Multiple sequence alignment - TraesCS7D01G213200

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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 TraesCS7D01G213200 chr7D 100.000 2201 0 0 1 2201 171373828 171371628 0.000000e+00 4065.0
1 TraesCS7D01G213200 chr7D 100.000 328 0 0 2526 2853 171371303 171370976 8.740000e-170 606.0
2 TraesCS7D01G213200 chr7D 87.313 134 9 4 2607 2732 171372685 171372818 2.290000e-31 147.0
3 TraesCS7D01G213200 chr7B 93.142 1881 60 21 15 1864 137881798 137879956 0.000000e+00 2695.0
4 TraesCS7D01G213200 chr7B 93.529 340 16 4 1866 2201 137879786 137879449 4.240000e-138 501.0
5 TraesCS7D01G213200 chr7B 87.302 126 13 2 2607 2732 137880679 137880801 1.070000e-29 141.0
6 TraesCS7D01G213200 chr7A 94.531 1536 59 14 631 2147 174274655 174273126 0.000000e+00 2348.0
7 TraesCS7D01G213200 chr7A 93.263 668 14 10 2 648 174275329 174274672 0.000000e+00 955.0
8 TraesCS7D01G213200 chr7A 90.840 262 19 4 2594 2853 174221929 174221671 2.100000e-91 346.0
9 TraesCS7D01G213200 chr7A 87.313 134 9 2 2607 2732 174274135 174274268 2.290000e-31 147.0
10 TraesCS7D01G213200 chr7A 91.304 69 6 0 2526 2594 174272715 174272647 8.410000e-16 95.3
11 TraesCS7D01G213200 chr6B 87.111 225 28 1 1397 1620 566535486 566535710 1.310000e-63 254.0


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 TraesCS7D01G213200 chr7D 171370976 171373828 2852 True 2335.500000 4065 100.000000 1 2853 2 chr7D.!!$R1 2852
1 TraesCS7D01G213200 chr7B 137879449 137881798 2349 True 1598.000000 2695 93.335500 15 2201 2 chr7B.!!$R1 2186
2 TraesCS7D01G213200 chr7A 174272647 174275329 2682 True 1132.766667 2348 93.032667 2 2594 3 chr7A.!!$R2 2592

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
354 365 0.396811 ACCACCAACTACAGTGCCTC 59.603 55.0 0.0 0.0 32.48 4.70 F
355 366 0.687354 CCACCAACTACAGTGCCTCT 59.313 55.0 0.0 0.0 32.48 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1362 0.453390 GGCAACTGCATTAGACTGCC 59.547 55.000 3.76 2.17 45.07 4.85 R
1924 2175 1.275573 GGTCGGAACTAGCAACCTCTT 59.724 52.381 0.00 0.00 0.00 2.85 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
231 232 6.753913 TTATCTCCTCACAGCTATTTGGAT 57.246 37.500 0.00 0.00 0.00 3.41
354 365 0.396811 ACCACCAACTACAGTGCCTC 59.603 55.000 0.00 0.00 32.48 4.70
355 366 0.687354 CCACCAACTACAGTGCCTCT 59.313 55.000 0.00 0.00 32.48 3.69
356 367 1.072331 CCACCAACTACAGTGCCTCTT 59.928 52.381 0.00 0.00 32.48 2.85
357 368 2.487265 CCACCAACTACAGTGCCTCTTT 60.487 50.000 0.00 0.00 32.48 2.52
405 416 0.743345 GCGTTAGCCCGGTGAGAAAT 60.743 55.000 0.00 0.00 37.42 2.17
406 417 1.734163 CGTTAGCCCGGTGAGAAATT 58.266 50.000 0.00 0.00 0.00 1.82
487 498 1.144716 GCTCCCATCGATCAGCACA 59.855 57.895 13.33 0.00 0.00 4.57
488 499 0.879400 GCTCCCATCGATCAGCACAG 60.879 60.000 13.33 0.00 0.00 3.66
489 500 0.879400 CTCCCATCGATCAGCACAGC 60.879 60.000 0.00 0.00 0.00 4.40
490 501 1.153309 CCCATCGATCAGCACAGCA 60.153 57.895 0.00 0.00 0.00 4.41
491 502 1.434622 CCCATCGATCAGCACAGCAC 61.435 60.000 0.00 0.00 0.00 4.40
497 508 2.189191 GATCAGCACAGCACCTCCCA 62.189 60.000 0.00 0.00 0.00 4.37
543 554 1.478105 GAAGCACCCCATCATGAAACC 59.522 52.381 0.00 0.00 0.00 3.27
552 563 2.632028 CCATCATGAAACCCAACCACAA 59.368 45.455 0.00 0.00 0.00 3.33
563 574 1.270550 CCAACCACAAGAAGGACATGC 59.729 52.381 0.00 0.00 0.00 4.06
690 757 2.348998 GGAGCAGTCACCCACCTG 59.651 66.667 0.00 0.00 0.00 4.00
695 769 1.149174 CAGTCACCCACCTGTGCTT 59.851 57.895 0.00 0.00 36.17 3.91
700 774 2.674380 CCCACCTGTGCTTCAGCC 60.674 66.667 0.00 0.00 42.38 4.85
881 957 4.101585 TCACGATAAGCATCCAGGAAATCT 59.898 41.667 0.00 0.00 0.00 2.40
883 959 4.141620 ACGATAAGCATCCAGGAAATCTGT 60.142 41.667 0.00 0.00 41.83 3.41
959 1035 0.758734 CCTTCAGGTGTGTCTGGACA 59.241 55.000 0.00 0.00 39.32 4.02
972 1048 2.237143 GTCTGGACACTGGATCATGGAA 59.763 50.000 0.00 0.00 0.00 3.53
1107 1183 9.921637 CTATACTCCATTATTTCTCTGTTCTCC 57.078 37.037 0.00 0.00 0.00 3.71
1860 1942 7.936847 TCTTTGCTCCATGTACCGATTAAATAT 59.063 33.333 0.00 0.00 0.00 1.28
1861 1943 9.214957 CTTTGCTCCATGTACCGATTAAATATA 57.785 33.333 0.00 0.00 0.00 0.86
1862 1944 9.733556 TTTGCTCCATGTACCGATTAAATATAT 57.266 29.630 0.00 0.00 0.00 0.86
1916 2167 8.993121 GTGTAATAGATATGGACCAATCACAAG 58.007 37.037 0.00 0.00 0.00 3.16
1924 2175 4.541705 TGGACCAATCACAAGAAAAAGGA 58.458 39.130 0.00 0.00 0.00 3.36
2020 2275 6.251376 GGCGAAGTTGATACATAAAGCAAAAG 59.749 38.462 0.00 0.00 0.00 2.27
2088 2347 9.190858 GTATGTGATGCTAAGTGAAATCTAGAG 57.809 37.037 0.00 0.00 0.00 2.43
2137 2398 4.034975 GCAGTTGTCTATTGCCTCAGAATC 59.965 45.833 0.00 0.00 31.79 2.52
2151 2412 2.361119 TCAGAATCGTCGTATCAAGGGG 59.639 50.000 0.00 0.00 0.00 4.79
2152 2413 2.361119 CAGAATCGTCGTATCAAGGGGA 59.639 50.000 0.00 0.00 0.00 4.81
2153 2414 3.005897 CAGAATCGTCGTATCAAGGGGAT 59.994 47.826 0.00 0.00 40.14 3.85
2154 2415 4.217767 CAGAATCGTCGTATCAAGGGGATA 59.782 45.833 0.00 0.00 37.44 2.59
2155 2416 4.831155 AGAATCGTCGTATCAAGGGGATAA 59.169 41.667 0.00 0.00 40.11 1.75
2186 2447 7.657023 AAGACTTAACATCCTACTTCGGTAT 57.343 36.000 0.00 0.00 0.00 2.73
2583 2876 4.384056 ACATGCCAGCATCTATAGTTGTC 58.616 43.478 1.19 5.32 33.90 3.18
2591 2884 3.300857 CATCTATAGTTGTCGGTGCTCG 58.699 50.000 0.00 0.00 40.90 5.03
2599 2892 2.034532 TCGGTGCTCGACAGGGTA 59.965 61.111 0.00 0.00 43.74 3.69
2600 2893 2.181021 CGGTGCTCGACAGGGTAC 59.819 66.667 0.00 0.00 42.43 3.34
2601 2894 2.632544 CGGTGCTCGACAGGGTACA 61.633 63.158 0.00 0.00 42.43 2.90
2602 2895 1.898154 GGTGCTCGACAGGGTACAT 59.102 57.895 0.00 0.00 34.96 2.29
2603 2896 0.460284 GGTGCTCGACAGGGTACATG 60.460 60.000 0.00 0.00 34.96 3.21
2604 2897 1.084370 GTGCTCGACAGGGTACATGC 61.084 60.000 0.00 0.00 33.37 4.06
2605 2898 1.218047 GCTCGACAGGGTACATGCA 59.782 57.895 0.00 0.00 0.00 3.96
2606 2899 0.807667 GCTCGACAGGGTACATGCAG 60.808 60.000 0.00 0.00 0.00 4.41
2607 2900 0.807667 CTCGACAGGGTACATGCAGC 60.808 60.000 0.00 0.00 0.00 5.25
2608 2901 1.219124 CGACAGGGTACATGCAGCT 59.781 57.895 0.00 0.00 0.00 4.24
2609 2902 0.391661 CGACAGGGTACATGCAGCTT 60.392 55.000 0.00 0.00 0.00 3.74
2610 2903 1.826385 GACAGGGTACATGCAGCTTT 58.174 50.000 0.00 0.00 0.00 3.51
2611 2904 1.470098 GACAGGGTACATGCAGCTTTG 59.530 52.381 0.00 0.00 0.00 2.77
2612 2905 0.171903 CAGGGTACATGCAGCTTTGC 59.828 55.000 0.00 0.00 0.00 3.68
2613 2906 0.038744 AGGGTACATGCAGCTTTGCT 59.961 50.000 0.00 0.00 40.77 3.91
2614 2907 0.890683 GGGTACATGCAGCTTTGCTT 59.109 50.000 0.00 0.00 36.40 3.91
2615 2908 1.403249 GGGTACATGCAGCTTTGCTTG 60.403 52.381 10.99 10.99 43.06 4.01
2617 2910 2.589014 GTACATGCAGCTTTGCTTGTC 58.411 47.619 18.74 10.03 45.86 3.18
2618 2911 0.039798 ACATGCAGCTTTGCTTGTCG 60.040 50.000 12.08 0.00 45.86 4.35
2619 2912 0.039798 CATGCAGCTTTGCTTGTCGT 60.040 50.000 0.00 0.00 36.40 4.34
2620 2913 1.197492 CATGCAGCTTTGCTTGTCGTA 59.803 47.619 0.00 0.00 36.40 3.43
2621 2914 0.586319 TGCAGCTTTGCTTGTCGTAC 59.414 50.000 0.00 0.00 36.40 3.67
2622 2915 0.451135 GCAGCTTTGCTTGTCGTACG 60.451 55.000 9.53 9.53 36.40 3.67
2623 2916 0.859232 CAGCTTTGCTTGTCGTACGT 59.141 50.000 16.05 0.00 36.40 3.57
2624 2917 2.055838 CAGCTTTGCTTGTCGTACGTA 58.944 47.619 16.05 2.87 36.40 3.57
2625 2918 2.090658 CAGCTTTGCTTGTCGTACGTAG 59.909 50.000 16.05 12.03 36.40 3.51
2626 2919 1.201780 GCTTTGCTTGTCGTACGTAGC 60.202 52.381 23.10 23.10 0.00 3.58
2627 2920 2.325761 CTTTGCTTGTCGTACGTAGCT 58.674 47.619 26.84 0.00 34.77 3.32
2628 2921 3.495193 CTTTGCTTGTCGTACGTAGCTA 58.505 45.455 26.84 21.21 34.77 3.32
2629 2922 3.557577 TTGCTTGTCGTACGTAGCTAA 57.442 42.857 26.84 20.01 34.77 3.09
2630 2923 3.127081 TGCTTGTCGTACGTAGCTAAG 57.873 47.619 26.84 19.63 34.77 2.18
2631 2924 1.844962 GCTTGTCGTACGTAGCTAAGC 59.155 52.381 22.81 21.17 33.32 3.09
2632 2925 2.477525 GCTTGTCGTACGTAGCTAAGCT 60.478 50.000 22.81 0.00 43.41 3.74
2633 2926 3.242543 GCTTGTCGTACGTAGCTAAGCTA 60.243 47.826 22.81 0.00 40.44 3.32
2634 2927 4.516359 CTTGTCGTACGTAGCTAAGCTAG 58.484 47.826 16.05 0.00 42.11 3.42
2635 2928 3.785486 TGTCGTACGTAGCTAAGCTAGA 58.215 45.455 16.05 1.03 42.11 2.43
2636 2929 3.801050 TGTCGTACGTAGCTAAGCTAGAG 59.199 47.826 16.05 0.00 42.11 2.43
2637 2930 3.184178 GTCGTACGTAGCTAAGCTAGAGG 59.816 52.174 16.05 0.00 42.11 3.69
2638 2931 3.068732 TCGTACGTAGCTAAGCTAGAGGA 59.931 47.826 16.05 0.00 42.11 3.71
2639 2932 3.184178 CGTACGTAGCTAAGCTAGAGGAC 59.816 52.174 7.22 0.00 42.11 3.85
2640 2933 2.211806 ACGTAGCTAAGCTAGAGGACG 58.788 52.381 6.59 1.66 42.11 4.79
2641 2934 1.532007 CGTAGCTAAGCTAGAGGACGG 59.468 57.143 0.00 0.00 42.11 4.79
2642 2935 2.806019 CGTAGCTAAGCTAGAGGACGGA 60.806 54.545 0.00 0.00 42.11 4.69
2643 2936 1.975660 AGCTAAGCTAGAGGACGGAG 58.024 55.000 0.00 0.00 36.99 4.63
2644 2937 1.491332 AGCTAAGCTAGAGGACGGAGA 59.509 52.381 0.00 0.00 36.99 3.71
2645 2938 1.877443 GCTAAGCTAGAGGACGGAGAG 59.123 57.143 0.00 0.00 0.00 3.20
2646 2939 2.485835 GCTAAGCTAGAGGACGGAGAGA 60.486 54.545 0.00 0.00 0.00 3.10
2647 2940 2.810870 AAGCTAGAGGACGGAGAGAA 57.189 50.000 0.00 0.00 0.00 2.87
2648 2941 2.810870 AGCTAGAGGACGGAGAGAAA 57.189 50.000 0.00 0.00 0.00 2.52
2649 2942 3.306472 AGCTAGAGGACGGAGAGAAAT 57.694 47.619 0.00 0.00 0.00 2.17
2650 2943 4.440826 AGCTAGAGGACGGAGAGAAATA 57.559 45.455 0.00 0.00 0.00 1.40
2651 2944 4.794334 AGCTAGAGGACGGAGAGAAATAA 58.206 43.478 0.00 0.00 0.00 1.40
2652 2945 5.390387 AGCTAGAGGACGGAGAGAAATAAT 58.610 41.667 0.00 0.00 0.00 1.28
2653 2946 5.242838 AGCTAGAGGACGGAGAGAAATAATG 59.757 44.000 0.00 0.00 0.00 1.90
2654 2947 4.946478 AGAGGACGGAGAGAAATAATGG 57.054 45.455 0.00 0.00 0.00 3.16
2655 2948 4.547671 AGAGGACGGAGAGAAATAATGGA 58.452 43.478 0.00 0.00 0.00 3.41
2656 2949 4.586841 AGAGGACGGAGAGAAATAATGGAG 59.413 45.833 0.00 0.00 0.00 3.86
2657 2950 4.290942 AGGACGGAGAGAAATAATGGAGT 58.709 43.478 0.00 0.00 0.00 3.85
2658 2951 5.455872 AGGACGGAGAGAAATAATGGAGTA 58.544 41.667 0.00 0.00 0.00 2.59
2659 2952 6.078664 AGGACGGAGAGAAATAATGGAGTAT 58.921 40.000 0.00 0.00 0.00 2.12
2660 2953 7.239438 AGGACGGAGAGAAATAATGGAGTATA 58.761 38.462 0.00 0.00 0.00 1.47
2661 2954 7.394923 AGGACGGAGAGAAATAATGGAGTATAG 59.605 40.741 0.00 0.00 0.00 1.31
2662 2955 7.177041 GGACGGAGAGAAATAATGGAGTATAGT 59.823 40.741 0.00 0.00 0.00 2.12
2663 2956 8.113173 ACGGAGAGAAATAATGGAGTATAGTC 57.887 38.462 0.00 0.00 0.00 2.59
2664 2957 7.094720 ACGGAGAGAAATAATGGAGTATAGTCG 60.095 40.741 1.45 0.00 0.00 4.18
2665 2958 7.119407 CGGAGAGAAATAATGGAGTATAGTCGA 59.881 40.741 1.45 0.00 0.00 4.20
2666 2959 8.794553 GGAGAGAAATAATGGAGTATAGTCGAA 58.205 37.037 1.45 0.00 0.00 3.71
2667 2960 9.834628 GAGAGAAATAATGGAGTATAGTCGAAG 57.165 37.037 1.45 0.00 0.00 3.79
2668 2961 9.357161 AGAGAAATAATGGAGTATAGTCGAAGT 57.643 33.333 1.45 0.00 0.00 3.01
2669 2962 9.400638 GAGAAATAATGGAGTATAGTCGAAGTG 57.599 37.037 1.45 0.00 0.00 3.16
2670 2963 8.361139 AGAAATAATGGAGTATAGTCGAAGTGG 58.639 37.037 1.45 0.00 0.00 4.00
2671 2964 7.834881 AATAATGGAGTATAGTCGAAGTGGA 57.165 36.000 1.45 0.00 0.00 4.02
2672 2965 5.776173 AATGGAGTATAGTCGAAGTGGAG 57.224 43.478 1.45 0.00 0.00 3.86
2673 2966 4.498894 TGGAGTATAGTCGAAGTGGAGA 57.501 45.455 1.45 0.00 0.00 3.71
2674 2967 4.452825 TGGAGTATAGTCGAAGTGGAGAG 58.547 47.826 1.45 0.00 0.00 3.20
2675 2968 3.816523 GGAGTATAGTCGAAGTGGAGAGG 59.183 52.174 1.45 0.00 0.00 3.69
2676 2969 4.444591 GGAGTATAGTCGAAGTGGAGAGGA 60.445 50.000 1.45 0.00 0.00 3.71
2677 2970 4.710324 AGTATAGTCGAAGTGGAGAGGAG 58.290 47.826 0.00 0.00 0.00 3.69
2678 2971 3.935818 ATAGTCGAAGTGGAGAGGAGA 57.064 47.619 0.00 0.00 0.00 3.71
2679 2972 2.588464 AGTCGAAGTGGAGAGGAGAA 57.412 50.000 0.00 0.00 0.00 2.87
2680 2973 2.877866 AGTCGAAGTGGAGAGGAGAAA 58.122 47.619 0.00 0.00 0.00 2.52
2681 2974 2.823154 AGTCGAAGTGGAGAGGAGAAAG 59.177 50.000 0.00 0.00 0.00 2.62
2682 2975 2.820787 GTCGAAGTGGAGAGGAGAAAGA 59.179 50.000 0.00 0.00 0.00 2.52
2683 2976 3.085533 TCGAAGTGGAGAGGAGAAAGAG 58.914 50.000 0.00 0.00 0.00 2.85
2684 2977 3.085533 CGAAGTGGAGAGGAGAAAGAGA 58.914 50.000 0.00 0.00 0.00 3.10
2685 2978 3.128589 CGAAGTGGAGAGGAGAAAGAGAG 59.871 52.174 0.00 0.00 0.00 3.20
2686 2979 3.100207 AGTGGAGAGGAGAAAGAGAGG 57.900 52.381 0.00 0.00 0.00 3.69
2687 2980 2.652348 AGTGGAGAGGAGAAAGAGAGGA 59.348 50.000 0.00 0.00 0.00 3.71
2688 2981 3.272020 AGTGGAGAGGAGAAAGAGAGGAT 59.728 47.826 0.00 0.00 0.00 3.24
2689 2982 4.480537 AGTGGAGAGGAGAAAGAGAGGATA 59.519 45.833 0.00 0.00 0.00 2.59
2690 2983 4.827284 GTGGAGAGGAGAAAGAGAGGATAG 59.173 50.000 0.00 0.00 0.00 2.08
2691 2984 4.141041 TGGAGAGGAGAAAGAGAGGATAGG 60.141 50.000 0.00 0.00 0.00 2.57
2692 2985 3.826729 GAGAGGAGAAAGAGAGGATAGGC 59.173 52.174 0.00 0.00 0.00 3.93
2693 2986 2.556622 GAGGAGAAAGAGAGGATAGGCG 59.443 54.545 0.00 0.00 0.00 5.52
2694 2987 1.616374 GGAGAAAGAGAGGATAGGCGG 59.384 57.143 0.00 0.00 0.00 6.13
2695 2988 1.616374 GAGAAAGAGAGGATAGGCGGG 59.384 57.143 0.00 0.00 0.00 6.13
2696 2989 0.682292 GAAAGAGAGGATAGGCGGGG 59.318 60.000 0.00 0.00 0.00 5.73
2697 2990 0.764752 AAAGAGAGGATAGGCGGGGG 60.765 60.000 0.00 0.00 0.00 5.40
2698 2991 1.665948 AAGAGAGGATAGGCGGGGGA 61.666 60.000 0.00 0.00 0.00 4.81
2699 2992 1.608046 GAGAGGATAGGCGGGGGAG 60.608 68.421 0.00 0.00 0.00 4.30
2700 2993 2.201771 GAGGATAGGCGGGGGAGT 59.798 66.667 0.00 0.00 0.00 3.85
2701 2994 1.909287 GAGGATAGGCGGGGGAGTC 60.909 68.421 0.00 0.00 0.00 3.36
2702 2995 2.201771 GGATAGGCGGGGGAGTCT 59.798 66.667 0.00 0.00 0.00 3.24
2703 2996 1.459730 GGATAGGCGGGGGAGTCTT 60.460 63.158 0.00 0.00 0.00 3.01
2704 2997 1.749033 GATAGGCGGGGGAGTCTTG 59.251 63.158 0.00 0.00 0.00 3.02
2705 2998 1.003051 ATAGGCGGGGGAGTCTTGT 59.997 57.895 0.00 0.00 0.00 3.16
2706 2999 1.338136 ATAGGCGGGGGAGTCTTGTG 61.338 60.000 0.00 0.00 0.00 3.33
2707 3000 2.449967 TAGGCGGGGGAGTCTTGTGA 62.450 60.000 0.00 0.00 0.00 3.58
2708 3001 2.747686 GCGGGGGAGTCTTGTGAA 59.252 61.111 0.00 0.00 0.00 3.18
2709 3002 1.671379 GCGGGGGAGTCTTGTGAAC 60.671 63.158 0.00 0.00 0.00 3.18
2710 3003 1.374252 CGGGGGAGTCTTGTGAACG 60.374 63.158 0.00 0.00 0.00 3.95
2711 3004 1.003718 GGGGGAGTCTTGTGAACGG 60.004 63.158 0.00 0.00 0.00 4.44
2712 3005 1.477685 GGGGGAGTCTTGTGAACGGA 61.478 60.000 0.00 0.00 0.00 4.69
2713 3006 0.395312 GGGGAGTCTTGTGAACGGAA 59.605 55.000 0.00 0.00 0.00 4.30
2714 3007 1.608283 GGGGAGTCTTGTGAACGGAAG 60.608 57.143 0.00 0.00 0.00 3.46
2715 3008 1.608283 GGGAGTCTTGTGAACGGAAGG 60.608 57.143 0.00 0.00 0.00 3.46
2716 3009 1.343465 GGAGTCTTGTGAACGGAAGGA 59.657 52.381 0.00 0.00 0.00 3.36
2717 3010 2.224209 GGAGTCTTGTGAACGGAAGGAA 60.224 50.000 0.00 0.00 0.00 3.36
2718 3011 3.060602 GAGTCTTGTGAACGGAAGGAAG 58.939 50.000 0.00 0.00 0.00 3.46
2719 3012 2.698797 AGTCTTGTGAACGGAAGGAAGA 59.301 45.455 0.00 0.00 0.00 2.87
2720 3013 3.060602 GTCTTGTGAACGGAAGGAAGAG 58.939 50.000 0.00 0.00 0.00 2.85
2721 3014 2.963101 TCTTGTGAACGGAAGGAAGAGA 59.037 45.455 0.00 0.00 0.00 3.10
2722 3015 3.005897 TCTTGTGAACGGAAGGAAGAGAG 59.994 47.826 0.00 0.00 0.00 3.20
2723 3016 2.594131 TGTGAACGGAAGGAAGAGAGA 58.406 47.619 0.00 0.00 0.00 3.10
2724 3017 2.296471 TGTGAACGGAAGGAAGAGAGAC 59.704 50.000 0.00 0.00 0.00 3.36
2725 3018 1.540267 TGAACGGAAGGAAGAGAGACG 59.460 52.381 0.00 0.00 0.00 4.18
2726 3019 1.811359 GAACGGAAGGAAGAGAGACGA 59.189 52.381 0.00 0.00 0.00 4.20
2727 3020 1.455248 ACGGAAGGAAGAGAGACGAG 58.545 55.000 0.00 0.00 0.00 4.18
2728 3021 1.271488 ACGGAAGGAAGAGAGACGAGT 60.271 52.381 0.00 0.00 0.00 4.18
2729 3022 1.131504 CGGAAGGAAGAGAGACGAGTG 59.868 57.143 0.00 0.00 0.00 3.51
2730 3023 1.474879 GGAAGGAAGAGAGACGAGTGG 59.525 57.143 0.00 0.00 0.00 4.00
2731 3024 2.164338 GAAGGAAGAGAGACGAGTGGT 58.836 52.381 0.00 0.00 0.00 4.16
2732 3025 2.296073 AGGAAGAGAGACGAGTGGTT 57.704 50.000 0.00 0.00 0.00 3.67
2733 3026 2.599677 AGGAAGAGAGACGAGTGGTTT 58.400 47.619 0.00 0.00 0.00 3.27
2734 3027 2.297597 AGGAAGAGAGACGAGTGGTTTG 59.702 50.000 0.00 0.00 0.00 2.93
2735 3028 2.296471 GGAAGAGAGACGAGTGGTTTGA 59.704 50.000 0.00 0.00 0.00 2.69
2736 3029 3.310246 GAAGAGAGACGAGTGGTTTGAC 58.690 50.000 0.00 0.00 0.00 3.18
2737 3030 2.307768 AGAGAGACGAGTGGTTTGACA 58.692 47.619 0.00 0.00 0.00 3.58
2738 3031 2.693591 AGAGAGACGAGTGGTTTGACAA 59.306 45.455 0.00 0.00 0.00 3.18
2739 3032 3.322254 AGAGAGACGAGTGGTTTGACAAT 59.678 43.478 0.00 0.00 0.00 2.71
2740 3033 4.058817 GAGAGACGAGTGGTTTGACAATT 58.941 43.478 0.00 0.00 0.00 2.32
2741 3034 4.451900 AGAGACGAGTGGTTTGACAATTT 58.548 39.130 0.00 0.00 0.00 1.82
2742 3035 4.273480 AGAGACGAGTGGTTTGACAATTTG 59.727 41.667 0.00 0.00 0.00 2.32
2743 3036 3.315191 AGACGAGTGGTTTGACAATTTGG 59.685 43.478 0.78 0.00 0.00 3.28
2744 3037 2.360801 ACGAGTGGTTTGACAATTTGGG 59.639 45.455 0.78 0.00 0.00 4.12
2745 3038 2.621055 CGAGTGGTTTGACAATTTGGGA 59.379 45.455 0.78 0.00 0.00 4.37
2746 3039 3.255642 CGAGTGGTTTGACAATTTGGGAT 59.744 43.478 0.78 0.00 0.00 3.85
2747 3040 4.615912 CGAGTGGTTTGACAATTTGGGATC 60.616 45.833 0.78 0.00 0.00 3.36
2748 3041 3.578282 AGTGGTTTGACAATTTGGGATCC 59.422 43.478 1.92 1.92 0.00 3.36
2749 3042 3.323403 GTGGTTTGACAATTTGGGATCCA 59.677 43.478 15.23 0.00 0.00 3.41
2750 3043 3.577848 TGGTTTGACAATTTGGGATCCAG 59.422 43.478 15.23 0.00 33.81 3.86
2751 3044 3.055891 GGTTTGACAATTTGGGATCCAGG 60.056 47.826 15.23 0.00 33.81 4.45
2752 3045 3.541242 TTGACAATTTGGGATCCAGGT 57.459 42.857 15.23 1.45 33.81 4.00
2753 3046 4.666412 TTGACAATTTGGGATCCAGGTA 57.334 40.909 15.23 0.00 33.81 3.08
2754 3047 4.879295 TGACAATTTGGGATCCAGGTAT 57.121 40.909 15.23 0.00 33.81 2.73
2755 3048 4.792068 TGACAATTTGGGATCCAGGTATC 58.208 43.478 15.23 2.58 33.81 2.24
2756 3049 4.145052 GACAATTTGGGATCCAGGTATCC 58.855 47.826 15.23 8.69 44.14 2.59
2757 3050 3.793827 ACAATTTGGGATCCAGGTATCCT 59.206 43.478 15.23 0.00 44.27 3.24
2758 3051 4.141158 ACAATTTGGGATCCAGGTATCCTC 60.141 45.833 15.23 7.94 44.27 3.71
2759 3052 3.438131 TTTGGGATCCAGGTATCCTCT 57.562 47.619 15.23 0.00 44.27 3.69
2760 3053 2.704190 TGGGATCCAGGTATCCTCTC 57.296 55.000 15.23 0.00 44.27 3.20
2761 3054 1.866269 TGGGATCCAGGTATCCTCTCA 59.134 52.381 15.23 0.00 44.27 3.27
2762 3055 2.250008 TGGGATCCAGGTATCCTCTCAA 59.750 50.000 15.23 0.00 44.27 3.02
2763 3056 3.311327 TGGGATCCAGGTATCCTCTCAAA 60.311 47.826 15.23 0.00 44.27 2.69
2764 3057 3.913163 GGGATCCAGGTATCCTCTCAAAT 59.087 47.826 15.23 0.00 44.27 2.32
2765 3058 5.094387 GGGATCCAGGTATCCTCTCAAATA 58.906 45.833 15.23 0.00 44.27 1.40
2766 3059 5.728741 GGGATCCAGGTATCCTCTCAAATAT 59.271 44.000 15.23 0.00 44.27 1.28
2767 3060 6.216456 GGGATCCAGGTATCCTCTCAAATATT 59.784 42.308 15.23 0.00 44.27 1.28
2768 3061 7.403231 GGGATCCAGGTATCCTCTCAAATATTA 59.597 40.741 15.23 0.00 44.27 0.98
2769 3062 8.826765 GGATCCAGGTATCCTCTCAAATATTAA 58.173 37.037 6.95 0.00 41.99 1.40
2792 3085 4.918810 ATTTTTATCATTCCCCACTCGC 57.081 40.909 0.00 0.00 0.00 5.03
2793 3086 2.341846 TTTATCATTCCCCACTCGCC 57.658 50.000 0.00 0.00 0.00 5.54
2794 3087 1.208706 TTATCATTCCCCACTCGCCA 58.791 50.000 0.00 0.00 0.00 5.69
2795 3088 1.208706 TATCATTCCCCACTCGCCAA 58.791 50.000 0.00 0.00 0.00 4.52
2796 3089 0.552848 ATCATTCCCCACTCGCCAAT 59.447 50.000 0.00 0.00 0.00 3.16
2797 3090 0.331278 TCATTCCCCACTCGCCAATT 59.669 50.000 0.00 0.00 0.00 2.32
2798 3091 0.457035 CATTCCCCACTCGCCAATTG 59.543 55.000 0.00 0.00 0.00 2.32
2799 3092 0.039618 ATTCCCCACTCGCCAATTGT 59.960 50.000 4.43 0.00 0.00 2.71
2800 3093 0.893270 TTCCCCACTCGCCAATTGTG 60.893 55.000 4.43 0.00 0.00 3.33
2811 3104 2.835580 CCAATTGTGGCCACATTTCA 57.164 45.000 37.97 24.24 41.52 2.69
2812 3105 2.690786 CCAATTGTGGCCACATTTCAG 58.309 47.619 37.97 26.25 41.52 3.02
2813 3106 2.299582 CCAATTGTGGCCACATTTCAGA 59.700 45.455 37.97 23.07 41.52 3.27
2814 3107 3.581755 CAATTGTGGCCACATTTCAGAG 58.418 45.455 37.97 22.67 41.52 3.35
2815 3108 2.655090 TTGTGGCCACATTTCAGAGA 57.345 45.000 37.97 18.77 41.52 3.10
2816 3109 2.655090 TGTGGCCACATTTCAGAGAA 57.345 45.000 34.74 7.90 36.21 2.87
2817 3110 2.229792 TGTGGCCACATTTCAGAGAAC 58.770 47.619 34.74 4.13 36.21 3.01
2818 3111 2.158623 TGTGGCCACATTTCAGAGAACT 60.159 45.455 34.74 0.00 36.21 3.01
2819 3112 2.485814 GTGGCCACATTTCAGAGAACTC 59.514 50.000 31.23 0.00 0.00 3.01
2820 3113 2.106338 TGGCCACATTTCAGAGAACTCA 59.894 45.455 0.00 0.00 0.00 3.41
2821 3114 2.485814 GGCCACATTTCAGAGAACTCAC 59.514 50.000 0.00 0.00 0.00 3.51
2822 3115 3.141398 GCCACATTTCAGAGAACTCACA 58.859 45.455 4.64 0.00 0.00 3.58
2823 3116 3.058639 GCCACATTTCAGAGAACTCACAC 60.059 47.826 4.64 0.00 0.00 3.82
2824 3117 3.499918 CCACATTTCAGAGAACTCACACC 59.500 47.826 4.64 0.00 0.00 4.16
2825 3118 3.499918 CACATTTCAGAGAACTCACACCC 59.500 47.826 4.64 0.00 0.00 4.61
2826 3119 2.526304 TTTCAGAGAACTCACACCCG 57.474 50.000 4.64 0.00 0.00 5.28
2827 3120 0.033504 TTCAGAGAACTCACACCCGC 59.966 55.000 4.64 0.00 0.00 6.13
2828 3121 1.374758 CAGAGAACTCACACCCGCC 60.375 63.158 4.64 0.00 0.00 6.13
2829 3122 1.837051 AGAGAACTCACACCCGCCA 60.837 57.895 4.64 0.00 0.00 5.69
2830 3123 1.194781 AGAGAACTCACACCCGCCAT 61.195 55.000 4.64 0.00 0.00 4.40
2831 3124 0.535335 GAGAACTCACACCCGCCATA 59.465 55.000 0.00 0.00 0.00 2.74
2832 3125 0.537188 AGAACTCACACCCGCCATAG 59.463 55.000 0.00 0.00 0.00 2.23
2833 3126 0.249398 GAACTCACACCCGCCATAGT 59.751 55.000 0.00 0.00 0.00 2.12
2834 3127 1.479323 GAACTCACACCCGCCATAGTA 59.521 52.381 0.00 0.00 0.00 1.82
2835 3128 0.822164 ACTCACACCCGCCATAGTAC 59.178 55.000 0.00 0.00 0.00 2.73
2836 3129 1.112113 CTCACACCCGCCATAGTACT 58.888 55.000 0.00 0.00 0.00 2.73
2837 3130 1.480954 CTCACACCCGCCATAGTACTT 59.519 52.381 0.00 0.00 0.00 2.24
2838 3131 1.903860 TCACACCCGCCATAGTACTTT 59.096 47.619 0.00 0.00 0.00 2.66
2839 3132 2.006888 CACACCCGCCATAGTACTTTG 58.993 52.381 0.00 3.05 0.00 2.77
2840 3133 1.014352 CACCCGCCATAGTACTTTGC 58.986 55.000 0.00 0.49 0.00 3.68
2841 3134 0.107361 ACCCGCCATAGTACTTTGCC 60.107 55.000 0.00 0.00 0.00 4.52
2842 3135 0.107410 CCCGCCATAGTACTTTGCCA 60.107 55.000 0.00 0.00 0.00 4.92
2843 3136 1.680555 CCCGCCATAGTACTTTGCCAA 60.681 52.381 0.00 0.00 0.00 4.52
2844 3137 1.670811 CCGCCATAGTACTTTGCCAAG 59.329 52.381 0.00 0.00 35.92 3.61
2845 3138 2.356135 CGCCATAGTACTTTGCCAAGT 58.644 47.619 8.41 8.41 45.73 3.16
2846 3139 2.095853 CGCCATAGTACTTTGCCAAGTG 59.904 50.000 13.20 0.00 43.54 3.16
2847 3140 3.343617 GCCATAGTACTTTGCCAAGTGA 58.656 45.455 13.20 0.00 43.54 3.41
2848 3141 3.756434 GCCATAGTACTTTGCCAAGTGAA 59.244 43.478 13.20 0.00 43.54 3.18
2849 3142 4.217550 GCCATAGTACTTTGCCAAGTGAAA 59.782 41.667 13.20 0.00 43.54 2.69
2850 3143 5.619981 GCCATAGTACTTTGCCAAGTGAAAG 60.620 44.000 13.20 2.10 43.54 2.62
2851 3144 5.705441 CCATAGTACTTTGCCAAGTGAAAGA 59.295 40.000 13.20 0.00 43.54 2.52
2852 3145 6.348540 CCATAGTACTTTGCCAAGTGAAAGAC 60.349 42.308 13.20 3.25 43.54 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
405 416 1.788308 CGGTCGACGCTTTCACTTTAA 59.212 47.619 9.92 0.00 34.82 1.52
406 417 1.411394 CGGTCGACGCTTTCACTTTA 58.589 50.000 9.92 0.00 34.82 1.85
487 498 1.607467 GGCATTGTTGGGAGGTGCT 60.607 57.895 0.00 0.00 36.15 4.40
488 499 1.470996 TTGGCATTGTTGGGAGGTGC 61.471 55.000 0.00 0.00 35.17 5.01
489 500 1.047002 TTTGGCATTGTTGGGAGGTG 58.953 50.000 0.00 0.00 0.00 4.00
490 501 2.028561 ATTTGGCATTGTTGGGAGGT 57.971 45.000 0.00 0.00 0.00 3.85
491 502 2.702261 CAATTTGGCATTGTTGGGAGG 58.298 47.619 0.00 0.00 0.00 4.30
543 554 1.270550 GCATGTCCTTCTTGTGGTTGG 59.729 52.381 0.00 0.00 0.00 3.77
552 563 3.972133 TCATCCATTTGCATGTCCTTCT 58.028 40.909 0.00 0.00 0.00 2.85
700 774 1.708193 TTCTTGCGAGCCATCATGCG 61.708 55.000 0.00 0.00 36.02 4.73
881 957 1.225855 GGCACGACACTCAATCAACA 58.774 50.000 0.00 0.00 0.00 3.33
959 1035 4.230502 AGGTAATTGGTTCCATGATCCAGT 59.769 41.667 0.00 0.00 33.64 4.00
972 1048 2.478292 AGGATCGTGGAGGTAATTGGT 58.522 47.619 0.00 0.00 0.00 3.67
1107 1183 0.685785 TAGCTGAGCCAGAGGACAGG 60.686 60.000 0.00 0.00 32.44 4.00
1286 1362 0.453390 GGCAACTGCATTAGACTGCC 59.547 55.000 3.76 2.17 45.07 4.85
1319 1395 2.294074 CGGAAGGTGGTTGAGAAACAA 58.706 47.619 0.00 0.00 36.02 2.83
1379 1458 4.235762 CCGGTCTATGGCGTGGGG 62.236 72.222 0.00 0.00 0.00 4.96
1814 1895 6.598753 AAGATTCGACGAACAGAAAGAAAA 57.401 33.333 13.38 0.00 0.00 2.29
1916 2167 5.048643 GGAACTAGCAACCTCTTCCTTTTTC 60.049 44.000 0.00 0.00 30.50 2.29
1924 2175 1.275573 GGTCGGAACTAGCAACCTCTT 59.724 52.381 0.00 0.00 0.00 2.85
2020 2275 7.117236 TGCTTTGATTGAGCATCTTTCAATTTC 59.883 33.333 2.41 0.00 44.63 2.17
2024 2279 5.456548 TGCTTTGATTGAGCATCTTTCAA 57.543 34.783 0.00 0.00 44.63 2.69
2088 2347 9.882996 CATAACATGTTGTGTATGGATTGTATC 57.117 33.333 23.01 0.00 41.14 2.24
2137 2398 4.940463 TCTTTTATCCCCTTGATACGACG 58.060 43.478 0.00 0.00 35.66 5.12
2533 2826 4.580995 AGGTTGAGTAGGAGACATATGACG 59.419 45.833 10.38 0.00 0.00 4.35
2536 2829 4.100035 TGCAGGTTGAGTAGGAGACATATG 59.900 45.833 0.00 0.00 0.00 1.78
2539 2832 2.540383 TGCAGGTTGAGTAGGAGACAT 58.460 47.619 0.00 0.00 0.00 3.06
2540 2833 2.009681 TGCAGGTTGAGTAGGAGACA 57.990 50.000 0.00 0.00 0.00 3.41
2583 2876 1.945354 ATGTACCCTGTCGAGCACCG 61.945 60.000 0.00 0.00 40.25 4.94
2591 2884 1.470098 CAAAGCTGCATGTACCCTGTC 59.530 52.381 1.02 0.00 0.00 3.51
2604 2897 0.859232 ACGTACGACAAGCAAAGCTG 59.141 50.000 24.41 0.00 39.62 4.24
2605 2898 2.325761 CTACGTACGACAAGCAAAGCT 58.674 47.619 24.41 0.00 42.56 3.74
2606 2899 1.201780 GCTACGTACGACAAGCAAAGC 60.202 52.381 24.41 12.37 35.05 3.51
2607 2900 2.325761 AGCTACGTACGACAAGCAAAG 58.674 47.619 29.25 13.91 37.44 2.77
2608 2901 2.427232 AGCTACGTACGACAAGCAAA 57.573 45.000 29.25 6.52 37.44 3.68
2609 2902 3.495193 CTTAGCTACGTACGACAAGCAA 58.505 45.455 29.25 22.36 37.44 3.91
2610 2903 2.730090 GCTTAGCTACGTACGACAAGCA 60.730 50.000 29.25 18.86 37.46 3.91
2611 2904 1.844962 GCTTAGCTACGTACGACAAGC 59.155 52.381 24.41 24.31 35.16 4.01
2612 2905 3.402058 AGCTTAGCTACGTACGACAAG 57.598 47.619 24.41 16.27 36.99 3.16
2613 2906 4.183865 TCTAGCTTAGCTACGTACGACAA 58.816 43.478 24.41 5.91 40.44 3.18
2614 2907 3.785486 TCTAGCTTAGCTACGTACGACA 58.215 45.455 24.41 8.23 40.44 4.35
2615 2908 3.184178 CCTCTAGCTTAGCTACGTACGAC 59.816 52.174 24.41 10.85 40.44 4.34
2616 2909 3.068732 TCCTCTAGCTTAGCTACGTACGA 59.931 47.826 24.41 5.02 40.44 3.43
2617 2910 3.184178 GTCCTCTAGCTTAGCTACGTACG 59.816 52.174 15.01 15.01 40.44 3.67
2618 2911 3.184178 CGTCCTCTAGCTTAGCTACGTAC 59.816 52.174 10.21 5.69 40.44 3.67
2619 2912 3.388308 CGTCCTCTAGCTTAGCTACGTA 58.612 50.000 10.21 0.00 40.44 3.57
2620 2913 2.211806 CGTCCTCTAGCTTAGCTACGT 58.788 52.381 10.21 0.00 40.44 3.57
2621 2914 1.532007 CCGTCCTCTAGCTTAGCTACG 59.468 57.143 16.60 16.60 40.44 3.51
2622 2915 2.809696 CTCCGTCCTCTAGCTTAGCTAC 59.190 54.545 10.21 1.80 40.44 3.58
2623 2916 2.704596 TCTCCGTCCTCTAGCTTAGCTA 59.295 50.000 13.70 13.70 40.44 3.32
2624 2917 1.491332 TCTCCGTCCTCTAGCTTAGCT 59.509 52.381 12.67 12.67 43.41 3.32
2625 2918 1.877443 CTCTCCGTCCTCTAGCTTAGC 59.123 57.143 0.00 0.00 0.00 3.09
2626 2919 3.478857 TCTCTCCGTCCTCTAGCTTAG 57.521 52.381 0.00 0.00 0.00 2.18
2627 2920 3.928005 TTCTCTCCGTCCTCTAGCTTA 57.072 47.619 0.00 0.00 0.00 3.09
2628 2921 2.810870 TTCTCTCCGTCCTCTAGCTT 57.189 50.000 0.00 0.00 0.00 3.74
2629 2922 2.810870 TTTCTCTCCGTCCTCTAGCT 57.189 50.000 0.00 0.00 0.00 3.32
2630 2923 5.465935 CATTATTTCTCTCCGTCCTCTAGC 58.534 45.833 0.00 0.00 0.00 3.42
2631 2924 5.770663 TCCATTATTTCTCTCCGTCCTCTAG 59.229 44.000 0.00 0.00 0.00 2.43
2632 2925 5.702266 TCCATTATTTCTCTCCGTCCTCTA 58.298 41.667 0.00 0.00 0.00 2.43
2633 2926 4.547671 TCCATTATTTCTCTCCGTCCTCT 58.452 43.478 0.00 0.00 0.00 3.69
2634 2927 4.342665 ACTCCATTATTTCTCTCCGTCCTC 59.657 45.833 0.00 0.00 0.00 3.71
2635 2928 4.290942 ACTCCATTATTTCTCTCCGTCCT 58.709 43.478 0.00 0.00 0.00 3.85
2636 2929 4.674281 ACTCCATTATTTCTCTCCGTCC 57.326 45.455 0.00 0.00 0.00 4.79
2637 2930 8.113173 ACTATACTCCATTATTTCTCTCCGTC 57.887 38.462 0.00 0.00 0.00 4.79
2638 2931 7.094720 CGACTATACTCCATTATTTCTCTCCGT 60.095 40.741 0.00 0.00 0.00 4.69
2639 2932 7.119407 TCGACTATACTCCATTATTTCTCTCCG 59.881 40.741 0.00 0.00 0.00 4.63
2640 2933 8.338072 TCGACTATACTCCATTATTTCTCTCC 57.662 38.462 0.00 0.00 0.00 3.71
2641 2934 9.834628 CTTCGACTATACTCCATTATTTCTCTC 57.165 37.037 0.00 0.00 0.00 3.20
2642 2935 9.357161 ACTTCGACTATACTCCATTATTTCTCT 57.643 33.333 0.00 0.00 0.00 3.10
2643 2936 9.400638 CACTTCGACTATACTCCATTATTTCTC 57.599 37.037 0.00 0.00 0.00 2.87
2644 2937 8.361139 CCACTTCGACTATACTCCATTATTTCT 58.639 37.037 0.00 0.00 0.00 2.52
2645 2938 8.358148 TCCACTTCGACTATACTCCATTATTTC 58.642 37.037 0.00 0.00 0.00 2.17
2646 2939 8.246430 TCCACTTCGACTATACTCCATTATTT 57.754 34.615 0.00 0.00 0.00 1.40
2647 2940 7.724506 TCTCCACTTCGACTATACTCCATTATT 59.275 37.037 0.00 0.00 0.00 1.40
2648 2941 7.232188 TCTCCACTTCGACTATACTCCATTAT 58.768 38.462 0.00 0.00 0.00 1.28
2649 2942 6.598503 TCTCCACTTCGACTATACTCCATTA 58.401 40.000 0.00 0.00 0.00 1.90
2650 2943 5.446860 TCTCCACTTCGACTATACTCCATT 58.553 41.667 0.00 0.00 0.00 3.16
2651 2944 5.050126 TCTCCACTTCGACTATACTCCAT 57.950 43.478 0.00 0.00 0.00 3.41
2652 2945 4.452825 CTCTCCACTTCGACTATACTCCA 58.547 47.826 0.00 0.00 0.00 3.86
2653 2946 3.816523 CCTCTCCACTTCGACTATACTCC 59.183 52.174 0.00 0.00 0.00 3.85
2654 2947 4.706035 TCCTCTCCACTTCGACTATACTC 58.294 47.826 0.00 0.00 0.00 2.59
2655 2948 4.409574 TCTCCTCTCCACTTCGACTATACT 59.590 45.833 0.00 0.00 0.00 2.12
2656 2949 4.706035 TCTCCTCTCCACTTCGACTATAC 58.294 47.826 0.00 0.00 0.00 1.47
2657 2950 5.369409 TTCTCCTCTCCACTTCGACTATA 57.631 43.478 0.00 0.00 0.00 1.31
2658 2951 3.935818 TCTCCTCTCCACTTCGACTAT 57.064 47.619 0.00 0.00 0.00 2.12
2659 2952 3.715638 TTCTCCTCTCCACTTCGACTA 57.284 47.619 0.00 0.00 0.00 2.59
2660 2953 2.588464 TTCTCCTCTCCACTTCGACT 57.412 50.000 0.00 0.00 0.00 4.18
2661 2954 2.820787 TCTTTCTCCTCTCCACTTCGAC 59.179 50.000 0.00 0.00 0.00 4.20
2662 2955 3.085533 CTCTTTCTCCTCTCCACTTCGA 58.914 50.000 0.00 0.00 0.00 3.71
2663 2956 3.085533 TCTCTTTCTCCTCTCCACTTCG 58.914 50.000 0.00 0.00 0.00 3.79
2664 2957 3.447229 CCTCTCTTTCTCCTCTCCACTTC 59.553 52.174 0.00 0.00 0.00 3.01
2665 2958 3.076785 TCCTCTCTTTCTCCTCTCCACTT 59.923 47.826 0.00 0.00 0.00 3.16
2666 2959 2.652348 TCCTCTCTTTCTCCTCTCCACT 59.348 50.000 0.00 0.00 0.00 4.00
2667 2960 3.094484 TCCTCTCTTTCTCCTCTCCAC 57.906 52.381 0.00 0.00 0.00 4.02
2668 2961 4.141041 CCTATCCTCTCTTTCTCCTCTCCA 60.141 50.000 0.00 0.00 0.00 3.86
2669 2962 4.407365 CCTATCCTCTCTTTCTCCTCTCC 58.593 52.174 0.00 0.00 0.00 3.71
2670 2963 3.826729 GCCTATCCTCTCTTTCTCCTCTC 59.173 52.174 0.00 0.00 0.00 3.20
2671 2964 3.750599 CGCCTATCCTCTCTTTCTCCTCT 60.751 52.174 0.00 0.00 0.00 3.69
2672 2965 2.556622 CGCCTATCCTCTCTTTCTCCTC 59.443 54.545 0.00 0.00 0.00 3.71
2673 2966 2.593026 CGCCTATCCTCTCTTTCTCCT 58.407 52.381 0.00 0.00 0.00 3.69
2674 2967 1.616374 CCGCCTATCCTCTCTTTCTCC 59.384 57.143 0.00 0.00 0.00 3.71
2675 2968 1.616374 CCCGCCTATCCTCTCTTTCTC 59.384 57.143 0.00 0.00 0.00 2.87
2676 2969 1.710816 CCCGCCTATCCTCTCTTTCT 58.289 55.000 0.00 0.00 0.00 2.52
2677 2970 0.682292 CCCCGCCTATCCTCTCTTTC 59.318 60.000 0.00 0.00 0.00 2.62
2678 2971 0.764752 CCCCCGCCTATCCTCTCTTT 60.765 60.000 0.00 0.00 0.00 2.52
2679 2972 1.152226 CCCCCGCCTATCCTCTCTT 60.152 63.158 0.00 0.00 0.00 2.85
2680 2973 2.087857 CTCCCCCGCCTATCCTCTCT 62.088 65.000 0.00 0.00 0.00 3.10
2681 2974 1.608046 CTCCCCCGCCTATCCTCTC 60.608 68.421 0.00 0.00 0.00 3.20
2682 2975 2.374781 GACTCCCCCGCCTATCCTCT 62.375 65.000 0.00 0.00 0.00 3.69
2683 2976 1.909287 GACTCCCCCGCCTATCCTC 60.909 68.421 0.00 0.00 0.00 3.71
2684 2977 1.962570 AAGACTCCCCCGCCTATCCT 61.963 60.000 0.00 0.00 0.00 3.24
2685 2978 1.459730 AAGACTCCCCCGCCTATCC 60.460 63.158 0.00 0.00 0.00 2.59
2686 2979 1.049289 ACAAGACTCCCCCGCCTATC 61.049 60.000 0.00 0.00 0.00 2.08
2687 2980 1.003051 ACAAGACTCCCCCGCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
2688 2981 1.987855 CACAAGACTCCCCCGCCTA 60.988 63.158 0.00 0.00 0.00 3.93
2689 2982 3.322466 CACAAGACTCCCCCGCCT 61.322 66.667 0.00 0.00 0.00 5.52
2690 2983 2.890766 TTCACAAGACTCCCCCGCC 61.891 63.158 0.00 0.00 0.00 6.13
2691 2984 1.671379 GTTCACAAGACTCCCCCGC 60.671 63.158 0.00 0.00 0.00 6.13
2692 2985 1.374252 CGTTCACAAGACTCCCCCG 60.374 63.158 0.00 0.00 0.00 5.73
2693 2986 1.003718 CCGTTCACAAGACTCCCCC 60.004 63.158 0.00 0.00 0.00 5.40
2694 2987 0.395312 TTCCGTTCACAAGACTCCCC 59.605 55.000 0.00 0.00 0.00 4.81
2695 2988 1.608283 CCTTCCGTTCACAAGACTCCC 60.608 57.143 0.00 0.00 0.00 4.30
2696 2989 1.343465 TCCTTCCGTTCACAAGACTCC 59.657 52.381 0.00 0.00 0.00 3.85
2697 2990 2.814280 TCCTTCCGTTCACAAGACTC 57.186 50.000 0.00 0.00 0.00 3.36
2698 2991 2.698797 TCTTCCTTCCGTTCACAAGACT 59.301 45.455 0.00 0.00 0.00 3.24
2699 2992 3.060602 CTCTTCCTTCCGTTCACAAGAC 58.939 50.000 0.00 0.00 0.00 3.01
2700 2993 2.963101 TCTCTTCCTTCCGTTCACAAGA 59.037 45.455 0.00 0.00 0.00 3.02
2701 2994 3.005897 TCTCTCTTCCTTCCGTTCACAAG 59.994 47.826 0.00 0.00 0.00 3.16
2702 2995 2.963101 TCTCTCTTCCTTCCGTTCACAA 59.037 45.455 0.00 0.00 0.00 3.33
2703 2996 2.296471 GTCTCTCTTCCTTCCGTTCACA 59.704 50.000 0.00 0.00 0.00 3.58
2704 2997 2.668834 CGTCTCTCTTCCTTCCGTTCAC 60.669 54.545 0.00 0.00 0.00 3.18
2705 2998 1.540267 CGTCTCTCTTCCTTCCGTTCA 59.460 52.381 0.00 0.00 0.00 3.18
2706 2999 1.811359 TCGTCTCTCTTCCTTCCGTTC 59.189 52.381 0.00 0.00 0.00 3.95
2707 3000 1.813786 CTCGTCTCTCTTCCTTCCGTT 59.186 52.381 0.00 0.00 0.00 4.44
2708 3001 1.271488 ACTCGTCTCTCTTCCTTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
2709 3002 1.131504 CACTCGTCTCTCTTCCTTCCG 59.868 57.143 0.00 0.00 0.00 4.30
2710 3003 1.474879 CCACTCGTCTCTCTTCCTTCC 59.525 57.143 0.00 0.00 0.00 3.46
2711 3004 2.164338 ACCACTCGTCTCTCTTCCTTC 58.836 52.381 0.00 0.00 0.00 3.46
2712 3005 2.296073 ACCACTCGTCTCTCTTCCTT 57.704 50.000 0.00 0.00 0.00 3.36
2713 3006 2.296073 AACCACTCGTCTCTCTTCCT 57.704 50.000 0.00 0.00 0.00 3.36
2714 3007 2.296471 TCAAACCACTCGTCTCTCTTCC 59.704 50.000 0.00 0.00 0.00 3.46
2715 3008 3.243434 TGTCAAACCACTCGTCTCTCTTC 60.243 47.826 0.00 0.00 0.00 2.87
2716 3009 2.693591 TGTCAAACCACTCGTCTCTCTT 59.306 45.455 0.00 0.00 0.00 2.85
2717 3010 2.307768 TGTCAAACCACTCGTCTCTCT 58.692 47.619 0.00 0.00 0.00 3.10
2718 3011 2.795175 TGTCAAACCACTCGTCTCTC 57.205 50.000 0.00 0.00 0.00 3.20
2719 3012 3.753294 ATTGTCAAACCACTCGTCTCT 57.247 42.857 0.00 0.00 0.00 3.10
2720 3013 4.527564 CAAATTGTCAAACCACTCGTCTC 58.472 43.478 0.00 0.00 0.00 3.36
2721 3014 3.315191 CCAAATTGTCAAACCACTCGTCT 59.685 43.478 0.00 0.00 0.00 4.18
2722 3015 3.550030 CCCAAATTGTCAAACCACTCGTC 60.550 47.826 0.00 0.00 0.00 4.20
2723 3016 2.360801 CCCAAATTGTCAAACCACTCGT 59.639 45.455 0.00 0.00 0.00 4.18
2724 3017 2.621055 TCCCAAATTGTCAAACCACTCG 59.379 45.455 0.00 0.00 0.00 4.18
2725 3018 4.321974 GGATCCCAAATTGTCAAACCACTC 60.322 45.833 0.00 0.00 0.00 3.51
2726 3019 3.578282 GGATCCCAAATTGTCAAACCACT 59.422 43.478 0.00 0.00 0.00 4.00
2727 3020 3.323403 TGGATCCCAAATTGTCAAACCAC 59.677 43.478 9.90 0.00 0.00 4.16
2728 3021 3.577848 CTGGATCCCAAATTGTCAAACCA 59.422 43.478 9.90 0.00 30.80 3.67
2729 3022 3.055891 CCTGGATCCCAAATTGTCAAACC 60.056 47.826 9.90 0.00 30.80 3.27
2730 3023 3.578282 ACCTGGATCCCAAATTGTCAAAC 59.422 43.478 9.90 0.00 30.80 2.93
2731 3024 3.855668 ACCTGGATCCCAAATTGTCAAA 58.144 40.909 9.90 0.00 30.80 2.69
2732 3025 3.541242 ACCTGGATCCCAAATTGTCAA 57.459 42.857 9.90 0.00 30.80 3.18
2733 3026 4.386312 GGATACCTGGATCCCAAATTGTCA 60.386 45.833 9.90 0.00 39.74 3.58
2734 3027 4.141158 AGGATACCTGGATCCCAAATTGTC 60.141 45.833 9.90 0.00 45.85 3.18
2735 3028 3.793827 AGGATACCTGGATCCCAAATTGT 59.206 43.478 9.90 0.00 45.85 2.71
2736 3029 4.105377 AGAGGATACCTGGATCCCAAATTG 59.895 45.833 9.90 0.00 45.85 2.32
2737 3030 4.319515 AGAGGATACCTGGATCCCAAATT 58.680 43.478 9.90 0.00 45.85 1.82
2738 3031 3.913163 GAGAGGATACCTGGATCCCAAAT 59.087 47.826 9.90 0.00 45.85 2.32
2739 3032 3.311327 TGAGAGGATACCTGGATCCCAAA 60.311 47.826 9.90 0.00 45.85 3.28
2740 3033 2.250008 TGAGAGGATACCTGGATCCCAA 59.750 50.000 9.90 0.00 45.85 4.12
2741 3034 1.866269 TGAGAGGATACCTGGATCCCA 59.134 52.381 9.90 8.85 45.85 4.37
2742 3035 2.704190 TGAGAGGATACCTGGATCCC 57.296 55.000 9.90 7.82 45.85 3.85
2743 3036 6.882768 ATATTTGAGAGGATACCTGGATCC 57.117 41.667 4.20 4.20 45.16 3.36
2766 3059 8.573035 GCGAGTGGGGAATGATAAAAATATTAA 58.427 33.333 0.00 0.00 0.00 1.40
2767 3060 7.175990 GGCGAGTGGGGAATGATAAAAATATTA 59.824 37.037 0.00 0.00 0.00 0.98
2768 3061 6.015434 GGCGAGTGGGGAATGATAAAAATATT 60.015 38.462 0.00 0.00 0.00 1.28
2769 3062 5.476945 GGCGAGTGGGGAATGATAAAAATAT 59.523 40.000 0.00 0.00 0.00 1.28
2770 3063 4.825085 GGCGAGTGGGGAATGATAAAAATA 59.175 41.667 0.00 0.00 0.00 1.40
2771 3064 3.636764 GGCGAGTGGGGAATGATAAAAAT 59.363 43.478 0.00 0.00 0.00 1.82
2772 3065 3.020984 GGCGAGTGGGGAATGATAAAAA 58.979 45.455 0.00 0.00 0.00 1.94
2773 3066 2.025793 TGGCGAGTGGGGAATGATAAAA 60.026 45.455 0.00 0.00 0.00 1.52
2774 3067 1.562008 TGGCGAGTGGGGAATGATAAA 59.438 47.619 0.00 0.00 0.00 1.40
2775 3068 1.208706 TGGCGAGTGGGGAATGATAA 58.791 50.000 0.00 0.00 0.00 1.75
2776 3069 1.208706 TTGGCGAGTGGGGAATGATA 58.791 50.000 0.00 0.00 0.00 2.15
2777 3070 0.552848 ATTGGCGAGTGGGGAATGAT 59.447 50.000 0.00 0.00 0.00 2.45
2778 3071 0.331278 AATTGGCGAGTGGGGAATGA 59.669 50.000 0.00 0.00 0.00 2.57
2779 3072 0.457035 CAATTGGCGAGTGGGGAATG 59.543 55.000 0.00 0.00 0.00 2.67
2780 3073 0.039618 ACAATTGGCGAGTGGGGAAT 59.960 50.000 10.83 0.00 0.00 3.01
2781 3074 0.893270 CACAATTGGCGAGTGGGGAA 60.893 55.000 10.83 0.00 0.00 3.97
2782 3075 1.303236 CACAATTGGCGAGTGGGGA 60.303 57.895 10.83 0.00 0.00 4.81
2783 3076 2.342650 CCACAATTGGCGAGTGGGG 61.343 63.158 9.42 9.42 46.98 4.96
2784 3077 3.277133 CCACAATTGGCGAGTGGG 58.723 61.111 10.83 1.70 46.98 4.61
2792 3085 2.299582 TCTGAAATGTGGCCACAATTGG 59.700 45.455 37.55 28.25 45.41 3.16
2793 3086 3.256383 TCTCTGAAATGTGGCCACAATTG 59.744 43.478 37.55 25.62 45.41 2.32
2794 3087 3.499338 TCTCTGAAATGTGGCCACAATT 58.501 40.909 40.48 37.12 45.41 2.32
2795 3088 3.159213 TCTCTGAAATGTGGCCACAAT 57.841 42.857 40.48 31.25 45.41 2.71
2796 3089 2.622942 GTTCTCTGAAATGTGGCCACAA 59.377 45.455 40.48 24.01 45.41 3.33
2797 3090 2.158623 AGTTCTCTGAAATGTGGCCACA 60.159 45.455 39.23 39.23 46.44 4.17
2798 3091 2.485814 GAGTTCTCTGAAATGTGGCCAC 59.514 50.000 29.67 29.67 0.00 5.01
2799 3092 2.106338 TGAGTTCTCTGAAATGTGGCCA 59.894 45.455 0.00 0.00 0.00 5.36
2800 3093 2.485814 GTGAGTTCTCTGAAATGTGGCC 59.514 50.000 0.00 0.00 0.00 5.36
2801 3094 3.058639 GTGTGAGTTCTCTGAAATGTGGC 60.059 47.826 1.53 0.00 0.00 5.01
2802 3095 3.499918 GGTGTGAGTTCTCTGAAATGTGG 59.500 47.826 1.53 0.00 0.00 4.17
2803 3096 3.499918 GGGTGTGAGTTCTCTGAAATGTG 59.500 47.826 1.53 0.00 0.00 3.21
2804 3097 3.744660 GGGTGTGAGTTCTCTGAAATGT 58.255 45.455 1.53 0.00 0.00 2.71
2805 3098 2.738846 CGGGTGTGAGTTCTCTGAAATG 59.261 50.000 1.53 0.00 0.00 2.32
2806 3099 2.872038 GCGGGTGTGAGTTCTCTGAAAT 60.872 50.000 1.53 0.00 0.00 2.17
2807 3100 1.540363 GCGGGTGTGAGTTCTCTGAAA 60.540 52.381 1.53 0.00 0.00 2.69
2808 3101 0.033504 GCGGGTGTGAGTTCTCTGAA 59.966 55.000 1.53 0.00 0.00 3.02
2809 3102 1.666011 GCGGGTGTGAGTTCTCTGA 59.334 57.895 1.53 0.00 0.00 3.27
2810 3103 1.374758 GGCGGGTGTGAGTTCTCTG 60.375 63.158 1.53 0.00 0.00 3.35
2811 3104 1.194781 ATGGCGGGTGTGAGTTCTCT 61.195 55.000 1.53 0.00 0.00 3.10
2812 3105 0.535335 TATGGCGGGTGTGAGTTCTC 59.465 55.000 0.00 0.00 0.00 2.87
2813 3106 0.537188 CTATGGCGGGTGTGAGTTCT 59.463 55.000 0.00 0.00 0.00 3.01
2814 3107 0.249398 ACTATGGCGGGTGTGAGTTC 59.751 55.000 0.00 0.00 0.00 3.01
2815 3108 1.206371 GTACTATGGCGGGTGTGAGTT 59.794 52.381 0.00 0.00 0.00 3.01
2816 3109 0.822164 GTACTATGGCGGGTGTGAGT 59.178 55.000 0.00 0.00 0.00 3.41
2817 3110 1.112113 AGTACTATGGCGGGTGTGAG 58.888 55.000 0.00 0.00 0.00 3.51
2818 3111 1.563924 AAGTACTATGGCGGGTGTGA 58.436 50.000 0.00 0.00 0.00 3.58
2819 3112 2.006888 CAAAGTACTATGGCGGGTGTG 58.993 52.381 0.00 0.00 0.00 3.82
2820 3113 1.677820 GCAAAGTACTATGGCGGGTGT 60.678 52.381 0.00 0.00 0.00 4.16
2821 3114 1.014352 GCAAAGTACTATGGCGGGTG 58.986 55.000 0.00 0.00 0.00 4.61
2822 3115 0.107361 GGCAAAGTACTATGGCGGGT 60.107 55.000 0.00 0.00 32.19 5.28
2823 3116 0.107410 TGGCAAAGTACTATGGCGGG 60.107 55.000 0.00 0.00 44.38 6.13
2824 3117 1.670811 CTTGGCAAAGTACTATGGCGG 59.329 52.381 0.00 0.00 44.38 6.13
2825 3118 2.095853 CACTTGGCAAAGTACTATGGCG 59.904 50.000 6.06 0.00 45.07 5.69
2826 3119 3.343617 TCACTTGGCAAAGTACTATGGC 58.656 45.455 6.06 0.00 45.07 4.40
2827 3120 5.705441 TCTTTCACTTGGCAAAGTACTATGG 59.295 40.000 6.06 0.00 45.07 2.74
2828 3121 6.603095 GTCTTTCACTTGGCAAAGTACTATG 58.397 40.000 6.06 0.00 45.07 2.23
2829 3122 6.803154 GTCTTTCACTTGGCAAAGTACTAT 57.197 37.500 6.06 0.00 45.07 2.12


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

AutoCloner maintained by Alex Coulton.