Multiple sequence alignment - TraesCS5D01G136300

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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 TraesCS5D01G136300 chr5D 100.000 3004 0 0 1 3004 216997554 217000557 0.000000e+00 5548.0
1 TraesCS5D01G136300 chr5D 85.000 220 26 4 2787 3003 207020651 207020866 1.810000e-52 217.0
2 TraesCS5D01G136300 chr5A 96.598 2616 41 20 63 2643 287609284 287611886 0.000000e+00 4294.0
3 TraesCS5D01G136300 chr5B 95.589 2607 53 21 63 2643 232787052 232784482 0.000000e+00 4120.0
4 TraesCS5D01G136300 chr5B 96.970 33 1 0 2784 2816 636965884 636965916 4.180000e-04 56.5
5 TraesCS5D01G136300 chr2B 91.354 347 24 3 2643 2985 747677087 747676743 1.260000e-128 470.0
6 TraesCS5D01G136300 chr6D 92.949 156 5 2 2642 2791 56204872 56204717 3.900000e-54 222.0
7 TraesCS5D01G136300 chr6D 92.715 151 7 1 2642 2788 75293298 75293448 6.520000e-52 215.0
8 TraesCS5D01G136300 chr6D 84.545 110 14 3 2784 2891 38562809 38562701 4.100000e-19 106.0
9 TraesCS5D01G136300 chr6D 83.838 99 14 2 2784 2881 38544364 38544267 3.190000e-15 93.5
10 TraesCS5D01G136300 chr3B 92.763 152 6 1 2642 2788 164641137 164640986 6.520000e-52 215.0
11 TraesCS5D01G136300 chr3D 92.053 151 7 1 2643 2788 149689575 149689725 1.090000e-49 207.0
12 TraesCS5D01G136300 chr3D 93.243 74 3 2 1 73 523510582 523510510 1.140000e-19 108.0
13 TraesCS5D01G136300 chr3D 85.294 102 9 4 2785 2881 568931719 568931619 1.910000e-17 100.0
14 TraesCS5D01G136300 chr2D 92.000 150 9 3 2642 2788 70385360 70385509 1.090000e-49 207.0
15 TraesCS5D01G136300 chr1D 91.275 149 10 1 2643 2788 5693006 5693154 1.830000e-47 200.0
16 TraesCS5D01G136300 chr3A 86.842 152 16 3 2642 2789 589836660 589836509 1.850000e-37 167.0
17 TraesCS5D01G136300 chr3A 97.101 69 2 0 1 69 463140666 463140734 1.890000e-22 117.0
18 TraesCS5D01G136300 chr3A 92.500 80 4 2 1 79 377426417 377426495 2.450000e-21 113.0
19 TraesCS5D01G136300 chr7B 85.443 158 19 4 2635 2788 81415351 81415194 8.620000e-36 161.0
20 TraesCS5D01G136300 chr7B 95.652 69 3 0 1 69 354759875 354759807 8.800000e-21 111.0
21 TraesCS5D01G136300 chr4A 96.970 66 2 0 1 66 17384210 17384145 8.800000e-21 111.0
22 TraesCS5D01G136300 chr4A 95.714 70 2 1 1 69 120037528 120037459 8.800000e-21 111.0
23 TraesCS5D01G136300 chr6A 94.366 71 3 1 1 70 389904282 389904212 1.140000e-19 108.0
24 TraesCS5D01G136300 chr6A 93.243 74 4 1 2 74 389904487 389904560 1.140000e-19 108.0
25 TraesCS5D01G136300 chr4D 95.522 67 3 0 1 67 498393564 498393630 1.140000e-19 108.0
26 TraesCS5D01G136300 chr4D 77.885 104 16 6 2786 2885 255533457 255533357 1.160000e-04 58.4
27 TraesCS5D01G136300 chrUn 90.000 50 5 0 2787 2836 147943792 147943743 6.950000e-07 65.8


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 TraesCS5D01G136300 chr5D 216997554 217000557 3003 False 5548 5548 100.000 1 3004 1 chr5D.!!$F2 3003
1 TraesCS5D01G136300 chr5A 287609284 287611886 2602 False 4294 4294 96.598 63 2643 1 chr5A.!!$F1 2580
2 TraesCS5D01G136300 chr5B 232784482 232787052 2570 True 4120 4120 95.589 63 2643 1 chr5B.!!$R1 2580

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
220 222 0.178873 TCCACAAGGGCCTACTTCCT 60.179 55.0 6.41 0.0 36.21 3.36 F
1055 1084 0.464036 TCGCAACAACCAGACAGAGT 59.536 50.0 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1138 2.620627 CCCCACAATAAGAGGTTCCACC 60.621 54.545 0.0 0.0 38.99 4.61 R
2830 2877 0.172352 ATGTAAAATTGCCACGCCGG 59.828 50.000 0.0 0.0 38.11 6.13 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
24 25 7.466746 AAAATCTAGAGTGGCATAAGCAAAA 57.533 32.000 0.00 0.00 44.61 2.44
25 26 7.651027 AAATCTAGAGTGGCATAAGCAAAAT 57.349 32.000 0.00 0.00 44.61 1.82
26 27 7.651027 AATCTAGAGTGGCATAAGCAAAATT 57.349 32.000 0.00 0.00 44.61 1.82
27 28 6.441093 TCTAGAGTGGCATAAGCAAAATTG 57.559 37.500 0.00 0.00 44.61 2.32
28 29 4.460948 AGAGTGGCATAAGCAAAATTGG 57.539 40.909 0.00 0.00 44.61 3.16
29 30 2.931969 GAGTGGCATAAGCAAAATTGGC 59.068 45.455 0.00 0.00 44.61 4.52
30 31 2.302445 AGTGGCATAAGCAAAATTGGCA 59.698 40.909 0.00 0.00 44.61 4.92
31 32 3.072944 GTGGCATAAGCAAAATTGGCAA 58.927 40.909 0.68 0.68 44.76 4.52
32 33 3.501445 GTGGCATAAGCAAAATTGGCAAA 59.499 39.130 3.01 0.00 44.76 3.68
33 34 4.023365 GTGGCATAAGCAAAATTGGCAAAA 60.023 37.500 3.01 0.00 44.76 2.44
34 35 4.215827 TGGCATAAGCAAAATTGGCAAAAG 59.784 37.500 3.01 0.00 44.61 2.27
35 36 4.160594 GCATAAGCAAAATTGGCAAAAGC 58.839 39.130 3.01 6.24 41.58 3.51
36 37 4.083164 GCATAAGCAAAATTGGCAAAAGCT 60.083 37.500 3.01 8.57 41.58 3.74
37 38 5.122082 GCATAAGCAAAATTGGCAAAAGCTA 59.878 36.000 15.85 8.06 41.58 3.32
38 39 6.348376 GCATAAGCAAAATTGGCAAAAGCTAA 60.348 34.615 15.85 0.00 41.58 3.09
39 40 7.583230 CATAAGCAAAATTGGCAAAAGCTAAA 58.417 30.769 15.85 10.03 0.00 1.85
40 41 5.678132 AGCAAAATTGGCAAAAGCTAAAG 57.322 34.783 3.01 0.00 0.00 1.85
41 42 5.125356 AGCAAAATTGGCAAAAGCTAAAGT 58.875 33.333 3.01 0.00 0.00 2.66
42 43 5.007921 AGCAAAATTGGCAAAAGCTAAAGTG 59.992 36.000 3.01 0.00 0.00 3.16
43 44 5.750650 CAAAATTGGCAAAAGCTAAAGTGG 58.249 37.500 3.01 0.00 0.00 4.00
44 45 2.524569 TTGGCAAAAGCTAAAGTGGC 57.475 45.000 0.00 0.00 37.09 5.01
45 46 1.407936 TGGCAAAAGCTAAAGTGGCA 58.592 45.000 9.97 9.97 43.41 4.92
46 47 1.759445 TGGCAAAAGCTAAAGTGGCAA 59.241 42.857 11.18 0.00 42.78 4.52
47 48 2.169352 TGGCAAAAGCTAAAGTGGCAAA 59.831 40.909 11.18 0.00 42.78 3.68
48 49 3.202097 GGCAAAAGCTAAAGTGGCAAAA 58.798 40.909 0.00 0.00 36.61 2.44
49 50 3.625313 GGCAAAAGCTAAAGTGGCAAAAA 59.375 39.130 0.00 0.00 36.61 1.94
50 51 4.495679 GGCAAAAGCTAAAGTGGCAAAAAC 60.496 41.667 0.00 0.00 36.61 2.43
51 52 4.094146 GCAAAAGCTAAAGTGGCAAAAACA 59.906 37.500 0.00 0.00 0.00 2.83
52 53 5.391416 GCAAAAGCTAAAGTGGCAAAAACAA 60.391 36.000 0.00 0.00 0.00 2.83
53 54 6.606768 CAAAAGCTAAAGTGGCAAAAACAAA 58.393 32.000 0.00 0.00 0.00 2.83
54 55 6.421377 AAAGCTAAAGTGGCAAAAACAAAG 57.579 33.333 0.00 0.00 0.00 2.77
55 56 5.084818 AGCTAAAGTGGCAAAAACAAAGT 57.915 34.783 0.00 0.00 0.00 2.66
56 57 5.487433 AGCTAAAGTGGCAAAAACAAAGTT 58.513 33.333 0.00 0.00 0.00 2.66
57 58 5.937540 AGCTAAAGTGGCAAAAACAAAGTTT 59.062 32.000 0.00 0.00 0.00 2.66
58 59 6.429692 AGCTAAAGTGGCAAAAACAAAGTTTT 59.570 30.769 2.26 2.26 0.00 2.43
59 60 6.740905 GCTAAAGTGGCAAAAACAAAGTTTTC 59.259 34.615 8.16 0.00 0.00 2.29
60 61 5.621197 AAGTGGCAAAAACAAAGTTTTCC 57.379 34.783 8.16 7.10 0.00 3.13
61 62 4.006989 AGTGGCAAAAACAAAGTTTTCCC 58.993 39.130 8.16 11.39 0.00 3.97
219 221 0.253327 CTCCACAAGGGCCTACTTCC 59.747 60.000 6.41 0.00 36.21 3.46
220 222 0.178873 TCCACAAGGGCCTACTTCCT 60.179 55.000 6.41 0.00 36.21 3.36
221 223 0.698818 CCACAAGGGCCTACTTCCTT 59.301 55.000 6.41 0.00 43.55 3.36
324 332 3.794717 TGCAATGTGACTGCAAATTTGT 58.205 36.364 19.03 0.00 46.47 2.83
530 555 6.712998 TGTTTCCGAAAGAAATAACATGGAGA 59.287 34.615 0.00 0.00 45.99 3.71
705 731 5.493133 ACGAAGATAAAACAAGTGTGCAA 57.507 34.783 0.00 0.00 0.00 4.08
1055 1084 0.464036 TCGCAACAACCAGACAGAGT 59.536 50.000 0.00 0.00 0.00 3.24
1109 1138 2.418746 CCTTCCAACCATGTCTAGGTCG 60.419 54.545 0.00 0.00 38.76 4.79
1283 1312 2.113139 CAAGGGGGTGACTTGCGT 59.887 61.111 0.00 0.00 38.89 5.24
1287 1316 2.112297 GGGGTGACTTGCGTTCCA 59.888 61.111 0.00 0.00 0.00 3.53
1298 1327 1.674359 TGCGTTCCATGTTCACACTT 58.326 45.000 0.00 0.00 0.00 3.16
1302 1331 3.363970 GCGTTCCATGTTCACACTTGTAG 60.364 47.826 0.00 0.00 0.00 2.74
1557 1588 1.599542 GCACATCTCCGTATTGCCTTC 59.400 52.381 0.00 0.00 0.00 3.46
1592 1623 9.620259 AAGACTGTTTTCTGAAGACTTCTAATT 57.380 29.630 16.02 0.00 0.00 1.40
1618 1649 7.777440 TGGAGCCATTTTGTCATATATGTTACA 59.223 33.333 12.42 7.75 0.00 2.41
1675 1706 2.579410 TGCTTCTTTTGGTAGGTCCC 57.421 50.000 0.00 0.00 34.77 4.46
1684 1715 1.719529 TGGTAGGTCCCTTCGAACAA 58.280 50.000 0.00 0.00 34.77 2.83
2322 2353 0.608856 ATGTCGCATGCTGGTTCCAA 60.609 50.000 17.13 0.00 0.00 3.53
2434 2465 4.862641 AACCCTCCTAACTGTATTGCAT 57.137 40.909 0.00 0.00 0.00 3.96
2499 2530 2.173569 AGGATCACCCACTAGAAATGCC 59.826 50.000 0.00 0.00 37.41 4.40
2545 2591 3.264193 TGCCTTCATCATGTCCTTACACT 59.736 43.478 0.00 0.00 38.78 3.55
2629 2675 0.400594 AAACTGACCCTCTTTCCCCG 59.599 55.000 0.00 0.00 0.00 5.73
2638 2685 1.404843 CTCTTTCCCCGTCCTCTAGG 58.595 60.000 0.00 0.00 0.00 3.02
2658 2705 7.642082 CTAGGAATACTAGTATAATGCCCGT 57.358 40.000 15.74 0.00 43.47 5.28
2659 2706 6.282199 AGGAATACTAGTATAATGCCCGTG 57.718 41.667 15.74 0.00 0.00 4.94
2660 2707 4.868734 GGAATACTAGTATAATGCCCGTGC 59.131 45.833 15.74 0.00 38.26 5.34
2661 2708 2.433868 ACTAGTATAATGCCCGTGCG 57.566 50.000 0.00 0.00 41.78 5.34
2662 2709 1.684983 ACTAGTATAATGCCCGTGCGT 59.315 47.619 0.00 0.00 41.78 5.24
2664 2711 1.295792 AGTATAATGCCCGTGCGTTG 58.704 50.000 7.64 0.00 46.06 4.10
2665 2712 0.316689 GTATAATGCCCGTGCGTTGC 60.317 55.000 7.64 0.00 46.06 4.17
2666 2713 1.440938 TATAATGCCCGTGCGTTGCC 61.441 55.000 7.64 0.00 46.06 4.52
2681 2728 4.002797 GCCACGGGCTTTTGAGAT 57.997 55.556 7.58 0.00 46.69 2.75
2682 2729 3.168773 GCCACGGGCTTTTGAGATA 57.831 52.632 7.58 0.00 46.69 1.98
2683 2730 1.680338 GCCACGGGCTTTTGAGATAT 58.320 50.000 7.58 0.00 46.69 1.63
2684 2731 2.024414 GCCACGGGCTTTTGAGATATT 58.976 47.619 7.58 0.00 46.69 1.28
2685 2732 2.427095 GCCACGGGCTTTTGAGATATTT 59.573 45.455 7.58 0.00 46.69 1.40
2686 2733 3.119137 GCCACGGGCTTTTGAGATATTTT 60.119 43.478 7.58 0.00 46.69 1.82
2687 2734 4.423732 CCACGGGCTTTTGAGATATTTTG 58.576 43.478 0.00 0.00 0.00 2.44
2688 2735 3.859386 CACGGGCTTTTGAGATATTTTGC 59.141 43.478 0.00 0.00 0.00 3.68
2689 2736 3.763897 ACGGGCTTTTGAGATATTTTGCT 59.236 39.130 0.00 0.00 0.00 3.91
2690 2737 4.947388 ACGGGCTTTTGAGATATTTTGCTA 59.053 37.500 0.00 0.00 0.00 3.49
2691 2738 5.066505 ACGGGCTTTTGAGATATTTTGCTAG 59.933 40.000 0.00 0.00 0.00 3.42
2692 2739 5.296780 CGGGCTTTTGAGATATTTTGCTAGA 59.703 40.000 0.00 0.00 0.00 2.43
2693 2740 6.183360 CGGGCTTTTGAGATATTTTGCTAGAA 60.183 38.462 0.00 0.00 0.00 2.10
2694 2741 7.469181 CGGGCTTTTGAGATATTTTGCTAGAAT 60.469 37.037 0.00 0.00 0.00 2.40
2695 2742 8.200120 GGGCTTTTGAGATATTTTGCTAGAATT 58.800 33.333 0.00 0.00 0.00 2.17
2789 2836 9.561069 AGTCAACTTCACTTACATTGTAAATCT 57.439 29.630 10.32 0.00 0.00 2.40
2811 2858 7.562454 TCTTTTCCTAATAATAAAGCACGGG 57.438 36.000 0.00 0.00 0.00 5.28
2812 2859 7.114095 TCTTTTCCTAATAATAAAGCACGGGT 58.886 34.615 0.00 0.00 0.00 5.28
2813 2860 7.612633 TCTTTTCCTAATAATAAAGCACGGGTT 59.387 33.333 0.00 0.00 0.00 4.11
2814 2861 6.687081 TTCCTAATAATAAAGCACGGGTTG 57.313 37.500 0.00 0.00 0.00 3.77
2815 2862 5.991861 TCCTAATAATAAAGCACGGGTTGA 58.008 37.500 0.00 0.00 0.00 3.18
2816 2863 6.053005 TCCTAATAATAAAGCACGGGTTGAG 58.947 40.000 0.00 0.00 0.00 3.02
2817 2864 4.632538 AATAATAAAGCACGGGTTGAGC 57.367 40.909 0.00 0.00 0.00 4.26
2818 2865 1.904287 AATAAAGCACGGGTTGAGCA 58.096 45.000 0.00 0.00 36.53 4.26
2819 2866 2.128771 ATAAAGCACGGGTTGAGCAT 57.871 45.000 0.00 0.00 36.53 3.79
2820 2867 1.164411 TAAAGCACGGGTTGAGCATG 58.836 50.000 0.00 0.00 36.53 4.06
2821 2868 0.823356 AAAGCACGGGTTGAGCATGT 60.823 50.000 0.00 0.00 36.53 3.21
2822 2869 1.237285 AAGCACGGGTTGAGCATGTC 61.237 55.000 0.00 0.00 36.53 3.06
2823 2870 3.027170 GCACGGGTTGAGCATGTCG 62.027 63.158 0.00 0.00 33.95 4.35
2824 2871 2.047274 ACGGGTTGAGCATGTCGG 60.047 61.111 0.00 0.00 0.00 4.79
2825 2872 2.819595 CGGGTTGAGCATGTCGGG 60.820 66.667 0.00 0.00 0.00 5.14
2826 2873 2.351276 GGGTTGAGCATGTCGGGT 59.649 61.111 0.00 0.00 0.00 5.28
2827 2874 1.303317 GGGTTGAGCATGTCGGGTT 60.303 57.895 0.00 0.00 0.00 4.11
2828 2875 1.305930 GGGTTGAGCATGTCGGGTTC 61.306 60.000 0.00 0.00 0.00 3.62
2829 2876 0.605319 GGTTGAGCATGTCGGGTTCA 60.605 55.000 0.00 0.00 0.00 3.18
2830 2877 0.517316 GTTGAGCATGTCGGGTTCAC 59.483 55.000 0.00 0.00 0.00 3.18
2831 2878 0.605319 TTGAGCATGTCGGGTTCACC 60.605 55.000 0.00 0.00 0.00 4.02
2842 2889 3.361977 GTTCACCGGCGTGGCAAT 61.362 61.111 6.01 0.00 43.94 3.56
2843 2890 2.596046 TTCACCGGCGTGGCAATT 60.596 55.556 6.01 0.00 43.94 2.32
2844 2891 2.196925 TTCACCGGCGTGGCAATTT 61.197 52.632 6.01 0.00 43.94 1.82
2845 2892 1.739338 TTCACCGGCGTGGCAATTTT 61.739 50.000 6.01 0.00 43.94 1.82
2846 2893 0.889638 TCACCGGCGTGGCAATTTTA 60.890 50.000 6.01 0.00 43.94 1.52
2847 2894 0.731174 CACCGGCGTGGCAATTTTAC 60.731 55.000 6.01 0.00 43.94 2.01
2848 2895 1.173444 ACCGGCGTGGCAATTTTACA 61.173 50.000 6.01 0.00 43.94 2.41
2849 2896 0.172352 CCGGCGTGGCAATTTTACAT 59.828 50.000 6.01 0.00 0.00 2.29
2850 2897 1.402259 CCGGCGTGGCAATTTTACATA 59.598 47.619 6.01 0.00 0.00 2.29
2851 2898 2.159366 CCGGCGTGGCAATTTTACATAA 60.159 45.455 6.01 0.00 0.00 1.90
2852 2899 3.502920 CGGCGTGGCAATTTTACATAAA 58.497 40.909 0.00 0.00 0.00 1.40
2853 2900 3.921021 CGGCGTGGCAATTTTACATAAAA 59.079 39.130 0.00 0.00 39.25 1.52
2854 2901 4.031201 CGGCGTGGCAATTTTACATAAAAG 59.969 41.667 0.00 0.00 38.42 2.27
2855 2902 4.926832 GGCGTGGCAATTTTACATAAAAGT 59.073 37.500 0.00 0.00 38.42 2.66
2856 2903 5.061684 GGCGTGGCAATTTTACATAAAAGTC 59.938 40.000 0.00 0.00 38.42 3.01
2857 2904 5.061684 GCGTGGCAATTTTACATAAAAGTCC 59.938 40.000 0.00 5.13 38.42 3.85
2858 2905 5.575218 CGTGGCAATTTTACATAAAAGTCCC 59.425 40.000 0.00 1.10 38.42 4.46
2859 2906 6.571537 CGTGGCAATTTTACATAAAAGTCCCT 60.572 38.462 6.20 0.00 38.42 4.20
2860 2907 7.158697 GTGGCAATTTTACATAAAAGTCCCTT 58.841 34.615 6.20 0.00 38.42 3.95
2861 2908 7.330946 GTGGCAATTTTACATAAAAGTCCCTTC 59.669 37.037 6.20 0.00 38.42 3.46
2862 2909 7.015682 TGGCAATTTTACATAAAAGTCCCTTCA 59.984 33.333 6.20 0.00 38.42 3.02
2863 2910 8.040727 GGCAATTTTACATAAAAGTCCCTTCAT 58.959 33.333 3.42 0.00 38.42 2.57
2864 2911 9.435688 GCAATTTTACATAAAAGTCCCTTCATT 57.564 29.630 3.42 0.00 38.42 2.57
2871 2918 7.611770 ACATAAAAGTCCCTTCATTTTTAGGC 58.388 34.615 0.00 0.00 32.88 3.93
2872 2919 7.234577 ACATAAAAGTCCCTTCATTTTTAGGCA 59.765 33.333 0.00 0.00 32.88 4.75
2873 2920 6.493189 AAAAGTCCCTTCATTTTTAGGCAA 57.507 33.333 0.00 0.00 0.00 4.52
2874 2921 6.686484 AAAGTCCCTTCATTTTTAGGCAAT 57.314 33.333 0.00 0.00 0.00 3.56
2875 2922 6.686484 AAGTCCCTTCATTTTTAGGCAATT 57.314 33.333 0.00 0.00 0.00 2.32
2876 2923 7.790782 AAGTCCCTTCATTTTTAGGCAATTA 57.209 32.000 0.00 0.00 0.00 1.40
2877 2924 7.790782 AGTCCCTTCATTTTTAGGCAATTAA 57.209 32.000 0.00 0.00 0.00 1.40
2878 2925 7.840931 AGTCCCTTCATTTTTAGGCAATTAAG 58.159 34.615 0.00 0.00 0.00 1.85
2879 2926 6.535150 GTCCCTTCATTTTTAGGCAATTAAGC 59.465 38.462 0.00 0.00 0.00 3.09
2887 2934 2.482326 GGCAATTAAGCCGCAGACT 58.518 52.632 0.00 0.00 46.12 3.24
2888 2935 1.663695 GGCAATTAAGCCGCAGACTA 58.336 50.000 0.00 0.00 46.12 2.59
2889 2936 2.222027 GGCAATTAAGCCGCAGACTAT 58.778 47.619 0.00 0.00 46.12 2.12
2890 2937 2.224314 GGCAATTAAGCCGCAGACTATC 59.776 50.000 0.00 0.00 46.12 2.08
2891 2938 2.872245 GCAATTAAGCCGCAGACTATCA 59.128 45.455 0.00 0.00 0.00 2.15
2892 2939 3.499918 GCAATTAAGCCGCAGACTATCAT 59.500 43.478 0.00 0.00 0.00 2.45
2893 2940 4.377841 GCAATTAAGCCGCAGACTATCATC 60.378 45.833 0.00 0.00 0.00 2.92
2894 2941 4.607293 ATTAAGCCGCAGACTATCATCA 57.393 40.909 0.00 0.00 0.00 3.07
2895 2942 2.988010 AAGCCGCAGACTATCATCAA 57.012 45.000 0.00 0.00 0.00 2.57
2896 2943 2.522836 AGCCGCAGACTATCATCAAG 57.477 50.000 0.00 0.00 0.00 3.02
2897 2944 1.759445 AGCCGCAGACTATCATCAAGT 59.241 47.619 0.00 0.00 0.00 3.16
2898 2945 2.131183 GCCGCAGACTATCATCAAGTC 58.869 52.381 0.00 0.00 43.06 3.01
2899 2946 2.389059 CCGCAGACTATCATCAAGTCG 58.611 52.381 0.00 0.00 46.46 4.18
2900 2947 2.389059 CGCAGACTATCATCAAGTCGG 58.611 52.381 0.00 0.00 46.46 4.79
2902 2949 3.443099 CAGACTATCATCAAGTCGGCA 57.557 47.619 0.00 0.00 46.46 5.69
2903 2950 3.785486 CAGACTATCATCAAGTCGGCAA 58.215 45.455 0.00 0.00 46.46 4.52
2904 2951 4.183865 CAGACTATCATCAAGTCGGCAAA 58.816 43.478 0.00 0.00 46.46 3.68
2905 2952 4.631377 CAGACTATCATCAAGTCGGCAAAA 59.369 41.667 0.00 0.00 46.46 2.44
2906 2953 5.122239 CAGACTATCATCAAGTCGGCAAAAA 59.878 40.000 0.00 0.00 46.46 1.94
2907 2954 5.352569 AGACTATCATCAAGTCGGCAAAAAG 59.647 40.000 0.00 0.00 46.46 2.27
2908 2955 5.245531 ACTATCATCAAGTCGGCAAAAAGA 58.754 37.500 0.00 0.00 0.00 2.52
2909 2956 5.705441 ACTATCATCAAGTCGGCAAAAAGAA 59.295 36.000 0.00 0.00 0.00 2.52
2910 2957 5.649782 ATCATCAAGTCGGCAAAAAGAAT 57.350 34.783 0.00 0.00 0.00 2.40
2911 2958 5.046910 TCATCAAGTCGGCAAAAAGAATC 57.953 39.130 0.00 0.00 0.00 2.52
2912 2959 3.536158 TCAAGTCGGCAAAAAGAATCG 57.464 42.857 0.00 0.00 0.00 3.34
2913 2960 2.875933 TCAAGTCGGCAAAAAGAATCGT 59.124 40.909 0.00 0.00 0.00 3.73
2914 2961 3.314080 TCAAGTCGGCAAAAAGAATCGTT 59.686 39.130 0.00 0.00 0.00 3.85
2915 2962 3.982576 AGTCGGCAAAAAGAATCGTTT 57.017 38.095 0.00 0.00 0.00 3.60
2916 2963 4.301637 AGTCGGCAAAAAGAATCGTTTT 57.698 36.364 1.18 1.18 0.00 2.43
2917 2964 4.678622 AGTCGGCAAAAAGAATCGTTTTT 58.321 34.783 4.23 1.72 39.65 1.94
2953 3000 8.874744 TTTTAAAATAAACCCCTTGACTTTCG 57.125 30.769 0.00 0.00 0.00 3.46
2954 3001 5.462530 AAAATAAACCCCTTGACTTTCGG 57.537 39.130 0.00 0.00 0.00 4.30
2955 3002 3.801307 ATAAACCCCTTGACTTTCGGT 57.199 42.857 0.00 0.00 0.00 4.69
2956 3003 1.977056 AAACCCCTTGACTTTCGGTC 58.023 50.000 0.00 0.00 44.70 4.79
2965 3012 0.645868 GACTTTCGGTCGTAGCATGC 59.354 55.000 10.51 10.51 35.07 4.06
2967 3014 1.752501 CTTTCGGTCGTAGCATGCGG 61.753 60.000 13.01 6.06 46.86 5.69
2968 3015 2.215465 TTTCGGTCGTAGCATGCGGA 62.215 55.000 13.01 8.55 46.86 5.54
2969 3016 2.011741 TTCGGTCGTAGCATGCGGAT 62.012 55.000 13.01 0.00 46.86 4.18
2970 3017 2.302952 CGGTCGTAGCATGCGGATG 61.303 63.158 13.21 13.21 46.86 3.51
2971 3018 1.956170 GGTCGTAGCATGCGGATGG 60.956 63.158 19.11 1.70 46.86 3.51
2972 3019 1.067416 GTCGTAGCATGCGGATGGA 59.933 57.895 19.11 4.27 46.86 3.41
2973 3020 0.319900 GTCGTAGCATGCGGATGGAT 60.320 55.000 19.11 0.78 46.86 3.41
2974 3021 1.067846 GTCGTAGCATGCGGATGGATA 60.068 52.381 19.11 0.00 46.86 2.59
2975 3022 1.824852 TCGTAGCATGCGGATGGATAT 59.175 47.619 19.11 0.00 46.86 1.63
2976 3023 2.159240 TCGTAGCATGCGGATGGATATC 60.159 50.000 19.11 1.08 46.86 1.63
2977 3024 2.196749 GTAGCATGCGGATGGATATCG 58.803 52.381 19.11 0.00 33.98 2.92
2978 3025 0.897621 AGCATGCGGATGGATATCGA 59.102 50.000 19.11 0.00 33.98 3.59
2979 3026 1.002366 GCATGCGGATGGATATCGAC 58.998 55.000 19.11 0.00 33.98 4.20
2980 3027 1.271876 CATGCGGATGGATATCGACG 58.728 55.000 9.36 0.08 33.98 5.12
2981 3028 1.135402 CATGCGGATGGATATCGACGA 60.135 52.381 9.36 0.00 33.98 4.20
2982 3029 0.240145 TGCGGATGGATATCGACGAC 59.760 55.000 0.00 0.00 33.98 4.34
2983 3030 0.793478 GCGGATGGATATCGACGACG 60.793 60.000 0.00 0.00 41.26 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.466746 TTTTGCTTATGCCACTCTAGATTTT 57.533 32.000 0.00 0.00 38.71 1.82
1 2 7.651027 ATTTTGCTTATGCCACTCTAGATTT 57.349 32.000 0.00 0.00 38.71 2.17
2 3 7.417116 CCAATTTTGCTTATGCCACTCTAGATT 60.417 37.037 0.00 0.00 38.71 2.40
3 4 6.040166 CCAATTTTGCTTATGCCACTCTAGAT 59.960 38.462 0.00 0.00 38.71 1.98
4 5 5.357878 CCAATTTTGCTTATGCCACTCTAGA 59.642 40.000 0.00 0.00 38.71 2.43
5 6 5.585390 CCAATTTTGCTTATGCCACTCTAG 58.415 41.667 0.00 0.00 38.71 2.43
6 7 4.142182 GCCAATTTTGCTTATGCCACTCTA 60.142 41.667 0.00 0.00 38.71 2.43
7 8 3.368739 GCCAATTTTGCTTATGCCACTCT 60.369 43.478 0.00 0.00 38.71 3.24
8 9 2.931969 GCCAATTTTGCTTATGCCACTC 59.068 45.455 0.00 0.00 38.71 3.51
9 10 2.302445 TGCCAATTTTGCTTATGCCACT 59.698 40.909 0.00 0.00 38.71 4.00
10 11 2.697654 TGCCAATTTTGCTTATGCCAC 58.302 42.857 0.00 0.00 38.71 5.01
11 12 3.413846 TTGCCAATTTTGCTTATGCCA 57.586 38.095 0.00 0.00 38.71 4.92
12 13 4.725359 CTTTTGCCAATTTTGCTTATGCC 58.275 39.130 0.00 0.00 38.71 4.40
13 14 4.160594 GCTTTTGCCAATTTTGCTTATGC 58.839 39.130 0.00 0.00 40.15 3.14
29 30 5.793026 TGTTTTTGCCACTTTAGCTTTTG 57.207 34.783 0.00 0.00 0.00 2.44
30 31 6.429692 ACTTTGTTTTTGCCACTTTAGCTTTT 59.570 30.769 0.00 0.00 0.00 2.27
31 32 5.937540 ACTTTGTTTTTGCCACTTTAGCTTT 59.062 32.000 0.00 0.00 0.00 3.51
32 33 5.487433 ACTTTGTTTTTGCCACTTTAGCTT 58.513 33.333 0.00 0.00 0.00 3.74
33 34 5.084818 ACTTTGTTTTTGCCACTTTAGCT 57.915 34.783 0.00 0.00 0.00 3.32
34 35 5.794687 AACTTTGTTTTTGCCACTTTAGC 57.205 34.783 0.00 0.00 0.00 3.09
35 36 7.240674 GGAAAACTTTGTTTTTGCCACTTTAG 58.759 34.615 9.36 0.00 32.30 1.85
36 37 7.135089 GGAAAACTTTGTTTTTGCCACTTTA 57.865 32.000 9.36 0.00 32.30 1.85
37 38 6.007936 GGAAAACTTTGTTTTTGCCACTTT 57.992 33.333 9.36 0.00 32.30 2.66
38 39 5.621197 GGAAAACTTTGTTTTTGCCACTT 57.379 34.783 9.36 0.00 32.30 3.16
43 44 8.972262 TTATTTTGGGAAAACTTTGTTTTTGC 57.028 26.923 9.36 0.00 36.39 3.68
55 56 8.889717 CGCTCTCTAAGTATTATTTTGGGAAAA 58.110 33.333 0.00 0.00 34.41 2.29
56 57 7.497909 CCGCTCTCTAAGTATTATTTTGGGAAA 59.502 37.037 0.00 0.00 0.00 3.13
57 58 6.990349 CCGCTCTCTAAGTATTATTTTGGGAA 59.010 38.462 0.00 0.00 0.00 3.97
58 59 6.325545 TCCGCTCTCTAAGTATTATTTTGGGA 59.674 38.462 0.00 0.00 0.00 4.37
59 60 6.522054 TCCGCTCTCTAAGTATTATTTTGGG 58.478 40.000 0.00 0.00 0.00 4.12
60 61 8.608844 ATTCCGCTCTCTAAGTATTATTTTGG 57.391 34.615 0.00 0.00 0.00 3.28
219 221 0.601558 ATTGTCTGCAGCAAGGCAAG 59.398 50.000 22.06 0.00 44.48 4.01
220 222 1.042229 AATTGTCTGCAGCAAGGCAA 58.958 45.000 22.06 12.39 45.28 4.52
221 223 0.315886 CAATTGTCTGCAGCAAGGCA 59.684 50.000 22.06 9.25 42.53 4.75
222 224 1.012486 GCAATTGTCTGCAGCAAGGC 61.012 55.000 22.06 21.99 42.17 4.35
433 454 7.944729 ATCTTATGTTGTACTCAGCCATTTT 57.055 32.000 0.00 0.00 0.00 1.82
437 458 6.379988 TGACTATCTTATGTTGTACTCAGCCA 59.620 38.462 0.00 0.00 0.00 4.75
438 459 6.806751 TGACTATCTTATGTTGTACTCAGCC 58.193 40.000 0.00 0.00 0.00 4.85
439 460 6.419413 GCTGACTATCTTATGTTGTACTCAGC 59.581 42.308 8.53 8.53 37.71 4.26
1055 1084 5.968528 ATTTTGGTCTTGCACGGTAAATA 57.031 34.783 0.00 0.00 0.00 1.40
1109 1138 2.620627 CCCCACAATAAGAGGTTCCACC 60.621 54.545 0.00 0.00 38.99 4.61
1283 1312 4.133820 CACCTACAAGTGTGAACATGGAA 58.866 43.478 0.00 0.00 34.37 3.53
1287 1316 3.207265 TGCACCTACAAGTGTGAACAT 57.793 42.857 0.00 0.00 40.04 2.71
1298 1327 5.067153 CCGGATTGAATTAAATGCACCTACA 59.933 40.000 7.71 0.00 0.00 2.74
1302 1331 3.383185 TCCCGGATTGAATTAAATGCACC 59.617 43.478 0.73 0.00 0.00 5.01
1360 1389 4.864704 TTGTGGCCATTAGGAAGAAAAC 57.135 40.909 9.72 0.00 36.89 2.43
1557 1588 9.212641 TCTTCAGAAAACAGTCTTCTTCATATG 57.787 33.333 0.00 0.00 30.58 1.78
1592 1623 7.777440 TGTAACATATATGACAAAATGGCTCCA 59.223 33.333 19.63 0.00 0.00 3.86
1618 1649 9.435570 AGGTATATCAGTAACAATCCTGTAAGT 57.564 33.333 0.00 0.00 33.45 2.24
1675 1706 8.970691 ATAGACCAATTCAAATTTGTTCGAAG 57.029 30.769 17.47 6.68 0.00 3.79
1684 1715 9.039165 AGAACATGGAATAGACCAATTCAAATT 57.961 29.630 0.00 0.00 43.47 1.82
2322 2353 1.539827 GCCGAAAAGGTGCACATAACT 59.460 47.619 20.43 2.99 43.70 2.24
2391 2422 6.307155 GTTTTCATTGTTCTATGAGGTGACG 58.693 40.000 0.00 0.00 36.03 4.35
2434 2465 4.342862 GCCTCTCTGAATATAGTGGCAA 57.657 45.455 10.19 0.00 46.67 4.52
2499 2530 1.974875 GGGTGGGGGCGTACTTTTG 60.975 63.158 0.00 0.00 0.00 2.44
2545 2591 5.895636 AATGGATATTGTTTTGTCGCTGA 57.104 34.783 0.00 0.00 0.00 4.26
2608 2654 2.238898 CGGGGAAAGAGGGTCAGTTTAT 59.761 50.000 0.00 0.00 0.00 1.40
2629 2675 8.905850 GGCATTATACTAGTATTCCTAGAGGAC 58.094 40.741 20.21 1.76 45.21 3.85
2638 2685 4.561606 CGCACGGGCATTATACTAGTATTC 59.438 45.833 20.21 7.85 41.24 1.75
2643 2690 2.433868 ACGCACGGGCATTATACTAG 57.566 50.000 11.77 0.00 41.24 2.57
2644 2691 2.475818 CAACGCACGGGCATTATACTA 58.524 47.619 11.77 0.00 41.24 1.82
2645 2692 1.295792 CAACGCACGGGCATTATACT 58.704 50.000 11.77 0.00 41.24 2.12
2646 2693 0.316689 GCAACGCACGGGCATTATAC 60.317 55.000 11.77 0.00 41.24 1.47
2647 2694 1.440938 GGCAACGCACGGGCATTATA 61.441 55.000 11.77 0.00 41.24 0.98
2648 2695 2.770589 GGCAACGCACGGGCATTAT 61.771 57.895 11.77 0.00 41.24 1.28
2649 2696 3.436055 GGCAACGCACGGGCATTA 61.436 61.111 11.77 0.00 41.24 1.90
2665 2712 4.423732 CAAAATATCTCAAAAGCCCGTGG 58.576 43.478 0.00 0.00 0.00 4.94
2666 2713 3.859386 GCAAAATATCTCAAAAGCCCGTG 59.141 43.478 0.00 0.00 0.00 4.94
2667 2714 3.763897 AGCAAAATATCTCAAAAGCCCGT 59.236 39.130 0.00 0.00 0.00 5.28
2668 2715 4.376340 AGCAAAATATCTCAAAAGCCCG 57.624 40.909 0.00 0.00 0.00 6.13
2669 2716 6.699575 TCTAGCAAAATATCTCAAAAGCCC 57.300 37.500 0.00 0.00 0.00 5.19
2763 2810 9.561069 AGATTTACAATGTAAGTGAAGTTGACT 57.439 29.630 5.88 0.00 34.17 3.41
2785 2832 8.630037 CCCGTGCTTTATTATTAGGAAAAGATT 58.370 33.333 0.00 0.00 31.96 2.40
2786 2833 7.778382 ACCCGTGCTTTATTATTAGGAAAAGAT 59.222 33.333 0.00 0.00 31.96 2.40
2787 2834 7.114095 ACCCGTGCTTTATTATTAGGAAAAGA 58.886 34.615 0.00 0.00 31.96 2.52
2788 2835 7.329588 ACCCGTGCTTTATTATTAGGAAAAG 57.670 36.000 0.00 0.00 33.15 2.27
2789 2836 7.393796 TCAACCCGTGCTTTATTATTAGGAAAA 59.606 33.333 0.00 0.00 0.00 2.29
2790 2837 6.885376 TCAACCCGTGCTTTATTATTAGGAAA 59.115 34.615 0.00 0.00 0.00 3.13
2791 2838 6.416415 TCAACCCGTGCTTTATTATTAGGAA 58.584 36.000 0.00 0.00 0.00 3.36
2792 2839 5.991861 TCAACCCGTGCTTTATTATTAGGA 58.008 37.500 0.00 0.00 0.00 2.94
2793 2840 5.277828 GCTCAACCCGTGCTTTATTATTAGG 60.278 44.000 0.00 0.00 0.00 2.69
2794 2841 5.295787 TGCTCAACCCGTGCTTTATTATTAG 59.704 40.000 0.00 0.00 35.11 1.73
2795 2842 5.186942 TGCTCAACCCGTGCTTTATTATTA 58.813 37.500 0.00 0.00 35.11 0.98
2796 2843 4.013728 TGCTCAACCCGTGCTTTATTATT 58.986 39.130 0.00 0.00 35.11 1.40
2797 2844 3.616219 TGCTCAACCCGTGCTTTATTAT 58.384 40.909 0.00 0.00 35.11 1.28
2798 2845 3.060736 TGCTCAACCCGTGCTTTATTA 57.939 42.857 0.00 0.00 35.11 0.98
2799 2846 1.904287 TGCTCAACCCGTGCTTTATT 58.096 45.000 0.00 0.00 35.11 1.40
2800 2847 1.745087 CATGCTCAACCCGTGCTTTAT 59.255 47.619 0.00 0.00 35.11 1.40
2801 2848 1.164411 CATGCTCAACCCGTGCTTTA 58.836 50.000 0.00 0.00 35.11 1.85
2802 2849 0.823356 ACATGCTCAACCCGTGCTTT 60.823 50.000 0.00 0.00 35.11 3.51
2803 2850 1.228245 ACATGCTCAACCCGTGCTT 60.228 52.632 0.00 0.00 35.11 3.91
2804 2851 1.672356 GACATGCTCAACCCGTGCT 60.672 57.895 0.00 0.00 35.11 4.40
2805 2852 2.870372 GACATGCTCAACCCGTGC 59.130 61.111 0.00 0.00 34.62 5.34
2806 2853 2.390599 CCGACATGCTCAACCCGTG 61.391 63.158 0.00 0.00 0.00 4.94
2807 2854 2.047274 CCGACATGCTCAACCCGT 60.047 61.111 0.00 0.00 0.00 5.28
2808 2855 2.819595 CCCGACATGCTCAACCCG 60.820 66.667 0.00 0.00 0.00 5.28
2809 2856 1.303317 AACCCGACATGCTCAACCC 60.303 57.895 0.00 0.00 0.00 4.11
2810 2857 0.605319 TGAACCCGACATGCTCAACC 60.605 55.000 0.00 0.00 0.00 3.77
2811 2858 0.517316 GTGAACCCGACATGCTCAAC 59.483 55.000 0.00 0.00 0.00 3.18
2812 2859 0.605319 GGTGAACCCGACATGCTCAA 60.605 55.000 0.00 0.00 0.00 3.02
2813 2860 1.003839 GGTGAACCCGACATGCTCA 60.004 57.895 0.00 0.00 0.00 4.26
2814 2861 3.890674 GGTGAACCCGACATGCTC 58.109 61.111 0.00 0.00 0.00 4.26
2828 2875 0.731174 GTAAAATTGCCACGCCGGTG 60.731 55.000 14.93 14.93 43.99 4.94
2829 2876 1.173444 TGTAAAATTGCCACGCCGGT 61.173 50.000 1.90 0.00 36.97 5.28
2830 2877 0.172352 ATGTAAAATTGCCACGCCGG 59.828 50.000 0.00 0.00 38.11 6.13
2831 2878 2.834574 TATGTAAAATTGCCACGCCG 57.165 45.000 0.00 0.00 0.00 6.46
2832 2879 4.926832 ACTTTTATGTAAAATTGCCACGCC 59.073 37.500 0.00 0.00 34.95 5.68
2833 2880 5.061684 GGACTTTTATGTAAAATTGCCACGC 59.938 40.000 0.00 0.00 34.95 5.34
2834 2881 5.575218 GGGACTTTTATGTAAAATTGCCACG 59.425 40.000 16.03 0.00 42.10 4.94
2835 2882 6.697395 AGGGACTTTTATGTAAAATTGCCAC 58.303 36.000 20.20 8.66 43.68 5.01
2836 2883 6.926630 AGGGACTTTTATGTAAAATTGCCA 57.073 33.333 20.20 0.00 43.68 4.92
2854 2901 6.535150 GCTTAATTGCCTAAAAATGAAGGGAC 59.465 38.462 0.00 0.00 32.32 4.46
2855 2902 6.639563 GCTTAATTGCCTAAAAATGAAGGGA 58.360 36.000 0.00 0.00 33.17 4.20
2856 2903 6.908870 GCTTAATTGCCTAAAAATGAAGGG 57.091 37.500 0.00 0.00 33.17 3.95
2870 2917 2.872245 TGATAGTCTGCGGCTTAATTGC 59.128 45.455 0.00 0.00 0.00 3.56
2871 2918 4.751600 TGATGATAGTCTGCGGCTTAATTG 59.248 41.667 0.00 0.00 0.00 2.32
2872 2919 4.960938 TGATGATAGTCTGCGGCTTAATT 58.039 39.130 0.00 0.00 0.00 1.40
2873 2920 4.607293 TGATGATAGTCTGCGGCTTAAT 57.393 40.909 0.00 0.00 0.00 1.40
2874 2921 4.141937 ACTTGATGATAGTCTGCGGCTTAA 60.142 41.667 0.00 0.00 0.00 1.85
2875 2922 3.384789 ACTTGATGATAGTCTGCGGCTTA 59.615 43.478 0.00 0.00 0.00 3.09
2876 2923 2.169352 ACTTGATGATAGTCTGCGGCTT 59.831 45.455 0.00 0.00 0.00 4.35
2877 2924 1.759445 ACTTGATGATAGTCTGCGGCT 59.241 47.619 0.00 0.00 0.00 5.52
2878 2925 2.131183 GACTTGATGATAGTCTGCGGC 58.869 52.381 0.00 0.00 39.12 6.53
2879 2926 2.389059 CGACTTGATGATAGTCTGCGG 58.611 52.381 0.00 0.00 39.86 5.69
2880 2927 2.389059 CCGACTTGATGATAGTCTGCG 58.611 52.381 0.00 0.00 39.86 5.18
2881 2928 2.131183 GCCGACTTGATGATAGTCTGC 58.869 52.381 0.00 0.00 42.67 4.26
2882 2929 3.443099 TGCCGACTTGATGATAGTCTG 57.557 47.619 0.00 0.00 39.86 3.51
2883 2930 4.471904 TTTGCCGACTTGATGATAGTCT 57.528 40.909 0.00 0.00 39.86 3.24
2884 2931 5.351465 TCTTTTTGCCGACTTGATGATAGTC 59.649 40.000 0.00 0.00 38.88 2.59
2885 2932 5.245531 TCTTTTTGCCGACTTGATGATAGT 58.754 37.500 0.00 0.00 0.00 2.12
2886 2933 5.801350 TCTTTTTGCCGACTTGATGATAG 57.199 39.130 0.00 0.00 0.00 2.08
2887 2934 6.456853 CGATTCTTTTTGCCGACTTGATGATA 60.457 38.462 0.00 0.00 0.00 2.15
2888 2935 5.644644 GATTCTTTTTGCCGACTTGATGAT 58.355 37.500 0.00 0.00 0.00 2.45
2889 2936 4.378356 CGATTCTTTTTGCCGACTTGATGA 60.378 41.667 0.00 0.00 0.00 2.92
2890 2937 3.848019 CGATTCTTTTTGCCGACTTGATG 59.152 43.478 0.00 0.00 0.00 3.07
2891 2938 3.502211 ACGATTCTTTTTGCCGACTTGAT 59.498 39.130 0.00 0.00 0.00 2.57
2892 2939 2.875933 ACGATTCTTTTTGCCGACTTGA 59.124 40.909 0.00 0.00 0.00 3.02
2893 2940 3.268013 ACGATTCTTTTTGCCGACTTG 57.732 42.857 0.00 0.00 0.00 3.16
2894 2941 3.982576 AACGATTCTTTTTGCCGACTT 57.017 38.095 0.00 0.00 0.00 3.01
2895 2942 3.982576 AAACGATTCTTTTTGCCGACT 57.017 38.095 0.00 0.00 0.00 4.18
2927 2974 9.315525 CGAAAGTCAAGGGGTTTATTTTAAAAA 57.684 29.630 4.44 0.00 0.00 1.94
2928 2975 7.927092 CCGAAAGTCAAGGGGTTTATTTTAAAA 59.073 33.333 2.51 2.51 0.00 1.52
2929 2976 7.069702 ACCGAAAGTCAAGGGGTTTATTTTAAA 59.930 33.333 0.00 0.00 0.00 1.52
2930 2977 6.550481 ACCGAAAGTCAAGGGGTTTATTTTAA 59.450 34.615 0.00 0.00 0.00 1.52
2931 2978 6.069994 ACCGAAAGTCAAGGGGTTTATTTTA 58.930 36.000 0.00 0.00 0.00 1.52
2932 2979 4.897076 ACCGAAAGTCAAGGGGTTTATTTT 59.103 37.500 0.00 0.00 0.00 1.82
2933 2980 4.476297 ACCGAAAGTCAAGGGGTTTATTT 58.524 39.130 0.00 0.00 0.00 1.40
2934 2981 4.077108 GACCGAAAGTCAAGGGGTTTATT 58.923 43.478 0.00 0.00 45.55 1.40
2935 2982 3.682696 GACCGAAAGTCAAGGGGTTTAT 58.317 45.455 0.00 0.00 45.55 1.40
2936 2983 2.548493 CGACCGAAAGTCAAGGGGTTTA 60.548 50.000 0.00 0.00 46.69 2.01
2937 2984 1.812708 CGACCGAAAGTCAAGGGGTTT 60.813 52.381 0.00 0.00 46.69 3.27
2938 2985 0.250166 CGACCGAAAGTCAAGGGGTT 60.250 55.000 0.00 0.00 46.69 4.11
2939 2986 1.370064 CGACCGAAAGTCAAGGGGT 59.630 57.895 0.00 0.00 46.69 4.95
2940 2987 0.604578 TACGACCGAAAGTCAAGGGG 59.395 55.000 0.00 0.00 46.69 4.79
2941 2988 1.992170 CTACGACCGAAAGTCAAGGG 58.008 55.000 0.00 0.00 46.69 3.95
2942 2989 1.336517 TGCTACGACCGAAAGTCAAGG 60.337 52.381 0.00 0.00 46.69 3.61
2943 2990 2.060326 TGCTACGACCGAAAGTCAAG 57.940 50.000 0.00 0.00 46.69 3.02
2944 2991 2.333926 CATGCTACGACCGAAAGTCAA 58.666 47.619 0.00 0.00 46.69 3.18
2945 2992 1.990799 CATGCTACGACCGAAAGTCA 58.009 50.000 0.00 0.00 46.69 3.41
2946 2993 0.645868 GCATGCTACGACCGAAAGTC 59.354 55.000 11.37 0.00 42.54 3.01
2947 2994 1.076533 CGCATGCTACGACCGAAAGT 61.077 55.000 17.13 0.00 0.00 2.66
2948 2995 1.631072 CGCATGCTACGACCGAAAG 59.369 57.895 17.13 0.00 0.00 2.62
2949 2996 1.807981 CCGCATGCTACGACCGAAA 60.808 57.895 17.13 0.00 0.00 3.46
2950 2997 2.011741 ATCCGCATGCTACGACCGAA 62.012 55.000 17.13 0.00 0.00 4.30
2951 2998 2.486663 ATCCGCATGCTACGACCGA 61.487 57.895 17.13 0.00 0.00 4.69
2952 2999 2.027605 ATCCGCATGCTACGACCG 59.972 61.111 17.13 0.00 0.00 4.79
2953 3000 1.956170 CCATCCGCATGCTACGACC 60.956 63.158 17.13 0.00 0.00 4.79
2954 3001 0.319900 ATCCATCCGCATGCTACGAC 60.320 55.000 17.13 0.00 0.00 4.34
2955 3002 1.253100 TATCCATCCGCATGCTACGA 58.747 50.000 17.13 8.75 0.00 3.43
2956 3003 2.196749 GATATCCATCCGCATGCTACG 58.803 52.381 17.13 2.91 0.00 3.51
2957 3004 2.159240 TCGATATCCATCCGCATGCTAC 60.159 50.000 17.13 0.00 0.00 3.58
2958 3005 2.099405 TCGATATCCATCCGCATGCTA 58.901 47.619 17.13 3.87 0.00 3.49
2959 3006 0.897621 TCGATATCCATCCGCATGCT 59.102 50.000 17.13 0.00 0.00 3.79
2960 3007 1.002366 GTCGATATCCATCCGCATGC 58.998 55.000 7.91 7.91 0.00 4.06
2961 3008 1.135402 TCGTCGATATCCATCCGCATG 60.135 52.381 0.00 0.00 0.00 4.06
2962 3009 1.135373 GTCGTCGATATCCATCCGCAT 60.135 52.381 0.00 0.00 0.00 4.73
2963 3010 0.240145 GTCGTCGATATCCATCCGCA 59.760 55.000 0.00 0.00 0.00 5.69
2964 3011 0.793478 CGTCGTCGATATCCATCCGC 60.793 60.000 0.00 0.00 39.71 5.54
2965 3012 0.794473 TCGTCGTCGATATCCATCCG 59.206 55.000 0.00 0.00 41.35 4.18
2966 3013 1.130749 CCTCGTCGTCGATATCCATCC 59.869 57.143 5.00 0.00 45.21 3.51
2967 3014 1.130749 CCCTCGTCGTCGATATCCATC 59.869 57.143 5.00 0.00 45.21 3.51
2968 3015 1.166129 CCCTCGTCGTCGATATCCAT 58.834 55.000 5.00 0.00 45.21 3.41
2969 3016 1.512996 GCCCTCGTCGTCGATATCCA 61.513 60.000 5.00 0.00 45.21 3.41
2970 3017 1.209640 GCCCTCGTCGTCGATATCC 59.790 63.158 5.00 0.00 45.21 2.59
2971 3018 1.154450 CGCCCTCGTCGTCGATATC 60.154 63.158 5.00 0.00 45.21 1.63
2972 3019 2.614446 CCGCCCTCGTCGTCGATAT 61.614 63.158 5.00 0.00 45.21 1.63
2973 3020 3.274586 CCGCCCTCGTCGTCGATA 61.275 66.667 5.00 0.00 45.21 2.92


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

AutoCloner maintained by Alex Coulton.