Multiple sequence alignment - TraesCS6D01G171700

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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 TraesCS6D01G171700 chr6D 100.000 3260 0 0 1 3260 158076155 158072896 0.000000e+00 6021
1 TraesCS6D01G171700 chr6D 83.673 343 48 4 2786 3125 384213717 384214054 1.890000e-82 316
2 TraesCS6D01G171700 chr6D 82.121 330 47 6 2789 3117 456649851 456649533 4.140000e-69 272
3 TraesCS6D01G171700 chr6A 95.023 2813 97 12 1 2794 213148045 213150833 0.000000e+00 4379
4 TraesCS6D01G171700 chr6A 89.437 142 9 2 3119 3260 213150825 213150960 1.200000e-39 174
5 TraesCS6D01G171700 chr6B 97.010 2609 69 5 1 2609 288792658 288795257 0.000000e+00 4377
6 TraesCS6D01G171700 chr4B 86.203 1754 188 30 582 2292 175473909 175475651 0.000000e+00 1849
7 TraesCS6D01G171700 chr4B 80.882 340 52 5 2787 3125 11595131 11594804 4.170000e-64 255
8 TraesCS6D01G171700 chr4D 85.000 1880 215 35 471 2295 115045350 115047217 0.000000e+00 1847
9 TraesCS6D01G171700 chr4A 84.902 1881 215 36 471 2295 462222217 462220350 0.000000e+00 1836
10 TraesCS6D01G171700 chr3D 83.871 341 44 3 2787 3127 378044928 378044599 6.790000e-82 315
11 TraesCS6D01G171700 chr3D 88.770 187 20 1 2789 2975 335683810 335683625 9.100000e-56 228
12 TraesCS6D01G171700 chr5A 83.384 331 43 2 2793 3122 705956127 705956446 2.460000e-76 296
13 TraesCS6D01G171700 chr3B 83.483 333 40 5 2787 3119 134620417 134620734 2.460000e-76 296
14 TraesCS6D01G171700 chr3B 83.333 336 41 5 2787 3122 135352724 135352404 2.460000e-76 296
15 TraesCS6D01G171700 chr1D 82.941 340 43 4 2787 3122 34024549 34024877 3.180000e-75 292


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 TraesCS6D01G171700 chr6D 158072896 158076155 3259 True 6021.0 6021 100.000 1 3260 1 chr6D.!!$R1 3259
1 TraesCS6D01G171700 chr6A 213148045 213150960 2915 False 2276.5 4379 92.230 1 3260 2 chr6A.!!$F1 3259
2 TraesCS6D01G171700 chr6B 288792658 288795257 2599 False 4377.0 4377 97.010 1 2609 1 chr6B.!!$F1 2608
3 TraesCS6D01G171700 chr4B 175473909 175475651 1742 False 1849.0 1849 86.203 582 2292 1 chr4B.!!$F1 1710
4 TraesCS6D01G171700 chr4D 115045350 115047217 1867 False 1847.0 1847 85.000 471 2295 1 chr4D.!!$F1 1824
5 TraesCS6D01G171700 chr4A 462220350 462222217 1867 True 1836.0 1836 84.902 471 2295 1 chr4A.!!$R1 1824

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
185 186 0.112995 TCCTTGTGGGCTTTGCTGAT 59.887 50.000 0.0 0.0 34.39 2.90 F
207 208 1.378531 TGACATTTACGGCATGGAGC 58.621 50.000 0.0 0.0 44.65 4.70 F
466 479 3.387962 AGAGGCAGGGAGTTGATTATGA 58.612 45.455 0.0 0.0 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1976 0.037975 CCATCTTTGGGTGCACAAGC 60.038 55.000 20.43 0.39 39.56 4.01 R
2106 2177 3.340814 ACGCTTTCCATGTGAATCTCT 57.659 42.857 0.00 0.00 31.67 3.10 R
2303 2374 1.476891 ACGTACGATGATCTTGCAGGT 59.523 47.619 24.41 0.00 0.00 4.00 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
58 59 6.230472 TCAGACAGCAAGCATAACTAAAAGA 58.770 36.000 0.00 0.00 0.00 2.52
130 131 1.305219 TAGACGCCCAACATGCTTGC 61.305 55.000 0.00 0.00 0.00 4.01
131 132 2.598394 ACGCCCAACATGCTTGCT 60.598 55.556 0.00 0.00 0.00 3.91
169 170 8.908903 TGTTACATGTTTTATGACTTTGTTCCT 58.091 29.630 2.30 0.00 0.00 3.36
185 186 0.112995 TCCTTGTGGGCTTTGCTGAT 59.887 50.000 0.00 0.00 34.39 2.90
207 208 1.378531 TGACATTTACGGCATGGAGC 58.621 50.000 0.00 0.00 44.65 4.70
243 244 5.399013 GTTGGTACATGAAGGGAAAATTCG 58.601 41.667 0.00 0.00 39.30 3.34
404 405 6.162079 CACCATCATCATCAGTGTAGGATAC 58.838 44.000 0.00 0.00 43.42 2.24
463 476 4.534500 TGTAAAGAGGCAGGGAGTTGATTA 59.466 41.667 0.00 0.00 0.00 1.75
464 477 4.870021 AAAGAGGCAGGGAGTTGATTAT 57.130 40.909 0.00 0.00 0.00 1.28
465 478 3.853355 AGAGGCAGGGAGTTGATTATG 57.147 47.619 0.00 0.00 0.00 1.90
466 479 3.387962 AGAGGCAGGGAGTTGATTATGA 58.612 45.455 0.00 0.00 0.00 2.15
467 480 3.979347 AGAGGCAGGGAGTTGATTATGAT 59.021 43.478 0.00 0.00 0.00 2.45
468 481 4.414846 AGAGGCAGGGAGTTGATTATGATT 59.585 41.667 0.00 0.00 0.00 2.57
469 482 5.608437 AGAGGCAGGGAGTTGATTATGATTA 59.392 40.000 0.00 0.00 0.00 1.75
576 589 8.230472 ACCATATGTCTTGAAATGAATCTTCC 57.770 34.615 1.24 0.00 0.00 3.46
989 1051 5.215160 CAACTAACTTTGTTGATCCTGTGC 58.785 41.667 9.69 0.00 45.27 4.57
1332 1403 3.701205 TCTGAAATACAGGAGCAGCAA 57.299 42.857 0.00 0.00 45.76 3.91
1347 1418 4.351192 AGCAGCAAAACTTGTTAAAGACG 58.649 39.130 0.00 0.00 36.84 4.18
1470 1541 8.707938 AAACAAAACTGGAGAAGAAATTGAAG 57.292 30.769 0.00 0.00 0.00 3.02
1572 1643 7.278868 AGCTTGTTTACATCTACTGCTGATAAC 59.721 37.037 0.00 0.00 0.00 1.89
1716 1787 6.233434 TCACAAGAAGTATGCATTTGAGTCT 58.767 36.000 3.54 0.00 0.00 3.24
1763 1834 5.532779 GTGGTTTCCATCAAGAGAACTTCTT 59.467 40.000 0.00 0.00 40.45 2.52
2106 2177 0.681733 AGAAGGCAAGCGAGTTCTCA 59.318 50.000 0.00 0.00 0.00 3.27
2303 2374 2.107041 ATTCCGGGCGTCTCACACAA 62.107 55.000 0.00 0.00 0.00 3.33
2438 2509 4.447724 TCGAAGACTGTAATGTGTGCTTTC 59.552 41.667 0.00 0.00 0.00 2.62
2513 2584 7.656707 AGTTATGAAAAATTGTCAATGTGGC 57.343 32.000 0.00 0.00 0.00 5.01
2522 2593 1.002544 TGTCAATGTGGCGTGGATGTA 59.997 47.619 0.00 0.00 0.00 2.29
2615 2687 6.542370 TGGCTTTTCTACTGCCTAATAATGAC 59.458 38.462 0.00 0.00 46.23 3.06
2675 2765 1.299541 GTGTAGACGGAATGGGCATG 58.700 55.000 0.00 0.00 0.00 4.06
2696 2786 2.979813 GTGCAGCAAATTGTTTAGGACG 59.020 45.455 0.00 0.00 0.00 4.79
2698 2788 2.606795 GCAGCAAATTGTTTAGGACGCA 60.607 45.455 0.00 0.00 0.00 5.24
2699 2789 2.979813 CAGCAAATTGTTTAGGACGCAC 59.020 45.455 0.00 0.00 0.00 5.34
2700 2790 2.884639 AGCAAATTGTTTAGGACGCACT 59.115 40.909 0.00 0.00 0.00 4.40
2701 2791 2.979813 GCAAATTGTTTAGGACGCACTG 59.020 45.455 0.00 0.00 0.00 3.66
2702 2792 3.304391 GCAAATTGTTTAGGACGCACTGA 60.304 43.478 0.00 0.00 0.00 3.41
2711 2801 1.335182 AGGACGCACTGAGTATGATCG 59.665 52.381 0.00 0.00 0.00 3.69
2729 2819 0.777631 CGTTTGATTTTGCTGTGCCG 59.222 50.000 0.00 0.00 0.00 5.69
2793 2883 3.458163 CGAGGGTCGCTAAGGGCA 61.458 66.667 0.00 0.00 41.91 5.36
2794 2884 2.797278 CGAGGGTCGCTAAGGGCAT 61.797 63.158 0.00 0.00 41.91 4.40
2795 2885 1.227674 GAGGGTCGCTAAGGGCATG 60.228 63.158 0.00 0.00 41.91 4.06
2796 2886 2.203209 GGGTCGCTAAGGGCATGG 60.203 66.667 0.00 0.00 41.91 3.66
2797 2887 2.902343 GGTCGCTAAGGGCATGGC 60.902 66.667 11.56 11.56 41.91 4.40
2812 2902 4.585070 GGCCAATGCATAGCCTCA 57.415 55.556 26.05 0.00 43.62 3.86
2813 2903 3.047039 GGCCAATGCATAGCCTCAT 57.953 52.632 26.05 0.00 43.62 2.90
2814 2904 0.601558 GGCCAATGCATAGCCTCATG 59.398 55.000 26.05 8.97 43.62 3.07
2815 2905 0.601558 GCCAATGCATAGCCTCATGG 59.398 55.000 0.00 2.91 37.47 3.66
2816 2906 1.991121 CCAATGCATAGCCTCATGGT 58.009 50.000 0.00 0.00 35.27 3.55
2817 2907 1.611977 CCAATGCATAGCCTCATGGTG 59.388 52.381 0.00 0.00 35.27 4.17
2818 2908 2.578786 CAATGCATAGCCTCATGGTGA 58.421 47.619 0.00 0.00 35.27 4.02
2819 2909 3.154710 CAATGCATAGCCTCATGGTGAT 58.845 45.455 0.00 0.00 35.27 3.06
2820 2910 2.265589 TGCATAGCCTCATGGTGATG 57.734 50.000 0.00 0.00 35.27 3.07
2821 2911 0.879765 GCATAGCCTCATGGTGATGC 59.120 55.000 0.00 0.00 42.17 3.91
2822 2912 1.531423 CATAGCCTCATGGTGATGCC 58.469 55.000 4.03 0.00 38.54 4.40
2823 2913 0.403271 ATAGCCTCATGGTGATGCCC 59.597 55.000 4.03 0.00 38.54 5.36
2824 2914 1.708993 TAGCCTCATGGTGATGCCCC 61.709 60.000 4.03 0.00 38.54 5.80
2825 2915 3.009275 CCTCATGGTGATGCCCCA 58.991 61.111 0.00 0.00 36.04 4.96
2826 2916 1.540166 CCTCATGGTGATGCCCCAT 59.460 57.895 0.00 0.00 43.53 4.00
2829 2919 4.690849 ATGGTGATGCCCCATGTG 57.309 55.556 0.00 0.00 41.17 3.21
2830 2920 1.759299 ATGGTGATGCCCCATGTGC 60.759 57.895 0.00 0.00 41.17 4.57
2831 2921 3.149648 GGTGATGCCCCATGTGCC 61.150 66.667 2.39 0.00 0.00 5.01
2832 2922 2.362760 GTGATGCCCCATGTGCCA 60.363 61.111 2.39 0.00 0.00 4.92
2833 2923 1.759299 GTGATGCCCCATGTGCCAT 60.759 57.895 2.39 0.00 0.00 4.40
2834 2924 0.467844 GTGATGCCCCATGTGCCATA 60.468 55.000 2.39 0.00 0.00 2.74
2835 2925 0.483770 TGATGCCCCATGTGCCATAT 59.516 50.000 2.39 0.00 0.00 1.78
2836 2926 1.709679 TGATGCCCCATGTGCCATATA 59.290 47.619 2.39 0.00 0.00 0.86
2837 2927 2.291089 TGATGCCCCATGTGCCATATAG 60.291 50.000 2.39 0.00 0.00 1.31
2838 2928 0.405198 TGCCCCATGTGCCATATAGG 59.595 55.000 2.39 0.00 41.84 2.57
2839 2929 0.698238 GCCCCATGTGCCATATAGGA 59.302 55.000 0.00 0.00 41.22 2.94
2840 2930 1.285962 GCCCCATGTGCCATATAGGAT 59.714 52.381 0.00 0.00 41.22 3.24
2841 2931 2.291800 GCCCCATGTGCCATATAGGATT 60.292 50.000 0.00 0.00 41.22 3.01
2842 2932 3.359033 CCCCATGTGCCATATAGGATTG 58.641 50.000 0.00 0.00 41.22 2.67
2843 2933 3.359033 CCCATGTGCCATATAGGATTGG 58.641 50.000 0.00 0.00 41.22 3.16
2844 2934 3.010472 CCCATGTGCCATATAGGATTGGA 59.990 47.826 0.00 0.00 41.22 3.53
2845 2935 4.325579 CCCATGTGCCATATAGGATTGGAT 60.326 45.833 0.00 0.00 41.22 3.41
2846 2936 4.643334 CCATGTGCCATATAGGATTGGATG 59.357 45.833 0.00 0.00 41.22 3.51
2847 2937 4.999469 TGTGCCATATAGGATTGGATGT 57.001 40.909 0.00 0.00 41.22 3.06
2848 2938 5.323382 TGTGCCATATAGGATTGGATGTT 57.677 39.130 0.00 0.00 41.22 2.71
2849 2939 6.446909 TGTGCCATATAGGATTGGATGTTA 57.553 37.500 0.00 0.00 41.22 2.41
2850 2940 6.475504 TGTGCCATATAGGATTGGATGTTAG 58.524 40.000 0.00 0.00 41.22 2.34
2851 2941 5.882557 GTGCCATATAGGATTGGATGTTAGG 59.117 44.000 0.00 0.00 41.22 2.69
2852 2942 5.044919 TGCCATATAGGATTGGATGTTAGGG 60.045 44.000 0.00 0.00 41.22 3.53
2853 2943 5.191722 GCCATATAGGATTGGATGTTAGGGA 59.808 44.000 0.00 0.00 41.22 4.20
2854 2944 6.297010 GCCATATAGGATTGGATGTTAGGGAA 60.297 42.308 0.00 0.00 41.22 3.97
2855 2945 7.698912 CCATATAGGATTGGATGTTAGGGAAA 58.301 38.462 0.00 0.00 41.22 3.13
2856 2946 8.339247 CCATATAGGATTGGATGTTAGGGAAAT 58.661 37.037 0.00 0.00 41.22 2.17
2857 2947 9.759473 CATATAGGATTGGATGTTAGGGAAATT 57.241 33.333 0.00 0.00 0.00 1.82
2860 2950 6.614657 AGGATTGGATGTTAGGGAAATTAGG 58.385 40.000 0.00 0.00 0.00 2.69
2861 2951 6.162241 AGGATTGGATGTTAGGGAAATTAGGT 59.838 38.462 0.00 0.00 0.00 3.08
2862 2952 6.839134 GGATTGGATGTTAGGGAAATTAGGTT 59.161 38.462 0.00 0.00 0.00 3.50
2863 2953 7.014326 GGATTGGATGTTAGGGAAATTAGGTTC 59.986 40.741 0.00 0.00 0.00 3.62
2864 2954 5.433526 TGGATGTTAGGGAAATTAGGTTCG 58.566 41.667 0.00 0.00 0.00 3.95
2865 2955 4.820173 GGATGTTAGGGAAATTAGGTTCGG 59.180 45.833 0.00 0.00 0.00 4.30
2866 2956 5.397109 GGATGTTAGGGAAATTAGGTTCGGA 60.397 44.000 0.00 0.00 0.00 4.55
2867 2957 5.703730 TGTTAGGGAAATTAGGTTCGGAT 57.296 39.130 0.00 0.00 0.00 4.18
2868 2958 6.811634 TGTTAGGGAAATTAGGTTCGGATA 57.188 37.500 0.00 0.00 0.00 2.59
2869 2959 7.197901 TGTTAGGGAAATTAGGTTCGGATAA 57.802 36.000 0.00 0.00 0.00 1.75
2870 2960 7.277396 TGTTAGGGAAATTAGGTTCGGATAAG 58.723 38.462 0.00 0.00 0.00 1.73
2871 2961 5.306114 AGGGAAATTAGGTTCGGATAAGG 57.694 43.478 0.00 0.00 0.00 2.69
2872 2962 4.973211 AGGGAAATTAGGTTCGGATAAGGA 59.027 41.667 0.00 0.00 0.00 3.36
2873 2963 5.430745 AGGGAAATTAGGTTCGGATAAGGAA 59.569 40.000 0.00 0.00 0.00 3.36
2874 2964 5.763698 GGGAAATTAGGTTCGGATAAGGAAG 59.236 44.000 0.00 0.00 0.00 3.46
2875 2965 5.238868 GGAAATTAGGTTCGGATAAGGAAGC 59.761 44.000 0.00 0.00 41.06 3.86
2876 2966 3.447918 TTAGGTTCGGATAAGGAAGCG 57.552 47.619 0.00 0.00 44.35 4.68
2877 2967 1.481871 AGGTTCGGATAAGGAAGCGA 58.518 50.000 0.00 0.00 44.35 4.93
2878 2968 1.409427 AGGTTCGGATAAGGAAGCGAG 59.591 52.381 0.00 0.00 44.35 5.03
2879 2969 1.407979 GGTTCGGATAAGGAAGCGAGA 59.592 52.381 0.00 0.00 32.96 4.04
2880 2970 2.036089 GGTTCGGATAAGGAAGCGAGAT 59.964 50.000 0.00 0.00 32.96 2.75
2881 2971 3.310246 GTTCGGATAAGGAAGCGAGATC 58.690 50.000 0.00 0.00 0.00 2.75
2882 2972 1.887198 TCGGATAAGGAAGCGAGATCC 59.113 52.381 0.00 0.00 37.22 3.36
2884 2974 2.094957 CGGATAAGGAAGCGAGATCCTC 60.095 54.545 4.79 0.00 46.65 3.71
2885 2975 3.161866 GGATAAGGAAGCGAGATCCTCT 58.838 50.000 4.79 0.00 46.65 3.69
2886 2976 3.056891 GGATAAGGAAGCGAGATCCTCTG 60.057 52.174 4.79 0.00 46.65 3.35
2887 2977 1.859302 AAGGAAGCGAGATCCTCTGT 58.141 50.000 4.79 0.00 46.65 3.41
2888 2978 2.738587 AGGAAGCGAGATCCTCTGTA 57.261 50.000 0.00 0.00 44.01 2.74
2889 2979 3.019799 AGGAAGCGAGATCCTCTGTAA 57.980 47.619 0.00 0.00 44.01 2.41
2890 2980 2.955660 AGGAAGCGAGATCCTCTGTAAG 59.044 50.000 0.00 0.00 44.01 2.34
2891 2981 2.952978 GGAAGCGAGATCCTCTGTAAGA 59.047 50.000 0.00 0.00 43.69 2.10
2901 2991 3.358554 TCTGTAAGAGACGGGTGCT 57.641 52.632 0.00 0.00 38.67 4.40
2902 2992 1.629043 TCTGTAAGAGACGGGTGCTT 58.371 50.000 0.00 0.00 38.67 3.91
2903 2993 1.272490 TCTGTAAGAGACGGGTGCTTG 59.728 52.381 0.00 0.00 38.67 4.01
2904 2994 0.320374 TGTAAGAGACGGGTGCTTGG 59.680 55.000 0.00 0.00 0.00 3.61
2905 2995 0.391263 GTAAGAGACGGGTGCTTGGG 60.391 60.000 0.00 0.00 0.00 4.12
2906 2996 1.550130 TAAGAGACGGGTGCTTGGGG 61.550 60.000 0.00 0.00 0.00 4.96
2907 2997 3.319198 GAGACGGGTGCTTGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
2908 2998 3.316573 GAGACGGGTGCTTGGGGAG 62.317 68.421 0.00 0.00 0.00 4.30
2909 2999 3.319198 GACGGGTGCTTGGGGAGA 61.319 66.667 0.00 0.00 0.00 3.71
2910 3000 2.852075 ACGGGTGCTTGGGGAGAA 60.852 61.111 0.00 0.00 0.00 2.87
2911 3001 2.406002 GACGGGTGCTTGGGGAGAAA 62.406 60.000 0.00 0.00 0.00 2.52
2912 3002 1.228429 CGGGTGCTTGGGGAGAAAA 60.228 57.895 0.00 0.00 0.00 2.29
2913 3003 0.825840 CGGGTGCTTGGGGAGAAAAA 60.826 55.000 0.00 0.00 0.00 1.94
2914 3004 1.644509 GGGTGCTTGGGGAGAAAAAT 58.355 50.000 0.00 0.00 0.00 1.82
2915 3005 1.977854 GGGTGCTTGGGGAGAAAAATT 59.022 47.619 0.00 0.00 0.00 1.82
2916 3006 2.289631 GGGTGCTTGGGGAGAAAAATTG 60.290 50.000 0.00 0.00 0.00 2.32
2917 3007 2.368548 GGTGCTTGGGGAGAAAAATTGT 59.631 45.455 0.00 0.00 0.00 2.71
2918 3008 3.392882 GTGCTTGGGGAGAAAAATTGTG 58.607 45.455 0.00 0.00 0.00 3.33
2919 3009 2.368221 TGCTTGGGGAGAAAAATTGTGG 59.632 45.455 0.00 0.00 0.00 4.17
2920 3010 2.632512 GCTTGGGGAGAAAAATTGTGGA 59.367 45.455 0.00 0.00 0.00 4.02
2921 3011 3.554960 GCTTGGGGAGAAAAATTGTGGAC 60.555 47.826 0.00 0.00 0.00 4.02
2922 3012 2.604139 TGGGGAGAAAAATTGTGGACC 58.396 47.619 0.00 0.00 0.00 4.46
2923 3013 1.544246 GGGGAGAAAAATTGTGGACCG 59.456 52.381 0.00 0.00 0.00 4.79
2924 3014 2.510613 GGGAGAAAAATTGTGGACCGA 58.489 47.619 0.00 0.00 0.00 4.69
2925 3015 3.089284 GGGAGAAAAATTGTGGACCGAT 58.911 45.455 0.00 0.00 0.00 4.18
2926 3016 3.119495 GGGAGAAAAATTGTGGACCGATG 60.119 47.826 0.00 0.00 0.00 3.84
2927 3017 3.506067 GGAGAAAAATTGTGGACCGATGT 59.494 43.478 0.00 0.00 0.00 3.06
2928 3018 4.698304 GGAGAAAAATTGTGGACCGATGTA 59.302 41.667 0.00 0.00 0.00 2.29
2929 3019 5.182380 GGAGAAAAATTGTGGACCGATGTAA 59.818 40.000 0.00 0.00 0.00 2.41
2930 3020 6.294286 GGAGAAAAATTGTGGACCGATGTAAA 60.294 38.462 0.00 0.00 0.00 2.01
2931 3021 7.045126 AGAAAAATTGTGGACCGATGTAAAA 57.955 32.000 0.00 0.00 0.00 1.52
2932 3022 7.493367 AGAAAAATTGTGGACCGATGTAAAAA 58.507 30.769 0.00 0.00 0.00 1.94
2933 3023 7.651704 AGAAAAATTGTGGACCGATGTAAAAAG 59.348 33.333 0.00 0.00 0.00 2.27
2934 3024 3.907894 TTGTGGACCGATGTAAAAAGC 57.092 42.857 0.00 0.00 0.00 3.51
2935 3025 3.134574 TGTGGACCGATGTAAAAAGCT 57.865 42.857 0.00 0.00 0.00 3.74
2936 3026 2.811431 TGTGGACCGATGTAAAAAGCTG 59.189 45.455 0.00 0.00 0.00 4.24
2937 3027 3.071479 GTGGACCGATGTAAAAAGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
2938 3028 3.500680 GTGGACCGATGTAAAAAGCTGAA 59.499 43.478 0.00 0.00 0.00 3.02
2939 3029 4.023536 GTGGACCGATGTAAAAAGCTGAAA 60.024 41.667 0.00 0.00 0.00 2.69
2940 3030 4.580995 TGGACCGATGTAAAAAGCTGAAAA 59.419 37.500 0.00 0.00 0.00 2.29
2941 3031 5.067936 TGGACCGATGTAAAAAGCTGAAAAA 59.932 36.000 0.00 0.00 0.00 1.94
2965 3055 9.466497 AAAATTGAAATAAGGAGTAGAGATGCA 57.534 29.630 0.00 0.00 0.00 3.96
2966 3056 9.638176 AAATTGAAATAAGGAGTAGAGATGCAT 57.362 29.630 0.00 0.00 0.00 3.96
2969 3059 9.716531 TTGAAATAAGGAGTAGAGATGCATATG 57.283 33.333 0.00 0.00 0.00 1.78
2970 3060 8.874156 TGAAATAAGGAGTAGAGATGCATATGT 58.126 33.333 0.00 0.00 0.00 2.29
2976 3066 9.760926 AAGGAGTAGAGATGCATATGTATTAGA 57.239 33.333 7.78 0.00 0.00 2.10
2977 3067 9.407380 AGGAGTAGAGATGCATATGTATTAGAG 57.593 37.037 7.78 0.00 0.00 2.43
2978 3068 9.184523 GGAGTAGAGATGCATATGTATTAGAGT 57.815 37.037 7.78 0.00 0.00 3.24
3020 3110 7.732222 TTTTTATTATTTGATGAGGGCCACT 57.268 32.000 6.18 0.00 0.00 4.00
3021 3111 8.830915 TTTTTATTATTTGATGAGGGCCACTA 57.169 30.769 6.18 0.00 0.00 2.74
3022 3112 8.830915 TTTTATTATTTGATGAGGGCCACTAA 57.169 30.769 6.18 0.00 0.00 2.24
3023 3113 9.432982 TTTTATTATTTGATGAGGGCCACTAAT 57.567 29.630 6.18 0.00 0.00 1.73
3025 3115 9.739276 TTATTATTTGATGAGGGCCACTAATAG 57.261 33.333 6.18 0.00 0.00 1.73
3026 3116 5.653255 ATTTGATGAGGGCCACTAATAGT 57.347 39.130 6.18 0.00 0.00 2.12
3027 3117 6.763715 ATTTGATGAGGGCCACTAATAGTA 57.236 37.500 6.18 0.00 0.00 1.82
3028 3118 5.808366 TTGATGAGGGCCACTAATAGTAG 57.192 43.478 6.18 0.00 0.00 2.57
3029 3119 3.578716 TGATGAGGGCCACTAATAGTAGC 59.421 47.826 6.18 2.19 31.96 3.58
3030 3120 3.330126 TGAGGGCCACTAATAGTAGCT 57.670 47.619 6.18 0.00 33.32 3.32
3031 3121 3.654273 TGAGGGCCACTAATAGTAGCTT 58.346 45.455 6.18 0.33 33.32 3.74
3032 3122 4.811498 TGAGGGCCACTAATAGTAGCTTA 58.189 43.478 6.18 0.00 33.32 3.09
3033 3123 4.587684 TGAGGGCCACTAATAGTAGCTTAC 59.412 45.833 6.18 2.61 33.32 2.34
3034 3124 4.817286 AGGGCCACTAATAGTAGCTTACT 58.183 43.478 6.18 4.60 42.68 2.24
3035 3125 5.217400 AGGGCCACTAATAGTAGCTTACTT 58.783 41.667 6.18 0.00 40.14 2.24
3036 3126 5.666265 AGGGCCACTAATAGTAGCTTACTTT 59.334 40.000 6.18 0.00 40.14 2.66
3037 3127 5.758784 GGGCCACTAATAGTAGCTTACTTTG 59.241 44.000 10.39 0.00 40.14 2.77
3038 3128 5.758784 GGCCACTAATAGTAGCTTACTTTGG 59.241 44.000 10.39 0.00 40.14 3.28
3039 3129 5.758784 GCCACTAATAGTAGCTTACTTTGGG 59.241 44.000 3.62 0.00 40.14 4.12
3040 3130 6.289064 CCACTAATAGTAGCTTACTTTGGGG 58.711 44.000 0.00 0.00 40.14 4.96
3041 3131 6.099269 CCACTAATAGTAGCTTACTTTGGGGA 59.901 42.308 0.00 0.00 40.14 4.81
3042 3132 7.210873 CACTAATAGTAGCTTACTTTGGGGAG 58.789 42.308 0.00 0.00 40.14 4.30
3043 3133 7.069578 CACTAATAGTAGCTTACTTTGGGGAGA 59.930 40.741 0.00 0.00 40.14 3.71
3044 3134 6.886178 AATAGTAGCTTACTTTGGGGAGAA 57.114 37.500 0.00 0.00 40.14 2.87
3045 3135 6.886178 ATAGTAGCTTACTTTGGGGAGAAA 57.114 37.500 0.00 0.00 40.14 2.52
3046 3136 5.578157 AGTAGCTTACTTTGGGGAGAAAA 57.422 39.130 0.00 0.00 34.86 2.29
3047 3137 5.948842 AGTAGCTTACTTTGGGGAGAAAAA 58.051 37.500 0.00 0.00 34.86 1.94
3048 3138 6.552932 AGTAGCTTACTTTGGGGAGAAAAAT 58.447 36.000 0.00 0.00 34.86 1.82
3049 3139 5.984695 AGCTTACTTTGGGGAGAAAAATC 57.015 39.130 0.00 0.00 0.00 2.17
3050 3140 5.393866 AGCTTACTTTGGGGAGAAAAATCA 58.606 37.500 0.00 0.00 0.00 2.57
3051 3141 5.838521 AGCTTACTTTGGGGAGAAAAATCAA 59.161 36.000 0.00 0.00 0.00 2.57
3052 3142 6.498303 AGCTTACTTTGGGGAGAAAAATCAAT 59.502 34.615 0.00 0.00 0.00 2.57
3053 3143 6.591448 GCTTACTTTGGGGAGAAAAATCAATG 59.409 38.462 0.00 0.00 0.00 2.82
3054 3144 4.898320 ACTTTGGGGAGAAAAATCAATGC 58.102 39.130 0.00 0.00 0.00 3.56
3055 3145 4.347583 ACTTTGGGGAGAAAAATCAATGCA 59.652 37.500 0.00 0.00 0.00 3.96
3056 3146 4.540359 TTGGGGAGAAAAATCAATGCAG 57.460 40.909 0.00 0.00 0.00 4.41
3057 3147 3.509442 TGGGGAGAAAAATCAATGCAGT 58.491 40.909 0.00 0.00 0.00 4.40
3058 3148 3.903090 TGGGGAGAAAAATCAATGCAGTT 59.097 39.130 0.00 0.00 0.00 3.16
3059 3149 4.248058 GGGGAGAAAAATCAATGCAGTTG 58.752 43.478 0.00 0.00 39.25 3.16
3060 3150 3.681417 GGGAGAAAAATCAATGCAGTTGC 59.319 43.478 0.00 0.00 37.74 4.17
3061 3151 3.681417 GGAGAAAAATCAATGCAGTTGCC 59.319 43.478 1.06 0.00 41.18 4.52
3062 3152 4.562143 GGAGAAAAATCAATGCAGTTGCCT 60.562 41.667 1.06 0.00 41.18 4.75
3063 3153 4.964593 AGAAAAATCAATGCAGTTGCCTT 58.035 34.783 1.06 0.00 41.18 4.35
3064 3154 6.100404 AGAAAAATCAATGCAGTTGCCTTA 57.900 33.333 1.06 0.00 41.18 2.69
3065 3155 6.523840 AGAAAAATCAATGCAGTTGCCTTAA 58.476 32.000 1.06 0.00 41.18 1.85
3066 3156 6.647895 AGAAAAATCAATGCAGTTGCCTTAAG 59.352 34.615 1.06 0.00 41.18 1.85
3067 3157 3.515330 ATCAATGCAGTTGCCTTAAGC 57.485 42.857 1.06 0.00 41.18 3.09
3068 3158 1.545582 TCAATGCAGTTGCCTTAAGCC 59.454 47.619 1.06 0.00 42.71 4.35
3069 3159 1.273048 CAATGCAGTTGCCTTAAGCCA 59.727 47.619 1.06 0.00 42.71 4.75
3070 3160 0.890683 ATGCAGTTGCCTTAAGCCAC 59.109 50.000 1.06 0.00 42.71 5.01
3071 3161 1.178534 TGCAGTTGCCTTAAGCCACC 61.179 55.000 1.06 0.00 42.71 4.61
3072 3162 0.895559 GCAGTTGCCTTAAGCCACCT 60.896 55.000 0.00 0.00 42.71 4.00
3073 3163 1.620822 CAGTTGCCTTAAGCCACCTT 58.379 50.000 0.00 0.00 42.71 3.50
3074 3164 1.963515 CAGTTGCCTTAAGCCACCTTT 59.036 47.619 0.00 0.00 42.71 3.11
3075 3165 2.365293 CAGTTGCCTTAAGCCACCTTTT 59.635 45.455 0.00 0.00 42.71 2.27
3076 3166 3.038280 AGTTGCCTTAAGCCACCTTTTT 58.962 40.909 0.00 0.00 42.71 1.94
3094 3184 4.734398 TTTTTCATGGGGCATGTGTATC 57.266 40.909 0.00 0.00 41.98 2.24
3095 3185 2.363306 TTCATGGGGCATGTGTATCC 57.637 50.000 0.00 0.00 41.98 2.59
3096 3186 1.220703 TCATGGGGCATGTGTATCCA 58.779 50.000 0.00 0.00 41.98 3.41
3097 3187 1.782140 TCATGGGGCATGTGTATCCAT 59.218 47.619 0.00 0.00 41.98 3.41
3098 3188 2.985311 TCATGGGGCATGTGTATCCATA 59.015 45.455 0.00 0.00 41.98 2.74
3099 3189 3.592877 TCATGGGGCATGTGTATCCATAT 59.407 43.478 0.00 0.00 41.98 1.78
3100 3190 3.438216 TGGGGCATGTGTATCCATATG 57.562 47.619 0.00 0.00 41.61 1.78
3109 3199 7.080353 CATGTGTATCCATATGCTACCATTG 57.920 40.000 0.00 0.00 34.09 2.82
3110 3200 6.186420 TGTGTATCCATATGCTACCATTGT 57.814 37.500 0.00 0.00 32.85 2.71
3111 3201 6.600388 TGTGTATCCATATGCTACCATTGTT 58.400 36.000 0.00 0.00 32.85 2.83
3112 3202 6.710295 TGTGTATCCATATGCTACCATTGTTC 59.290 38.462 0.00 0.00 32.85 3.18
3113 3203 6.710295 GTGTATCCATATGCTACCATTGTTCA 59.290 38.462 0.00 0.00 32.85 3.18
3114 3204 7.391554 GTGTATCCATATGCTACCATTGTTCAT 59.608 37.037 0.00 0.00 32.85 2.57
3115 3205 6.829229 ATCCATATGCTACCATTGTTCATG 57.171 37.500 0.00 0.00 32.85 3.07
3116 3206 4.520111 TCCATATGCTACCATTGTTCATGC 59.480 41.667 0.00 0.00 32.85 4.06
3117 3207 4.321452 CCATATGCTACCATTGTTCATGCC 60.321 45.833 0.00 0.00 32.85 4.40
3130 3220 3.199727 TGTTCATGCCCTAAGAGCACATA 59.800 43.478 0.00 0.00 44.40 2.29
3131 3221 4.141413 TGTTCATGCCCTAAGAGCACATAT 60.141 41.667 0.00 0.00 44.40 1.78
3132 3222 5.071653 TGTTCATGCCCTAAGAGCACATATA 59.928 40.000 0.00 0.00 44.40 0.86
3159 3249 5.562298 AGTAAACTAGAAGAGCCAAACCA 57.438 39.130 0.00 0.00 0.00 3.67
3160 3250 5.937111 AGTAAACTAGAAGAGCCAAACCAA 58.063 37.500 0.00 0.00 0.00 3.67
3169 3259 4.313020 AGAGCCAAACCAATGATCTTCT 57.687 40.909 0.00 0.00 0.00 2.85
3180 3270 8.591114 AACCAATGATCTTCTCAGAATTGATT 57.409 30.769 0.06 0.00 37.28 2.57
3181 3271 8.591114 ACCAATGATCTTCTCAGAATTGATTT 57.409 30.769 0.06 0.00 37.28 2.17
3182 3272 9.032624 ACCAATGATCTTCTCAGAATTGATTTT 57.967 29.630 0.06 0.00 37.28 1.82
3183 3273 9.517609 CCAATGATCTTCTCAGAATTGATTTTC 57.482 33.333 0.06 0.00 37.28 2.29
3249 3339 4.685628 GCTTTAGCAGCTCATATGAGACTC 59.314 45.833 32.38 19.64 46.27 3.36
3250 3340 5.738495 GCTTTAGCAGCTCATATGAGACTCA 60.738 44.000 32.38 15.99 46.27 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.781934 AGTGGCTGAACTGTCTTTTAGTT 58.218 39.130 0.00 0.00 40.84 2.24
58 59 1.071385 CCAGAGAAGTGGCTGAACTGT 59.929 52.381 0.00 0.00 34.06 3.55
169 170 2.433604 TCAAAATCAGCAAAGCCCACAA 59.566 40.909 0.00 0.00 0.00 3.33
185 186 3.366883 GCTCCATGCCGTAAATGTCAAAA 60.367 43.478 0.00 0.00 35.15 2.44
207 208 2.288579 TGTACCAACCGTCTACTGCAAG 60.289 50.000 0.00 0.00 42.29 4.01
404 405 8.402472 TCCATATTAAAAAGCTTAACCATCACG 58.598 33.333 0.00 0.00 0.00 4.35
426 427 2.766263 TCTTTACAGGTCGCTGATCCAT 59.234 45.455 0.00 0.00 0.00 3.41
576 589 3.576078 TTACTCATTAGGGTGCCATGG 57.424 47.619 7.63 7.63 0.00 3.66
868 905 9.077885 ACATAACAGGAAAAATAGCTGAAAAGA 57.922 29.630 0.00 0.00 0.00 2.52
880 917 6.016192 TGCATAAACGGACATAACAGGAAAAA 60.016 34.615 0.00 0.00 0.00 1.94
989 1051 1.261619 GCCGGATCATTACTTCTTGCG 59.738 52.381 5.05 0.00 0.00 4.85
1332 1403 5.351458 ACCTCGTACGTCTTTAACAAGTTT 58.649 37.500 16.05 0.00 0.00 2.66
1347 1418 5.069501 ACTTCTTTACCATGACCTCGTAC 57.930 43.478 0.00 0.00 0.00 3.67
1470 1541 3.056821 CCTTGTTAAGTAAGCCCCTTTGC 60.057 47.826 0.00 0.00 0.00 3.68
1572 1643 5.929697 ACTCATGTATTGATTGGTATGCG 57.070 39.130 0.00 0.00 32.72 4.73
1716 1787 7.440198 CACTGAAGATTCTCTGGCAGATATAA 58.560 38.462 19.11 12.96 34.96 0.98
1763 1834 1.016627 GGCATTAGCAGCGTCAATCA 58.983 50.000 0.00 0.00 44.61 2.57
1767 1838 1.020861 CAGTGGCATTAGCAGCGTCA 61.021 55.000 0.00 0.00 44.61 4.35
1770 1841 0.523072 AAACAGTGGCATTAGCAGCG 59.477 50.000 0.00 0.00 44.61 5.18
1903 1974 4.542833 CCATCTTTGGGTGCACAAGCAG 62.543 54.545 20.43 8.98 42.50 4.24
1905 1976 0.037975 CCATCTTTGGGTGCACAAGC 60.038 55.000 20.43 0.39 39.56 4.01
2106 2177 3.340814 ACGCTTTCCATGTGAATCTCT 57.659 42.857 0.00 0.00 31.67 3.10
2252 2323 4.817517 CAACCCTAACACTTATCAGTCGT 58.182 43.478 0.00 0.00 0.00 4.34
2303 2374 1.476891 ACGTACGATGATCTTGCAGGT 59.523 47.619 24.41 0.00 0.00 4.00
2438 2509 8.246180 AGGATTTACATGCATTACAAAACAGAG 58.754 33.333 0.00 0.00 0.00 3.35
2526 2597 4.542697 TGGCTGTACAGTCACCATATAGA 58.457 43.478 25.90 0.00 38.26 1.98
2675 2765 2.979813 CGTCCTAAACAATTTGCTGCAC 59.020 45.455 0.00 0.00 0.00 4.57
2696 2786 5.725110 AATCAAACGATCATACTCAGTGC 57.275 39.130 0.00 0.00 0.00 4.40
2698 2788 6.372659 AGCAAAATCAAACGATCATACTCAGT 59.627 34.615 0.00 0.00 0.00 3.41
2699 2789 6.685828 CAGCAAAATCAAACGATCATACTCAG 59.314 38.462 0.00 0.00 0.00 3.35
2700 2790 6.149308 ACAGCAAAATCAAACGATCATACTCA 59.851 34.615 0.00 0.00 0.00 3.41
2701 2791 6.467047 CACAGCAAAATCAAACGATCATACTC 59.533 38.462 0.00 0.00 0.00 2.59
2702 2792 6.317088 CACAGCAAAATCAAACGATCATACT 58.683 36.000 0.00 0.00 0.00 2.12
2711 2801 1.139163 CCGGCACAGCAAAATCAAAC 58.861 50.000 0.00 0.00 0.00 2.93
2795 2885 0.601558 CATGAGGCTATGCATTGGCC 59.398 55.000 26.45 26.29 45.57 5.36
2796 2886 0.601558 CCATGAGGCTATGCATTGGC 59.398 55.000 23.68 23.68 41.68 4.52
2797 2887 1.611977 CACCATGAGGCTATGCATTGG 59.388 52.381 3.54 7.19 39.06 3.16
2798 2888 2.578786 TCACCATGAGGCTATGCATTG 58.421 47.619 3.54 3.55 39.06 2.82
2799 2889 3.154710 CATCACCATGAGGCTATGCATT 58.845 45.455 3.54 0.00 39.06 3.56
2800 2890 2.791655 CATCACCATGAGGCTATGCAT 58.208 47.619 3.79 3.79 39.06 3.96
2801 2891 2.265589 CATCACCATGAGGCTATGCA 57.734 50.000 0.00 0.00 39.06 3.96
2808 2898 1.540166 ATGGGGCATCACCATGAGG 59.460 57.895 0.00 0.00 46.57 3.86
2813 2903 2.362760 GCACATGGGGCATCACCA 60.363 61.111 0.00 0.00 42.05 4.17
2814 2904 3.149648 GGCACATGGGGCATCACC 61.150 66.667 18.06 0.00 37.93 4.02
2815 2905 2.362760 TGGCACATGGGGCATCAC 60.363 61.111 22.03 0.00 38.55 3.06
2827 2917 5.882557 CCTAACATCCAATCCTATATGGCAC 59.117 44.000 0.00 0.00 36.62 5.01
2828 2918 5.044919 CCCTAACATCCAATCCTATATGGCA 60.045 44.000 0.00 0.00 36.62 4.92
2829 2919 5.191722 TCCCTAACATCCAATCCTATATGGC 59.808 44.000 0.00 0.00 36.62 4.40
2830 2920 6.891306 TCCCTAACATCCAATCCTATATGG 57.109 41.667 0.00 0.00 38.09 2.74
2831 2921 9.759473 AATTTCCCTAACATCCAATCCTATATG 57.241 33.333 0.00 0.00 0.00 1.78
2834 2924 8.394040 CCTAATTTCCCTAACATCCAATCCTAT 58.606 37.037 0.00 0.00 0.00 2.57
2835 2925 7.352522 ACCTAATTTCCCTAACATCCAATCCTA 59.647 37.037 0.00 0.00 0.00 2.94
2836 2926 6.162241 ACCTAATTTCCCTAACATCCAATCCT 59.838 38.462 0.00 0.00 0.00 3.24
2837 2927 6.373759 ACCTAATTTCCCTAACATCCAATCC 58.626 40.000 0.00 0.00 0.00 3.01
2838 2928 7.255139 CGAACCTAATTTCCCTAACATCCAATC 60.255 40.741 0.00 0.00 0.00 2.67
2839 2929 6.546034 CGAACCTAATTTCCCTAACATCCAAT 59.454 38.462 0.00 0.00 0.00 3.16
2840 2930 5.883673 CGAACCTAATTTCCCTAACATCCAA 59.116 40.000 0.00 0.00 0.00 3.53
2841 2931 5.433526 CGAACCTAATTTCCCTAACATCCA 58.566 41.667 0.00 0.00 0.00 3.41
2842 2932 4.820173 CCGAACCTAATTTCCCTAACATCC 59.180 45.833 0.00 0.00 0.00 3.51
2843 2933 5.677567 TCCGAACCTAATTTCCCTAACATC 58.322 41.667 0.00 0.00 0.00 3.06
2844 2934 5.703730 TCCGAACCTAATTTCCCTAACAT 57.296 39.130 0.00 0.00 0.00 2.71
2845 2935 5.703730 ATCCGAACCTAATTTCCCTAACA 57.296 39.130 0.00 0.00 0.00 2.41
2846 2936 6.709397 CCTTATCCGAACCTAATTTCCCTAAC 59.291 42.308 0.00 0.00 0.00 2.34
2847 2937 6.616548 TCCTTATCCGAACCTAATTTCCCTAA 59.383 38.462 0.00 0.00 0.00 2.69
2848 2938 6.145336 TCCTTATCCGAACCTAATTTCCCTA 58.855 40.000 0.00 0.00 0.00 3.53
2849 2939 4.973211 TCCTTATCCGAACCTAATTTCCCT 59.027 41.667 0.00 0.00 0.00 4.20
2850 2940 5.300411 TCCTTATCCGAACCTAATTTCCC 57.700 43.478 0.00 0.00 0.00 3.97
2851 2941 5.238868 GCTTCCTTATCCGAACCTAATTTCC 59.761 44.000 0.00 0.00 0.00 3.13
2852 2942 5.050295 CGCTTCCTTATCCGAACCTAATTTC 60.050 44.000 0.00 0.00 0.00 2.17
2853 2943 4.814771 CGCTTCCTTATCCGAACCTAATTT 59.185 41.667 0.00 0.00 0.00 1.82
2854 2944 4.100498 TCGCTTCCTTATCCGAACCTAATT 59.900 41.667 0.00 0.00 0.00 1.40
2855 2945 3.640029 TCGCTTCCTTATCCGAACCTAAT 59.360 43.478 0.00 0.00 0.00 1.73
2856 2946 3.025978 TCGCTTCCTTATCCGAACCTAA 58.974 45.455 0.00 0.00 0.00 2.69
2857 2947 2.621998 CTCGCTTCCTTATCCGAACCTA 59.378 50.000 0.00 0.00 0.00 3.08
2858 2948 1.409427 CTCGCTTCCTTATCCGAACCT 59.591 52.381 0.00 0.00 0.00 3.50
2859 2949 1.407979 TCTCGCTTCCTTATCCGAACC 59.592 52.381 0.00 0.00 0.00 3.62
2860 2950 2.865343 TCTCGCTTCCTTATCCGAAC 57.135 50.000 0.00 0.00 0.00 3.95
2861 2951 2.296471 GGATCTCGCTTCCTTATCCGAA 59.704 50.000 0.00 0.00 0.00 4.30
2862 2952 1.887198 GGATCTCGCTTCCTTATCCGA 59.113 52.381 0.00 0.00 0.00 4.55
2863 2953 1.889829 AGGATCTCGCTTCCTTATCCG 59.110 52.381 0.00 0.00 40.84 4.18
2864 2954 3.586100 GAGGATCTCGCTTCCTTATCC 57.414 52.381 0.00 0.00 43.75 2.59
2878 2968 2.359531 CACCCGTCTCTTACAGAGGATC 59.640 54.545 0.93 0.00 42.54 3.36
2879 2969 2.379972 CACCCGTCTCTTACAGAGGAT 58.620 52.381 0.93 0.00 42.54 3.24
2880 2970 1.835494 CACCCGTCTCTTACAGAGGA 58.165 55.000 0.93 0.00 42.54 3.71
2881 2971 0.173708 GCACCCGTCTCTTACAGAGG 59.826 60.000 0.93 0.00 42.54 3.69
2882 2972 1.178276 AGCACCCGTCTCTTACAGAG 58.822 55.000 0.00 0.00 43.64 3.35
2883 2973 1.272490 CAAGCACCCGTCTCTTACAGA 59.728 52.381 0.00 0.00 0.00 3.41
2884 2974 1.673033 CCAAGCACCCGTCTCTTACAG 60.673 57.143 0.00 0.00 0.00 2.74
2885 2975 0.320374 CCAAGCACCCGTCTCTTACA 59.680 55.000 0.00 0.00 0.00 2.41
2886 2976 0.391263 CCCAAGCACCCGTCTCTTAC 60.391 60.000 0.00 0.00 0.00 2.34
2887 2977 1.550130 CCCCAAGCACCCGTCTCTTA 61.550 60.000 0.00 0.00 0.00 2.10
2888 2978 2.750350 CCCAAGCACCCGTCTCTT 59.250 61.111 0.00 0.00 0.00 2.85
2889 2979 3.322466 CCCCAAGCACCCGTCTCT 61.322 66.667 0.00 0.00 0.00 3.10
2890 2980 3.316573 CTCCCCAAGCACCCGTCTC 62.317 68.421 0.00 0.00 0.00 3.36
2891 2981 3.322466 CTCCCCAAGCACCCGTCT 61.322 66.667 0.00 0.00 0.00 4.18
2892 2982 2.406002 TTTCTCCCCAAGCACCCGTC 62.406 60.000 0.00 0.00 0.00 4.79
2893 2983 2.002018 TTTTCTCCCCAAGCACCCGT 62.002 55.000 0.00 0.00 0.00 5.28
2894 2984 0.825840 TTTTTCTCCCCAAGCACCCG 60.826 55.000 0.00 0.00 0.00 5.28
2895 2985 1.644509 ATTTTTCTCCCCAAGCACCC 58.355 50.000 0.00 0.00 0.00 4.61
2896 2986 2.368548 ACAATTTTTCTCCCCAAGCACC 59.631 45.455 0.00 0.00 0.00 5.01
2897 2987 3.392882 CACAATTTTTCTCCCCAAGCAC 58.607 45.455 0.00 0.00 0.00 4.40
2898 2988 2.368221 CCACAATTTTTCTCCCCAAGCA 59.632 45.455 0.00 0.00 0.00 3.91
2899 2989 2.632512 TCCACAATTTTTCTCCCCAAGC 59.367 45.455 0.00 0.00 0.00 4.01
2900 2990 3.006859 GGTCCACAATTTTTCTCCCCAAG 59.993 47.826 0.00 0.00 0.00 3.61
2901 2991 2.969262 GGTCCACAATTTTTCTCCCCAA 59.031 45.455 0.00 0.00 0.00 4.12
2902 2992 2.604139 GGTCCACAATTTTTCTCCCCA 58.396 47.619 0.00 0.00 0.00 4.96
2903 2993 1.544246 CGGTCCACAATTTTTCTCCCC 59.456 52.381 0.00 0.00 0.00 4.81
2904 2994 2.510613 TCGGTCCACAATTTTTCTCCC 58.489 47.619 0.00 0.00 0.00 4.30
2905 2995 3.506067 ACATCGGTCCACAATTTTTCTCC 59.494 43.478 0.00 0.00 0.00 3.71
2906 2996 4.766404 ACATCGGTCCACAATTTTTCTC 57.234 40.909 0.00 0.00 0.00 2.87
2907 2997 6.642707 TTTACATCGGTCCACAATTTTTCT 57.357 33.333 0.00 0.00 0.00 2.52
2908 2998 7.568679 GCTTTTTACATCGGTCCACAATTTTTC 60.569 37.037 0.00 0.00 0.00 2.29
2909 2999 6.201997 GCTTTTTACATCGGTCCACAATTTTT 59.798 34.615 0.00 0.00 0.00 1.94
2910 3000 5.694458 GCTTTTTACATCGGTCCACAATTTT 59.306 36.000 0.00 0.00 0.00 1.82
2911 3001 5.010617 AGCTTTTTACATCGGTCCACAATTT 59.989 36.000 0.00 0.00 0.00 1.82
2912 3002 4.522789 AGCTTTTTACATCGGTCCACAATT 59.477 37.500 0.00 0.00 0.00 2.32
2913 3003 4.079253 AGCTTTTTACATCGGTCCACAAT 58.921 39.130 0.00 0.00 0.00 2.71
2914 3004 3.252215 CAGCTTTTTACATCGGTCCACAA 59.748 43.478 0.00 0.00 0.00 3.33
2915 3005 2.811431 CAGCTTTTTACATCGGTCCACA 59.189 45.455 0.00 0.00 0.00 4.17
2916 3006 3.071479 TCAGCTTTTTACATCGGTCCAC 58.929 45.455 0.00 0.00 0.00 4.02
2917 3007 3.410631 TCAGCTTTTTACATCGGTCCA 57.589 42.857 0.00 0.00 0.00 4.02
2918 3008 4.759516 TTTCAGCTTTTTACATCGGTCC 57.240 40.909 0.00 0.00 0.00 4.46
2939 3029 9.466497 TGCATCTCTACTCCTTATTTCAATTTT 57.534 29.630 0.00 0.00 0.00 1.82
2940 3030 9.638176 ATGCATCTCTACTCCTTATTTCAATTT 57.362 29.630 0.00 0.00 0.00 1.82
2943 3033 9.716531 CATATGCATCTCTACTCCTTATTTCAA 57.283 33.333 0.19 0.00 0.00 2.69
2944 3034 8.874156 ACATATGCATCTCTACTCCTTATTTCA 58.126 33.333 0.19 0.00 0.00 2.69
2950 3040 9.760926 TCTAATACATATGCATCTCTACTCCTT 57.239 33.333 0.19 0.00 0.00 3.36
2951 3041 9.407380 CTCTAATACATATGCATCTCTACTCCT 57.593 37.037 0.19 0.00 0.00 3.69
2952 3042 9.184523 ACTCTAATACATATGCATCTCTACTCC 57.815 37.037 0.19 0.00 0.00 3.85
2996 3086 7.732222 AGTGGCCCTCATCAAATAATAAAAA 57.268 32.000 0.00 0.00 0.00 1.94
2997 3087 8.830915 TTAGTGGCCCTCATCAAATAATAAAA 57.169 30.769 0.00 0.00 0.00 1.52
2999 3089 9.739276 CTATTAGTGGCCCTCATCAAATAATAA 57.261 33.333 0.00 0.00 0.00 1.40
3000 3090 8.890472 ACTATTAGTGGCCCTCATCAAATAATA 58.110 33.333 0.00 0.00 0.00 0.98
3001 3091 7.759607 ACTATTAGTGGCCCTCATCAAATAAT 58.240 34.615 0.00 0.00 0.00 1.28
3002 3092 7.149202 ACTATTAGTGGCCCTCATCAAATAA 57.851 36.000 0.00 0.00 0.00 1.40
3003 3093 6.763715 ACTATTAGTGGCCCTCATCAAATA 57.236 37.500 0.00 0.00 0.00 1.40
3004 3094 5.653255 ACTATTAGTGGCCCTCATCAAAT 57.347 39.130 0.00 0.00 0.00 2.32
3005 3095 5.454755 GCTACTATTAGTGGCCCTCATCAAA 60.455 44.000 18.53 0.00 45.53 2.69
3006 3096 4.040461 GCTACTATTAGTGGCCCTCATCAA 59.960 45.833 18.53 0.00 45.53 2.57
3007 3097 3.578716 GCTACTATTAGTGGCCCTCATCA 59.421 47.826 18.53 0.00 45.53 3.07
3008 3098 4.195225 GCTACTATTAGTGGCCCTCATC 57.805 50.000 18.53 0.00 45.53 2.92
3016 3106 6.099269 TCCCCAAAGTAAGCTACTATTAGTGG 59.901 42.308 6.60 4.74 38.26 4.00
3017 3107 7.069578 TCTCCCCAAAGTAAGCTACTATTAGTG 59.930 40.741 6.60 0.00 38.26 2.74
3018 3108 7.130775 TCTCCCCAAAGTAAGCTACTATTAGT 58.869 38.462 1.30 1.30 38.26 2.24
3019 3109 7.598759 TCTCCCCAAAGTAAGCTACTATTAG 57.401 40.000 0.00 0.00 38.26 1.73
3020 3110 7.983166 TTCTCCCCAAAGTAAGCTACTATTA 57.017 36.000 0.00 0.00 38.26 0.98
3021 3111 6.886178 TTCTCCCCAAAGTAAGCTACTATT 57.114 37.500 0.00 0.00 38.26 1.73
3022 3112 6.886178 TTTCTCCCCAAAGTAAGCTACTAT 57.114 37.500 0.00 0.00 38.26 2.12
3023 3113 6.691255 TTTTCTCCCCAAAGTAAGCTACTA 57.309 37.500 0.00 0.00 38.26 1.82
3024 3114 5.578157 TTTTCTCCCCAAAGTAAGCTACT 57.422 39.130 0.00 0.00 41.73 2.57
3025 3115 6.433093 TGATTTTTCTCCCCAAAGTAAGCTAC 59.567 38.462 0.00 0.00 0.00 3.58
3026 3116 6.548321 TGATTTTTCTCCCCAAAGTAAGCTA 58.452 36.000 0.00 0.00 0.00 3.32
3027 3117 5.393866 TGATTTTTCTCCCCAAAGTAAGCT 58.606 37.500 0.00 0.00 0.00 3.74
3028 3118 5.722021 TGATTTTTCTCCCCAAAGTAAGC 57.278 39.130 0.00 0.00 0.00 3.09
3029 3119 6.591448 GCATTGATTTTTCTCCCCAAAGTAAG 59.409 38.462 0.00 0.00 0.00 2.34
3030 3120 6.042552 TGCATTGATTTTTCTCCCCAAAGTAA 59.957 34.615 0.00 0.00 0.00 2.24
3031 3121 5.541868 TGCATTGATTTTTCTCCCCAAAGTA 59.458 36.000 0.00 0.00 0.00 2.24
3032 3122 4.347583 TGCATTGATTTTTCTCCCCAAAGT 59.652 37.500 0.00 0.00 0.00 2.66
3033 3123 4.897140 TGCATTGATTTTTCTCCCCAAAG 58.103 39.130 0.00 0.00 0.00 2.77
3034 3124 4.347583 ACTGCATTGATTTTTCTCCCCAAA 59.652 37.500 0.00 0.00 0.00 3.28
3035 3125 3.903090 ACTGCATTGATTTTTCTCCCCAA 59.097 39.130 0.00 0.00 0.00 4.12
3036 3126 3.509442 ACTGCATTGATTTTTCTCCCCA 58.491 40.909 0.00 0.00 0.00 4.96
3037 3127 4.248058 CAACTGCATTGATTTTTCTCCCC 58.752 43.478 0.00 0.00 41.23 4.81
3038 3128 3.681417 GCAACTGCATTGATTTTTCTCCC 59.319 43.478 11.52 0.00 41.23 4.30
3039 3129 3.681417 GGCAACTGCATTGATTTTTCTCC 59.319 43.478 11.52 0.08 41.23 3.71
3040 3130 4.916099 GGCAACTGCATTGATTTTTCTC 57.084 40.909 11.52 0.00 41.23 2.87
3073 3163 3.450457 GGATACACATGCCCCATGAAAAA 59.550 43.478 11.78 0.00 43.81 1.94
3074 3164 3.030291 GGATACACATGCCCCATGAAAA 58.970 45.455 11.78 0.00 43.81 2.29
3075 3165 2.024560 TGGATACACATGCCCCATGAAA 60.025 45.455 11.78 0.00 46.17 2.69
3076 3166 1.568123 TGGATACACATGCCCCATGAA 59.432 47.619 11.78 0.00 46.17 2.57
3077 3167 1.220703 TGGATACACATGCCCCATGA 58.779 50.000 11.78 0.00 46.17 3.07
3078 3168 3.825436 TGGATACACATGCCCCATG 57.175 52.632 3.80 3.80 46.17 3.66
3089 3179 7.391275 CATGAACAATGGTAGCATATGGATACA 59.609 37.037 8.04 3.67 40.15 2.29
3090 3180 7.627088 GCATGAACAATGGTAGCATATGGATAC 60.627 40.741 8.04 0.00 37.65 2.24
3091 3181 6.375174 GCATGAACAATGGTAGCATATGGATA 59.625 38.462 8.04 0.00 36.71 2.59
3092 3182 5.184479 GCATGAACAATGGTAGCATATGGAT 59.816 40.000 8.04 3.33 36.71 3.41
3093 3183 4.520111 GCATGAACAATGGTAGCATATGGA 59.480 41.667 8.04 0.00 36.71 3.41
3094 3184 4.321452 GGCATGAACAATGGTAGCATATGG 60.321 45.833 8.04 3.90 36.71 2.74
3095 3185 4.321452 GGGCATGAACAATGGTAGCATATG 60.321 45.833 8.04 8.82 36.71 1.78
3096 3186 3.828451 GGGCATGAACAATGGTAGCATAT 59.172 43.478 8.04 0.00 36.71 1.78
3097 3187 3.117550 AGGGCATGAACAATGGTAGCATA 60.118 43.478 8.04 0.00 36.71 3.14
3098 3188 2.034124 GGGCATGAACAATGGTAGCAT 58.966 47.619 0.40 0.40 36.71 3.79
3099 3189 1.005805 AGGGCATGAACAATGGTAGCA 59.994 47.619 0.00 0.00 36.71 3.49
3100 3190 1.767759 AGGGCATGAACAATGGTAGC 58.232 50.000 0.00 0.00 36.71 3.58
3101 3191 4.780815 TCTTAGGGCATGAACAATGGTAG 58.219 43.478 0.00 0.00 36.71 3.18
3102 3192 4.780815 CTCTTAGGGCATGAACAATGGTA 58.219 43.478 0.00 0.00 36.71 3.25
3103 3193 3.624777 CTCTTAGGGCATGAACAATGGT 58.375 45.455 0.00 0.00 36.71 3.55
3104 3194 2.360165 GCTCTTAGGGCATGAACAATGG 59.640 50.000 0.00 0.00 36.71 3.16
3105 3195 3.018856 TGCTCTTAGGGCATGAACAATG 58.981 45.455 1.11 0.00 39.49 2.82
3106 3196 3.019564 GTGCTCTTAGGGCATGAACAAT 58.980 45.455 10.96 0.00 41.86 2.71
3107 3197 2.224744 TGTGCTCTTAGGGCATGAACAA 60.225 45.455 10.96 0.00 41.86 2.83
3108 3198 1.350684 TGTGCTCTTAGGGCATGAACA 59.649 47.619 10.96 0.00 41.86 3.18
3109 3199 2.113860 TGTGCTCTTAGGGCATGAAC 57.886 50.000 10.96 0.00 41.86 3.18
3110 3200 4.712051 ATATGTGCTCTTAGGGCATGAA 57.288 40.909 10.96 0.00 41.86 2.57
3111 3201 5.823861 TTATATGTGCTCTTAGGGCATGA 57.176 39.130 10.96 0.00 41.86 3.07
3112 3202 8.565896 TTTATTATATGTGCTCTTAGGGCATG 57.434 34.615 10.96 0.00 41.86 4.06
3113 3203 8.386264 ACTTTATTATATGTGCTCTTAGGGCAT 58.614 33.333 10.96 0.00 41.86 4.40
3114 3204 7.745717 ACTTTATTATATGTGCTCTTAGGGCA 58.254 34.615 1.11 1.11 37.36 5.36
3115 3205 9.720769 TTACTTTATTATATGTGCTCTTAGGGC 57.279 33.333 0.00 0.00 0.00 5.19
3132 3222 9.011095 GGTTTGGCTCTTCTAGTTTACTTTATT 57.989 33.333 0.00 0.00 0.00 1.40
3196 3286 5.567037 ATGGGATATCGATGGAAAGTTGA 57.433 39.130 8.54 0.00 0.00 3.18
3208 3298 2.233271 AGCAGCCAAAATGGGATATCG 58.767 47.619 0.00 0.00 38.19 2.92


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

AutoCloner maintained by Alex Coulton.