Multiple sequence alignment - TraesCS6D01G225300

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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 TraesCS6D01G225300 chr6D 100.000 6187 0 0 1 6187 317075139 317081325 0.000000e+00 11426.0
1 TraesCS6D01G225300 chr6D 99.442 717 3 1 1 716 317066328 317067044 0.000000e+00 1301.0
2 TraesCS6D01G225300 chr6D 89.764 127 7 5 3641 3764 391925993 391925870 2.310000e-34 158.0
3 TraesCS6D01G225300 chr6B 98.381 3459 50 5 2119 5576 507473182 507469729 0.000000e+00 6072.0
4 TraesCS6D01G225300 chr6B 91.695 1180 56 18 980 2142 507477642 507476488 0.000000e+00 1598.0
5 TraesCS6D01G225300 chr6B 96.994 499 15 0 5689 6187 507469666 507469168 0.000000e+00 839.0
6 TraesCS6D01G225300 chr6B 81.576 863 115 30 10 859 507482934 507482103 0.000000e+00 673.0
7 TraesCS6D01G225300 chr6B 88.976 127 8 5 3641 3764 585524848 585524725 1.070000e-32 152.0
8 TraesCS6D01G225300 chr6A 96.735 2879 48 14 1001 3865 454675340 454678186 0.000000e+00 4754.0
9 TraesCS6D01G225300 chr6A 97.018 1643 40 6 4014 5649 454678189 454679829 0.000000e+00 2754.0
10 TraesCS6D01G225300 chr6A 97.809 502 11 0 5686 6187 454679828 454680329 0.000000e+00 867.0
11 TraesCS6D01G225300 chr4B 92.126 127 5 4 3641 3764 479155622 479155498 2.290000e-39 174.0
12 TraesCS6D01G225300 chr3B 93.750 112 5 2 3643 3754 672778075 672778184 3.840000e-37 167.0
13 TraesCS6D01G225300 chr3B 89.831 118 11 1 3647 3764 178386658 178386542 3.860000e-32 150.0
14 TraesCS6D01G225300 chr7B 94.444 108 5 1 3647 3754 357651484 357651590 1.380000e-36 165.0
15 TraesCS6D01G225300 chr2A 90.678 118 10 1 3637 3754 205917590 205917706 8.300000e-34 156.0
16 TraesCS6D01G225300 chr2A 87.324 71 8 1 1166 1236 642911854 642911923 5.140000e-11 80.5
17 TraesCS6D01G225300 chr2B 86.765 68 8 1 1166 1233 584719643 584719709 2.390000e-09 75.0


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 TraesCS6D01G225300 chr6D 317075139 317081325 6186 False 11426.000000 11426 100.000000 1 6187 1 chr6D.!!$F2 6186
1 TraesCS6D01G225300 chr6D 317066328 317067044 716 False 1301.000000 1301 99.442000 1 716 1 chr6D.!!$F1 715
2 TraesCS6D01G225300 chr6B 507469168 507477642 8474 True 2836.333333 6072 95.690000 980 6187 3 chr6B.!!$R3 5207
3 TraesCS6D01G225300 chr6B 507482103 507482934 831 True 673.000000 673 81.576000 10 859 1 chr6B.!!$R1 849
4 TraesCS6D01G225300 chr6A 454675340 454680329 4989 False 2791.666667 4754 97.187333 1001 6187 3 chr6A.!!$F1 5186

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
967 977 0.108138 TTTCGCCTCTAGCTTCAGCC 60.108 55.000 0.00 0.0 43.38 4.85 F
1510 1536 0.247894 CTCGAGAGGTCTTCTTCGCG 60.248 60.000 6.58 0.0 42.16 5.87 F
1729 1756 1.133136 ACCCTAGATCGGTGCCTATGT 60.133 52.381 0.00 0.0 30.39 2.29 F
1730 1757 2.109480 ACCCTAGATCGGTGCCTATGTA 59.891 50.000 0.00 0.0 30.39 2.29 F
3537 6909 0.811281 CTTCAAAGCATCCCCCGTTC 59.189 55.000 0.00 0.0 0.00 3.95 F
4448 7820 5.760253 AGGAAATACGACCATATCAAAGCTG 59.240 40.000 0.00 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1942 1.305201 ACAAGAAACATTCGCACCGT 58.695 45.000 0.00 0.00 34.02 4.83 R
2884 6256 9.691362 GGTGAAACATTGTTTACTGAATAACAT 57.309 29.630 14.49 0.00 39.98 2.71 R
3537 6909 4.176271 GCCCATTTTAGTAAAAGCAGCAG 58.824 43.478 13.25 1.62 33.22 4.24 R
3729 7101 5.078256 ACTCCCTCCGATCGATATTACTTT 58.922 41.667 18.66 0.00 0.00 2.66 R
4658 8030 0.734889 ATTTTCGCCCATCAAGCTCG 59.265 50.000 0.00 0.00 0.00 5.03 R
5701 9084 0.179111 GCGGCTATGTGCAGTAGTCA 60.179 55.000 10.31 0.00 45.15 3.41 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
374 376 1.683365 TACCCTGTCGGCCACCTAC 60.683 63.158 2.24 0.00 33.26 3.18
655 665 9.729023 TCACCATATATTTAAAAATGCTTCGTG 57.271 29.630 0.00 1.90 0.00 4.35
656 666 9.515020 CACCATATATTTAAAAATGCTTCGTGT 57.485 29.630 0.00 0.00 0.00 4.49
657 667 9.515020 ACCATATATTTAAAAATGCTTCGTGTG 57.485 29.630 0.00 0.00 0.00 3.82
658 668 9.515020 CCATATATTTAAAAATGCTTCGTGTGT 57.485 29.630 0.00 0.00 0.00 3.72
664 674 9.953697 ATTTAAAAATGCTTCGTGTGTACTAAA 57.046 25.926 0.00 0.00 0.00 1.85
665 675 9.784680 TTTAAAAATGCTTCGTGTGTACTAAAA 57.215 25.926 0.00 0.00 0.00 1.52
666 676 9.784680 TTAAAAATGCTTCGTGTGTACTAAAAA 57.215 25.926 0.00 0.00 0.00 1.94
712 722 8.969260 AGTTCATCATATACTGAAAATGCTCA 57.031 30.769 1.77 0.00 37.44 4.26
713 723 9.399797 AGTTCATCATATACTGAAAATGCTCAA 57.600 29.630 1.77 0.00 37.44 3.02
716 726 9.346005 TCATCATATACTGAAAATGCTCAATGT 57.654 29.630 0.00 0.00 37.44 2.71
724 734 8.109705 ACTGAAAATGCTCAATGTATACAACA 57.890 30.769 10.14 4.24 43.86 3.33
725 735 8.575589 ACTGAAAATGCTCAATGTATACAACAA 58.424 29.630 10.14 0.00 42.70 2.83
726 736 9.409312 CTGAAAATGCTCAATGTATACAACAAA 57.591 29.630 10.14 0.00 42.70 2.83
727 737 9.755804 TGAAAATGCTCAATGTATACAACAAAA 57.244 25.926 10.14 0.00 42.70 2.44
782 792 9.139174 AGTGTGTATTTAAATAATGTTTGCTGC 57.861 29.630 9.48 0.00 0.00 5.25
783 793 8.101510 GTGTGTATTTAAATAATGTTTGCTGCG 58.898 33.333 9.48 0.00 0.00 5.18
784 794 7.810282 TGTGTATTTAAATAATGTTTGCTGCGT 59.190 29.630 9.48 0.00 0.00 5.24
785 795 9.279904 GTGTATTTAAATAATGTTTGCTGCGTA 57.720 29.630 9.48 0.00 0.00 4.42
786 796 9.279904 TGTATTTAAATAATGTTTGCTGCGTAC 57.720 29.630 9.48 0.00 0.00 3.67
787 797 9.498307 GTATTTAAATAATGTTTGCTGCGTACT 57.502 29.630 9.48 0.00 0.00 2.73
796 806 8.980143 AATGTTTGCTGCGTACTAATAAAATT 57.020 26.923 0.00 0.00 0.00 1.82
797 807 8.980143 ATGTTTGCTGCGTACTAATAAAATTT 57.020 26.923 0.00 0.00 0.00 1.82
798 808 8.442605 TGTTTGCTGCGTACTAATAAAATTTC 57.557 30.769 0.00 0.00 0.00 2.17
799 809 8.076781 TGTTTGCTGCGTACTAATAAAATTTCA 58.923 29.630 0.00 0.00 0.00 2.69
800 810 8.575454 GTTTGCTGCGTACTAATAAAATTTCAG 58.425 33.333 0.00 0.00 0.00 3.02
801 811 7.372451 TGCTGCGTACTAATAAAATTTCAGT 57.628 32.000 0.00 0.00 0.00 3.41
802 812 7.240674 TGCTGCGTACTAATAAAATTTCAGTG 58.759 34.615 0.00 0.00 0.00 3.66
803 813 7.094975 TGCTGCGTACTAATAAAATTTCAGTGT 60.095 33.333 0.00 0.00 0.00 3.55
804 814 7.216317 GCTGCGTACTAATAAAATTTCAGTGTG 59.784 37.037 0.00 0.00 0.00 3.82
805 815 8.090250 TGCGTACTAATAAAATTTCAGTGTGT 57.910 30.769 0.00 0.00 0.00 3.72
806 816 9.205719 TGCGTACTAATAAAATTTCAGTGTGTA 57.794 29.630 0.00 0.00 0.00 2.90
821 831 7.962934 TCAGTGTGTATTTGAAAAAGAAACG 57.037 32.000 0.00 0.00 0.00 3.60
822 832 7.753659 TCAGTGTGTATTTGAAAAAGAAACGA 58.246 30.769 0.00 0.00 0.00 3.85
823 833 8.402472 TCAGTGTGTATTTGAAAAAGAAACGAT 58.598 29.630 0.00 0.00 0.00 3.73
824 834 9.658475 CAGTGTGTATTTGAAAAAGAAACGATA 57.342 29.630 0.00 0.00 0.00 2.92
861 871 8.554835 AAAACAAATCCGAAAAAGAAAAAGGA 57.445 26.923 0.00 0.00 0.00 3.36
862 872 8.554835 AAACAAATCCGAAAAAGAAAAAGGAA 57.445 26.923 0.00 0.00 0.00 3.36
863 873 8.554835 AACAAATCCGAAAAAGAAAAAGGAAA 57.445 26.923 0.00 0.00 0.00 3.13
864 874 8.554835 ACAAATCCGAAAAAGAAAAAGGAAAA 57.445 26.923 0.00 0.00 0.00 2.29
865 875 9.004717 ACAAATCCGAAAAAGAAAAAGGAAAAA 57.995 25.926 0.00 0.00 0.00 1.94
868 878 7.780008 TCCGAAAAAGAAAAAGGAAAAATCC 57.220 32.000 0.00 0.00 0.00 3.01
869 879 6.764085 TCCGAAAAAGAAAAAGGAAAAATCCC 59.236 34.615 0.00 0.00 0.00 3.85
870 880 6.540551 CCGAAAAAGAAAAAGGAAAAATCCCA 59.459 34.615 0.00 0.00 0.00 4.37
871 881 7.066404 CCGAAAAAGAAAAAGGAAAAATCCCAA 59.934 33.333 0.00 0.00 0.00 4.12
872 882 8.122330 CGAAAAAGAAAAAGGAAAAATCCCAAG 58.878 33.333 0.00 0.00 0.00 3.61
873 883 9.173021 GAAAAAGAAAAAGGAAAAATCCCAAGA 57.827 29.630 0.00 0.00 0.00 3.02
874 884 9.527157 AAAAAGAAAAAGGAAAAATCCCAAGAA 57.473 25.926 0.00 0.00 0.00 2.52
875 885 9.527157 AAAAGAAAAAGGAAAAATCCCAAGAAA 57.473 25.926 0.00 0.00 0.00 2.52
876 886 9.527157 AAAGAAAAAGGAAAAATCCCAAGAAAA 57.473 25.926 0.00 0.00 0.00 2.29
877 887 9.527157 AAGAAAAAGGAAAAATCCCAAGAAAAA 57.473 25.926 0.00 0.00 0.00 1.94
878 888 8.956426 AGAAAAAGGAAAAATCCCAAGAAAAAC 58.044 29.630 0.00 0.00 0.00 2.43
879 889 6.918892 AAAGGAAAAATCCCAAGAAAAACG 57.081 33.333 0.00 0.00 0.00 3.60
880 890 4.377021 AGGAAAAATCCCAAGAAAAACGC 58.623 39.130 0.00 0.00 0.00 4.84
881 891 4.123506 GGAAAAATCCCAAGAAAAACGCA 58.876 39.130 0.00 0.00 0.00 5.24
882 892 4.025229 GGAAAAATCCCAAGAAAAACGCAC 60.025 41.667 0.00 0.00 0.00 5.34
883 893 3.810310 AAATCCCAAGAAAAACGCACA 57.190 38.095 0.00 0.00 0.00 4.57
884 894 2.793278 ATCCCAAGAAAAACGCACAC 57.207 45.000 0.00 0.00 0.00 3.82
885 895 1.464734 TCCCAAGAAAAACGCACACA 58.535 45.000 0.00 0.00 0.00 3.72
886 896 1.819288 TCCCAAGAAAAACGCACACAA 59.181 42.857 0.00 0.00 0.00 3.33
887 897 2.159310 TCCCAAGAAAAACGCACACAAG 60.159 45.455 0.00 0.00 0.00 3.16
888 898 2.159310 CCCAAGAAAAACGCACACAAGA 60.159 45.455 0.00 0.00 0.00 3.02
889 899 3.506810 CCAAGAAAAACGCACACAAGAA 58.493 40.909 0.00 0.00 0.00 2.52
890 900 3.923461 CCAAGAAAAACGCACACAAGAAA 59.077 39.130 0.00 0.00 0.00 2.52
891 901 4.387256 CCAAGAAAAACGCACACAAGAAAA 59.613 37.500 0.00 0.00 0.00 2.29
892 902 5.305036 CAAGAAAAACGCACACAAGAAAAC 58.695 37.500 0.00 0.00 0.00 2.43
893 903 4.805219 AGAAAAACGCACACAAGAAAACT 58.195 34.783 0.00 0.00 0.00 2.66
894 904 5.945155 AGAAAAACGCACACAAGAAAACTA 58.055 33.333 0.00 0.00 0.00 2.24
895 905 6.027749 AGAAAAACGCACACAAGAAAACTAG 58.972 36.000 0.00 0.00 0.00 2.57
896 906 3.334272 AACGCACACAAGAAAACTAGC 57.666 42.857 0.00 0.00 0.00 3.42
897 907 2.561569 ACGCACACAAGAAAACTAGCT 58.438 42.857 0.00 0.00 0.00 3.32
898 908 2.943033 ACGCACACAAGAAAACTAGCTT 59.057 40.909 0.00 0.00 0.00 3.74
899 909 3.002348 ACGCACACAAGAAAACTAGCTTC 59.998 43.478 0.00 0.00 0.00 3.86
900 910 3.248602 CGCACACAAGAAAACTAGCTTCT 59.751 43.478 0.00 2.52 34.56 2.85
901 911 4.531332 GCACACAAGAAAACTAGCTTCTG 58.469 43.478 8.13 6.02 33.40 3.02
902 912 4.531332 CACACAAGAAAACTAGCTTCTGC 58.469 43.478 8.13 0.00 33.40 4.26
912 922 4.245054 GCTTCTGCTCACGAACGA 57.755 55.556 0.14 0.00 36.03 3.85
913 923 2.517598 GCTTCTGCTCACGAACGAA 58.482 52.632 0.14 0.00 36.03 3.85
914 924 0.859232 GCTTCTGCTCACGAACGAAA 59.141 50.000 0.14 0.00 36.03 3.46
915 925 1.260561 GCTTCTGCTCACGAACGAAAA 59.739 47.619 0.14 0.00 36.03 2.29
916 926 2.892613 CTTCTGCTCACGAACGAAAAC 58.107 47.619 0.14 0.00 0.00 2.43
917 927 1.929230 TCTGCTCACGAACGAAAACA 58.071 45.000 0.14 0.00 0.00 2.83
918 928 2.272678 TCTGCTCACGAACGAAAACAA 58.727 42.857 0.14 0.00 0.00 2.83
919 929 2.673862 TCTGCTCACGAACGAAAACAAA 59.326 40.909 0.14 0.00 0.00 2.83
920 930 3.125487 TCTGCTCACGAACGAAAACAAAA 59.875 39.130 0.14 0.00 0.00 2.44
921 931 3.421741 TGCTCACGAACGAAAACAAAAG 58.578 40.909 0.14 0.00 0.00 2.27
922 932 2.781646 GCTCACGAACGAAAACAAAAGG 59.218 45.455 0.14 0.00 0.00 3.11
923 933 3.486209 GCTCACGAACGAAAACAAAAGGA 60.486 43.478 0.14 0.00 0.00 3.36
924 934 4.654015 CTCACGAACGAAAACAAAAGGAA 58.346 39.130 0.14 0.00 0.00 3.36
925 935 4.654015 TCACGAACGAAAACAAAAGGAAG 58.346 39.130 0.14 0.00 0.00 3.46
926 936 3.239712 CACGAACGAAAACAAAAGGAAGC 59.760 43.478 0.14 0.00 0.00 3.86
927 937 2.787129 CGAACGAAAACAAAAGGAAGCC 59.213 45.455 0.00 0.00 0.00 4.35
928 938 3.732471 CGAACGAAAACAAAAGGAAGCCA 60.732 43.478 0.00 0.00 0.00 4.75
929 939 3.436700 ACGAAAACAAAAGGAAGCCAG 57.563 42.857 0.00 0.00 0.00 4.85
930 940 3.020984 ACGAAAACAAAAGGAAGCCAGA 58.979 40.909 0.00 0.00 0.00 3.86
931 941 3.445805 ACGAAAACAAAAGGAAGCCAGAA 59.554 39.130 0.00 0.00 0.00 3.02
932 942 3.796717 CGAAAACAAAAGGAAGCCAGAAC 59.203 43.478 0.00 0.00 0.00 3.01
933 943 3.436700 AAACAAAAGGAAGCCAGAACG 57.563 42.857 0.00 0.00 0.00 3.95
934 944 0.668535 ACAAAAGGAAGCCAGAACGC 59.331 50.000 0.00 0.00 0.00 4.84
935 945 0.667993 CAAAAGGAAGCCAGAACGCA 59.332 50.000 0.00 0.00 0.00 5.24
936 946 0.954452 AAAAGGAAGCCAGAACGCAG 59.046 50.000 0.00 0.00 0.00 5.18
937 947 0.108585 AAAGGAAGCCAGAACGCAGA 59.891 50.000 0.00 0.00 0.00 4.26
938 948 0.108585 AAGGAAGCCAGAACGCAGAA 59.891 50.000 0.00 0.00 0.00 3.02
939 949 0.326264 AGGAAGCCAGAACGCAGAAT 59.674 50.000 0.00 0.00 0.00 2.40
940 950 0.729690 GGAAGCCAGAACGCAGAATC 59.270 55.000 0.00 0.00 0.00 2.52
941 951 1.442769 GAAGCCAGAACGCAGAATCA 58.557 50.000 0.00 0.00 0.00 2.57
942 952 1.806542 GAAGCCAGAACGCAGAATCAA 59.193 47.619 0.00 0.00 0.00 2.57
943 953 1.896220 AGCCAGAACGCAGAATCAAA 58.104 45.000 0.00 0.00 0.00 2.69
944 954 1.537202 AGCCAGAACGCAGAATCAAAC 59.463 47.619 0.00 0.00 0.00 2.93
945 955 1.266718 GCCAGAACGCAGAATCAAACA 59.733 47.619 0.00 0.00 0.00 2.83
946 956 2.918131 GCCAGAACGCAGAATCAAACAC 60.918 50.000 0.00 0.00 0.00 3.32
947 957 2.290367 CCAGAACGCAGAATCAAACACA 59.710 45.455 0.00 0.00 0.00 3.72
948 958 3.058016 CCAGAACGCAGAATCAAACACAT 60.058 43.478 0.00 0.00 0.00 3.21
949 959 4.539870 CAGAACGCAGAATCAAACACATT 58.460 39.130 0.00 0.00 0.00 2.71
950 960 4.977963 CAGAACGCAGAATCAAACACATTT 59.022 37.500 0.00 0.00 0.00 2.32
951 961 5.116074 CAGAACGCAGAATCAAACACATTTC 59.884 40.000 0.00 0.00 0.00 2.17
952 962 3.554524 ACGCAGAATCAAACACATTTCG 58.445 40.909 0.00 0.00 0.00 3.46
953 963 2.339400 CGCAGAATCAAACACATTTCGC 59.661 45.455 0.00 0.00 0.00 4.70
954 964 2.663119 GCAGAATCAAACACATTTCGCC 59.337 45.455 0.00 0.00 0.00 5.54
955 965 3.612479 GCAGAATCAAACACATTTCGCCT 60.612 43.478 0.00 0.00 0.00 5.52
956 966 4.161333 CAGAATCAAACACATTTCGCCTC 58.839 43.478 0.00 0.00 0.00 4.70
957 967 4.074970 AGAATCAAACACATTTCGCCTCT 58.925 39.130 0.00 0.00 0.00 3.69
958 968 5.122239 CAGAATCAAACACATTTCGCCTCTA 59.878 40.000 0.00 0.00 0.00 2.43
959 969 5.352569 AGAATCAAACACATTTCGCCTCTAG 59.647 40.000 0.00 0.00 0.00 2.43
960 970 2.742053 TCAAACACATTTCGCCTCTAGC 59.258 45.455 0.00 0.00 38.52 3.42
961 971 2.744202 CAAACACATTTCGCCTCTAGCT 59.256 45.455 0.00 0.00 40.39 3.32
962 972 2.770164 ACACATTTCGCCTCTAGCTT 57.230 45.000 0.00 0.00 40.39 3.74
963 973 2.622436 ACACATTTCGCCTCTAGCTTC 58.378 47.619 0.00 0.00 40.39 3.86
964 974 2.028112 ACACATTTCGCCTCTAGCTTCA 60.028 45.455 0.00 0.00 40.39 3.02
965 975 2.606725 CACATTTCGCCTCTAGCTTCAG 59.393 50.000 0.00 0.00 40.39 3.02
966 976 1.596727 CATTTCGCCTCTAGCTTCAGC 59.403 52.381 0.00 0.00 40.39 4.26
967 977 0.108138 TTTCGCCTCTAGCTTCAGCC 60.108 55.000 0.00 0.00 43.38 4.85
968 978 2.279120 CGCCTCTAGCTTCAGCCG 60.279 66.667 0.00 0.00 43.38 5.52
969 979 2.107953 GCCTCTAGCTTCAGCCGG 59.892 66.667 0.00 0.00 43.38 6.13
970 980 2.107953 CCTCTAGCTTCAGCCGGC 59.892 66.667 21.89 21.89 43.38 6.13
971 981 2.279120 CTCTAGCTTCAGCCGGCG 60.279 66.667 23.20 16.49 43.38 6.46
972 982 3.068691 TCTAGCTTCAGCCGGCGT 61.069 61.111 23.20 6.69 43.38 5.68
973 983 2.583593 CTAGCTTCAGCCGGCGTC 60.584 66.667 23.20 9.53 43.38 5.19
974 984 3.356639 CTAGCTTCAGCCGGCGTCA 62.357 63.158 23.20 5.74 43.38 4.35
975 985 2.635229 CTAGCTTCAGCCGGCGTCAT 62.635 60.000 23.20 8.99 43.38 3.06
976 986 1.388837 TAGCTTCAGCCGGCGTCATA 61.389 55.000 23.20 7.91 43.38 2.15
977 987 1.595382 GCTTCAGCCGGCGTCATAT 60.595 57.895 23.20 0.00 34.31 1.78
978 988 1.160329 GCTTCAGCCGGCGTCATATT 61.160 55.000 23.20 0.00 34.31 1.28
1015 1025 1.103803 GTAGATGTGCTCGGACTCCA 58.896 55.000 0.00 0.00 0.00 3.86
1017 1027 0.534412 AGATGTGCTCGGACTCCAAG 59.466 55.000 0.00 0.00 0.00 3.61
1128 1140 3.223589 GCCTCGCCTCTCCTCTCC 61.224 72.222 0.00 0.00 0.00 3.71
1129 1141 2.600731 CCTCGCCTCTCCTCTCCT 59.399 66.667 0.00 0.00 0.00 3.69
1130 1142 1.528309 CCTCGCCTCTCCTCTCCTC 60.528 68.421 0.00 0.00 0.00 3.71
1133 1145 1.528309 CGCCTCTCCTCTCCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
1134 1146 1.930520 GCCTCTCCTCTCCTCTCCT 59.069 63.158 0.00 0.00 0.00 3.69
1225 1241 0.320683 CATGAACCAGGTGAGCACGA 60.321 55.000 0.00 0.00 0.00 4.35
1510 1536 0.247894 CTCGAGAGGTCTTCTTCGCG 60.248 60.000 6.58 0.00 42.16 5.87
1603 1629 1.220206 CGATGCTTCTGCCACCTCT 59.780 57.895 0.00 0.00 38.71 3.69
1643 1670 2.286772 CGGCTGTGTTGTTCTGTTTACC 60.287 50.000 0.00 0.00 0.00 2.85
1727 1754 2.400467 AACCCTAGATCGGTGCCTAT 57.600 50.000 0.00 0.00 32.55 2.57
1728 1755 1.633774 ACCCTAGATCGGTGCCTATG 58.366 55.000 0.00 0.00 30.39 2.23
1729 1756 1.133136 ACCCTAGATCGGTGCCTATGT 60.133 52.381 0.00 0.00 30.39 2.29
1730 1757 2.109480 ACCCTAGATCGGTGCCTATGTA 59.891 50.000 0.00 0.00 30.39 2.29
1731 1758 2.755655 CCCTAGATCGGTGCCTATGTAG 59.244 54.545 0.00 1.49 0.00 2.74
1732 1759 3.561528 CCCTAGATCGGTGCCTATGTAGA 60.562 52.174 8.02 0.00 0.00 2.59
1733 1760 3.692101 CCTAGATCGGTGCCTATGTAGAG 59.308 52.174 8.02 0.00 0.00 2.43
1734 1761 3.231207 AGATCGGTGCCTATGTAGAGT 57.769 47.619 0.00 0.00 0.00 3.24
1735 1762 3.150767 AGATCGGTGCCTATGTAGAGTC 58.849 50.000 0.00 0.00 0.00 3.36
1782 1809 4.783227 TCTTCCTAGCATACCTTCCAACTT 59.217 41.667 0.00 0.00 0.00 2.66
1792 1820 3.053826 ACCTTCCAACTTTGAGGTAGGT 58.946 45.455 4.21 4.21 46.89 3.08
1911 1942 5.306937 TGTCTGAAATAGAGTCTTGGTTCCA 59.693 40.000 0.00 0.00 35.70 3.53
2117 2151 4.093998 CACAGTCTGGCACATTATTCTGTC 59.906 45.833 4.53 0.00 38.20 3.51
2884 6256 6.183360 CCCTGTCTATATTGCATTTTTCAGCA 60.183 38.462 0.00 0.00 39.32 4.41
3537 6909 0.811281 CTTCAAAGCATCCCCCGTTC 59.189 55.000 0.00 0.00 0.00 3.95
3729 7101 6.697455 GTCTAGATACATCAATTTCAGCGACA 59.303 38.462 0.00 0.00 0.00 4.35
3960 7332 6.304683 GCACCTATTTAACAAGCTTAAACACG 59.695 38.462 0.00 0.00 0.00 4.49
4448 7820 5.760253 AGGAAATACGACCATATCAAAGCTG 59.240 40.000 0.00 0.00 0.00 4.24
4658 8030 3.308530 GCATGCAACAGGTGAACTTTAC 58.691 45.455 14.21 0.00 0.00 2.01
4670 8042 3.125316 GTGAACTTTACGAGCTTGATGGG 59.875 47.826 8.31 0.00 0.00 4.00
5407 8790 7.996098 AAATGTGTACTATACTTTTGGTGCT 57.004 32.000 0.00 0.00 0.00 4.40
5584 8967 5.618798 GCTCTCGCATTTCTTTCATATTTCG 59.381 40.000 0.00 0.00 35.78 3.46
5642 9025 8.459635 GTGTAGAAAGGAAATATCTCCAAAACC 58.540 37.037 0.00 0.00 38.02 3.27
5649 9032 6.373495 AGGAAATATCTCCAAAACCAACGTAC 59.627 38.462 0.00 0.00 38.02 3.67
5650 9033 6.373495 GGAAATATCTCCAAAACCAACGTACT 59.627 38.462 0.00 0.00 35.36 2.73
5651 9034 6.980051 AATATCTCCAAAACCAACGTACTC 57.020 37.500 0.00 0.00 0.00 2.59
5652 9035 3.116079 TCTCCAAAACCAACGTACTCC 57.884 47.619 0.00 0.00 0.00 3.85
5653 9036 2.148768 CTCCAAAACCAACGTACTCCC 58.851 52.381 0.00 0.00 0.00 4.30
5654 9037 1.770061 TCCAAAACCAACGTACTCCCT 59.230 47.619 0.00 0.00 0.00 4.20
5655 9038 2.148768 CCAAAACCAACGTACTCCCTC 58.851 52.381 0.00 0.00 0.00 4.30
5656 9039 2.148768 CAAAACCAACGTACTCCCTCC 58.851 52.381 0.00 0.00 0.00 4.30
5657 9040 0.319405 AAACCAACGTACTCCCTCCG 59.681 55.000 0.00 0.00 0.00 4.63
5658 9041 0.829182 AACCAACGTACTCCCTCCGT 60.829 55.000 0.00 0.00 36.17 4.69
5659 9042 0.829182 ACCAACGTACTCCCTCCGTT 60.829 55.000 0.00 0.00 44.81 4.44
5660 9043 0.108945 CCAACGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 42.34 3.95
5661 9044 0.886563 CAACGTACTCCCTCCGTTCT 59.113 55.000 0.00 0.00 42.34 3.01
5662 9045 2.086869 CAACGTACTCCCTCCGTTCTA 58.913 52.381 0.00 0.00 42.34 2.10
5663 9046 2.686915 CAACGTACTCCCTCCGTTCTAT 59.313 50.000 0.00 0.00 42.34 1.98
5664 9047 3.845781 ACGTACTCCCTCCGTTCTATA 57.154 47.619 0.00 0.00 0.00 1.31
5665 9048 4.363991 ACGTACTCCCTCCGTTCTATAT 57.636 45.455 0.00 0.00 0.00 0.86
5666 9049 5.489792 ACGTACTCCCTCCGTTCTATATA 57.510 43.478 0.00 0.00 0.00 0.86
5667 9050 5.869579 ACGTACTCCCTCCGTTCTATATAA 58.130 41.667 0.00 0.00 0.00 0.98
5668 9051 6.299141 ACGTACTCCCTCCGTTCTATATAAA 58.701 40.000 0.00 0.00 0.00 1.40
5669 9052 6.944862 ACGTACTCCCTCCGTTCTATATAAAT 59.055 38.462 0.00 0.00 0.00 1.40
5670 9053 8.103305 ACGTACTCCCTCCGTTCTATATAAATA 58.897 37.037 0.00 0.00 0.00 1.40
5671 9054 8.394121 CGTACTCCCTCCGTTCTATATAAATAC 58.606 40.741 0.00 0.00 0.00 1.89
5672 9055 7.388460 ACTCCCTCCGTTCTATATAAATACG 57.612 40.000 0.00 0.00 0.00 3.06
5673 9056 6.944862 ACTCCCTCCGTTCTATATAAATACGT 59.055 38.462 0.00 0.00 0.00 3.57
5674 9057 7.120432 ACTCCCTCCGTTCTATATAAATACGTC 59.880 40.741 0.00 0.00 0.00 4.34
5675 9058 7.170965 TCCCTCCGTTCTATATAAATACGTCT 58.829 38.462 0.00 0.00 0.00 4.18
5676 9059 8.321353 TCCCTCCGTTCTATATAAATACGTCTA 58.679 37.037 0.00 0.00 0.00 2.59
5677 9060 8.610896 CCCTCCGTTCTATATAAATACGTCTAG 58.389 40.741 0.00 0.00 0.00 2.43
5678 9061 9.376075 CCTCCGTTCTATATAAATACGTCTAGA 57.624 37.037 0.00 0.00 0.00 2.43
5718 9101 2.672961 TGTGACTACTGCACATAGCC 57.327 50.000 0.00 0.00 44.83 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 297 1.975660 GCCCATTTATAAGCGGGACA 58.024 50.000 20.33 0.00 41.62 4.02
374 376 3.827898 GAGGTCTCCTCGTGGGCG 61.828 72.222 3.23 0.00 41.08 6.13
639 649 9.784680 TTTTAGTACACACGAAGCATTTTTAAA 57.215 25.926 0.00 0.00 0.00 1.52
640 650 9.784680 TTTTTAGTACACACGAAGCATTTTTAA 57.215 25.926 0.00 0.00 0.00 1.52
686 696 9.399797 TGAGCATTTTCAGTATATGATGAACTT 57.600 29.630 4.43 0.00 37.89 2.66
687 697 8.969260 TGAGCATTTTCAGTATATGATGAACT 57.031 30.769 4.43 0.27 37.89 3.01
690 700 9.346005 ACATTGAGCATTTTCAGTATATGATGA 57.654 29.630 0.00 0.00 37.89 2.92
698 708 9.225436 TGTTGTATACATTGAGCATTTTCAGTA 57.775 29.630 6.36 0.00 0.00 2.74
699 709 8.109705 TGTTGTATACATTGAGCATTTTCAGT 57.890 30.769 6.36 0.00 0.00 3.41
700 710 8.969121 TTGTTGTATACATTGAGCATTTTCAG 57.031 30.769 6.36 0.00 36.44 3.02
701 711 9.755804 TTTTGTTGTATACATTGAGCATTTTCA 57.244 25.926 6.36 0.00 36.44 2.69
756 766 9.139174 GCAGCAAACATTATTTAAATACACACT 57.861 29.630 7.43 0.00 0.00 3.55
757 767 8.101510 CGCAGCAAACATTATTTAAATACACAC 58.898 33.333 7.43 0.00 0.00 3.82
758 768 7.810282 ACGCAGCAAACATTATTTAAATACACA 59.190 29.630 7.43 0.00 0.00 3.72
759 769 8.168681 ACGCAGCAAACATTATTTAAATACAC 57.831 30.769 7.43 0.00 0.00 2.90
760 770 9.279904 GTACGCAGCAAACATTATTTAAATACA 57.720 29.630 7.43 0.87 0.00 2.29
761 771 9.498307 AGTACGCAGCAAACATTATTTAAATAC 57.502 29.630 7.43 0.00 0.00 1.89
771 781 8.980143 AATTTTATTAGTACGCAGCAAACATT 57.020 26.923 0.00 0.00 0.00 2.71
772 782 8.980143 AAATTTTATTAGTACGCAGCAAACAT 57.020 26.923 0.00 0.00 0.00 2.71
773 783 8.076781 TGAAATTTTATTAGTACGCAGCAAACA 58.923 29.630 0.00 0.00 0.00 2.83
774 784 8.442605 TGAAATTTTATTAGTACGCAGCAAAC 57.557 30.769 0.00 0.00 0.00 2.93
775 785 8.293867 ACTGAAATTTTATTAGTACGCAGCAAA 58.706 29.630 0.00 0.00 0.00 3.68
776 786 7.748683 CACTGAAATTTTATTAGTACGCAGCAA 59.251 33.333 0.00 0.00 0.00 3.91
777 787 7.094975 ACACTGAAATTTTATTAGTACGCAGCA 60.095 33.333 0.00 0.00 0.00 4.41
778 788 7.216317 CACACTGAAATTTTATTAGTACGCAGC 59.784 37.037 0.00 0.00 0.00 5.25
779 789 8.227791 ACACACTGAAATTTTATTAGTACGCAG 58.772 33.333 0.00 0.00 0.00 5.18
780 790 8.090250 ACACACTGAAATTTTATTAGTACGCA 57.910 30.769 0.00 0.00 0.00 5.24
795 805 8.855279 CGTTTCTTTTTCAAATACACACTGAAA 58.145 29.630 0.00 0.00 37.30 2.69
796 806 8.237949 TCGTTTCTTTTTCAAATACACACTGAA 58.762 29.630 0.00 0.00 0.00 3.02
797 807 7.753659 TCGTTTCTTTTTCAAATACACACTGA 58.246 30.769 0.00 0.00 0.00 3.41
798 808 7.962934 TCGTTTCTTTTTCAAATACACACTG 57.037 32.000 0.00 0.00 0.00 3.66
835 845 9.004717 TCCTTTTTCTTTTTCGGATTTGTTTTT 57.995 25.926 0.00 0.00 0.00 1.94
836 846 8.554835 TCCTTTTTCTTTTTCGGATTTGTTTT 57.445 26.923 0.00 0.00 0.00 2.43
837 847 8.554835 TTCCTTTTTCTTTTTCGGATTTGTTT 57.445 26.923 0.00 0.00 0.00 2.83
838 848 8.554835 TTTCCTTTTTCTTTTTCGGATTTGTT 57.445 26.923 0.00 0.00 0.00 2.83
839 849 8.554835 TTTTCCTTTTTCTTTTTCGGATTTGT 57.445 26.923 0.00 0.00 0.00 2.83
842 852 8.836413 GGATTTTTCCTTTTTCTTTTTCGGATT 58.164 29.630 0.00 0.00 0.00 3.01
843 853 7.444183 GGGATTTTTCCTTTTTCTTTTTCGGAT 59.556 33.333 0.00 0.00 0.00 4.18
844 854 6.764085 GGGATTTTTCCTTTTTCTTTTTCGGA 59.236 34.615 0.00 0.00 0.00 4.55
845 855 6.540551 TGGGATTTTTCCTTTTTCTTTTTCGG 59.459 34.615 0.00 0.00 0.00 4.30
846 856 7.546778 TGGGATTTTTCCTTTTTCTTTTTCG 57.453 32.000 0.00 0.00 0.00 3.46
847 857 9.173021 TCTTGGGATTTTTCCTTTTTCTTTTTC 57.827 29.630 0.00 0.00 0.00 2.29
848 858 9.527157 TTCTTGGGATTTTTCCTTTTTCTTTTT 57.473 25.926 0.00 0.00 0.00 1.94
849 859 9.527157 TTTCTTGGGATTTTTCCTTTTTCTTTT 57.473 25.926 0.00 0.00 0.00 2.27
850 860 9.527157 TTTTCTTGGGATTTTTCCTTTTTCTTT 57.473 25.926 0.00 0.00 0.00 2.52
851 861 9.527157 TTTTTCTTGGGATTTTTCCTTTTTCTT 57.473 25.926 0.00 0.00 0.00 2.52
852 862 8.956426 GTTTTTCTTGGGATTTTTCCTTTTTCT 58.044 29.630 0.00 0.00 0.00 2.52
853 863 7.908082 CGTTTTTCTTGGGATTTTTCCTTTTTC 59.092 33.333 0.00 0.00 0.00 2.29
854 864 7.627513 GCGTTTTTCTTGGGATTTTTCCTTTTT 60.628 33.333 0.00 0.00 0.00 1.94
855 865 6.183360 GCGTTTTTCTTGGGATTTTTCCTTTT 60.183 34.615 0.00 0.00 0.00 2.27
856 866 5.295787 GCGTTTTTCTTGGGATTTTTCCTTT 59.704 36.000 0.00 0.00 0.00 3.11
857 867 4.814234 GCGTTTTTCTTGGGATTTTTCCTT 59.186 37.500 0.00 0.00 0.00 3.36
858 868 4.141824 TGCGTTTTTCTTGGGATTTTTCCT 60.142 37.500 0.00 0.00 0.00 3.36
859 869 4.025229 GTGCGTTTTTCTTGGGATTTTTCC 60.025 41.667 0.00 0.00 0.00 3.13
860 870 4.568760 TGTGCGTTTTTCTTGGGATTTTTC 59.431 37.500 0.00 0.00 0.00 2.29
861 871 4.331443 GTGTGCGTTTTTCTTGGGATTTTT 59.669 37.500 0.00 0.00 0.00 1.94
862 872 3.868661 GTGTGCGTTTTTCTTGGGATTTT 59.131 39.130 0.00 0.00 0.00 1.82
863 873 3.118956 TGTGTGCGTTTTTCTTGGGATTT 60.119 39.130 0.00 0.00 0.00 2.17
864 874 2.428890 TGTGTGCGTTTTTCTTGGGATT 59.571 40.909 0.00 0.00 0.00 3.01
865 875 2.028130 TGTGTGCGTTTTTCTTGGGAT 58.972 42.857 0.00 0.00 0.00 3.85
866 876 1.464734 TGTGTGCGTTTTTCTTGGGA 58.535 45.000 0.00 0.00 0.00 4.37
867 877 2.159310 TCTTGTGTGCGTTTTTCTTGGG 60.159 45.455 0.00 0.00 0.00 4.12
868 878 3.143807 TCTTGTGTGCGTTTTTCTTGG 57.856 42.857 0.00 0.00 0.00 3.61
869 879 5.118510 AGTTTTCTTGTGTGCGTTTTTCTTG 59.881 36.000 0.00 0.00 0.00 3.02
870 880 5.227152 AGTTTTCTTGTGTGCGTTTTTCTT 58.773 33.333 0.00 0.00 0.00 2.52
871 881 4.805219 AGTTTTCTTGTGTGCGTTTTTCT 58.195 34.783 0.00 0.00 0.00 2.52
872 882 5.275741 GCTAGTTTTCTTGTGTGCGTTTTTC 60.276 40.000 0.00 0.00 0.00 2.29
873 883 4.561213 GCTAGTTTTCTTGTGTGCGTTTTT 59.439 37.500 0.00 0.00 0.00 1.94
874 884 4.102649 GCTAGTTTTCTTGTGTGCGTTTT 58.897 39.130 0.00 0.00 0.00 2.43
875 885 3.377172 AGCTAGTTTTCTTGTGTGCGTTT 59.623 39.130 0.00 0.00 0.00 3.60
876 886 2.943033 AGCTAGTTTTCTTGTGTGCGTT 59.057 40.909 0.00 0.00 0.00 4.84
877 887 2.561569 AGCTAGTTTTCTTGTGTGCGT 58.438 42.857 0.00 0.00 0.00 5.24
878 888 3.248602 AGAAGCTAGTTTTCTTGTGTGCG 59.751 43.478 5.99 0.00 30.98 5.34
879 889 4.531332 CAGAAGCTAGTTTTCTTGTGTGC 58.469 43.478 8.39 0.00 32.75 4.57
880 890 4.531332 GCAGAAGCTAGTTTTCTTGTGTG 58.469 43.478 8.39 1.83 36.37 3.82
881 891 4.820284 GCAGAAGCTAGTTTTCTTGTGT 57.180 40.909 8.39 0.00 36.37 3.72
895 905 0.859232 TTTCGTTCGTGAGCAGAAGC 59.141 50.000 0.00 0.00 42.56 3.86
896 906 2.284150 TGTTTTCGTTCGTGAGCAGAAG 59.716 45.455 0.00 0.00 0.00 2.85
897 907 2.272678 TGTTTTCGTTCGTGAGCAGAA 58.727 42.857 0.00 0.00 0.00 3.02
898 908 1.929230 TGTTTTCGTTCGTGAGCAGA 58.071 45.000 0.00 0.00 0.00 4.26
899 909 2.730183 TTGTTTTCGTTCGTGAGCAG 57.270 45.000 0.00 0.00 0.00 4.24
900 910 3.421741 CTTTTGTTTTCGTTCGTGAGCA 58.578 40.909 0.00 0.00 0.00 4.26
901 911 2.781646 CCTTTTGTTTTCGTTCGTGAGC 59.218 45.455 0.00 0.00 0.00 4.26
902 912 4.267357 TCCTTTTGTTTTCGTTCGTGAG 57.733 40.909 0.00 0.00 0.00 3.51
903 913 4.654015 CTTCCTTTTGTTTTCGTTCGTGA 58.346 39.130 0.00 0.00 0.00 4.35
904 914 3.239712 GCTTCCTTTTGTTTTCGTTCGTG 59.760 43.478 0.00 0.00 0.00 4.35
905 915 3.431856 GCTTCCTTTTGTTTTCGTTCGT 58.568 40.909 0.00 0.00 0.00 3.85
906 916 2.787129 GGCTTCCTTTTGTTTTCGTTCG 59.213 45.455 0.00 0.00 0.00 3.95
907 917 3.776340 TGGCTTCCTTTTGTTTTCGTTC 58.224 40.909 0.00 0.00 0.00 3.95
908 918 3.445805 TCTGGCTTCCTTTTGTTTTCGTT 59.554 39.130 0.00 0.00 0.00 3.85
909 919 3.020984 TCTGGCTTCCTTTTGTTTTCGT 58.979 40.909 0.00 0.00 0.00 3.85
910 920 3.708563 TCTGGCTTCCTTTTGTTTTCG 57.291 42.857 0.00 0.00 0.00 3.46
911 921 3.796717 CGTTCTGGCTTCCTTTTGTTTTC 59.203 43.478 0.00 0.00 0.00 2.29
912 922 3.780902 CGTTCTGGCTTCCTTTTGTTTT 58.219 40.909 0.00 0.00 0.00 2.43
913 923 2.481276 GCGTTCTGGCTTCCTTTTGTTT 60.481 45.455 0.00 0.00 0.00 2.83
914 924 1.067060 GCGTTCTGGCTTCCTTTTGTT 59.933 47.619 0.00 0.00 0.00 2.83
915 925 0.668535 GCGTTCTGGCTTCCTTTTGT 59.331 50.000 0.00 0.00 0.00 2.83
916 926 0.667993 TGCGTTCTGGCTTCCTTTTG 59.332 50.000 0.00 0.00 0.00 2.44
917 927 0.954452 CTGCGTTCTGGCTTCCTTTT 59.046 50.000 0.00 0.00 0.00 2.27
918 928 0.108585 TCTGCGTTCTGGCTTCCTTT 59.891 50.000 0.00 0.00 0.00 3.11
919 929 0.108585 TTCTGCGTTCTGGCTTCCTT 59.891 50.000 0.00 0.00 0.00 3.36
920 930 0.326264 ATTCTGCGTTCTGGCTTCCT 59.674 50.000 0.00 0.00 0.00 3.36
921 931 0.729690 GATTCTGCGTTCTGGCTTCC 59.270 55.000 0.00 0.00 0.00 3.46
922 932 1.442769 TGATTCTGCGTTCTGGCTTC 58.557 50.000 0.00 0.00 0.00 3.86
923 933 1.896220 TTGATTCTGCGTTCTGGCTT 58.104 45.000 0.00 0.00 0.00 4.35
924 934 1.537202 GTTTGATTCTGCGTTCTGGCT 59.463 47.619 0.00 0.00 0.00 4.75
925 935 1.266718 TGTTTGATTCTGCGTTCTGGC 59.733 47.619 0.00 0.00 0.00 4.85
926 936 2.290367 TGTGTTTGATTCTGCGTTCTGG 59.710 45.455 0.00 0.00 0.00 3.86
927 937 3.607422 TGTGTTTGATTCTGCGTTCTG 57.393 42.857 0.00 0.00 0.00 3.02
928 938 4.836125 AATGTGTTTGATTCTGCGTTCT 57.164 36.364 0.00 0.00 0.00 3.01
929 939 4.087085 CGAAATGTGTTTGATTCTGCGTTC 59.913 41.667 0.00 0.00 0.00 3.95
930 940 3.974401 CGAAATGTGTTTGATTCTGCGTT 59.026 39.130 0.00 0.00 0.00 4.84
931 941 3.554524 CGAAATGTGTTTGATTCTGCGT 58.445 40.909 0.00 0.00 0.00 5.24
932 942 2.339400 GCGAAATGTGTTTGATTCTGCG 59.661 45.455 0.00 0.00 0.00 5.18
933 943 2.663119 GGCGAAATGTGTTTGATTCTGC 59.337 45.455 0.00 0.00 0.00 4.26
934 944 4.083110 AGAGGCGAAATGTGTTTGATTCTG 60.083 41.667 0.00 0.00 0.00 3.02
935 945 4.074970 AGAGGCGAAATGTGTTTGATTCT 58.925 39.130 0.00 0.00 0.00 2.40
936 946 4.425577 AGAGGCGAAATGTGTTTGATTC 57.574 40.909 0.00 0.00 0.00 2.52
937 947 4.142600 GCTAGAGGCGAAATGTGTTTGATT 60.143 41.667 0.00 0.00 0.00 2.57
938 948 3.375299 GCTAGAGGCGAAATGTGTTTGAT 59.625 43.478 0.00 0.00 0.00 2.57
939 949 2.742053 GCTAGAGGCGAAATGTGTTTGA 59.258 45.455 0.00 0.00 0.00 2.69
940 950 3.122937 GCTAGAGGCGAAATGTGTTTG 57.877 47.619 0.00 0.00 0.00 2.93
952 962 2.107953 CCGGCTGAAGCTAGAGGC 59.892 66.667 8.09 8.09 41.70 4.70
953 963 2.107953 GCCGGCTGAAGCTAGAGG 59.892 66.667 22.15 2.83 41.70 3.69
954 964 2.279120 CGCCGGCTGAAGCTAGAG 60.279 66.667 26.68 0.00 41.70 2.43
955 965 3.064987 GACGCCGGCTGAAGCTAGA 62.065 63.158 26.68 0.00 41.70 2.43
956 966 2.583593 GACGCCGGCTGAAGCTAG 60.584 66.667 26.68 8.67 41.70 3.42
957 967 1.388837 TATGACGCCGGCTGAAGCTA 61.389 55.000 26.68 5.55 41.70 3.32
958 968 2.032860 ATATGACGCCGGCTGAAGCT 62.033 55.000 26.68 6.60 41.70 3.74
959 969 1.160329 AATATGACGCCGGCTGAAGC 61.160 55.000 26.68 9.33 41.14 3.86
960 970 0.583438 CAATATGACGCCGGCTGAAG 59.417 55.000 26.68 11.62 0.00 3.02
961 971 0.813610 CCAATATGACGCCGGCTGAA 60.814 55.000 26.68 9.79 0.00 3.02
962 972 1.227527 CCAATATGACGCCGGCTGA 60.228 57.895 26.68 8.26 0.00 4.26
963 973 0.603707 ATCCAATATGACGCCGGCTG 60.604 55.000 26.68 20.24 0.00 4.85
964 974 0.320771 GATCCAATATGACGCCGGCT 60.321 55.000 26.68 11.91 0.00 5.52
965 975 1.298859 GGATCCAATATGACGCCGGC 61.299 60.000 19.07 19.07 0.00 6.13
966 976 0.034756 TGGATCCAATATGACGCCGG 59.965 55.000 13.46 0.00 0.00 6.13
967 977 1.148310 GTGGATCCAATATGACGCCG 58.852 55.000 18.20 0.00 0.00 6.46
968 978 1.523758 GGTGGATCCAATATGACGCC 58.476 55.000 18.20 7.04 35.97 5.68
969 979 1.148310 CGGTGGATCCAATATGACGC 58.852 55.000 18.20 0.45 35.57 5.19
970 980 1.148310 GCGGTGGATCCAATATGACG 58.852 55.000 18.20 14.70 35.57 4.35
971 981 1.523758 GGCGGTGGATCCAATATGAC 58.476 55.000 18.20 4.84 35.57 3.06
972 982 0.400213 GGGCGGTGGATCCAATATGA 59.600 55.000 18.20 0.00 35.57 2.15
973 983 0.110295 TGGGCGGTGGATCCAATATG 59.890 55.000 18.20 7.70 35.57 1.78
974 984 0.110486 GTGGGCGGTGGATCCAATAT 59.890 55.000 18.20 0.00 35.57 1.28
975 985 1.529796 GTGGGCGGTGGATCCAATA 59.470 57.895 18.20 0.00 35.57 1.90
976 986 2.275418 GTGGGCGGTGGATCCAAT 59.725 61.111 18.20 0.00 35.57 3.16
977 987 4.402528 CGTGGGCGGTGGATCCAA 62.403 66.667 18.20 0.00 35.57 3.53
1015 1025 1.142870 TGGTACAGCAGCAACTTCCTT 59.857 47.619 0.00 0.00 0.00 3.36
1017 1027 0.875059 GTGGTACAGCAGCAACTTCC 59.125 55.000 0.00 0.00 41.80 3.46
1110 1122 3.591835 GAGAGGAGAGGCGAGGCG 61.592 72.222 0.00 0.00 0.00 5.52
1111 1123 3.223589 GGAGAGGAGAGGCGAGGC 61.224 72.222 0.00 0.00 0.00 4.70
1114 1126 1.529796 GAGAGGAGAGGAGAGGCGA 59.470 63.158 0.00 0.00 0.00 5.54
1128 1140 4.127171 CGTAGGAAGAAGAGAGAGGAGAG 58.873 52.174 0.00 0.00 0.00 3.20
1129 1141 3.683281 GCGTAGGAAGAAGAGAGAGGAGA 60.683 52.174 0.00 0.00 0.00 3.71
1130 1142 2.616842 GCGTAGGAAGAAGAGAGAGGAG 59.383 54.545 0.00 0.00 0.00 3.69
1133 1145 1.268335 GCGCGTAGGAAGAAGAGAGAG 60.268 57.143 8.43 0.00 0.00 3.20
1134 1146 0.733729 GCGCGTAGGAAGAAGAGAGA 59.266 55.000 8.43 0.00 0.00 3.10
1331 1357 0.741221 GTCCCCAGATGAACTGCGAC 60.741 60.000 0.00 0.00 44.52 5.19
1333 1359 0.742281 CAGTCCCCAGATGAACTGCG 60.742 60.000 0.00 0.00 44.52 5.18
1510 1536 5.965334 ACAATTTCACATCGCATAATCGAAC 59.035 36.000 0.00 0.00 42.15 3.95
1603 1629 3.927817 TACCTTGCCCCCTGCCGTA 62.928 63.158 0.00 0.00 40.16 4.02
1643 1670 2.083774 TGCGCTATGGAGGAACAAAAG 58.916 47.619 9.73 0.00 0.00 2.27
1704 1731 2.169978 AGGCACCGATCTAGGGTTAAAC 59.830 50.000 0.00 0.00 34.97 2.01
1727 1754 4.822685 AGACCTTCTCTACGACTCTACA 57.177 45.455 0.00 0.00 0.00 2.74
1728 1755 7.790823 AATTAGACCTTCTCTACGACTCTAC 57.209 40.000 0.00 0.00 30.56 2.59
1729 1756 9.896645 TTAAATTAGACCTTCTCTACGACTCTA 57.103 33.333 0.00 0.00 30.56 2.43
1730 1757 8.676401 GTTAAATTAGACCTTCTCTACGACTCT 58.324 37.037 0.00 0.00 30.56 3.24
1731 1758 8.676401 AGTTAAATTAGACCTTCTCTACGACTC 58.324 37.037 0.00 0.00 30.56 3.36
1732 1759 8.460428 CAGTTAAATTAGACCTTCTCTACGACT 58.540 37.037 0.00 0.00 30.56 4.18
1733 1760 8.242739 ACAGTTAAATTAGACCTTCTCTACGAC 58.757 37.037 0.00 0.00 30.56 4.34
1734 1761 8.345724 ACAGTTAAATTAGACCTTCTCTACGA 57.654 34.615 0.00 0.00 30.56 3.43
1735 1762 8.460428 AGACAGTTAAATTAGACCTTCTCTACG 58.540 37.037 0.00 0.00 30.56 3.51
1763 1790 4.843728 TCAAAGTTGGAAGGTATGCTAGG 58.156 43.478 0.00 0.00 0.00 3.02
1782 1809 6.424883 TGGTTAACAAAAGAACCTACCTCAA 58.575 36.000 8.10 0.00 44.63 3.02
1792 1820 7.385478 GTGAAAAACACCTGGTTAACAAAAGAA 59.615 33.333 8.10 0.00 43.05 2.52
1911 1942 1.305201 ACAAGAAACATTCGCACCGT 58.695 45.000 0.00 0.00 34.02 4.83
2884 6256 9.691362 GGTGAAACATTGTTTACTGAATAACAT 57.309 29.630 14.49 0.00 39.98 2.71
3537 6909 4.176271 GCCCATTTTAGTAAAAGCAGCAG 58.824 43.478 13.25 1.62 33.22 4.24
3729 7101 5.078256 ACTCCCTCCGATCGATATTACTTT 58.922 41.667 18.66 0.00 0.00 2.66
3941 7313 6.488817 ACGTTCGTGTTTAAGCTTGTTAAAT 58.511 32.000 9.86 0.00 0.00 1.40
3960 7332 5.462398 CCTAAAGTAGCCATGTGATACGTTC 59.538 44.000 11.64 0.00 0.00 3.95
4026 7398 4.339247 CCTCAACTGCAAAGAAGAAAGGAA 59.661 41.667 0.00 0.00 0.00 3.36
4658 8030 0.734889 ATTTTCGCCCATCAAGCTCG 59.265 50.000 0.00 0.00 0.00 5.03
4670 8042 5.806286 TGAGATATCGGTTTTGATTTTCGC 58.194 37.500 0.00 0.00 0.00 4.70
5365 8746 7.444299 ACACATTTTTCAATCCAGCAACTAAT 58.556 30.769 0.00 0.00 0.00 1.73
5366 8747 6.815089 ACACATTTTTCAATCCAGCAACTAA 58.185 32.000 0.00 0.00 0.00 2.24
5649 9032 7.336427 AGACGTATTTATATAGAACGGAGGGAG 59.664 40.741 14.28 0.00 37.86 4.30
5650 9033 7.170965 AGACGTATTTATATAGAACGGAGGGA 58.829 38.462 14.28 0.00 37.86 4.20
5651 9034 7.388460 AGACGTATTTATATAGAACGGAGGG 57.612 40.000 14.28 0.00 37.86 4.30
5652 9035 9.376075 TCTAGACGTATTTATATAGAACGGAGG 57.624 37.037 14.28 5.75 37.86 4.30
5685 9068 9.127277 TGCAGTAGTCACATACAGTACATAATA 57.873 33.333 0.00 0.00 0.00 0.98
5686 9069 7.921214 GTGCAGTAGTCACATACAGTACATAAT 59.079 37.037 0.00 0.00 31.29 1.28
5687 9070 7.094118 TGTGCAGTAGTCACATACAGTACATAA 60.094 37.037 0.00 0.00 39.29 1.90
5701 9084 0.179111 GCGGCTATGTGCAGTAGTCA 60.179 55.000 10.31 0.00 45.15 3.41
5848 9231 1.140589 CGAGATGAAGAGGCACGCT 59.859 57.895 0.00 0.00 43.09 5.07


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

AutoCloner maintained by Alex Coulton.