Multiple sequence alignment - TraesCS7A01G307600

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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 TraesCS7A01G307600 chr7A 100.000 4028 0 0 1 4028 434744416 434740389 0.000000e+00 7439
1 TraesCS7A01G307600 chr7D 95.018 3312 81 19 764 4028 386362735 386359461 0.000000e+00 5125
2 TraesCS7A01G307600 chr7D 94.073 658 37 2 1 656 579057134 579056477 0.000000e+00 998
3 TraesCS7A01G307600 chr7B 96.012 2633 90 9 828 3451 380541268 380538642 0.000000e+00 4266
4 TraesCS7A01G307600 chr7B 93.874 555 8 2 3499 4028 380538653 380538100 0.000000e+00 813
5 TraesCS7A01G307600 chr1D 94.073 658 37 2 1 656 233339931 233340588 0.000000e+00 998
6 TraesCS7A01G307600 chr1D 96.610 59 2 0 466 524 111394604 111394662 9.210000e-17 99
7 TraesCS7A01G307600 chr6D 93.245 607 38 2 1 606 10799283 10798679 0.000000e+00 891
8 TraesCS7A01G307600 chr1A 89.314 627 57 4 34 656 586990472 586989852 0.000000e+00 778
9 TraesCS7A01G307600 chr2A 88.867 503 53 3 156 656 750805176 750805677 2.060000e-172 616


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 TraesCS7A01G307600 chr7A 434740389 434744416 4027 True 7439.0 7439 100.000 1 4028 1 chr7A.!!$R1 4027
1 TraesCS7A01G307600 chr7D 386359461 386362735 3274 True 5125.0 5125 95.018 764 4028 1 chr7D.!!$R1 3264
2 TraesCS7A01G307600 chr7D 579056477 579057134 657 True 998.0 998 94.073 1 656 1 chr7D.!!$R2 655
3 TraesCS7A01G307600 chr7B 380538100 380541268 3168 True 2539.5 4266 94.943 828 4028 2 chr7B.!!$R1 3200
4 TraesCS7A01G307600 chr1D 233339931 233340588 657 False 998.0 998 94.073 1 656 1 chr1D.!!$F2 655
5 TraesCS7A01G307600 chr6D 10798679 10799283 604 True 891.0 891 93.245 1 606 1 chr6D.!!$R1 605
6 TraesCS7A01G307600 chr1A 586989852 586990472 620 True 778.0 778 89.314 34 656 1 chr1A.!!$R1 622
7 TraesCS7A01G307600 chr2A 750805176 750805677 501 False 616.0 616 88.867 156 656 1 chr2A.!!$F1 500

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
559 564 0.034337 AAAGGCTGCGTCGTCCTTAA 59.966 50.000 13.29 0.0 39.14 1.85 F
672 677 0.250166 AAACGAAGACCAACGAGGGG 60.250 55.000 0.00 0.0 43.89 4.79 F
707 712 0.311790 ACCAAAGCGAAGACGACGTA 59.688 50.000 0.00 0.0 42.66 3.57 F
870 887 0.397187 TATCCCGTCCCTCTCTCTCG 59.603 60.000 0.00 0.0 0.00 4.04 F
1419 1440 1.274167 GACCAGTACATGTGGAACCGA 59.726 52.381 9.11 0.0 38.57 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1761 0.179094 CAATCCGCCCGCACTTACTA 60.179 55.000 0.0 0.0 0.00 1.82 R
1908 1929 2.263077 AGCATCGTCGAGAATGTGAAC 58.737 47.619 0.0 0.0 0.00 3.18 R
2067 2088 2.322161 CTCTCAAAAACATGCCTTGCG 58.678 47.619 0.0 0.0 0.00 4.85 R
2328 2349 3.806316 AAAAGTTCGATAACACAGGCG 57.194 42.857 0.0 0.0 38.12 5.52 R
3353 3383 3.057033 GCAGACATGACAAGGCAAAGATT 60.057 43.478 0.0 0.0 0.00 2.40 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
56 57 5.066593 AGTTTCAGAATCCTGTTTCCACTC 58.933 41.667 0.00 0.00 41.16 3.51
177 178 1.349357 GAGTCCTCTGAAGCCTGGTTT 59.651 52.381 0.00 0.00 0.00 3.27
189 190 1.110442 CCTGGTTTGTGCAAGGTGAA 58.890 50.000 0.00 0.00 0.00 3.18
226 227 3.069318 AGGGACGGTCGAAGAGGC 61.069 66.667 1.43 0.00 36.95 4.70
230 231 3.909258 GACGGTCGAAGAGGCGCAA 62.909 63.158 10.83 0.00 36.95 4.85
255 256 2.095617 CAGCAATTTGTCGTGATGAGCA 60.096 45.455 0.00 0.00 0.00 4.26
299 302 2.758009 CTGTTGTTTTGAATGGCCAGG 58.242 47.619 13.05 0.00 0.00 4.45
308 311 1.976404 TGAATGGCCAGGCAAATTCAA 59.024 42.857 27.72 17.00 38.90 2.69
387 391 6.927294 ATTAGGAAGATAAAAGTTGCCTCG 57.073 37.500 0.00 0.00 0.00 4.63
393 397 3.947834 AGATAAAAGTTGCCTCGGATTGG 59.052 43.478 0.00 0.00 0.00 3.16
467 472 3.973206 TTTGCGAGAAGTGGAGGATAA 57.027 42.857 0.00 0.00 0.00 1.75
492 497 7.686434 AGGCTAAATTGTTTACTCTAGTGGAA 58.314 34.615 0.00 0.00 0.00 3.53
559 564 0.034337 AAAGGCTGCGTCGTCCTTAA 59.966 50.000 13.29 0.00 39.14 1.85
613 618 9.823647 CTTTATCAGATATCTGTAACACACCTT 57.176 33.333 27.80 7.72 44.12 3.50
628 633 6.627395 ACACACCTTTGAATGTTTCGATTA 57.373 33.333 0.00 0.00 0.00 1.75
671 676 1.589803 AAAACGAAGACCAACGAGGG 58.410 50.000 0.00 0.00 43.89 4.30
672 677 0.250166 AAACGAAGACCAACGAGGGG 60.250 55.000 0.00 0.00 43.89 4.79
673 678 1.117142 AACGAAGACCAACGAGGGGA 61.117 55.000 0.00 0.00 43.89 4.81
674 679 1.215647 CGAAGACCAACGAGGGGAG 59.784 63.158 0.00 0.00 43.89 4.30
675 680 1.248785 CGAAGACCAACGAGGGGAGA 61.249 60.000 0.00 0.00 43.89 3.71
676 681 0.974383 GAAGACCAACGAGGGGAGAA 59.026 55.000 0.00 0.00 43.89 2.87
677 682 1.346722 GAAGACCAACGAGGGGAGAAA 59.653 52.381 0.00 0.00 43.89 2.52
678 683 0.685660 AGACCAACGAGGGGAGAAAC 59.314 55.000 0.00 0.00 43.89 2.78
679 684 0.395312 GACCAACGAGGGGAGAAACA 59.605 55.000 0.00 0.00 43.89 2.83
680 685 1.003233 GACCAACGAGGGGAGAAACAT 59.997 52.381 0.00 0.00 43.89 2.71
681 686 1.271379 ACCAACGAGGGGAGAAACATG 60.271 52.381 0.00 0.00 43.89 3.21
682 687 1.003118 CCAACGAGGGGAGAAACATGA 59.997 52.381 0.00 0.00 0.00 3.07
683 688 2.552155 CCAACGAGGGGAGAAACATGAA 60.552 50.000 0.00 0.00 0.00 2.57
684 689 3.146066 CAACGAGGGGAGAAACATGAAA 58.854 45.455 0.00 0.00 0.00 2.69
685 690 2.779506 ACGAGGGGAGAAACATGAAAC 58.220 47.619 0.00 0.00 0.00 2.78
686 691 1.732259 CGAGGGGAGAAACATGAAACG 59.268 52.381 0.00 0.00 0.00 3.60
687 692 2.084546 GAGGGGAGAAACATGAAACGG 58.915 52.381 0.00 0.00 0.00 4.44
688 693 1.702957 AGGGGAGAAACATGAAACGGA 59.297 47.619 0.00 0.00 0.00 4.69
689 694 1.810755 GGGGAGAAACATGAAACGGAC 59.189 52.381 0.00 0.00 0.00 4.79
690 695 1.810755 GGGAGAAACATGAAACGGACC 59.189 52.381 0.00 0.00 0.00 4.46
691 696 2.500229 GGAGAAACATGAAACGGACCA 58.500 47.619 0.00 0.00 0.00 4.02
692 697 2.882137 GGAGAAACATGAAACGGACCAA 59.118 45.455 0.00 0.00 0.00 3.67
693 698 3.316868 GGAGAAACATGAAACGGACCAAA 59.683 43.478 0.00 0.00 0.00 3.28
694 699 4.537015 GAGAAACATGAAACGGACCAAAG 58.463 43.478 0.00 0.00 0.00 2.77
695 700 2.793278 AACATGAAACGGACCAAAGC 57.207 45.000 0.00 0.00 0.00 3.51
696 701 0.591170 ACATGAAACGGACCAAAGCG 59.409 50.000 0.00 0.00 0.00 4.68
697 702 0.871722 CATGAAACGGACCAAAGCGA 59.128 50.000 0.00 0.00 0.00 4.93
698 703 1.265635 CATGAAACGGACCAAAGCGAA 59.734 47.619 0.00 0.00 0.00 4.70
699 704 0.941542 TGAAACGGACCAAAGCGAAG 59.058 50.000 0.00 0.00 0.00 3.79
700 705 1.223187 GAAACGGACCAAAGCGAAGA 58.777 50.000 0.00 0.00 0.00 2.87
701 706 0.942252 AAACGGACCAAAGCGAAGAC 59.058 50.000 0.00 0.00 0.00 3.01
702 707 1.219522 AACGGACCAAAGCGAAGACG 61.220 55.000 0.00 0.00 42.93 4.18
703 708 1.372499 CGGACCAAAGCGAAGACGA 60.372 57.895 0.00 0.00 42.66 4.20
704 709 1.615107 CGGACCAAAGCGAAGACGAC 61.615 60.000 0.00 0.00 42.66 4.34
705 710 1.615107 GGACCAAAGCGAAGACGACG 61.615 60.000 0.00 0.00 42.66 5.12
706 711 0.938168 GACCAAAGCGAAGACGACGT 60.938 55.000 0.00 0.00 42.66 4.34
707 712 0.311790 ACCAAAGCGAAGACGACGTA 59.688 50.000 0.00 0.00 42.66 3.57
708 713 1.068055 ACCAAAGCGAAGACGACGTAT 60.068 47.619 0.00 0.00 42.66 3.06
709 714 1.582502 CCAAAGCGAAGACGACGTATC 59.417 52.381 0.00 1.51 42.66 2.24
710 715 2.247637 CAAAGCGAAGACGACGTATCA 58.752 47.619 0.00 0.00 42.66 2.15
711 716 2.624316 AAGCGAAGACGACGTATCAA 57.376 45.000 0.00 0.00 42.66 2.57
712 717 2.624316 AGCGAAGACGACGTATCAAA 57.376 45.000 0.00 0.00 42.66 2.69
713 718 2.937591 AGCGAAGACGACGTATCAAAA 58.062 42.857 0.00 0.00 42.66 2.44
714 719 3.311106 AGCGAAGACGACGTATCAAAAA 58.689 40.909 0.00 0.00 42.66 1.94
736 741 8.899887 AAAAAGATCAAATTATGGGAGAAGGA 57.100 30.769 0.00 0.00 0.00 3.36
737 742 8.899887 AAAAGATCAAATTATGGGAGAAGGAA 57.100 30.769 0.00 0.00 0.00 3.36
738 743 8.530804 AAAGATCAAATTATGGGAGAAGGAAG 57.469 34.615 0.00 0.00 0.00 3.46
739 744 6.067350 AGATCAAATTATGGGAGAAGGAAGC 58.933 40.000 0.00 0.00 0.00 3.86
740 745 5.191727 TCAAATTATGGGAGAAGGAAGCA 57.808 39.130 0.00 0.00 0.00 3.91
741 746 5.579047 TCAAATTATGGGAGAAGGAAGCAA 58.421 37.500 0.00 0.00 0.00 3.91
742 747 6.197168 TCAAATTATGGGAGAAGGAAGCAAT 58.803 36.000 0.00 0.00 0.00 3.56
743 748 7.353525 TCAAATTATGGGAGAAGGAAGCAATA 58.646 34.615 0.00 0.00 0.00 1.90
744 749 7.503566 TCAAATTATGGGAGAAGGAAGCAATAG 59.496 37.037 0.00 0.00 0.00 1.73
745 750 2.717639 TGGGAGAAGGAAGCAATAGC 57.282 50.000 0.00 0.00 42.56 2.97
746 751 1.212935 TGGGAGAAGGAAGCAATAGCC 59.787 52.381 0.00 0.00 43.56 3.93
747 752 1.477740 GGGAGAAGGAAGCAATAGCCC 60.478 57.143 0.00 0.00 43.56 5.19
748 753 1.492599 GGAGAAGGAAGCAATAGCCCT 59.507 52.381 0.00 0.00 43.56 5.19
749 754 2.092158 GGAGAAGGAAGCAATAGCCCTT 60.092 50.000 0.00 0.00 42.70 3.95
750 755 3.625853 GAGAAGGAAGCAATAGCCCTTT 58.374 45.455 0.00 0.00 40.91 3.11
751 756 4.019858 GAGAAGGAAGCAATAGCCCTTTT 58.980 43.478 0.00 0.00 40.91 2.27
752 757 5.193099 AGAAGGAAGCAATAGCCCTTTTA 57.807 39.130 0.00 0.00 40.91 1.52
753 758 5.770919 AGAAGGAAGCAATAGCCCTTTTAT 58.229 37.500 0.00 0.00 40.91 1.40
754 759 6.197903 AGAAGGAAGCAATAGCCCTTTTATT 58.802 36.000 0.00 0.00 40.91 1.40
755 760 7.354312 AGAAGGAAGCAATAGCCCTTTTATTA 58.646 34.615 0.00 0.00 40.91 0.98
756 761 8.007153 AGAAGGAAGCAATAGCCCTTTTATTAT 58.993 33.333 0.00 0.00 40.91 1.28
757 762 8.553085 AAGGAAGCAATAGCCCTTTTATTATT 57.447 30.769 0.00 0.00 38.70 1.40
758 763 9.654919 AAGGAAGCAATAGCCCTTTTATTATTA 57.345 29.630 0.00 0.00 38.70 0.98
759 764 9.301897 AGGAAGCAATAGCCCTTTTATTATTAG 57.698 33.333 0.00 0.00 43.56 1.73
760 765 9.297037 GGAAGCAATAGCCCTTTTATTATTAGA 57.703 33.333 0.00 0.00 43.56 2.10
839 856 1.728971 GCATGGACTGACACTTTCGAG 59.271 52.381 0.00 0.00 0.00 4.04
846 863 2.057316 CTGACACTTTCGAGCTCACAG 58.943 52.381 15.40 8.33 0.00 3.66
857 874 0.955178 AGCTCACAGACGATATCCCG 59.045 55.000 0.00 0.00 0.00 5.14
868 885 1.003812 CGATATCCCGTCCCTCTCTCT 59.996 57.143 0.00 0.00 0.00 3.10
870 887 0.397187 TATCCCGTCCCTCTCTCTCG 59.603 60.000 0.00 0.00 0.00 4.04
871 888 2.969300 ATCCCGTCCCTCTCTCTCGC 62.969 65.000 0.00 0.00 0.00 5.03
873 890 2.124487 CGTCCCTCTCTCTCGCCT 60.124 66.667 0.00 0.00 0.00 5.52
888 905 4.101448 CCTCCCCCTCCACTTGCG 62.101 72.222 0.00 0.00 0.00 4.85
922 939 4.653888 ACCCCAAAACCCTCGCCG 62.654 66.667 0.00 0.00 0.00 6.46
924 941 2.596338 CCCAAAACCCTCGCCGTT 60.596 61.111 0.00 0.00 0.00 4.44
925 942 2.622962 CCCAAAACCCTCGCCGTTC 61.623 63.158 0.00 0.00 0.00 3.95
926 943 2.554272 CAAAACCCTCGCCGTTCG 59.446 61.111 0.00 0.00 40.15 3.95
965 986 4.853924 TTTCTCCAAATTTCAGCTCACC 57.146 40.909 0.00 0.00 0.00 4.02
998 1019 1.337118 GGCTTGGTTTCCAATCCACA 58.663 50.000 14.17 0.00 45.87 4.17
999 1020 1.901833 GGCTTGGTTTCCAATCCACAT 59.098 47.619 14.17 0.00 45.87 3.21
1027 1048 4.390556 AGCTCACTCCCCTCCGCT 62.391 66.667 0.00 0.00 0.00 5.52
1419 1440 1.274167 GACCAGTACATGTGGAACCGA 59.726 52.381 9.11 0.00 38.57 4.69
1656 1677 3.284449 GTGTTGGGGTCGGTGCAC 61.284 66.667 8.80 8.80 0.00 4.57
1740 1761 3.525268 TGTGCACTCATCGACATGTAT 57.475 42.857 19.41 0.00 0.00 2.29
1908 1929 2.825836 GGTGCCGGCTTGGATCAG 60.826 66.667 29.70 0.00 42.00 2.90
2026 2047 1.551430 TGGACATTGTCGGGAATACGT 59.449 47.619 10.56 0.00 32.65 3.57
2067 2088 1.280457 AGTGGGGTCAGATGGAAGAC 58.720 55.000 0.00 0.00 0.00 3.01
2112 2133 2.634940 GCCTAGCAGGAACCTGATATCA 59.365 50.000 22.96 5.07 46.30 2.15
2691 2712 9.618890 TTCTTTAATGATAGTCTCAATCCCAAG 57.381 33.333 0.00 0.00 37.44 3.61
3203 3225 2.833794 TCTACACCAGAGTTGTTGCAC 58.166 47.619 0.00 0.00 0.00 4.57
3239 3261 9.454859 AAGTTATTTCCTAGATGTTCTTTCTGG 57.545 33.333 0.00 0.00 0.00 3.86
3338 3368 8.931775 GTTAATCAAAGCATATTTTCCGGTTTT 58.068 29.630 0.00 0.00 0.00 2.43
3353 3383 5.878627 TCCGGTTTTATGAGGTTTCCTTAA 58.121 37.500 0.00 0.00 31.76 1.85
3378 3408 0.671472 TGCCTTGTCATGTCTGCTCG 60.671 55.000 0.00 0.00 0.00 5.03
3614 3647 8.350722 AGTTTGATTCTCATTGATATGCATGTC 58.649 33.333 15.93 15.93 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.922407 TCTTCATCATGAATAGCTCTTCTTCG 59.078 38.462 12.51 2.38 35.59 3.79
177 178 2.296752 CCATCAACATTCACCTTGCACA 59.703 45.455 0.00 0.00 0.00 4.57
189 190 3.372349 CCTGGACAATCCTCCATCAACAT 60.372 47.826 0.00 0.00 39.72 2.71
226 227 1.187704 CGACAAATTGCTGTTGTTGCG 59.812 47.619 0.00 0.12 39.29 4.85
230 231 3.314913 TCATCACGACAAATTGCTGTTGT 59.685 39.130 0.00 0.00 43.42 3.32
299 302 4.553323 AGCTTCAGACATGTTGAATTTGC 58.447 39.130 17.82 17.15 34.33 3.68
308 311 4.063689 GCATGCTATAGCTTCAGACATGT 58.936 43.478 24.61 0.00 42.66 3.21
387 391 1.541588 GTGACAACTTCCAGCCAATCC 59.458 52.381 0.00 0.00 0.00 3.01
393 397 6.017109 TCTGAAAATTAGTGACAACTTCCAGC 60.017 38.462 0.00 0.00 37.88 4.85
467 472 7.253905 TCCACTAGAGTAAACAATTTAGCCT 57.746 36.000 0.00 0.00 0.00 4.58
492 497 2.968574 CTCCCTATACTCATGCACCACT 59.031 50.000 0.00 0.00 0.00 4.00
559 564 0.944386 CAAATATAACGGCCTGCGCT 59.056 50.000 9.73 0.00 34.44 5.92
656 661 1.215647 CTCCCCTCGTTGGTCTTCG 59.784 63.158 0.00 0.00 0.00 3.79
657 662 0.974383 TTCTCCCCTCGTTGGTCTTC 59.026 55.000 0.00 0.00 0.00 2.87
658 663 1.071857 GTTTCTCCCCTCGTTGGTCTT 59.928 52.381 0.00 0.00 0.00 3.01
659 664 0.685660 GTTTCTCCCCTCGTTGGTCT 59.314 55.000 0.00 0.00 0.00 3.85
660 665 0.395312 TGTTTCTCCCCTCGTTGGTC 59.605 55.000 0.00 0.00 0.00 4.02
661 666 1.064825 ATGTTTCTCCCCTCGTTGGT 58.935 50.000 0.00 0.00 0.00 3.67
662 667 1.003118 TCATGTTTCTCCCCTCGTTGG 59.997 52.381 0.00 0.00 0.00 3.77
663 668 2.472695 TCATGTTTCTCCCCTCGTTG 57.527 50.000 0.00 0.00 0.00 4.10
664 669 3.146847 GTTTCATGTTTCTCCCCTCGTT 58.853 45.455 0.00 0.00 0.00 3.85
665 670 2.779506 GTTTCATGTTTCTCCCCTCGT 58.220 47.619 0.00 0.00 0.00 4.18
666 671 1.732259 CGTTTCATGTTTCTCCCCTCG 59.268 52.381 0.00 0.00 0.00 4.63
667 672 2.084546 CCGTTTCATGTTTCTCCCCTC 58.915 52.381 0.00 0.00 0.00 4.30
668 673 1.702957 TCCGTTTCATGTTTCTCCCCT 59.297 47.619 0.00 0.00 0.00 4.79
669 674 1.810755 GTCCGTTTCATGTTTCTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
670 675 1.810755 GGTCCGTTTCATGTTTCTCCC 59.189 52.381 0.00 0.00 0.00 4.30
671 676 2.500229 TGGTCCGTTTCATGTTTCTCC 58.500 47.619 0.00 0.00 0.00 3.71
672 677 4.537015 CTTTGGTCCGTTTCATGTTTCTC 58.463 43.478 0.00 0.00 0.00 2.87
673 678 3.243401 GCTTTGGTCCGTTTCATGTTTCT 60.243 43.478 0.00 0.00 0.00 2.52
674 679 3.049912 GCTTTGGTCCGTTTCATGTTTC 58.950 45.455 0.00 0.00 0.00 2.78
675 680 2.542824 CGCTTTGGTCCGTTTCATGTTT 60.543 45.455 0.00 0.00 0.00 2.83
676 681 1.001815 CGCTTTGGTCCGTTTCATGTT 60.002 47.619 0.00 0.00 0.00 2.71
677 682 0.591170 CGCTTTGGTCCGTTTCATGT 59.409 50.000 0.00 0.00 0.00 3.21
678 683 0.871722 TCGCTTTGGTCCGTTTCATG 59.128 50.000 0.00 0.00 0.00 3.07
679 684 1.535462 CTTCGCTTTGGTCCGTTTCAT 59.465 47.619 0.00 0.00 0.00 2.57
680 685 0.941542 CTTCGCTTTGGTCCGTTTCA 59.058 50.000 0.00 0.00 0.00 2.69
681 686 1.070108 GTCTTCGCTTTGGTCCGTTTC 60.070 52.381 0.00 0.00 0.00 2.78
682 687 0.942252 GTCTTCGCTTTGGTCCGTTT 59.058 50.000 0.00 0.00 0.00 3.60
683 688 1.219522 CGTCTTCGCTTTGGTCCGTT 61.220 55.000 0.00 0.00 0.00 4.44
684 689 1.663702 CGTCTTCGCTTTGGTCCGT 60.664 57.895 0.00 0.00 0.00 4.69
685 690 1.372499 TCGTCTTCGCTTTGGTCCG 60.372 57.895 0.00 0.00 36.96 4.79
686 691 1.615107 CGTCGTCTTCGCTTTGGTCC 61.615 60.000 0.00 0.00 36.96 4.46
687 692 0.938168 ACGTCGTCTTCGCTTTGGTC 60.938 55.000 0.00 0.00 36.96 4.02
688 693 0.311790 TACGTCGTCTTCGCTTTGGT 59.688 50.000 0.00 0.00 36.96 3.67
689 694 1.582502 GATACGTCGTCTTCGCTTTGG 59.417 52.381 0.00 0.00 36.96 3.28
690 695 2.247637 TGATACGTCGTCTTCGCTTTG 58.752 47.619 0.00 0.00 36.96 2.77
691 696 2.624316 TGATACGTCGTCTTCGCTTT 57.376 45.000 0.00 0.00 36.96 3.51
692 697 2.624316 TTGATACGTCGTCTTCGCTT 57.376 45.000 0.00 0.00 36.96 4.68
693 698 2.624316 TTTGATACGTCGTCTTCGCT 57.376 45.000 0.00 0.00 36.96 4.93
694 699 3.693300 TTTTTGATACGTCGTCTTCGC 57.307 42.857 0.00 0.00 36.96 4.70
711 716 8.899887 TCCTTCTCCCATAATTTGATCTTTTT 57.100 30.769 0.00 0.00 0.00 1.94
712 717 8.899887 TTCCTTCTCCCATAATTTGATCTTTT 57.100 30.769 0.00 0.00 0.00 2.27
713 718 7.069208 GCTTCCTTCTCCCATAATTTGATCTTT 59.931 37.037 0.00 0.00 0.00 2.52
714 719 6.548993 GCTTCCTTCTCCCATAATTTGATCTT 59.451 38.462 0.00 0.00 0.00 2.40
715 720 6.067350 GCTTCCTTCTCCCATAATTTGATCT 58.933 40.000 0.00 0.00 0.00 2.75
716 721 5.829924 TGCTTCCTTCTCCCATAATTTGATC 59.170 40.000 0.00 0.00 0.00 2.92
717 722 5.769835 TGCTTCCTTCTCCCATAATTTGAT 58.230 37.500 0.00 0.00 0.00 2.57
718 723 5.191727 TGCTTCCTTCTCCCATAATTTGA 57.808 39.130 0.00 0.00 0.00 2.69
719 724 5.920193 TTGCTTCCTTCTCCCATAATTTG 57.080 39.130 0.00 0.00 0.00 2.32
720 725 6.266330 GCTATTGCTTCCTTCTCCCATAATTT 59.734 38.462 0.00 0.00 36.03 1.82
721 726 5.772169 GCTATTGCTTCCTTCTCCCATAATT 59.228 40.000 0.00 0.00 36.03 1.40
722 727 5.320277 GCTATTGCTTCCTTCTCCCATAAT 58.680 41.667 0.00 0.00 36.03 1.28
723 728 4.446311 GGCTATTGCTTCCTTCTCCCATAA 60.446 45.833 0.00 0.00 39.59 1.90
724 729 3.073062 GGCTATTGCTTCCTTCTCCCATA 59.927 47.826 0.00 0.00 39.59 2.74
725 730 2.158549 GGCTATTGCTTCCTTCTCCCAT 60.159 50.000 0.00 0.00 39.59 4.00
726 731 1.212935 GGCTATTGCTTCCTTCTCCCA 59.787 52.381 0.00 0.00 39.59 4.37
727 732 1.477740 GGGCTATTGCTTCCTTCTCCC 60.478 57.143 0.00 0.00 39.59 4.30
728 733 1.492599 AGGGCTATTGCTTCCTTCTCC 59.507 52.381 0.00 0.00 39.59 3.71
729 734 3.289407 AAGGGCTATTGCTTCCTTCTC 57.711 47.619 4.34 0.00 36.54 2.87
730 735 3.746792 AAAGGGCTATTGCTTCCTTCT 57.253 42.857 9.40 0.49 39.04 2.85
731 736 6.471233 AATAAAAGGGCTATTGCTTCCTTC 57.529 37.500 9.40 0.00 39.04 3.46
732 737 8.553085 AATAATAAAAGGGCTATTGCTTCCTT 57.447 30.769 4.34 4.34 40.79 3.36
733 738 9.301897 CTAATAATAAAAGGGCTATTGCTTCCT 57.698 33.333 0.00 0.00 39.59 3.36
734 739 9.297037 TCTAATAATAAAAGGGCTATTGCTTCC 57.703 33.333 0.00 0.00 39.59 3.46
799 804 8.884323 TCCATGCTCCTATATAAACAGAGAATT 58.116 33.333 0.00 0.00 0.00 2.17
801 806 7.510685 AGTCCATGCTCCTATATAAACAGAGAA 59.489 37.037 0.00 0.00 0.00 2.87
802 807 7.013220 AGTCCATGCTCCTATATAAACAGAGA 58.987 38.462 0.00 0.00 0.00 3.10
803 808 7.039434 TCAGTCCATGCTCCTATATAAACAGAG 60.039 40.741 0.00 0.00 0.00 3.35
804 809 6.782494 TCAGTCCATGCTCCTATATAAACAGA 59.218 38.462 0.00 0.00 0.00 3.41
805 810 6.870965 GTCAGTCCATGCTCCTATATAAACAG 59.129 42.308 0.00 0.00 0.00 3.16
806 811 6.326323 TGTCAGTCCATGCTCCTATATAAACA 59.674 38.462 0.00 0.00 0.00 2.83
807 812 6.647067 GTGTCAGTCCATGCTCCTATATAAAC 59.353 42.308 0.00 0.00 0.00 2.01
808 813 6.554982 AGTGTCAGTCCATGCTCCTATATAAA 59.445 38.462 0.00 0.00 0.00 1.40
809 814 6.077993 AGTGTCAGTCCATGCTCCTATATAA 58.922 40.000 0.00 0.00 0.00 0.98
810 815 5.645201 AGTGTCAGTCCATGCTCCTATATA 58.355 41.667 0.00 0.00 0.00 0.86
811 816 4.487804 AGTGTCAGTCCATGCTCCTATAT 58.512 43.478 0.00 0.00 0.00 0.86
812 817 3.916035 AGTGTCAGTCCATGCTCCTATA 58.084 45.455 0.00 0.00 0.00 1.31
813 818 2.756907 AGTGTCAGTCCATGCTCCTAT 58.243 47.619 0.00 0.00 0.00 2.57
814 819 2.238084 AGTGTCAGTCCATGCTCCTA 57.762 50.000 0.00 0.00 0.00 2.94
817 822 1.728971 CGAAAGTGTCAGTCCATGCTC 59.271 52.381 0.00 0.00 0.00 4.26
839 856 0.669077 ACGGGATATCGTCTGTGAGC 59.331 55.000 0.00 0.00 39.34 4.26
857 874 1.826487 GGAGGCGAGAGAGAGGGAC 60.826 68.421 0.00 0.00 0.00 4.46
868 885 4.332543 AAGTGGAGGGGGAGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
870 887 4.432741 GCAAGTGGAGGGGGAGGC 62.433 72.222 0.00 0.00 0.00 4.70
871 888 4.101448 CGCAAGTGGAGGGGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
888 905 0.105964 GGTTCTGGGTTGGGTTTTGC 59.894 55.000 0.00 0.00 0.00 3.68
922 939 0.521735 GTGGTGGATTTGAGGCGAAC 59.478 55.000 0.00 0.00 0.00 3.95
924 941 1.002624 GGTGGTGGATTTGAGGCGA 60.003 57.895 0.00 0.00 0.00 5.54
925 942 0.680921 ATGGTGGTGGATTTGAGGCG 60.681 55.000 0.00 0.00 0.00 5.52
926 943 1.560505 AATGGTGGTGGATTTGAGGC 58.439 50.000 0.00 0.00 0.00 4.70
928 945 3.445096 GGAGAAATGGTGGTGGATTTGAG 59.555 47.826 0.00 0.00 0.00 3.02
1027 1048 1.612442 GGTAGTGGAGTGGGAGGCA 60.612 63.158 0.00 0.00 0.00 4.75
1071 1092 2.888998 GACGGTGTTGGTCGTTGCC 61.889 63.158 0.00 0.00 39.88 4.52
1171 1192 4.554036 GAGATGGACGGGGCTGCC 62.554 72.222 11.05 11.05 0.00 4.85
1185 1206 3.077556 GCGCAGAGGGAAGGGAGA 61.078 66.667 0.30 0.00 0.00 3.71
1419 1440 1.272648 ACCAAATACATGCCCAGCACT 60.273 47.619 0.00 0.00 43.04 4.40
1563 1584 2.683933 TCCCAGAGCTCCCCGAAC 60.684 66.667 10.93 0.00 0.00 3.95
1740 1761 0.179094 CAATCCGCCCGCACTTACTA 60.179 55.000 0.00 0.00 0.00 1.82
1908 1929 2.263077 AGCATCGTCGAGAATGTGAAC 58.737 47.619 0.00 0.00 0.00 3.18
2026 2047 5.764686 ACTTGCAATACAGATCAACAAGTGA 59.235 36.000 0.00 0.00 43.22 3.41
2067 2088 2.322161 CTCTCAAAAACATGCCTTGCG 58.678 47.619 0.00 0.00 0.00 4.85
2328 2349 3.806316 AAAAGTTCGATAACACAGGCG 57.194 42.857 0.00 0.00 38.12 5.52
2367 2388 5.936956 CCTTATCACTGAATAGGCTTCATCC 59.063 44.000 0.00 0.00 0.00 3.51
2691 2712 5.249420 AGCCTTTGGTAGATTTCTGAACTC 58.751 41.667 0.00 0.00 0.00 3.01
2951 2972 6.294286 GCTAGCATCTCTTACGGTAATCTCTT 60.294 42.308 10.63 0.00 0.00 2.85
3079 3101 6.039717 GCATGCCTAGATCACAAGGAATTAAA 59.960 38.462 6.36 0.00 34.58 1.52
3338 3368 7.182060 AGGCAAAGATTTAAGGAAACCTCATA 58.818 34.615 0.00 0.00 30.89 2.15
3353 3383 3.057033 GCAGACATGACAAGGCAAAGATT 60.057 43.478 0.00 0.00 0.00 2.40
3489 3522 6.131544 TGTTTAGCTTCAGAACCTTCAAAC 57.868 37.500 0.00 0.00 0.00 2.93
3614 3647 5.695851 AATAACAAGGAAAGACACAGCAG 57.304 39.130 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.