Multiple sequence alignment - TraesCS5A01G094600

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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 TraesCS5A01G094600 chr5A 100.000 2958 0 0 1 2958 131646282 131643325 0.000000e+00 5463.0
1 TraesCS5A01G094600 chr5B 93.866 1777 59 24 383 2116 133894262 133892493 0.000000e+00 2632.0
2 TraesCS5A01G094600 chr5B 92.791 430 26 2 2145 2569 133892496 133892067 4.190000e-173 617.0
3 TraesCS5A01G094600 chr5B 96.215 317 12 0 1 317 133894577 133894261 1.220000e-143 520.0
4 TraesCS5A01G094600 chr5D 95.936 1255 32 4 556 1793 120789777 120788525 0.000000e+00 2017.0
5 TraesCS5A01G094600 chr5D 93.156 789 45 8 1883 2667 120788521 120787738 0.000000e+00 1149.0
6 TraesCS5A01G094600 chr5D 92.857 476 32 1 1 476 120790250 120789777 0.000000e+00 689.0
7 TraesCS5A01G094600 chr5D 88.542 96 10 1 465 559 498655274 498655369 6.700000e-22 115.0
8 TraesCS5A01G094600 chr5D 88.636 88 10 0 472 559 430065272 430065185 1.120000e-19 108.0
9 TraesCS5A01G094600 chr5D 93.548 62 4 0 2651 2712 120787715 120787654 3.140000e-15 93.5
10 TraesCS5A01G094600 chr1D 88.400 250 28 1 2710 2958 33389363 33389612 1.720000e-77 300.0
11 TraesCS5A01G094600 chr1D 84.167 120 10 7 451 562 260568823 260568941 1.120000e-19 108.0
12 TraesCS5A01G094600 chr1A 88.608 237 24 3 2723 2958 386793686 386793920 4.830000e-73 285.0
13 TraesCS5A01G094600 chr1A 85.062 241 35 1 2719 2958 360042654 360042894 8.190000e-61 244.0
14 TraesCS5A01G094600 chr1A 89.362 94 10 0 465 558 396427717 396427624 5.180000e-23 119.0
15 TraesCS5A01G094600 chr6A 91.765 85 7 0 475 559 616434185 616434269 5.180000e-23 119.0
16 TraesCS5A01G094600 chr6A 90.588 85 8 0 475 559 616583904 616583988 2.410000e-21 113.0
17 TraesCS5A01G094600 chr7B 90.588 85 8 0 475 559 203137495 203137579 2.410000e-21 113.0
18 TraesCS5A01G094600 chr7D 83.146 89 15 0 472 560 124782780 124782692 6.800000e-12 82.4
19 TraesCS5A01G094600 chr7D 82.667 75 10 2 2573 2646 228665608 228665680 2.460000e-06 63.9
20 TraesCS5A01G094600 chr2A 87.879 66 8 0 2579 2644 613691170 613691235 8.790000e-11 78.7


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 TraesCS5A01G094600 chr5A 131643325 131646282 2957 True 5463.000000 5463 100.000000 1 2958 1 chr5A.!!$R1 2957
1 TraesCS5A01G094600 chr5B 133892067 133894577 2510 True 1256.333333 2632 94.290667 1 2569 3 chr5B.!!$R1 2568
2 TraesCS5A01G094600 chr5D 120787654 120790250 2596 True 987.125000 2017 93.874250 1 2712 4 chr5D.!!$R2 2711

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
179 180 0.318360 TTCGTGTGTGCGATTCTCGT 60.318 50.0 0.0 0.0 42.81 4.18 F
1007 1025 0.762082 TGCTGCCAAACCATCCCAAA 60.762 50.0 0.0 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1835 0.034896 AGCCCAACCTGTACTTCACG 59.965 55.0 0.0 0.0 0.00 4.35 R
2894 2997 0.038599 ATTGGTGGAGCAGCATGACA 59.961 50.0 0.0 0.0 41.53 3.58 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
41 42 7.254522 GCAGTGACAAAATTTGTGTGATCAAAT 60.255 33.333 16.78 0.00 45.52 2.32
125 126 4.661993 TCACTGATAACAAATCGTGTGC 57.338 40.909 0.00 0.00 40.60 4.57
134 135 4.771590 ACAAATCGTGTGCATTGAATCT 57.228 36.364 2.61 0.00 39.72 2.40
179 180 0.318360 TTCGTGTGTGCGATTCTCGT 60.318 50.000 0.00 0.00 42.81 4.18
269 270 1.070577 GTGTGTGATTGACTGTGCGAC 60.071 52.381 0.00 0.00 0.00 5.19
310 311 5.227238 GCAATGAGCATATATGTACTGGC 57.773 43.478 14.14 7.83 44.79 4.85
313 314 2.233676 TGAGCATATATGTACTGGCGGG 59.766 50.000 14.14 0.00 0.00 6.13
315 316 2.903784 AGCATATATGTACTGGCGGGAA 59.096 45.455 14.14 0.00 0.00 3.97
320 321 6.542370 GCATATATGTACTGGCGGGAATTTAT 59.458 38.462 14.14 0.00 0.00 1.40
371 372 9.181061 GGACTACAATTAAGTTATGCCCTAAAA 57.819 33.333 0.00 0.00 0.00 1.52
448 449 9.434275 TCTCTTACCAATATTATGAGTCCAGAA 57.566 33.333 0.00 0.00 0.00 3.02
453 454 7.283329 ACCAATATTATGAGTCCAGAACCTTC 58.717 38.462 0.00 0.00 0.00 3.46
487 488 8.392479 AGATTTTATATAGTACTCCCTCCGTCT 58.608 37.037 0.00 0.00 0.00 4.18
498 499 7.830201 AGTACTCCCTCCGTCTCATAATATAAG 59.170 40.741 0.00 0.00 0.00 1.73
503 504 6.202937 CCTCCGTCTCATAATATAAGATCGC 58.797 44.000 0.00 0.00 0.00 4.58
504 505 6.132791 TCCGTCTCATAATATAAGATCGCC 57.867 41.667 0.00 0.00 0.00 5.54
520 521 1.678627 TCGCCTTGCAAGCTAAAACAA 59.321 42.857 21.43 0.00 0.00 2.83
534 535 9.109533 CAAGCTAAAACAATTTGCAAAATGATC 57.890 29.630 29.22 9.39 0.00 2.92
593 594 1.474879 GCAAGCTTAACCGGCCAAATA 59.525 47.619 0.00 0.00 0.00 1.40
594 595 2.094442 GCAAGCTTAACCGGCCAAATAA 60.094 45.455 0.00 0.00 0.00 1.40
799 809 2.159254 GCCACTGCTTGTTGAAGTTTGA 60.159 45.455 0.00 0.00 30.38 2.69
816 826 3.564053 TTGAACCCAAAACCGTCTAGT 57.436 42.857 0.00 0.00 0.00 2.57
1007 1025 0.762082 TGCTGCCAAACCATCCCAAA 60.762 50.000 0.00 0.00 0.00 3.28
1099 1126 1.508088 CTTCCATCACTTTGCCGCC 59.492 57.895 0.00 0.00 0.00 6.13
1559 1586 9.696572 AGAATAATCTAAGTGACCTAGTGTGTA 57.303 33.333 0.00 0.00 32.88 2.90
1778 1835 6.689669 CGTTTTCATCCCAACCGTATATTTTC 59.310 38.462 0.00 0.00 0.00 2.29
1801 1858 0.989602 AAGTACAGGTTGGGCTACCC 59.010 55.000 0.00 0.00 45.71 3.69
1820 1877 6.128172 GCTACCCATTTGCTATGACATGTATC 60.128 42.308 0.00 0.00 0.00 2.24
1821 1878 4.756642 ACCCATTTGCTATGACATGTATCG 59.243 41.667 0.00 0.00 0.00 2.92
1874 1931 6.976349 GGATTTATATATCCGCACACGATACA 59.024 38.462 6.47 0.00 43.93 2.29
1881 1938 3.586892 TCCGCACACGATACATTAACAA 58.413 40.909 0.00 0.00 43.93 2.83
1935 1992 1.555075 ACGGCCTCTGTATCATTGTGT 59.445 47.619 0.00 0.00 0.00 3.72
1938 1995 2.098117 GGCCTCTGTATCATTGTGTTGC 59.902 50.000 0.00 0.00 0.00 4.17
2058 2117 7.848223 TTACATGACTCAAACACATATCCTG 57.152 36.000 0.00 0.00 0.00 3.86
2123 2182 6.642707 ATTAACCGAAACATGTTTTCCTGA 57.357 33.333 24.02 10.19 32.11 3.86
2143 2202 1.800805 ATGTCAACGCAGTCTCCAAG 58.199 50.000 0.00 0.00 45.00 3.61
2159 2218 9.442047 CAGTCTCCAAGATGTAGATAAGTTTTT 57.558 33.333 0.00 0.00 0.00 1.94
2358 2423 8.049117 TGGAACAAGTCTCTTTGCATATAAGAT 58.951 33.333 0.00 0.00 31.92 2.40
2382 2447 5.050295 TCACTATATAGCACGTGAGTTCTCG 60.050 44.000 22.23 4.48 46.40 4.04
2390 2455 3.244579 GCACGTGAGTTCTCGTACTTTTT 59.755 43.478 22.23 0.00 46.40 1.94
2396 2461 6.636044 CGTGAGTTCTCGTACTTTTTACTCTT 59.364 38.462 0.00 0.00 33.50 2.85
2413 2478 5.186996 ACTCTTGTGTGAAAAATCGCATT 57.813 34.783 0.00 0.00 32.43 3.56
2430 2495 4.333649 TCGCATTTGAAAATTTGGTTTGCA 59.666 33.333 11.48 0.00 33.39 4.08
2432 2497 5.052502 CGCATTTGAAAATTTGGTTTGCAAC 60.053 36.000 0.00 0.00 43.47 4.17
2566 2631 1.827789 TGCTGCGCAGAAAACCCTT 60.828 52.632 40.21 0.00 33.32 3.95
2570 2635 2.695359 CTGCGCAGAAAACCCTTACTA 58.305 47.619 33.66 0.00 0.00 1.82
2576 2641 5.506815 GCGCAGAAAACCCTTACTAAAGTTT 60.507 40.000 0.30 0.00 34.02 2.66
2605 2670 0.898789 TTCTCGTGACTCCAGGGACC 60.899 60.000 0.00 0.00 0.00 4.46
2623 2688 1.486310 ACCATATCTCGGTGTGTGCAT 59.514 47.619 0.00 0.00 34.69 3.96
2649 2714 4.631813 GCAAACACATTAGTCCCTCACTAG 59.368 45.833 0.00 0.00 38.90 2.57
2660 2763 2.642311 TCCCTCACTAGATTGCACCAAA 59.358 45.455 0.00 0.00 0.00 3.28
2701 2804 4.272489 CAAGATAAGTTCCTGGGCAATCA 58.728 43.478 0.00 0.00 0.00 2.57
2712 2815 0.623723 GGGCAATCACCCCTAGTCAA 59.376 55.000 0.00 0.00 45.00 3.18
2713 2816 1.682087 GGGCAATCACCCCTAGTCAAC 60.682 57.143 0.00 0.00 45.00 3.18
2714 2817 1.282157 GGCAATCACCCCTAGTCAACT 59.718 52.381 0.00 0.00 0.00 3.16
2715 2818 2.633488 GCAATCACCCCTAGTCAACTC 58.367 52.381 0.00 0.00 0.00 3.01
2716 2819 2.681097 GCAATCACCCCTAGTCAACTCC 60.681 54.545 0.00 0.00 0.00 3.85
2717 2820 1.880941 ATCACCCCTAGTCAACTCCC 58.119 55.000 0.00 0.00 0.00 4.30
2718 2821 0.613853 TCACCCCTAGTCAACTCCCG 60.614 60.000 0.00 0.00 0.00 5.14
2719 2822 1.988406 ACCCCTAGTCAACTCCCGC 60.988 63.158 0.00 0.00 0.00 6.13
2720 2823 1.987855 CCCCTAGTCAACTCCCGCA 60.988 63.158 0.00 0.00 0.00 5.69
2721 2824 1.517832 CCCTAGTCAACTCCCGCAG 59.482 63.158 0.00 0.00 0.00 5.18
2722 2825 0.970937 CCCTAGTCAACTCCCGCAGA 60.971 60.000 0.00 0.00 0.00 4.26
2730 2833 3.288484 CTCCCGCAGAGCAGTGTA 58.712 61.111 0.00 0.00 35.31 2.90
2731 2834 1.140589 CTCCCGCAGAGCAGTGTAG 59.859 63.158 0.00 0.00 35.31 2.74
2732 2835 2.510238 CCCGCAGAGCAGTGTAGC 60.510 66.667 0.00 0.00 0.00 3.58
2733 2836 2.510238 CCGCAGAGCAGTGTAGCC 60.510 66.667 0.00 0.00 34.23 3.93
2734 2837 2.510238 CGCAGAGCAGTGTAGCCC 60.510 66.667 0.00 0.00 34.23 5.19
2735 2838 2.985456 GCAGAGCAGTGTAGCCCT 59.015 61.111 0.00 0.00 34.23 5.19
2736 2839 1.449246 GCAGAGCAGTGTAGCCCTG 60.449 63.158 0.00 0.00 42.52 4.45
2737 2840 1.892819 GCAGAGCAGTGTAGCCCTGA 61.893 60.000 1.53 0.00 42.26 3.86
2738 2841 0.610174 CAGAGCAGTGTAGCCCTGAA 59.390 55.000 0.00 0.00 42.26 3.02
2739 2842 0.610687 AGAGCAGTGTAGCCCTGAAC 59.389 55.000 0.00 0.00 34.23 3.18
2740 2843 0.391793 GAGCAGTGTAGCCCTGAACC 60.392 60.000 0.00 0.00 34.23 3.62
2741 2844 0.838122 AGCAGTGTAGCCCTGAACCT 60.838 55.000 0.00 0.00 34.23 3.50
2742 2845 0.902531 GCAGTGTAGCCCTGAACCTA 59.097 55.000 0.00 0.00 31.38 3.08
2743 2846 1.486726 GCAGTGTAGCCCTGAACCTAT 59.513 52.381 0.00 0.00 31.38 2.57
2744 2847 2.483889 GCAGTGTAGCCCTGAACCTATC 60.484 54.545 0.00 0.00 31.38 2.08
2745 2848 3.034635 CAGTGTAGCCCTGAACCTATCT 58.965 50.000 0.00 0.00 31.38 1.98
2746 2849 3.068873 CAGTGTAGCCCTGAACCTATCTC 59.931 52.174 0.00 0.00 31.38 2.75
2747 2850 3.031736 GTGTAGCCCTGAACCTATCTCA 58.968 50.000 0.00 0.00 0.00 3.27
2748 2851 3.451178 GTGTAGCCCTGAACCTATCTCAA 59.549 47.826 0.00 0.00 0.00 3.02
2749 2852 3.451178 TGTAGCCCTGAACCTATCTCAAC 59.549 47.826 0.00 0.00 0.00 3.18
2750 2853 1.840635 AGCCCTGAACCTATCTCAACC 59.159 52.381 0.00 0.00 0.00 3.77
2751 2854 1.840635 GCCCTGAACCTATCTCAACCT 59.159 52.381 0.00 0.00 0.00 3.50
2752 2855 2.158885 GCCCTGAACCTATCTCAACCTC 60.159 54.545 0.00 0.00 0.00 3.85
2753 2856 3.379452 CCCTGAACCTATCTCAACCTCT 58.621 50.000 0.00 0.00 0.00 3.69
2754 2857 3.777522 CCCTGAACCTATCTCAACCTCTT 59.222 47.826 0.00 0.00 0.00 2.85
2755 2858 4.141824 CCCTGAACCTATCTCAACCTCTTC 60.142 50.000 0.00 0.00 0.00 2.87
2756 2859 4.141824 CCTGAACCTATCTCAACCTCTTCC 60.142 50.000 0.00 0.00 0.00 3.46
2757 2860 4.425772 TGAACCTATCTCAACCTCTTCCA 58.574 43.478 0.00 0.00 0.00 3.53
2758 2861 4.223032 TGAACCTATCTCAACCTCTTCCAC 59.777 45.833 0.00 0.00 0.00 4.02
2759 2862 3.108376 ACCTATCTCAACCTCTTCCACC 58.892 50.000 0.00 0.00 0.00 4.61
2760 2863 3.246167 ACCTATCTCAACCTCTTCCACCT 60.246 47.826 0.00 0.00 0.00 4.00
2761 2864 3.386402 CCTATCTCAACCTCTTCCACCTC 59.614 52.174 0.00 0.00 0.00 3.85
2762 2865 2.398754 TCTCAACCTCTTCCACCTCA 57.601 50.000 0.00 0.00 0.00 3.86
2763 2866 2.251818 TCTCAACCTCTTCCACCTCAG 58.748 52.381 0.00 0.00 0.00 3.35
2764 2867 0.687354 TCAACCTCTTCCACCTCAGC 59.313 55.000 0.00 0.00 0.00 4.26
2765 2868 0.322008 CAACCTCTTCCACCTCAGCC 60.322 60.000 0.00 0.00 0.00 4.85
2766 2869 1.492993 AACCTCTTCCACCTCAGCCC 61.493 60.000 0.00 0.00 0.00 5.19
2767 2870 1.614824 CCTCTTCCACCTCAGCCCT 60.615 63.158 0.00 0.00 0.00 5.19
2768 2871 1.621672 CCTCTTCCACCTCAGCCCTC 61.622 65.000 0.00 0.00 0.00 4.30
2769 2872 1.613630 TCTTCCACCTCAGCCCTCC 60.614 63.158 0.00 0.00 0.00 4.30
2770 2873 1.920325 CTTCCACCTCAGCCCTCCA 60.920 63.158 0.00 0.00 0.00 3.86
2771 2874 2.190488 CTTCCACCTCAGCCCTCCAC 62.190 65.000 0.00 0.00 0.00 4.02
2772 2875 2.930019 CCACCTCAGCCCTCCACA 60.930 66.667 0.00 0.00 0.00 4.17
2773 2876 2.528818 CCACCTCAGCCCTCCACAA 61.529 63.158 0.00 0.00 0.00 3.33
2774 2877 1.302832 CACCTCAGCCCTCCACAAC 60.303 63.158 0.00 0.00 0.00 3.32
2775 2878 1.770110 ACCTCAGCCCTCCACAACA 60.770 57.895 0.00 0.00 0.00 3.33
2776 2879 1.352622 ACCTCAGCCCTCCACAACAA 61.353 55.000 0.00 0.00 0.00 2.83
2777 2880 0.890996 CCTCAGCCCTCCACAACAAC 60.891 60.000 0.00 0.00 0.00 3.32
2778 2881 0.179020 CTCAGCCCTCCACAACAACA 60.179 55.000 0.00 0.00 0.00 3.33
2779 2882 0.179020 TCAGCCCTCCACAACAACAG 60.179 55.000 0.00 0.00 0.00 3.16
2780 2883 1.151450 AGCCCTCCACAACAACAGG 59.849 57.895 0.00 0.00 0.00 4.00
2781 2884 1.150536 GCCCTCCACAACAACAGGA 59.849 57.895 0.00 0.00 0.00 3.86
2782 2885 0.467290 GCCCTCCACAACAACAGGAA 60.467 55.000 0.00 0.00 0.00 3.36
2783 2886 1.609208 CCCTCCACAACAACAGGAAG 58.391 55.000 0.00 0.00 0.00 3.46
2784 2887 1.142870 CCCTCCACAACAACAGGAAGA 59.857 52.381 0.00 0.00 0.00 2.87
2785 2888 2.498167 CCTCCACAACAACAGGAAGAG 58.502 52.381 0.00 0.00 0.00 2.85
2786 2889 2.498167 CTCCACAACAACAGGAAGAGG 58.502 52.381 0.00 0.00 0.00 3.69
2787 2890 2.104792 CTCCACAACAACAGGAAGAGGA 59.895 50.000 0.00 0.00 0.00 3.71
2788 2891 2.507886 TCCACAACAACAGGAAGAGGAA 59.492 45.455 0.00 0.00 0.00 3.36
2789 2892 2.880890 CCACAACAACAGGAAGAGGAAG 59.119 50.000 0.00 0.00 0.00 3.46
2790 2893 3.433598 CCACAACAACAGGAAGAGGAAGA 60.434 47.826 0.00 0.00 0.00 2.87
2791 2894 4.199310 CACAACAACAGGAAGAGGAAGAA 58.801 43.478 0.00 0.00 0.00 2.52
2792 2895 4.035675 CACAACAACAGGAAGAGGAAGAAC 59.964 45.833 0.00 0.00 0.00 3.01
2793 2896 4.199310 CAACAACAGGAAGAGGAAGAACA 58.801 43.478 0.00 0.00 0.00 3.18
2794 2897 4.503714 ACAACAGGAAGAGGAAGAACAA 57.496 40.909 0.00 0.00 0.00 2.83
2795 2898 5.053978 ACAACAGGAAGAGGAAGAACAAT 57.946 39.130 0.00 0.00 0.00 2.71
2796 2899 6.187727 ACAACAGGAAGAGGAAGAACAATA 57.812 37.500 0.00 0.00 0.00 1.90
2797 2900 6.784031 ACAACAGGAAGAGGAAGAACAATAT 58.216 36.000 0.00 0.00 0.00 1.28
2798 2901 6.881602 ACAACAGGAAGAGGAAGAACAATATC 59.118 38.462 0.00 0.00 0.00 1.63
2799 2902 5.995446 ACAGGAAGAGGAAGAACAATATCC 58.005 41.667 0.00 0.00 0.00 2.59
2800 2903 5.104318 ACAGGAAGAGGAAGAACAATATCCC 60.104 44.000 0.00 0.00 33.55 3.85
2801 2904 5.131809 CAGGAAGAGGAAGAACAATATCCCT 59.868 44.000 0.00 0.00 33.55 4.20
2802 2905 5.368230 AGGAAGAGGAAGAACAATATCCCTC 59.632 44.000 0.00 0.00 40.21 4.30
2804 2907 5.885449 AGAGGAAGAACAATATCCCTCTG 57.115 43.478 7.84 0.00 46.12 3.35
2805 2908 4.657969 AGAGGAAGAACAATATCCCTCTGG 59.342 45.833 7.84 0.00 46.12 3.86
2806 2909 4.375313 AGGAAGAACAATATCCCTCTGGT 58.625 43.478 0.00 0.00 33.55 4.00
2807 2910 4.790790 AGGAAGAACAATATCCCTCTGGTT 59.209 41.667 0.00 0.00 33.55 3.67
2808 2911 4.884164 GGAAGAACAATATCCCTCTGGTTG 59.116 45.833 0.00 0.00 0.00 3.77
2809 2912 5.339200 GGAAGAACAATATCCCTCTGGTTGA 60.339 44.000 0.00 0.00 0.00 3.18
2810 2913 5.365021 AGAACAATATCCCTCTGGTTGAG 57.635 43.478 0.00 0.00 42.30 3.02
2811 2914 5.032846 AGAACAATATCCCTCTGGTTGAGA 58.967 41.667 0.00 0.00 45.39 3.27
2812 2915 4.762289 ACAATATCCCTCTGGTTGAGAC 57.238 45.455 0.00 0.00 45.39 3.36
2813 2916 4.104086 ACAATATCCCTCTGGTTGAGACA 58.896 43.478 0.00 0.00 45.39 3.41
2814 2917 4.163078 ACAATATCCCTCTGGTTGAGACAG 59.837 45.833 0.00 0.00 45.39 3.51
2815 2918 1.577736 ATCCCTCTGGTTGAGACAGG 58.422 55.000 0.00 0.00 45.39 4.00
2816 2919 1.194781 TCCCTCTGGTTGAGACAGGC 61.195 60.000 0.00 0.00 45.39 4.85
2817 2920 1.079543 CCTCTGGTTGAGACAGGCG 60.080 63.158 0.00 0.00 45.39 5.52
2818 2921 1.668294 CTCTGGTTGAGACAGGCGT 59.332 57.895 0.00 0.00 45.39 5.68
2819 2922 0.888619 CTCTGGTTGAGACAGGCGTA 59.111 55.000 0.00 0.00 45.39 4.42
2820 2923 1.272490 CTCTGGTTGAGACAGGCGTAA 59.728 52.381 0.00 0.00 45.39 3.18
2821 2924 1.272490 TCTGGTTGAGACAGGCGTAAG 59.728 52.381 0.00 0.00 36.62 2.34
2822 2925 0.320374 TGGTTGAGACAGGCGTAAGG 59.680 55.000 0.00 0.00 38.28 2.69
2823 2926 0.606604 GGTTGAGACAGGCGTAAGGA 59.393 55.000 0.00 0.00 38.28 3.36
2824 2927 1.404315 GGTTGAGACAGGCGTAAGGAG 60.404 57.143 0.00 0.00 38.28 3.69
2825 2928 1.544691 GTTGAGACAGGCGTAAGGAGA 59.455 52.381 0.00 0.00 38.28 3.71
2826 2929 1.919240 TGAGACAGGCGTAAGGAGAA 58.081 50.000 0.00 0.00 38.28 2.87
2827 2930 1.819288 TGAGACAGGCGTAAGGAGAAG 59.181 52.381 0.00 0.00 38.28 2.85
2828 2931 1.819903 GAGACAGGCGTAAGGAGAAGT 59.180 52.381 0.00 0.00 38.28 3.01
2829 2932 2.231721 GAGACAGGCGTAAGGAGAAGTT 59.768 50.000 0.00 0.00 38.28 2.66
2830 2933 2.028930 AGACAGGCGTAAGGAGAAGTTG 60.029 50.000 0.00 0.00 38.28 3.16
2831 2934 1.692519 ACAGGCGTAAGGAGAAGTTGT 59.307 47.619 0.00 0.00 38.28 3.32
2832 2935 2.895404 ACAGGCGTAAGGAGAAGTTGTA 59.105 45.455 0.00 0.00 38.28 2.41
2833 2936 3.056749 ACAGGCGTAAGGAGAAGTTGTAG 60.057 47.826 0.00 0.00 38.28 2.74
2834 2937 3.192844 CAGGCGTAAGGAGAAGTTGTAGA 59.807 47.826 0.00 0.00 38.28 2.59
2835 2938 4.024670 AGGCGTAAGGAGAAGTTGTAGAT 58.975 43.478 0.00 0.00 38.28 1.98
2836 2939 4.466726 AGGCGTAAGGAGAAGTTGTAGATT 59.533 41.667 0.00 0.00 38.28 2.40
2837 2940 4.567159 GGCGTAAGGAGAAGTTGTAGATTG 59.433 45.833 0.00 0.00 38.28 2.67
2838 2941 5.408356 GCGTAAGGAGAAGTTGTAGATTGA 58.592 41.667 0.00 0.00 38.28 2.57
2839 2942 5.867716 GCGTAAGGAGAAGTTGTAGATTGAA 59.132 40.000 0.00 0.00 38.28 2.69
2840 2943 6.535508 GCGTAAGGAGAAGTTGTAGATTGAAT 59.464 38.462 0.00 0.00 38.28 2.57
2841 2944 7.064728 GCGTAAGGAGAAGTTGTAGATTGAATT 59.935 37.037 0.00 0.00 38.28 2.17
2842 2945 8.936864 CGTAAGGAGAAGTTGTAGATTGAATTT 58.063 33.333 0.00 0.00 0.00 1.82
2884 2987 8.506168 AAAAATCTGTGTGTAGAGACAAAGAA 57.494 30.769 3.97 0.00 42.33 2.52
2885 2988 8.682936 AAAATCTGTGTGTAGAGACAAAGAAT 57.317 30.769 3.97 0.00 42.33 2.40
2886 2989 7.664082 AATCTGTGTGTAGAGACAAAGAATG 57.336 36.000 3.97 0.00 42.33 2.67
2887 2990 6.763355 ATCTGTGTGTAGAGACAAAGAATGT 58.237 36.000 3.97 0.00 42.33 2.71
2900 3003 6.492007 ACAAAGAATGTCTAGCTTGTCATG 57.508 37.500 8.42 1.18 37.96 3.07
2901 3004 5.106396 ACAAAGAATGTCTAGCTTGTCATGC 60.106 40.000 8.42 6.92 37.96 4.06
2902 3005 4.484537 AGAATGTCTAGCTTGTCATGCT 57.515 40.909 16.59 16.59 43.79 3.79
2903 3006 4.190001 AGAATGTCTAGCTTGTCATGCTG 58.810 43.478 20.46 11.84 41.32 4.41
2904 3007 1.730501 TGTCTAGCTTGTCATGCTGC 58.269 50.000 20.46 12.08 41.32 5.25
2905 3008 1.277273 TGTCTAGCTTGTCATGCTGCT 59.723 47.619 20.46 8.86 41.32 4.24
2906 3009 1.932511 GTCTAGCTTGTCATGCTGCTC 59.067 52.381 20.46 8.60 41.32 4.26
2907 3010 1.134580 TCTAGCTTGTCATGCTGCTCC 60.135 52.381 20.46 0.00 41.32 4.70
2908 3011 0.614812 TAGCTTGTCATGCTGCTCCA 59.385 50.000 20.46 0.42 41.32 3.86
2909 3012 0.959372 AGCTTGTCATGCTGCTCCAC 60.959 55.000 12.16 0.00 39.56 4.02
2910 3013 1.930908 GCTTGTCATGCTGCTCCACC 61.931 60.000 0.00 0.00 0.00 4.61
2911 3014 0.607217 CTTGTCATGCTGCTCCACCA 60.607 55.000 0.00 0.00 0.00 4.17
2912 3015 0.178995 TTGTCATGCTGCTCCACCAA 60.179 50.000 0.00 0.00 0.00 3.67
2913 3016 0.038599 TGTCATGCTGCTCCACCAAT 59.961 50.000 0.00 0.00 0.00 3.16
2914 3017 0.737219 GTCATGCTGCTCCACCAATC 59.263 55.000 0.00 0.00 0.00 2.67
2915 3018 0.394762 TCATGCTGCTCCACCAATCC 60.395 55.000 0.00 0.00 0.00 3.01
2916 3019 0.395311 CATGCTGCTCCACCAATCCT 60.395 55.000 0.00 0.00 0.00 3.24
2917 3020 0.333993 ATGCTGCTCCACCAATCCTT 59.666 50.000 0.00 0.00 0.00 3.36
2918 3021 0.112995 TGCTGCTCCACCAATCCTTT 59.887 50.000 0.00 0.00 0.00 3.11
2919 3022 0.813821 GCTGCTCCACCAATCCTTTC 59.186 55.000 0.00 0.00 0.00 2.62
2920 3023 1.887956 GCTGCTCCACCAATCCTTTCA 60.888 52.381 0.00 0.00 0.00 2.69
2921 3024 2.089980 CTGCTCCACCAATCCTTTCAG 58.910 52.381 0.00 0.00 0.00 3.02
2922 3025 0.813821 GCTCCACCAATCCTTTCAGC 59.186 55.000 0.00 0.00 0.00 4.26
2923 3026 1.615384 GCTCCACCAATCCTTTCAGCT 60.615 52.381 0.00 0.00 0.00 4.24
2924 3027 2.356125 GCTCCACCAATCCTTTCAGCTA 60.356 50.000 0.00 0.00 0.00 3.32
2925 3028 3.873801 GCTCCACCAATCCTTTCAGCTAA 60.874 47.826 0.00 0.00 0.00 3.09
2926 3029 4.335416 CTCCACCAATCCTTTCAGCTAAA 58.665 43.478 0.00 0.00 0.00 1.85
2927 3030 4.735369 TCCACCAATCCTTTCAGCTAAAA 58.265 39.130 0.00 0.00 0.00 1.52
2928 3031 5.332743 TCCACCAATCCTTTCAGCTAAAAT 58.667 37.500 0.00 0.00 0.00 1.82
2929 3032 5.418840 TCCACCAATCCTTTCAGCTAAAATC 59.581 40.000 0.00 0.00 0.00 2.17
2930 3033 5.185635 CCACCAATCCTTTCAGCTAAAATCA 59.814 40.000 0.00 0.00 0.00 2.57
2931 3034 6.127253 CCACCAATCCTTTCAGCTAAAATCAT 60.127 38.462 0.00 0.00 0.00 2.45
2932 3035 7.325694 CACCAATCCTTTCAGCTAAAATCATT 58.674 34.615 0.00 0.00 0.00 2.57
2933 3036 8.469200 CACCAATCCTTTCAGCTAAAATCATTA 58.531 33.333 0.00 0.00 0.00 1.90
2934 3037 9.034800 ACCAATCCTTTCAGCTAAAATCATTAA 57.965 29.630 0.00 0.00 0.00 1.40
2935 3038 9.525409 CCAATCCTTTCAGCTAAAATCATTAAG 57.475 33.333 0.00 0.00 0.00 1.85
2938 3041 9.692325 ATCCTTTCAGCTAAAATCATTAAGAGT 57.308 29.630 0.00 0.00 0.00 3.24
2939 3042 9.167311 TCCTTTCAGCTAAAATCATTAAGAGTC 57.833 33.333 0.00 0.00 0.00 3.36
2940 3043 9.171877 CCTTTCAGCTAAAATCATTAAGAGTCT 57.828 33.333 0.00 0.00 0.00 3.24
2941 3044 9.985318 CTTTCAGCTAAAATCATTAAGAGTCTG 57.015 33.333 0.00 0.00 0.00 3.51
2942 3045 9.725019 TTTCAGCTAAAATCATTAAGAGTCTGA 57.275 29.630 0.00 0.00 0.00 3.27
2943 3046 9.725019 TTCAGCTAAAATCATTAAGAGTCTGAA 57.275 29.630 0.00 0.00 34.54 3.02
2944 3047 9.896645 TCAGCTAAAATCATTAAGAGTCTGAAT 57.103 29.630 0.00 0.00 0.00 2.57
2957 3060 7.750229 AAGAGTCTGAATACTTCATTTTGCA 57.250 32.000 0.00 0.00 39.30 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.943449 TAACCGTGCGTGATGTATGA 57.057 45.000 0.00 0.00 0.00 2.15
112 113 4.919168 CAGATTCAATGCACACGATTTGTT 59.081 37.500 0.00 0.00 35.67 2.83
134 135 4.832266 AGGCAGGATCATTTGTTTTGTACA 59.168 37.500 0.00 0.00 34.12 2.90
269 270 0.029300 CACACAGTTCAAAGCCCGTG 59.971 55.000 0.00 0.00 0.00 4.94
340 341 8.528643 GGGCATAACTTAATTGTAGTCCTTTTT 58.471 33.333 0.00 0.00 0.00 1.94
371 372 6.406624 GGTTTCAGCATGGATCATCATTTTCT 60.407 38.462 0.00 0.00 36.16 2.52
438 439 5.623956 TGTAAAAGAAGGTTCTGGACTCA 57.376 39.130 0.00 0.00 37.65 3.41
483 484 6.020281 GCAAGGCGATCTTATATTATGAGACG 60.020 42.308 0.62 7.74 33.68 4.18
487 488 6.092670 GCTTGCAAGGCGATCTTATATTATGA 59.907 38.462 27.10 0.00 33.68 2.15
498 499 2.095263 TGTTTTAGCTTGCAAGGCGATC 60.095 45.455 27.10 10.53 34.52 3.69
503 504 4.272991 TGCAAATTGTTTTAGCTTGCAAGG 59.727 37.500 27.10 9.80 46.77 3.61
504 505 5.406767 TGCAAATTGTTTTAGCTTGCAAG 57.593 34.783 22.44 22.44 46.77 4.01
534 535 7.067251 GGTACTCCCTCCGTCTCATAATATAAG 59.933 44.444 0.00 0.00 0.00 1.73
544 545 2.725221 TAAGGTACTCCCTCCGTCTC 57.275 55.000 0.00 0.00 45.47 3.36
593 594 2.424246 TCGATCACACATGCATGCATTT 59.576 40.909 30.32 21.99 33.90 2.32
594 595 2.018515 TCGATCACACATGCATGCATT 58.981 42.857 30.32 18.23 33.90 3.56
799 809 4.248058 CGATTACTAGACGGTTTTGGGTT 58.752 43.478 0.00 0.00 0.00 4.11
1051 1077 0.606673 GAAGGGTGTTGGTCAGCTCC 60.607 60.000 0.00 0.00 43.26 4.70
1099 1126 4.103103 TCGCAGTGGTCGAGCTCG 62.103 66.667 30.03 30.03 41.45 5.03
1110 1137 2.299013 TCTTGTGATGTAACCTCGCAGT 59.701 45.455 0.00 0.00 34.84 4.40
1674 1701 7.609960 AGTGAATAGGCACACATCTAGATATG 58.390 38.462 9.51 9.51 41.19 1.78
1778 1835 0.034896 AGCCCAACCTGTACTTCACG 59.965 55.000 0.00 0.00 0.00 4.35
1801 1858 5.049886 ACTGCGATACATGTCATAGCAAATG 60.050 40.000 0.00 4.59 34.30 2.32
1802 1859 5.049886 CACTGCGATACATGTCATAGCAAAT 60.050 40.000 0.00 2.21 34.30 2.32
1820 1877 3.609103 AAGAAACAAAGTAGCACTGCG 57.391 42.857 0.00 0.00 0.00 5.18
1821 1878 3.487207 GCAAAGAAACAAAGTAGCACTGC 59.513 43.478 0.00 0.00 0.00 4.40
1888 1945 7.865889 GGGTCACTATGTTTTCGAAAAAGAATT 59.134 33.333 24.04 10.22 0.00 2.17
1889 1946 7.013846 TGGGTCACTATGTTTTCGAAAAAGAAT 59.986 33.333 24.04 18.70 0.00 2.40
1891 1948 5.823570 TGGGTCACTATGTTTTCGAAAAAGA 59.176 36.000 24.04 14.37 0.00 2.52
1905 1962 1.001760 AGAGGCCGTGGGTCACTAT 59.998 57.895 0.00 0.00 31.34 2.12
1906 1963 1.982395 CAGAGGCCGTGGGTCACTA 60.982 63.158 0.00 0.00 31.34 2.74
2000 2059 1.200020 CGGTTGGGTCTTGAGCATTTC 59.800 52.381 2.24 0.00 0.00 2.17
2058 2117 2.359848 GGTTTGGTTGTGGAGTGGTAAC 59.640 50.000 0.00 0.00 0.00 2.50
2123 2182 2.146342 CTTGGAGACTGCGTTGACATT 58.854 47.619 0.00 0.00 0.00 2.71
2304 2365 7.016153 TCCAGTTCTATAACATGTCTTTGGT 57.984 36.000 0.00 0.00 38.12 3.67
2358 2423 5.050295 CGAGAACTCACGTGCTATATAGTGA 60.050 44.000 11.67 6.94 40.77 3.41
2390 2455 5.940192 ATGCGATTTTTCACACAAGAGTA 57.060 34.783 0.00 0.00 0.00 2.59
2396 2461 6.653273 TTTTCAAATGCGATTTTTCACACA 57.347 29.167 0.00 0.00 0.00 3.72
2413 2478 4.932200 ACTCGTTGCAAACCAAATTTTCAA 59.068 33.333 0.00 0.00 46.28 2.69
2430 2495 9.832445 ATAACACATAATTTCCAGATACTCGTT 57.168 29.630 0.00 0.00 0.00 3.85
2479 2544 2.557056 TGTCGAAGTTGACCCTGACTAG 59.443 50.000 0.00 0.00 38.11 2.57
2566 2631 9.918630 ACGAGAAGTTTGCTATAAACTTTAGTA 57.081 29.630 16.16 0.00 46.81 1.82
2570 2635 7.441458 AGTCACGAGAAGTTTGCTATAAACTTT 59.559 33.333 16.16 8.58 46.81 2.66
2576 2641 4.461431 TGGAGTCACGAGAAGTTTGCTATA 59.539 41.667 0.00 0.00 0.00 1.31
2588 2653 0.972983 ATGGTCCCTGGAGTCACGAG 60.973 60.000 0.00 0.00 0.00 4.18
2605 2670 3.185188 GCTAATGCACACACCGAGATATG 59.815 47.826 0.00 0.00 39.41 1.78
2623 2688 5.001232 GTGAGGGACTAATGTGTTTGCTAA 58.999 41.667 0.00 0.00 41.55 3.09
2631 2696 5.053145 GCAATCTAGTGAGGGACTAATGTG 58.947 45.833 0.00 0.00 41.55 3.21
2640 2705 2.787473 TTGGTGCAATCTAGTGAGGG 57.213 50.000 0.00 0.00 0.00 4.30
2701 2804 1.988406 GCGGGAGTTGACTAGGGGT 60.988 63.158 0.00 0.00 0.00 4.95
2705 2808 0.179124 GCTCTGCGGGAGTTGACTAG 60.179 60.000 8.05 0.00 43.62 2.57
2712 2815 1.599606 CTACACTGCTCTGCGGGAGT 61.600 60.000 8.05 4.11 43.62 3.85
2713 2816 1.140589 CTACACTGCTCTGCGGGAG 59.859 63.158 3.35 0.00 44.49 4.30
2714 2817 3.006756 GCTACACTGCTCTGCGGGA 62.007 63.158 3.35 0.00 39.57 5.14
2715 2818 2.510238 GCTACACTGCTCTGCGGG 60.510 66.667 3.35 0.00 39.57 6.13
2716 2819 2.510238 GGCTACACTGCTCTGCGG 60.510 66.667 0.00 0.00 41.29 5.69
2717 2820 2.510238 GGGCTACACTGCTCTGCG 60.510 66.667 0.00 0.00 0.00 5.18
2718 2821 2.985456 AGGGCTACACTGCTCTGC 59.015 61.111 0.00 0.00 42.99 4.26
2720 2823 0.610687 GTTCAGGGCTACACTGCTCT 59.389 55.000 0.00 0.00 45.99 4.09
2721 2824 0.391793 GGTTCAGGGCTACACTGCTC 60.392 60.000 0.00 0.00 35.94 4.26
2722 2825 0.838122 AGGTTCAGGGCTACACTGCT 60.838 55.000 0.00 0.00 35.94 4.24
2723 2826 0.902531 TAGGTTCAGGGCTACACTGC 59.097 55.000 0.00 0.00 35.94 4.40
2724 2827 3.034635 AGATAGGTTCAGGGCTACACTG 58.965 50.000 0.00 0.00 37.30 3.66
2725 2828 3.301274 GAGATAGGTTCAGGGCTACACT 58.699 50.000 0.00 0.00 0.00 3.55
2726 2829 3.031736 TGAGATAGGTTCAGGGCTACAC 58.968 50.000 0.00 0.00 0.00 2.90
2727 2830 3.398318 TGAGATAGGTTCAGGGCTACA 57.602 47.619 0.00 0.00 0.00 2.74
2728 2831 3.181464 GGTTGAGATAGGTTCAGGGCTAC 60.181 52.174 0.00 0.00 0.00 3.58
2729 2832 3.039011 GGTTGAGATAGGTTCAGGGCTA 58.961 50.000 0.00 0.00 0.00 3.93
2730 2833 1.840635 GGTTGAGATAGGTTCAGGGCT 59.159 52.381 0.00 0.00 0.00 5.19
2731 2834 1.840635 AGGTTGAGATAGGTTCAGGGC 59.159 52.381 0.00 0.00 0.00 5.19
2732 2835 3.379452 AGAGGTTGAGATAGGTTCAGGG 58.621 50.000 0.00 0.00 0.00 4.45
2733 2836 4.141824 GGAAGAGGTTGAGATAGGTTCAGG 60.142 50.000 0.00 0.00 0.00 3.86
2734 2837 4.467795 TGGAAGAGGTTGAGATAGGTTCAG 59.532 45.833 0.00 0.00 0.00 3.02
2735 2838 4.223032 GTGGAAGAGGTTGAGATAGGTTCA 59.777 45.833 0.00 0.00 0.00 3.18
2736 2839 4.383226 GGTGGAAGAGGTTGAGATAGGTTC 60.383 50.000 0.00 0.00 0.00 3.62
2737 2840 3.519913 GGTGGAAGAGGTTGAGATAGGTT 59.480 47.826 0.00 0.00 0.00 3.50
2738 2841 3.108376 GGTGGAAGAGGTTGAGATAGGT 58.892 50.000 0.00 0.00 0.00 3.08
2739 2842 3.379452 AGGTGGAAGAGGTTGAGATAGG 58.621 50.000 0.00 0.00 0.00 2.57
2740 2843 4.026744 TGAGGTGGAAGAGGTTGAGATAG 58.973 47.826 0.00 0.00 0.00 2.08
2741 2844 4.026744 CTGAGGTGGAAGAGGTTGAGATA 58.973 47.826 0.00 0.00 0.00 1.98
2742 2845 2.836981 CTGAGGTGGAAGAGGTTGAGAT 59.163 50.000 0.00 0.00 0.00 2.75
2743 2846 2.251818 CTGAGGTGGAAGAGGTTGAGA 58.748 52.381 0.00 0.00 0.00 3.27
2744 2847 1.338579 GCTGAGGTGGAAGAGGTTGAG 60.339 57.143 0.00 0.00 0.00 3.02
2745 2848 0.687354 GCTGAGGTGGAAGAGGTTGA 59.313 55.000 0.00 0.00 0.00 3.18
2746 2849 0.322008 GGCTGAGGTGGAAGAGGTTG 60.322 60.000 0.00 0.00 0.00 3.77
2747 2850 1.492993 GGGCTGAGGTGGAAGAGGTT 61.493 60.000 0.00 0.00 0.00 3.50
2748 2851 1.920835 GGGCTGAGGTGGAAGAGGT 60.921 63.158 0.00 0.00 0.00 3.85
2749 2852 1.614824 AGGGCTGAGGTGGAAGAGG 60.615 63.158 0.00 0.00 0.00 3.69
2750 2853 1.621672 GGAGGGCTGAGGTGGAAGAG 61.622 65.000 0.00 0.00 0.00 2.85
2751 2854 1.613630 GGAGGGCTGAGGTGGAAGA 60.614 63.158 0.00 0.00 0.00 2.87
2752 2855 1.920325 TGGAGGGCTGAGGTGGAAG 60.920 63.158 0.00 0.00 0.00 3.46
2753 2856 2.206900 TGGAGGGCTGAGGTGGAA 59.793 61.111 0.00 0.00 0.00 3.53
2754 2857 2.607750 GTGGAGGGCTGAGGTGGA 60.608 66.667 0.00 0.00 0.00 4.02
2755 2858 2.528818 TTGTGGAGGGCTGAGGTGG 61.529 63.158 0.00 0.00 0.00 4.61
2756 2859 1.302832 GTTGTGGAGGGCTGAGGTG 60.303 63.158 0.00 0.00 0.00 4.00
2757 2860 1.352622 TTGTTGTGGAGGGCTGAGGT 61.353 55.000 0.00 0.00 0.00 3.85
2758 2861 0.890996 GTTGTTGTGGAGGGCTGAGG 60.891 60.000 0.00 0.00 0.00 3.86
2759 2862 0.179020 TGTTGTTGTGGAGGGCTGAG 60.179 55.000 0.00 0.00 0.00 3.35
2760 2863 0.179020 CTGTTGTTGTGGAGGGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
2761 2864 1.174712 CCTGTTGTTGTGGAGGGCTG 61.175 60.000 0.00 0.00 0.00 4.85
2762 2865 1.151450 CCTGTTGTTGTGGAGGGCT 59.849 57.895 0.00 0.00 0.00 5.19
2763 2866 0.467290 TTCCTGTTGTTGTGGAGGGC 60.467 55.000 0.00 0.00 0.00 5.19
2764 2867 1.142870 TCTTCCTGTTGTTGTGGAGGG 59.857 52.381 0.00 0.00 0.00 4.30
2765 2868 2.498167 CTCTTCCTGTTGTTGTGGAGG 58.502 52.381 0.00 0.00 0.00 4.30
2766 2869 2.104792 TCCTCTTCCTGTTGTTGTGGAG 59.895 50.000 0.00 0.00 0.00 3.86
2767 2870 2.123589 TCCTCTTCCTGTTGTTGTGGA 58.876 47.619 0.00 0.00 0.00 4.02
2768 2871 2.638480 TCCTCTTCCTGTTGTTGTGG 57.362 50.000 0.00 0.00 0.00 4.17
2769 2872 3.808728 TCTTCCTCTTCCTGTTGTTGTG 58.191 45.455 0.00 0.00 0.00 3.33
2770 2873 4.200092 GTTCTTCCTCTTCCTGTTGTTGT 58.800 43.478 0.00 0.00 0.00 3.32
2771 2874 4.199310 TGTTCTTCCTCTTCCTGTTGTTG 58.801 43.478 0.00 0.00 0.00 3.33
2772 2875 4.503714 TGTTCTTCCTCTTCCTGTTGTT 57.496 40.909 0.00 0.00 0.00 2.83
2773 2876 4.503714 TTGTTCTTCCTCTTCCTGTTGT 57.496 40.909 0.00 0.00 0.00 3.32
2774 2877 6.317391 GGATATTGTTCTTCCTCTTCCTGTTG 59.683 42.308 0.00 0.00 0.00 3.33
2775 2878 6.418946 GGATATTGTTCTTCCTCTTCCTGTT 58.581 40.000 0.00 0.00 0.00 3.16
2776 2879 5.104318 GGGATATTGTTCTTCCTCTTCCTGT 60.104 44.000 0.00 0.00 0.00 4.00
2777 2880 5.131809 AGGGATATTGTTCTTCCTCTTCCTG 59.868 44.000 0.00 0.00 0.00 3.86
2778 2881 5.292815 AGGGATATTGTTCTTCCTCTTCCT 58.707 41.667 0.00 0.00 0.00 3.36
2779 2882 5.368230 AGAGGGATATTGTTCTTCCTCTTCC 59.632 44.000 0.00 0.00 46.12 3.46
2780 2883 6.287525 CAGAGGGATATTGTTCTTCCTCTTC 58.712 44.000 6.93 0.00 46.12 2.87
2781 2884 5.131809 CCAGAGGGATATTGTTCTTCCTCTT 59.868 44.000 6.93 0.00 46.12 2.85
2783 2886 4.410555 ACCAGAGGGATATTGTTCTTCCTC 59.589 45.833 0.00 0.00 40.61 3.71
2784 2887 4.375313 ACCAGAGGGATATTGTTCTTCCT 58.625 43.478 0.00 0.00 38.05 3.36
2785 2888 4.779993 ACCAGAGGGATATTGTTCTTCC 57.220 45.455 0.00 0.00 38.05 3.46
2786 2889 5.745227 TCAACCAGAGGGATATTGTTCTTC 58.255 41.667 0.00 0.00 38.05 2.87
2787 2890 5.488919 TCTCAACCAGAGGGATATTGTTCTT 59.511 40.000 0.00 0.00 44.81 2.52
2788 2891 5.032846 TCTCAACCAGAGGGATATTGTTCT 58.967 41.667 0.00 0.00 44.81 3.01
2789 2892 5.119694 GTCTCAACCAGAGGGATATTGTTC 58.880 45.833 0.00 0.00 44.81 3.18
2790 2893 4.536090 TGTCTCAACCAGAGGGATATTGTT 59.464 41.667 0.00 0.00 44.81 2.83
2791 2894 4.104086 TGTCTCAACCAGAGGGATATTGT 58.896 43.478 0.00 0.00 44.81 2.71
2792 2895 4.444022 CCTGTCTCAACCAGAGGGATATTG 60.444 50.000 0.00 0.00 44.81 1.90
2793 2896 3.713764 CCTGTCTCAACCAGAGGGATATT 59.286 47.826 0.00 0.00 44.81 1.28
2794 2897 3.312890 CCTGTCTCAACCAGAGGGATAT 58.687 50.000 0.00 0.00 44.81 1.63
2795 2898 2.752030 CCTGTCTCAACCAGAGGGATA 58.248 52.381 0.00 0.00 44.81 2.59
2796 2899 1.577736 CCTGTCTCAACCAGAGGGAT 58.422 55.000 0.00 0.00 44.81 3.85
2797 2900 1.194781 GCCTGTCTCAACCAGAGGGA 61.195 60.000 0.00 0.00 44.81 4.20
2798 2901 1.298014 GCCTGTCTCAACCAGAGGG 59.702 63.158 0.00 0.00 44.81 4.30
2799 2902 1.079543 CGCCTGTCTCAACCAGAGG 60.080 63.158 0.00 0.00 44.81 3.69
2800 2903 0.888619 TACGCCTGTCTCAACCAGAG 59.111 55.000 0.00 0.00 46.14 3.35
2801 2904 1.272490 CTTACGCCTGTCTCAACCAGA 59.728 52.381 0.00 0.00 31.38 3.86
2802 2905 1.673033 CCTTACGCCTGTCTCAACCAG 60.673 57.143 0.00 0.00 0.00 4.00
2803 2906 0.320374 CCTTACGCCTGTCTCAACCA 59.680 55.000 0.00 0.00 0.00 3.67
2804 2907 0.606604 TCCTTACGCCTGTCTCAACC 59.393 55.000 0.00 0.00 0.00 3.77
2805 2908 1.544691 TCTCCTTACGCCTGTCTCAAC 59.455 52.381 0.00 0.00 0.00 3.18
2806 2909 1.919240 TCTCCTTACGCCTGTCTCAA 58.081 50.000 0.00 0.00 0.00 3.02
2807 2910 1.819288 CTTCTCCTTACGCCTGTCTCA 59.181 52.381 0.00 0.00 0.00 3.27
2808 2911 1.819903 ACTTCTCCTTACGCCTGTCTC 59.180 52.381 0.00 0.00 0.00 3.36
2809 2912 1.926108 ACTTCTCCTTACGCCTGTCT 58.074 50.000 0.00 0.00 0.00 3.41
2810 2913 2.288886 ACAACTTCTCCTTACGCCTGTC 60.289 50.000 0.00 0.00 0.00 3.51
2811 2914 1.692519 ACAACTTCTCCTTACGCCTGT 59.307 47.619 0.00 0.00 0.00 4.00
2812 2915 2.457366 ACAACTTCTCCTTACGCCTG 57.543 50.000 0.00 0.00 0.00 4.85
2813 2916 3.428532 TCTACAACTTCTCCTTACGCCT 58.571 45.455 0.00 0.00 0.00 5.52
2814 2917 3.863142 TCTACAACTTCTCCTTACGCC 57.137 47.619 0.00 0.00 0.00 5.68
2815 2918 5.408356 TCAATCTACAACTTCTCCTTACGC 58.592 41.667 0.00 0.00 0.00 4.42
2816 2919 8.480643 AATTCAATCTACAACTTCTCCTTACG 57.519 34.615 0.00 0.00 0.00 3.18
2859 2962 8.506168 TTCTTTGTCTCTACACACAGATTTTT 57.494 30.769 0.00 0.00 33.97 1.94
2860 2963 8.562892 CATTCTTTGTCTCTACACACAGATTTT 58.437 33.333 0.00 0.00 33.97 1.82
2861 2964 7.716998 ACATTCTTTGTCTCTACACACAGATTT 59.283 33.333 0.00 0.00 33.97 2.17
2862 2965 7.220030 ACATTCTTTGTCTCTACACACAGATT 58.780 34.615 0.00 0.00 33.97 2.40
2863 2966 6.763355 ACATTCTTTGTCTCTACACACAGAT 58.237 36.000 0.00 0.00 33.97 2.90
2864 2967 6.161855 ACATTCTTTGTCTCTACACACAGA 57.838 37.500 0.00 0.00 34.61 3.41
2876 2979 8.957798 AGCATGACAAGCTAGACATTCTTTGTC 61.958 40.741 2.74 10.38 43.97 3.18
2877 2980 5.106396 GCATGACAAGCTAGACATTCTTTGT 60.106 40.000 0.00 0.00 42.79 2.83
2878 2981 5.123502 AGCATGACAAGCTAGACATTCTTTG 59.876 40.000 2.74 0.00 41.32 2.77
2879 2982 5.123502 CAGCATGACAAGCTAGACATTCTTT 59.876 40.000 4.61 0.00 41.14 2.52
2880 2983 4.634883 CAGCATGACAAGCTAGACATTCTT 59.365 41.667 4.61 0.00 41.14 2.52
2881 2984 4.190001 CAGCATGACAAGCTAGACATTCT 58.810 43.478 4.61 0.00 41.14 2.40
2882 2985 3.242673 GCAGCATGACAAGCTAGACATTC 60.243 47.826 4.61 0.00 41.14 2.67
2883 2986 2.681848 GCAGCATGACAAGCTAGACATT 59.318 45.455 4.61 0.00 41.14 2.71
2884 2987 2.093075 AGCAGCATGACAAGCTAGACAT 60.093 45.455 4.61 0.00 41.14 3.06
2885 2988 1.277273 AGCAGCATGACAAGCTAGACA 59.723 47.619 4.61 0.00 41.14 3.41
2886 2989 1.932511 GAGCAGCATGACAAGCTAGAC 59.067 52.381 4.61 0.00 41.14 2.59
2887 2990 1.134580 GGAGCAGCATGACAAGCTAGA 60.135 52.381 4.61 0.00 41.14 2.43
2888 2991 1.297664 GGAGCAGCATGACAAGCTAG 58.702 55.000 4.61 1.75 41.14 3.42
2889 2992 0.614812 TGGAGCAGCATGACAAGCTA 59.385 50.000 4.61 0.00 41.14 3.32
2890 2993 0.959372 GTGGAGCAGCATGACAAGCT 60.959 55.000 0.00 0.00 44.62 3.74
2891 2994 1.505353 GTGGAGCAGCATGACAAGC 59.495 57.895 0.00 0.00 39.69 4.01
2892 2995 0.607217 TGGTGGAGCAGCATGACAAG 60.607 55.000 0.00 0.00 39.69 3.16
2893 2996 0.178995 TTGGTGGAGCAGCATGACAA 60.179 50.000 0.00 0.00 41.53 3.18
2894 2997 0.038599 ATTGGTGGAGCAGCATGACA 59.961 50.000 0.00 0.00 41.53 3.58
2895 2998 0.737219 GATTGGTGGAGCAGCATGAC 59.263 55.000 0.00 0.00 41.53 3.06
2896 2999 0.394762 GGATTGGTGGAGCAGCATGA 60.395 55.000 0.00 0.00 41.53 3.07
2897 3000 0.395311 AGGATTGGTGGAGCAGCATG 60.395 55.000 0.00 0.00 41.53 4.06
2898 3001 0.333993 AAGGATTGGTGGAGCAGCAT 59.666 50.000 0.00 0.00 41.53 3.79
2899 3002 0.112995 AAAGGATTGGTGGAGCAGCA 59.887 50.000 0.00 0.00 40.20 4.41
2900 3003 0.813821 GAAAGGATTGGTGGAGCAGC 59.186 55.000 0.00 0.00 0.00 5.25
2901 3004 2.089980 CTGAAAGGATTGGTGGAGCAG 58.910 52.381 0.00 0.00 0.00 4.24
2902 3005 1.887956 GCTGAAAGGATTGGTGGAGCA 60.888 52.381 0.00 0.00 0.00 4.26
2903 3006 0.813821 GCTGAAAGGATTGGTGGAGC 59.186 55.000 0.00 0.00 0.00 4.70
2904 3007 2.503895 AGCTGAAAGGATTGGTGGAG 57.496 50.000 0.00 0.00 0.00 3.86
2905 3008 4.380843 TTTAGCTGAAAGGATTGGTGGA 57.619 40.909 0.00 0.00 0.00 4.02
2906 3009 5.185635 TGATTTTAGCTGAAAGGATTGGTGG 59.814 40.000 9.70 0.00 0.00 4.61
2907 3010 6.271488 TGATTTTAGCTGAAAGGATTGGTG 57.729 37.500 9.70 0.00 0.00 4.17
2908 3011 7.486407 AATGATTTTAGCTGAAAGGATTGGT 57.514 32.000 9.70 0.00 0.00 3.67
2909 3012 9.525409 CTTAATGATTTTAGCTGAAAGGATTGG 57.475 33.333 9.70 4.77 0.00 3.16
2912 3015 9.692325 ACTCTTAATGATTTTAGCTGAAAGGAT 57.308 29.630 9.70 1.41 0.00 3.24
2913 3016 9.167311 GACTCTTAATGATTTTAGCTGAAAGGA 57.833 33.333 9.70 0.00 0.00 3.36
2914 3017 9.171877 AGACTCTTAATGATTTTAGCTGAAAGG 57.828 33.333 9.70 0.00 0.00 3.11
2915 3018 9.985318 CAGACTCTTAATGATTTTAGCTGAAAG 57.015 33.333 9.70 0.00 0.00 2.62
2916 3019 9.725019 TCAGACTCTTAATGATTTTAGCTGAAA 57.275 29.630 6.09 6.09 0.00 2.69
2917 3020 9.725019 TTCAGACTCTTAATGATTTTAGCTGAA 57.275 29.630 0.00 0.00 35.78 3.02
2918 3021 9.896645 ATTCAGACTCTTAATGATTTTAGCTGA 57.103 29.630 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.