Multiple sequence alignment - TraesCS1D01G198900

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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 TraesCS1D01G198900 chr1D 100.000 4843 0 0 1 4843 280712061 280716903 0.000000e+00 8944
1 TraesCS1D01G198900 chr1D 91.545 615 43 9 175 783 339309110 339308499 0.000000e+00 839
2 TraesCS1D01G198900 chr1A 97.305 3747 76 10 1104 4843 352866645 352870373 0.000000e+00 6336
3 TraesCS1D01G198900 chr3D 91.433 677 44 10 115 780 86229258 86228585 0.000000e+00 917
4 TraesCS1D01G198900 chr3D 87.516 793 64 28 4 780 501425353 501426126 0.000000e+00 883
5 TraesCS1D01G198900 chr2D 91.150 678 45 10 115 780 375589891 375590565 0.000000e+00 905
6 TraesCS1D01G198900 chr2D 87.927 762 69 20 39 780 575237942 575238700 0.000000e+00 876
7 TraesCS1D01G198900 chr4D 89.014 710 51 22 89 780 461817006 461816306 0.000000e+00 854
8 TraesCS1D01G198900 chr3A 85.930 796 80 27 4 780 26628909 26629691 0.000000e+00 821
9 TraesCS1D01G198900 chr3A 90.145 619 45 14 175 781 734662702 734663316 0.000000e+00 791
10 TraesCS1D01G198900 chr5D 90.097 616 48 10 175 781 486198057 486197446 0.000000e+00 787
11 TraesCS1D01G198900 chr5A 84.394 660 61 21 33 663 491180474 491179828 1.150000e-170 610
12 TraesCS1D01G198900 chr1B 94.286 70 2 1 948 1017 381500070 381500137 6.630000e-19 106


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 TraesCS1D01G198900 chr1D 280712061 280716903 4842 False 8944 8944 100.000 1 4843 1 chr1D.!!$F1 4842
1 TraesCS1D01G198900 chr1D 339308499 339309110 611 True 839 839 91.545 175 783 1 chr1D.!!$R1 608
2 TraesCS1D01G198900 chr1A 352866645 352870373 3728 False 6336 6336 97.305 1104 4843 1 chr1A.!!$F1 3739
3 TraesCS1D01G198900 chr3D 86228585 86229258 673 True 917 917 91.433 115 780 1 chr3D.!!$R1 665
4 TraesCS1D01G198900 chr3D 501425353 501426126 773 False 883 883 87.516 4 780 1 chr3D.!!$F1 776
5 TraesCS1D01G198900 chr2D 375589891 375590565 674 False 905 905 91.150 115 780 1 chr2D.!!$F1 665
6 TraesCS1D01G198900 chr2D 575237942 575238700 758 False 876 876 87.927 39 780 1 chr2D.!!$F2 741
7 TraesCS1D01G198900 chr4D 461816306 461817006 700 True 854 854 89.014 89 780 1 chr4D.!!$R1 691
8 TraesCS1D01G198900 chr3A 26628909 26629691 782 False 821 821 85.930 4 780 1 chr3A.!!$F1 776
9 TraesCS1D01G198900 chr3A 734662702 734663316 614 False 791 791 90.145 175 781 1 chr3A.!!$F2 606
10 TraesCS1D01G198900 chr5D 486197446 486198057 611 True 787 787 90.097 175 781 1 chr5D.!!$R1 606
11 TraesCS1D01G198900 chr5A 491179828 491180474 646 True 610 610 84.394 33 663 1 chr5A.!!$R1 630

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
988 1056 0.106015 CCAATCCCCACCCTCCATTC 60.106 60.0 0.0 0.0 0.00 2.67 F
1676 1745 0.109153 TGCTCCTTGAAGCTCTTGCA 59.891 50.0 0.0 0.0 42.94 4.08 F
2049 2118 0.892358 AGTGTTGCAGGACATGGCTG 60.892 55.0 0.0 0.0 0.00 4.85 F
3596 3666 0.907230 GAGAGACCACAGAGGCCCTT 60.907 60.0 0.0 0.0 43.14 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2179 0.700564 TGCTTCTGAGAAATGCCCCT 59.299 50.000 4.29 0.0 0.00 4.79 R
3276 3345 0.036858 AGCTTGGAGGCTTCTTCGTC 60.037 55.000 0.00 0.0 39.86 4.20 R
3692 3762 8.678510 CAATACCATAAATAAACTTTAAGCGCG 58.321 33.333 0.00 0.0 0.00 6.86 R
4787 4862 1.899437 GAATGGGGTCACGCTCCTCA 61.899 60.000 0.00 0.0 38.99 3.86 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
139 143 1.398451 GGTGTCAAAATCGTGCGTCTG 60.398 52.381 0.00 0.00 0.00 3.51
437 477 1.447838 GGATCGACGAAAGCCTGCA 60.448 57.895 0.00 0.00 0.00 4.41
439 479 0.579156 GATCGACGAAAGCCTGCATC 59.421 55.000 0.00 0.00 0.00 3.91
469 524 1.205893 GGAGAGTTGATGGAGCGAAGT 59.794 52.381 0.00 0.00 0.00 3.01
592 648 4.149922 CGCGAAAGTAAATGACACAGAGAA 59.850 41.667 0.00 0.00 0.00 2.87
606 666 3.008375 CACAGAGAAATGGAGGAGACCAA 59.992 47.826 0.00 0.00 43.47 3.67
648 708 4.657504 AGAGATTACAATGATGGCTCCTCA 59.342 41.667 0.00 0.00 0.00 3.86
701 764 3.599730 AGTACCCACCTAACGTAAAGC 57.400 47.619 0.00 0.00 0.00 3.51
709 775 2.026915 ACCTAACGTAAAGCGGGGAAAT 60.027 45.455 0.00 0.00 46.52 2.17
781 849 2.840576 CCCCGGTTTCCCAACAGA 59.159 61.111 0.00 0.00 34.15 3.41
784 852 0.958822 CCCGGTTTCCCAACAGAAAG 59.041 55.000 0.00 0.00 36.45 2.62
785 853 0.958822 CCGGTTTCCCAACAGAAAGG 59.041 55.000 0.00 0.00 36.45 3.11
786 854 1.477923 CCGGTTTCCCAACAGAAAGGA 60.478 52.381 0.00 0.00 36.45 3.36
787 855 1.880027 CGGTTTCCCAACAGAAAGGAG 59.120 52.381 0.00 0.00 36.45 3.69
788 856 1.613925 GGTTTCCCAACAGAAAGGAGC 59.386 52.381 0.00 0.00 36.45 4.70
789 857 1.613925 GTTTCCCAACAGAAAGGAGCC 59.386 52.381 0.00 0.00 36.45 4.70
790 858 0.250727 TTCCCAACAGAAAGGAGCCG 60.251 55.000 0.00 0.00 0.00 5.52
791 859 1.073199 CCCAACAGAAAGGAGCCGT 59.927 57.895 0.00 0.00 0.00 5.68
792 860 0.955919 CCCAACAGAAAGGAGCCGTC 60.956 60.000 0.00 0.00 0.00 4.79
793 861 0.955919 CCAACAGAAAGGAGCCGTCC 60.956 60.000 0.00 0.00 44.33 4.79
801 869 4.452733 GGAGCCGTCCTGTTCCCG 62.453 72.222 0.00 0.00 40.17 5.14
802 870 3.692406 GAGCCGTCCTGTTCCCGT 61.692 66.667 0.00 0.00 0.00 5.28
803 871 3.934391 GAGCCGTCCTGTTCCCGTG 62.934 68.421 0.00 0.00 0.00 4.94
805 873 3.307906 CCGTCCTGTTCCCGTGGA 61.308 66.667 0.00 0.00 0.00 4.02
806 874 2.738480 CGTCCTGTTCCCGTGGAA 59.262 61.111 1.68 1.68 39.66 3.53
814 882 3.402833 TTCCCGTGGAACCCTATCA 57.597 52.632 1.68 0.00 36.71 2.15
815 883 1.659022 TTCCCGTGGAACCCTATCAA 58.341 50.000 1.68 0.00 36.71 2.57
816 884 1.887797 TCCCGTGGAACCCTATCAAT 58.112 50.000 0.00 0.00 0.00 2.57
817 885 1.766496 TCCCGTGGAACCCTATCAATC 59.234 52.381 0.00 0.00 0.00 2.67
818 886 1.202770 CCCGTGGAACCCTATCAATCC 60.203 57.143 0.00 0.00 0.00 3.01
819 887 1.202770 CCGTGGAACCCTATCAATCCC 60.203 57.143 0.00 0.00 0.00 3.85
820 888 1.540363 CGTGGAACCCTATCAATCCCG 60.540 57.143 0.00 0.00 0.00 5.14
821 889 0.472471 TGGAACCCTATCAATCCCGC 59.528 55.000 0.00 0.00 0.00 6.13
822 890 0.250770 GGAACCCTATCAATCCCGCC 60.251 60.000 0.00 0.00 0.00 6.13
823 891 0.602905 GAACCCTATCAATCCCGCCG 60.603 60.000 0.00 0.00 0.00 6.46
824 892 2.358737 CCCTATCAATCCCGCCGC 60.359 66.667 0.00 0.00 0.00 6.53
825 893 2.358737 CCTATCAATCCCGCCGCC 60.359 66.667 0.00 0.00 0.00 6.13
826 894 2.738521 CTATCAATCCCGCCGCCG 60.739 66.667 0.00 0.00 0.00 6.46
827 895 3.515316 CTATCAATCCCGCCGCCGT 62.515 63.158 0.00 0.00 0.00 5.68
828 896 3.800685 TATCAATCCCGCCGCCGTG 62.801 63.158 0.00 0.00 0.00 4.94
849 917 3.048602 CGTGTCCGGTGTCTCCTT 58.951 61.111 0.00 0.00 0.00 3.36
850 918 1.080705 CGTGTCCGGTGTCTCCTTC 60.081 63.158 0.00 0.00 0.00 3.46
851 919 1.080705 GTGTCCGGTGTCTCCTTCG 60.081 63.158 0.00 0.00 0.00 3.79
852 920 1.228337 TGTCCGGTGTCTCCTTCGA 60.228 57.895 0.00 0.00 0.00 3.71
853 921 1.212229 GTCCGGTGTCTCCTTCGAC 59.788 63.158 0.00 0.00 34.52 4.20
854 922 1.975407 TCCGGTGTCTCCTTCGACC 60.975 63.158 0.00 0.00 32.97 4.79
855 923 1.977544 CCGGTGTCTCCTTCGACCT 60.978 63.158 0.00 0.00 32.97 3.85
856 924 1.213013 CGGTGTCTCCTTCGACCTG 59.787 63.158 0.00 0.00 32.97 4.00
857 925 1.079750 GGTGTCTCCTTCGACCTGC 60.080 63.158 0.00 0.00 32.97 4.85
858 926 1.444553 GTGTCTCCTTCGACCTGCG 60.445 63.158 0.00 0.00 42.69 5.18
859 927 2.507324 GTCTCCTTCGACCTGCGC 60.507 66.667 0.00 0.00 40.61 6.09
860 928 3.760035 TCTCCTTCGACCTGCGCC 61.760 66.667 4.18 0.00 40.61 6.53
861 929 4.821589 CTCCTTCGACCTGCGCCC 62.822 72.222 4.18 0.00 40.61 6.13
863 931 4.394712 CCTTCGACCTGCGCCCTT 62.395 66.667 4.18 0.00 40.61 3.95
864 932 3.121030 CTTCGACCTGCGCCCTTG 61.121 66.667 4.18 0.00 40.61 3.61
870 938 4.504596 CCTGCGCCCTTGCCCATA 62.505 66.667 4.18 0.00 0.00 2.74
871 939 3.211963 CTGCGCCCTTGCCCATAC 61.212 66.667 4.18 0.00 0.00 2.39
897 965 4.351054 CCGTGCAGCCCCCTTCTT 62.351 66.667 0.00 0.00 0.00 2.52
898 966 3.058160 CGTGCAGCCCCCTTCTTG 61.058 66.667 0.00 0.00 0.00 3.02
899 967 2.677875 GTGCAGCCCCCTTCTTGG 60.678 66.667 0.00 0.00 0.00 3.61
904 972 4.372999 GCCCCCTTCTTGGCTGCT 62.373 66.667 0.00 0.00 44.46 4.24
905 973 2.442413 CCCCCTTCTTGGCTGCTT 59.558 61.111 0.00 0.00 0.00 3.91
906 974 1.680314 CCCCCTTCTTGGCTGCTTC 60.680 63.158 0.00 0.00 0.00 3.86
907 975 2.042831 CCCCTTCTTGGCTGCTTCG 61.043 63.158 0.00 0.00 0.00 3.79
908 976 2.694760 CCCTTCTTGGCTGCTTCGC 61.695 63.158 0.00 0.00 0.00 4.70
909 977 1.673665 CCTTCTTGGCTGCTTCGCT 60.674 57.895 0.00 0.00 0.00 4.93
910 978 1.500844 CTTCTTGGCTGCTTCGCTG 59.499 57.895 0.00 0.00 0.00 5.18
911 979 1.919956 CTTCTTGGCTGCTTCGCTGG 61.920 60.000 0.00 0.00 0.00 4.85
916 984 2.823147 GCTGCTTCGCTGGCTGAT 60.823 61.111 0.00 0.00 0.00 2.90
917 985 2.821688 GCTGCTTCGCTGGCTGATC 61.822 63.158 0.00 0.00 0.00 2.92
918 986 1.153409 CTGCTTCGCTGGCTGATCT 60.153 57.895 0.00 0.00 0.00 2.75
919 987 1.152989 CTGCTTCGCTGGCTGATCTC 61.153 60.000 0.00 0.00 0.00 2.75
920 988 1.886777 GCTTCGCTGGCTGATCTCC 60.887 63.158 0.00 0.00 0.00 3.71
921 989 1.227497 CTTCGCTGGCTGATCTCCC 60.227 63.158 0.00 0.00 0.00 4.30
922 990 1.964608 CTTCGCTGGCTGATCTCCCA 61.965 60.000 0.00 5.08 0.00 4.37
923 991 2.202987 CGCTGGCTGATCTCCCAC 60.203 66.667 0.00 0.00 0.00 4.61
924 992 2.191641 GCTGGCTGATCTCCCACC 59.808 66.667 0.00 0.00 0.00 4.61
925 993 2.914289 CTGGCTGATCTCCCACCC 59.086 66.667 0.00 0.00 0.00 4.61
926 994 1.692042 CTGGCTGATCTCCCACCCT 60.692 63.158 0.00 0.00 0.00 4.34
927 995 1.229951 TGGCTGATCTCCCACCCTT 60.230 57.895 0.00 0.00 0.00 3.95
928 996 0.846427 TGGCTGATCTCCCACCCTTT 60.846 55.000 0.00 0.00 0.00 3.11
929 997 0.394899 GGCTGATCTCCCACCCTTTG 60.395 60.000 0.00 0.00 0.00 2.77
930 998 0.620556 GCTGATCTCCCACCCTTTGA 59.379 55.000 0.00 0.00 0.00 2.69
931 999 1.213926 GCTGATCTCCCACCCTTTGAT 59.786 52.381 0.00 0.00 0.00 2.57
932 1000 2.747799 GCTGATCTCCCACCCTTTGATC 60.748 54.545 0.00 0.00 35.44 2.92
933 1001 1.846439 TGATCTCCCACCCTTTGATCC 59.154 52.381 0.00 0.00 34.36 3.36
934 1002 1.846439 GATCTCCCACCCTTTGATCCA 59.154 52.381 0.00 0.00 0.00 3.41
935 1003 1.753903 TCTCCCACCCTTTGATCCAA 58.246 50.000 0.00 0.00 0.00 3.53
936 1004 2.287584 TCTCCCACCCTTTGATCCAAT 58.712 47.619 0.00 0.00 0.00 3.16
937 1005 2.242196 TCTCCCACCCTTTGATCCAATC 59.758 50.000 0.00 0.00 0.00 2.67
938 1006 2.243221 CTCCCACCCTTTGATCCAATCT 59.757 50.000 0.00 0.00 0.00 2.40
939 1007 2.654385 TCCCACCCTTTGATCCAATCTT 59.346 45.455 0.00 0.00 0.00 2.40
940 1008 2.762327 CCCACCCTTTGATCCAATCTTG 59.238 50.000 0.00 0.00 0.00 3.02
951 1019 1.453155 CCAATCTTGGTGGAAGGTCG 58.547 55.000 0.55 0.00 43.43 4.79
952 1020 1.271379 CCAATCTTGGTGGAAGGTCGT 60.271 52.381 0.55 0.00 43.43 4.34
953 1021 2.076863 CAATCTTGGTGGAAGGTCGTC 58.923 52.381 0.00 0.00 31.85 4.20
954 1022 0.613777 ATCTTGGTGGAAGGTCGTCC 59.386 55.000 0.00 0.00 38.27 4.79
955 1023 0.761323 TCTTGGTGGAAGGTCGTCCA 60.761 55.000 0.51 1.58 45.72 4.02
959 1027 3.294750 TGGAAGGTCGTCCATCGG 58.705 61.111 0.51 0.00 42.97 4.18
960 1028 1.608336 TGGAAGGTCGTCCATCGGT 60.608 57.895 0.51 0.00 42.97 4.69
961 1029 1.141234 GGAAGGTCGTCCATCGGTC 59.859 63.158 0.51 0.00 40.32 4.79
962 1030 1.141234 GAAGGTCGTCCATCGGTCC 59.859 63.158 0.51 0.00 40.32 4.46
963 1031 2.294132 GAAGGTCGTCCATCGGTCCC 62.294 65.000 0.51 0.00 40.32 4.46
964 1032 3.846430 GGTCGTCCATCGGTCCCC 61.846 72.222 0.00 0.00 40.32 4.81
976 1044 3.805497 GTCCCCGGACCCAATCCC 61.805 72.222 0.73 0.00 46.04 3.85
979 1047 4.123545 CCCGGACCCAATCCCCAC 62.124 72.222 0.73 0.00 46.04 4.61
980 1048 4.123545 CCGGACCCAATCCCCACC 62.124 72.222 0.00 0.00 46.04 4.61
981 1049 4.123545 CGGACCCAATCCCCACCC 62.124 72.222 0.00 0.00 46.04 4.61
982 1050 2.617215 GGACCCAATCCCCACCCT 60.617 66.667 0.00 0.00 42.46 4.34
983 1051 2.690734 GGACCCAATCCCCACCCTC 61.691 68.421 0.00 0.00 42.46 4.30
984 1052 2.617215 ACCCAATCCCCACCCTCC 60.617 66.667 0.00 0.00 0.00 4.30
985 1053 2.616893 CCCAATCCCCACCCTCCA 60.617 66.667 0.00 0.00 0.00 3.86
986 1054 2.014550 CCCAATCCCCACCCTCCAT 61.015 63.158 0.00 0.00 0.00 3.41
987 1055 1.593166 CCCAATCCCCACCCTCCATT 61.593 60.000 0.00 0.00 0.00 3.16
988 1056 0.106015 CCAATCCCCACCCTCCATTC 60.106 60.000 0.00 0.00 0.00 2.67
989 1057 0.630673 CAATCCCCACCCTCCATTCA 59.369 55.000 0.00 0.00 0.00 2.57
990 1058 1.006998 CAATCCCCACCCTCCATTCAA 59.993 52.381 0.00 0.00 0.00 2.69
991 1059 1.624173 ATCCCCACCCTCCATTCAAT 58.376 50.000 0.00 0.00 0.00 2.57
992 1060 0.926293 TCCCCACCCTCCATTCAATC 59.074 55.000 0.00 0.00 0.00 2.67
993 1061 0.929244 CCCCACCCTCCATTCAATCT 59.071 55.000 0.00 0.00 0.00 2.40
994 1062 1.133668 CCCCACCCTCCATTCAATCTC 60.134 57.143 0.00 0.00 0.00 2.75
995 1063 1.133668 CCCACCCTCCATTCAATCTCC 60.134 57.143 0.00 0.00 0.00 3.71
996 1064 1.849039 CCACCCTCCATTCAATCTCCT 59.151 52.381 0.00 0.00 0.00 3.69
997 1065 2.158696 CCACCCTCCATTCAATCTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
998 1066 2.776536 CACCCTCCATTCAATCTCCTCT 59.223 50.000 0.00 0.00 0.00 3.69
999 1067 3.969976 CACCCTCCATTCAATCTCCTCTA 59.030 47.826 0.00 0.00 0.00 2.43
1000 1068 4.596643 CACCCTCCATTCAATCTCCTCTAT 59.403 45.833 0.00 0.00 0.00 1.98
1001 1069 5.072872 CACCCTCCATTCAATCTCCTCTATT 59.927 44.000 0.00 0.00 0.00 1.73
1002 1070 6.270927 CACCCTCCATTCAATCTCCTCTATTA 59.729 42.308 0.00 0.00 0.00 0.98
1003 1071 6.500049 ACCCTCCATTCAATCTCCTCTATTAG 59.500 42.308 0.00 0.00 0.00 1.73
1004 1072 6.405538 CCTCCATTCAATCTCCTCTATTAGC 58.594 44.000 0.00 0.00 0.00 3.09
1005 1073 6.213195 CCTCCATTCAATCTCCTCTATTAGCT 59.787 42.308 0.00 0.00 0.00 3.32
1006 1074 7.256619 CCTCCATTCAATCTCCTCTATTAGCTT 60.257 40.741 0.00 0.00 0.00 3.74
1007 1075 7.675062 TCCATTCAATCTCCTCTATTAGCTTC 58.325 38.462 0.00 0.00 0.00 3.86
1008 1076 7.512058 TCCATTCAATCTCCTCTATTAGCTTCT 59.488 37.037 0.00 0.00 0.00 2.85
1009 1077 8.811017 CCATTCAATCTCCTCTATTAGCTTCTA 58.189 37.037 0.00 0.00 0.00 2.10
1010 1078 9.638239 CATTCAATCTCCTCTATTAGCTTCTAC 57.362 37.037 0.00 0.00 0.00 2.59
1011 1079 7.768807 TCAATCTCCTCTATTAGCTTCTACC 57.231 40.000 0.00 0.00 0.00 3.18
1012 1080 6.431543 TCAATCTCCTCTATTAGCTTCTACCG 59.568 42.308 0.00 0.00 0.00 4.02
1013 1081 4.073549 TCTCCTCTATTAGCTTCTACCGC 58.926 47.826 0.00 0.00 0.00 5.68
1014 1082 3.155501 TCCTCTATTAGCTTCTACCGCC 58.844 50.000 0.00 0.00 0.00 6.13
1015 1083 2.231721 CCTCTATTAGCTTCTACCGCCC 59.768 54.545 0.00 0.00 0.00 6.13
1016 1084 3.158676 CTCTATTAGCTTCTACCGCCCT 58.841 50.000 0.00 0.00 0.00 5.19
1017 1085 3.155501 TCTATTAGCTTCTACCGCCCTC 58.844 50.000 0.00 0.00 0.00 4.30
1018 1086 1.789523 ATTAGCTTCTACCGCCCTCA 58.210 50.000 0.00 0.00 0.00 3.86
1019 1087 1.563924 TTAGCTTCTACCGCCCTCAA 58.436 50.000 0.00 0.00 0.00 3.02
1020 1088 0.822164 TAGCTTCTACCGCCCTCAAC 59.178 55.000 0.00 0.00 0.00 3.18
1021 1089 1.449778 GCTTCTACCGCCCTCAACC 60.450 63.158 0.00 0.00 0.00 3.77
1022 1090 1.153628 CTTCTACCGCCCTCAACCG 60.154 63.158 0.00 0.00 0.00 4.44
1023 1091 1.885163 CTTCTACCGCCCTCAACCGT 61.885 60.000 0.00 0.00 0.00 4.83
1024 1092 1.474332 TTCTACCGCCCTCAACCGTT 61.474 55.000 0.00 0.00 0.00 4.44
1025 1093 1.447314 CTACCGCCCTCAACCGTTC 60.447 63.158 0.00 0.00 0.00 3.95
1026 1094 2.847435 CTACCGCCCTCAACCGTTCC 62.847 65.000 0.00 0.00 0.00 3.62
1027 1095 4.323477 CCGCCCTCAACCGTTCCA 62.323 66.667 0.00 0.00 0.00 3.53
1028 1096 3.047877 CGCCCTCAACCGTTCCAC 61.048 66.667 0.00 0.00 0.00 4.02
1029 1097 2.112297 GCCCTCAACCGTTCCACA 59.888 61.111 0.00 0.00 0.00 4.17
1030 1098 1.303317 GCCCTCAACCGTTCCACAT 60.303 57.895 0.00 0.00 0.00 3.21
1031 1099 1.305930 GCCCTCAACCGTTCCACATC 61.306 60.000 0.00 0.00 0.00 3.06
1032 1100 1.019278 CCCTCAACCGTTCCACATCG 61.019 60.000 0.00 0.00 0.00 3.84
1033 1101 1.635663 CCTCAACCGTTCCACATCGC 61.636 60.000 0.00 0.00 0.00 4.58
1034 1102 0.948623 CTCAACCGTTCCACATCGCA 60.949 55.000 0.00 0.00 0.00 5.10
1035 1103 1.206578 CAACCGTTCCACATCGCAC 59.793 57.895 0.00 0.00 0.00 5.34
1036 1104 1.227704 AACCGTTCCACATCGCACA 60.228 52.632 0.00 0.00 0.00 4.57
1037 1105 0.605319 AACCGTTCCACATCGCACAT 60.605 50.000 0.00 0.00 0.00 3.21
1038 1106 1.019278 ACCGTTCCACATCGCACATC 61.019 55.000 0.00 0.00 0.00 3.06
1039 1107 1.705337 CCGTTCCACATCGCACATCC 61.705 60.000 0.00 0.00 0.00 3.51
1040 1108 1.018752 CGTTCCACATCGCACATCCA 61.019 55.000 0.00 0.00 0.00 3.41
1041 1109 1.382522 GTTCCACATCGCACATCCAT 58.617 50.000 0.00 0.00 0.00 3.41
1042 1110 1.331756 GTTCCACATCGCACATCCATC 59.668 52.381 0.00 0.00 0.00 3.51
1043 1111 0.179048 TCCACATCGCACATCCATCC 60.179 55.000 0.00 0.00 0.00 3.51
1044 1112 1.501337 CCACATCGCACATCCATCCG 61.501 60.000 0.00 0.00 0.00 4.18
1045 1113 1.889105 ACATCGCACATCCATCCGC 60.889 57.895 0.00 0.00 0.00 5.54
1046 1114 2.281070 ATCGCACATCCATCCGCC 60.281 61.111 0.00 0.00 0.00 6.13
1047 1115 3.105686 ATCGCACATCCATCCGCCA 62.106 57.895 0.00 0.00 0.00 5.69
1048 1116 2.401699 ATCGCACATCCATCCGCCAT 62.402 55.000 0.00 0.00 0.00 4.40
1049 1117 2.900167 CGCACATCCATCCGCCATG 61.900 63.158 0.00 0.00 0.00 3.66
1050 1118 1.526686 GCACATCCATCCGCCATGA 60.527 57.895 0.00 0.00 33.80 3.07
1051 1119 1.102809 GCACATCCATCCGCCATGAA 61.103 55.000 0.00 0.00 33.80 2.57
1052 1120 1.391577 CACATCCATCCGCCATGAAA 58.608 50.000 0.00 0.00 33.80 2.69
1053 1121 1.066002 CACATCCATCCGCCATGAAAC 59.934 52.381 0.00 0.00 33.80 2.78
1054 1122 0.670162 CATCCATCCGCCATGAAACC 59.330 55.000 0.00 0.00 33.80 3.27
1055 1123 0.258484 ATCCATCCGCCATGAAACCA 59.742 50.000 0.00 0.00 33.80 3.67
1056 1124 0.679640 TCCATCCGCCATGAAACCAC 60.680 55.000 0.00 0.00 33.80 4.16
1057 1125 1.666209 CCATCCGCCATGAAACCACC 61.666 60.000 0.00 0.00 33.80 4.61
1058 1126 0.964860 CATCCGCCATGAAACCACCA 60.965 55.000 0.00 0.00 33.80 4.17
1059 1127 0.965363 ATCCGCCATGAAACCACCAC 60.965 55.000 0.00 0.00 0.00 4.16
1060 1128 2.635443 CCGCCATGAAACCACCACC 61.635 63.158 0.00 0.00 0.00 4.61
1061 1129 2.635443 CGCCATGAAACCACCACCC 61.635 63.158 0.00 0.00 0.00 4.61
1062 1130 2.282783 GCCATGAAACCACCACCCC 61.283 63.158 0.00 0.00 0.00 4.95
1063 1131 1.154921 CCATGAAACCACCACCCCA 59.845 57.895 0.00 0.00 0.00 4.96
1064 1132 1.184970 CCATGAAACCACCACCCCAC 61.185 60.000 0.00 0.00 0.00 4.61
1065 1133 1.155155 ATGAAACCACCACCCCACC 59.845 57.895 0.00 0.00 0.00 4.61
1066 1134 1.660019 ATGAAACCACCACCCCACCA 61.660 55.000 0.00 0.00 0.00 4.17
1067 1135 1.830847 GAAACCACCACCCCACCAC 60.831 63.158 0.00 0.00 0.00 4.16
1068 1136 3.383031 AAACCACCACCCCACCACC 62.383 63.158 0.00 0.00 0.00 4.61
1071 1139 3.966543 CACCACCCCACCACCCTC 61.967 72.222 0.00 0.00 0.00 4.30
1072 1140 4.202030 ACCACCCCACCACCCTCT 62.202 66.667 0.00 0.00 0.00 3.69
1073 1141 3.330720 CCACCCCACCACCCTCTC 61.331 72.222 0.00 0.00 0.00 3.20
1074 1142 3.330720 CACCCCACCACCCTCTCC 61.331 72.222 0.00 0.00 0.00 3.71
1075 1143 3.542602 ACCCCACCACCCTCTCCT 61.543 66.667 0.00 0.00 0.00 3.69
1076 1144 2.689034 CCCCACCACCCTCTCCTC 60.689 72.222 0.00 0.00 0.00 3.71
1077 1145 2.689034 CCCACCACCCTCTCCTCC 60.689 72.222 0.00 0.00 0.00 4.30
1078 1146 2.452114 CCACCACCCTCTCCTCCT 59.548 66.667 0.00 0.00 0.00 3.69
1079 1147 1.687493 CCACCACCCTCTCCTCCTC 60.687 68.421 0.00 0.00 0.00 3.71
1080 1148 2.055042 CACCACCCTCTCCTCCTCG 61.055 68.421 0.00 0.00 0.00 4.63
1081 1149 3.151022 CCACCCTCTCCTCCTCGC 61.151 72.222 0.00 0.00 0.00 5.03
1082 1150 3.151022 CACCCTCTCCTCCTCGCC 61.151 72.222 0.00 0.00 0.00 5.54
1083 1151 3.673597 ACCCTCTCCTCCTCGCCA 61.674 66.667 0.00 0.00 0.00 5.69
1084 1152 2.123077 CCCTCTCCTCCTCGCCAT 60.123 66.667 0.00 0.00 0.00 4.40
1085 1153 2.206536 CCCTCTCCTCCTCGCCATC 61.207 68.421 0.00 0.00 0.00 3.51
1086 1154 2.206536 CCTCTCCTCCTCGCCATCC 61.207 68.421 0.00 0.00 0.00 3.51
1087 1155 2.519541 TCTCCTCCTCGCCATCCG 60.520 66.667 0.00 0.00 38.61 4.18
1088 1156 4.292178 CTCCTCCTCGCCATCCGC 62.292 72.222 0.00 0.00 36.73 5.54
1091 1159 4.899239 CTCCTCGCCATCCGCCAC 62.899 72.222 0.00 0.00 36.73 5.01
1232 1300 2.411701 CGCGACCTCGATTGCCTA 59.588 61.111 0.00 0.00 43.02 3.93
1386 1454 2.203451 ACGACCACGACCTCCTGT 60.203 61.111 0.00 0.00 42.66 4.00
1465 1533 2.584970 CGCTCGCCGCCTAATCAA 60.585 61.111 0.00 0.00 34.21 2.57
1577 1645 2.811317 CTCAACTCCTCCGCACGC 60.811 66.667 0.00 0.00 0.00 5.34
1675 1744 1.461559 ATGCTCCTTGAAGCTCTTGC 58.538 50.000 0.00 0.00 42.94 4.01
1676 1745 0.109153 TGCTCCTTGAAGCTCTTGCA 59.891 50.000 0.00 0.00 42.94 4.08
1679 1748 1.208614 CCTTGAAGCTCTTGCACGC 59.791 57.895 0.00 0.00 42.74 5.34
1726 1795 1.268999 GGTGTTTGCTGAAATGCGTGA 60.269 47.619 0.00 0.00 35.36 4.35
1804 1873 2.747686 GGCTGGAAAGGTGGACGA 59.252 61.111 0.00 0.00 0.00 4.20
1832 1901 6.370166 GTCTTAAGATGCTTGCAGAGTTAGTT 59.630 38.462 8.75 0.00 0.00 2.24
1926 1995 1.201880 GAGTAGACGAGGCTTTTCGGT 59.798 52.381 9.79 1.32 44.57 4.69
2049 2118 0.892358 AGTGTTGCAGGACATGGCTG 60.892 55.000 0.00 0.00 0.00 4.85
2110 2179 4.439974 GCTTATTGATTGCCATTGTCGGAA 60.440 41.667 0.00 0.00 0.00 4.30
2154 2223 4.022068 TCAGGTTGTTTGATGAAATGCTCC 60.022 41.667 0.00 0.00 0.00 4.70
2238 2307 1.670949 GGAGATGGAGCGTGCTGAGA 61.671 60.000 0.00 0.00 0.00 3.27
2258 2327 7.443302 TGAGAAGATATTGGAGGAGATGTTT 57.557 36.000 0.00 0.00 0.00 2.83
2262 2331 6.485830 AGATATTGGAGGAGATGTTTTCGA 57.514 37.500 0.00 0.00 0.00 3.71
2431 2500 4.729856 GCAGCTTTGCAAGGGCGG 62.730 66.667 10.89 14.72 45.35 6.13
2432 2501 4.060038 CAGCTTTGCAAGGGCGGG 62.060 66.667 10.89 8.33 45.35 6.13
2466 2535 3.960102 AGCAGTTGGAATTTGGTTGAAGA 59.040 39.130 0.00 0.00 0.00 2.87
2475 2544 6.323482 TGGAATTTGGTTGAAGATGTTGAAGA 59.677 34.615 0.00 0.00 0.00 2.87
2483 2552 7.340743 TGGTTGAAGATGTTGAAGAAAGGTTTA 59.659 33.333 0.00 0.00 0.00 2.01
2527 2596 2.533916 TGCATTGGTTCATGGGCTTTA 58.466 42.857 0.00 0.00 0.00 1.85
2538 2607 1.979809 TGGGCTTTATGAGGGGAAGA 58.020 50.000 0.00 0.00 0.00 2.87
2640 2709 1.237285 ACTAGGTTGCTGCAAAGGCG 61.237 55.000 17.80 8.80 45.35 5.52
2651 2720 4.580167 TGCTGCAAAGGCGATAAAATAGAT 59.420 37.500 0.00 0.00 45.35 1.98
2693 2762 4.916041 TGACATGATCAGAAGAGGGTTT 57.084 40.909 0.00 0.00 31.91 3.27
2948 3017 2.757868 TGCACTTATTGGTGGTTATGGC 59.242 45.455 0.00 0.00 37.65 4.40
2990 3059 4.218417 GGTGCAATTGATGTCCTTAACACT 59.782 41.667 10.34 0.00 41.75 3.55
3000 3069 8.589701 TGATGTCCTTAACACTATGAAGTCTA 57.410 34.615 0.00 0.00 41.75 2.59
3216 3285 1.322538 GCAAATGCGATCCAGGGGTT 61.323 55.000 0.00 0.00 0.00 4.11
3276 3345 9.283768 TGTATGCCTATTGTAAATCTGGTAATG 57.716 33.333 0.00 0.00 0.00 1.90
3278 3347 7.801716 TGCCTATTGTAAATCTGGTAATGAC 57.198 36.000 0.00 0.00 0.00 3.06
3596 3666 0.907230 GAGAGACCACAGAGGCCCTT 60.907 60.000 0.00 0.00 43.14 3.95
3692 3762 1.661341 CTATCCAACAGCAGCAGGTC 58.339 55.000 0.00 0.00 0.00 3.85
3716 3786 8.066000 GTCGCGCTTAAAGTTTATTTATGGTAT 58.934 33.333 5.56 0.00 0.00 2.73
3887 3958 9.099454 GAGTTCCTTTTATAAATCGACAGTGAT 57.901 33.333 0.00 0.00 0.00 3.06
3986 4057 6.041182 TGTGTAGCTGAAAACACTCTACCTAA 59.959 38.462 16.35 0.00 44.99 2.69
4024 4096 9.555727 GTATAGCACCCAATAGTATTCTGAAAA 57.444 33.333 0.00 0.00 0.00 2.29
4074 4146 6.016024 TGTTCTCAAGCAGCACATCTTTTATT 60.016 34.615 0.00 0.00 0.00 1.40
4088 4160 6.660949 ACATCTTTTATTCCTTCCCTTGACAG 59.339 38.462 0.00 0.00 0.00 3.51
4134 4206 6.867662 GCATAAGCATTGACTTGTACCTAT 57.132 37.500 0.00 0.00 41.58 2.57
4153 4225 6.775708 ACCTATTTACACAGCCTAACTTTGA 58.224 36.000 0.00 0.00 30.25 2.69
4157 4229 5.957842 TTACACAGCCTAACTTTGATTGG 57.042 39.130 0.00 0.00 30.25 3.16
4255 4327 8.794335 AAGGTAATGATTTCTTCTCTTGTACC 57.206 34.615 0.00 0.00 0.00 3.34
4257 4329 7.182930 AGGTAATGATTTCTTCTCTTGTACCCT 59.817 37.037 0.00 0.00 0.00 4.34
4266 4338 6.186234 TCTTCTCTTGTACCCTTAGGACTAC 58.814 44.000 0.00 0.00 36.73 2.73
4343 4415 2.978978 TCCCTTTTCTGAGATGGACACA 59.021 45.455 2.12 0.00 0.00 3.72
4515 4588 9.199982 CTGCACAAAAATATCAAGTTCATTTCT 57.800 29.630 0.00 0.00 0.00 2.52
4638 4713 2.151202 TCATCTGCCCGTCTGTTTTTC 58.849 47.619 0.00 0.00 0.00 2.29
4660 4735 1.624173 ATTGGTTCATCCCCTCCCAT 58.376 50.000 0.00 0.00 34.77 4.00
4671 4746 4.100084 CTCCCATCCACGCTGCCA 62.100 66.667 0.00 0.00 0.00 4.92
4709 4784 1.560505 AAAACACATGCCTCATCCCC 58.439 50.000 0.00 0.00 0.00 4.81
4710 4785 0.706433 AAACACATGCCTCATCCCCT 59.294 50.000 0.00 0.00 0.00 4.79
4711 4786 1.595311 AACACATGCCTCATCCCCTA 58.405 50.000 0.00 0.00 0.00 3.53
4712 4787 1.595311 ACACATGCCTCATCCCCTAA 58.405 50.000 0.00 0.00 0.00 2.69
4713 4788 2.138542 ACACATGCCTCATCCCCTAAT 58.861 47.619 0.00 0.00 0.00 1.73
4714 4789 2.107204 ACACATGCCTCATCCCCTAATC 59.893 50.000 0.00 0.00 0.00 1.75
4715 4790 2.374504 CACATGCCTCATCCCCTAATCT 59.625 50.000 0.00 0.00 0.00 2.40
4716 4791 3.059097 ACATGCCTCATCCCCTAATCTT 58.941 45.455 0.00 0.00 0.00 2.40
4717 4792 3.073650 ACATGCCTCATCCCCTAATCTTC 59.926 47.826 0.00 0.00 0.00 2.87
4718 4793 3.066208 TGCCTCATCCCCTAATCTTCT 57.934 47.619 0.00 0.00 0.00 2.85
4719 4794 2.975489 TGCCTCATCCCCTAATCTTCTC 59.025 50.000 0.00 0.00 0.00 2.87
4787 4862 1.907739 CCACACCGATCCCTGACAT 59.092 57.895 0.00 0.00 0.00 3.06
4800 4875 0.459237 CTGACATGAGGAGCGTGACC 60.459 60.000 0.00 0.00 36.97 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 90 1.028330 CCAGATGACGCTGTGCCAAT 61.028 55.000 0.00 0.00 34.06 3.16
120 124 1.937359 CAGACGCACGATTTTGACAC 58.063 50.000 0.00 0.00 0.00 3.67
437 477 2.234661 TCAACTCTCCGTCAAGCATGAT 59.765 45.455 0.00 0.00 38.01 2.45
439 479 2.084610 TCAACTCTCCGTCAAGCATG 57.915 50.000 0.00 0.00 0.00 4.06
469 524 1.424403 CGGAACACGTTATCAGCACA 58.576 50.000 0.00 0.00 37.93 4.57
562 617 4.034163 TGTCATTTACTTTCGCGTGTTTCA 59.966 37.500 5.77 0.00 0.00 2.69
564 619 4.201832 TGTGTCATTTACTTTCGCGTGTTT 60.202 37.500 5.77 0.00 0.00 2.83
592 648 8.336235 TGATTAATAAAGTTGGTCTCCTCCATT 58.664 33.333 0.00 0.00 37.33 3.16
648 708 5.928656 ACCCCTAGTCCCTATATAAAGCAT 58.071 41.667 0.00 0.00 0.00 3.79
690 753 2.353579 CCATTTCCCCGCTTTACGTTAG 59.646 50.000 0.00 0.00 41.42 2.34
701 764 4.522975 GCCCCTCCCATTTCCCCG 62.523 72.222 0.00 0.00 0.00 5.73
781 849 1.375326 GGAACAGGACGGCTCCTTT 59.625 57.895 3.15 2.82 45.77 3.11
784 852 4.452733 CGGGAACAGGACGGCTCC 62.453 72.222 0.00 0.00 36.71 4.70
785 853 3.692406 ACGGGAACAGGACGGCTC 61.692 66.667 0.00 0.00 0.00 4.70
786 854 4.003788 CACGGGAACAGGACGGCT 62.004 66.667 0.00 0.00 0.00 5.52
788 856 2.874664 TTCCACGGGAACAGGACGG 61.875 63.158 1.68 0.00 36.71 4.79
789 857 2.738480 TTCCACGGGAACAGGACG 59.262 61.111 1.68 0.00 36.71 4.79
796 864 1.659022 TTGATAGGGTTCCACGGGAA 58.341 50.000 1.68 1.68 39.66 3.97
797 865 1.766496 GATTGATAGGGTTCCACGGGA 59.234 52.381 0.00 0.00 0.00 5.14
798 866 1.202770 GGATTGATAGGGTTCCACGGG 60.203 57.143 0.00 0.00 0.00 5.28
799 867 1.202770 GGGATTGATAGGGTTCCACGG 60.203 57.143 0.00 0.00 0.00 4.94
800 868 1.540363 CGGGATTGATAGGGTTCCACG 60.540 57.143 0.00 0.00 0.00 4.94
801 869 1.814248 GCGGGATTGATAGGGTTCCAC 60.814 57.143 0.00 0.00 0.00 4.02
802 870 0.472471 GCGGGATTGATAGGGTTCCA 59.528 55.000 0.00 0.00 0.00 3.53
803 871 0.250770 GGCGGGATTGATAGGGTTCC 60.251 60.000 0.00 0.00 0.00 3.62
804 872 0.602905 CGGCGGGATTGATAGGGTTC 60.603 60.000 0.00 0.00 0.00 3.62
805 873 1.450211 CGGCGGGATTGATAGGGTT 59.550 57.895 0.00 0.00 0.00 4.11
806 874 3.148084 CGGCGGGATTGATAGGGT 58.852 61.111 0.00 0.00 0.00 4.34
807 875 2.358737 GCGGCGGGATTGATAGGG 60.359 66.667 9.78 0.00 0.00 3.53
808 876 2.358737 GGCGGCGGGATTGATAGG 60.359 66.667 9.78 0.00 0.00 2.57
809 877 2.738521 CGGCGGCGGGATTGATAG 60.739 66.667 25.36 0.00 0.00 2.08
810 878 3.542676 ACGGCGGCGGGATTGATA 61.543 61.111 35.05 0.00 0.00 2.15
832 900 1.080705 GAAGGAGACACCGGACACG 60.081 63.158 9.46 0.00 44.74 4.49
833 901 1.080705 CGAAGGAGACACCGGACAC 60.081 63.158 9.46 0.00 44.74 3.67
834 902 1.228337 TCGAAGGAGACACCGGACA 60.228 57.895 9.46 0.00 44.74 4.02
835 903 1.212229 GTCGAAGGAGACACCGGAC 59.788 63.158 9.46 0.00 44.74 4.79
836 904 1.975407 GGTCGAAGGAGACACCGGA 60.975 63.158 9.46 0.00 44.74 5.14
837 905 1.977544 AGGTCGAAGGAGACACCGG 60.978 63.158 0.00 0.00 44.74 5.28
838 906 1.213013 CAGGTCGAAGGAGACACCG 59.787 63.158 0.00 0.00 44.74 4.94
839 907 1.079750 GCAGGTCGAAGGAGACACC 60.080 63.158 0.00 0.00 42.62 4.16
840 908 1.444553 CGCAGGTCGAAGGAGACAC 60.445 63.158 0.00 0.00 42.62 3.67
841 909 2.962569 CGCAGGTCGAAGGAGACA 59.037 61.111 0.00 0.00 42.62 3.41
842 910 2.507324 GCGCAGGTCGAAGGAGAC 60.507 66.667 0.30 0.00 41.67 3.36
843 911 3.760035 GGCGCAGGTCGAAGGAGA 61.760 66.667 10.83 0.00 41.67 3.71
844 912 4.821589 GGGCGCAGGTCGAAGGAG 62.822 72.222 10.83 0.00 41.67 3.69
846 914 4.394712 AAGGGCGCAGGTCGAAGG 62.395 66.667 10.83 0.00 41.67 3.46
847 915 3.121030 CAAGGGCGCAGGTCGAAG 61.121 66.667 10.83 0.00 41.67 3.79
880 948 4.351054 AAGAAGGGGGCTGCACGG 62.351 66.667 0.50 0.00 0.00 4.94
881 949 3.058160 CAAGAAGGGGGCTGCACG 61.058 66.667 0.50 0.00 0.00 5.34
882 950 2.677875 CCAAGAAGGGGGCTGCAC 60.678 66.667 0.50 0.00 0.00 4.57
883 951 4.684134 GCCAAGAAGGGGGCTGCA 62.684 66.667 0.50 0.00 46.74 4.41
888 956 1.680314 GAAGCAGCCAAGAAGGGGG 60.680 63.158 0.00 0.00 38.09 5.40
889 957 2.042831 CGAAGCAGCCAAGAAGGGG 61.043 63.158 0.00 0.00 38.09 4.79
890 958 3.583383 CGAAGCAGCCAAGAAGGG 58.417 61.111 0.00 0.00 38.09 3.95
903 971 1.227497 GGGAGATCAGCCAGCGAAG 60.227 63.158 6.92 0.00 0.00 3.79
904 972 1.989508 TGGGAGATCAGCCAGCGAA 60.990 57.895 6.92 0.00 0.00 4.70
905 973 2.364186 TGGGAGATCAGCCAGCGA 60.364 61.111 6.92 0.00 0.00 4.93
906 974 2.202987 GTGGGAGATCAGCCAGCG 60.203 66.667 6.92 0.00 0.00 5.18
907 975 2.191641 GGTGGGAGATCAGCCAGC 59.808 66.667 6.92 0.00 0.00 4.85
911 979 0.620556 TCAAAGGGTGGGAGATCAGC 59.379 55.000 0.00 0.00 34.70 4.26
912 980 2.158696 GGATCAAAGGGTGGGAGATCAG 60.159 54.545 0.00 0.00 37.44 2.90
913 981 1.846439 GGATCAAAGGGTGGGAGATCA 59.154 52.381 0.00 0.00 37.44 2.92
914 982 1.846439 TGGATCAAAGGGTGGGAGATC 59.154 52.381 0.00 0.00 35.52 2.75
915 983 1.985622 TGGATCAAAGGGTGGGAGAT 58.014 50.000 0.00 0.00 0.00 2.75
916 984 1.753903 TTGGATCAAAGGGTGGGAGA 58.246 50.000 0.00 0.00 0.00 3.71
917 985 2.243221 AGATTGGATCAAAGGGTGGGAG 59.757 50.000 0.00 0.00 0.00 4.30
918 986 2.287584 AGATTGGATCAAAGGGTGGGA 58.712 47.619 0.00 0.00 0.00 4.37
919 987 2.762327 CAAGATTGGATCAAAGGGTGGG 59.238 50.000 0.00 0.00 0.00 4.61
933 1001 2.076863 GACGACCTTCCACCAAGATTG 58.923 52.381 0.00 0.00 33.29 2.67
934 1002 1.003233 GGACGACCTTCCACCAAGATT 59.997 52.381 0.00 0.00 35.49 2.40
935 1003 0.613777 GGACGACCTTCCACCAAGAT 59.386 55.000 0.00 0.00 35.49 2.40
936 1004 0.761323 TGGACGACCTTCCACCAAGA 60.761 55.000 5.33 0.00 41.00 3.02
937 1005 1.752198 TGGACGACCTTCCACCAAG 59.248 57.895 5.33 0.00 41.00 3.61
938 1006 3.973458 TGGACGACCTTCCACCAA 58.027 55.556 5.33 0.00 41.00 3.67
943 1011 1.141234 GACCGATGGACGACCTTCC 59.859 63.158 12.81 0.00 45.77 3.46
944 1012 1.141234 GGACCGATGGACGACCTTC 59.859 63.158 5.33 7.58 45.77 3.46
945 1013 2.356780 GGGACCGATGGACGACCTT 61.357 63.158 5.33 0.00 45.77 3.50
946 1014 2.758737 GGGACCGATGGACGACCT 60.759 66.667 5.33 0.00 45.77 3.85
947 1015 3.846430 GGGGACCGATGGACGACC 61.846 72.222 0.00 0.00 45.77 4.79
966 1034 2.690734 GGAGGGTGGGGATTGGGTC 61.691 68.421 0.00 0.00 0.00 4.46
967 1035 2.617215 GGAGGGTGGGGATTGGGT 60.617 66.667 0.00 0.00 0.00 4.51
968 1036 1.593166 AATGGAGGGTGGGGATTGGG 61.593 60.000 0.00 0.00 0.00 4.12
969 1037 0.106015 GAATGGAGGGTGGGGATTGG 60.106 60.000 0.00 0.00 0.00 3.16
970 1038 0.630673 TGAATGGAGGGTGGGGATTG 59.369 55.000 0.00 0.00 0.00 2.67
971 1039 1.392407 TTGAATGGAGGGTGGGGATT 58.608 50.000 0.00 0.00 0.00 3.01
972 1040 1.500736 GATTGAATGGAGGGTGGGGAT 59.499 52.381 0.00 0.00 0.00 3.85
973 1041 0.926293 GATTGAATGGAGGGTGGGGA 59.074 55.000 0.00 0.00 0.00 4.81
974 1042 0.929244 AGATTGAATGGAGGGTGGGG 59.071 55.000 0.00 0.00 0.00 4.96
975 1043 1.133668 GGAGATTGAATGGAGGGTGGG 60.134 57.143 0.00 0.00 0.00 4.61
976 1044 1.849039 AGGAGATTGAATGGAGGGTGG 59.151 52.381 0.00 0.00 0.00 4.61
977 1045 2.776536 AGAGGAGATTGAATGGAGGGTG 59.223 50.000 0.00 0.00 0.00 4.61
978 1046 3.142579 AGAGGAGATTGAATGGAGGGT 57.857 47.619 0.00 0.00 0.00 4.34
979 1047 5.839517 AATAGAGGAGATTGAATGGAGGG 57.160 43.478 0.00 0.00 0.00 4.30
980 1048 6.213195 AGCTAATAGAGGAGATTGAATGGAGG 59.787 42.308 0.00 0.00 0.00 4.30
981 1049 7.243604 AGCTAATAGAGGAGATTGAATGGAG 57.756 40.000 0.00 0.00 0.00 3.86
982 1050 7.512058 AGAAGCTAATAGAGGAGATTGAATGGA 59.488 37.037 0.00 0.00 0.00 3.41
983 1051 7.678837 AGAAGCTAATAGAGGAGATTGAATGG 58.321 38.462 0.00 0.00 0.00 3.16
984 1052 9.638239 GTAGAAGCTAATAGAGGAGATTGAATG 57.362 37.037 0.00 0.00 0.00 2.67
985 1053 8.811994 GGTAGAAGCTAATAGAGGAGATTGAAT 58.188 37.037 0.00 0.00 0.00 2.57
986 1054 7.040340 CGGTAGAAGCTAATAGAGGAGATTGAA 60.040 40.741 0.00 0.00 0.00 2.69
987 1055 6.431543 CGGTAGAAGCTAATAGAGGAGATTGA 59.568 42.308 0.00 0.00 0.00 2.57
988 1056 6.616947 CGGTAGAAGCTAATAGAGGAGATTG 58.383 44.000 0.00 0.00 0.00 2.67
989 1057 5.184287 GCGGTAGAAGCTAATAGAGGAGATT 59.816 44.000 0.00 0.00 0.00 2.40
990 1058 4.703093 GCGGTAGAAGCTAATAGAGGAGAT 59.297 45.833 0.00 0.00 0.00 2.75
991 1059 4.073549 GCGGTAGAAGCTAATAGAGGAGA 58.926 47.826 0.00 0.00 0.00 3.71
992 1060 3.191791 GGCGGTAGAAGCTAATAGAGGAG 59.808 52.174 0.00 0.00 34.52 3.69
993 1061 3.155501 GGCGGTAGAAGCTAATAGAGGA 58.844 50.000 0.00 0.00 34.52 3.71
994 1062 2.231721 GGGCGGTAGAAGCTAATAGAGG 59.768 54.545 0.00 0.00 34.52 3.69
995 1063 3.158676 AGGGCGGTAGAAGCTAATAGAG 58.841 50.000 0.00 0.00 34.52 2.43
996 1064 3.155501 GAGGGCGGTAGAAGCTAATAGA 58.844 50.000 0.00 0.00 34.52 1.98
997 1065 2.891580 TGAGGGCGGTAGAAGCTAATAG 59.108 50.000 0.00 0.00 34.52 1.73
998 1066 2.953453 TGAGGGCGGTAGAAGCTAATA 58.047 47.619 0.00 0.00 34.52 0.98
999 1067 1.789523 TGAGGGCGGTAGAAGCTAAT 58.210 50.000 0.00 0.00 34.52 1.73
1000 1068 1.206371 GTTGAGGGCGGTAGAAGCTAA 59.794 52.381 0.00 0.00 34.52 3.09
1001 1069 0.822164 GTTGAGGGCGGTAGAAGCTA 59.178 55.000 0.00 0.00 34.52 3.32
1002 1070 1.597461 GTTGAGGGCGGTAGAAGCT 59.403 57.895 0.00 0.00 34.52 3.74
1003 1071 1.449778 GGTTGAGGGCGGTAGAAGC 60.450 63.158 0.00 0.00 0.00 3.86
1004 1072 1.153628 CGGTTGAGGGCGGTAGAAG 60.154 63.158 0.00 0.00 0.00 2.85
1005 1073 1.474332 AACGGTTGAGGGCGGTAGAA 61.474 55.000 0.00 0.00 0.00 2.10
1006 1074 1.880819 GAACGGTTGAGGGCGGTAGA 61.881 60.000 0.00 0.00 0.00 2.59
1007 1075 1.447314 GAACGGTTGAGGGCGGTAG 60.447 63.158 0.00 0.00 0.00 3.18
1008 1076 2.658422 GAACGGTTGAGGGCGGTA 59.342 61.111 0.00 0.00 0.00 4.02
1009 1077 4.324991 GGAACGGTTGAGGGCGGT 62.325 66.667 0.00 0.00 0.00 5.68
1010 1078 4.323477 TGGAACGGTTGAGGGCGG 62.323 66.667 0.00 0.00 0.00 6.13
1011 1079 3.047877 GTGGAACGGTTGAGGGCG 61.048 66.667 0.00 0.00 0.00 6.13
1012 1080 1.303317 ATGTGGAACGGTTGAGGGC 60.303 57.895 0.00 0.00 42.39 5.19
1013 1081 1.019278 CGATGTGGAACGGTTGAGGG 61.019 60.000 0.00 0.00 42.39 4.30
1014 1082 1.635663 GCGATGTGGAACGGTTGAGG 61.636 60.000 0.00 0.00 42.39 3.86
1015 1083 0.948623 TGCGATGTGGAACGGTTGAG 60.949 55.000 0.00 0.00 42.39 3.02
1016 1084 1.069935 TGCGATGTGGAACGGTTGA 59.930 52.632 0.00 0.00 42.39 3.18
1017 1085 1.206578 GTGCGATGTGGAACGGTTG 59.793 57.895 0.00 0.00 42.39 3.77
1018 1086 0.605319 ATGTGCGATGTGGAACGGTT 60.605 50.000 0.00 0.00 42.39 4.44
1019 1087 1.003839 ATGTGCGATGTGGAACGGT 60.004 52.632 0.00 0.00 42.39 4.83
1020 1088 1.705337 GGATGTGCGATGTGGAACGG 61.705 60.000 0.00 0.00 42.39 4.44
1021 1089 1.018752 TGGATGTGCGATGTGGAACG 61.019 55.000 0.00 0.00 42.39 3.95
1022 1090 1.331756 GATGGATGTGCGATGTGGAAC 59.668 52.381 0.00 0.00 37.35 3.62
1023 1091 1.667236 GATGGATGTGCGATGTGGAA 58.333 50.000 0.00 0.00 0.00 3.53
1024 1092 0.179048 GGATGGATGTGCGATGTGGA 60.179 55.000 0.00 0.00 0.00 4.02
1025 1093 1.501337 CGGATGGATGTGCGATGTGG 61.501 60.000 0.00 0.00 34.67 4.17
1026 1094 1.936658 CGGATGGATGTGCGATGTG 59.063 57.895 0.00 0.00 34.67 3.21
1027 1095 1.889105 GCGGATGGATGTGCGATGT 60.889 57.895 0.00 0.00 34.67 3.06
1028 1096 2.610694 GGCGGATGGATGTGCGATG 61.611 63.158 0.00 0.00 34.67 3.84
1029 1097 2.281070 GGCGGATGGATGTGCGAT 60.281 61.111 0.00 0.00 34.67 4.58
1030 1098 3.105686 ATGGCGGATGGATGTGCGA 62.106 57.895 0.00 0.00 34.67 5.10
1031 1099 2.592574 ATGGCGGATGGATGTGCG 60.593 61.111 0.00 0.00 35.93 5.34
1032 1100 1.102809 TTCATGGCGGATGGATGTGC 61.103 55.000 0.00 0.00 32.26 4.57
1033 1101 1.066002 GTTTCATGGCGGATGGATGTG 59.934 52.381 0.00 0.00 32.26 3.21
1034 1102 1.392589 GTTTCATGGCGGATGGATGT 58.607 50.000 0.00 0.00 32.26 3.06
1035 1103 0.670162 GGTTTCATGGCGGATGGATG 59.330 55.000 0.00 0.00 32.26 3.51
1036 1104 0.258484 TGGTTTCATGGCGGATGGAT 59.742 50.000 0.00 0.00 32.26 3.41
1037 1105 0.679640 GTGGTTTCATGGCGGATGGA 60.680 55.000 0.00 0.00 32.26 3.41
1038 1106 1.666209 GGTGGTTTCATGGCGGATGG 61.666 60.000 0.00 0.00 32.26 3.51
1039 1107 0.964860 TGGTGGTTTCATGGCGGATG 60.965 55.000 0.00 0.00 0.00 3.51
1040 1108 0.965363 GTGGTGGTTTCATGGCGGAT 60.965 55.000 0.00 0.00 0.00 4.18
1041 1109 1.602323 GTGGTGGTTTCATGGCGGA 60.602 57.895 0.00 0.00 0.00 5.54
1042 1110 2.635443 GGTGGTGGTTTCATGGCGG 61.635 63.158 0.00 0.00 0.00 6.13
1043 1111 2.635443 GGGTGGTGGTTTCATGGCG 61.635 63.158 0.00 0.00 0.00 5.69
1044 1112 2.282783 GGGGTGGTGGTTTCATGGC 61.283 63.158 0.00 0.00 0.00 4.40
1045 1113 1.154921 TGGGGTGGTGGTTTCATGG 59.845 57.895 0.00 0.00 0.00 3.66
1046 1114 1.184970 GGTGGGGTGGTGGTTTCATG 61.185 60.000 0.00 0.00 0.00 3.07
1047 1115 1.155155 GGTGGGGTGGTGGTTTCAT 59.845 57.895 0.00 0.00 0.00 2.57
1048 1116 2.317378 TGGTGGGGTGGTGGTTTCA 61.317 57.895 0.00 0.00 0.00 2.69
1049 1117 1.830847 GTGGTGGGGTGGTGGTTTC 60.831 63.158 0.00 0.00 0.00 2.78
1050 1118 2.280753 GTGGTGGGGTGGTGGTTT 59.719 61.111 0.00 0.00 0.00 3.27
1051 1119 3.828023 GGTGGTGGGGTGGTGGTT 61.828 66.667 0.00 0.00 0.00 3.67
1054 1122 3.966543 GAGGGTGGTGGGGTGGTG 61.967 72.222 0.00 0.00 0.00 4.17
1055 1123 4.202030 AGAGGGTGGTGGGGTGGT 62.202 66.667 0.00 0.00 0.00 4.16
1056 1124 3.330720 GAGAGGGTGGTGGGGTGG 61.331 72.222 0.00 0.00 0.00 4.61
1057 1125 3.330720 GGAGAGGGTGGTGGGGTG 61.331 72.222 0.00 0.00 0.00 4.61
1058 1126 3.542602 AGGAGAGGGTGGTGGGGT 61.543 66.667 0.00 0.00 0.00 4.95
1059 1127 2.689034 GAGGAGAGGGTGGTGGGG 60.689 72.222 0.00 0.00 0.00 4.96
1060 1128 2.689034 GGAGGAGAGGGTGGTGGG 60.689 72.222 0.00 0.00 0.00 4.61
1061 1129 1.687493 GAGGAGGAGAGGGTGGTGG 60.687 68.421 0.00 0.00 0.00 4.61
1062 1130 2.055042 CGAGGAGGAGAGGGTGGTG 61.055 68.421 0.00 0.00 0.00 4.17
1063 1131 2.360980 CGAGGAGGAGAGGGTGGT 59.639 66.667 0.00 0.00 0.00 4.16
1064 1132 3.151022 GCGAGGAGGAGAGGGTGG 61.151 72.222 0.00 0.00 0.00 4.61
1065 1133 3.151022 GGCGAGGAGGAGAGGGTG 61.151 72.222 0.00 0.00 0.00 4.61
1066 1134 2.937959 GATGGCGAGGAGGAGAGGGT 62.938 65.000 0.00 0.00 0.00 4.34
1067 1135 2.123077 ATGGCGAGGAGGAGAGGG 60.123 66.667 0.00 0.00 0.00 4.30
1068 1136 2.206536 GGATGGCGAGGAGGAGAGG 61.207 68.421 0.00 0.00 0.00 3.69
1069 1137 2.560119 CGGATGGCGAGGAGGAGAG 61.560 68.421 0.00 0.00 0.00 3.20
1070 1138 2.519541 CGGATGGCGAGGAGGAGA 60.520 66.667 0.00 0.00 0.00 3.71
1071 1139 4.292178 GCGGATGGCGAGGAGGAG 62.292 72.222 0.00 0.00 0.00 3.69
1074 1142 4.899239 GTGGCGGATGGCGAGGAG 62.899 72.222 0.00 0.00 44.92 3.69
1196 1264 3.112709 GACGCGTCAGGTGAAGGC 61.113 66.667 33.09 2.59 0.00 4.35
1366 1434 4.736896 GGAGGTCGTGGTCGTGGC 62.737 72.222 0.00 0.00 38.33 5.01
1465 1533 1.685765 TGGTGATGTAGGAGGCGCT 60.686 57.895 7.64 0.00 0.00 5.92
1528 1596 3.669251 GGAGTAAATCCGATGAGGGAG 57.331 52.381 0.00 0.00 40.02 4.30
1804 1873 2.028112 TCTGCAAGCATCTTAAGACCGT 60.028 45.455 7.48 0.00 0.00 4.83
1926 1995 4.029520 CTCTCTTCCATCCTCTCCTTCAA 58.970 47.826 0.00 0.00 0.00 2.69
1973 2042 4.159135 AGACCATTGATCAGAATGCCAAAC 59.841 41.667 0.00 0.00 33.54 2.93
2110 2179 0.700564 TGCTTCTGAGAAATGCCCCT 59.299 50.000 4.29 0.00 0.00 4.79
2154 2223 3.190118 GCTGTTGACTTCATCTCCTTTGG 59.810 47.826 0.00 0.00 0.00 3.28
2197 2266 3.389329 CCCTTCCTTGCATAGAGCTCTAA 59.611 47.826 26.62 11.73 45.94 2.10
2238 2307 6.763610 GTCGAAAACATCTCCTCCAATATCTT 59.236 38.462 0.00 0.00 0.00 2.40
2258 2327 2.531771 TGAACTACCATCCCAGTCGAA 58.468 47.619 0.00 0.00 0.00 3.71
2262 2331 4.202673 ACCAAAATGAACTACCATCCCAGT 60.203 41.667 0.00 0.00 0.00 4.00
2431 2500 2.223805 CCAACTGCTTCTTGGTGTTTCC 60.224 50.000 0.00 0.00 34.50 3.13
2432 2501 2.687935 TCCAACTGCTTCTTGGTGTTTC 59.312 45.455 7.29 0.00 39.48 2.78
2466 2535 8.463930 TTGACAGATAAACCTTTCTTCAACAT 57.536 30.769 0.00 0.00 0.00 2.71
2475 2544 8.806146 AGTTGCAATATTGACAGATAAACCTTT 58.194 29.630 19.73 0.00 0.00 3.11
2483 2552 8.133627 GCATTAGAAGTTGCAATATTGACAGAT 58.866 33.333 19.73 6.41 38.72 2.90
2514 2583 2.091885 TCCCCTCATAAAGCCCATGAAC 60.092 50.000 0.00 0.00 32.20 3.18
2527 2596 2.243221 CCTTCCATGTTCTTCCCCTCAT 59.757 50.000 0.00 0.00 0.00 2.90
2538 2607 2.503356 CCTCAGTAGCTCCTTCCATGTT 59.497 50.000 0.00 0.00 0.00 2.71
2651 2720 5.000591 TCATCACGGAGTTTAATTGCTTCA 58.999 37.500 0.00 0.00 41.61 3.02
2948 3017 4.320494 GCACCAGAAATGTTACCAACTCTG 60.320 45.833 0.00 0.00 35.03 3.35
2990 3059 5.897250 TGGTCTTATGCCAGTAGACTTCATA 59.103 40.000 8.37 0.00 38.62 2.15
3000 3069 5.179452 ACATTAGTTGGTCTTATGCCAGT 57.821 39.130 0.00 0.00 36.87 4.00
3206 3275 2.068831 TTGGAGGTAAACCCCTGGAT 57.931 50.000 0.00 0.00 34.03 3.41
3276 3345 0.036858 AGCTTGGAGGCTTCTTCGTC 60.037 55.000 0.00 0.00 39.86 4.20
3692 3762 8.678510 CAATACCATAAATAAACTTTAAGCGCG 58.321 33.333 0.00 0.00 0.00 6.86
4062 4134 6.434028 TGTCAAGGGAAGGAATAAAAGATGTG 59.566 38.462 0.00 0.00 0.00 3.21
4074 4146 1.814429 TTCCACTGTCAAGGGAAGGA 58.186 50.000 1.63 0.00 35.84 3.36
4088 4160 8.676454 TGCATAACGTGTTATTATTTTTCCAC 57.324 30.769 2.56 0.00 33.79 4.02
4133 4205 6.572314 GCCAATCAAAGTTAGGCTGTGTAAAT 60.572 38.462 0.00 0.00 42.01 1.40
4134 4206 5.278758 GCCAATCAAAGTTAGGCTGTGTAAA 60.279 40.000 0.00 0.00 42.01 2.01
4153 4225 2.964464 TCAAGGTGTTGTCATTGCCAAT 59.036 40.909 0.00 0.00 34.98 3.16
4157 4229 2.733026 GCAATCAAGGTGTTGTCATTGC 59.267 45.455 8.09 8.09 36.77 3.56
4255 4327 5.160607 TGTGTTCAATGGTAGTCCTAAGG 57.839 43.478 0.00 0.00 34.23 2.69
4257 4329 9.747898 AATTAATGTGTTCAATGGTAGTCCTAA 57.252 29.630 0.00 0.00 34.23 2.69
4266 4338 6.070881 TGGGGAAGAATTAATGTGTTCAATGG 60.071 38.462 0.00 0.00 0.00 3.16
4343 4415 9.487790 TTCAAACTTTCAATTTCAAACTCACTT 57.512 25.926 0.00 0.00 0.00 3.16
4515 4588 7.561021 TGCAGTGATGTAGTACAAAAGAAAA 57.439 32.000 7.16 0.00 0.00 2.29
4525 4598 7.611770 AGTACAGATTTTGCAGTGATGTAGTA 58.388 34.615 0.00 0.00 0.00 1.82
4526 4599 6.467677 AGTACAGATTTTGCAGTGATGTAGT 58.532 36.000 0.00 0.00 0.00 2.73
4527 4600 6.974932 AGTACAGATTTTGCAGTGATGTAG 57.025 37.500 0.00 0.00 0.00 2.74
4623 4698 3.254657 CCAATAAGAAAAACAGACGGGCA 59.745 43.478 0.00 0.00 0.00 5.36
4638 4713 2.513738 TGGGAGGGGATGAACCAATAAG 59.486 50.000 0.00 0.00 41.20 1.73
4660 4735 2.725811 TTTTTCATGGCAGCGTGGA 58.274 47.368 0.00 0.00 0.00 4.02
4694 4769 2.374504 AGATTAGGGGATGAGGCATGTG 59.625 50.000 0.00 0.00 0.00 3.21
4698 4773 2.975489 GAGAAGATTAGGGGATGAGGCA 59.025 50.000 0.00 0.00 0.00 4.75
4707 4782 5.538433 CCTAGAGAGTTGGAGAAGATTAGGG 59.462 48.000 0.00 0.00 0.00 3.53
4708 4783 5.538433 CCCTAGAGAGTTGGAGAAGATTAGG 59.462 48.000 0.00 0.00 0.00 2.69
4709 4784 6.133356 ACCCTAGAGAGTTGGAGAAGATTAG 58.867 44.000 0.00 0.00 0.00 1.73
4710 4785 6.093617 ACCCTAGAGAGTTGGAGAAGATTA 57.906 41.667 0.00 0.00 0.00 1.75
4711 4786 4.954089 ACCCTAGAGAGTTGGAGAAGATT 58.046 43.478 0.00 0.00 0.00 2.40
4712 4787 4.618378 ACCCTAGAGAGTTGGAGAAGAT 57.382 45.455 0.00 0.00 0.00 2.40
4713 4788 4.345854 GAACCCTAGAGAGTTGGAGAAGA 58.654 47.826 0.00 0.00 0.00 2.87
4714 4789 3.449377 GGAACCCTAGAGAGTTGGAGAAG 59.551 52.174 0.00 0.00 0.00 2.85
4715 4790 3.442076 GGAACCCTAGAGAGTTGGAGAA 58.558 50.000 0.00 0.00 0.00 2.87
4716 4791 3.103080 GGAACCCTAGAGAGTTGGAGA 57.897 52.381 0.00 0.00 0.00 3.71
4787 4862 1.899437 GAATGGGGTCACGCTCCTCA 61.899 60.000 0.00 0.00 38.99 3.86


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

AutoCloner maintained by Alex Coulton.