGCATACGACT 59.001 50.000 37.83 26.57 35.80 4.18
703 731 0.718904 TGACGTTGCATGCATACGAC 59.281 50.000 37.83 33.77 35.80 4.34
704 732 1.327156 CATGACGTTGCATGCATACGA 59.673 47.619 37.83 26.57 39.19 3.43
705 733 1.733706 CATGACGTTGCATGCATACG 58.266 50.000 33.54 33.54 39.19 3.06
713 741 0.392863 ATGGCTAGCATGACGTTGCA 60.393 50.000 18.24 1.74 45.23 4.08
716 744 0.392863 TGCATGGCTAGCATGACGTT 60.393 50.000 23.07 0.00 37.02 3.99
781 809 7.249147 GTGTACGTTATCAGTTGATGAGTAGT 58.751 38.462 0.00 1.26 42.53 2.73
782 810 6.411203 CGTGTACGTTATCAGTTGATGAGTAG 59.589 42.308 0.00 0.00 36.52 2.57
787 1093 3.300944 CGCGTGTACGTTATCAGTTGATG 60.301 47.826 0.00 0.00 42.22 3.07
788 1094 2.850060 CGCGTGTACGTTATCAGTTGAT 59.150 45.455 0.00 0.00 42.22 2.57
797 1103 4.035054 GTACGCGCGTGTACGTTA 57.965 55.556 42.78 20.80 43.35 3.18
854 1190 1.490910 GGTATGAGGTAAAGGCTGGCT 59.509 52.381 0.00 0.00 0.00 4.75
858 1194 0.468648 GCGGGTATGAGGTAAAGGCT 59.531 55.000 0.00 0.00 0.00 4.58
865 1201 1.968050 CTTTCGGGCGGGTATGAGGT 61.968 60.000 0.00 0.00 0.00 3.85
867 1203 0.529992 GACTTTCGGGCGGGTATGAG 60.530 60.000 0.00 0.00 0.00 2.90
979 1322 1.202428 GGCTAGCTACTCGGAAGGTTG 60.202 57.143 15.72 0.00 0.00 3.77
983 1326 1.000283 CCATGGCTAGCTACTCGGAAG 60.000 57.143 15.72 0.00 0.00 3.46
986 1329 1.005630 GCCATGGCTAGCTACTCGG 60.006 63.158 29.98 11.35 38.26 4.63
1377 1724 0.820871 GCATCAGGTCGTCTCCTTCT 59.179 55.000 0.00 0.00 35.37 2.85
1417 1764 2.807045 GCGTGTCTGCGTCTCCTG 60.807 66.667 0.00 0.00 0.00 3.86
1461 1808 2.707849 GCACCCAAGCAGCATGAGG 61.708 63.158 0.00 1.52 39.69 3.86
1539 1886 1.303309 GCTGATACGCCTCTTTGCAT 58.697 50.000 0.00 0.00 0.00 3.96
1745 2101 0.674895 GCGATGTTCTTGGACCAGCT 60.675 55.000 0.00 0.00 0.00 4.24
1838 2316 2.554032 CACCACCCTGTCAATGTTCTTC 59.446 50.000 0.00 0.00 0.00 2.87
2178 2701 0.669318 GCGACCGAGTGAATGTCCAA 60.669 55.000 0.00 0.00 0.00 3.53
2376 2902 1.888512 CAAGCACATTAGGGCAGTTGT 59.111 47.619 0.00 0.00 0.00 3.32
2451 2982 2.031919 TTGCCGTGTACCCTGCAG 59.968 61.111 6.78 6.78 34.81 4.41
2582 3116 5.721000 TGCCATGATTTGAAAACCTTAGGAT 59.279 36.000 4.77 0.00 0.00 3.24
2608 3142 5.652014 CCATGTATGGTCTGGTTTACAACAT 59.348 40.000 2.66 0.00 43.05 2.71


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

AutoCloner maintained by Alex Coulton.