Multiple sequence alignment - TraesCS6A01G273900

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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 TraesCS6A01G273900 chr6A 100.000 4097 0 0 1 4097 500077047 500081143 0.000000e+00 7566
1 TraesCS6A01G273900 chr6B 95.670 3141 125 6 957 4097 539721177 539724306 0.000000e+00 5036
2 TraesCS6A01G273900 chr6B 91.193 704 51 7 74 773 155189041 155188345 0.000000e+00 946
3 TraesCS6A01G273900 chr6B 92.941 85 3 2 1 85 444442981 444442900 2.000000e-23 121
4 TraesCS6A01G273900 chr6B 90.000 90 5 2 1 90 617895164 617895249 3.350000e-21 113
5 TraesCS6A01G273900 chr6D 94.856 3227 134 18 884 4097 358321087 358324294 0.000000e+00 5011
6 TraesCS6A01G273900 chr6D 87.834 674 74 5 74 742 38519223 38519893 0.000000e+00 784
7 TraesCS6A01G273900 chr4A 90.986 588 48 3 74 658 711331729 711332314 0.000000e+00 787
8 TraesCS6A01G273900 chr2D 83.830 705 99 10 74 773 118818481 118819175 0.000000e+00 656
9 TraesCS6A01G273900 chr7A 82.222 675 104 12 112 778 690426996 690427662 5.940000e-158 568
10 TraesCS6A01G273900 chr7A 92.941 85 3 3 1 85 723192968 723193049 2.000000e-23 121
11 TraesCS6A01G273900 chr3B 98.611 72 1 0 1 72 127022256 127022327 1.200000e-25 128
12 TraesCS6A01G273900 chr1D 92.941 85 6 0 1 85 209037921 209037837 1.550000e-24 124
13 TraesCS6A01G273900 chr1D 90.000 90 5 2 1 90 105518535 105518450 3.350000e-21 113
14 TraesCS6A01G273900 chr3D 92.941 85 3 1 1 85 331753126 331753207 2.000000e-23 121
15 TraesCS6A01G273900 chr7B 91.111 90 4 2 1 90 145855825 145855740 7.190000e-23 119
16 TraesCS6A01G273900 chr4D 91.954 87 4 1 1 87 353332545 353332628 7.190000e-23 119


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 TraesCS6A01G273900 chr6A 500077047 500081143 4096 False 7566 7566 100.000 1 4097 1 chr6A.!!$F1 4096
1 TraesCS6A01G273900 chr6B 539721177 539724306 3129 False 5036 5036 95.670 957 4097 1 chr6B.!!$F1 3140
2 TraesCS6A01G273900 chr6B 155188345 155189041 696 True 946 946 91.193 74 773 1 chr6B.!!$R1 699
3 TraesCS6A01G273900 chr6D 358321087 358324294 3207 False 5011 5011 94.856 884 4097 1 chr6D.!!$F2 3213
4 TraesCS6A01G273900 chr6D 38519223 38519893 670 False 784 784 87.834 74 742 1 chr6D.!!$F1 668
5 TraesCS6A01G273900 chr4A 711331729 711332314 585 False 787 787 90.986 74 658 1 chr4A.!!$F1 584
6 TraesCS6A01G273900 chr2D 118818481 118819175 694 False 656 656 83.830 74 773 1 chr2D.!!$F1 699
7 TraesCS6A01G273900 chr7A 690426996 690427662 666 False 568 568 82.222 112 778 1 chr7A.!!$F1 666

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
43 44 0.039256 CCATTTGGTTGTGACTGCCG 60.039 55.0 0.00 0.0 0.00 5.69 F
912 919 0.312102 AGAAAAGCGCCTGAAACTGC 59.688 50.0 2.29 0.0 0.00 4.40 F
990 1003 0.531974 GTGCACACTTTCCCTCGTCA 60.532 55.0 13.17 0.0 0.00 4.35 F
2559 2572 0.538584 CATGCAGCCACTCTGGACTA 59.461 55.0 0.00 0.0 46.09 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1757 0.379669 GATTGCACAGCTCCAATCCG 59.620 55.0 15.45 0.0 40.73 4.18 R
2058 2071 0.323178 ACTGCATTGCCTTCTCCTGG 60.323 55.0 6.12 0.0 0.00 4.45 R
2620 2633 0.531532 ATGGCACTACGATGCTCTGC 60.532 55.0 10.09 0.0 45.38 4.26 R
3759 3774 0.514691 GCTAATCGCTGCCTGCATAC 59.485 55.0 0.00 0.0 43.06 2.39 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
21 22 3.458189 GTTCATTCTATGGACCTGACCG 58.542 50.000 0.00 0.00 32.40 4.79
22 23 3.026707 TCATTCTATGGACCTGACCGA 57.973 47.619 0.00 0.00 0.00 4.69
23 24 3.576861 TCATTCTATGGACCTGACCGAT 58.423 45.455 0.00 0.00 0.00 4.18
24 25 3.574396 TCATTCTATGGACCTGACCGATC 59.426 47.826 0.00 0.00 0.00 3.69
25 26 1.996798 TCTATGGACCTGACCGATCC 58.003 55.000 0.00 0.00 0.00 3.36
26 27 1.216930 TCTATGGACCTGACCGATCCA 59.783 52.381 0.00 0.00 46.36 3.41
27 28 3.247424 ATGGACCTGACCGATCCAT 57.753 52.632 0.00 0.00 46.03 3.41
28 29 3.006061 TGGACCTGACCGATCCATT 57.994 52.632 0.00 0.00 37.60 3.16
29 30 1.285280 TGGACCTGACCGATCCATTT 58.715 50.000 0.00 0.00 37.60 2.32
30 31 1.065491 TGGACCTGACCGATCCATTTG 60.065 52.381 0.00 0.00 37.60 2.32
31 32 1.668419 GACCTGACCGATCCATTTGG 58.332 55.000 0.00 0.00 34.63 3.28
32 33 0.991920 ACCTGACCGATCCATTTGGT 59.008 50.000 0.00 0.00 45.60 3.67
33 34 1.354368 ACCTGACCGATCCATTTGGTT 59.646 47.619 0.00 0.00 42.70 3.67
34 35 1.745087 CCTGACCGATCCATTTGGTTG 59.255 52.381 0.00 0.00 42.70 3.77
35 36 2.436417 CTGACCGATCCATTTGGTTGT 58.564 47.619 0.00 0.00 42.70 3.32
36 37 2.158559 TGACCGATCCATTTGGTTGTG 58.841 47.619 0.00 0.00 42.70 3.33
37 38 2.224646 TGACCGATCCATTTGGTTGTGA 60.225 45.455 0.00 0.00 42.70 3.58
38 39 2.159382 ACCGATCCATTTGGTTGTGAC 58.841 47.619 0.00 0.00 39.26 3.67
39 40 2.224769 ACCGATCCATTTGGTTGTGACT 60.225 45.455 0.00 0.00 39.26 3.41
40 41 2.162208 CCGATCCATTTGGTTGTGACTG 59.838 50.000 0.00 0.00 36.34 3.51
41 42 2.414559 CGATCCATTTGGTTGTGACTGC 60.415 50.000 0.00 0.00 36.34 4.40
42 43 1.327303 TCCATTTGGTTGTGACTGCC 58.673 50.000 0.00 0.00 36.34 4.85
43 44 0.039256 CCATTTGGTTGTGACTGCCG 60.039 55.000 0.00 0.00 0.00 5.69
44 45 0.950836 CATTTGGTTGTGACTGCCGA 59.049 50.000 0.00 0.00 0.00 5.54
45 46 1.336440 CATTTGGTTGTGACTGCCGAA 59.664 47.619 2.24 2.24 0.00 4.30
46 47 1.464734 TTTGGTTGTGACTGCCGAAA 58.535 45.000 0.00 0.00 0.00 3.46
47 48 1.464734 TTGGTTGTGACTGCCGAAAA 58.535 45.000 0.00 0.00 0.00 2.29
48 49 0.736053 TGGTTGTGACTGCCGAAAAC 59.264 50.000 0.00 0.00 0.00 2.43
49 50 0.736053 GGTTGTGACTGCCGAAAACA 59.264 50.000 0.00 0.00 0.00 2.83
50 51 1.268539 GGTTGTGACTGCCGAAAACAG 60.269 52.381 0.00 0.00 41.08 3.16
54 55 4.559502 ACTGCCGAAAACAGTGCT 57.440 50.000 0.00 0.00 46.38 4.40
55 56 2.024918 ACTGCCGAAAACAGTGCTG 58.975 52.632 0.00 0.00 46.38 4.41
56 57 1.283793 CTGCCGAAAACAGTGCTGG 59.716 57.895 4.11 0.00 34.19 4.85
57 58 1.153066 TGCCGAAAACAGTGCTGGA 60.153 52.632 4.11 0.00 34.19 3.86
58 59 1.165907 TGCCGAAAACAGTGCTGGAG 61.166 55.000 4.11 0.00 34.19 3.86
59 60 1.166531 GCCGAAAACAGTGCTGGAGT 61.167 55.000 4.11 0.00 34.19 3.85
60 61 1.308998 CCGAAAACAGTGCTGGAGTT 58.691 50.000 4.11 0.00 34.19 3.01
61 62 2.489971 CCGAAAACAGTGCTGGAGTTA 58.510 47.619 4.11 0.00 34.19 2.24
62 63 2.480419 CCGAAAACAGTGCTGGAGTTAG 59.520 50.000 4.11 0.00 34.19 2.34
63 64 3.390135 CGAAAACAGTGCTGGAGTTAGA 58.610 45.455 4.11 0.00 34.19 2.10
64 65 3.997021 CGAAAACAGTGCTGGAGTTAGAT 59.003 43.478 4.11 0.00 34.19 1.98
65 66 4.143030 CGAAAACAGTGCTGGAGTTAGATG 60.143 45.833 4.11 0.00 34.19 2.90
66 67 4.623932 AAACAGTGCTGGAGTTAGATGA 57.376 40.909 4.11 0.00 34.19 2.92
67 68 4.833478 AACAGTGCTGGAGTTAGATGAT 57.167 40.909 4.11 0.00 34.19 2.45
68 69 4.134379 ACAGTGCTGGAGTTAGATGATG 57.866 45.455 4.11 0.00 34.19 3.07
69 70 3.517100 ACAGTGCTGGAGTTAGATGATGT 59.483 43.478 4.11 0.00 34.19 3.06
70 71 4.019860 ACAGTGCTGGAGTTAGATGATGTT 60.020 41.667 4.11 0.00 34.19 2.71
71 72 4.331992 CAGTGCTGGAGTTAGATGATGTTG 59.668 45.833 0.00 0.00 0.00 3.33
72 73 4.019860 AGTGCTGGAGTTAGATGATGTTGT 60.020 41.667 0.00 0.00 0.00 3.32
110 111 1.010935 CGCGCTCTGAGCTCAAAAGA 61.011 55.000 25.59 14.82 39.60 2.52
161 162 2.634940 AGTGAAGTTCTTCTGCTGGCTA 59.365 45.455 12.74 0.00 0.00 3.93
162 163 3.262915 AGTGAAGTTCTTCTGCTGGCTAT 59.737 43.478 12.74 0.00 0.00 2.97
167 168 2.686915 GTTCTTCTGCTGGCTATTGCAT 59.313 45.455 0.66 0.00 41.91 3.96
197 198 2.816689 CTATGGTGCAACGATCGGTTA 58.183 47.619 20.98 0.75 36.41 2.85
361 362 0.319900 CCTGAAGACTGGTCACCACG 60.320 60.000 0.00 0.00 0.00 4.94
450 451 1.143183 TCGCTCACCGCCCTAATTC 59.857 57.895 0.00 0.00 36.73 2.17
506 510 3.476552 TCAAGAGGAAACAATCAAGCGT 58.523 40.909 0.00 0.00 0.00 5.07
520 524 4.093115 GCGTCAGCGACATCATCA 57.907 55.556 8.91 0.00 41.33 3.07
524 528 1.737029 CGTCAGCGACATCATCACCTT 60.737 52.381 8.91 0.00 41.33 3.50
525 529 1.662629 GTCAGCGACATCATCACCTTG 59.337 52.381 4.20 0.00 32.09 3.61
599 603 0.538118 CCTTTCGGGGATCCAACGTA 59.462 55.000 22.40 13.74 0.00 3.57
609 613 3.808174 GGGATCCAACGTAAGACATAAGC 59.192 47.826 15.23 0.00 43.62 3.09
610 614 4.439057 GGATCCAACGTAAGACATAAGCA 58.561 43.478 6.95 0.00 43.62 3.91
683 689 7.650504 TGAATTTTTGTTTTCATCTCTCTGCTG 59.349 33.333 0.00 0.00 0.00 4.41
693 699 3.117171 CTCTGCTGCTGACCGCAC 61.117 66.667 5.03 0.00 45.47 5.34
715 722 4.020128 ACTCTCGATCAGTTAGCCCTTTTT 60.020 41.667 0.00 0.00 0.00 1.94
742 749 4.662179 TCTCCCCTCTGCTAAATCAATGAT 59.338 41.667 0.00 0.00 0.00 2.45
809 816 9.836864 AAAAGAAAATAAGAAAAATGCACCTCT 57.163 25.926 0.00 0.00 0.00 3.69
810 817 9.836864 AAAGAAAATAAGAAAAATGCACCTCTT 57.163 25.926 0.00 0.00 32.95 2.85
811 818 9.481340 AAGAAAATAAGAAAAATGCACCTCTTC 57.519 29.630 0.00 0.00 30.90 2.87
812 819 8.090831 AGAAAATAAGAAAAATGCACCTCTTCC 58.909 33.333 0.00 0.00 30.90 3.46
813 820 7.544804 AAATAAGAAAAATGCACCTCTTCCT 57.455 32.000 0.00 0.00 30.90 3.36
814 821 4.861102 AAGAAAAATGCACCTCTTCCTG 57.139 40.909 0.00 0.00 0.00 3.86
815 822 2.560105 AGAAAAATGCACCTCTTCCTGC 59.440 45.455 0.00 0.00 0.00 4.85
819 826 3.751767 TGCACCTCTTCCTGCATTT 57.248 47.368 0.00 0.00 38.49 2.32
820 827 1.250328 TGCACCTCTTCCTGCATTTG 58.750 50.000 0.00 0.00 38.49 2.32
821 828 1.202915 TGCACCTCTTCCTGCATTTGA 60.203 47.619 0.00 0.00 38.49 2.69
822 829 1.888512 GCACCTCTTCCTGCATTTGAA 59.111 47.619 0.00 0.00 33.31 2.69
823 830 2.494870 GCACCTCTTCCTGCATTTGAAT 59.505 45.455 0.00 0.00 33.31 2.57
824 831 3.428589 GCACCTCTTCCTGCATTTGAATC 60.429 47.826 0.00 0.00 33.31 2.52
825 832 3.760151 CACCTCTTCCTGCATTTGAATCA 59.240 43.478 0.00 0.00 0.00 2.57
826 833 3.760684 ACCTCTTCCTGCATTTGAATCAC 59.239 43.478 0.00 0.00 0.00 3.06
827 834 3.181503 CCTCTTCCTGCATTTGAATCACG 60.182 47.826 0.00 0.00 0.00 4.35
828 835 3.673902 TCTTCCTGCATTTGAATCACGA 58.326 40.909 0.00 0.00 0.00 4.35
829 836 3.436704 TCTTCCTGCATTTGAATCACGAC 59.563 43.478 0.00 0.00 0.00 4.34
830 837 2.083774 TCCTGCATTTGAATCACGACC 58.916 47.619 0.00 0.00 0.00 4.79
831 838 1.811965 CCTGCATTTGAATCACGACCA 59.188 47.619 0.00 0.00 0.00 4.02
832 839 2.424601 CCTGCATTTGAATCACGACCAT 59.575 45.455 0.00 0.00 0.00 3.55
833 840 3.627123 CCTGCATTTGAATCACGACCATA 59.373 43.478 0.00 0.00 0.00 2.74
834 841 4.096231 CCTGCATTTGAATCACGACCATAA 59.904 41.667 0.00 0.00 0.00 1.90
835 842 4.980590 TGCATTTGAATCACGACCATAAC 58.019 39.130 0.00 0.00 0.00 1.89
836 843 4.028383 GCATTTGAATCACGACCATAACG 58.972 43.478 0.00 0.00 0.00 3.18
837 844 4.201773 GCATTTGAATCACGACCATAACGA 60.202 41.667 0.00 0.00 34.70 3.85
838 845 5.672570 GCATTTGAATCACGACCATAACGAA 60.673 40.000 0.00 0.00 34.70 3.85
839 846 5.926214 TTTGAATCACGACCATAACGAAA 57.074 34.783 0.00 0.00 34.70 3.46
840 847 5.926214 TTGAATCACGACCATAACGAAAA 57.074 34.783 0.00 0.00 34.70 2.29
841 848 6.489127 TTGAATCACGACCATAACGAAAAT 57.511 33.333 0.00 0.00 34.70 1.82
842 849 6.489127 TGAATCACGACCATAACGAAAATT 57.511 33.333 0.00 0.00 34.70 1.82
843 850 7.598189 TGAATCACGACCATAACGAAAATTA 57.402 32.000 0.00 0.00 34.70 1.40
844 851 7.457868 TGAATCACGACCATAACGAAAATTAC 58.542 34.615 0.00 0.00 34.70 1.89
845 852 6.971527 ATCACGACCATAACGAAAATTACA 57.028 33.333 0.00 0.00 34.70 2.41
846 853 6.782298 TCACGACCATAACGAAAATTACAA 57.218 33.333 0.00 0.00 34.70 2.41
847 854 7.187244 TCACGACCATAACGAAAATTACAAA 57.813 32.000 0.00 0.00 34.70 2.83
848 855 7.808672 TCACGACCATAACGAAAATTACAAAT 58.191 30.769 0.00 0.00 34.70 2.32
849 856 8.291032 TCACGACCATAACGAAAATTACAAATT 58.709 29.630 0.00 0.00 34.70 1.82
850 857 8.362304 CACGACCATAACGAAAATTACAAATTG 58.638 33.333 0.00 0.00 34.70 2.32
851 858 7.539366 ACGACCATAACGAAAATTACAAATTGG 59.461 33.333 0.00 0.00 34.70 3.16
852 859 7.008810 CGACCATAACGAAAATTACAAATTGGG 59.991 37.037 0.00 0.00 0.00 4.12
853 860 7.672240 ACCATAACGAAAATTACAAATTGGGT 58.328 30.769 0.00 0.00 0.00 4.51
854 861 8.151596 ACCATAACGAAAATTACAAATTGGGTT 58.848 29.630 0.00 0.00 0.00 4.11
855 862 8.439286 CCATAACGAAAATTACAAATTGGGTTG 58.561 33.333 0.00 0.00 34.52 3.77
856 863 5.915812 ACGAAAATTACAAATTGGGTTGC 57.084 34.783 0.00 0.00 31.29 4.17
857 864 4.446051 ACGAAAATTACAAATTGGGTTGCG 59.554 37.500 0.00 0.00 31.29 4.85
858 865 4.665394 CGAAAATTACAAATTGGGTTGCGC 60.665 41.667 0.00 0.00 31.29 6.09
859 866 3.393089 AATTACAAATTGGGTTGCGCA 57.607 38.095 5.66 5.66 31.29 6.09
860 867 2.141535 TTACAAATTGGGTTGCGCAC 57.858 45.000 11.12 5.37 31.29 5.34
861 868 1.032794 TACAAATTGGGTTGCGCACA 58.967 45.000 11.12 1.06 31.29 4.57
862 869 0.529555 ACAAATTGGGTTGCGCACAC 60.530 50.000 11.12 11.99 31.29 3.82
863 870 1.299773 AAATTGGGTTGCGCACACG 60.300 52.632 11.12 0.00 44.07 4.49
864 871 1.729470 AAATTGGGTTGCGCACACGA 61.729 50.000 11.12 7.16 43.93 4.35
865 872 1.523154 AATTGGGTTGCGCACACGAT 61.523 50.000 11.12 9.45 43.93 3.73
866 873 1.523154 ATTGGGTTGCGCACACGATT 61.523 50.000 11.12 0.00 43.93 3.34
867 874 2.123988 TTGGGTTGCGCACACGATTC 62.124 55.000 11.12 3.79 43.93 2.52
868 875 2.202171 GGTTGCGCACACGATTCG 60.202 61.111 11.12 4.14 43.93 3.34
869 876 2.202171 GTTGCGCACACGATTCGG 60.202 61.111 11.12 2.17 43.93 4.30
870 877 2.663520 TTGCGCACACGATTCGGT 60.664 55.556 11.12 2.81 43.93 4.69
871 878 2.949030 TTGCGCACACGATTCGGTG 61.949 57.895 11.12 17.77 43.93 4.94
875 882 4.147322 CACACGATTCGGTGCCGC 62.147 66.667 11.29 0.00 41.65 6.53
876 883 4.373116 ACACGATTCGGTGCCGCT 62.373 61.111 11.29 0.00 41.65 5.52
877 884 3.118454 CACGATTCGGTGCCGCTT 61.118 61.111 11.29 0.00 39.59 4.68
878 885 2.813908 ACGATTCGGTGCCGCTTC 60.814 61.111 11.29 4.42 39.59 3.86
879 886 3.913573 CGATTCGGTGCCGCTTCG 61.914 66.667 16.10 16.10 39.59 3.79
880 887 4.223964 GATTCGGTGCCGCTTCGC 62.224 66.667 5.64 0.00 39.59 4.70
891 898 2.343758 GCTTCGCAGTGGGTCTGA 59.656 61.111 7.12 0.00 46.27 3.27
904 911 1.134371 GGGTCTGATAGAAAAGCGCCT 60.134 52.381 2.29 0.00 0.00 5.52
909 916 3.684788 TCTGATAGAAAAGCGCCTGAAAC 59.315 43.478 2.29 0.00 0.00 2.78
910 917 3.674997 TGATAGAAAAGCGCCTGAAACT 58.325 40.909 2.29 0.00 0.00 2.66
911 918 3.436704 TGATAGAAAAGCGCCTGAAACTG 59.563 43.478 2.29 0.00 0.00 3.16
912 919 0.312102 AGAAAAGCGCCTGAAACTGC 59.688 50.000 2.29 0.00 0.00 4.40
917 924 0.952984 AGCGCCTGAAACTGCTCTTC 60.953 55.000 2.29 0.00 30.37 2.87
930 937 1.227089 CTCTTCTGGACCCGATGCG 60.227 63.158 0.00 0.00 0.00 4.73
932 939 1.227089 CTTCTGGACCCGATGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
933 940 3.371097 TTCTGGACCCGATGCGAGC 62.371 63.158 0.00 0.00 0.00 5.03
934 941 4.147449 CTGGACCCGATGCGAGCA 62.147 66.667 0.00 0.00 0.00 4.26
935 942 3.451556 CTGGACCCGATGCGAGCAT 62.452 63.158 10.66 10.66 39.69 3.79
936 943 2.203070 GGACCCGATGCGAGCATT 60.203 61.111 12.16 0.00 36.70 3.56
937 944 2.247437 GGACCCGATGCGAGCATTC 61.247 63.158 12.16 5.57 36.70 2.67
938 945 1.521457 GACCCGATGCGAGCATTCA 60.521 57.895 12.16 0.00 36.70 2.57
939 946 1.493950 GACCCGATGCGAGCATTCAG 61.494 60.000 12.16 7.01 36.70 3.02
940 947 1.227350 CCCGATGCGAGCATTCAGA 60.227 57.895 12.16 0.00 36.70 3.27
944 957 2.538333 CCGATGCGAGCATTCAGAAAAG 60.538 50.000 12.16 0.00 36.70 2.27
950 963 2.346847 CGAGCATTCAGAAAAGTCTCGG 59.653 50.000 16.29 6.49 38.48 4.63
951 964 3.330267 GAGCATTCAGAAAAGTCTCGGT 58.670 45.455 0.00 0.00 28.78 4.69
954 967 4.580580 AGCATTCAGAAAAGTCTCGGTTTT 59.419 37.500 0.00 0.00 28.78 2.43
955 968 4.676924 GCATTCAGAAAAGTCTCGGTTTTG 59.323 41.667 0.00 0.00 28.78 2.44
967 980 4.266502 GTCTCGGTTTTGATCTCTTCATCG 59.733 45.833 0.00 0.00 33.34 3.84
974 987 3.156511 TGATCTCTTCATCGTCAGTGC 57.843 47.619 0.00 0.00 0.00 4.40
990 1003 0.531974 GTGCACACTTTCCCTCGTCA 60.532 55.000 13.17 0.00 0.00 4.35
1128 1141 2.203938 TCCTCCCACCACCTCACC 60.204 66.667 0.00 0.00 0.00 4.02
1133 1146 2.650116 CCCACCACCTCACCTCTCG 61.650 68.421 0.00 0.00 0.00 4.04
1159 1172 4.835891 CGTCCTACCCTCCCGCCT 62.836 72.222 0.00 0.00 0.00 5.52
1190 1203 0.657840 CTGTTCGATGAAATCCCCGC 59.342 55.000 0.00 0.00 41.39 6.13
1476 1489 1.401539 GGCTCAATCAACGCCTTCAAC 60.402 52.381 0.00 0.00 40.62 3.18
1688 1701 2.953648 CCTGCCATGCATATGTTCTCAA 59.046 45.455 0.00 0.00 38.13 3.02
1744 1757 3.381272 TGCTATTCTTGGGCTTTACATGC 59.619 43.478 0.00 0.00 0.00 4.06
1758 1771 1.028330 ACATGCGGATTGGAGCTGTG 61.028 55.000 0.00 0.00 0.00 3.66
1782 1795 3.247006 TCTGCAAGGAGGTTATTCGAC 57.753 47.619 0.00 0.00 0.00 4.20
1860 1873 0.668706 CTGGACACACCTCTGAAGCG 60.669 60.000 0.00 0.00 39.86 4.68
2058 2071 1.428448 TGTACATGAAGTGCTCGTGC 58.572 50.000 0.00 1.71 43.87 5.34
2109 2122 3.056322 GGATGCCAAAGAAAGATGCAGTT 60.056 43.478 0.00 0.00 35.10 3.16
2127 2140 3.512516 GCTTGGGCAGCGGTCATC 61.513 66.667 0.00 0.00 39.29 2.92
2290 2303 4.706476 CCTTTTGTCTCCATGGCTATTTGA 59.294 41.667 6.96 0.00 0.00 2.69
2315 2328 8.918202 ATTAACACTGGTTTCTGTGATAAGAA 57.082 30.769 9.71 0.00 42.95 2.52
2415 2428 3.875727 CCACTGAGAAGGATATTGTGCTG 59.124 47.826 0.00 0.00 0.00 4.41
2559 2572 0.538584 CATGCAGCCACTCTGGACTA 59.461 55.000 0.00 0.00 46.09 2.59
2562 2575 1.272480 TGCAGCCACTCTGGACTAGTA 60.272 52.381 0.00 0.00 40.96 1.82
2566 2579 1.751924 GCCACTCTGGACTAGTACAGG 59.248 57.143 30.67 23.42 41.86 4.00
2595 2608 7.095229 GGAAAGTCCATTTTTAAAAGCATGACC 60.095 37.037 12.28 4.66 36.28 4.02
2620 2633 5.334646 CGAGTCTATGGAATCATGCCAAATG 60.335 44.000 7.32 0.00 39.21 2.32
2777 2790 1.403382 CCGTGACACAGAGATGAGTGG 60.403 57.143 6.37 0.00 39.99 4.00
2779 2792 2.681706 GTGACACAGAGATGAGTGGTG 58.318 52.381 0.00 0.00 39.99 4.17
2809 2822 3.084786 GCCAAACTACTCAAGCTGGATT 58.915 45.455 0.00 0.00 34.67 3.01
2814 2827 5.690464 AACTACTCAAGCTGGATTCTGAT 57.310 39.130 0.00 0.00 0.00 2.90
2836 2849 5.939764 TCATGTTGGCTACTACAATCTCT 57.060 39.130 0.01 0.00 36.02 3.10
2841 2854 5.246203 TGTTGGCTACTACAATCTCTTGACT 59.754 40.000 0.01 0.00 36.20 3.41
2872 2885 3.703556 TGCTTTTGATGAAAAGTGGGACA 59.296 39.130 17.10 5.20 46.77 4.02
2873 2886 4.161189 TGCTTTTGATGAAAAGTGGGACAA 59.839 37.500 17.10 0.00 46.77 3.18
2904 2917 6.303839 AGAGACTAGGGACATTATCAGAGAC 58.696 44.000 0.00 0.00 0.00 3.36
2938 2951 2.908428 TGCCTGGTTGCAGTGCAG 60.908 61.111 18.81 7.44 40.61 4.41
3070 3083 5.168526 TGATTGTTTCTTTCAGTTGGACG 57.831 39.130 0.00 0.00 0.00 4.79
3244 3257 8.410141 ACAGCTTAGTTTTGCACTAATTGTAAA 58.590 29.630 9.32 0.00 45.29 2.01
3329 3342 7.226128 ACAATCAGTCAATCAGCTATGTATGTG 59.774 37.037 0.00 0.00 0.00 3.21
3362 3375 2.240667 ACTTTATGGTCAGAGCATGGCT 59.759 45.455 22.95 2.16 43.88 4.75
3364 3377 3.475566 TTATGGTCAGAGCATGGCTAC 57.524 47.619 22.95 0.00 39.88 3.58
3387 3402 9.503427 CTACCTTTTTCCATAATTAAAGAAGCG 57.497 33.333 0.00 0.00 30.97 4.68
3389 3404 6.020678 CCTTTTTCCATAATTAAAGAAGCGCG 60.021 38.462 0.00 0.00 30.97 6.86
3478 3493 1.528586 CGTTTGTTCAGGTCTGCTCAG 59.471 52.381 0.00 0.00 0.00 3.35
3497 3512 4.221530 TCAGGACTCATGATATGTGAGCT 58.778 43.478 12.44 0.00 45.42 4.09
3505 3520 5.052481 TCATGATATGTGAGCTGTTAGTGC 58.948 41.667 0.00 0.00 0.00 4.40
3565 3580 7.058525 TCTGGAGATAATGAGTTTCATGCATT 58.941 34.615 0.00 0.00 37.15 3.56
3634 3649 0.736053 TTGCACTGTTTGACCGGTTC 59.264 50.000 9.42 2.34 0.00 3.62
3759 3774 4.808414 TGTCTCTTTCTCCTATGTGTGG 57.192 45.455 0.00 0.00 0.00 4.17
3769 3784 1.134128 CCTATGTGTGGTATGCAGGCA 60.134 52.381 0.00 0.00 0.00 4.75
3821 3838 1.206371 GTTACTCTTTCTGCGGGCCTA 59.794 52.381 0.84 0.00 0.00 3.93
3857 3883 4.785511 TCTGAGTGTGGTTAAGAGTAGC 57.214 45.455 0.00 0.00 0.00 3.58
3858 3884 4.149598 TCTGAGTGTGGTTAAGAGTAGCA 58.850 43.478 0.00 0.00 0.00 3.49
3859 3885 4.772624 TCTGAGTGTGGTTAAGAGTAGCAT 59.227 41.667 0.00 0.00 0.00 3.79
3860 3886 4.820897 TGAGTGTGGTTAAGAGTAGCATG 58.179 43.478 0.00 0.00 0.00 4.06
3861 3887 4.526650 TGAGTGTGGTTAAGAGTAGCATGA 59.473 41.667 0.00 0.00 0.00 3.07
3862 3888 5.187772 TGAGTGTGGTTAAGAGTAGCATGAT 59.812 40.000 0.00 0.00 0.00 2.45
3863 3889 5.423015 AGTGTGGTTAAGAGTAGCATGATG 58.577 41.667 0.00 0.00 0.00 3.07
3864 3890 4.034510 GTGTGGTTAAGAGTAGCATGATGC 59.965 45.833 9.89 9.89 45.46 3.91
3906 3932 3.433615 GTCTTTGTGGACTACATCAGCAC 59.566 47.826 0.00 0.00 39.48 4.40
3922 3948 1.962807 AGCACTGCCTTGCATTTGTTA 59.037 42.857 9.14 0.00 45.62 2.41
3965 3993 0.247460 CGCTCTGAACACCTGGATGA 59.753 55.000 0.00 0.00 0.00 2.92
3998 4026 7.931578 TTACCATAACAAAGGTGGAACTATG 57.068 36.000 0.00 0.00 38.87 2.23
4021 4049 3.255642 ACAATGTTTGCGTCTAATTGCCT 59.744 39.130 0.00 0.00 32.65 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.132289 TCGGTCAGGTCCATAGAATGAAC 59.868 47.826 0.00 0.00 0.00 3.18
1 2 3.371034 TCGGTCAGGTCCATAGAATGAA 58.629 45.455 0.00 0.00 0.00 2.57
2 3 3.026707 TCGGTCAGGTCCATAGAATGA 57.973 47.619 0.00 0.00 0.00 2.57
3 4 3.919216 GATCGGTCAGGTCCATAGAATG 58.081 50.000 0.00 0.00 0.00 2.67
12 13 1.065418 ACCAAATGGATCGGTCAGGTC 60.065 52.381 6.42 0.00 38.94 3.85
13 14 0.991920 ACCAAATGGATCGGTCAGGT 59.008 50.000 6.42 0.00 38.94 4.00
14 15 1.745087 CAACCAAATGGATCGGTCAGG 59.255 52.381 6.42 0.00 38.94 3.86
15 16 2.162208 CACAACCAAATGGATCGGTCAG 59.838 50.000 6.42 0.00 38.94 3.51
16 17 2.158559 CACAACCAAATGGATCGGTCA 58.841 47.619 6.42 0.00 38.94 4.02
17 18 2.161609 GTCACAACCAAATGGATCGGTC 59.838 50.000 6.42 0.00 38.94 4.79
18 19 2.159382 GTCACAACCAAATGGATCGGT 58.841 47.619 6.42 0.00 38.94 4.69
19 20 2.162208 CAGTCACAACCAAATGGATCGG 59.838 50.000 6.42 0.00 38.94 4.18
20 21 2.414559 GCAGTCACAACCAAATGGATCG 60.415 50.000 6.42 0.00 38.94 3.69
21 22 2.094545 GGCAGTCACAACCAAATGGATC 60.095 50.000 6.42 0.00 38.94 3.36
22 23 1.895131 GGCAGTCACAACCAAATGGAT 59.105 47.619 6.42 0.00 38.94 3.41
23 24 1.327303 GGCAGTCACAACCAAATGGA 58.673 50.000 6.42 0.00 38.94 3.41
24 25 0.039256 CGGCAGTCACAACCAAATGG 60.039 55.000 0.00 0.00 42.17 3.16
25 26 0.950836 TCGGCAGTCACAACCAAATG 59.049 50.000 0.00 0.00 0.00 2.32
26 27 1.686355 TTCGGCAGTCACAACCAAAT 58.314 45.000 0.00 0.00 0.00 2.32
27 28 1.464734 TTTCGGCAGTCACAACCAAA 58.535 45.000 0.00 0.00 0.00 3.28
28 29 1.133407 GTTTTCGGCAGTCACAACCAA 59.867 47.619 0.00 0.00 0.00 3.67
29 30 0.736053 GTTTTCGGCAGTCACAACCA 59.264 50.000 0.00 0.00 0.00 3.67
30 31 0.736053 TGTTTTCGGCAGTCACAACC 59.264 50.000 0.00 0.00 0.00 3.77
31 32 1.400494 ACTGTTTTCGGCAGTCACAAC 59.600 47.619 0.00 0.00 42.90 3.32
32 33 1.400142 CACTGTTTTCGGCAGTCACAA 59.600 47.619 0.00 0.00 44.43 3.33
33 34 1.013596 CACTGTTTTCGGCAGTCACA 58.986 50.000 0.00 0.00 44.43 3.58
34 35 0.317020 GCACTGTTTTCGGCAGTCAC 60.317 55.000 0.00 0.00 44.43 3.67
35 36 0.463654 AGCACTGTTTTCGGCAGTCA 60.464 50.000 0.00 0.00 44.43 3.41
36 37 0.040958 CAGCACTGTTTTCGGCAGTC 60.041 55.000 0.00 0.00 44.43 3.51
37 38 1.447317 CCAGCACTGTTTTCGGCAGT 61.447 55.000 0.00 0.00 46.86 4.40
38 39 1.165907 TCCAGCACTGTTTTCGGCAG 61.166 55.000 0.00 0.00 39.67 4.85
39 40 1.153066 TCCAGCACTGTTTTCGGCA 60.153 52.632 0.00 0.00 0.00 5.69
40 41 1.166531 ACTCCAGCACTGTTTTCGGC 61.167 55.000 0.00 0.00 0.00 5.54
41 42 1.308998 AACTCCAGCACTGTTTTCGG 58.691 50.000 0.00 0.00 0.00 4.30
42 43 3.390135 TCTAACTCCAGCACTGTTTTCG 58.610 45.455 0.00 0.00 0.00 3.46
43 44 4.997395 TCATCTAACTCCAGCACTGTTTTC 59.003 41.667 0.00 0.00 0.00 2.29
44 45 4.973168 TCATCTAACTCCAGCACTGTTTT 58.027 39.130 0.00 0.00 0.00 2.43
45 46 4.623932 TCATCTAACTCCAGCACTGTTT 57.376 40.909 0.00 0.00 0.00 2.83
46 47 4.019860 ACATCATCTAACTCCAGCACTGTT 60.020 41.667 0.00 0.00 0.00 3.16
47 48 3.517100 ACATCATCTAACTCCAGCACTGT 59.483 43.478 0.00 0.00 0.00 3.55
48 49 4.134379 ACATCATCTAACTCCAGCACTG 57.866 45.455 0.00 0.00 0.00 3.66
49 50 4.019860 ACAACATCATCTAACTCCAGCACT 60.020 41.667 0.00 0.00 0.00 4.40
50 51 4.256920 ACAACATCATCTAACTCCAGCAC 58.743 43.478 0.00 0.00 0.00 4.40
51 52 4.558226 ACAACATCATCTAACTCCAGCA 57.442 40.909 0.00 0.00 0.00 4.41
52 53 4.437930 GCAACAACATCATCTAACTCCAGC 60.438 45.833 0.00 0.00 0.00 4.85
53 54 4.696877 TGCAACAACATCATCTAACTCCAG 59.303 41.667 0.00 0.00 0.00 3.86
54 55 4.650734 TGCAACAACATCATCTAACTCCA 58.349 39.130 0.00 0.00 0.00 3.86
55 56 4.697352 ACTGCAACAACATCATCTAACTCC 59.303 41.667 0.00 0.00 0.00 3.85
56 57 5.869753 ACTGCAACAACATCATCTAACTC 57.130 39.130 0.00 0.00 0.00 3.01
57 58 6.639632 AAACTGCAACAACATCATCTAACT 57.360 33.333 0.00 0.00 0.00 2.24
58 59 6.917477 TGAAAACTGCAACAACATCATCTAAC 59.083 34.615 0.00 0.00 0.00 2.34
59 60 7.036996 TGAAAACTGCAACAACATCATCTAA 57.963 32.000 0.00 0.00 0.00 2.10
60 61 6.631971 TGAAAACTGCAACAACATCATCTA 57.368 33.333 0.00 0.00 0.00 1.98
61 62 5.518848 TGAAAACTGCAACAACATCATCT 57.481 34.783 0.00 0.00 0.00 2.90
62 63 5.332808 GCTTGAAAACTGCAACAACATCATC 60.333 40.000 0.00 0.00 0.00 2.92
63 64 4.508861 GCTTGAAAACTGCAACAACATCAT 59.491 37.500 0.00 0.00 0.00 2.45
64 65 3.864583 GCTTGAAAACTGCAACAACATCA 59.135 39.130 0.00 0.00 0.00 3.07
65 66 3.245990 GGCTTGAAAACTGCAACAACATC 59.754 43.478 0.00 0.00 0.00 3.06
66 67 3.197265 GGCTTGAAAACTGCAACAACAT 58.803 40.909 0.00 0.00 0.00 2.71
67 68 2.028658 TGGCTTGAAAACTGCAACAACA 60.029 40.909 0.00 0.00 0.00 3.33
68 69 2.604462 CTGGCTTGAAAACTGCAACAAC 59.396 45.455 0.00 0.00 0.00 3.32
69 70 2.891112 CTGGCTTGAAAACTGCAACAA 58.109 42.857 0.00 0.00 0.00 2.83
70 71 1.471327 GCTGGCTTGAAAACTGCAACA 60.471 47.619 0.00 0.00 0.00 3.33
71 72 1.211743 GCTGGCTTGAAAACTGCAAC 58.788 50.000 0.00 0.00 0.00 4.17
72 73 0.104671 GGCTGGCTTGAAAACTGCAA 59.895 50.000 0.00 0.00 0.00 4.08
110 111 1.577736 CCCAGGTCTTCCAGATGAGT 58.422 55.000 0.00 0.00 35.89 3.41
161 162 1.677576 CATAGCCGGTTGTGATGCAAT 59.322 47.619 9.51 0.00 39.55 3.56
162 163 1.093972 CATAGCCGGTTGTGATGCAA 58.906 50.000 9.51 0.00 34.16 4.08
167 168 1.376683 GCACCATAGCCGGTTGTGA 60.377 57.895 16.62 0.00 37.07 3.58
315 316 2.008268 GCGGCACATCCCTTCCATTG 62.008 60.000 0.00 0.00 0.00 2.82
316 317 1.754234 GCGGCACATCCCTTCCATT 60.754 57.895 0.00 0.00 0.00 3.16
346 347 1.069765 CTGCGTGGTGACCAGTCTT 59.930 57.895 3.58 0.00 32.34 3.01
361 362 4.819761 TCTCCATGGTCGCGCTGC 62.820 66.667 12.58 0.00 0.00 5.25
420 421 0.029567 GTGAGCGACAGTATCCCTCG 59.970 60.000 0.00 0.00 35.30 4.63
492 496 1.194547 TCGCTGACGCTTGATTGTTTC 59.805 47.619 0.00 0.00 39.84 2.78
495 499 0.599991 TGTCGCTGACGCTTGATTGT 60.600 50.000 4.65 0.00 39.84 2.71
498 502 0.108662 TGATGTCGCTGACGCTTGAT 60.109 50.000 4.65 0.00 39.84 2.57
499 503 0.108662 ATGATGTCGCTGACGCTTGA 60.109 50.000 4.65 0.00 39.84 3.02
506 510 1.550072 TCAAGGTGATGATGTCGCTGA 59.450 47.619 0.00 0.00 37.50 4.26
520 524 2.238144 CCAGGTCACATCTGATCAAGGT 59.762 50.000 0.00 0.00 34.36 3.50
524 528 1.483827 GCTCCAGGTCACATCTGATCA 59.516 52.381 0.00 0.00 34.36 2.92
525 529 1.483827 TGCTCCAGGTCACATCTGATC 59.516 52.381 0.00 0.00 34.36 2.92
562 566 1.291272 GGGTCGCTAAACAGGTCGT 59.709 57.895 0.00 0.00 0.00 4.34
564 568 0.323957 AAGGGGTCGCTAAACAGGTC 59.676 55.000 0.00 0.00 0.00 3.85
683 689 2.271607 TGATCGAGAGTGCGGTCAGC 62.272 60.000 0.00 0.00 45.50 4.26
692 698 2.445682 AGGGCTAACTGATCGAGAGT 57.554 50.000 0.00 0.00 0.00 3.24
693 699 3.810310 AAAGGGCTAACTGATCGAGAG 57.190 47.619 0.00 0.00 0.00 3.20
715 722 6.575244 TTGATTTAGCAGAGGGGAGAATAA 57.425 37.500 0.00 0.00 0.00 1.40
783 790 9.836864 AGAGGTGCATTTTTCTTATTTTCTTTT 57.163 25.926 0.00 0.00 0.00 2.27
784 791 9.836864 AAGAGGTGCATTTTTCTTATTTTCTTT 57.163 25.926 0.00 0.00 0.00 2.52
785 792 9.481340 GAAGAGGTGCATTTTTCTTATTTTCTT 57.519 29.630 0.00 0.00 30.49 2.52
786 793 8.090831 GGAAGAGGTGCATTTTTCTTATTTTCT 58.909 33.333 0.00 0.00 30.49 2.52
787 794 8.090831 AGGAAGAGGTGCATTTTTCTTATTTTC 58.909 33.333 0.00 0.00 30.49 2.29
788 795 7.874528 CAGGAAGAGGTGCATTTTTCTTATTTT 59.125 33.333 0.00 0.00 30.49 1.82
789 796 7.381323 CAGGAAGAGGTGCATTTTTCTTATTT 58.619 34.615 0.00 0.00 30.49 1.40
790 797 6.573094 GCAGGAAGAGGTGCATTTTTCTTATT 60.573 38.462 0.00 0.00 39.62 1.40
791 798 5.105595 GCAGGAAGAGGTGCATTTTTCTTAT 60.106 40.000 0.00 0.00 39.62 1.73
792 799 4.218417 GCAGGAAGAGGTGCATTTTTCTTA 59.782 41.667 0.00 0.00 39.62 2.10
793 800 3.006217 GCAGGAAGAGGTGCATTTTTCTT 59.994 43.478 0.00 0.00 39.62 2.52
794 801 2.560105 GCAGGAAGAGGTGCATTTTTCT 59.440 45.455 0.00 0.00 39.62 2.52
795 802 2.297033 TGCAGGAAGAGGTGCATTTTTC 59.703 45.455 0.00 0.00 44.70 2.29
796 803 2.318908 TGCAGGAAGAGGTGCATTTTT 58.681 42.857 0.00 0.00 44.70 1.94
797 804 1.999648 TGCAGGAAGAGGTGCATTTT 58.000 45.000 0.00 0.00 44.70 1.82
798 805 3.751767 TGCAGGAAGAGGTGCATTT 57.248 47.368 0.00 0.00 44.70 2.32
802 809 1.538047 TCAAATGCAGGAAGAGGTGC 58.462 50.000 0.00 0.00 40.29 5.01
803 810 3.760151 TGATTCAAATGCAGGAAGAGGTG 59.240 43.478 0.00 0.00 0.00 4.00
804 811 3.760684 GTGATTCAAATGCAGGAAGAGGT 59.239 43.478 0.00 0.00 0.00 3.85
805 812 3.181503 CGTGATTCAAATGCAGGAAGAGG 60.182 47.826 0.00 0.00 0.00 3.69
806 813 3.686241 TCGTGATTCAAATGCAGGAAGAG 59.314 43.478 0.00 0.00 0.00 2.85
807 814 3.436704 GTCGTGATTCAAATGCAGGAAGA 59.563 43.478 0.00 0.00 0.00 2.87
808 815 3.426695 GGTCGTGATTCAAATGCAGGAAG 60.427 47.826 0.00 0.00 0.00 3.46
809 816 2.487762 GGTCGTGATTCAAATGCAGGAA 59.512 45.455 0.00 0.00 0.00 3.36
810 817 2.083774 GGTCGTGATTCAAATGCAGGA 58.916 47.619 0.00 0.00 0.00 3.86
811 818 1.811965 TGGTCGTGATTCAAATGCAGG 59.188 47.619 0.00 0.00 0.00 4.85
812 819 3.770263 ATGGTCGTGATTCAAATGCAG 57.230 42.857 0.00 0.00 0.00 4.41
813 820 4.436718 CGTTATGGTCGTGATTCAAATGCA 60.437 41.667 0.00 0.00 0.00 3.96
814 821 4.028383 CGTTATGGTCGTGATTCAAATGC 58.972 43.478 0.00 0.00 0.00 3.56
815 822 5.463499 TCGTTATGGTCGTGATTCAAATG 57.537 39.130 0.00 0.00 0.00 2.32
816 823 6.489127 TTTCGTTATGGTCGTGATTCAAAT 57.511 33.333 0.00 0.00 0.00 2.32
817 824 5.926214 TTTCGTTATGGTCGTGATTCAAA 57.074 34.783 0.00 0.00 0.00 2.69
818 825 5.926214 TTTTCGTTATGGTCGTGATTCAA 57.074 34.783 0.00 0.00 0.00 2.69
819 826 6.489127 AATTTTCGTTATGGTCGTGATTCA 57.511 33.333 0.00 0.00 0.00 2.57
820 827 7.457868 TGTAATTTTCGTTATGGTCGTGATTC 58.542 34.615 0.00 0.00 0.00 2.52
821 828 7.367159 TGTAATTTTCGTTATGGTCGTGATT 57.633 32.000 0.00 0.00 0.00 2.57
822 829 6.971527 TGTAATTTTCGTTATGGTCGTGAT 57.028 33.333 0.00 0.00 0.00 3.06
823 830 6.782298 TTGTAATTTTCGTTATGGTCGTGA 57.218 33.333 0.00 0.00 0.00 4.35
824 831 8.362304 CAATTTGTAATTTTCGTTATGGTCGTG 58.638 33.333 0.00 0.00 0.00 4.35
825 832 7.539366 CCAATTTGTAATTTTCGTTATGGTCGT 59.461 33.333 0.00 0.00 0.00 4.34
826 833 7.008810 CCCAATTTGTAATTTTCGTTATGGTCG 59.991 37.037 0.00 0.00 0.00 4.79
827 834 7.815549 ACCCAATTTGTAATTTTCGTTATGGTC 59.184 33.333 0.00 0.00 0.00 4.02
828 835 7.672240 ACCCAATTTGTAATTTTCGTTATGGT 58.328 30.769 0.00 0.00 0.00 3.55
829 836 8.439286 CAACCCAATTTGTAATTTTCGTTATGG 58.561 33.333 0.00 0.00 0.00 2.74
830 837 7.954786 GCAACCCAATTTGTAATTTTCGTTATG 59.045 33.333 0.00 0.00 0.00 1.90
831 838 7.148722 CGCAACCCAATTTGTAATTTTCGTTAT 60.149 33.333 0.00 0.00 0.00 1.89
832 839 6.144080 CGCAACCCAATTTGTAATTTTCGTTA 59.856 34.615 0.00 0.00 0.00 3.18
833 840 5.050702 CGCAACCCAATTTGTAATTTTCGTT 60.051 36.000 0.00 0.00 0.00 3.85
834 841 4.446051 CGCAACCCAATTTGTAATTTTCGT 59.554 37.500 0.00 0.00 0.00 3.85
835 842 4.665394 GCGCAACCCAATTTGTAATTTTCG 60.665 41.667 0.30 0.00 0.00 3.46
836 843 4.212214 TGCGCAACCCAATTTGTAATTTTC 59.788 37.500 8.16 0.00 0.00 2.29
837 844 4.024472 GTGCGCAACCCAATTTGTAATTTT 60.024 37.500 14.00 0.00 0.00 1.82
838 845 3.496507 GTGCGCAACCCAATTTGTAATTT 59.503 39.130 14.00 0.00 0.00 1.82
839 846 3.063485 GTGCGCAACCCAATTTGTAATT 58.937 40.909 14.00 0.00 0.00 1.40
840 847 2.036475 TGTGCGCAACCCAATTTGTAAT 59.964 40.909 14.00 0.00 0.00 1.89
841 848 1.409064 TGTGCGCAACCCAATTTGTAA 59.591 42.857 14.00 0.00 0.00 2.41
842 849 1.032794 TGTGCGCAACCCAATTTGTA 58.967 45.000 14.00 0.00 0.00 2.41
843 850 0.529555 GTGTGCGCAACCCAATTTGT 60.530 50.000 14.00 0.00 0.00 2.83
844 851 1.547292 CGTGTGCGCAACCCAATTTG 61.547 55.000 14.00 0.00 0.00 2.32
845 852 1.299773 CGTGTGCGCAACCCAATTT 60.300 52.632 14.00 0.00 0.00 1.82
846 853 1.523154 ATCGTGTGCGCAACCCAATT 61.523 50.000 14.00 0.00 38.14 2.32
847 854 1.523154 AATCGTGTGCGCAACCCAAT 61.523 50.000 14.00 0.00 38.14 3.16
848 855 2.123988 GAATCGTGTGCGCAACCCAA 62.124 55.000 14.00 0.00 38.14 4.12
849 856 2.593148 AATCGTGTGCGCAACCCA 60.593 55.556 14.00 2.47 38.14 4.51
850 857 2.175811 GAATCGTGTGCGCAACCC 59.824 61.111 14.00 0.00 38.14 4.11
851 858 2.202171 CGAATCGTGTGCGCAACC 60.202 61.111 14.00 4.22 38.14 3.77
852 859 2.202171 CCGAATCGTGTGCGCAAC 60.202 61.111 14.00 12.18 38.14 4.17
853 860 2.663520 ACCGAATCGTGTGCGCAA 60.664 55.556 14.00 0.00 38.14 4.85
854 861 3.410516 CACCGAATCGTGTGCGCA 61.411 61.111 5.66 5.66 38.14 6.09
855 862 4.794241 GCACCGAATCGTGTGCGC 62.794 66.667 24.71 0.00 41.22 6.09
856 863 4.147322 GGCACCGAATCGTGTGCG 62.147 66.667 28.56 8.31 46.52 5.34
857 864 4.147322 CGGCACCGAATCGTGTGC 62.147 66.667 28.22 28.22 45.64 4.57
858 865 4.147322 GCGGCACCGAATCGTGTG 62.147 66.667 14.43 16.16 42.83 3.82
859 866 3.876589 AAGCGGCACCGAATCGTGT 62.877 57.895 14.43 0.00 42.83 4.49
860 867 3.083600 GAAGCGGCACCGAATCGTG 62.084 63.158 14.43 1.46 42.83 4.35
861 868 2.813908 GAAGCGGCACCGAATCGT 60.814 61.111 14.43 0.00 42.83 3.73
862 869 3.913573 CGAAGCGGCACCGAATCG 61.914 66.667 14.43 16.68 42.83 3.34
875 882 1.751351 TCTATCAGACCCACTGCGAAG 59.249 52.381 0.00 0.00 45.38 3.79
876 883 1.847328 TCTATCAGACCCACTGCGAA 58.153 50.000 0.00 0.00 45.38 4.70
877 884 1.847328 TTCTATCAGACCCACTGCGA 58.153 50.000 0.00 0.00 45.38 5.10
878 885 2.672961 TTTCTATCAGACCCACTGCG 57.327 50.000 0.00 0.00 45.38 5.18
879 886 2.680339 GCTTTTCTATCAGACCCACTGC 59.320 50.000 0.00 0.00 45.38 4.40
880 887 2.932614 CGCTTTTCTATCAGACCCACTG 59.067 50.000 0.00 0.00 46.97 3.66
881 888 2.678190 GCGCTTTTCTATCAGACCCACT 60.678 50.000 0.00 0.00 0.00 4.00
882 889 1.666189 GCGCTTTTCTATCAGACCCAC 59.334 52.381 0.00 0.00 0.00 4.61
886 893 2.893637 TCAGGCGCTTTTCTATCAGAC 58.106 47.619 7.64 0.00 0.00 3.51
891 898 2.162408 GCAGTTTCAGGCGCTTTTCTAT 59.838 45.455 7.64 0.00 0.00 1.98
904 911 1.072331 GGGTCCAGAAGAGCAGTTTCA 59.928 52.381 0.00 0.00 45.21 2.69
909 916 0.179089 CATCGGGTCCAGAAGAGCAG 60.179 60.000 0.00 0.00 45.21 4.24
910 917 1.900351 CATCGGGTCCAGAAGAGCA 59.100 57.895 0.00 0.00 45.21 4.26
911 918 1.522580 GCATCGGGTCCAGAAGAGC 60.523 63.158 0.00 0.00 42.55 4.09
912 919 1.227089 CGCATCGGGTCCAGAAGAG 60.227 63.158 0.00 0.00 0.00 2.85
917 924 2.930385 AATGCTCGCATCGGGTCCAG 62.930 60.000 4.68 0.00 35.31 3.86
930 937 3.330267 ACCGAGACTTTTCTGAATGCTC 58.670 45.455 0.00 0.00 29.47 4.26
932 939 4.489679 AAACCGAGACTTTTCTGAATGC 57.510 40.909 0.00 0.00 29.47 3.56
933 940 6.060028 TCAAAACCGAGACTTTTCTGAATG 57.940 37.500 0.00 0.00 29.47 2.67
934 941 6.712547 AGATCAAAACCGAGACTTTTCTGAAT 59.287 34.615 0.00 0.00 29.47 2.57
935 942 6.055588 AGATCAAAACCGAGACTTTTCTGAA 58.944 36.000 0.00 0.00 29.47 3.02
936 943 5.611374 AGATCAAAACCGAGACTTTTCTGA 58.389 37.500 0.00 0.00 29.47 3.27
937 944 5.698545 AGAGATCAAAACCGAGACTTTTCTG 59.301 40.000 0.00 0.00 29.47 3.02
938 945 5.859495 AGAGATCAAAACCGAGACTTTTCT 58.141 37.500 0.00 0.00 33.37 2.52
939 946 6.202954 TGAAGAGATCAAAACCGAGACTTTTC 59.797 38.462 0.00 0.00 34.30 2.29
940 947 6.055588 TGAAGAGATCAAAACCGAGACTTTT 58.944 36.000 0.00 0.00 34.30 2.27
944 957 4.266502 CGATGAAGAGATCAAAACCGAGAC 59.733 45.833 0.00 0.00 42.54 3.36
950 963 5.669848 GCACTGACGATGAAGAGATCAAAAC 60.670 44.000 0.00 0.00 42.54 2.43
951 964 4.389992 GCACTGACGATGAAGAGATCAAAA 59.610 41.667 0.00 0.00 42.54 2.44
954 967 2.493278 TGCACTGACGATGAAGAGATCA 59.507 45.455 0.00 0.00 43.67 2.92
955 968 2.857152 GTGCACTGACGATGAAGAGATC 59.143 50.000 10.32 0.00 0.00 2.75
967 980 1.230324 GAGGGAAAGTGTGCACTGAC 58.770 55.000 19.41 8.91 41.58 3.51
974 987 1.605712 GGAGTGACGAGGGAAAGTGTG 60.606 57.143 0.00 0.00 0.00 3.82
1128 1141 2.098680 GACGCGAGGACACGAGAG 59.901 66.667 15.93 0.00 36.92 3.20
1133 1146 2.488820 GGTAGGACGCGAGGACAC 59.511 66.667 15.93 3.42 0.00 3.67
1159 1172 2.357034 GAACAGGTGGCGAGCGAA 60.357 61.111 0.00 0.00 0.00 4.70
1414 1427 2.779951 TACATCTGCACAAGCGCGGT 62.780 55.000 4.23 4.23 46.23 5.68
1476 1489 2.087009 GTCTGGTTCCTCGAACGCG 61.087 63.158 3.53 3.53 42.78 6.01
1688 1701 4.322049 CCAAGTCGTACTCCAAGTCATTCT 60.322 45.833 0.00 0.00 0.00 2.40
1704 1717 1.197721 GCATTCACCAGAACCAAGTCG 59.802 52.381 0.00 0.00 36.39 4.18
1744 1757 0.379669 GATTGCACAGCTCCAATCCG 59.620 55.000 15.45 0.00 40.73 4.18
1758 1771 3.242870 CGAATAACCTCCTTGCAGATTGC 60.243 47.826 0.00 0.00 45.29 3.56
1782 1795 1.678627 ACGTCTCTCTCCATCATTCCG 59.321 52.381 0.00 0.00 0.00 4.30
1860 1873 9.237846 GCAACCATTTTCTTATATAAGCTCAAC 57.762 33.333 16.37 0.00 33.40 3.18
1867 1880 6.238897 CCTGCCGCAACCATTTTCTTATATAA 60.239 38.462 0.00 0.00 0.00 0.98
2058 2071 0.323178 ACTGCATTGCCTTCTCCTGG 60.323 55.000 6.12 0.00 0.00 4.45
2118 2131 1.204941 GTAAGACCACTGATGACCGCT 59.795 52.381 0.00 0.00 0.00 5.52
2127 2140 3.496331 ACCATTTTGGGTAAGACCACTG 58.504 45.455 0.00 0.00 43.37 3.66
2290 2303 8.918202 TTCTTATCACAGAAACCAGTGTTAAT 57.082 30.769 0.00 0.00 37.07 1.40
2315 2328 1.039233 AAGTGCAGCTGCCACAAACT 61.039 50.000 34.64 26.60 41.18 2.66
2415 2428 2.170187 ACCTGAGATCATTGAGCTCCAC 59.830 50.000 24.84 5.91 43.48 4.02
2490 2503 6.598064 GGCTATTAGGTTTAACTGAAGAAGCA 59.402 38.462 14.65 0.00 0.00 3.91
2559 2572 5.584551 AAATGGACTTTCCTTCCTGTACT 57.415 39.130 0.00 0.00 37.46 2.73
2562 2575 7.669089 TTTAAAAATGGACTTTCCTTCCTGT 57.331 32.000 0.00 0.00 37.46 4.00
2566 2579 8.498358 CATGCTTTTAAAAATGGACTTTCCTTC 58.502 33.333 1.66 0.00 37.46 3.46
2595 2608 2.037641 TGGCATGATTCCATAGACTCGG 59.962 50.000 0.00 0.00 0.00 4.63
2620 2633 0.531532 ATGGCACTACGATGCTCTGC 60.532 55.000 10.09 0.00 45.38 4.26
2691 2704 1.003580 GCTCTCCCACCTGTTTCATGA 59.996 52.381 0.00 0.00 0.00 3.07
2777 2790 1.804748 GTAGTTTGGCAGCTACCACAC 59.195 52.381 13.55 13.55 40.19 3.82
2779 2792 2.289444 TGAGTAGTTTGGCAGCTACCAC 60.289 50.000 20.34 16.55 40.19 4.16
2809 2822 5.675684 TTGTAGTAGCCAACATGATCAGA 57.324 39.130 0.00 0.00 0.00 3.27
2814 2827 5.939764 AGAGATTGTAGTAGCCAACATGA 57.060 39.130 0.00 0.00 0.00 3.07
2853 2866 6.232581 ACATTGTCCCACTTTTCATCAAAA 57.767 33.333 0.00 0.00 0.00 2.44
2873 2886 9.213777 TGATAATGTCCCTAGTCTCTTTTACAT 57.786 33.333 0.00 0.00 0.00 2.29
2925 2938 1.047801 TCTCTACTGCACTGCAACCA 58.952 50.000 4.99 0.00 38.41 3.67
2938 2951 6.854892 GTGTGCATTGCATTATTGATCTCTAC 59.145 38.462 15.49 0.00 41.91 2.59
3070 3083 4.918810 AATCTTCAAACACCAAGTGACC 57.081 40.909 0.96 0.00 36.96 4.02
3244 3257 8.204836 GGAAGTGTCTGTCCTACATATACAATT 58.795 37.037 0.00 0.00 31.21 2.32
3345 3358 1.694150 GGTAGCCATGCTCTGACCATA 59.306 52.381 0.00 0.00 40.44 2.74
3362 3375 7.971722 GCGCTTCTTTAATTATGGAAAAAGGTA 59.028 33.333 0.00 0.00 31.37 3.08
3364 3377 6.020678 CGCGCTTCTTTAATTATGGAAAAAGG 60.021 38.462 5.56 0.00 31.37 3.11
3478 3493 4.333913 ACAGCTCACATATCATGAGTCC 57.666 45.455 12.88 1.19 44.60 3.85
3497 3512 2.671888 CGACTACGAGAGAGCACTAACA 59.328 50.000 0.00 0.00 42.66 2.41
3505 3520 2.619147 TGACTTCCGACTACGAGAGAG 58.381 52.381 0.00 0.00 42.66 3.20
3508 3523 4.261072 GCATAATGACTTCCGACTACGAGA 60.261 45.833 0.00 0.00 42.66 4.04
3509 3524 3.975670 GCATAATGACTTCCGACTACGAG 59.024 47.826 0.00 0.00 42.66 4.18
3565 3580 2.036217 CTGCAAAAGCATTGGAGGTTCA 59.964 45.455 13.63 0.00 34.74 3.18
3759 3774 0.514691 GCTAATCGCTGCCTGCATAC 59.485 55.000 0.00 0.00 43.06 2.39
3769 3784 3.522553 GTTTCTGTACCTGCTAATCGCT 58.477 45.455 0.00 0.00 40.11 4.93
3879 3905 2.047061 TGTAGTCCACAAAGACTGGCT 58.953 47.619 4.49 0.00 46.54 4.75
3906 3932 5.697633 ACAAAAGATAACAAATGCAAGGCAG 59.302 36.000 0.00 0.00 43.65 4.85
3943 3971 0.976641 TCCAGGTGTTCAGAGCGATT 59.023 50.000 0.00 0.00 0.00 3.34
3998 4026 3.608073 GGCAATTAGACGCAAACATTGTC 59.392 43.478 0.00 0.00 0.00 3.18
4021 4049 1.550327 TCATAAACCAATGCGGCCAA 58.450 45.000 2.24 0.00 39.03 4.52


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

AutoCloner maintained by Alex Coulton.