Multiple sequence alignment - TraesCS2D01G271300

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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 TraesCS2D01G271300 chr2D 100.000 4222 0 0 1 4222 334313330 334317551 0.000000e+00 7797
1 TraesCS2D01G271300 chr2B 95.051 2930 100 13 851 3761 402675897 402678800 0.000000e+00 4566
2 TraesCS2D01G271300 chr2B 96.129 465 16 2 3760 4222 402678890 402679354 0.000000e+00 758
3 TraesCS2D01G271300 chr2B 84.371 755 109 8 1 752 772237123 772237871 0.000000e+00 732
4 TraesCS2D01G271300 chr2A 94.672 1220 52 6 1516 2733 445332281 445333489 0.000000e+00 1881
5 TraesCS2D01G271300 chr2A 96.699 1121 18 6 2744 3851 445335747 445336861 0.000000e+00 1847
6 TraesCS2D01G271300 chr2A 96.731 673 19 2 851 1520 445331529 445332201 0.000000e+00 1118
7 TraesCS2D01G271300 chr2A 94.570 221 11 1 4002 4222 445362805 445363024 1.450000e-89 340
8 TraesCS2D01G271300 chr2A 97.647 170 3 1 3852 4021 445361446 445361614 1.490000e-74 291
9 TraesCS2D01G271300 chr2A 95.833 72 3 0 4009 4080 445362739 445362810 2.670000e-22 117
10 TraesCS2D01G271300 chr1B 85.270 740 98 11 1 734 95376977 95376243 0.000000e+00 752
11 TraesCS2D01G271300 chr1B 84.636 729 95 11 3 722 520239283 520240003 0.000000e+00 710
12 TraesCS2D01G271300 chr3B 84.840 752 94 13 1 734 383837909 383837160 0.000000e+00 739
13 TraesCS2D01G271300 chr6D 84.543 744 108 7 1 742 457272095 457272833 0.000000e+00 730
14 TraesCS2D01G271300 chr6A 83.990 762 113 8 1 759 604257536 604258291 0.000000e+00 723
15 TraesCS2D01G271300 chr6B 84.658 730 103 9 1 726 515014031 515014755 0.000000e+00 719
16 TraesCS2D01G271300 chr6B 83.706 761 120 4 1 759 695903185 695903943 0.000000e+00 715
17 TraesCS2D01G271300 chr5A 83.574 761 118 6 1 759 531348892 531348137 0.000000e+00 706
18 TraesCS2D01G271300 chr1D 81.629 577 79 13 204 759 338373978 338374548 1.790000e-123 453


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 TraesCS2D01G271300 chr2D 334313330 334317551 4221 False 7797.000000 7797 100.000000 1 4222 1 chr2D.!!$F1 4221
1 TraesCS2D01G271300 chr2B 402675897 402679354 3457 False 2662.000000 4566 95.590000 851 4222 2 chr2B.!!$F2 3371
2 TraesCS2D01G271300 chr2B 772237123 772237871 748 False 732.000000 732 84.371000 1 752 1 chr2B.!!$F1 751
3 TraesCS2D01G271300 chr2A 445331529 445336861 5332 False 1615.333333 1881 96.034000 851 3851 3 chr2A.!!$F1 3000
4 TraesCS2D01G271300 chr2A 445361446 445363024 1578 False 249.333333 340 96.016667 3852 4222 3 chr2A.!!$F2 370
5 TraesCS2D01G271300 chr1B 95376243 95376977 734 True 752.000000 752 85.270000 1 734 1 chr1B.!!$R1 733
6 TraesCS2D01G271300 chr1B 520239283 520240003 720 False 710.000000 710 84.636000 3 722 1 chr1B.!!$F1 719
7 TraesCS2D01G271300 chr3B 383837160 383837909 749 True 739.000000 739 84.840000 1 734 1 chr3B.!!$R1 733
8 TraesCS2D01G271300 chr6D 457272095 457272833 738 False 730.000000 730 84.543000 1 742 1 chr6D.!!$F1 741
9 TraesCS2D01G271300 chr6A 604257536 604258291 755 False 723.000000 723 83.990000 1 759 1 chr6A.!!$F1 758
10 TraesCS2D01G271300 chr6B 515014031 515014755 724 False 719.000000 719 84.658000 1 726 1 chr6B.!!$F1 725
11 TraesCS2D01G271300 chr6B 695903185 695903943 758 False 715.000000 715 83.706000 1 759 1 chr6B.!!$F2 758
12 TraesCS2D01G271300 chr5A 531348137 531348892 755 True 706.000000 706 83.574000 1 759 1 chr5A.!!$R1 758
13 TraesCS2D01G271300 chr1D 338373978 338374548 570 False 453.000000 453 81.629000 204 759 1 chr1D.!!$F1 555

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
817 865 0.030369 CGGGTCGCCTACTGTGATAC 59.970 60.0 0.0 0.00 35.57 2.24 F
916 964 0.106967 GATCACTTGGGCCCTTCCTC 60.107 60.0 25.7 8.56 34.39 3.71 F
1081 1131 1.915078 CTCGCCTTCAACCCCCATCT 61.915 60.0 0.0 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2651 2794 1.000060 GCTGTTTCTGCAAATGGCTCA 60.000 47.619 0.0 0.0 45.15 4.26 R
2655 2798 3.983344 GTGTAAGCTGTTTCTGCAAATGG 59.017 43.478 0.0 0.0 0.00 3.16 R
3402 5792 7.607991 TGAGGTGAAAGAGAAGATAAATTCCAC 59.392 37.037 0.0 0.0 0.00 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
95 96 1.078918 GCTTTCTTTGGCATGCCCC 60.079 57.895 33.44 10.83 34.56 5.80
184 187 1.765314 CCTCCTTGCCACTATACTGCT 59.235 52.381 0.00 0.00 0.00 4.24
212 217 3.263170 ACATGAGTACAACATGGGCTACA 59.737 43.478 25.50 0.00 46.19 2.74
224 229 4.165950 ACATGGGCTACAATCTGGTTGATA 59.834 41.667 7.81 0.00 40.37 2.15
250 257 1.501582 ATCCTCTGTGGGCTACCTTC 58.498 55.000 0.00 0.00 37.76 3.46
251 258 0.116342 TCCTCTGTGGGCTACCTTCA 59.884 55.000 0.00 0.00 37.76 3.02
256 263 1.556911 CTGTGGGCTACCTTCATCAGT 59.443 52.381 0.00 0.00 37.76 3.41
298 308 3.633986 CCAGAAAAAGTCTCACTTTGCCT 59.366 43.478 2.44 1.20 46.78 4.75
330 341 2.100584 AGCAGCTAGAAAGATGTCGAGG 59.899 50.000 0.00 0.00 41.33 4.63
331 342 2.099921 GCAGCTAGAAAGATGTCGAGGA 59.900 50.000 0.00 0.00 41.33 3.71
335 346 1.859302 AGAAAGATGTCGAGGAGGCT 58.141 50.000 0.00 0.00 0.00 4.58
353 364 1.321474 CTTTTGGAGTTCTGCAGGCA 58.679 50.000 15.13 0.00 0.00 4.75
421 433 2.092212 CCTTGTGGGAGGTGATAGCATT 60.092 50.000 0.00 0.00 37.23 3.56
424 436 4.853468 TGTGGGAGGTGATAGCATTTTA 57.147 40.909 0.00 0.00 0.00 1.52
455 467 2.496871 GCACAACATGATCATTGGGGAA 59.503 45.455 5.16 0.00 29.46 3.97
471 483 1.692762 GGGAAGAGGGTGAGGATGCTA 60.693 57.143 0.00 0.00 0.00 3.49
492 505 3.600388 ACCGCAACTCTAGAATTTGAGG 58.400 45.455 23.97 23.97 43.57 3.86
498 511 5.877012 GCAACTCTAGAATTTGAGGACATGA 59.123 40.000 15.06 0.00 34.84 3.07
504 517 7.270779 TCTAGAATTTGAGGACATGAGTGATG 58.729 38.462 0.00 0.00 38.15 3.07
553 566 5.095490 GGCCACATTTGAAGAGTTTATTCG 58.905 41.667 0.00 0.00 0.00 3.34
564 577 7.988737 TGAAGAGTTTATTCGAATGCATCAAT 58.011 30.769 20.87 1.68 0.00 2.57
585 598 5.659440 ATAAATTCGGCATTGACCAACTT 57.341 34.783 0.00 0.00 0.00 2.66
588 601 2.552599 TCGGCATTGACCAACTTACA 57.447 45.000 0.00 0.00 0.00 2.41
596 609 2.930950 TGACCAACTTACAAGCAGCTT 58.069 42.857 0.21 0.21 0.00 3.74
599 612 4.884744 TGACCAACTTACAAGCAGCTTAAA 59.115 37.500 7.52 4.68 0.00 1.52
625 638 7.506361 AAGATCAGATTGAGCATATATGGGA 57.494 36.000 14.51 0.00 34.77 4.37
633 646 9.866655 AGATTGAGCATATATGGGAAGTTAAAA 57.133 29.630 14.51 0.00 0.00 1.52
657 671 9.683069 AAAGAGACAACAATGTTGAAATATGAC 57.317 29.630 30.09 12.68 40.74 3.06
727 774 1.962092 GCGGCTATTTGAACGTGCGA 61.962 55.000 0.00 0.00 0.00 5.10
759 807 1.411041 ATTAGGGAGGCCAGACGTAC 58.589 55.000 5.01 0.00 0.00 3.67
760 808 1.033746 TTAGGGAGGCCAGACGTACG 61.034 60.000 15.01 15.01 0.00 3.67
761 809 2.202236 TAGGGAGGCCAGACGTACGT 62.202 60.000 23.04 23.04 0.00 3.57
762 810 2.181021 GGAGGCCAGACGTACGTG 59.819 66.667 28.16 12.97 0.00 4.49
763 811 2.181021 GAGGCCAGACGTACGTGG 59.819 66.667 28.16 22.29 36.85 4.94
764 812 3.352338 GAGGCCAGACGTACGTGGG 62.352 68.421 28.16 25.81 34.06 4.61
765 813 3.376078 GGCCAGACGTACGTGGGA 61.376 66.667 29.90 0.00 34.06 4.37
766 814 2.126189 GCCAGACGTACGTGGGAC 60.126 66.667 29.90 20.17 34.06 4.46
767 815 2.570181 CCAGACGTACGTGGGACC 59.430 66.667 28.16 11.00 0.00 4.46
768 816 2.270257 CCAGACGTACGTGGGACCA 61.270 63.158 28.16 0.00 0.00 4.02
769 817 1.601419 CCAGACGTACGTGGGACCAT 61.601 60.000 28.16 0.00 0.00 3.55
770 818 0.245539 CAGACGTACGTGGGACCATT 59.754 55.000 28.16 0.00 0.00 3.16
771 819 0.529378 AGACGTACGTGGGACCATTC 59.471 55.000 28.16 7.79 0.00 2.67
772 820 0.459063 GACGTACGTGGGACCATTCC 60.459 60.000 28.16 2.86 41.95 3.01
773 821 1.517694 CGTACGTGGGACCATTCCG 60.518 63.158 7.22 0.00 43.94 4.30
774 822 1.812507 GTACGTGGGACCATTCCGC 60.813 63.158 0.00 0.00 43.94 5.54
777 825 4.090588 GTGGGACCATTCCGCGGA 62.091 66.667 27.28 27.28 43.94 5.54
778 826 3.087253 TGGGACCATTCCGCGGAT 61.087 61.111 31.56 14.91 43.94 4.18
779 827 2.591715 GGGACCATTCCGCGGATG 60.592 66.667 31.56 26.09 43.94 3.51
780 828 2.591715 GGACCATTCCGCGGATGG 60.592 66.667 35.24 35.24 41.10 3.51
781 829 2.504032 GACCATTCCGCGGATGGA 59.496 61.111 39.64 26.23 38.75 3.41
782 830 1.071471 GACCATTCCGCGGATGGAT 59.929 57.895 39.64 29.76 38.00 3.41
783 831 1.227943 ACCATTCCGCGGATGGATG 60.228 57.895 39.64 33.23 38.00 3.51
784 832 2.620112 CCATTCCGCGGATGGATGC 61.620 63.158 34.55 0.00 38.00 3.91
785 833 1.893335 CATTCCGCGGATGGATGCA 60.893 57.895 31.56 13.03 38.00 3.96
786 834 1.893808 ATTCCGCGGATGGATGCAC 60.894 57.895 31.56 0.00 38.00 4.57
787 835 4.889856 TCCGCGGATGGATGCACG 62.890 66.667 27.28 0.00 31.53 5.34
788 836 4.889856 CCGCGGATGGATGCACGA 62.890 66.667 24.07 0.00 0.00 4.35
789 837 3.333189 CGCGGATGGATGCACGAG 61.333 66.667 0.00 0.00 0.00 4.18
790 838 2.106938 GCGGATGGATGCACGAGA 59.893 61.111 1.35 0.00 0.00 4.04
791 839 1.521457 GCGGATGGATGCACGAGAA 60.521 57.895 1.35 0.00 0.00 2.87
792 840 1.089481 GCGGATGGATGCACGAGAAA 61.089 55.000 1.35 0.00 0.00 2.52
793 841 1.368641 CGGATGGATGCACGAGAAAA 58.631 50.000 0.00 0.00 0.00 2.29
794 842 1.942657 CGGATGGATGCACGAGAAAAT 59.057 47.619 0.00 0.00 0.00 1.82
795 843 2.355756 CGGATGGATGCACGAGAAAATT 59.644 45.455 0.00 0.00 0.00 1.82
796 844 3.181497 CGGATGGATGCACGAGAAAATTT 60.181 43.478 0.00 0.00 0.00 1.82
797 845 4.107622 GGATGGATGCACGAGAAAATTTG 58.892 43.478 0.00 0.00 0.00 2.32
798 846 2.945278 TGGATGCACGAGAAAATTTGC 58.055 42.857 0.00 0.00 35.45 3.68
799 847 1.913403 GGATGCACGAGAAAATTTGCG 59.087 47.619 0.00 0.00 37.82 4.85
800 848 1.913403 GATGCACGAGAAAATTTGCGG 59.087 47.619 11.42 2.06 37.82 5.69
801 849 0.039617 TGCACGAGAAAATTTGCGGG 60.040 50.000 11.42 8.99 37.82 6.13
802 850 0.039527 GCACGAGAAAATTTGCGGGT 60.040 50.000 10.85 1.93 0.00 5.28
803 851 1.963747 CACGAGAAAATTTGCGGGTC 58.036 50.000 11.42 0.00 0.00 4.46
804 852 0.515564 ACGAGAAAATTTGCGGGTCG 59.484 50.000 5.08 5.08 0.00 4.79
815 863 3.207354 CGGGTCGCCTACTGTGAT 58.793 61.111 0.00 0.00 35.57 3.06
816 864 2.411535 CGGGTCGCCTACTGTGATA 58.588 57.895 0.00 0.00 35.57 2.15
817 865 0.030369 CGGGTCGCCTACTGTGATAC 59.970 60.000 0.00 0.00 35.57 2.24
818 866 0.030369 GGGTCGCCTACTGTGATACG 59.970 60.000 0.00 0.00 35.57 3.06
819 867 0.030369 GGTCGCCTACTGTGATACGG 59.970 60.000 0.00 0.00 35.57 4.02
820 868 0.737219 GTCGCCTACTGTGATACGGT 59.263 55.000 0.00 0.00 41.33 4.83
821 869 1.942657 GTCGCCTACTGTGATACGGTA 59.057 52.381 1.18 1.18 38.84 4.02
822 870 2.355756 GTCGCCTACTGTGATACGGTAA 59.644 50.000 2.65 0.00 39.27 2.85
823 871 3.016031 TCGCCTACTGTGATACGGTAAA 58.984 45.455 2.65 0.00 39.27 2.01
824 872 3.065786 TCGCCTACTGTGATACGGTAAAG 59.934 47.826 2.65 0.00 39.27 1.85
825 873 3.065786 CGCCTACTGTGATACGGTAAAGA 59.934 47.826 2.65 0.00 39.27 2.52
826 874 4.439153 CGCCTACTGTGATACGGTAAAGAA 60.439 45.833 2.65 0.00 39.27 2.52
827 875 5.413499 GCCTACTGTGATACGGTAAAGAAA 58.587 41.667 2.65 0.00 39.27 2.52
828 876 5.870978 GCCTACTGTGATACGGTAAAGAAAA 59.129 40.000 2.65 0.00 39.27 2.29
829 877 6.369615 GCCTACTGTGATACGGTAAAGAAAAA 59.630 38.462 2.65 0.00 39.27 1.94
830 878 7.622880 GCCTACTGTGATACGGTAAAGAAAAAC 60.623 40.741 2.65 0.00 39.27 2.43
831 879 6.219302 ACTGTGATACGGTAAAGAAAAACG 57.781 37.500 0.00 0.00 35.60 3.60
832 880 5.984926 ACTGTGATACGGTAAAGAAAAACGA 59.015 36.000 0.00 0.00 35.60 3.85
833 881 6.647895 ACTGTGATACGGTAAAGAAAAACGAT 59.352 34.615 0.00 0.00 35.60 3.73
834 882 6.823531 TGTGATACGGTAAAGAAAAACGATG 58.176 36.000 0.00 0.00 0.00 3.84
835 883 5.731263 GTGATACGGTAAAGAAAAACGATGC 59.269 40.000 0.00 0.00 0.00 3.91
836 884 5.408909 TGATACGGTAAAGAAAAACGATGCA 59.591 36.000 0.00 0.00 0.00 3.96
837 885 4.759516 ACGGTAAAGAAAAACGATGCAT 57.240 36.364 0.00 0.00 0.00 3.96
838 886 5.116069 ACGGTAAAGAAAAACGATGCATT 57.884 34.783 0.00 0.00 0.00 3.56
839 887 5.525199 ACGGTAAAGAAAAACGATGCATTT 58.475 33.333 0.00 0.00 0.00 2.32
840 888 5.980715 ACGGTAAAGAAAAACGATGCATTTT 59.019 32.000 0.00 0.00 0.00 1.82
841 889 6.477360 ACGGTAAAGAAAAACGATGCATTTTT 59.523 30.769 8.58 8.58 40.94 1.94
883 931 2.868839 GCATTTGCTTGCACTGTTCCAT 60.869 45.455 0.00 0.00 42.31 3.41
916 964 0.106967 GATCACTTGGGCCCTTCCTC 60.107 60.000 25.70 8.56 34.39 3.71
1081 1131 1.915078 CTCGCCTTCAACCCCCATCT 61.915 60.000 0.00 0.00 0.00 2.90
1137 1187 3.012518 CAAATCCATCTCGTTCTTGGCT 58.987 45.455 0.00 0.00 0.00 4.75
1362 1412 4.767255 CTGCACCCAGAGGCGGAC 62.767 72.222 0.00 0.00 41.77 4.79
1435 1485 2.508663 GCGGCCTCGTCAAGTACC 60.509 66.667 0.00 0.00 38.89 3.34
1464 1514 3.000727 CGACCAACTCCAGGTAATGAAC 58.999 50.000 0.00 0.00 40.09 3.18
1507 1557 9.258629 TCCATCCAAGATTTTTCAGTTATTCAT 57.741 29.630 0.00 0.00 0.00 2.57
1535 1669 6.796426 TGATGTACTTGTCTAGTATGCTCAC 58.204 40.000 0.00 0.00 41.26 3.51
1595 1729 5.589452 CGGACAAGTGACTACTCCTTAGTAT 59.411 44.000 6.84 0.00 41.48 2.12
1628 1762 5.127491 TGTGGACGAACTGGAAATTTTAGT 58.873 37.500 0.00 0.00 0.00 2.24
1629 1763 6.289834 TGTGGACGAACTGGAAATTTTAGTA 58.710 36.000 8.81 0.00 0.00 1.82
1630 1764 6.766944 TGTGGACGAACTGGAAATTTTAGTAA 59.233 34.615 8.81 0.00 0.00 2.24
1631 1765 7.041644 TGTGGACGAACTGGAAATTTTAGTAAG 60.042 37.037 8.81 8.54 0.00 2.34
1632 1766 6.993902 TGGACGAACTGGAAATTTTAGTAAGT 59.006 34.615 8.81 10.80 0.00 2.24
1633 1767 8.149647 TGGACGAACTGGAAATTTTAGTAAGTA 58.850 33.333 8.81 0.00 0.00 2.24
1634 1768 8.438513 GGACGAACTGGAAATTTTAGTAAGTAC 58.561 37.037 8.81 8.90 0.00 2.73
1675 1809 5.288712 CGTTGCTATTAGGTGAAGTGTACAG 59.711 44.000 0.00 0.00 0.00 2.74
1701 1835 8.072567 GCTTACTTAATGATTATGCTGGAAGTG 58.927 37.037 0.00 0.00 35.30 3.16
1745 1879 4.404691 GGTGCCAACCTTCCTGAG 57.595 61.111 0.00 0.00 43.84 3.35
1805 1939 2.484264 GCTTCACTCTACGGTTGCATTT 59.516 45.455 0.00 0.00 0.00 2.32
1823 1957 9.579610 GTTGCATTTTGTTATGTTTATTGACAC 57.420 29.630 0.00 0.00 31.30 3.67
2151 2287 7.822822 ACCAGGTATCACTTACAATTTAGACAC 59.177 37.037 0.00 0.00 31.99 3.67
2368 2511 6.885922 ACAGTTTTAGTTGAGACTGGTAACT 58.114 36.000 7.20 0.00 42.81 2.24
2369 2512 6.761714 ACAGTTTTAGTTGAGACTGGTAACTG 59.238 38.462 18.18 18.18 44.52 3.16
2651 2794 2.066262 CCACACAATTCGTTCTACGCT 58.934 47.619 0.00 0.00 42.21 5.07
2655 2798 1.993370 ACAATTCGTTCTACGCTGAGC 59.007 47.619 0.00 0.00 42.21 4.26
3425 5815 6.095580 GGGTGGAATTTATCTTCTCTTTCACC 59.904 42.308 2.98 2.98 0.00 4.02
3486 5876 7.339721 TGTTGATTAACTAACCTGTTTTGGTCA 59.660 33.333 1.75 0.00 37.22 4.02
3691 6086 5.545658 AGGTTTGCACGTATTGACTAATG 57.454 39.130 0.00 0.00 0.00 1.90
3825 6319 1.242076 CCGGCCTTCAATGGATGATC 58.758 55.000 0.00 0.00 38.03 2.92
4000 6495 2.432510 GGATCAACCTACAGGACCAGAG 59.567 54.545 1.29 0.00 38.94 3.35
4019 7723 0.605319 GAATCAACGTGTGGGAGGCA 60.605 55.000 0.00 0.00 0.00 4.75
4068 7772 0.753867 TAGGCCACGACAGTTGTTCA 59.246 50.000 5.01 0.00 0.00 3.18
4144 7848 0.301687 CCTCAATTTCGGTCATCGCG 59.698 55.000 0.00 0.00 39.05 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.005450 TGGGCTTCTTAACATGACCCC 59.995 52.381 0.00 0.00 34.83 4.95
95 96 3.686241 ACATTGATGTCATTGTGAGACCG 59.314 43.478 9.11 0.00 38.54 4.79
184 187 5.436175 CCCATGTTGTACTCATGTCCATTA 58.564 41.667 21.03 0.00 40.43 1.90
212 217 9.253832 CAGAGGATAGATACTATCAACCAGATT 57.746 37.037 16.93 0.00 38.19 2.40
224 229 3.913370 AGCCCACAGAGGATAGATACT 57.087 47.619 0.00 0.00 41.22 2.12
250 257 6.927936 CCAACTGGTTAGAGATGATACTGATG 59.072 42.308 0.00 0.00 0.00 3.07
251 258 6.463614 GCCAACTGGTTAGAGATGATACTGAT 60.464 42.308 0.00 0.00 37.57 2.90
256 263 4.037222 TGGCCAACTGGTTAGAGATGATA 58.963 43.478 0.61 0.00 37.57 2.15
298 308 6.759272 TCTTTCTAGCTGCTTCTTGTCTTTA 58.241 36.000 7.79 0.00 0.00 1.85
330 341 1.538950 CTGCAGAACTCCAAAAGCCTC 59.461 52.381 8.42 0.00 0.00 4.70
331 342 1.613836 CTGCAGAACTCCAAAAGCCT 58.386 50.000 8.42 0.00 0.00 4.58
335 346 1.032014 GTGCCTGCAGAACTCCAAAA 58.968 50.000 17.39 0.00 0.00 2.44
353 364 1.269206 CCATGAGCAACTGCAAAACGT 60.269 47.619 4.22 0.00 45.16 3.99
416 428 5.585820 TGTGCATGATCACATAAAATGCT 57.414 34.783 14.40 0.00 43.17 3.79
451 463 0.985490 AGCATCCTCACCCTCTTCCC 60.985 60.000 0.00 0.00 0.00 3.97
455 467 0.757188 CGGTAGCATCCTCACCCTCT 60.757 60.000 0.00 0.00 0.00 3.69
471 483 3.260884 TCCTCAAATTCTAGAGTTGCGGT 59.739 43.478 19.13 0.00 30.74 5.68
492 505 4.615949 AGTTCGATAGCATCACTCATGTC 58.384 43.478 0.00 0.00 34.56 3.06
498 511 5.105752 GTCTGAAAGTTCGATAGCATCACT 58.894 41.667 0.00 0.00 33.76 3.41
504 517 4.111375 TCTGGTCTGAAAGTTCGATAGC 57.889 45.455 0.00 0.00 33.76 2.97
553 566 6.421501 TCAATGCCGAATTTATTGATGCATTC 59.578 34.615 0.00 0.00 43.74 2.67
564 577 5.473846 TGTAAGTTGGTCAATGCCGAATTTA 59.526 36.000 2.95 0.00 32.97 1.40
599 612 8.388589 TCCCATATATGCTCAATCTGATCTTTT 58.611 33.333 7.24 0.00 0.00 2.27
607 620 9.866655 TTTTAACTTCCCATATATGCTCAATCT 57.133 29.630 7.24 0.00 0.00 2.40
618 631 8.934023 TTGTTGTCTCTTTTAACTTCCCATAT 57.066 30.769 0.00 0.00 0.00 1.78
625 638 9.921637 TTTCAACATTGTTGTCTCTTTTAACTT 57.078 25.926 24.71 0.00 34.06 2.66
633 646 8.394971 TGTCATATTTCAACATTGTTGTCTCT 57.605 30.769 24.71 13.07 34.06 3.10
655 668 6.089820 CCACATGCAACAATAGTTCAAATGTC 59.910 38.462 0.00 0.00 35.28 3.06
657 671 5.163933 GCCACATGCAACAATAGTTCAAATG 60.164 40.000 0.00 0.00 40.77 2.32
668 715 4.305769 GTTCAAATAGCCACATGCAACAA 58.694 39.130 0.00 0.00 44.83 2.83
746 794 2.181021 CCACGTACGTCTGGCCTC 59.819 66.667 19.94 0.00 0.00 4.70
755 803 1.517694 CGGAATGGTCCCACGTACG 60.518 63.158 15.01 15.01 41.44 3.67
760 808 3.400599 ATCCGCGGAATGGTCCCAC 62.401 63.158 34.66 0.00 41.44 4.61
761 809 3.087253 ATCCGCGGAATGGTCCCA 61.087 61.111 34.66 5.74 41.44 4.37
762 810 2.591715 CATCCGCGGAATGGTCCC 60.592 66.667 34.66 0.00 41.44 4.46
763 811 2.397413 ATCCATCCGCGGAATGGTCC 62.397 60.000 35.10 0.00 38.95 4.46
764 812 1.071471 ATCCATCCGCGGAATGGTC 59.929 57.895 35.10 0.00 38.95 4.02
765 813 1.227943 CATCCATCCGCGGAATGGT 60.228 57.895 35.10 24.61 38.95 3.55
766 814 2.620112 GCATCCATCCGCGGAATGG 61.620 63.158 33.23 33.23 38.95 3.16
767 815 1.893335 TGCATCCATCCGCGGAATG 60.893 57.895 34.66 29.92 38.95 2.67
768 816 1.893808 GTGCATCCATCCGCGGAAT 60.894 57.895 34.66 19.19 38.95 3.01
769 817 2.513666 GTGCATCCATCCGCGGAA 60.514 61.111 34.66 17.45 38.95 4.30
770 818 4.889856 CGTGCATCCATCCGCGGA 62.890 66.667 33.12 33.12 40.07 5.54
771 819 4.889856 TCGTGCATCCATCCGCGG 62.890 66.667 22.12 22.12 35.81 6.46
772 820 3.333189 CTCGTGCATCCATCCGCG 61.333 66.667 0.00 0.00 36.39 6.46
773 821 1.089481 TTTCTCGTGCATCCATCCGC 61.089 55.000 0.00 0.00 0.00 5.54
774 822 1.368641 TTTTCTCGTGCATCCATCCG 58.631 50.000 0.00 0.00 0.00 4.18
775 823 4.107622 CAAATTTTCTCGTGCATCCATCC 58.892 43.478 0.00 0.00 0.00 3.51
776 824 3.549070 GCAAATTTTCTCGTGCATCCATC 59.451 43.478 0.00 0.00 36.97 3.51
777 825 3.514645 GCAAATTTTCTCGTGCATCCAT 58.485 40.909 0.00 0.00 36.97 3.41
778 826 2.668001 CGCAAATTTTCTCGTGCATCCA 60.668 45.455 0.00 0.00 36.80 3.41
779 827 1.913403 CGCAAATTTTCTCGTGCATCC 59.087 47.619 0.00 0.00 36.80 3.51
780 828 1.913403 CCGCAAATTTTCTCGTGCATC 59.087 47.619 0.00 0.00 36.80 3.91
781 829 1.402720 CCCGCAAATTTTCTCGTGCAT 60.403 47.619 0.00 0.00 36.80 3.96
782 830 0.039617 CCCGCAAATTTTCTCGTGCA 60.040 50.000 0.00 0.00 36.80 4.57
783 831 0.039527 ACCCGCAAATTTTCTCGTGC 60.040 50.000 0.00 0.00 0.00 5.34
784 832 1.724654 CGACCCGCAAATTTTCTCGTG 60.725 52.381 0.00 0.00 0.00 4.35
785 833 0.515564 CGACCCGCAAATTTTCTCGT 59.484 50.000 0.00 0.00 0.00 4.18
786 834 3.290098 CGACCCGCAAATTTTCTCG 57.710 52.632 0.00 0.00 0.00 4.04
798 846 0.030369 GTATCACAGTAGGCGACCCG 59.970 60.000 0.00 0.00 35.76 5.28
799 847 0.030369 CGTATCACAGTAGGCGACCC 59.970 60.000 0.00 0.00 0.00 4.46
800 848 0.030369 CCGTATCACAGTAGGCGACC 59.970 60.000 0.00 0.00 0.00 4.79
801 849 0.737219 ACCGTATCACAGTAGGCGAC 59.263 55.000 0.00 0.00 0.00 5.19
802 850 2.330440 TACCGTATCACAGTAGGCGA 57.670 50.000 0.00 0.00 0.00 5.54
803 851 3.065786 TCTTTACCGTATCACAGTAGGCG 59.934 47.826 0.00 0.00 0.00 5.52
804 852 4.644103 TCTTTACCGTATCACAGTAGGC 57.356 45.455 0.00 0.00 0.00 3.93
805 853 7.411157 CGTTTTTCTTTACCGTATCACAGTAGG 60.411 40.741 0.00 0.00 0.00 3.18
806 854 7.326789 TCGTTTTTCTTTACCGTATCACAGTAG 59.673 37.037 0.00 0.00 0.00 2.57
807 855 7.144661 TCGTTTTTCTTTACCGTATCACAGTA 58.855 34.615 0.00 0.00 0.00 2.74
808 856 5.984926 TCGTTTTTCTTTACCGTATCACAGT 59.015 36.000 0.00 0.00 0.00 3.55
809 857 6.456447 TCGTTTTTCTTTACCGTATCACAG 57.544 37.500 0.00 0.00 0.00 3.66
810 858 6.619018 GCATCGTTTTTCTTTACCGTATCACA 60.619 38.462 0.00 0.00 0.00 3.58
811 859 5.731263 GCATCGTTTTTCTTTACCGTATCAC 59.269 40.000 0.00 0.00 0.00 3.06
812 860 5.408909 TGCATCGTTTTTCTTTACCGTATCA 59.591 36.000 0.00 0.00 0.00 2.15
813 861 5.860641 TGCATCGTTTTTCTTTACCGTATC 58.139 37.500 0.00 0.00 0.00 2.24
814 862 5.866335 TGCATCGTTTTTCTTTACCGTAT 57.134 34.783 0.00 0.00 0.00 3.06
815 863 5.866335 ATGCATCGTTTTTCTTTACCGTA 57.134 34.783 0.00 0.00 0.00 4.02
816 864 4.759516 ATGCATCGTTTTTCTTTACCGT 57.240 36.364 0.00 0.00 0.00 4.83
817 865 6.446659 AAAATGCATCGTTTTTCTTTACCG 57.553 33.333 0.00 0.00 29.58 4.02
883 931 0.546122 GTGATCCACAGGCCCATGTA 59.454 55.000 0.00 0.00 34.08 2.29
946 994 3.039588 GTTCGTCTCCGCCGCAAA 61.040 61.111 0.00 0.00 0.00 3.68
1081 1131 2.920912 AACTCGGGTCCTGGCGAA 60.921 61.111 0.00 0.00 0.00 4.70
1229 1279 1.825474 CCGGCTTCTTCTCCTCTACAA 59.175 52.381 0.00 0.00 0.00 2.41
1230 1280 1.475403 CCGGCTTCTTCTCCTCTACA 58.525 55.000 0.00 0.00 0.00 2.74
1353 1403 1.306642 CGTACAGAGTGTCCGCCTCT 61.307 60.000 0.00 0.00 39.87 3.69
1362 1412 0.811915 CCTCCTCCACGTACAGAGTG 59.188 60.000 8.19 0.00 39.19 3.51
1435 1485 0.613853 TGGAGTTGGTCGAGGGGTAG 60.614 60.000 0.00 0.00 0.00 3.18
1464 1514 1.203928 GGACGAGTTCTCATGCATCG 58.796 55.000 0.00 0.00 39.22 3.84
1507 1557 8.011844 AGCATACTAGACAAGTACATCATTGA 57.988 34.615 0.00 0.00 43.47 2.57
1595 1729 6.124340 TCCAGTTCGTCCACATAGATACTAA 58.876 40.000 0.00 0.00 0.00 2.24
1629 1763 9.367444 CAACGTTCCTCTTAATTGATAGTACTT 57.633 33.333 0.00 0.00 0.00 2.24
1630 1764 7.491696 GCAACGTTCCTCTTAATTGATAGTACT 59.508 37.037 0.00 0.00 0.00 2.73
1631 1765 7.491696 AGCAACGTTCCTCTTAATTGATAGTAC 59.508 37.037 0.00 0.00 0.00 2.73
1632 1766 7.553334 AGCAACGTTCCTCTTAATTGATAGTA 58.447 34.615 0.00 0.00 0.00 1.82
1633 1767 6.407202 AGCAACGTTCCTCTTAATTGATAGT 58.593 36.000 0.00 0.00 0.00 2.12
1634 1768 6.910536 AGCAACGTTCCTCTTAATTGATAG 57.089 37.500 0.00 0.00 0.00 2.08
1645 1779 4.119442 TCACCTAATAGCAACGTTCCTC 57.881 45.455 0.00 0.00 0.00 3.71
1654 1788 4.466370 AGCTGTACACTTCACCTAATAGCA 59.534 41.667 0.00 0.00 0.00 3.49
1675 1809 8.072567 CACTTCCAGCATAATCATTAAGTAAGC 58.927 37.037 0.00 0.00 0.00 3.09
1701 1835 8.421784 TGGTATTATCTCACCAAGTGAATCTAC 58.578 37.037 0.00 0.00 42.26 2.59
1745 1879 2.092375 AGCTAGCCCAATCCTGGTAAAC 60.092 50.000 12.13 0.00 41.72 2.01
1805 1939 8.696374 TCCCAAAAGTGTCAATAAACATAACAA 58.304 29.630 0.00 0.00 0.00 2.83
1823 1957 8.299570 GCAGACCATGTATTATATTCCCAAAAG 58.700 37.037 0.00 0.00 0.00 2.27
1840 1974 2.273370 GCACTTCATTGCAGACCATG 57.727 50.000 0.00 0.00 42.49 3.66
2151 2287 5.210715 GTCAAGAGACAATGCAAAGACAAG 58.789 41.667 0.00 0.00 44.34 3.16
2368 2511 5.820423 GTGAATGCATAATGTACTACCCACA 59.180 40.000 0.00 0.00 0.00 4.17
2369 2512 5.820423 TGTGAATGCATAATGTACTACCCAC 59.180 40.000 0.00 0.00 0.00 4.61
2651 2794 1.000060 GCTGTTTCTGCAAATGGCTCA 60.000 47.619 0.00 0.00 45.15 4.26
2655 2798 3.983344 GTGTAAGCTGTTTCTGCAAATGG 59.017 43.478 0.00 0.00 0.00 3.16
3402 5792 7.607991 TGAGGTGAAAGAGAAGATAAATTCCAC 59.392 37.037 0.00 0.00 0.00 4.02
3691 6086 7.602517 ACAGATACAGACTATTTCTTTGTGC 57.397 36.000 0.00 0.00 28.96 4.57
3726 6129 8.038862 AGTATATGGTTGAGATTTGGATGAGT 57.961 34.615 0.00 0.00 0.00 3.41
3807 6301 0.870393 CGATCATCCATTGAAGGCCG 59.130 55.000 0.00 0.00 38.03 6.13
3825 6319 4.560128 TCTTGAAGAGAGAATGGTTGTCG 58.440 43.478 0.00 0.00 0.00 4.35
3901 6396 3.129813 TCATCAAGCATGATTTCTGCCAC 59.870 43.478 0.71 0.00 43.89 5.01
4000 6495 0.605319 TGCCTCCCACACGTTGATTC 60.605 55.000 0.00 0.00 0.00 2.52
4019 7723 3.554934 TGCAAACATTCTCCAGTCAACT 58.445 40.909 0.00 0.00 0.00 3.16
4068 7772 1.551883 GGGAATGACTTGCTTGGCATT 59.448 47.619 9.72 9.72 38.76 3.56


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

AutoCloner maintained by Alex Coulton.