Multiple sequence alignment - TraesCS3D01G200200

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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 TraesCS3D01G200200 chr3D 100.000 3020 0 0 1 3020 230761421 230758402 0.000000e+00 5578
1 TraesCS3D01G200200 chr3D 97.183 426 9 2 2595 3020 408376056 408376478 0.000000e+00 717
2 TraesCS3D01G200200 chr3D 96.956 427 10 2 2594 3020 86739982 86739559 0.000000e+00 713
3 TraesCS3D01G200200 chr7A 94.517 2608 122 11 1 2594 198207876 198210476 0.000000e+00 4004
4 TraesCS3D01G200200 chr7A 89.873 79 8 0 287 365 75031877 75031799 5.330000e-18 102
5 TraesCS3D01G200200 chr1A 89.841 2648 200 28 1 2598 334381733 334384361 0.000000e+00 3336
6 TraesCS3D01G200200 chr5B 93.182 1980 119 6 1 1971 45810883 45812855 0.000000e+00 2894
7 TraesCS3D01G200200 chr5B 92.825 1979 129 3 1 1971 314980829 314978856 0.000000e+00 2856
8 TraesCS3D01G200200 chr5D 88.094 2083 181 24 523 2597 189464605 189466628 0.000000e+00 2410
9 TraesCS3D01G200200 chr5D 96.956 427 9 2 2594 3020 499416724 499417146 0.000000e+00 713
10 TraesCS3D01G200200 chr5D 96.128 439 13 2 2582 3020 539159443 539159877 0.000000e+00 713
11 TraesCS3D01G200200 chr5D 96.729 428 12 2 2593 3020 256405934 256405509 0.000000e+00 712
12 TraesCS3D01G200200 chr5D 96.956 427 8 3 2594 3020 535124582 535125003 0.000000e+00 712
13 TraesCS3D01G200200 chr1D 90.629 1654 143 8 954 2597 298421162 298422813 0.000000e+00 2185
14 TraesCS3D01G200200 chr1D 84.874 1428 181 24 584 1996 360152320 360150913 0.000000e+00 1408
15 TraesCS3D01G200200 chr1D 96.963 428 10 3 2594 3020 96674380 96674805 0.000000e+00 715
16 TraesCS3D01G200200 chr1D 77.439 164 37 0 588 751 356875385 356875548 6.890000e-17 99
17 TraesCS3D01G200200 chr5A 90.678 1652 139 8 954 2597 31941173 31942817 0.000000e+00 2183
18 TraesCS3D01G200200 chr5A 90.534 1648 142 7 954 2594 31841109 31842749 0.000000e+00 2167
19 TraesCS3D01G200200 chr5A 90.375 1652 144 8 954 2597 31810790 31812434 0.000000e+00 2156
20 TraesCS3D01G200200 chr5A 90.315 1652 145 8 954 2597 31602930 31604574 0.000000e+00 2150
21 TraesCS3D01G200200 chr6D 85.532 1880 200 27 1 1824 356192514 356190651 0.000000e+00 1899
22 TraesCS3D01G200200 chr1B 87.722 619 74 2 458 1075 227837818 227837201 0.000000e+00 721
23 TraesCS3D01G200200 chr1B 83.965 343 43 3 116 446 227838202 227837860 4.860000e-83 318
24 TraesCS3D01G200200 chr2D 96.956 427 9 3 2594 3020 131231599 131232021 0.000000e+00 713
25 TraesCS3D01G200200 chr7D 96.956 427 8 3 2594 3020 414115624 414115203 0.000000e+00 712
26 TraesCS3D01G200200 chr7D 83.511 376 48 4 3 365 496935328 496935702 3.730000e-89 339
27 TraesCS3D01G200200 chr3A 75.862 406 89 9 514 915 582374497 582374897 6.600000e-47 198
28 TraesCS3D01G200200 chr4D 72.775 382 97 7 588 966 127117005 127117382 4.090000e-24 122


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 TraesCS3D01G200200 chr3D 230758402 230761421 3019 True 5578.0 5578 100.0000 1 3020 1 chr3D.!!$R2 3019
1 TraesCS3D01G200200 chr7A 198207876 198210476 2600 False 4004.0 4004 94.5170 1 2594 1 chr7A.!!$F1 2593
2 TraesCS3D01G200200 chr1A 334381733 334384361 2628 False 3336.0 3336 89.8410 1 2598 1 chr1A.!!$F1 2597
3 TraesCS3D01G200200 chr5B 45810883 45812855 1972 False 2894.0 2894 93.1820 1 1971 1 chr5B.!!$F1 1970
4 TraesCS3D01G200200 chr5B 314978856 314980829 1973 True 2856.0 2856 92.8250 1 1971 1 chr5B.!!$R1 1970
5 TraesCS3D01G200200 chr5D 189464605 189466628 2023 False 2410.0 2410 88.0940 523 2597 1 chr5D.!!$F1 2074
6 TraesCS3D01G200200 chr1D 298421162 298422813 1651 False 2185.0 2185 90.6290 954 2597 1 chr1D.!!$F2 1643
7 TraesCS3D01G200200 chr1D 360150913 360152320 1407 True 1408.0 1408 84.8740 584 1996 1 chr1D.!!$R1 1412
8 TraesCS3D01G200200 chr5A 31941173 31942817 1644 False 2183.0 2183 90.6780 954 2597 1 chr5A.!!$F4 1643
9 TraesCS3D01G200200 chr5A 31841109 31842749 1640 False 2167.0 2167 90.5340 954 2594 1 chr5A.!!$F3 1640
10 TraesCS3D01G200200 chr5A 31810790 31812434 1644 False 2156.0 2156 90.3750 954 2597 1 chr5A.!!$F2 1643
11 TraesCS3D01G200200 chr5A 31602930 31604574 1644 False 2150.0 2150 90.3150 954 2597 1 chr5A.!!$F1 1643
12 TraesCS3D01G200200 chr6D 356190651 356192514 1863 True 1899.0 1899 85.5320 1 1824 1 chr6D.!!$R1 1823
13 TraesCS3D01G200200 chr1B 227837201 227838202 1001 True 519.5 721 85.8435 116 1075 2 chr1B.!!$R1 959

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
267 269 0.179116 CTGCTGATCTGGTGACTCGG 60.179 60.000 1.46 0.0 0.0 4.63 F
847 903 2.308722 GCCATGGAGGGTCAGGGAA 61.309 63.158 18.40 0.0 40.7 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1355 0.867753 CGAACTCGGCGAAGATGAGG 60.868 60.0 12.13 0.00 35.15 3.86 R
2822 2921 0.109458 CTGGATCACGTTCGTTCCGA 60.109 55.0 10.21 0.37 0.00 4.55 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
93 95 1.074248 GTGGAAGGCCTTTCGGGAA 59.926 57.895 21.54 0.00 36.62 3.97
142 144 2.806945 AAATCGGGAAAGATGCCTCA 57.193 45.000 0.00 0.00 34.24 3.86
210 212 4.233789 GTGAGATATCCTCTGATTCGCAC 58.766 47.826 0.00 0.00 42.44 5.34
243 245 1.817740 GCTGGGCCCAATTTCGCTATA 60.818 52.381 28.29 0.00 0.00 1.31
267 269 0.179116 CTGCTGATCTGGTGACTCGG 60.179 60.000 1.46 0.00 0.00 4.63
285 287 4.020573 ACTCGGGATTTGGGGAAAAATTTC 60.021 41.667 0.00 0.00 36.46 2.17
366 380 4.772483 AGAGGAATCAGTGGGGATCATAT 58.228 43.478 0.00 0.00 0.00 1.78
621 668 5.959512 TCATTTGAGGGAAAGGGAGTTTTA 58.040 37.500 0.00 0.00 0.00 1.52
847 903 2.308722 GCCATGGAGGGTCAGGGAA 61.309 63.158 18.40 0.00 40.70 3.97
1269 1355 1.227060 GCATTTCAAGCGGGATGGC 60.227 57.895 0.00 0.00 0.00 4.40
1376 1462 1.349259 CCGTTCGTGCTTAAGACGGG 61.349 60.000 19.73 12.68 37.43 5.28
1431 1517 1.050988 AGGTGCTGGAGGTATCGCAT 61.051 55.000 0.00 0.00 34.60 4.73
1596 1682 4.385825 TGTACTGTGAGTTTTGTGGGATC 58.614 43.478 0.00 0.00 0.00 3.36
1612 1698 2.036089 GGGATCGTGGGTCATACTTCTC 59.964 54.545 0.00 0.00 0.00 2.87
1642 1728 6.648879 TTTGTAAAATCCCAGGTGAGAAAG 57.351 37.500 0.00 0.00 0.00 2.62
1801 1887 2.130821 TAACGCCAAGCCCATGGACA 62.131 55.000 15.22 0.00 43.54 4.02
2169 2265 4.603535 GGGTTGGCAGTGCTGGGT 62.604 66.667 16.11 0.00 0.00 4.51
2276 2372 0.397941 GCTGCTGGCCATAGTGGATA 59.602 55.000 5.51 0.00 40.96 2.59
2332 2428 1.076485 GGTGGAGGCAGCCATTCAT 60.076 57.895 15.80 0.00 40.68 2.57
2416 2513 1.003580 CTCTTTCAGGGGCTGTTGCTA 59.996 52.381 0.00 0.00 39.59 3.49
2491 2589 3.004862 GCTGGGAAAAATTTGATGCAGG 58.995 45.455 0.00 0.00 0.00 4.85
2553 2652 5.407502 GGAGTTTCTAAGAGAGCAGAGAAC 58.592 45.833 0.00 0.00 0.00 3.01
2606 2705 5.601662 GAGAATCCCATTGATACGTCTTCA 58.398 41.667 0.00 0.00 31.83 3.02
2607 2706 5.989477 AGAATCCCATTGATACGTCTTCAA 58.011 37.500 14.12 14.12 37.49 2.69
2608 2707 5.817816 AGAATCCCATTGATACGTCTTCAAC 59.182 40.000 14.06 3.01 36.02 3.18
2609 2708 4.570772 AATCCCATTGATACGTCTTCAACG 59.429 41.667 14.06 7.82 44.74 4.10
2669 2768 5.146010 TCTGTTTTTGGACATTATTGGGC 57.854 39.130 0.00 0.00 0.00 5.36
2670 2769 4.837860 TCTGTTTTTGGACATTATTGGGCT 59.162 37.500 0.00 0.00 0.00 5.19
2671 2770 5.306678 TCTGTTTTTGGACATTATTGGGCTT 59.693 36.000 0.00 0.00 0.00 4.35
2672 2771 5.934781 TGTTTTTGGACATTATTGGGCTTT 58.065 33.333 0.00 0.00 0.00 3.51
2673 2772 7.015682 TCTGTTTTTGGACATTATTGGGCTTTA 59.984 33.333 0.00 0.00 0.00 1.85
2674 2773 7.684529 TGTTTTTGGACATTATTGGGCTTTAT 58.315 30.769 0.00 0.00 0.00 1.40
2675 2774 8.160106 TGTTTTTGGACATTATTGGGCTTTATT 58.840 29.630 0.00 0.00 0.00 1.40
2676 2775 9.660180 GTTTTTGGACATTATTGGGCTTTATTA 57.340 29.630 0.00 0.00 0.00 0.98
2680 2779 9.647918 TTGGACATTATTGGGCTTTATTATACA 57.352 29.630 0.00 0.00 0.00 2.29
2681 2780 9.073475 TGGACATTATTGGGCTTTATTATACAC 57.927 33.333 0.00 0.00 0.00 2.90
2682 2781 9.297037 GGACATTATTGGGCTTTATTATACACT 57.703 33.333 0.00 0.00 0.00 3.55
2715 2814 7.634671 ATTTTTGGGACTAACCTATTAACCG 57.365 36.000 0.00 0.00 38.98 4.44
2716 2815 4.758773 TTGGGACTAACCTATTAACCGG 57.241 45.455 0.00 0.00 38.98 5.28
2717 2816 3.992999 TGGGACTAACCTATTAACCGGA 58.007 45.455 9.46 0.00 38.98 5.14
2718 2817 3.962718 TGGGACTAACCTATTAACCGGAG 59.037 47.826 9.46 0.00 38.98 4.63
2719 2818 4.597404 GGACTAACCTATTAACCGGAGG 57.403 50.000 9.46 6.51 45.59 4.30
2720 2819 3.244009 GGACTAACCTATTAACCGGAGGC 60.244 52.174 9.46 0.00 44.44 4.70
2721 2820 6.309757 GGACTAACCTATTAACCGGAGGCC 62.310 54.167 9.46 0.00 44.44 5.19
2735 2834 3.464494 GGCCCAGCCCAGAATTGC 61.464 66.667 0.00 0.00 44.06 3.56
2736 2835 2.363406 GCCCAGCCCAGAATTGCT 60.363 61.111 0.00 0.00 38.67 3.91
2764 2863 5.371115 TTTTTGCCTATTTCAGAGTTCCG 57.629 39.130 0.00 0.00 0.00 4.30
2765 2864 2.024176 TGCCTATTTCAGAGTTCCGC 57.976 50.000 0.00 0.00 0.00 5.54
2766 2865 1.277842 TGCCTATTTCAGAGTTCCGCA 59.722 47.619 0.00 0.00 0.00 5.69
2767 2866 1.936547 GCCTATTTCAGAGTTCCGCAG 59.063 52.381 0.00 0.00 0.00 5.18
2768 2867 2.418746 GCCTATTTCAGAGTTCCGCAGA 60.419 50.000 0.00 0.00 0.00 4.26
2769 2868 3.861840 CCTATTTCAGAGTTCCGCAGAA 58.138 45.455 0.00 0.00 0.00 3.02
2770 2869 4.253685 CCTATTTCAGAGTTCCGCAGAAA 58.746 43.478 0.00 0.00 32.58 2.52
2771 2870 4.695455 CCTATTTCAGAGTTCCGCAGAAAA 59.305 41.667 0.00 0.00 32.58 2.29
2772 2871 5.181245 CCTATTTCAGAGTTCCGCAGAAAAA 59.819 40.000 0.00 0.00 32.58 1.94
2773 2872 4.552166 TTTCAGAGTTCCGCAGAAAAAG 57.448 40.909 0.00 0.00 32.58 2.27
2774 2873 3.469008 TCAGAGTTCCGCAGAAAAAGA 57.531 42.857 0.00 0.00 32.58 2.52
2775 2874 3.804036 TCAGAGTTCCGCAGAAAAAGAA 58.196 40.909 0.00 0.00 32.58 2.52
2776 2875 4.389374 TCAGAGTTCCGCAGAAAAAGAAT 58.611 39.130 0.00 0.00 32.58 2.40
2777 2876 5.547465 TCAGAGTTCCGCAGAAAAAGAATA 58.453 37.500 0.00 0.00 32.58 1.75
2778 2877 6.173339 TCAGAGTTCCGCAGAAAAAGAATAT 58.827 36.000 0.00 0.00 32.58 1.28
2779 2878 6.313905 TCAGAGTTCCGCAGAAAAAGAATATC 59.686 38.462 0.00 0.00 32.58 1.63
2780 2879 6.092670 CAGAGTTCCGCAGAAAAAGAATATCA 59.907 38.462 0.00 0.00 32.58 2.15
2781 2880 6.655003 AGAGTTCCGCAGAAAAAGAATATCAA 59.345 34.615 0.00 0.00 32.58 2.57
2782 2881 7.174946 AGAGTTCCGCAGAAAAAGAATATCAAA 59.825 33.333 0.00 0.00 32.58 2.69
2783 2882 7.084486 AGTTCCGCAGAAAAAGAATATCAAAC 58.916 34.615 0.00 0.00 32.58 2.93
2784 2883 5.627172 TCCGCAGAAAAAGAATATCAAACG 58.373 37.500 0.00 0.00 0.00 3.60
2785 2884 4.793216 CCGCAGAAAAAGAATATCAAACGG 59.207 41.667 0.00 0.00 0.00 4.44
2786 2885 5.391523 CCGCAGAAAAAGAATATCAAACGGA 60.392 40.000 0.00 0.00 36.59 4.69
2787 2886 5.734498 CGCAGAAAAAGAATATCAAACGGAG 59.266 40.000 0.00 0.00 0.00 4.63
2789 2888 6.743172 GCAGAAAAAGAATATCAAACGGAGTC 59.257 38.462 0.00 0.00 45.00 3.36
2790 2889 7.244192 CAGAAAAAGAATATCAAACGGAGTCC 58.756 38.462 0.00 0.00 45.00 3.85
2791 2890 6.940298 AGAAAAAGAATATCAAACGGAGTCCA 59.060 34.615 10.49 0.00 45.00 4.02
2792 2891 7.447238 AGAAAAAGAATATCAAACGGAGTCCAA 59.553 33.333 10.49 0.00 45.00 3.53
2793 2892 7.519032 AAAAGAATATCAAACGGAGTCCAAA 57.481 32.000 10.49 0.00 45.00 3.28
2794 2893 6.496338 AAGAATATCAAACGGAGTCCAAAC 57.504 37.500 10.49 0.00 45.00 2.93
2795 2894 4.630069 AGAATATCAAACGGAGTCCAAACG 59.370 41.667 10.49 0.00 45.00 3.60
2796 2895 1.519408 ATCAAACGGAGTCCAAACGG 58.481 50.000 10.49 0.00 45.00 4.44
2797 2896 1.161563 TCAAACGGAGTCCAAACGGC 61.162 55.000 10.49 0.00 45.00 5.68
2798 2897 1.153127 AAACGGAGTCCAAACGGCA 60.153 52.632 10.49 0.00 45.00 5.69
2799 2898 0.536460 AAACGGAGTCCAAACGGCAT 60.536 50.000 10.49 0.00 45.00 4.40
2800 2899 1.234615 AACGGAGTCCAAACGGCATG 61.235 55.000 10.49 0.00 45.00 4.06
2801 2900 1.375396 CGGAGTCCAAACGGCATGA 60.375 57.895 10.49 0.00 0.00 3.07
2802 2901 0.953471 CGGAGTCCAAACGGCATGAA 60.953 55.000 10.49 0.00 0.00 2.57
2803 2902 1.243902 GGAGTCCAAACGGCATGAAA 58.756 50.000 3.60 0.00 0.00 2.69
2804 2903 1.068541 GGAGTCCAAACGGCATGAAAC 60.069 52.381 3.60 0.00 0.00 2.78
2805 2904 0.958822 AGTCCAAACGGCATGAAACC 59.041 50.000 0.00 0.00 0.00 3.27
2806 2905 0.958822 GTCCAAACGGCATGAAACCT 59.041 50.000 0.00 0.00 0.00 3.50
2807 2906 1.339929 GTCCAAACGGCATGAAACCTT 59.660 47.619 0.00 0.00 0.00 3.50
2808 2907 1.611491 TCCAAACGGCATGAAACCTTC 59.389 47.619 0.00 0.00 0.00 3.46
2809 2908 1.665735 CCAAACGGCATGAAACCTTCG 60.666 52.381 0.00 0.00 0.00 3.79
2810 2909 0.596082 AAACGGCATGAAACCTTCGG 59.404 50.000 0.00 0.00 0.00 4.30
2811 2910 1.241315 AACGGCATGAAACCTTCGGG 61.241 55.000 0.00 0.00 41.87 5.14
2812 2911 1.376683 CGGCATGAAACCTTCGGGA 60.377 57.895 0.00 0.00 38.77 5.14
2813 2912 0.958382 CGGCATGAAACCTTCGGGAA 60.958 55.000 0.00 0.00 38.77 3.97
2814 2913 0.526211 GGCATGAAACCTTCGGGAAC 59.474 55.000 0.00 0.00 38.77 3.62
2828 2927 2.606717 GGGAACGTGATTTTCGGAAC 57.393 50.000 0.00 0.00 0.00 3.62
2842 2941 3.806591 GGAACGAACGTGATCCAGA 57.193 52.632 11.58 0.00 32.08 3.86
2843 2942 1.630148 GGAACGAACGTGATCCAGAG 58.370 55.000 11.58 0.00 32.08 3.35
2844 2943 1.630148 GAACGAACGTGATCCAGAGG 58.370 55.000 0.00 0.00 0.00 3.69
2845 2944 1.201647 GAACGAACGTGATCCAGAGGA 59.798 52.381 0.00 0.00 35.55 3.71
2846 2945 0.526662 ACGAACGTGATCCAGAGGAC 59.473 55.000 0.00 0.00 32.98 3.85
2847 2946 0.811915 CGAACGTGATCCAGAGGACT 59.188 55.000 0.00 0.00 32.98 3.85
2848 2947 1.202582 CGAACGTGATCCAGAGGACTT 59.797 52.381 0.00 0.00 32.98 3.01
2849 2948 2.611518 GAACGTGATCCAGAGGACTTG 58.388 52.381 0.00 0.00 32.98 3.16
2850 2949 0.898320 ACGTGATCCAGAGGACTTGG 59.102 55.000 0.00 0.00 32.98 3.61
2851 2950 1.186200 CGTGATCCAGAGGACTTGGA 58.814 55.000 0.00 0.00 32.98 3.53
2852 2951 1.134965 CGTGATCCAGAGGACTTGGAC 60.135 57.143 0.00 0.00 32.98 4.02
2853 2952 1.208293 GTGATCCAGAGGACTTGGACC 59.792 57.143 0.00 0.00 32.98 4.46
2854 2953 0.833949 GATCCAGAGGACTTGGACCC 59.166 60.000 0.00 0.00 32.98 4.46
2855 2954 0.419459 ATCCAGAGGACTTGGACCCT 59.581 55.000 0.00 0.00 32.98 4.34
2856 2955 1.089978 TCCAGAGGACTTGGACCCTA 58.910 55.000 0.00 0.00 31.84 3.53
2857 2956 1.196012 CCAGAGGACTTGGACCCTAC 58.804 60.000 0.00 0.00 31.84 3.18
2858 2957 0.818296 CAGAGGACTTGGACCCTACG 59.182 60.000 0.00 0.00 31.84 3.51
2859 2958 0.408700 AGAGGACTTGGACCCTACGT 59.591 55.000 0.00 0.00 31.84 3.57
2860 2959 0.816373 GAGGACTTGGACCCTACGTC 59.184 60.000 0.00 0.00 41.15 4.34
2861 2960 0.113776 AGGACTTGGACCCTACGTCA 59.886 55.000 0.00 0.00 43.95 4.35
2862 2961 0.971386 GGACTTGGACCCTACGTCAA 59.029 55.000 0.00 0.00 43.95 3.18
2863 2962 1.067071 GGACTTGGACCCTACGTCAAG 60.067 57.143 10.01 10.01 43.95 3.02
2864 2963 1.891150 GACTTGGACCCTACGTCAAGA 59.109 52.381 16.57 0.00 43.95 3.02
2865 2964 1.617357 ACTTGGACCCTACGTCAAGAC 59.383 52.381 16.57 0.00 43.95 3.01
2866 2965 1.616865 CTTGGACCCTACGTCAAGACA 59.383 52.381 6.58 0.00 43.95 3.41
2867 2966 1.933021 TGGACCCTACGTCAAGACAT 58.067 50.000 0.00 0.00 43.95 3.06
2868 2967 1.822990 TGGACCCTACGTCAAGACATC 59.177 52.381 0.00 0.00 43.95 3.06
2869 2968 1.822990 GGACCCTACGTCAAGACATCA 59.177 52.381 0.00 0.00 43.95 3.07
2870 2969 2.232941 GGACCCTACGTCAAGACATCAA 59.767 50.000 0.00 0.00 43.95 2.57
2871 2970 3.251571 GACCCTACGTCAAGACATCAAC 58.748 50.000 0.00 0.00 41.54 3.18
2872 2971 2.028385 ACCCTACGTCAAGACATCAACC 60.028 50.000 0.00 0.00 0.00 3.77
2873 2972 2.028476 CCCTACGTCAAGACATCAACCA 60.028 50.000 0.00 0.00 0.00 3.67
2874 2973 3.254060 CCTACGTCAAGACATCAACCAG 58.746 50.000 0.00 0.00 0.00 4.00
2875 2974 2.169832 ACGTCAAGACATCAACCAGG 57.830 50.000 0.72 0.00 0.00 4.45
2876 2975 1.691976 ACGTCAAGACATCAACCAGGA 59.308 47.619 0.00 0.00 0.00 3.86
2877 2976 2.104111 ACGTCAAGACATCAACCAGGAA 59.896 45.455 0.00 0.00 0.00 3.36
2878 2977 2.738846 CGTCAAGACATCAACCAGGAAG 59.261 50.000 0.00 0.00 0.00 3.46
2879 2978 3.077359 GTCAAGACATCAACCAGGAAGG 58.923 50.000 0.00 0.00 45.67 3.46
2880 2979 1.815003 CAAGACATCAACCAGGAAGGC 59.185 52.381 0.00 0.00 43.14 4.35
2881 2980 1.067295 AGACATCAACCAGGAAGGCA 58.933 50.000 0.00 0.00 43.14 4.75
2882 2981 1.168714 GACATCAACCAGGAAGGCAC 58.831 55.000 0.00 0.00 43.14 5.01
2883 2982 0.478072 ACATCAACCAGGAAGGCACA 59.522 50.000 0.00 0.00 43.14 4.57
2884 2983 1.133513 ACATCAACCAGGAAGGCACAA 60.134 47.619 0.00 0.00 43.14 3.33
2885 2984 1.542915 CATCAACCAGGAAGGCACAAG 59.457 52.381 0.00 0.00 43.14 3.16
2886 2985 0.178992 TCAACCAGGAAGGCACAAGG 60.179 55.000 0.00 0.00 43.14 3.61
2887 2986 0.468029 CAACCAGGAAGGCACAAGGT 60.468 55.000 0.00 0.00 43.14 3.50
2888 2987 1.145571 AACCAGGAAGGCACAAGGTA 58.854 50.000 0.00 0.00 43.14 3.08
2889 2988 0.693049 ACCAGGAAGGCACAAGGTAG 59.307 55.000 0.00 0.00 43.14 3.18
2890 2989 0.035056 CCAGGAAGGCACAAGGTAGG 60.035 60.000 0.00 0.00 0.00 3.18
2891 2990 0.035056 CAGGAAGGCACAAGGTAGGG 60.035 60.000 0.00 0.00 0.00 3.53
2892 2991 1.208165 AGGAAGGCACAAGGTAGGGG 61.208 60.000 0.00 0.00 0.00 4.79
2893 2992 1.303282 GAAGGCACAAGGTAGGGGG 59.697 63.158 0.00 0.00 0.00 5.40
2931 3030 4.394712 GTGCCCTCCACCCTCGTG 62.395 72.222 0.00 0.00 38.55 4.35
2942 3041 4.047125 CCTCGTGGGCCCCATGTT 62.047 66.667 22.27 0.00 41.03 2.71
2943 3042 2.751436 CTCGTGGGCCCCATGTTG 60.751 66.667 22.27 11.88 41.03 3.33
2946 3045 3.070576 GTGGGCCCCATGTTGCTC 61.071 66.667 22.27 0.59 35.28 4.26
2947 3046 4.380945 TGGGCCCCATGTTGCTCC 62.381 66.667 22.27 3.56 0.00 4.70
2948 3047 4.380945 GGGCCCCATGTTGCTCCA 62.381 66.667 12.23 0.00 0.00 3.86
2949 3048 3.070576 GGCCCCATGTTGCTCCAC 61.071 66.667 0.00 0.00 0.00 4.02
2950 3049 3.070576 GCCCCATGTTGCTCCACC 61.071 66.667 0.00 0.00 0.00 4.61
2951 3050 2.751436 CCCCATGTTGCTCCACCG 60.751 66.667 0.00 0.00 0.00 4.94
2952 3051 2.350895 CCCATGTTGCTCCACCGA 59.649 61.111 0.00 0.00 0.00 4.69
2953 3052 2.040544 CCCATGTTGCTCCACCGAC 61.041 63.158 0.00 0.00 0.00 4.79
2954 3053 2.390599 CCATGTTGCTCCACCGACG 61.391 63.158 0.00 0.00 0.00 5.12
2955 3054 1.667830 CATGTTGCTCCACCGACGT 60.668 57.895 0.00 0.00 0.00 4.34
2956 3055 0.389296 CATGTTGCTCCACCGACGTA 60.389 55.000 0.00 0.00 0.00 3.57
2957 3056 0.389426 ATGTTGCTCCACCGACGTAC 60.389 55.000 0.00 0.00 0.00 3.67
2958 3057 1.288127 GTTGCTCCACCGACGTACT 59.712 57.895 0.00 0.00 0.00 2.73
2959 3058 0.319297 GTTGCTCCACCGACGTACTT 60.319 55.000 0.00 0.00 0.00 2.24
2960 3059 0.038892 TTGCTCCACCGACGTACTTC 60.039 55.000 0.00 0.00 0.00 3.01
2961 3060 0.892358 TGCTCCACCGACGTACTTCT 60.892 55.000 0.00 0.00 0.00 2.85
2962 3061 0.243095 GCTCCACCGACGTACTTCTT 59.757 55.000 0.00 0.00 0.00 2.52
2963 3062 1.731750 GCTCCACCGACGTACTTCTTC 60.732 57.143 0.00 0.00 0.00 2.87
2964 3063 0.883833 TCCACCGACGTACTTCTTCC 59.116 55.000 0.00 0.00 0.00 3.46
2965 3064 0.886563 CCACCGACGTACTTCTTCCT 59.113 55.000 0.00 0.00 0.00 3.36
2966 3065 1.135460 CCACCGACGTACTTCTTCCTC 60.135 57.143 0.00 0.00 0.00 3.71
2967 3066 1.135460 CACCGACGTACTTCTTCCTCC 60.135 57.143 0.00 0.00 0.00 4.30
2968 3067 1.271817 ACCGACGTACTTCTTCCTCCT 60.272 52.381 0.00 0.00 0.00 3.69
2969 3068 2.026822 ACCGACGTACTTCTTCCTCCTA 60.027 50.000 0.00 0.00 0.00 2.94
2970 3069 3.212685 CCGACGTACTTCTTCCTCCTAT 58.787 50.000 0.00 0.00 0.00 2.57
2971 3070 4.141620 ACCGACGTACTTCTTCCTCCTATA 60.142 45.833 0.00 0.00 0.00 1.31
2972 3071 5.002516 CCGACGTACTTCTTCCTCCTATAT 58.997 45.833 0.00 0.00 0.00 0.86
2973 3072 6.169094 CCGACGTACTTCTTCCTCCTATATA 58.831 44.000 0.00 0.00 0.00 0.86
2974 3073 6.822676 CCGACGTACTTCTTCCTCCTATATAT 59.177 42.308 0.00 0.00 0.00 0.86
2975 3074 7.984050 CCGACGTACTTCTTCCTCCTATATATA 59.016 40.741 0.00 0.00 0.00 0.86
2976 3075 8.816144 CGACGTACTTCTTCCTCCTATATATAC 58.184 40.741 0.00 0.00 0.00 1.47
2977 3076 9.108284 GACGTACTTCTTCCTCCTATATATACC 57.892 40.741 0.00 0.00 0.00 2.73
2978 3077 8.834733 ACGTACTTCTTCCTCCTATATATACCT 58.165 37.037 0.00 0.00 0.00 3.08
2982 3081 8.834733 ACTTCTTCCTCCTATATATACCTACGT 58.165 37.037 0.00 0.00 0.00 3.57
2985 3084 8.709308 TCTTCCTCCTATATATACCTACGTACC 58.291 40.741 0.00 0.00 0.00 3.34
2986 3085 7.380423 TCCTCCTATATATACCTACGTACCC 57.620 44.000 0.00 0.00 0.00 3.69
2987 3086 6.330250 TCCTCCTATATATACCTACGTACCCC 59.670 46.154 0.00 0.00 0.00 4.95
2988 3087 6.466470 CCTCCTATATATACCTACGTACCCCC 60.466 50.000 0.00 0.00 0.00 5.40
2989 3088 5.976244 TCCTATATATACCTACGTACCCCCA 59.024 44.000 0.00 0.00 0.00 4.96
2990 3089 6.450024 TCCTATATATACCTACGTACCCCCAA 59.550 42.308 0.00 0.00 0.00 4.12
2991 3090 7.036205 TCCTATATATACCTACGTACCCCCAAA 60.036 40.741 0.00 0.00 0.00 3.28
2992 3091 6.857437 ATATATACCTACGTACCCCCAAAC 57.143 41.667 0.00 0.00 0.00 2.93
2993 3092 2.621556 TACCTACGTACCCCCAAACT 57.378 50.000 0.00 0.00 0.00 2.66
2994 3093 2.621556 ACCTACGTACCCCCAAACTA 57.378 50.000 0.00 0.00 0.00 2.24
2995 3094 2.179427 ACCTACGTACCCCCAAACTAC 58.821 52.381 0.00 0.00 0.00 2.73
2996 3095 1.482182 CCTACGTACCCCCAAACTACC 59.518 57.143 0.00 0.00 0.00 3.18
2997 3096 2.178580 CTACGTACCCCCAAACTACCA 58.821 52.381 0.00 0.00 0.00 3.25
2998 3097 0.978907 ACGTACCCCCAAACTACCAG 59.021 55.000 0.00 0.00 0.00 4.00
2999 3098 1.269012 CGTACCCCCAAACTACCAGA 58.731 55.000 0.00 0.00 0.00 3.86
3000 3099 1.835531 CGTACCCCCAAACTACCAGAT 59.164 52.381 0.00 0.00 0.00 2.90
3001 3100 3.033184 CGTACCCCCAAACTACCAGATA 58.967 50.000 0.00 0.00 0.00 1.98
3002 3101 3.181472 CGTACCCCCAAACTACCAGATAC 60.181 52.174 0.00 0.00 0.00 2.24
3003 3102 1.835531 ACCCCCAAACTACCAGATACG 59.164 52.381 0.00 0.00 0.00 3.06
3004 3103 1.140252 CCCCCAAACTACCAGATACGG 59.860 57.143 0.00 0.00 0.00 4.02
3005 3104 2.112998 CCCCAAACTACCAGATACGGA 58.887 52.381 0.00 0.00 0.00 4.69
3006 3105 2.102588 CCCCAAACTACCAGATACGGAG 59.897 54.545 0.00 0.00 0.00 4.63
3007 3106 2.483188 CCCAAACTACCAGATACGGAGC 60.483 54.545 0.00 0.00 0.00 4.70
3008 3107 2.483188 CCAAACTACCAGATACGGAGCC 60.483 54.545 0.00 0.00 0.00 4.70
3009 3108 2.154567 AACTACCAGATACGGAGCCA 57.845 50.000 0.00 0.00 0.00 4.75
3010 3109 2.154567 ACTACCAGATACGGAGCCAA 57.845 50.000 0.00 0.00 0.00 4.52
3011 3110 2.463752 ACTACCAGATACGGAGCCAAA 58.536 47.619 0.00 0.00 0.00 3.28
3012 3111 2.835764 ACTACCAGATACGGAGCCAAAA 59.164 45.455 0.00 0.00 0.00 2.44
3013 3112 2.871096 ACCAGATACGGAGCCAAAAA 57.129 45.000 0.00 0.00 0.00 1.94
3014 3113 2.433436 ACCAGATACGGAGCCAAAAAC 58.567 47.619 0.00 0.00 0.00 2.43
3015 3114 1.743394 CCAGATACGGAGCCAAAAACC 59.257 52.381 0.00 0.00 0.00 3.27
3016 3115 2.618045 CCAGATACGGAGCCAAAAACCT 60.618 50.000 0.00 0.00 0.00 3.50
3017 3116 3.370103 CCAGATACGGAGCCAAAAACCTA 60.370 47.826 0.00 0.00 0.00 3.08
3018 3117 4.258543 CAGATACGGAGCCAAAAACCTAA 58.741 43.478 0.00 0.00 0.00 2.69
3019 3118 4.881850 CAGATACGGAGCCAAAAACCTAAT 59.118 41.667 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 0.693049 GAAAGGCCTTCCACTCCTGA 59.307 55.000 20.79 0.00 33.74 3.86
93 95 6.463614 CCATCTTGATTAACCTCCTCGATCTT 60.464 42.308 0.00 0.00 0.00 2.40
142 144 4.630644 TCACTCTTCTCCTTGAATGCTT 57.369 40.909 0.00 0.00 33.71 3.91
210 212 4.148825 CCAGCCGGACCTTCCTCG 62.149 72.222 5.05 0.00 33.30 4.63
243 245 2.636893 AGTCACCAGATCAGCAGTTTCT 59.363 45.455 0.00 0.00 0.00 2.52
267 269 4.020573 ACCTCGAAATTTTTCCCCAAATCC 60.021 41.667 0.00 0.00 33.68 3.01
285 287 3.887621 TCAGGATTAAAGACCACCTCG 57.112 47.619 0.00 0.00 0.00 4.63
847 903 6.015918 TCCCCAAAATATCACACACATTCTT 58.984 36.000 0.00 0.00 0.00 2.52
1269 1355 0.867753 CGAACTCGGCGAAGATGAGG 60.868 60.000 12.13 0.00 35.15 3.86
1376 1462 2.106166 TCGAGAGACCACCCTATACTCC 59.894 54.545 0.00 0.00 33.31 3.85
1431 1517 6.782298 TTTTCAACGATTACATGGTTACGA 57.218 33.333 0.00 0.00 29.78 3.43
1596 1682 3.017442 TCTCTGAGAAGTATGACCCACG 58.983 50.000 4.57 0.00 0.00 4.94
1633 1719 2.027653 AGCAAGCTACTCCTTTCTCACC 60.028 50.000 0.00 0.00 0.00 4.02
1642 1728 2.389715 TCTAGGGAAGCAAGCTACTCC 58.610 52.381 4.54 4.54 0.00 3.85
1801 1887 1.003355 CAGTGGCCACCTTGACGAT 60.003 57.895 32.29 8.36 0.00 3.73
1885 1971 3.330720 CTCCTGAACCCGGCCCTT 61.331 66.667 0.00 0.00 0.00 3.95
2004 2092 2.191354 CTGGTCATGCGTTGCACCAG 62.191 60.000 12.97 12.97 43.04 4.00
2049 2138 2.047179 GAGCCACAGGAACCCGAC 60.047 66.667 0.00 0.00 0.00 4.79
2050 2139 1.415672 AAAGAGCCACAGGAACCCGA 61.416 55.000 0.00 0.00 0.00 5.14
2181 2277 1.303888 CTGGCCATGCAGAACACCT 60.304 57.895 5.51 0.00 0.00 4.00
2276 2372 1.074167 CCCTCCTGGCCAGTAGGAT 60.074 63.158 38.79 0.00 43.10 3.24
2332 2428 2.721167 CGGCTGTAGCTGCACCCTA 61.721 63.158 13.49 0.00 40.93 3.53
2491 2589 0.605083 CCCTTCCTCTTTTGCTTGCC 59.395 55.000 0.00 0.00 0.00 4.52
2553 2652 4.558538 ACCTATAGTTACCTTACGTGCG 57.441 45.455 0.00 0.00 0.00 5.34
2643 2742 7.986889 GCCCAATAATGTCCAAAAACAGAATAT 59.013 33.333 0.00 0.00 31.50 1.28
2644 2743 7.180051 AGCCCAATAATGTCCAAAAACAGAATA 59.820 33.333 0.00 0.00 31.50 1.75
2645 2744 6.013466 AGCCCAATAATGTCCAAAAACAGAAT 60.013 34.615 0.00 0.00 31.50 2.40
2646 2745 5.306678 AGCCCAATAATGTCCAAAAACAGAA 59.693 36.000 0.00 0.00 31.50 3.02
2647 2746 4.837860 AGCCCAATAATGTCCAAAAACAGA 59.162 37.500 0.00 0.00 31.50 3.41
2648 2747 5.151297 AGCCCAATAATGTCCAAAAACAG 57.849 39.130 0.00 0.00 31.50 3.16
2649 2748 5.559148 AAGCCCAATAATGTCCAAAAACA 57.441 34.783 0.00 0.00 0.00 2.83
2650 2749 8.560355 AATAAAGCCCAATAATGTCCAAAAAC 57.440 30.769 0.00 0.00 0.00 2.43
2654 2753 9.647918 TGTATAATAAAGCCCAATAATGTCCAA 57.352 29.630 0.00 0.00 0.00 3.53
2655 2754 9.073475 GTGTATAATAAAGCCCAATAATGTCCA 57.927 33.333 0.00 0.00 0.00 4.02
2656 2755 9.297037 AGTGTATAATAAAGCCCAATAATGTCC 57.703 33.333 0.00 0.00 0.00 4.02
2689 2788 9.176460 CGGTTAATAGGTTAGTCCCAAAAATAA 57.824 33.333 0.00 0.00 36.75 1.40
2690 2789 7.774625 CCGGTTAATAGGTTAGTCCCAAAAATA 59.225 37.037 0.00 0.00 36.75 1.40
2691 2790 6.604396 CCGGTTAATAGGTTAGTCCCAAAAAT 59.396 38.462 0.00 0.00 36.75 1.82
2692 2791 5.945191 CCGGTTAATAGGTTAGTCCCAAAAA 59.055 40.000 0.00 0.00 36.75 1.94
2693 2792 5.250313 TCCGGTTAATAGGTTAGTCCCAAAA 59.750 40.000 0.00 0.00 36.75 2.44
2694 2793 4.782156 TCCGGTTAATAGGTTAGTCCCAAA 59.218 41.667 0.00 0.00 36.75 3.28
2695 2794 4.360889 TCCGGTTAATAGGTTAGTCCCAA 58.639 43.478 0.00 0.00 36.75 4.12
2696 2795 3.962718 CTCCGGTTAATAGGTTAGTCCCA 59.037 47.826 0.00 0.00 36.75 4.37
2697 2796 3.323115 CCTCCGGTTAATAGGTTAGTCCC 59.677 52.174 0.00 0.00 36.75 4.46
2698 2797 3.244009 GCCTCCGGTTAATAGGTTAGTCC 60.244 52.174 0.00 0.00 32.67 3.85
2699 2798 3.244009 GGCCTCCGGTTAATAGGTTAGTC 60.244 52.174 0.00 0.00 32.67 2.59
2700 2799 2.702478 GGCCTCCGGTTAATAGGTTAGT 59.298 50.000 0.00 0.00 32.67 2.24
2701 2800 2.038164 GGGCCTCCGGTTAATAGGTTAG 59.962 54.545 0.84 0.00 32.67 2.34
2702 2801 2.049372 GGGCCTCCGGTTAATAGGTTA 58.951 52.381 0.84 0.00 32.67 2.85
2703 2802 0.841961 GGGCCTCCGGTTAATAGGTT 59.158 55.000 0.84 0.00 32.67 3.50
2704 2803 0.326808 TGGGCCTCCGGTTAATAGGT 60.327 55.000 4.53 0.00 35.24 3.08
2705 2804 0.396811 CTGGGCCTCCGGTTAATAGG 59.603 60.000 4.53 0.51 34.69 2.57
2706 2805 0.250338 GCTGGGCCTCCGGTTAATAG 60.250 60.000 4.53 0.00 41.53 1.73
2707 2806 1.702022 GGCTGGGCCTCCGGTTAATA 61.702 60.000 4.53 0.00 46.69 0.98
2708 2807 2.595655 GCTGGGCCTCCGGTTAAT 59.404 61.111 4.53 0.00 41.53 1.40
2709 2808 3.723922 GGCTGGGCCTCCGGTTAA 61.724 66.667 4.53 0.00 46.69 2.01
2719 2818 2.363406 AGCAATTCTGGGCTGGGC 60.363 61.111 0.00 0.00 39.30 5.36
2742 2841 4.320935 GCGGAACTCTGAAATAGGCAAAAA 60.321 41.667 0.00 0.00 0.00 1.94
2743 2842 3.190535 GCGGAACTCTGAAATAGGCAAAA 59.809 43.478 0.00 0.00 0.00 2.44
2744 2843 2.747446 GCGGAACTCTGAAATAGGCAAA 59.253 45.455 0.00 0.00 0.00 3.68
2745 2844 2.290008 TGCGGAACTCTGAAATAGGCAA 60.290 45.455 0.00 0.00 0.00 4.52
2746 2845 1.277842 TGCGGAACTCTGAAATAGGCA 59.722 47.619 0.00 0.00 0.00 4.75
2747 2846 1.936547 CTGCGGAACTCTGAAATAGGC 59.063 52.381 0.00 0.00 0.00 3.93
2748 2847 3.526931 TCTGCGGAACTCTGAAATAGG 57.473 47.619 0.00 0.00 0.00 2.57
2749 2848 5.862924 TTTTCTGCGGAACTCTGAAATAG 57.137 39.130 7.69 0.00 39.82 1.73
2750 2849 5.995282 TCTTTTTCTGCGGAACTCTGAAATA 59.005 36.000 7.69 0.00 39.82 1.40
2751 2850 4.821805 TCTTTTTCTGCGGAACTCTGAAAT 59.178 37.500 7.69 0.00 39.82 2.17
2752 2851 4.196193 TCTTTTTCTGCGGAACTCTGAAA 58.804 39.130 7.69 4.74 38.76 2.69
2753 2852 3.804036 TCTTTTTCTGCGGAACTCTGAA 58.196 40.909 7.69 0.00 0.00 3.02
2754 2853 3.469008 TCTTTTTCTGCGGAACTCTGA 57.531 42.857 7.69 1.60 0.00 3.27
2755 2854 4.756084 ATTCTTTTTCTGCGGAACTCTG 57.244 40.909 7.69 0.00 0.00 3.35
2756 2855 6.173339 TGATATTCTTTTTCTGCGGAACTCT 58.827 36.000 7.69 0.00 0.00 3.24
2757 2856 6.422776 TGATATTCTTTTTCTGCGGAACTC 57.577 37.500 7.69 0.00 0.00 3.01
2758 2857 6.817765 TTGATATTCTTTTTCTGCGGAACT 57.182 33.333 7.69 0.00 0.00 3.01
2759 2858 6.032460 CGTTTGATATTCTTTTTCTGCGGAAC 59.968 38.462 7.69 0.00 0.00 3.62
2760 2859 6.083630 CGTTTGATATTCTTTTTCTGCGGAA 58.916 36.000 3.13 3.13 0.00 4.30
2761 2860 5.391523 CCGTTTGATATTCTTTTTCTGCGGA 60.392 40.000 0.00 0.00 35.57 5.54
2762 2861 4.793216 CCGTTTGATATTCTTTTTCTGCGG 59.207 41.667 0.00 0.00 0.00 5.69
2763 2862 5.627172 TCCGTTTGATATTCTTTTTCTGCG 58.373 37.500 0.00 0.00 0.00 5.18
2764 2863 6.612306 ACTCCGTTTGATATTCTTTTTCTGC 58.388 36.000 0.00 0.00 0.00 4.26
2765 2864 7.094805 TGGACTCCGTTTGATATTCTTTTTCTG 60.095 37.037 0.00 0.00 0.00 3.02
2766 2865 6.940298 TGGACTCCGTTTGATATTCTTTTTCT 59.060 34.615 0.00 0.00 0.00 2.52
2767 2866 7.141100 TGGACTCCGTTTGATATTCTTTTTC 57.859 36.000 0.00 0.00 0.00 2.29
2768 2867 7.519032 TTGGACTCCGTTTGATATTCTTTTT 57.481 32.000 0.00 0.00 0.00 1.94
2769 2868 7.368059 GTTTGGACTCCGTTTGATATTCTTTT 58.632 34.615 0.00 0.00 0.00 2.27
2770 2869 6.348213 CGTTTGGACTCCGTTTGATATTCTTT 60.348 38.462 0.00 0.00 0.00 2.52
2771 2870 5.121768 CGTTTGGACTCCGTTTGATATTCTT 59.878 40.000 0.00 0.00 0.00 2.52
2772 2871 4.630069 CGTTTGGACTCCGTTTGATATTCT 59.370 41.667 0.00 0.00 0.00 2.40
2773 2872 4.201783 CCGTTTGGACTCCGTTTGATATTC 60.202 45.833 0.00 0.00 37.49 1.75
2774 2873 3.687698 CCGTTTGGACTCCGTTTGATATT 59.312 43.478 0.00 0.00 37.49 1.28
2775 2874 3.267483 CCGTTTGGACTCCGTTTGATAT 58.733 45.455 0.00 0.00 37.49 1.63
2776 2875 2.690786 CCGTTTGGACTCCGTTTGATA 58.309 47.619 0.00 0.00 37.49 2.15
2777 2876 1.519408 CCGTTTGGACTCCGTTTGAT 58.481 50.000 0.00 0.00 37.49 2.57
2778 2877 1.161563 GCCGTTTGGACTCCGTTTGA 61.162 55.000 0.00 0.00 37.49 2.69
2779 2878 1.281656 GCCGTTTGGACTCCGTTTG 59.718 57.895 0.00 0.00 37.49 2.93
2780 2879 0.536460 ATGCCGTTTGGACTCCGTTT 60.536 50.000 0.00 0.00 37.49 3.60
2781 2880 1.072505 ATGCCGTTTGGACTCCGTT 59.927 52.632 0.00 0.00 37.49 4.44
2782 2881 1.671054 CATGCCGTTTGGACTCCGT 60.671 57.895 0.00 0.00 37.49 4.69
2783 2882 0.953471 TTCATGCCGTTTGGACTCCG 60.953 55.000 0.00 0.00 37.49 4.63
2784 2883 1.068541 GTTTCATGCCGTTTGGACTCC 60.069 52.381 0.00 0.00 37.49 3.85
2785 2884 1.068541 GGTTTCATGCCGTTTGGACTC 60.069 52.381 0.00 0.00 37.49 3.36
2786 2885 0.958822 GGTTTCATGCCGTTTGGACT 59.041 50.000 0.00 0.00 37.49 3.85
2787 2886 0.958822 AGGTTTCATGCCGTTTGGAC 59.041 50.000 0.00 0.00 37.49 4.02
2788 2887 1.611491 GAAGGTTTCATGCCGTTTGGA 59.389 47.619 0.00 0.00 37.49 3.53
2789 2888 1.665735 CGAAGGTTTCATGCCGTTTGG 60.666 52.381 0.00 0.00 38.77 3.28
2790 2889 1.685302 CGAAGGTTTCATGCCGTTTG 58.315 50.000 0.00 0.00 0.00 2.93
2805 2904 1.127951 CCGAAAATCACGTTCCCGAAG 59.872 52.381 0.00 0.00 37.88 3.79
2806 2905 1.149987 CCGAAAATCACGTTCCCGAA 58.850 50.000 0.00 0.00 37.88 4.30
2807 2906 0.317799 TCCGAAAATCACGTTCCCGA 59.682 50.000 0.00 0.00 37.88 5.14
2808 2907 1.136169 GTTCCGAAAATCACGTTCCCG 60.136 52.381 0.00 0.00 40.83 5.14
2809 2908 1.136169 CGTTCCGAAAATCACGTTCCC 60.136 52.381 0.00 0.00 0.00 3.97
2810 2909 1.794116 TCGTTCCGAAAATCACGTTCC 59.206 47.619 0.00 0.00 34.24 3.62
2811 2910 3.508648 TTCGTTCCGAAAATCACGTTC 57.491 42.857 0.00 0.00 43.00 3.95
2821 2920 0.314618 TGGATCACGTTCGTTCCGAA 59.685 50.000 10.21 0.00 43.75 4.30
2822 2921 0.109458 CTGGATCACGTTCGTTCCGA 60.109 55.000 10.21 0.37 0.00 4.55
2823 2922 0.109458 TCTGGATCACGTTCGTTCCG 60.109 55.000 10.21 6.59 0.00 4.30
2824 2923 1.630148 CTCTGGATCACGTTCGTTCC 58.370 55.000 8.55 8.55 0.00 3.62
2825 2924 1.201647 TCCTCTGGATCACGTTCGTTC 59.798 52.381 0.00 0.00 0.00 3.95
2826 2925 1.067776 GTCCTCTGGATCACGTTCGTT 60.068 52.381 0.00 0.00 32.73 3.85
2827 2926 0.526662 GTCCTCTGGATCACGTTCGT 59.473 55.000 0.00 0.00 32.73 3.85
2828 2927 0.811915 AGTCCTCTGGATCACGTTCG 59.188 55.000 0.00 0.00 32.73 3.95
2829 2928 2.611518 CAAGTCCTCTGGATCACGTTC 58.388 52.381 0.00 0.00 32.73 3.95
2830 2929 1.276421 CCAAGTCCTCTGGATCACGTT 59.724 52.381 0.00 0.00 32.73 3.99
2831 2930 0.898320 CCAAGTCCTCTGGATCACGT 59.102 55.000 0.00 0.00 32.73 4.49
2832 2931 1.134965 GTCCAAGTCCTCTGGATCACG 60.135 57.143 0.00 0.00 32.73 4.35
2833 2932 1.208293 GGTCCAAGTCCTCTGGATCAC 59.792 57.143 0.00 0.00 33.26 3.06
2834 2933 1.573108 GGTCCAAGTCCTCTGGATCA 58.427 55.000 0.00 0.00 33.26 2.92
2835 2934 0.833949 GGGTCCAAGTCCTCTGGATC 59.166 60.000 0.00 0.00 32.73 3.36
2836 2935 0.419459 AGGGTCCAAGTCCTCTGGAT 59.581 55.000 0.00 0.00 32.73 3.41
2837 2936 1.089978 TAGGGTCCAAGTCCTCTGGA 58.910 55.000 0.00 0.00 34.75 3.86
2838 2937 1.196012 GTAGGGTCCAAGTCCTCTGG 58.804 60.000 0.00 0.00 34.75 3.86
2839 2938 0.818296 CGTAGGGTCCAAGTCCTCTG 59.182 60.000 0.00 0.00 34.75 3.35
2840 2939 0.408700 ACGTAGGGTCCAAGTCCTCT 59.591 55.000 0.00 0.00 34.75 3.69
2841 2940 0.816373 GACGTAGGGTCCAAGTCCTC 59.184 60.000 0.00 0.00 39.90 3.71
2842 2941 0.113776 TGACGTAGGGTCCAAGTCCT 59.886 55.000 0.00 0.00 45.46 3.85
2843 2942 0.971386 TTGACGTAGGGTCCAAGTCC 59.029 55.000 0.00 0.00 45.46 3.85
2844 2943 1.891150 TCTTGACGTAGGGTCCAAGTC 59.109 52.381 10.96 0.00 45.46 3.01
2845 2944 1.617357 GTCTTGACGTAGGGTCCAAGT 59.383 52.381 10.96 0.00 45.46 3.16
2846 2945 1.616865 TGTCTTGACGTAGGGTCCAAG 59.383 52.381 6.17 6.17 45.46 3.61
2847 2946 1.707106 TGTCTTGACGTAGGGTCCAA 58.293 50.000 0.00 0.00 45.46 3.53
2848 2947 1.822990 GATGTCTTGACGTAGGGTCCA 59.177 52.381 0.00 0.00 45.46 4.02
2849 2948 1.822990 TGATGTCTTGACGTAGGGTCC 59.177 52.381 0.00 0.00 45.46 4.46
2850 2949 3.251571 GTTGATGTCTTGACGTAGGGTC 58.748 50.000 0.00 0.00 46.27 4.46
2851 2950 2.028385 GGTTGATGTCTTGACGTAGGGT 60.028 50.000 0.00 0.00 0.00 4.34
2852 2951 2.028476 TGGTTGATGTCTTGACGTAGGG 60.028 50.000 0.00 0.00 0.00 3.53
2853 2952 3.254060 CTGGTTGATGTCTTGACGTAGG 58.746 50.000 0.00 0.00 0.00 3.18
2854 2953 3.056821 TCCTGGTTGATGTCTTGACGTAG 60.057 47.826 0.00 0.00 0.00 3.51
2855 2954 2.894765 TCCTGGTTGATGTCTTGACGTA 59.105 45.455 0.00 0.00 0.00 3.57
2856 2955 1.691976 TCCTGGTTGATGTCTTGACGT 59.308 47.619 0.00 0.00 0.00 4.34
2857 2956 2.455674 TCCTGGTTGATGTCTTGACG 57.544 50.000 0.00 0.00 0.00 4.35
2858 2957 3.077359 CCTTCCTGGTTGATGTCTTGAC 58.923 50.000 0.00 0.00 0.00 3.18
2859 2958 2.553028 GCCTTCCTGGTTGATGTCTTGA 60.553 50.000 0.00 0.00 38.35 3.02
2860 2959 1.815003 GCCTTCCTGGTTGATGTCTTG 59.185 52.381 0.00 0.00 38.35 3.02
2861 2960 1.425066 TGCCTTCCTGGTTGATGTCTT 59.575 47.619 0.00 0.00 38.35 3.01
2862 2961 1.067295 TGCCTTCCTGGTTGATGTCT 58.933 50.000 0.00 0.00 38.35 3.41
2863 2962 1.168714 GTGCCTTCCTGGTTGATGTC 58.831 55.000 0.00 0.00 38.35 3.06
2864 2963 0.478072 TGTGCCTTCCTGGTTGATGT 59.522 50.000 0.00 0.00 38.35 3.06
2865 2964 1.542915 CTTGTGCCTTCCTGGTTGATG 59.457 52.381 0.00 0.00 38.35 3.07
2866 2965 1.548582 CCTTGTGCCTTCCTGGTTGAT 60.549 52.381 0.00 0.00 38.35 2.57
2867 2966 0.178992 CCTTGTGCCTTCCTGGTTGA 60.179 55.000 0.00 0.00 38.35 3.18
2868 2967 0.468029 ACCTTGTGCCTTCCTGGTTG 60.468 55.000 0.00 0.00 38.35 3.77
2869 2968 1.073923 CTACCTTGTGCCTTCCTGGTT 59.926 52.381 0.00 0.00 38.35 3.67
2870 2969 0.693049 CTACCTTGTGCCTTCCTGGT 59.307 55.000 0.00 0.00 38.35 4.00
2871 2970 0.035056 CCTACCTTGTGCCTTCCTGG 60.035 60.000 0.00 0.00 39.35 4.45
2872 2971 0.035056 CCCTACCTTGTGCCTTCCTG 60.035 60.000 0.00 0.00 0.00 3.86
2873 2972 1.208165 CCCCTACCTTGTGCCTTCCT 61.208 60.000 0.00 0.00 0.00 3.36
2874 2973 1.303282 CCCCTACCTTGTGCCTTCC 59.697 63.158 0.00 0.00 0.00 3.46
2875 2974 1.303282 CCCCCTACCTTGTGCCTTC 59.697 63.158 0.00 0.00 0.00 3.46
2876 2975 3.508048 CCCCCTACCTTGTGCCTT 58.492 61.111 0.00 0.00 0.00 4.35
2914 3013 4.394712 CACGAGGGTGGAGGGCAC 62.395 72.222 0.00 0.00 40.58 5.01
2925 3024 4.047125 AACATGGGGCCCACGAGG 62.047 66.667 31.54 19.99 35.80 4.63
2926 3025 2.751436 CAACATGGGGCCCACGAG 60.751 66.667 31.54 23.00 35.80 4.18
2929 3028 3.070576 GAGCAACATGGGGCCCAC 61.071 66.667 31.54 15.53 35.80 4.61
2930 3029 4.380945 GGAGCAACATGGGGCCCA 62.381 66.667 30.97 30.97 38.19 5.36
2931 3030 4.380945 TGGAGCAACATGGGGCCC 62.381 66.667 18.17 18.17 0.00 5.80
2932 3031 3.070576 GTGGAGCAACATGGGGCC 61.071 66.667 0.00 0.00 0.00 5.80
2933 3032 3.070576 GGTGGAGCAACATGGGGC 61.071 66.667 0.00 0.00 0.00 5.80
2934 3033 2.751436 CGGTGGAGCAACATGGGG 60.751 66.667 0.00 0.00 0.00 4.96
2935 3034 2.040544 GTCGGTGGAGCAACATGGG 61.041 63.158 0.00 0.00 0.00 4.00
2936 3035 2.390599 CGTCGGTGGAGCAACATGG 61.391 63.158 0.00 0.00 0.00 3.66
2937 3036 0.389296 TACGTCGGTGGAGCAACATG 60.389 55.000 0.00 0.00 0.00 3.21
2938 3037 0.389426 GTACGTCGGTGGAGCAACAT 60.389 55.000 0.00 0.00 0.00 2.71
2939 3038 1.007038 GTACGTCGGTGGAGCAACA 60.007 57.895 0.00 0.00 0.00 3.33
2940 3039 0.319297 AAGTACGTCGGTGGAGCAAC 60.319 55.000 0.00 0.00 0.00 4.17
2941 3040 0.038892 GAAGTACGTCGGTGGAGCAA 60.039 55.000 0.00 0.00 0.00 3.91
2942 3041 0.892358 AGAAGTACGTCGGTGGAGCA 60.892 55.000 3.05 0.00 0.00 4.26
2943 3042 0.243095 AAGAAGTACGTCGGTGGAGC 59.757 55.000 3.05 0.00 0.00 4.70
2944 3043 1.135460 GGAAGAAGTACGTCGGTGGAG 60.135 57.143 3.05 0.00 0.00 3.86
2945 3044 0.883833 GGAAGAAGTACGTCGGTGGA 59.116 55.000 3.05 0.00 0.00 4.02
2946 3045 0.886563 AGGAAGAAGTACGTCGGTGG 59.113 55.000 3.05 0.00 0.00 4.61
2947 3046 1.135460 GGAGGAAGAAGTACGTCGGTG 60.135 57.143 3.05 0.00 0.00 4.94
2948 3047 1.172175 GGAGGAAGAAGTACGTCGGT 58.828 55.000 3.05 0.00 0.00 4.69
2949 3048 1.461559 AGGAGGAAGAAGTACGTCGG 58.538 55.000 3.05 0.00 0.00 4.79
2950 3049 7.846644 ATATATAGGAGGAAGAAGTACGTCG 57.153 40.000 3.05 0.00 0.00 5.12
2951 3050 9.108284 GGTATATATAGGAGGAAGAAGTACGTC 57.892 40.741 0.00 0.00 0.00 4.34
2952 3051 8.834733 AGGTATATATAGGAGGAAGAAGTACGT 58.165 37.037 0.00 0.00 0.00 3.57
2956 3055 8.834733 ACGTAGGTATATATAGGAGGAAGAAGT 58.165 37.037 0.00 0.00 0.00 3.01
2959 3058 8.709308 GGTACGTAGGTATATATAGGAGGAAGA 58.291 40.741 0.00 0.00 0.00 2.87
2960 3059 7.936301 GGGTACGTAGGTATATATAGGAGGAAG 59.064 44.444 0.00 0.00 0.00 3.46
2961 3060 7.147302 GGGGTACGTAGGTATATATAGGAGGAA 60.147 44.444 0.00 0.00 0.00 3.36
2962 3061 6.330250 GGGGTACGTAGGTATATATAGGAGGA 59.670 46.154 0.00 0.00 0.00 3.71
2963 3062 6.466470 GGGGGTACGTAGGTATATATAGGAGG 60.466 50.000 0.00 0.00 0.00 4.30
2964 3063 6.101734 TGGGGGTACGTAGGTATATATAGGAG 59.898 46.154 0.00 0.00 0.00 3.69
2965 3064 5.976244 TGGGGGTACGTAGGTATATATAGGA 59.024 44.000 0.00 0.00 0.00 2.94
2966 3065 6.266131 TGGGGGTACGTAGGTATATATAGG 57.734 45.833 0.00 0.00 0.00 2.57
2967 3066 7.836183 AGTTTGGGGGTACGTAGGTATATATAG 59.164 40.741 0.00 0.00 0.00 1.31
2968 3067 7.708624 AGTTTGGGGGTACGTAGGTATATATA 58.291 38.462 0.00 0.00 0.00 0.86
2969 3068 6.565036 AGTTTGGGGGTACGTAGGTATATAT 58.435 40.000 0.00 0.00 0.00 0.86
2970 3069 5.964288 AGTTTGGGGGTACGTAGGTATATA 58.036 41.667 0.00 0.00 0.00 0.86
2971 3070 4.819610 AGTTTGGGGGTACGTAGGTATAT 58.180 43.478 0.00 0.00 0.00 0.86
2972 3071 4.264373 AGTTTGGGGGTACGTAGGTATA 57.736 45.455 0.00 0.00 0.00 1.47
2973 3072 3.120468 AGTTTGGGGGTACGTAGGTAT 57.880 47.619 0.00 0.00 0.00 2.73
2974 3073 2.621556 AGTTTGGGGGTACGTAGGTA 57.378 50.000 0.00 0.00 0.00 3.08
2975 3074 2.179427 GTAGTTTGGGGGTACGTAGGT 58.821 52.381 0.00 0.00 0.00 3.08
2976 3075 1.482182 GGTAGTTTGGGGGTACGTAGG 59.518 57.143 0.00 0.00 0.00 3.18
2977 3076 2.167075 CTGGTAGTTTGGGGGTACGTAG 59.833 54.545 0.00 0.00 0.00 3.51
2978 3077 2.178580 CTGGTAGTTTGGGGGTACGTA 58.821 52.381 0.00 0.00 0.00 3.57
2979 3078 0.978907 CTGGTAGTTTGGGGGTACGT 59.021 55.000 0.00 0.00 0.00 3.57
2980 3079 1.269012 TCTGGTAGTTTGGGGGTACG 58.731 55.000 0.00 0.00 0.00 3.67
2981 3080 3.181472 CGTATCTGGTAGTTTGGGGGTAC 60.181 52.174 0.00 0.00 0.00 3.34
2982 3081 3.033184 CGTATCTGGTAGTTTGGGGGTA 58.967 50.000 0.00 0.00 0.00 3.69
2983 3082 1.835531 CGTATCTGGTAGTTTGGGGGT 59.164 52.381 0.00 0.00 0.00 4.95
2984 3083 1.140252 CCGTATCTGGTAGTTTGGGGG 59.860 57.143 0.00 0.00 0.00 5.40
2985 3084 2.102588 CTCCGTATCTGGTAGTTTGGGG 59.897 54.545 0.00 0.00 0.00 4.96
2986 3085 2.483188 GCTCCGTATCTGGTAGTTTGGG 60.483 54.545 0.00 0.00 0.00 4.12
2987 3086 2.483188 GGCTCCGTATCTGGTAGTTTGG 60.483 54.545 0.00 0.00 0.00 3.28
2988 3087 2.167693 TGGCTCCGTATCTGGTAGTTTG 59.832 50.000 0.00 0.00 0.00 2.93
2989 3088 2.463752 TGGCTCCGTATCTGGTAGTTT 58.536 47.619 0.00 0.00 0.00 2.66
2990 3089 2.154567 TGGCTCCGTATCTGGTAGTT 57.845 50.000 0.00 0.00 0.00 2.24
2991 3090 2.154567 TTGGCTCCGTATCTGGTAGT 57.845 50.000 0.00 0.00 0.00 2.73
2992 3091 3.536956 TTTTGGCTCCGTATCTGGTAG 57.463 47.619 0.00 0.00 0.00 3.18
2993 3092 3.602483 GTTTTTGGCTCCGTATCTGGTA 58.398 45.455 0.00 0.00 0.00 3.25
2994 3093 2.433436 GTTTTTGGCTCCGTATCTGGT 58.567 47.619 0.00 0.00 0.00 4.00
2995 3094 1.743394 GGTTTTTGGCTCCGTATCTGG 59.257 52.381 0.00 0.00 0.00 3.86
2996 3095 2.711542 AGGTTTTTGGCTCCGTATCTG 58.288 47.619 0.00 0.00 0.00 2.90
2997 3096 4.563140 TTAGGTTTTTGGCTCCGTATCT 57.437 40.909 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.