Multiple sequence alignment - TraesCS7A01G198600

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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 TraesCS7A01G198600 chr7A 100.000 2786 0 0 1 2786 159732126 159729341 0.000000e+00 5145.0
1 TraesCS7A01G198600 chr7A 96.622 740 19 4 1 740 732057555 732056822 0.000000e+00 1223.0
2 TraesCS7A01G198600 chr5B 97.436 741 16 3 1 740 551809725 551808987 0.000000e+00 1260.0
3 TraesCS7A01G198600 chr5B 96.501 743 21 3 1 743 590556164 590556901 0.000000e+00 1223.0
4 TraesCS7A01G198600 chr3B 97.031 741 21 1 1 741 768201824 768201085 0.000000e+00 1245.0
5 TraesCS7A01G198600 chr3B 93.103 58 4 0 845 902 175775301 175775358 4.940000e-13 86.1
6 TraesCS7A01G198600 chr7B 96.900 742 18 3 1 742 706158808 706159544 0.000000e+00 1238.0
7 TraesCS7A01G198600 chr7B 96.622 740 20 3 1 740 721101108 721100374 0.000000e+00 1223.0
8 TraesCS7A01G198600 chr7B 96.643 566 18 1 2077 2642 119312440 119313004 0.000000e+00 939.0
9 TraesCS7A01G198600 chr7B 85.653 697 79 11 976 1657 119287636 119288326 0.000000e+00 713.0
10 TraesCS7A01G198600 chr7B 93.539 356 22 1 1648 2003 119311935 119312289 1.900000e-146 529.0
11 TraesCS7A01G198600 chr7B 95.425 153 6 1 2634 2786 119316217 119316368 2.770000e-60 243.0
12 TraesCS7A01G198600 chr7B 94.483 145 8 0 1648 1792 119289177 119289321 1.000000e-54 224.0
13 TraesCS7A01G198600 chr7B 96.667 60 2 0 2001 2060 119312395 119312454 1.770000e-17 100.0
14 TraesCS7A01G198600 chr7B 83.562 73 12 0 829 901 6934063 6934135 4.980000e-08 69.4
15 TraesCS7A01G198600 chr6B 96.757 740 23 1 1 740 489488103 489487365 0.000000e+00 1232.0
16 TraesCS7A01G198600 chr6B 96.361 742 21 4 1 742 662219197 662219932 0.000000e+00 1216.0
17 TraesCS7A01G198600 chr4A 96.757 740 19 4 2 740 118993081 118993816 0.000000e+00 1229.0
18 TraesCS7A01G198600 chr7D 92.672 232 16 1 2385 2616 156830382 156830612 1.600000e-87 333.0
19 TraesCS7A01G198600 chr7D 95.000 180 9 0 2607 2786 156862388 156862567 1.630000e-72 283.0
20 TraesCS7A01G198600 chr6A 92.265 181 14 0 739 919 12221005 12220825 9.900000e-65 257.0
21 TraesCS7A01G198600 chr2B 87.931 58 7 0 845 902 526414203 526414146 4.980000e-08 69.4


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 TraesCS7A01G198600 chr7A 159729341 159732126 2785 True 5145.00 5145 100.0000 1 2786 1 chr7A.!!$R1 2785
1 TraesCS7A01G198600 chr7A 732056822 732057555 733 True 1223.00 1223 96.6220 1 740 1 chr7A.!!$R2 739
2 TraesCS7A01G198600 chr5B 551808987 551809725 738 True 1260.00 1260 97.4360 1 740 1 chr5B.!!$R1 739
3 TraesCS7A01G198600 chr5B 590556164 590556901 737 False 1223.00 1223 96.5010 1 743 1 chr5B.!!$F1 742
4 TraesCS7A01G198600 chr3B 768201085 768201824 739 True 1245.00 1245 97.0310 1 741 1 chr3B.!!$R1 740
5 TraesCS7A01G198600 chr7B 706158808 706159544 736 False 1238.00 1238 96.9000 1 742 1 chr7B.!!$F2 741
6 TraesCS7A01G198600 chr7B 721100374 721101108 734 True 1223.00 1223 96.6220 1 740 1 chr7B.!!$R1 739
7 TraesCS7A01G198600 chr7B 119287636 119289321 1685 False 468.50 713 90.0680 976 1792 2 chr7B.!!$F3 816
8 TraesCS7A01G198600 chr7B 119311935 119316368 4433 False 452.75 939 95.5685 1648 2786 4 chr7B.!!$F4 1138
9 TraesCS7A01G198600 chr6B 489487365 489488103 738 True 1232.00 1232 96.7570 1 740 1 chr6B.!!$R1 739
10 TraesCS7A01G198600 chr6B 662219197 662219932 735 False 1216.00 1216 96.3610 1 742 1 chr6B.!!$F1 741
11 TraesCS7A01G198600 chr4A 118993081 118993816 735 False 1229.00 1229 96.7570 2 740 1 chr4A.!!$F1 738


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
957 967 0.03467 AAATCTCCAGCAGCCACCTC 60.035 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2693 6914 0.388649 ACGCTTCAGCTTGGTAGACG 60.389 55.0 0.0 0.0 39.32 4.18 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.322816 GGCTTGCAGGAAGGATGTCA 60.323 55.000 0.00 0.00 31.56 3.58
90 91 2.744202 GTGTGCTCCAATCTTGATTCGT 59.256 45.455 0.00 0.00 0.00 3.85
274 275 2.038837 GCTACCGGCAACTTGGACC 61.039 63.158 0.00 0.00 41.35 4.46
518 519 2.675844 TGTTGATAATTGAACGCCGAGG 59.324 45.455 0.00 0.00 0.00 4.63
585 586 2.476519 GCCGTTTATTCGCCGAAATTGA 60.477 45.455 2.60 0.00 0.00 2.57
709 715 1.668751 GGCGATTTTTATGCGTCCTGA 59.331 47.619 0.00 0.00 0.00 3.86
710 716 2.286418 GGCGATTTTTATGCGTCCTGAG 60.286 50.000 0.00 0.00 0.00 3.35
711 717 2.286418 GCGATTTTTATGCGTCCTGAGG 60.286 50.000 0.00 0.00 0.00 3.86
712 718 2.287915 CGATTTTTATGCGTCCTGAGGG 59.712 50.000 0.00 0.00 0.00 4.30
713 719 2.122783 TTTTTATGCGTCCTGAGGGG 57.877 50.000 0.00 0.00 0.00 4.79
714 720 1.281419 TTTTATGCGTCCTGAGGGGA 58.719 50.000 0.00 0.00 42.77 4.81
743 753 1.453669 GGCTGGAGATGCCCTAAGG 59.546 63.158 0.00 0.00 44.32 2.69
760 770 2.587753 GCATTAGCCACCGCGCTA 60.588 61.111 5.56 0.00 40.39 4.26
761 771 2.882366 GCATTAGCCACCGCGCTAC 61.882 63.158 5.56 0.00 41.01 3.58
762 772 2.279252 ATTAGCCACCGCGCTACG 60.279 61.111 5.56 0.00 41.01 3.51
773 783 2.778679 CGCTACGCCTTCAGTTGC 59.221 61.111 0.00 0.00 37.08 4.17
780 790 2.998668 CGCCTTCAGTTGCGTTATAG 57.001 50.000 0.00 0.00 45.43 1.31
781 791 1.593006 CGCCTTCAGTTGCGTTATAGG 59.407 52.381 0.00 0.00 45.43 2.57
782 792 2.737359 CGCCTTCAGTTGCGTTATAGGA 60.737 50.000 0.00 0.00 45.43 2.94
783 793 3.467803 GCCTTCAGTTGCGTTATAGGAT 58.532 45.455 0.00 0.00 0.00 3.24
784 794 4.628074 GCCTTCAGTTGCGTTATAGGATA 58.372 43.478 0.00 0.00 0.00 2.59
785 795 5.238583 GCCTTCAGTTGCGTTATAGGATAT 58.761 41.667 0.00 0.00 0.00 1.63
786 796 6.395629 GCCTTCAGTTGCGTTATAGGATATA 58.604 40.000 0.00 0.00 0.00 0.86
787 797 6.310711 GCCTTCAGTTGCGTTATAGGATATAC 59.689 42.308 0.00 0.00 0.00 1.47
788 798 6.812160 CCTTCAGTTGCGTTATAGGATATACC 59.188 42.308 0.00 0.00 39.35 2.73
789 799 6.904463 TCAGTTGCGTTATAGGATATACCA 57.096 37.500 0.00 0.00 42.04 3.25
790 800 6.920817 TCAGTTGCGTTATAGGATATACCAG 58.079 40.000 0.00 0.00 42.04 4.00
791 801 6.492429 TCAGTTGCGTTATAGGATATACCAGT 59.508 38.462 0.00 0.00 42.04 4.00
792 802 7.666804 TCAGTTGCGTTATAGGATATACCAGTA 59.333 37.037 0.00 0.00 42.04 2.74
793 803 8.467598 CAGTTGCGTTATAGGATATACCAGTAT 58.532 37.037 0.00 0.00 42.04 2.12
794 804 9.690913 AGTTGCGTTATAGGATATACCAGTATA 57.309 33.333 0.19 0.19 42.04 1.47
797 807 9.910267 TGCGTTATAGGATATACCAGTATAAGA 57.090 33.333 1.81 0.00 42.04 2.10
806 816 9.668497 GGATATACCAGTATAAGAACCAAATCC 57.332 37.037 1.81 0.00 38.79 3.01
809 819 8.747538 ATACCAGTATAAGAACCAAATCCAAC 57.252 34.615 0.00 0.00 0.00 3.77
810 820 5.646360 ACCAGTATAAGAACCAAATCCAACG 59.354 40.000 0.00 0.00 0.00 4.10
811 821 5.065988 CCAGTATAAGAACCAAATCCAACGG 59.934 44.000 0.00 0.00 0.00 4.44
812 822 5.065988 CAGTATAAGAACCAAATCCAACGGG 59.934 44.000 0.00 0.00 0.00 5.28
826 836 4.939271 TCCAACGGGATTTTGAGAAAAAC 58.061 39.130 0.00 0.00 38.64 2.43
827 837 4.055360 CCAACGGGATTTTGAGAAAAACC 58.945 43.478 0.00 0.00 41.19 3.27
832 842 4.304110 GGGATTTTGAGAAAAACCGAACC 58.696 43.478 0.00 0.00 42.39 3.62
833 843 3.978855 GGATTTTGAGAAAAACCGAACCG 59.021 43.478 0.00 0.00 34.30 4.44
834 844 4.498513 GGATTTTGAGAAAAACCGAACCGT 60.499 41.667 0.00 0.00 34.30 4.83
835 845 4.437772 TTTTGAGAAAAACCGAACCGTT 57.562 36.364 0.00 0.00 0.00 4.44
836 846 3.678915 TTGAGAAAAACCGAACCGTTC 57.321 42.857 0.76 0.76 0.00 3.95
837 847 2.908916 TGAGAAAAACCGAACCGTTCT 58.091 42.857 9.55 0.00 0.00 3.01
838 848 2.610374 TGAGAAAAACCGAACCGTTCTG 59.390 45.455 9.55 5.49 0.00 3.02
839 849 2.610833 GAGAAAAACCGAACCGTTCTGT 59.389 45.455 9.55 6.13 0.00 3.41
840 850 3.011818 AGAAAAACCGAACCGTTCTGTT 58.988 40.909 13.52 13.52 38.50 3.16
841 851 3.064408 AGAAAAACCGAACCGTTCTGTTC 59.936 43.478 18.00 8.93 36.32 3.18
842 852 2.027003 AAACCGAACCGTTCTGTTCA 57.973 45.000 18.00 0.00 43.84 3.18
843 853 2.249844 AACCGAACCGTTCTGTTCAT 57.750 45.000 13.52 0.00 43.84 2.57
844 854 2.249844 ACCGAACCGTTCTGTTCATT 57.750 45.000 9.55 0.00 43.84 2.57
845 855 2.567985 ACCGAACCGTTCTGTTCATTT 58.432 42.857 9.55 0.00 43.84 2.32
846 856 3.731089 ACCGAACCGTTCTGTTCATTTA 58.269 40.909 9.55 0.00 43.84 1.40
847 857 4.320870 ACCGAACCGTTCTGTTCATTTAT 58.679 39.130 9.55 0.00 43.84 1.40
848 858 4.153475 ACCGAACCGTTCTGTTCATTTATG 59.847 41.667 9.55 0.00 43.84 1.90
849 859 4.436852 CCGAACCGTTCTGTTCATTTATGG 60.437 45.833 9.55 0.00 43.84 2.74
850 860 4.436852 CGAACCGTTCTGTTCATTTATGGG 60.437 45.833 9.55 0.00 43.84 4.00
851 861 4.028993 ACCGTTCTGTTCATTTATGGGT 57.971 40.909 0.00 0.00 0.00 4.51
852 862 3.756434 ACCGTTCTGTTCATTTATGGGTG 59.244 43.478 0.00 0.00 0.00 4.61
853 863 4.006989 CCGTTCTGTTCATTTATGGGTGA 58.993 43.478 0.00 0.00 0.00 4.02
854 864 4.640201 CCGTTCTGTTCATTTATGGGTGAT 59.360 41.667 0.00 0.00 0.00 3.06
855 865 5.820423 CCGTTCTGTTCATTTATGGGTGATA 59.180 40.000 0.00 0.00 0.00 2.15
856 866 6.486657 CCGTTCTGTTCATTTATGGGTGATAT 59.513 38.462 0.00 0.00 0.00 1.63
857 867 7.355017 CGTTCTGTTCATTTATGGGTGATATG 58.645 38.462 0.00 0.00 0.00 1.78
858 868 7.520453 CGTTCTGTTCATTTATGGGTGATATGG 60.520 40.741 0.00 0.00 0.00 2.74
859 869 6.910191 TCTGTTCATTTATGGGTGATATGGT 58.090 36.000 0.00 0.00 0.00 3.55
860 870 6.772233 TCTGTTCATTTATGGGTGATATGGTG 59.228 38.462 0.00 0.00 0.00 4.17
861 871 6.667661 TGTTCATTTATGGGTGATATGGTGA 58.332 36.000 0.00 0.00 0.00 4.02
862 872 6.772233 TGTTCATTTATGGGTGATATGGTGAG 59.228 38.462 0.00 0.00 0.00 3.51
863 873 6.514012 TCATTTATGGGTGATATGGTGAGT 57.486 37.500 0.00 0.00 0.00 3.41
864 874 7.625498 TCATTTATGGGTGATATGGTGAGTA 57.375 36.000 0.00 0.00 0.00 2.59
865 875 8.040002 TCATTTATGGGTGATATGGTGAGTAA 57.960 34.615 0.00 0.00 0.00 2.24
866 876 8.668653 TCATTTATGGGTGATATGGTGAGTAAT 58.331 33.333 0.00 0.00 0.00 1.89
867 877 9.300681 CATTTATGGGTGATATGGTGAGTAATT 57.699 33.333 0.00 0.00 0.00 1.40
868 878 9.881773 ATTTATGGGTGATATGGTGAGTAATTT 57.118 29.630 0.00 0.00 0.00 1.82
871 881 8.868522 ATGGGTGATATGGTGAGTAATTTATG 57.131 34.615 0.00 0.00 0.00 1.90
872 882 7.811282 TGGGTGATATGGTGAGTAATTTATGT 58.189 34.615 0.00 0.00 0.00 2.29
873 883 7.936847 TGGGTGATATGGTGAGTAATTTATGTC 59.063 37.037 0.00 0.00 0.00 3.06
874 884 7.936847 GGGTGATATGGTGAGTAATTTATGTCA 59.063 37.037 0.00 0.00 0.00 3.58
875 885 9.337396 GGTGATATGGTGAGTAATTTATGTCAA 57.663 33.333 0.00 0.00 0.00 3.18
880 890 7.359262 TGGTGAGTAATTTATGTCAACTTCG 57.641 36.000 7.78 0.00 0.00 3.79
881 891 7.156000 TGGTGAGTAATTTATGTCAACTTCGA 58.844 34.615 7.78 0.00 0.00 3.71
882 892 7.330946 TGGTGAGTAATTTATGTCAACTTCGAG 59.669 37.037 7.78 0.00 0.00 4.04
883 893 7.201530 GGTGAGTAATTTATGTCAACTTCGAGG 60.202 40.741 0.00 0.00 0.00 4.63
884 894 6.816640 TGAGTAATTTATGTCAACTTCGAGGG 59.183 38.462 0.00 0.00 0.00 4.30
885 895 6.708285 AGTAATTTATGTCAACTTCGAGGGT 58.292 36.000 0.00 0.00 0.00 4.34
886 896 7.844009 AGTAATTTATGTCAACTTCGAGGGTA 58.156 34.615 0.00 0.00 0.00 3.69
887 897 8.316214 AGTAATTTATGTCAACTTCGAGGGTAA 58.684 33.333 0.00 0.00 0.00 2.85
888 898 9.106070 GTAATTTATGTCAACTTCGAGGGTAAT 57.894 33.333 0.00 0.00 0.00 1.89
889 899 8.575649 AATTTATGTCAACTTCGAGGGTAATT 57.424 30.769 0.00 0.00 0.00 1.40
890 900 7.989416 TTTATGTCAACTTCGAGGGTAATTT 57.011 32.000 0.00 0.00 0.00 1.82
891 901 7.989416 TTATGTCAACTTCGAGGGTAATTTT 57.011 32.000 0.00 0.00 0.00 1.82
892 902 9.504708 TTTATGTCAACTTCGAGGGTAATTTTA 57.495 29.630 0.00 0.00 0.00 1.52
893 903 7.989416 ATGTCAACTTCGAGGGTAATTTTAA 57.011 32.000 0.00 0.00 0.00 1.52
894 904 7.989416 TGTCAACTTCGAGGGTAATTTTAAT 57.011 32.000 0.00 0.00 0.00 1.40
895 905 7.812648 TGTCAACTTCGAGGGTAATTTTAATG 58.187 34.615 0.00 0.00 0.00 1.90
896 906 7.662258 TGTCAACTTCGAGGGTAATTTTAATGA 59.338 33.333 0.00 0.00 0.00 2.57
897 907 7.961283 GTCAACTTCGAGGGTAATTTTAATGAC 59.039 37.037 0.00 1.73 0.00 3.06
898 908 6.657836 ACTTCGAGGGTAATTTTAATGACG 57.342 37.500 0.00 0.00 0.00 4.35
899 909 6.168389 ACTTCGAGGGTAATTTTAATGACGT 58.832 36.000 0.00 0.00 0.00 4.34
900 910 7.322664 ACTTCGAGGGTAATTTTAATGACGTA 58.677 34.615 0.00 0.00 0.00 3.57
901 911 7.276438 ACTTCGAGGGTAATTTTAATGACGTAC 59.724 37.037 0.00 0.00 0.00 3.67
902 912 6.629128 TCGAGGGTAATTTTAATGACGTACA 58.371 36.000 0.00 0.00 0.00 2.90
903 913 7.095910 TCGAGGGTAATTTTAATGACGTACAA 58.904 34.615 0.00 0.00 0.00 2.41
904 914 7.063308 TCGAGGGTAATTTTAATGACGTACAAC 59.937 37.037 0.00 0.00 0.00 3.32
905 915 7.381766 AGGGTAATTTTAATGACGTACAACC 57.618 36.000 0.00 0.00 0.00 3.77
906 916 6.941436 AGGGTAATTTTAATGACGTACAACCA 59.059 34.615 0.00 0.00 0.00 3.67
907 917 7.120138 AGGGTAATTTTAATGACGTACAACCAG 59.880 37.037 0.00 0.00 0.00 4.00
908 918 7.119553 GGGTAATTTTAATGACGTACAACCAGA 59.880 37.037 0.00 0.00 0.00 3.86
909 919 8.505625 GGTAATTTTAATGACGTACAACCAGAA 58.494 33.333 0.00 0.00 0.00 3.02
910 920 9.537848 GTAATTTTAATGACGTACAACCAGAAG 57.462 33.333 0.00 0.00 0.00 2.85
911 921 5.600908 TTTAATGACGTACAACCAGAAGC 57.399 39.130 0.00 0.00 0.00 3.86
912 922 2.831685 ATGACGTACAACCAGAAGCA 57.168 45.000 0.00 0.00 0.00 3.91
913 923 1.860676 TGACGTACAACCAGAAGCAC 58.139 50.000 0.00 0.00 0.00 4.40
914 924 1.411246 TGACGTACAACCAGAAGCACT 59.589 47.619 0.00 0.00 0.00 4.40
915 925 2.624364 TGACGTACAACCAGAAGCACTA 59.376 45.455 0.00 0.00 0.00 2.74
916 926 3.243336 GACGTACAACCAGAAGCACTAG 58.757 50.000 0.00 0.00 0.00 2.57
917 927 2.626743 ACGTACAACCAGAAGCACTAGT 59.373 45.455 0.00 0.00 0.00 2.57
918 928 3.243336 CGTACAACCAGAAGCACTAGTC 58.757 50.000 0.00 0.00 0.00 2.59
919 929 3.305131 CGTACAACCAGAAGCACTAGTCA 60.305 47.826 0.00 0.00 0.00 3.41
920 930 3.838244 ACAACCAGAAGCACTAGTCAA 57.162 42.857 0.00 0.00 0.00 3.18
921 931 4.150897 ACAACCAGAAGCACTAGTCAAA 57.849 40.909 0.00 0.00 0.00 2.69
922 932 4.523083 ACAACCAGAAGCACTAGTCAAAA 58.477 39.130 0.00 0.00 0.00 2.44
923 933 5.133221 ACAACCAGAAGCACTAGTCAAAAT 58.867 37.500 0.00 0.00 0.00 1.82
924 934 5.594317 ACAACCAGAAGCACTAGTCAAAATT 59.406 36.000 0.00 0.00 0.00 1.82
925 935 6.770785 ACAACCAGAAGCACTAGTCAAAATTA 59.229 34.615 0.00 0.00 0.00 1.40
926 936 7.448469 ACAACCAGAAGCACTAGTCAAAATTAT 59.552 33.333 0.00 0.00 0.00 1.28
927 937 7.617041 ACCAGAAGCACTAGTCAAAATTATC 57.383 36.000 0.00 0.00 0.00 1.75
928 938 7.168219 ACCAGAAGCACTAGTCAAAATTATCA 58.832 34.615 0.00 0.00 0.00 2.15
929 939 7.665559 ACCAGAAGCACTAGTCAAAATTATCAA 59.334 33.333 0.00 0.00 0.00 2.57
930 940 8.514594 CCAGAAGCACTAGTCAAAATTATCAAA 58.485 33.333 0.00 0.00 0.00 2.69
935 945 9.143631 AGCACTAGTCAAAATTATCAAATTTGC 57.856 29.630 13.54 0.00 43.04 3.68
936 946 8.382875 GCACTAGTCAAAATTATCAAATTTGCC 58.617 33.333 13.54 0.00 43.04 4.52
937 947 8.872845 CACTAGTCAAAATTATCAAATTTGCCC 58.127 33.333 13.54 0.00 43.04 5.36
938 948 8.592809 ACTAGTCAAAATTATCAAATTTGCCCA 58.407 29.630 13.54 0.00 43.04 5.36
939 949 9.434420 CTAGTCAAAATTATCAAATTTGCCCAA 57.566 29.630 13.54 7.25 43.04 4.12
940 950 8.688747 AGTCAAAATTATCAAATTTGCCCAAA 57.311 26.923 13.54 5.27 43.04 3.28
941 951 9.299465 AGTCAAAATTATCAAATTTGCCCAAAT 57.701 25.926 13.54 4.11 43.04 2.32
942 952 9.558648 GTCAAAATTATCAAATTTGCCCAAATC 57.441 29.630 13.54 0.00 43.04 2.17
943 953 9.517868 TCAAAATTATCAAATTTGCCCAAATCT 57.482 25.926 13.54 0.00 43.04 2.40
944 954 9.777575 CAAAATTATCAAATTTGCCCAAATCTC 57.222 29.630 13.54 0.00 43.04 2.75
945 955 8.510243 AAATTATCAAATTTGCCCAAATCTCC 57.490 30.769 13.54 0.00 42.41 3.71
946 956 6.617782 TTATCAAATTTGCCCAAATCTCCA 57.382 33.333 13.54 0.00 39.88 3.86
947 957 4.540359 TCAAATTTGCCCAAATCTCCAG 57.460 40.909 13.54 0.00 39.88 3.86
948 958 3.004862 CAAATTTGCCCAAATCTCCAGC 58.995 45.455 5.01 0.00 39.88 4.85
949 959 1.941377 ATTTGCCCAAATCTCCAGCA 58.059 45.000 0.57 0.00 36.34 4.41
950 960 1.259609 TTTGCCCAAATCTCCAGCAG 58.740 50.000 0.00 0.00 34.45 4.24
951 961 1.252904 TTGCCCAAATCTCCAGCAGC 61.253 55.000 0.00 0.00 34.45 5.25
952 962 2.421399 GCCCAAATCTCCAGCAGCC 61.421 63.158 0.00 0.00 0.00 4.85
953 963 1.000521 CCCAAATCTCCAGCAGCCA 60.001 57.895 0.00 0.00 0.00 4.75
954 964 1.318158 CCCAAATCTCCAGCAGCCAC 61.318 60.000 0.00 0.00 0.00 5.01
955 965 1.318158 CCAAATCTCCAGCAGCCACC 61.318 60.000 0.00 0.00 0.00 4.61
956 966 0.323178 CAAATCTCCAGCAGCCACCT 60.323 55.000 0.00 0.00 0.00 4.00
957 967 0.034670 AAATCTCCAGCAGCCACCTC 60.035 55.000 0.00 0.00 0.00 3.85
958 968 1.919600 AATCTCCAGCAGCCACCTCC 61.920 60.000 0.00 0.00 0.00 4.30
959 969 4.106925 CTCCAGCAGCCACCTCCC 62.107 72.222 0.00 0.00 0.00 4.30
1007 1017 3.188786 GTGCGGCCAGATGACGAC 61.189 66.667 2.24 0.00 0.00 4.34
1034 1044 2.041265 AGGCCTGTCCCCCAGTAG 59.959 66.667 3.11 0.00 39.74 2.57
1037 1047 2.301738 GCCTGTCCCCCAGTAGCTT 61.302 63.158 0.00 0.00 39.74 3.74
1044 1054 0.974010 CCCCCAGTAGCTTGGTCGTA 60.974 60.000 3.76 0.00 36.45 3.43
1050 1064 3.055080 TAGCTTGGTCGTACCGGCG 62.055 63.158 0.00 0.00 42.58 6.46
1081 1095 2.380410 CCGTCCTTCTTTGCCGTCG 61.380 63.158 0.00 0.00 0.00 5.12
1082 1096 1.663702 CGTCCTTCTTTGCCGTCGT 60.664 57.895 0.00 0.00 0.00 4.34
1084 1098 0.599204 GTCCTTCTTTGCCGTCGTCA 60.599 55.000 0.00 0.00 0.00 4.35
1101 1115 2.022902 ATCGACGACAGCGCTACG 59.977 61.111 26.42 26.42 42.48 3.51
1103 1117 4.456253 CGACGACAGCGCTACGGT 62.456 66.667 29.48 19.66 42.48 4.83
1151 1171 2.125673 CGACACGGGTGGACATCC 60.126 66.667 0.00 0.00 34.19 3.51
1211 1231 0.887387 CGGCCCAAGTTCGAGGAAAA 60.887 55.000 0.00 0.00 0.00 2.29
1221 1241 1.741770 CGAGGAAAAGACCCCAGCG 60.742 63.158 0.00 0.00 0.00 5.18
1306 1329 3.785499 GAAACGGCGCTTCGGGTC 61.785 66.667 6.90 1.39 0.00 4.46
1309 1332 2.438951 AAACGGCGCTTCGGGTCTTA 62.439 55.000 6.90 0.00 0.00 2.10
1310 1333 2.125832 CGGCGCTTCGGGTCTTAA 60.126 61.111 7.64 0.00 0.00 1.85
1315 1347 1.593469 GCGCTTCGGGTCTTAAGATTC 59.407 52.381 8.75 4.47 0.00 2.52
1333 1365 4.509737 GGGTAGCTGGTCGCCGTC 62.510 72.222 0.00 0.00 40.39 4.79
1335 1367 3.450115 GTAGCTGGTCGCCGTCCT 61.450 66.667 0.00 0.00 40.39 3.85
1336 1368 3.138798 TAGCTGGTCGCCGTCCTC 61.139 66.667 0.00 0.00 40.39 3.71
1339 1371 3.129502 CTGGTCGCCGTCCTCGTA 61.130 66.667 1.46 0.00 35.01 3.43
1340 1372 3.392595 CTGGTCGCCGTCCTCGTAC 62.393 68.421 1.46 0.00 35.01 3.67
1341 1373 3.434319 GGTCGCCGTCCTCGTACA 61.434 66.667 0.00 0.00 35.01 2.90
1342 1374 2.099831 GTCGCCGTCCTCGTACAG 59.900 66.667 0.00 0.00 35.01 2.74
1343 1375 2.046988 TCGCCGTCCTCGTACAGA 60.047 61.111 0.00 0.00 35.01 3.41
1344 1376 2.099831 CGCCGTCCTCGTACAGAC 59.900 66.667 0.00 0.00 35.01 3.51
1345 1377 2.683859 CGCCGTCCTCGTACAGACA 61.684 63.158 8.04 0.00 33.08 3.41
1346 1378 1.154073 GCCGTCCTCGTACAGACAC 60.154 63.158 8.04 0.00 33.08 3.67
1347 1379 1.505353 CCGTCCTCGTACAGACACC 59.495 63.158 8.04 0.00 33.08 4.16
1348 1380 0.959372 CCGTCCTCGTACAGACACCT 60.959 60.000 8.04 0.00 33.08 4.00
1349 1381 0.447011 CGTCCTCGTACAGACACCTC 59.553 60.000 8.04 0.00 33.08 3.85
1353 1385 0.447011 CTCGTACAGACACCTCCGAC 59.553 60.000 0.00 0.00 0.00 4.79
1368 1400 0.878523 CCGACAAAGGTGCGTCTTCA 60.879 55.000 0.00 0.00 0.00 3.02
1415 1447 2.456119 CGGCCGTCACATCTGAAGC 61.456 63.158 19.50 0.00 0.00 3.86
1422 1454 0.745486 TCACATCTGAAGCCATGCCG 60.745 55.000 0.00 0.00 0.00 5.69
1454 1486 1.074872 CGGCGGAAACTAGTTCGTCC 61.075 60.000 8.95 12.09 37.08 4.79
1461 1493 2.719426 AACTAGTTCGTCCGTCCTTG 57.281 50.000 1.12 0.00 0.00 3.61
1462 1494 0.886563 ACTAGTTCGTCCGTCCTTGG 59.113 55.000 0.00 0.00 0.00 3.61
1485 1517 0.319641 GACCAGTTCGCTTCCTTCGT 60.320 55.000 0.00 0.00 0.00 3.85
1486 1518 0.600255 ACCAGTTCGCTTCCTTCGTG 60.600 55.000 0.00 0.00 0.00 4.35
1494 1526 1.351153 GCTTCCTTCGTGTCAGTAGC 58.649 55.000 0.00 0.00 0.00 3.58
1524 1556 1.721664 CCTCCATGGCTGTTGATGCG 61.722 60.000 6.96 0.00 0.00 4.73
1532 1564 0.730494 GCTGTTGATGCGTTGAAGGC 60.730 55.000 2.45 2.45 0.00 4.35
1536 1568 1.243342 TTGATGCGTTGAAGGCAGGG 61.243 55.000 17.74 0.00 42.60 4.45
1559 1591 1.270041 GGACCTGAAGATCGCCATCTC 60.270 57.143 0.00 0.00 38.55 2.75
1560 1592 1.410517 GACCTGAAGATCGCCATCTCA 59.589 52.381 0.00 0.00 38.55 3.27
1578 1610 3.133946 GAGGATCTCCCACTCGGC 58.866 66.667 0.00 0.00 37.41 5.54
1748 2640 1.102154 ACGCAGTCCAGAGATCTGAG 58.898 55.000 11.44 2.20 41.85 3.35
1761 2653 0.529337 ATCTGAGCCTGTCGATTGCG 60.529 55.000 0.00 0.00 39.35 4.85
1781 2673 2.165641 CGAGGGACACAGCTATGTTACA 59.834 50.000 0.00 0.00 37.65 2.41
1795 2687 5.334260 GCTATGTTACACTAGAGCTAGACCG 60.334 48.000 11.28 2.56 36.97 4.79
1798 2690 5.491070 TGTTACACTAGAGCTAGACCGTTA 58.509 41.667 11.28 0.00 36.97 3.18
1804 2696 4.756135 ACTAGAGCTAGACCGTTACATAGC 59.244 45.833 11.28 0.00 40.74 2.97
1830 2722 8.865001 CAACTACTGTAGCTTAGTCAAGAAATC 58.135 37.037 14.55 0.00 33.20 2.17
1877 2769 7.016153 TGTCTTGTACTGGATTTAGTGGATT 57.984 36.000 0.00 0.00 32.19 3.01
1934 2826 2.335316 ACTGCCTTCGGTGTTGTTTA 57.665 45.000 0.00 0.00 0.00 2.01
1962 2854 9.232082 CAAAGTTGTTTAATGTCGAATCTTCAA 57.768 29.630 0.00 0.00 0.00 2.69
1973 2865 5.050091 TGTCGAATCTTCAAAGTGCTCTTTC 60.050 40.000 10.72 0.00 41.31 2.62
1990 2882 5.637387 GCTCTTTCTTTGTGTTGTTGGAAAA 59.363 36.000 0.00 0.00 0.00 2.29
1994 2886 4.677584 TCTTTGTGTTGTTGGAAAATCCG 58.322 39.130 0.00 0.00 40.17 4.18
2035 3035 1.134280 TGGTGGGGTTTTTGTTGCATG 60.134 47.619 0.00 0.00 0.00 4.06
2057 3057 6.729690 TGGAATTCCAACAAGTTCTCATTT 57.270 33.333 25.13 0.00 44.35 2.32
2058 3058 7.123355 TGGAATTCCAACAAGTTCTCATTTT 57.877 32.000 25.13 0.00 44.35 1.82
2059 3059 7.209475 TGGAATTCCAACAAGTTCTCATTTTC 58.791 34.615 25.13 0.00 44.35 2.29
2060 3060 7.069826 TGGAATTCCAACAAGTTCTCATTTTCT 59.930 33.333 25.13 0.00 44.35 2.52
2061 3061 7.928167 GGAATTCCAACAAGTTCTCATTTTCTT 59.072 33.333 20.04 0.00 35.64 2.52
2062 3062 9.317936 GAATTCCAACAAGTTCTCATTTTCTTT 57.682 29.630 0.00 0.00 0.00 2.52
2063 3063 9.671279 AATTCCAACAAGTTCTCATTTTCTTTT 57.329 25.926 0.00 0.00 0.00 2.27
2064 3064 9.671279 ATTCCAACAAGTTCTCATTTTCTTTTT 57.329 25.926 0.00 0.00 0.00 1.94
2101 3101 9.305925 ACAAGTTCTCATTTTCAAATTCACTTC 57.694 29.630 0.00 0.00 0.00 3.01
2132 3132 6.524933 CGACAGAAGATCAGTAACTGTTACAG 59.475 42.308 27.12 21.05 41.01 2.74
2187 3187 3.564225 GGAGACTAATTGTTTATGGCCCG 59.436 47.826 0.00 0.00 0.00 6.13
2306 3306 6.307800 GTGTATGTGTATGTTGCCAAATTCAC 59.692 38.462 0.00 0.00 0.00 3.18
2344 3344 3.302350 GCTTCGCTCTCTGAAATGAATCG 60.302 47.826 0.00 0.00 0.00 3.34
2355 3355 6.566141 TCTGAAATGAATCGGTATAACGACA 58.434 36.000 16.46 10.55 46.64 4.35
2356 3356 7.036829 TCTGAAATGAATCGGTATAACGACAA 58.963 34.615 16.46 4.32 46.64 3.18
2357 3357 6.996106 TGAAATGAATCGGTATAACGACAAC 58.004 36.000 16.46 10.22 46.64 3.32
2359 3359 6.583912 AATGAATCGGTATAACGACAACTG 57.416 37.500 16.46 0.00 46.64 3.16
2435 3435 5.865085 TGGTATAGTAATGCACAATCCTCC 58.135 41.667 0.00 0.00 0.00 4.30
2439 3439 3.733337 AGTAATGCACAATCCTCCGATC 58.267 45.455 0.00 0.00 0.00 3.69
2479 3479 6.595326 TGTGAGTCTTTATTAGTGCTGATTGG 59.405 38.462 0.00 0.00 0.00 3.16
2517 3517 2.806608 ACTCAACCTTGCATTGCTTG 57.193 45.000 10.49 6.14 0.00 4.01
2550 3550 9.847224 GTAAATTCTGACCATTTTCCTCCTATA 57.153 33.333 0.00 0.00 0.00 1.31
2589 3589 4.762251 ACTATTCAGAGGGCAAGTTTGTTC 59.238 41.667 0.00 0.00 0.00 3.18
2634 3634 3.305964 CTGATGCTGTTTTGCTGACTTG 58.694 45.455 0.00 0.00 0.00 3.16
2658 6879 3.477210 AGTTCTGTTTCTGTCTGGGAC 57.523 47.619 0.00 0.00 0.00 4.46
2685 6906 0.614812 TTAGCCAGTCTCATGCAGCA 59.385 50.000 0.00 0.00 0.00 4.41
2703 6924 1.398390 GCAGCAATTCCGTCTACCAAG 59.602 52.381 0.00 0.00 0.00 3.61
2764 6985 2.294979 AGTTGACACCGGAAAAGGTTC 58.705 47.619 9.46 0.00 43.00 3.62
2767 6988 1.153127 ACACCGGAAAAGGTTCGCA 60.153 52.632 9.46 0.00 43.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.050339 CACACCAAATGCCCGCTT 58.950 55.556 0.00 0.00 0.00 4.68
518 519 4.364409 GACGTGGTTTCGCCGTGC 62.364 66.667 0.00 0.00 41.21 5.34
534 535 3.162666 ACGAGAATAGGCCCATATTCGA 58.837 45.455 19.04 0.00 43.79 3.71
585 586 1.123246 AATTGGCCCACTTTGCAGCT 61.123 50.000 0.00 0.00 0.00 4.24
687 689 1.021968 GGACGCATAAAAATCGCCCT 58.978 50.000 0.00 0.00 0.00 5.19
743 753 2.587753 TAGCGCGGTGGCTAATGC 60.588 61.111 23.02 0.00 42.26 3.56
744 754 2.585869 CGTAGCGCGGTGGCTAATG 61.586 63.158 23.02 1.36 46.31 1.90
745 755 2.279252 CGTAGCGCGGTGGCTAAT 60.279 61.111 23.02 0.00 46.31 1.73
762 772 2.901249 TCCTATAACGCAACTGAAGGC 58.099 47.619 0.00 0.00 0.00 4.35
763 773 6.812160 GGTATATCCTATAACGCAACTGAAGG 59.188 42.308 0.00 0.00 0.00 3.46
764 774 7.375834 TGGTATATCCTATAACGCAACTGAAG 58.624 38.462 0.00 0.00 37.07 3.02
765 775 7.014905 ACTGGTATATCCTATAACGCAACTGAA 59.985 37.037 0.00 0.00 37.07 3.02
766 776 6.492429 ACTGGTATATCCTATAACGCAACTGA 59.508 38.462 0.00 0.00 37.07 3.41
767 777 6.688578 ACTGGTATATCCTATAACGCAACTG 58.311 40.000 0.00 0.00 37.07 3.16
768 778 6.912951 ACTGGTATATCCTATAACGCAACT 57.087 37.500 0.00 0.00 37.07 3.16
771 781 9.910267 TCTTATACTGGTATATCCTATAACGCA 57.090 33.333 1.91 0.00 37.07 5.24
780 790 9.668497 GGATTTGGTTCTTATACTGGTATATCC 57.332 37.037 1.91 0.00 0.00 2.59
783 793 9.841295 GTTGGATTTGGTTCTTATACTGGTATA 57.159 33.333 0.00 0.00 0.00 1.47
784 794 7.497909 CGTTGGATTTGGTTCTTATACTGGTAT 59.502 37.037 0.00 0.00 0.00 2.73
785 795 6.819649 CGTTGGATTTGGTTCTTATACTGGTA 59.180 38.462 0.00 0.00 0.00 3.25
786 796 5.646360 CGTTGGATTTGGTTCTTATACTGGT 59.354 40.000 0.00 0.00 0.00 4.00
787 797 5.065988 CCGTTGGATTTGGTTCTTATACTGG 59.934 44.000 0.00 0.00 0.00 4.00
788 798 5.065988 CCCGTTGGATTTGGTTCTTATACTG 59.934 44.000 0.00 0.00 0.00 2.74
789 799 5.045432 TCCCGTTGGATTTGGTTCTTATACT 60.045 40.000 0.00 0.00 35.03 2.12
790 800 5.187687 TCCCGTTGGATTTGGTTCTTATAC 58.812 41.667 0.00 0.00 35.03 1.47
791 801 5.438698 TCCCGTTGGATTTGGTTCTTATA 57.561 39.130 0.00 0.00 35.03 0.98
792 802 4.310022 TCCCGTTGGATTTGGTTCTTAT 57.690 40.909 0.00 0.00 35.03 1.73
793 803 3.791953 TCCCGTTGGATTTGGTTCTTA 57.208 42.857 0.00 0.00 35.03 2.10
794 804 2.668144 TCCCGTTGGATTTGGTTCTT 57.332 45.000 0.00 0.00 35.03 2.52
805 815 4.055360 GGTTTTTCTCAAAATCCCGTTGG 58.945 43.478 0.00 0.00 35.25 3.77
806 816 3.733727 CGGTTTTTCTCAAAATCCCGTTG 59.266 43.478 10.15 0.00 38.94 4.10
807 817 3.633065 TCGGTTTTTCTCAAAATCCCGTT 59.367 39.130 14.78 0.00 41.79 4.44
808 818 3.215975 TCGGTTTTTCTCAAAATCCCGT 58.784 40.909 14.78 0.00 41.79 5.28
809 819 3.907894 TCGGTTTTTCTCAAAATCCCG 57.092 42.857 11.36 11.36 42.14 5.14
810 820 4.304110 GGTTCGGTTTTTCTCAAAATCCC 58.696 43.478 4.10 0.00 37.07 3.85
811 821 3.978855 CGGTTCGGTTTTTCTCAAAATCC 59.021 43.478 0.45 0.45 37.04 3.01
812 822 4.603985 ACGGTTCGGTTTTTCTCAAAATC 58.396 39.130 0.00 0.00 34.35 2.17
813 823 4.642445 ACGGTTCGGTTTTTCTCAAAAT 57.358 36.364 0.00 0.00 34.35 1.82
814 824 4.156373 AGAACGGTTCGGTTTTTCTCAAAA 59.844 37.500 14.70 0.00 34.02 2.44
815 825 3.690628 AGAACGGTTCGGTTTTTCTCAAA 59.309 39.130 14.70 0.00 34.02 2.69
816 826 3.064271 CAGAACGGTTCGGTTTTTCTCAA 59.936 43.478 14.70 0.00 34.02 3.02
817 827 2.610374 CAGAACGGTTCGGTTTTTCTCA 59.390 45.455 14.70 0.00 34.02 3.27
818 828 2.610833 ACAGAACGGTTCGGTTTTTCTC 59.389 45.455 18.81 0.00 34.38 2.87
819 829 2.635714 ACAGAACGGTTCGGTTTTTCT 58.364 42.857 18.81 0.00 34.38 2.52
820 830 3.357021 GAACAGAACGGTTCGGTTTTTC 58.643 45.455 30.33 19.38 45.72 2.29
821 831 3.409851 GAACAGAACGGTTCGGTTTTT 57.590 42.857 30.33 15.91 45.72 1.94
828 838 4.457949 ACCCATAAATGAACAGAACGGTTC 59.542 41.667 12.91 12.91 45.75 3.62
829 839 4.217550 CACCCATAAATGAACAGAACGGTT 59.782 41.667 0.00 0.00 0.00 4.44
830 840 3.756434 CACCCATAAATGAACAGAACGGT 59.244 43.478 0.00 0.00 0.00 4.83
831 841 4.006989 TCACCCATAAATGAACAGAACGG 58.993 43.478 0.00 0.00 0.00 4.44
832 842 5.818136 ATCACCCATAAATGAACAGAACG 57.182 39.130 0.00 0.00 0.00 3.95
833 843 7.285401 ACCATATCACCCATAAATGAACAGAAC 59.715 37.037 0.00 0.00 0.00 3.01
834 844 7.285172 CACCATATCACCCATAAATGAACAGAA 59.715 37.037 0.00 0.00 0.00 3.02
835 845 6.772233 CACCATATCACCCATAAATGAACAGA 59.228 38.462 0.00 0.00 0.00 3.41
836 846 6.772233 TCACCATATCACCCATAAATGAACAG 59.228 38.462 0.00 0.00 0.00 3.16
837 847 6.667661 TCACCATATCACCCATAAATGAACA 58.332 36.000 0.00 0.00 0.00 3.18
838 848 6.772716 ACTCACCATATCACCCATAAATGAAC 59.227 38.462 0.00 0.00 0.00 3.18
839 849 6.910191 ACTCACCATATCACCCATAAATGAA 58.090 36.000 0.00 0.00 0.00 2.57
840 850 6.514012 ACTCACCATATCACCCATAAATGA 57.486 37.500 0.00 0.00 0.00 2.57
841 851 8.868522 ATTACTCACCATATCACCCATAAATG 57.131 34.615 0.00 0.00 0.00 2.32
842 852 9.881773 AAATTACTCACCATATCACCCATAAAT 57.118 29.630 0.00 0.00 0.00 1.40
845 855 9.958180 CATAAATTACTCACCATATCACCCATA 57.042 33.333 0.00 0.00 0.00 2.74
846 856 8.448008 ACATAAATTACTCACCATATCACCCAT 58.552 33.333 0.00 0.00 0.00 4.00
847 857 7.811282 ACATAAATTACTCACCATATCACCCA 58.189 34.615 0.00 0.00 0.00 4.51
848 858 7.936847 TGACATAAATTACTCACCATATCACCC 59.063 37.037 0.00 0.00 0.00 4.61
849 859 8.902540 TGACATAAATTACTCACCATATCACC 57.097 34.615 0.00 0.00 0.00 4.02
854 864 9.093970 CGAAGTTGACATAAATTACTCACCATA 57.906 33.333 0.00 0.00 0.00 2.74
855 865 7.822334 TCGAAGTTGACATAAATTACTCACCAT 59.178 33.333 0.00 0.00 0.00 3.55
856 866 7.156000 TCGAAGTTGACATAAATTACTCACCA 58.844 34.615 0.00 0.00 0.00 4.17
857 867 7.201530 CCTCGAAGTTGACATAAATTACTCACC 60.202 40.741 0.00 0.00 0.00 4.02
858 868 7.201530 CCCTCGAAGTTGACATAAATTACTCAC 60.202 40.741 0.00 0.00 0.00 3.51
859 869 6.816640 CCCTCGAAGTTGACATAAATTACTCA 59.183 38.462 0.00 0.00 0.00 3.41
860 870 6.817140 ACCCTCGAAGTTGACATAAATTACTC 59.183 38.462 0.00 0.00 0.00 2.59
861 871 6.708285 ACCCTCGAAGTTGACATAAATTACT 58.292 36.000 0.00 0.00 0.00 2.24
862 872 6.980051 ACCCTCGAAGTTGACATAAATTAC 57.020 37.500 0.00 0.00 0.00 1.89
863 873 9.675464 AATTACCCTCGAAGTTGACATAAATTA 57.325 29.630 0.00 0.00 0.00 1.40
864 874 8.575649 AATTACCCTCGAAGTTGACATAAATT 57.424 30.769 0.00 0.00 0.00 1.82
865 875 8.575649 AAATTACCCTCGAAGTTGACATAAAT 57.424 30.769 0.00 0.00 0.00 1.40
866 876 7.989416 AAATTACCCTCGAAGTTGACATAAA 57.011 32.000 0.00 0.00 0.00 1.40
867 877 7.989416 AAAATTACCCTCGAAGTTGACATAA 57.011 32.000 0.00 0.00 0.00 1.90
868 878 9.675464 ATTAAAATTACCCTCGAAGTTGACATA 57.325 29.630 0.00 0.00 0.00 2.29
869 879 7.989416 TTAAAATTACCCTCGAAGTTGACAT 57.011 32.000 0.00 0.00 0.00 3.06
870 880 7.662258 TCATTAAAATTACCCTCGAAGTTGACA 59.338 33.333 0.00 0.00 0.00 3.58
871 881 7.961283 GTCATTAAAATTACCCTCGAAGTTGAC 59.039 37.037 0.00 0.00 0.00 3.18
872 882 7.148540 CGTCATTAAAATTACCCTCGAAGTTGA 60.149 37.037 0.00 0.00 0.00 3.18
873 883 6.959311 CGTCATTAAAATTACCCTCGAAGTTG 59.041 38.462 0.00 0.00 0.00 3.16
874 884 6.652062 ACGTCATTAAAATTACCCTCGAAGTT 59.348 34.615 0.00 0.00 0.00 2.66
875 885 6.168389 ACGTCATTAAAATTACCCTCGAAGT 58.832 36.000 0.00 0.00 0.00 3.01
876 886 6.657836 ACGTCATTAAAATTACCCTCGAAG 57.342 37.500 0.00 0.00 0.00 3.79
877 887 7.095910 TGTACGTCATTAAAATTACCCTCGAA 58.904 34.615 0.00 0.00 0.00 3.71
878 888 6.629128 TGTACGTCATTAAAATTACCCTCGA 58.371 36.000 0.00 0.00 0.00 4.04
879 889 6.890663 TGTACGTCATTAAAATTACCCTCG 57.109 37.500 0.00 0.00 0.00 4.63
880 890 7.119553 TGGTTGTACGTCATTAAAATTACCCTC 59.880 37.037 0.00 0.00 0.00 4.30
881 891 6.941436 TGGTTGTACGTCATTAAAATTACCCT 59.059 34.615 0.00 0.00 0.00 4.34
882 892 7.119553 TCTGGTTGTACGTCATTAAAATTACCC 59.880 37.037 0.00 0.00 0.00 3.69
883 893 8.031848 TCTGGTTGTACGTCATTAAAATTACC 57.968 34.615 0.00 0.00 0.00 2.85
884 894 9.537848 CTTCTGGTTGTACGTCATTAAAATTAC 57.462 33.333 0.00 0.00 0.00 1.89
885 895 8.231837 GCTTCTGGTTGTACGTCATTAAAATTA 58.768 33.333 0.00 0.00 0.00 1.40
886 896 7.081976 GCTTCTGGTTGTACGTCATTAAAATT 58.918 34.615 0.00 0.00 0.00 1.82
887 897 6.205853 TGCTTCTGGTTGTACGTCATTAAAAT 59.794 34.615 0.00 0.00 0.00 1.82
888 898 5.527951 TGCTTCTGGTTGTACGTCATTAAAA 59.472 36.000 0.00 0.00 0.00 1.52
889 899 5.049954 GTGCTTCTGGTTGTACGTCATTAAA 60.050 40.000 0.00 0.00 0.00 1.52
890 900 4.449743 GTGCTTCTGGTTGTACGTCATTAA 59.550 41.667 0.00 0.00 0.00 1.40
891 901 3.991773 GTGCTTCTGGTTGTACGTCATTA 59.008 43.478 0.00 0.00 0.00 1.90
892 902 2.806244 GTGCTTCTGGTTGTACGTCATT 59.194 45.455 0.00 0.00 0.00 2.57
893 903 2.037251 AGTGCTTCTGGTTGTACGTCAT 59.963 45.455 0.00 0.00 0.00 3.06
894 904 1.411246 AGTGCTTCTGGTTGTACGTCA 59.589 47.619 0.00 0.00 0.00 4.35
895 905 2.150397 AGTGCTTCTGGTTGTACGTC 57.850 50.000 0.00 0.00 0.00 4.34
896 906 2.626743 ACTAGTGCTTCTGGTTGTACGT 59.373 45.455 0.00 0.00 34.16 3.57
897 907 3.243336 GACTAGTGCTTCTGGTTGTACG 58.757 50.000 0.00 0.00 37.98 3.67
898 908 4.252971 TGACTAGTGCTTCTGGTTGTAC 57.747 45.455 0.00 0.00 37.98 2.90
899 909 4.948341 TTGACTAGTGCTTCTGGTTGTA 57.052 40.909 0.00 0.00 37.98 2.41
900 910 3.838244 TTGACTAGTGCTTCTGGTTGT 57.162 42.857 0.00 0.00 37.98 3.32
901 911 5.695851 ATTTTGACTAGTGCTTCTGGTTG 57.304 39.130 0.00 0.00 37.98 3.77
902 912 7.665559 TGATAATTTTGACTAGTGCTTCTGGTT 59.334 33.333 0.00 0.00 37.98 3.67
903 913 7.168219 TGATAATTTTGACTAGTGCTTCTGGT 58.832 34.615 0.00 0.00 40.54 4.00
904 914 7.615582 TGATAATTTTGACTAGTGCTTCTGG 57.384 36.000 0.00 0.00 0.00 3.86
909 919 9.143631 GCAAATTTGATAATTTTGACTAGTGCT 57.856 29.630 22.31 0.00 40.97 4.40
910 920 8.382875 GGCAAATTTGATAATTTTGACTAGTGC 58.617 33.333 22.31 0.00 40.97 4.40
911 921 8.872845 GGGCAAATTTGATAATTTTGACTAGTG 58.127 33.333 22.31 0.00 40.97 2.74
912 922 8.592809 TGGGCAAATTTGATAATTTTGACTAGT 58.407 29.630 22.31 0.00 40.97 2.57
913 923 9.434420 TTGGGCAAATTTGATAATTTTGACTAG 57.566 29.630 22.31 0.00 40.97 2.57
914 924 9.784531 TTTGGGCAAATTTGATAATTTTGACTA 57.215 25.926 22.31 5.98 40.97 2.59
915 925 8.688747 TTTGGGCAAATTTGATAATTTTGACT 57.311 26.923 22.31 0.00 40.97 3.41
916 926 9.558648 GATTTGGGCAAATTTGATAATTTTGAC 57.441 29.630 22.31 8.77 40.97 3.18
917 927 9.517868 AGATTTGGGCAAATTTGATAATTTTGA 57.482 25.926 22.31 0.00 40.97 2.69
918 928 9.777575 GAGATTTGGGCAAATTTGATAATTTTG 57.222 29.630 22.31 0.00 40.97 2.44
919 929 8.959548 GGAGATTTGGGCAAATTTGATAATTTT 58.040 29.630 22.31 5.14 40.97 1.82
920 930 8.108364 TGGAGATTTGGGCAAATTTGATAATTT 58.892 29.630 22.31 9.32 43.09 1.82
921 931 7.631933 TGGAGATTTGGGCAAATTTGATAATT 58.368 30.769 22.31 8.91 40.77 1.40
922 932 7.197901 TGGAGATTTGGGCAAATTTGATAAT 57.802 32.000 22.31 13.16 40.77 1.28
923 933 6.617782 TGGAGATTTGGGCAAATTTGATAA 57.382 33.333 22.31 9.76 40.77 1.75
924 934 5.395546 GCTGGAGATTTGGGCAAATTTGATA 60.396 40.000 22.31 4.00 40.77 2.15
925 935 4.624604 GCTGGAGATTTGGGCAAATTTGAT 60.625 41.667 22.31 5.70 40.77 2.57
926 936 3.306919 GCTGGAGATTTGGGCAAATTTGA 60.307 43.478 22.31 0.36 40.77 2.69
927 937 3.004862 GCTGGAGATTTGGGCAAATTTG 58.995 45.455 14.03 14.03 40.77 2.32
928 938 2.638855 TGCTGGAGATTTGGGCAAATTT 59.361 40.909 0.00 0.00 40.77 1.82
929 939 2.235402 CTGCTGGAGATTTGGGCAAATT 59.765 45.455 0.00 0.00 40.77 1.82
930 940 1.829222 CTGCTGGAGATTTGGGCAAAT 59.171 47.619 0.00 0.00 43.14 2.32
931 941 1.259609 CTGCTGGAGATTTGGGCAAA 58.740 50.000 0.00 0.00 32.43 3.68
932 942 1.252904 GCTGCTGGAGATTTGGGCAA 61.253 55.000 0.00 0.00 32.43 4.52
933 943 1.679977 GCTGCTGGAGATTTGGGCA 60.680 57.895 0.00 0.00 0.00 5.36
934 944 2.421399 GGCTGCTGGAGATTTGGGC 61.421 63.158 0.00 0.00 0.00 5.36
935 945 1.000521 TGGCTGCTGGAGATTTGGG 60.001 57.895 0.00 0.00 0.00 4.12
936 946 1.318158 GGTGGCTGCTGGAGATTTGG 61.318 60.000 0.00 0.00 0.00 3.28
937 947 0.323178 AGGTGGCTGCTGGAGATTTG 60.323 55.000 0.00 0.00 0.00 2.32
938 948 0.034670 GAGGTGGCTGCTGGAGATTT 60.035 55.000 0.00 0.00 0.00 2.17
939 949 1.606531 GAGGTGGCTGCTGGAGATT 59.393 57.895 0.00 0.00 0.00 2.40
940 950 2.373707 GGAGGTGGCTGCTGGAGAT 61.374 63.158 0.00 0.00 0.00 2.75
941 951 3.005539 GGAGGTGGCTGCTGGAGA 61.006 66.667 0.00 0.00 0.00 3.71
942 952 4.106925 GGGAGGTGGCTGCTGGAG 62.107 72.222 0.00 0.00 0.00 3.86
989 999 4.794439 TCGTCATCTGGCCGCACG 62.794 66.667 0.00 1.55 0.00 5.34
997 1007 2.579787 GTCGCCCGTCGTCATCTG 60.580 66.667 0.00 0.00 39.67 2.90
1065 1079 0.599204 TGACGACGGCAAAGAAGGAC 60.599 55.000 0.00 0.00 0.00 3.85
1066 1080 0.320374 ATGACGACGGCAAAGAAGGA 59.680 50.000 7.85 0.00 0.00 3.36
1081 1095 1.062047 TAGCGCTGTCGTCGATGAC 59.938 57.895 27.30 27.30 39.37 3.06
1082 1096 1.062047 GTAGCGCTGTCGTCGATGA 59.938 57.895 22.90 2.39 38.14 2.92
1084 1098 2.022902 CGTAGCGCTGTCGTCGAT 59.977 61.111 22.90 0.00 38.14 3.59
1139 1159 4.838152 CGCCTGGATGTCCACCCG 62.838 72.222 0.00 0.32 42.01 5.28
1193 1213 0.881796 CTTTTCCTCGAACTTGGGCC 59.118 55.000 0.00 0.00 0.00 5.80
1234 1254 1.293498 TCGGAGACAGCTTCTTGCC 59.707 57.895 0.00 0.00 44.23 4.52
1274 1297 2.646175 TTTCCAGAGGAGGACGCGG 61.646 63.158 12.47 0.00 37.42 6.46
1277 1300 1.215647 CCGTTTCCAGAGGAGGACG 59.784 63.158 13.60 13.60 40.32 4.79
1305 1328 3.371965 ACCAGCTACCCGAATCTTAAGA 58.628 45.455 7.82 7.82 0.00 2.10
1306 1329 3.718815 GACCAGCTACCCGAATCTTAAG 58.281 50.000 0.00 0.00 0.00 1.85
1309 1332 0.460311 CGACCAGCTACCCGAATCTT 59.540 55.000 0.00 0.00 0.00 2.40
1310 1333 2.017559 GCGACCAGCTACCCGAATCT 62.018 60.000 5.20 0.00 44.04 2.40
1331 1363 0.810016 GGAGGTGTCTGTACGAGGAC 59.190 60.000 0.00 6.52 0.00 3.85
1332 1364 0.675837 CGGAGGTGTCTGTACGAGGA 60.676 60.000 0.00 0.00 0.00 3.71
1333 1365 0.675837 TCGGAGGTGTCTGTACGAGG 60.676 60.000 0.00 0.00 0.00 4.63
1335 1367 0.250424 TGTCGGAGGTGTCTGTACGA 60.250 55.000 0.00 0.00 0.00 3.43
1336 1368 0.594602 TTGTCGGAGGTGTCTGTACG 59.405 55.000 0.00 0.00 0.00 3.67
1337 1369 2.609737 CCTTTGTCGGAGGTGTCTGTAC 60.610 54.545 0.00 0.00 0.00 2.90
1338 1370 1.616865 CCTTTGTCGGAGGTGTCTGTA 59.383 52.381 0.00 0.00 0.00 2.74
1339 1371 0.393077 CCTTTGTCGGAGGTGTCTGT 59.607 55.000 0.00 0.00 0.00 3.41
1340 1372 0.393077 ACCTTTGTCGGAGGTGTCTG 59.607 55.000 0.00 0.00 45.59 3.51
1341 1373 2.836020 ACCTTTGTCGGAGGTGTCT 58.164 52.632 0.00 0.00 45.59 3.41
1346 1378 2.027625 GACGCACCTTTGTCGGAGG 61.028 63.158 0.00 0.00 40.24 4.30
1347 1379 0.600255 AAGACGCACCTTTGTCGGAG 60.600 55.000 0.00 0.00 40.05 4.63
1348 1380 0.599204 GAAGACGCACCTTTGTCGGA 60.599 55.000 0.00 0.00 40.05 4.55
1349 1381 0.878523 TGAAGACGCACCTTTGTCGG 60.879 55.000 0.00 0.00 40.05 4.79
1360 1392 2.507324 GAGCCGAGGTGAAGACGC 60.507 66.667 0.00 0.00 0.00 5.19
1407 1439 2.517875 GGCGGCATGGCTTCAGAT 60.518 61.111 18.09 0.00 40.72 2.90
1430 1462 1.012486 AACTAGTTTCCGCCGCTTCG 61.012 55.000 1.12 0.00 0.00 3.79
1435 1467 1.074872 GGACGAACTAGTTTCCGCCG 61.075 60.000 10.02 10.58 0.00 6.46
1440 1472 2.985139 CAAGGACGGACGAACTAGTTTC 59.015 50.000 10.02 4.12 0.00 2.78
1461 1493 0.673956 GGAAGCGAACTGGTCCTTCC 60.674 60.000 20.04 20.04 41.99 3.46
1462 1494 0.321996 AGGAAGCGAACTGGTCCTTC 59.678 55.000 12.65 12.65 34.92 3.46
1485 1517 1.676916 GCATCAGCCTTGCTACTGACA 60.677 52.381 0.00 0.00 45.19 3.58
1486 1518 1.012841 GCATCAGCCTTGCTACTGAC 58.987 55.000 0.00 0.00 45.19 3.51
1508 1540 0.457166 CAACGCATCAACAGCCATGG 60.457 55.000 7.63 7.63 0.00 3.66
1521 1553 4.577677 TGCCCTGCCTTCAACGCA 62.578 61.111 0.00 0.00 34.41 5.24
1524 1556 1.973812 GTCCTGCCCTGCCTTCAAC 60.974 63.158 0.00 0.00 0.00 3.18
1536 1568 1.522580 GGCGATCTTCAGGTCCTGC 60.523 63.158 14.64 0.00 0.00 4.85
1559 1591 1.743321 GCCGAGTGGGAGATCCTCTG 61.743 65.000 0.00 0.00 39.29 3.35
1560 1592 1.456705 GCCGAGTGGGAGATCCTCT 60.457 63.158 0.00 0.00 41.66 3.69
1578 1610 2.202987 GCCACATCAGAGGCCTCG 60.203 66.667 26.95 20.71 44.66 4.63
1588 1620 1.009829 AGAATCGCTTTCGCCACATC 58.990 50.000 0.00 0.00 39.46 3.06
1597 1629 2.095415 GGTAAAACGGCAGAATCGCTTT 60.095 45.455 0.00 0.00 32.04 3.51
1611 1643 2.733671 GAGGACGCGCGGGTAAAAC 61.734 63.158 35.22 18.40 0.00 2.43
1638 1670 0.819259 TGCACAGGAGCAACAAGTCC 60.819 55.000 0.00 0.00 42.46 3.85
1746 2638 1.880340 CCTCGCAATCGACAGGCTC 60.880 63.158 0.00 0.00 40.21 4.70
1748 2640 2.892425 CCCTCGCAATCGACAGGC 60.892 66.667 0.00 0.00 40.21 4.85
1761 2653 3.195825 AGTGTAACATAGCTGTGTCCCTC 59.804 47.826 17.08 10.64 41.43 4.30
1781 2673 4.756135 GCTATGTAACGGTCTAGCTCTAGT 59.244 45.833 0.00 0.00 34.98 2.57
1804 2696 8.764524 ATTTCTTGACTAAGCTACAGTAGTTG 57.235 34.615 9.42 0.00 33.82 3.16
1877 2769 6.992123 AGTCGAAACCAGATCATTGCATAATA 59.008 34.615 0.00 0.00 0.00 0.98
1934 2826 9.612620 GAAGATTCGACATTAAACAACTTTGAT 57.387 29.630 0.00 0.00 0.00 2.57
1962 2854 5.163513 CAACAACACAAAGAAAGAGCACTT 58.836 37.500 0.00 0.00 38.05 3.16
1973 2865 4.677584 TCGGATTTTCCAACAACACAAAG 58.322 39.130 0.00 0.00 35.91 2.77
1990 2882 2.092914 GGACAAACTCCAATCCTCGGAT 60.093 50.000 0.00 0.00 39.21 4.18
1994 2886 1.003233 ACCGGACAAACTCCAATCCTC 59.997 52.381 9.46 0.00 39.39 3.71
2035 3035 7.436933 AGAAAATGAGAACTTGTTGGAATTCC 58.563 34.615 18.17 18.17 0.00 3.01
2061 3061 9.487790 AATGAGAACTTGTTTGTCTTTCAAAAA 57.512 25.926 0.00 0.00 45.84 1.94
2062 3062 9.487790 AAATGAGAACTTGTTTGTCTTTCAAAA 57.512 25.926 0.00 0.00 45.84 2.44
2063 3063 9.487790 AAAATGAGAACTTGTTTGTCTTTCAAA 57.512 25.926 0.00 0.00 42.79 2.69
2064 3064 9.139174 GAAAATGAGAACTTGTTTGTCTTTCAA 57.861 29.630 0.00 0.00 29.11 2.69
2065 3065 8.303156 TGAAAATGAGAACTTGTTTGTCTTTCA 58.697 29.630 0.00 0.00 33.13 2.69
2066 3066 8.687824 TGAAAATGAGAACTTGTTTGTCTTTC 57.312 30.769 0.00 0.00 29.22 2.62
2067 3067 9.487790 TTTGAAAATGAGAACTTGTTTGTCTTT 57.512 25.926 0.00 0.00 0.00 2.52
2068 3068 9.657419 ATTTGAAAATGAGAACTTGTTTGTCTT 57.343 25.926 0.00 0.00 0.00 3.01
2069 3069 9.657419 AATTTGAAAATGAGAACTTGTTTGTCT 57.343 25.926 0.00 0.00 0.00 3.41
2070 3070 9.906111 GAATTTGAAAATGAGAACTTGTTTGTC 57.094 29.630 0.00 0.00 0.00 3.18
2071 3071 9.434420 TGAATTTGAAAATGAGAACTTGTTTGT 57.566 25.926 0.00 0.00 0.00 2.83
2072 3072 9.693157 GTGAATTTGAAAATGAGAACTTGTTTG 57.307 29.630 0.00 0.00 0.00 2.93
2073 3073 9.657419 AGTGAATTTGAAAATGAGAACTTGTTT 57.343 25.926 0.00 0.00 0.00 2.83
2074 3074 9.657419 AAGTGAATTTGAAAATGAGAACTTGTT 57.343 25.926 0.00 0.00 0.00 2.83
2075 3075 9.305925 GAAGTGAATTTGAAAATGAGAACTTGT 57.694 29.630 8.90 0.00 0.00 3.16
2101 3101 6.252441 CAGTTACTGATCTTCTGTCGCTAAAG 59.748 42.308 6.50 0.00 32.44 1.85
2174 3174 2.685897 GCACTTATCGGGCCATAAACAA 59.314 45.455 4.39 0.00 0.00 2.83
2187 3187 0.950116 GCCCATCTGCTGCACTTATC 59.050 55.000 0.00 0.00 0.00 1.75
2306 3306 2.045536 GCCCTGCCAGTCTTCCTG 60.046 66.667 0.00 0.00 41.15 3.86
2344 3344 6.567050 TGTCTAATCCAGTTGTCGTTATACC 58.433 40.000 0.00 0.00 0.00 2.73
2355 3355 6.183360 TGTGTTTGCATTTGTCTAATCCAGTT 60.183 34.615 0.00 0.00 0.00 3.16
2356 3356 5.301551 TGTGTTTGCATTTGTCTAATCCAGT 59.698 36.000 0.00 0.00 0.00 4.00
2357 3357 5.771469 TGTGTTTGCATTTGTCTAATCCAG 58.229 37.500 0.00 0.00 0.00 3.86
2359 3359 6.446318 TCTTGTGTTTGCATTTGTCTAATCC 58.554 36.000 0.00 0.00 0.00 3.01
2435 3435 6.931281 ACTCACATCAATTATGGTAAGGATCG 59.069 38.462 0.00 0.00 40.16 3.69
2439 3439 8.511604 AAAGACTCACATCAATTATGGTAAGG 57.488 34.615 0.00 0.00 40.16 2.69
2472 3472 3.710209 AGAGACAAAGTCCCCAATCAG 57.290 47.619 0.00 0.00 32.18 2.90
2479 3479 2.561858 AGTTCGGTAGAGACAAAGTCCC 59.438 50.000 0.00 0.00 32.18 4.46
2517 3517 8.023706 GGAAAATGGTCAGAATTTACTTGAGTC 58.976 37.037 0.00 0.00 0.00 3.36
2589 3589 8.887717 CAGGATTTTCAATTACTCTCTTACCTG 58.112 37.037 0.00 0.00 33.24 4.00
2612 3612 1.884579 AGTCAGCAAAACAGCATCAGG 59.115 47.619 0.00 0.00 36.85 3.86
2634 3634 4.065789 CCCAGACAGAAACAGAACTAACC 58.934 47.826 0.00 0.00 0.00 2.85
2658 6879 3.685139 TGAGACTGGCTAACCTGAAAG 57.315 47.619 0.00 0.00 38.25 2.62
2685 6906 1.279271 AGCTTGGTAGACGGAATTGCT 59.721 47.619 0.00 0.00 0.00 3.91
2693 6914 0.388649 ACGCTTCAGCTTGGTAGACG 60.389 55.000 0.00 0.00 39.32 4.18
2703 6924 2.784380 CGTACTTATCAGACGCTTCAGC 59.216 50.000 0.00 0.00 37.78 4.26
2718 6939 8.050778 TCCTTTTGCATTTTGATATCGTACTT 57.949 30.769 0.00 0.00 0.00 2.24
2764 6985 1.372128 GGCAAGCAAAGAACCTGCG 60.372 57.895 0.00 0.00 44.75 5.18
2767 6988 2.044452 GCAGGCAAGCAAAGAACCT 58.956 52.632 0.00 0.00 0.00 3.50



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

AutoCloner maintained by Alex Coulton.