Multiple sequence alignment - TraesCS3B01G287200

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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 TraesCS3B01G287200 chr3B 100.000 3114 0 0 1 3114 459445088 459441975 0.000 5751.0
1 TraesCS3B01G287200 chr3D 92.303 1767 71 29 1 1742 357800514 357798788 0.000 2449.0
2 TraesCS3B01G287200 chr3D 91.365 938 62 12 1742 2675 357798740 357797818 0.000 1266.0
3 TraesCS3B01G287200 chr3A 92.996 1128 46 19 590 1696 477332041 477330926 0.000 1615.0
4 TraesCS3B01G287200 chr3A 92.756 635 25 2 1742 2373 477330846 477330230 0.000 898.0
5 TraesCS3B01G287200 chr3A 90.183 601 37 9 1 592 477332740 477332153 0.000 763.0
6 TraesCS3B01G287200 chr4D 96.970 33 0 1 3070 3101 62708397 62708365 0.002 54.7


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 TraesCS3B01G287200 chr3B 459441975 459445088 3113 True 5751.0 5751 100.000000 1 3114 1 chr3B.!!$R1 3113
1 TraesCS3B01G287200 chr3D 357797818 357800514 2696 True 1857.5 2449 91.834000 1 2675 2 chr3D.!!$R1 2674
2 TraesCS3B01G287200 chr3A 477330230 477332740 2510 True 1092.0 1615 91.978333 1 2373 3 chr3A.!!$R1 2372

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
961 1104 0.107654 AGGCAGACGTGGAAATAGCC 60.108 55.0 0.0 0.0 40.85 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2734 2945 0.105964 CCTCCAACATATCGGCCGAA 59.894 55.0 34.66 21.47 0.0 4.3 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
23 24 0.517316 GGCAAACTGACGTGGTGATC 59.483 55.000 0.00 0.00 0.00 2.92
176 186 7.831193 ACTTATATTTGGCTCAACTGATGACTT 59.169 33.333 0.00 0.00 33.47 3.01
181 191 5.016051 TGGCTCAACTGATGACTTATCTC 57.984 43.478 0.00 0.00 36.71 2.75
212 222 3.429492 TGAGCATAGAATTGCCAAACCA 58.571 40.909 0.00 0.00 43.83 3.67
320 330 1.882989 GCTCCGCTTCTCAGAGGTGT 61.883 60.000 0.00 0.00 40.81 4.16
363 373 4.835891 CCTAGGGCCGGAGACCGT 62.836 72.222 5.05 0.34 46.80 4.83
365 375 2.757099 TAGGGCCGGAGACCGTTC 60.757 66.667 5.05 1.05 46.80 3.95
388 398 1.010419 CAAATGACGGCCAAGCAAGC 61.010 55.000 2.24 0.00 0.00 4.01
557 571 4.537688 ACCAGGAAAGATTCTTCAGATCCA 59.462 41.667 14.42 0.00 0.00 3.41
593 607 7.436430 CGATAGTCTGTAGATAGCTGGTAAA 57.564 40.000 0.00 0.00 0.00 2.01
594 608 8.046294 CGATAGTCTGTAGATAGCTGGTAAAT 57.954 38.462 0.00 0.00 0.00 1.40
595 609 8.516234 CGATAGTCTGTAGATAGCTGGTAAATT 58.484 37.037 0.00 0.00 0.00 1.82
799 938 1.112113 GCAGTCTCCCGTTCCATAGA 58.888 55.000 0.00 0.00 0.00 1.98
865 1008 4.611355 GCCGATGATTCAACCATACAATCG 60.611 45.833 0.00 0.00 30.35 3.34
923 1066 2.566529 GCTACAAAAGCCACGGCC 59.433 61.111 3.95 0.00 46.25 6.13
924 1067 2.867472 CTACAAAAGCCACGGCCG 59.133 61.111 26.86 26.86 43.17 6.13
925 1068 2.670251 TACAAAAGCCACGGCCGG 60.670 61.111 31.76 18.27 43.17 6.13
957 1100 0.250513 GAGGAGGCAGACGTGGAAAT 59.749 55.000 0.00 0.00 0.00 2.17
958 1101 1.480954 GAGGAGGCAGACGTGGAAATA 59.519 52.381 0.00 0.00 0.00 1.40
959 1102 1.482593 AGGAGGCAGACGTGGAAATAG 59.517 52.381 0.00 0.00 0.00 1.73
960 1103 1.291132 GAGGCAGACGTGGAAATAGC 58.709 55.000 0.00 0.00 0.00 2.97
961 1104 0.107654 AGGCAGACGTGGAAATAGCC 60.108 55.000 0.00 0.00 40.85 3.93
963 1106 1.448985 GCAGACGTGGAAATAGCCAA 58.551 50.000 0.00 0.00 40.20 4.52
965 1108 2.935238 GCAGACGTGGAAATAGCCAAGA 60.935 50.000 0.00 0.00 40.20 3.02
966 1109 3.535561 CAGACGTGGAAATAGCCAAGAT 58.464 45.455 0.00 0.00 40.20 2.40
967 1110 4.693283 CAGACGTGGAAATAGCCAAGATA 58.307 43.478 0.00 0.00 40.20 1.98
968 1111 4.508124 CAGACGTGGAAATAGCCAAGATAC 59.492 45.833 0.00 0.00 40.20 2.24
969 1112 4.161565 AGACGTGGAAATAGCCAAGATACA 59.838 41.667 0.00 0.00 40.20 2.29
970 1113 4.839121 ACGTGGAAATAGCCAAGATACAA 58.161 39.130 0.00 0.00 40.20 2.41
983 1126 5.059833 CCAAGATACAATACAAGGAGGCTC 58.940 45.833 5.78 5.78 0.00 4.70
1098 1241 1.556911 CTCTCCCCAGTGTAAGCATGT 59.443 52.381 0.00 0.00 0.00 3.21
1103 1248 5.427157 TCTCCCCAGTGTAAGCATGTTATAA 59.573 40.000 0.00 0.00 0.00 0.98
1111 1256 8.623903 CAGTGTAAGCATGTTATAAATGGATGT 58.376 33.333 0.00 0.00 0.00 3.06
1252 1402 3.292481 TTCGACGGGCTCCCCTACT 62.292 63.158 0.00 0.00 42.67 2.57
1293 1443 1.427809 TCATCTGCCTCTGGTATGGG 58.572 55.000 0.00 0.00 0.00 4.00
1430 1580 2.421107 GGGTAATTTCCTTCCCGTCCTC 60.421 54.545 0.73 0.00 0.00 3.71
1439 1590 2.047560 CCCGTCCTCAACCCGTTC 60.048 66.667 0.00 0.00 0.00 3.95
1452 1603 1.337823 ACCCGTTCCACTTTCATCTCG 60.338 52.381 0.00 0.00 0.00 4.04
1503 1659 6.711277 TGCAATACTTCTTCCTGTACTGAAT 58.289 36.000 0.60 0.00 0.00 2.57
1511 1667 7.873505 ACTTCTTCCTGTACTGAATTCTGTTAC 59.126 37.037 21.17 16.42 0.00 2.50
1514 1670 4.081862 TCCTGTACTGAATTCTGTTACCCG 60.082 45.833 21.17 7.75 0.00 5.28
1515 1671 4.322499 CCTGTACTGAATTCTGTTACCCGT 60.322 45.833 21.17 0.00 0.00 5.28
1704 1860 2.279918 GTACGCCGCCCGATCAAT 60.280 61.111 0.65 0.00 41.02 2.57
1738 1894 7.713073 CCTCATCAAAATTTCTCCTACCTAGAC 59.287 40.741 0.00 0.00 0.00 2.59
1739 1895 8.146053 TCATCAAAATTTCTCCTACCTAGACA 57.854 34.615 0.00 0.00 0.00 3.41
1740 1896 8.772250 TCATCAAAATTTCTCCTACCTAGACAT 58.228 33.333 0.00 0.00 0.00 3.06
1870 2075 1.598924 CCTCTTTCGCGGTATACGGAC 60.599 57.143 14.13 5.02 44.51 4.79
1957 2162 5.010112 ACTTGAATCGATGTATCTGTCGGAT 59.990 40.000 0.00 0.00 38.34 4.18
1958 2163 5.048153 TGAATCGATGTATCTGTCGGATC 57.952 43.478 0.00 0.00 38.34 3.36
1959 2164 3.748868 ATCGATGTATCTGTCGGATCG 57.251 47.619 0.00 0.00 38.34 3.69
1960 2165 1.804748 TCGATGTATCTGTCGGATCGG 59.195 52.381 0.00 0.00 38.34 4.18
1961 2166 1.804748 CGATGTATCTGTCGGATCGGA 59.195 52.381 0.00 0.00 35.98 4.55
1966 2171 0.034059 ATCTGTCGGATCGGAATGCC 59.966 55.000 4.31 0.00 0.00 4.40
2069 2274 2.159421 GCACTCTACGCTTACTACAGCA 60.159 50.000 0.00 0.00 40.09 4.41
2090 2295 3.958798 CAGGAAATGGAGATGCAAGGATT 59.041 43.478 0.00 0.00 0.00 3.01
2092 2297 3.956199 GGAAATGGAGATGCAAGGATTCA 59.044 43.478 0.00 0.00 0.00 2.57
2161 2366 2.420058 TTAGCTTGGCTAGAAAGGGC 57.580 50.000 0.00 0.00 42.34 5.19
2270 2475 5.535333 GCCTACGCCTCTGTTTATATGTTA 58.465 41.667 0.00 0.00 0.00 2.41
2291 2498 9.965902 ATGTTACTCAAGTATCATTCTTTTCCT 57.034 29.630 7.58 0.00 37.55 3.36
2292 2499 9.219603 TGTTACTCAAGTATCATTCTTTTCCTG 57.780 33.333 0.00 0.00 0.00 3.86
2332 2542 7.047891 GGATATTTTGTTTGATTCCCCCTTTC 58.952 38.462 0.00 0.00 0.00 2.62
2376 2586 7.550196 ACACAAATATTTCAATTCTGGGCATTC 59.450 33.333 0.00 0.00 0.00 2.67
2378 2588 8.323567 ACAAATATTTCAATTCTGGGCATTCTT 58.676 29.630 0.00 0.00 0.00 2.52
2443 2653 8.275758 TGTACATTTTATACCACCACACCATAT 58.724 33.333 0.00 0.00 0.00 1.78
2495 2705 2.817844 GGTAGCCAAGAAAAACGACCAT 59.182 45.455 0.00 0.00 0.00 3.55
2497 2707 4.261867 GGTAGCCAAGAAAAACGACCATTT 60.262 41.667 0.00 0.00 0.00 2.32
2500 2710 2.799978 CCAAGAAAAACGACCATTTGGC 59.200 45.455 0.00 0.00 39.32 4.52
2532 2743 6.317857 GTGGCTATCTCAAAAACAATGAGTC 58.682 40.000 3.72 0.00 43.77 3.36
2535 2746 7.025963 GGCTATCTCAAAAACAATGAGTCAAG 58.974 38.462 0.00 0.00 43.77 3.02
2542 2753 8.824159 TCAAAAACAATGAGTCAAGAAAAACA 57.176 26.923 0.00 0.00 0.00 2.83
2619 2830 9.453325 ACAAACCTAAAAACACAACGTATTATG 57.547 29.630 0.00 0.00 0.00 1.90
2668 2879 5.921004 TGTCTTGCAATTTTTATGCCAAC 57.079 34.783 0.00 0.00 43.16 3.77
2672 2883 7.066766 TGTCTTGCAATTTTTATGCCAACTTTT 59.933 29.630 0.00 0.00 43.16 2.27
2687 2898 5.719173 CCAACTTTTGGTTTCTGAAACTCA 58.281 37.500 26.93 20.90 45.93 3.41
2688 2899 6.162777 CCAACTTTTGGTTTCTGAAACTCAA 58.837 36.000 26.93 24.20 45.93 3.02
2689 2900 6.648725 CCAACTTTTGGTTTCTGAAACTCAAA 59.351 34.615 27.23 27.23 45.93 2.69
2690 2901 7.360017 CCAACTTTTGGTTTCTGAAACTCAAAC 60.360 37.037 28.96 17.71 45.93 2.93
2691 2902 6.754193 ACTTTTGGTTTCTGAAACTCAAACA 58.246 32.000 28.96 22.72 39.23 2.83
2692 2903 7.386059 ACTTTTGGTTTCTGAAACTCAAACAT 58.614 30.769 28.96 22.44 39.23 2.71
2693 2904 7.331687 ACTTTTGGTTTCTGAAACTCAAACATG 59.668 33.333 28.96 24.92 39.23 3.21
2694 2905 6.522625 TTGGTTTCTGAAACTCAAACATGA 57.477 33.333 26.93 9.27 41.14 3.07
2695 2906 6.522625 TGGTTTCTGAAACTCAAACATGAA 57.477 33.333 26.93 2.90 41.14 2.57
2696 2907 6.329496 TGGTTTCTGAAACTCAAACATGAAC 58.671 36.000 26.93 10.70 41.14 3.18
2697 2908 5.455525 GGTTTCTGAAACTCAAACATGAACG 59.544 40.000 26.93 0.00 41.14 3.95
2698 2909 5.811399 TTCTGAAACTCAAACATGAACGT 57.189 34.783 0.00 0.00 0.00 3.99
2699 2910 6.912203 TTCTGAAACTCAAACATGAACGTA 57.088 33.333 0.00 0.00 0.00 3.57
2700 2911 6.912203 TCTGAAACTCAAACATGAACGTAA 57.088 33.333 0.00 0.00 0.00 3.18
2718 2929 5.486095 CGTAAGTTACGTAACCACTTGTC 57.514 43.478 29.87 15.96 46.41 3.18
2719 2930 4.382754 CGTAAGTTACGTAACCACTTGTCC 59.617 45.833 29.87 12.41 46.41 4.02
2720 2931 4.677673 AAGTTACGTAACCACTTGTCCT 57.322 40.909 29.87 9.61 36.88 3.85
2721 2932 4.248691 AGTTACGTAACCACTTGTCCTC 57.751 45.455 29.87 5.56 36.88 3.71
2722 2933 3.006217 AGTTACGTAACCACTTGTCCTCC 59.994 47.826 29.87 5.37 36.88 4.30
2723 2934 1.416243 ACGTAACCACTTGTCCTCCA 58.584 50.000 0.00 0.00 0.00 3.86
2724 2935 1.343465 ACGTAACCACTTGTCCTCCAG 59.657 52.381 0.00 0.00 0.00 3.86
2725 2936 1.343465 CGTAACCACTTGTCCTCCAGT 59.657 52.381 0.00 0.00 0.00 4.00
2726 2937 2.767505 GTAACCACTTGTCCTCCAGTG 58.232 52.381 0.00 0.00 0.00 3.66
2728 2939 1.302832 CCACTTGTCCTCCAGTGGC 60.303 63.158 3.51 0.00 44.11 5.01
2729 2940 1.669115 CACTTGTCCTCCAGTGGCG 60.669 63.158 3.51 0.00 0.00 5.69
2730 2941 2.046892 CTTGTCCTCCAGTGGCGG 60.047 66.667 12.36 12.36 0.00 6.13
2731 2942 2.525629 TTGTCCTCCAGTGGCGGA 60.526 61.111 17.28 17.28 33.75 5.54
2746 2957 4.268687 GGAGCTTCGGCCGATATG 57.731 61.111 31.56 22.18 43.01 1.78
2747 2958 1.367840 GGAGCTTCGGCCGATATGT 59.632 57.895 31.56 14.33 43.01 2.29
2748 2959 0.249911 GGAGCTTCGGCCGATATGTT 60.250 55.000 31.56 19.57 43.01 2.71
2749 2960 0.861837 GAGCTTCGGCCGATATGTTG 59.138 55.000 31.56 15.40 43.01 3.33
2750 2961 0.532862 AGCTTCGGCCGATATGTTGG 60.533 55.000 31.56 13.61 43.01 3.77
2751 2962 0.531974 GCTTCGGCCGATATGTTGGA 60.532 55.000 31.56 10.56 34.32 3.53
2752 2963 1.502231 CTTCGGCCGATATGTTGGAG 58.498 55.000 31.56 17.00 0.00 3.86
2753 2964 0.105964 TTCGGCCGATATGTTGGAGG 59.894 55.000 31.56 0.00 0.00 4.30
2754 2965 1.301716 CGGCCGATATGTTGGAGGG 60.302 63.158 24.07 0.00 0.00 4.30
2755 2966 1.600916 GGCCGATATGTTGGAGGGC 60.601 63.158 0.00 0.00 40.27 5.19
2756 2967 1.148273 GCCGATATGTTGGAGGGCA 59.852 57.895 0.00 0.00 40.24 5.36
2757 2968 0.465460 GCCGATATGTTGGAGGGCAA 60.465 55.000 0.00 0.00 40.24 4.52
2758 2969 1.819305 GCCGATATGTTGGAGGGCAAT 60.819 52.381 0.00 0.00 40.24 3.56
2759 2970 1.881973 CCGATATGTTGGAGGGCAATG 59.118 52.381 0.00 0.00 0.00 2.82
2760 2971 1.881973 CGATATGTTGGAGGGCAATGG 59.118 52.381 0.00 0.00 0.00 3.16
2761 2972 2.242043 GATATGTTGGAGGGCAATGGG 58.758 52.381 0.00 0.00 0.00 4.00
2762 2973 0.396974 TATGTTGGAGGGCAATGGGC 60.397 55.000 0.00 0.00 43.74 5.36
2763 2974 3.451894 GTTGGAGGGCAATGGGCG 61.452 66.667 0.00 0.00 46.16 6.13
2764 2975 4.757355 TTGGAGGGCAATGGGCGG 62.757 66.667 0.00 0.00 46.16 6.13
2767 2978 4.424711 GAGGGCAATGGGCGGACA 62.425 66.667 0.00 0.00 46.16 4.02
2768 2979 3.721370 GAGGGCAATGGGCGGACAT 62.721 63.158 0.00 0.00 46.16 3.06
2769 2980 3.530260 GGGCAATGGGCGGACATG 61.530 66.667 0.00 0.00 46.16 3.21
2770 2981 2.755469 GGCAATGGGCGGACATGT 60.755 61.111 0.00 0.00 46.16 3.21
2771 2982 1.453015 GGCAATGGGCGGACATGTA 60.453 57.895 0.00 0.00 46.16 2.29
2772 2983 0.823356 GGCAATGGGCGGACATGTAT 60.823 55.000 0.00 0.00 46.16 2.29
2773 2984 0.593128 GCAATGGGCGGACATGTATC 59.407 55.000 0.00 0.00 0.00 2.24
2774 2985 0.867746 CAATGGGCGGACATGTATCG 59.132 55.000 14.43 14.43 0.00 2.92
2794 3005 3.607422 GCATGCTGCGTTACATATCAA 57.393 42.857 11.37 0.00 31.71 2.57
2795 3006 3.548587 GCATGCTGCGTTACATATCAAG 58.451 45.455 11.37 0.00 31.71 3.02
2796 3007 3.548587 CATGCTGCGTTACATATCAAGC 58.451 45.455 0.00 0.00 0.00 4.01
2797 3008 1.592543 TGCTGCGTTACATATCAAGCG 59.407 47.619 0.00 0.00 0.00 4.68
2798 3009 1.070577 GCTGCGTTACATATCAAGCGG 60.071 52.381 0.00 0.00 0.00 5.52
2799 3010 2.201732 CTGCGTTACATATCAAGCGGT 58.798 47.619 0.00 0.00 0.00 5.68
2800 3011 2.198406 TGCGTTACATATCAAGCGGTC 58.802 47.619 0.00 0.00 0.00 4.79
2801 3012 1.189446 GCGTTACATATCAAGCGGTCG 59.811 52.381 0.00 0.00 0.00 4.79
2802 3013 1.189446 CGTTACATATCAAGCGGTCGC 59.811 52.381 7.32 7.32 42.33 5.19
2803 3014 1.525619 GTTACATATCAAGCGGTCGCC 59.474 52.381 11.95 0.00 43.17 5.54
2804 3015 1.037493 TACATATCAAGCGGTCGCCT 58.963 50.000 11.95 0.00 43.17 5.52
2805 3016 1.037493 ACATATCAAGCGGTCGCCTA 58.963 50.000 11.95 0.00 43.17 3.93
2806 3017 1.269621 ACATATCAAGCGGTCGCCTAC 60.270 52.381 11.95 0.00 43.17 3.18
2807 3018 1.037493 ATATCAAGCGGTCGCCTACA 58.963 50.000 11.95 0.00 43.17 2.74
2808 3019 0.384309 TATCAAGCGGTCGCCTACAG 59.616 55.000 11.95 0.00 43.17 2.74
2809 3020 1.320344 ATCAAGCGGTCGCCTACAGA 61.320 55.000 11.95 3.87 43.17 3.41
2810 3021 1.805945 CAAGCGGTCGCCTACAGAC 60.806 63.158 11.95 0.00 43.17 3.51
2815 3026 4.340620 GTCGCCTACAGACCTCCT 57.659 61.111 0.00 0.00 32.78 3.69
2816 3027 2.108568 GTCGCCTACAGACCTCCTC 58.891 63.158 0.00 0.00 32.78 3.71
2817 3028 1.451567 TCGCCTACAGACCTCCTCG 60.452 63.158 0.00 0.00 0.00 4.63
2818 3029 1.749638 CGCCTACAGACCTCCTCGT 60.750 63.158 0.00 0.00 0.00 4.18
2819 3030 1.716826 CGCCTACAGACCTCCTCGTC 61.717 65.000 0.00 0.00 0.00 4.20
2820 3031 1.716826 GCCTACAGACCTCCTCGTCG 61.717 65.000 0.00 0.00 37.85 5.12
2821 3032 1.716826 CCTACAGACCTCCTCGTCGC 61.717 65.000 0.00 0.00 37.85 5.19
2822 3033 0.745128 CTACAGACCTCCTCGTCGCT 60.745 60.000 0.00 0.00 37.85 4.93
2823 3034 0.538584 TACAGACCTCCTCGTCGCTA 59.461 55.000 0.00 0.00 37.85 4.26
2824 3035 0.745128 ACAGACCTCCTCGTCGCTAG 60.745 60.000 0.00 0.00 37.85 3.42
2825 3036 1.820481 AGACCTCCTCGTCGCTAGC 60.820 63.158 4.06 4.06 37.85 3.42
2826 3037 2.045242 ACCTCCTCGTCGCTAGCA 60.045 61.111 16.45 0.00 0.00 3.49
2827 3038 1.448922 GACCTCCTCGTCGCTAGCAT 61.449 60.000 16.45 0.00 0.00 3.79
2828 3039 1.007964 CCTCCTCGTCGCTAGCATG 60.008 63.158 16.45 7.70 0.00 4.06
2829 3040 1.007964 CTCCTCGTCGCTAGCATGG 60.008 63.158 16.45 8.63 0.00 3.66
2830 3041 1.729470 CTCCTCGTCGCTAGCATGGT 61.729 60.000 16.45 1.62 0.00 3.55
2831 3042 1.589993 CCTCGTCGCTAGCATGGTG 60.590 63.158 16.45 3.49 0.00 4.17
2832 3043 1.589993 CTCGTCGCTAGCATGGTGG 60.590 63.158 16.45 5.65 0.00 4.61
2833 3044 2.586079 CGTCGCTAGCATGGTGGG 60.586 66.667 16.45 6.39 0.00 4.61
2834 3045 2.203070 GTCGCTAGCATGGTGGGG 60.203 66.667 17.52 17.52 0.00 4.96
2835 3046 2.687200 TCGCTAGCATGGTGGGGT 60.687 61.111 21.56 0.00 0.00 4.95
2836 3047 2.514592 CGCTAGCATGGTGGGGTG 60.515 66.667 16.45 5.56 0.00 4.61
2837 3048 2.124151 GCTAGCATGGTGGGGTGG 60.124 66.667 10.63 0.00 0.00 4.61
2838 3049 2.679342 GCTAGCATGGTGGGGTGGA 61.679 63.158 10.63 0.00 0.00 4.02
2839 3050 1.224592 CTAGCATGGTGGGGTGGAC 59.775 63.158 7.89 0.00 0.00 4.02
2840 3051 2.270874 CTAGCATGGTGGGGTGGACC 62.271 65.000 7.89 0.00 39.11 4.46
2842 3053 4.424711 CATGGTGGGGTGGACCGG 62.425 72.222 0.00 0.00 41.60 5.28
2849 3060 3.413300 GGGTGGACCGGCCCATTA 61.413 66.667 14.50 0.00 44.23 1.90
2850 3061 2.192175 GGTGGACCGGCCCATTAG 59.808 66.667 14.50 0.00 38.66 1.73
2851 3062 2.516225 GTGGACCGGCCCATTAGC 60.516 66.667 14.50 0.00 38.66 3.09
2852 3063 4.169696 TGGACCGGCCCATTAGCG 62.170 66.667 4.87 0.00 34.97 4.26
2854 3065 4.849310 GACCGGCCCATTAGCGCA 62.849 66.667 11.47 0.00 0.00 6.09
2857 3068 3.876198 CGGCCCATTAGCGCACAC 61.876 66.667 11.47 0.00 0.00 3.82
2858 3069 3.518068 GGCCCATTAGCGCACACC 61.518 66.667 11.47 0.00 0.00 4.16
2859 3070 2.438434 GCCCATTAGCGCACACCT 60.438 61.111 11.47 0.00 0.00 4.00
2860 3071 2.764314 GCCCATTAGCGCACACCTG 61.764 63.158 11.47 0.00 0.00 4.00
2861 3072 2.114670 CCCATTAGCGCACACCTGG 61.115 63.158 11.47 8.83 0.00 4.45
2862 3073 2.114670 CCATTAGCGCACACCTGGG 61.115 63.158 11.47 0.00 0.00 4.45
2863 3074 1.078497 CATTAGCGCACACCTGGGA 60.078 57.895 11.47 0.00 31.89 4.37
2864 3075 0.464373 CATTAGCGCACACCTGGGAT 60.464 55.000 11.47 0.00 32.93 3.85
2865 3076 0.179045 ATTAGCGCACACCTGGGATC 60.179 55.000 11.47 0.00 30.50 3.36
2866 3077 2.572095 TTAGCGCACACCTGGGATCG 62.572 60.000 11.47 0.00 30.50 3.69
2868 3079 4.457496 CGCACACCTGGGATCGCT 62.457 66.667 11.46 0.00 31.89 4.93
2869 3080 2.512515 GCACACCTGGGATCGCTC 60.513 66.667 11.46 0.00 0.00 5.03
2870 3081 2.202797 CACACCTGGGATCGCTCG 60.203 66.667 11.46 3.44 0.00 5.03
2871 3082 4.148825 ACACCTGGGATCGCTCGC 62.149 66.667 11.46 0.00 35.01 5.03
2872 3083 3.842923 CACCTGGGATCGCTCGCT 61.843 66.667 11.46 0.00 35.45 4.93
2873 3084 3.532155 ACCTGGGATCGCTCGCTC 61.532 66.667 11.46 0.00 35.45 5.03
2874 3085 4.292178 CCTGGGATCGCTCGCTCC 62.292 72.222 11.46 3.76 35.45 4.70
2877 3088 4.292178 GGGATCGCTCGCTCCCAG 62.292 72.222 22.08 0.00 46.73 4.45
2878 3089 3.532155 GGATCGCTCGCTCCCAGT 61.532 66.667 1.02 0.00 0.00 4.00
2879 3090 2.194212 GGATCGCTCGCTCCCAGTA 61.194 63.158 1.02 0.00 0.00 2.74
2880 3091 1.528292 GGATCGCTCGCTCCCAGTAT 61.528 60.000 1.02 0.00 0.00 2.12
2881 3092 1.166129 GATCGCTCGCTCCCAGTATA 58.834 55.000 0.00 0.00 0.00 1.47
2882 3093 1.746220 GATCGCTCGCTCCCAGTATAT 59.254 52.381 0.00 0.00 0.00 0.86
2883 3094 2.484742 TCGCTCGCTCCCAGTATATA 57.515 50.000 0.00 0.00 0.00 0.86
2884 3095 3.000684 TCGCTCGCTCCCAGTATATAT 57.999 47.619 0.00 0.00 0.00 0.86
2885 3096 2.683362 TCGCTCGCTCCCAGTATATATG 59.317 50.000 0.00 0.00 0.00 1.78
2886 3097 2.423892 CGCTCGCTCCCAGTATATATGT 59.576 50.000 0.00 0.00 0.00 2.29
2887 3098 3.626217 CGCTCGCTCCCAGTATATATGTA 59.374 47.826 0.00 0.00 0.00 2.29
2888 3099 4.276183 CGCTCGCTCCCAGTATATATGTAT 59.724 45.833 0.00 0.00 0.00 2.29
2889 3100 5.524284 GCTCGCTCCCAGTATATATGTATG 58.476 45.833 0.00 0.00 0.00 2.39
2890 3101 5.508153 GCTCGCTCCCAGTATATATGTATGG 60.508 48.000 0.00 1.00 0.00 2.74
2891 3102 5.516044 TCGCTCCCAGTATATATGTATGGT 58.484 41.667 10.20 0.00 0.00 3.55
2892 3103 5.359860 TCGCTCCCAGTATATATGTATGGTG 59.640 44.000 10.20 5.75 0.00 4.17
2893 3104 5.127194 CGCTCCCAGTATATATGTATGGTGT 59.873 44.000 10.20 0.00 0.00 4.16
2894 3105 6.351033 CGCTCCCAGTATATATGTATGGTGTT 60.351 42.308 10.20 0.00 0.00 3.32
2895 3106 7.042335 GCTCCCAGTATATATGTATGGTGTTC 58.958 42.308 10.20 0.00 0.00 3.18
2896 3107 7.490657 TCCCAGTATATATGTATGGTGTTCC 57.509 40.000 10.20 0.00 0.00 3.62
2924 3135 5.591643 AAAAAGCATACGTACTGTCTGTG 57.408 39.130 0.00 0.00 0.00 3.66
2925 3136 3.936372 AAGCATACGTACTGTCTGTGT 57.064 42.857 0.00 0.00 0.00 3.72
2926 3137 3.217599 AGCATACGTACTGTCTGTGTG 57.782 47.619 0.00 5.20 0.00 3.82
2927 3138 2.094700 AGCATACGTACTGTCTGTGTGG 60.095 50.000 0.00 0.00 0.00 4.17
2928 3139 2.352421 GCATACGTACTGTCTGTGTGGT 60.352 50.000 0.00 0.00 0.00 4.16
2929 3140 3.859627 GCATACGTACTGTCTGTGTGGTT 60.860 47.826 0.00 0.00 0.00 3.67
2930 3141 2.973694 ACGTACTGTCTGTGTGGTTT 57.026 45.000 0.00 0.00 0.00 3.27
2931 3142 3.255969 ACGTACTGTCTGTGTGGTTTT 57.744 42.857 0.00 0.00 0.00 2.43
2932 3143 3.602483 ACGTACTGTCTGTGTGGTTTTT 58.398 40.909 0.00 0.00 0.00 1.94
2960 3171 6.548441 TTCTTGTTTTTCCCACTACATACG 57.452 37.500 0.00 0.00 0.00 3.06
2961 3172 5.856156 TCTTGTTTTTCCCACTACATACGA 58.144 37.500 0.00 0.00 0.00 3.43
2962 3173 6.469410 TCTTGTTTTTCCCACTACATACGAT 58.531 36.000 0.00 0.00 0.00 3.73
2963 3174 6.938030 TCTTGTTTTTCCCACTACATACGATT 59.062 34.615 0.00 0.00 0.00 3.34
2964 3175 7.446013 TCTTGTTTTTCCCACTACATACGATTT 59.554 33.333 0.00 0.00 0.00 2.17
2965 3176 7.513371 TGTTTTTCCCACTACATACGATTTT 57.487 32.000 0.00 0.00 0.00 1.82
2966 3177 8.618702 TGTTTTTCCCACTACATACGATTTTA 57.381 30.769 0.00 0.00 0.00 1.52
2967 3178 9.064706 TGTTTTTCCCACTACATACGATTTTAA 57.935 29.630 0.00 0.00 0.00 1.52
2968 3179 9.896263 GTTTTTCCCACTACATACGATTTTAAA 57.104 29.630 0.00 0.00 0.00 1.52
3009 3220 9.626045 AAAAATTCACGGATTAAAGTCATCTTC 57.374 29.630 0.00 0.00 32.90 2.87
3010 3221 7.921786 AATTCACGGATTAAAGTCATCTTCA 57.078 32.000 0.00 0.00 32.90 3.02
3011 3222 7.921786 ATTCACGGATTAAAGTCATCTTCAA 57.078 32.000 0.00 0.00 32.90 2.69
3012 3223 7.921786 TTCACGGATTAAAGTCATCTTCAAT 57.078 32.000 0.00 0.00 32.90 2.57
3013 3224 7.307493 TCACGGATTAAAGTCATCTTCAATG 57.693 36.000 0.00 0.00 32.90 2.82
3014 3225 6.878923 TCACGGATTAAAGTCATCTTCAATGT 59.121 34.615 0.00 0.00 32.90 2.71
3015 3226 7.390440 TCACGGATTAAAGTCATCTTCAATGTT 59.610 33.333 0.00 0.00 32.90 2.71
3016 3227 8.023128 CACGGATTAAAGTCATCTTCAATGTTT 58.977 33.333 0.00 0.00 32.90 2.83
3017 3228 8.576442 ACGGATTAAAGTCATCTTCAATGTTTT 58.424 29.630 0.00 0.00 32.90 2.43
3018 3229 9.410556 CGGATTAAAGTCATCTTCAATGTTTTT 57.589 29.630 0.00 0.00 32.90 1.94
3024 3235 9.447157 AAAGTCATCTTCAATGTTTTTGGAAAA 57.553 25.926 0.00 0.00 32.90 2.29
3025 3236 9.447157 AAGTCATCTTCAATGTTTTTGGAAAAA 57.553 25.926 0.00 0.00 35.67 1.94
3073 3284 8.641499 TGAATGTGAATTCAAAACAAGGTTAC 57.359 30.769 10.35 0.00 37.59 2.50
3074 3285 8.253810 TGAATGTGAATTCAAAACAAGGTTACA 58.746 29.630 10.35 0.00 37.59 2.41
3075 3286 9.092876 GAATGTGAATTCAAAACAAGGTTACAA 57.907 29.630 10.35 0.00 0.00 2.41
3076 3287 9.442047 AATGTGAATTCAAAACAAGGTTACAAA 57.558 25.926 10.35 0.00 0.00 2.83
3077 3288 9.612066 ATGTGAATTCAAAACAAGGTTACAAAT 57.388 25.926 10.35 0.00 0.00 2.32
3078 3289 9.442047 TGTGAATTCAAAACAAGGTTACAAATT 57.558 25.926 10.35 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.069273 CCTCAACAAGATCACCACGTC 58.931 52.381 0.00 0.00 0.00 4.34
13 14 1.416401 ACCTCAACAAGATCACCACGT 59.584 47.619 0.00 0.00 0.00 4.49
93 94 2.599677 TCGGGGTAAAACTTGCCATTT 58.400 42.857 0.00 0.00 37.12 2.32
95 96 2.525105 ATCGGGGTAAAACTTGCCAT 57.475 45.000 0.00 0.00 37.12 4.40
97 98 3.322369 CAAAATCGGGGTAAAACTTGCC 58.678 45.455 0.00 0.00 34.30 4.52
98 99 2.734606 GCAAAATCGGGGTAAAACTTGC 59.265 45.455 0.00 0.00 0.00 4.01
99 100 2.983803 CGCAAAATCGGGGTAAAACTTG 59.016 45.455 0.00 0.00 0.00 3.16
100 101 2.885894 TCGCAAAATCGGGGTAAAACTT 59.114 40.909 0.00 0.00 0.00 2.66
101 102 2.506444 TCGCAAAATCGGGGTAAAACT 58.494 42.857 0.00 0.00 0.00 2.66
102 103 2.993449 TCGCAAAATCGGGGTAAAAC 57.007 45.000 0.00 0.00 0.00 2.43
103 104 2.351932 GCTTCGCAAAATCGGGGTAAAA 60.352 45.455 0.00 0.00 0.00 1.52
176 186 6.946340 TCTATGCTCAAAACTTGTGGAGATA 58.054 36.000 0.00 0.00 0.00 1.98
181 191 5.346822 GCAATTCTATGCTCAAAACTTGTGG 59.653 40.000 0.00 0.00 43.06 4.17
212 222 2.574006 TCAGCAAGGAGAAATGCAGT 57.426 45.000 0.00 0.00 44.95 4.40
320 330 0.672401 GAAGATTGGACGGCCGACAA 60.672 55.000 35.90 32.72 36.79 3.18
363 373 0.535328 TTGGCCGTCATTTGACCGAA 60.535 50.000 0.00 0.00 41.86 4.30
365 375 1.501741 CTTGGCCGTCATTTGACCG 59.498 57.895 0.00 0.38 41.86 4.79
388 398 3.583882 AAGGTTGGATGGCCACCGG 62.584 63.158 8.16 0.00 45.94 5.28
515 529 4.862371 TGGTGTCCAGGTAGTTTCTTTTT 58.138 39.130 0.00 0.00 0.00 1.94
516 530 4.513406 TGGTGTCCAGGTAGTTTCTTTT 57.487 40.909 0.00 0.00 0.00 2.27
557 571 2.993899 CAGACTATCGTTTTCTGCGGTT 59.006 45.455 0.00 0.00 30.90 4.44
613 742 1.654954 CTGGCAAGATCACTGCTGGC 61.655 60.000 16.60 8.47 32.43 4.85
614 743 0.322277 ACTGGCAAGATCACTGCTGG 60.322 55.000 16.60 12.50 0.00 4.85
616 745 0.959372 GCACTGGCAAGATCACTGCT 60.959 55.000 16.60 0.00 40.72 4.24
617 746 1.505353 GCACTGGCAAGATCACTGC 59.495 57.895 10.52 10.52 40.72 4.40
619 748 0.671781 GACGCACTGGCAAGATCACT 60.672 55.000 0.00 0.00 41.24 3.41
620 749 0.950555 TGACGCACTGGCAAGATCAC 60.951 55.000 0.00 0.00 41.24 3.06
721 857 1.134995 TGTCTTGCCTCTGCTGATACG 60.135 52.381 0.00 0.00 38.71 3.06
812 955 1.143183 GGGAACGCGCCTCTTCATA 59.857 57.895 5.73 0.00 0.00 2.15
865 1008 0.755327 AACCCCACAGCCACAAGTTC 60.755 55.000 0.00 0.00 0.00 3.01
923 1066 0.320374 TCCTCAGCACTGTAAACCCG 59.680 55.000 0.00 0.00 0.00 5.28
924 1067 1.339151 CCTCCTCAGCACTGTAAACCC 60.339 57.143 0.00 0.00 0.00 4.11
925 1068 1.946283 GCCTCCTCAGCACTGTAAACC 60.946 57.143 0.00 0.00 0.00 3.27
926 1069 1.270839 TGCCTCCTCAGCACTGTAAAC 60.271 52.381 0.00 0.00 34.69 2.01
927 1070 1.002430 CTGCCTCCTCAGCACTGTAAA 59.998 52.381 0.00 0.00 36.01 2.01
957 1100 5.454755 GCCTCCTTGTATTGTATCTTGGCTA 60.455 44.000 0.00 0.00 33.45 3.93
958 1101 4.687219 GCCTCCTTGTATTGTATCTTGGCT 60.687 45.833 0.00 0.00 33.45 4.75
959 1102 3.565902 GCCTCCTTGTATTGTATCTTGGC 59.434 47.826 0.00 0.00 0.00 4.52
960 1103 5.041191 AGCCTCCTTGTATTGTATCTTGG 57.959 43.478 0.00 0.00 0.00 3.61
961 1104 5.059833 GGAGCCTCCTTGTATTGTATCTTG 58.940 45.833 2.64 0.00 32.53 3.02
963 1106 4.561752 AGGAGCCTCCTTGTATTGTATCT 58.438 43.478 7.68 0.00 46.91 1.98
983 1126 6.183360 GGAGTCCATGAATGAAAGATTGAAGG 60.183 42.308 3.60 0.00 0.00 3.46
1098 1241 6.151985 ACGAAACCAGCAACATCCATTTATAA 59.848 34.615 0.00 0.00 0.00 0.98
1103 1248 2.238521 ACGAAACCAGCAACATCCATT 58.761 42.857 0.00 0.00 0.00 3.16
1111 1256 1.819288 TCAAACCAACGAAACCAGCAA 59.181 42.857 0.00 0.00 0.00 3.91
1252 1402 0.035881 CAGTTGAGCAGGGAGAGCAA 59.964 55.000 0.00 0.00 0.00 3.91
1293 1443 4.779733 TCGGAGACCCAGGGGAGC 62.780 72.222 11.37 2.55 38.96 4.70
1430 1580 2.484264 GAGATGAAAGTGGAACGGGTTG 59.516 50.000 0.00 0.00 45.86 3.77
1439 1590 3.403038 ACTGTTTCCGAGATGAAAGTGG 58.597 45.455 0.00 0.00 35.04 4.00
1452 1603 0.179012 TTCCCCGTTGGACTGTTTCC 60.179 55.000 0.00 0.00 45.11 3.13
1503 1659 2.438763 TGGAGGAAAACGGGTAACAGAA 59.561 45.455 0.00 0.00 39.74 3.02
1511 1667 1.073199 AGCTGTGGAGGAAAACGGG 59.927 57.895 0.00 0.00 0.00 5.28
1695 1851 1.072159 GGAGCCCAGATTGATCGGG 59.928 63.158 13.24 13.24 41.13 5.14
1699 1855 2.415624 TGATGAGGAGCCCAGATTGAT 58.584 47.619 0.00 0.00 0.00 2.57
1704 1860 3.744940 AATTTTGATGAGGAGCCCAGA 57.255 42.857 0.00 0.00 0.00 3.86
1738 1894 3.931468 GGAGACATGTGTGAGAACAGATG 59.069 47.826 1.15 12.80 44.08 2.90
1739 1895 3.580022 TGGAGACATGTGTGAGAACAGAT 59.420 43.478 1.15 0.00 32.52 2.90
1740 1896 2.965147 TGGAGACATGTGTGAGAACAGA 59.035 45.455 1.15 0.00 32.52 3.41
1870 2075 0.740164 AAGAGATCACGCAGCAGCAG 60.740 55.000 0.82 0.00 42.27 4.24
1953 2158 2.537560 GCACAGGCATTCCGATCCG 61.538 63.158 0.00 0.00 40.72 4.18
1957 2162 1.375908 GTCAGCACAGGCATTCCGA 60.376 57.895 0.00 0.00 44.61 4.55
1958 2163 2.743752 CGTCAGCACAGGCATTCCG 61.744 63.158 0.00 0.00 44.61 4.30
1959 2164 0.745845 ATCGTCAGCACAGGCATTCC 60.746 55.000 0.00 0.00 44.61 3.01
1960 2165 1.089920 AATCGTCAGCACAGGCATTC 58.910 50.000 0.00 0.00 44.61 2.67
1961 2166 0.806868 CAATCGTCAGCACAGGCATT 59.193 50.000 0.00 0.00 44.61 3.56
1966 2171 1.728971 GAAGTCCAATCGTCAGCACAG 59.271 52.381 0.00 0.00 0.00 3.66
2050 2255 2.683867 CCTGCTGTAGTAAGCGTAGAGT 59.316 50.000 0.00 0.00 46.65 3.24
2069 2274 3.967467 ATCCTTGCATCTCCATTTCCT 57.033 42.857 0.00 0.00 0.00 3.36
2161 2366 1.295423 CTACAGAACCCCACACCCG 59.705 63.158 0.00 0.00 0.00 5.28
2212 2417 5.117355 ACAAACTGATTCAGCATCAACTG 57.883 39.130 13.64 3.77 41.66 3.16
2270 2475 8.378565 TCTTCAGGAAAAGAATGATACTTGAGT 58.621 33.333 0.00 0.00 32.42 3.41
2291 2498 1.600058 ATCCCCCTCTGCATTCTTCA 58.400 50.000 0.00 0.00 0.00 3.02
2292 2499 4.379302 AATATCCCCCTCTGCATTCTTC 57.621 45.455 0.00 0.00 0.00 2.87
2421 2631 9.883142 AAAAATATGGTGTGGTGGTATAAAATG 57.117 29.630 0.00 0.00 0.00 2.32
2467 2677 4.685628 CGTTTTTCTTGGCTACCTACGTAA 59.314 41.667 0.00 0.00 0.00 3.18
2471 2681 3.434641 GGTCGTTTTTCTTGGCTACCTAC 59.565 47.826 0.00 0.00 0.00 3.18
2476 2686 4.261825 CCAAATGGTCGTTTTTCTTGGCTA 60.262 41.667 0.00 0.00 0.00 3.93
2479 2689 2.799978 GCCAAATGGTCGTTTTTCTTGG 59.200 45.455 0.71 0.00 37.57 3.61
2480 2690 3.452474 TGCCAAATGGTCGTTTTTCTTG 58.548 40.909 0.71 0.00 37.57 3.02
2495 2705 0.403655 TAGCCACCACTCATGCCAAA 59.596 50.000 0.00 0.00 0.00 3.28
2497 2707 0.181114 GATAGCCACCACTCATGCCA 59.819 55.000 0.00 0.00 0.00 4.92
2500 2710 3.548745 TTGAGATAGCCACCACTCATG 57.451 47.619 0.00 0.00 38.79 3.07
2539 2750 9.862371 TGTGTTTGTGTATTTTGTTCTTATGTT 57.138 25.926 0.00 0.00 0.00 2.71
2640 2851 6.852345 GGCATAAAAATTGCAAGACAACAAAG 59.148 34.615 4.94 0.00 42.27 2.77
2668 2879 7.545265 TCATGTTTGAGTTTCAGAAACCAAAAG 59.455 33.333 27.06 22.20 42.34 2.27
2672 2883 6.329496 GTTCATGTTTGAGTTTCAGAAACCA 58.671 36.000 20.47 15.34 42.34 3.67
2674 2885 6.027749 ACGTTCATGTTTGAGTTTCAGAAAC 58.972 36.000 17.11 17.11 41.69 2.78
2675 2886 6.189677 ACGTTCATGTTTGAGTTTCAGAAA 57.810 33.333 0.00 0.00 32.27 2.52
2676 2887 5.811399 ACGTTCATGTTTGAGTTTCAGAA 57.189 34.783 0.00 0.00 32.27 3.02
2677 2888 6.537301 ACTTACGTTCATGTTTGAGTTTCAGA 59.463 34.615 0.00 0.00 32.27 3.27
2678 2889 6.715464 ACTTACGTTCATGTTTGAGTTTCAG 58.285 36.000 0.00 0.00 32.27 3.02
2679 2890 6.671614 ACTTACGTTCATGTTTGAGTTTCA 57.328 33.333 0.00 0.00 32.27 2.69
2680 2891 7.317269 CGTAACTTACGTTCATGTTTGAGTTTC 59.683 37.037 12.37 0.00 46.41 2.78
2681 2892 7.121272 CGTAACTTACGTTCATGTTTGAGTTT 58.879 34.615 12.37 0.00 46.41 2.66
2682 2893 6.642917 CGTAACTTACGTTCATGTTTGAGTT 58.357 36.000 12.37 0.60 46.41 3.01
2683 2894 6.206600 CGTAACTTACGTTCATGTTTGAGT 57.793 37.500 12.37 0.00 46.41 3.41
2697 2908 5.532557 AGGACAAGTGGTTACGTAACTTAC 58.467 41.667 31.35 27.91 36.47 2.34
2698 2909 5.278957 GGAGGACAAGTGGTTACGTAACTTA 60.279 44.000 31.35 20.63 36.47 2.24
2699 2910 4.502087 GGAGGACAAGTGGTTACGTAACTT 60.502 45.833 31.35 19.06 36.47 2.66
2700 2911 3.006217 GGAGGACAAGTGGTTACGTAACT 59.994 47.826 31.35 14.49 36.47 2.24
2701 2912 3.243839 TGGAGGACAAGTGGTTACGTAAC 60.244 47.826 26.72 26.72 35.50 2.50
2702 2913 2.964464 TGGAGGACAAGTGGTTACGTAA 59.036 45.455 3.29 3.29 0.00 3.18
2703 2914 2.559668 CTGGAGGACAAGTGGTTACGTA 59.440 50.000 0.00 0.00 0.00 3.57
2704 2915 1.343465 CTGGAGGACAAGTGGTTACGT 59.657 52.381 0.00 0.00 0.00 3.57
2705 2916 1.343465 ACTGGAGGACAAGTGGTTACG 59.657 52.381 0.00 0.00 0.00 3.18
2706 2917 2.550208 CCACTGGAGGACAAGTGGTTAC 60.550 54.545 13.76 0.00 40.49 2.50
2707 2918 1.697432 CCACTGGAGGACAAGTGGTTA 59.303 52.381 13.76 0.00 40.49 2.85
2708 2919 0.474184 CCACTGGAGGACAAGTGGTT 59.526 55.000 13.76 0.00 40.49 3.67
2709 2920 2.056906 GCCACTGGAGGACAAGTGGT 62.057 60.000 20.41 0.00 43.91 4.16
2710 2921 1.302832 GCCACTGGAGGACAAGTGG 60.303 63.158 16.71 16.71 44.39 4.00
2711 2922 1.669115 CGCCACTGGAGGACAAGTG 60.669 63.158 0.00 0.00 0.00 3.16
2712 2923 2.743718 CGCCACTGGAGGACAAGT 59.256 61.111 0.00 0.00 0.00 3.16
2713 2924 2.046892 CCGCCACTGGAGGACAAG 60.047 66.667 12.46 0.00 45.77 3.16
2714 2925 2.525629 TCCGCCACTGGAGGACAA 60.526 61.111 16.21 0.00 46.40 3.18
2715 2926 2.997315 CTCCGCCACTGGAGGACA 60.997 66.667 16.21 0.00 46.40 4.02
2720 2931 4.069232 CGAAGCTCCGCCACTGGA 62.069 66.667 0.00 0.00 36.37 3.86
2727 2938 3.575351 ATATCGGCCGAAGCTCCGC 62.575 63.158 34.66 0.00 44.91 5.54
2728 2939 1.734477 CATATCGGCCGAAGCTCCG 60.734 63.158 34.66 13.70 46.52 4.63
2729 2940 0.249911 AACATATCGGCCGAAGCTCC 60.250 55.000 34.66 0.00 39.73 4.70
2730 2941 0.861837 CAACATATCGGCCGAAGCTC 59.138 55.000 34.66 0.00 39.73 4.09
2731 2942 0.532862 CCAACATATCGGCCGAAGCT 60.533 55.000 34.66 19.24 39.73 3.74
2732 2943 0.531974 TCCAACATATCGGCCGAAGC 60.532 55.000 34.66 0.00 38.76 3.86
2733 2944 1.502231 CTCCAACATATCGGCCGAAG 58.498 55.000 34.66 25.94 0.00 3.79
2734 2945 0.105964 CCTCCAACATATCGGCCGAA 59.894 55.000 34.66 21.47 0.00 4.30
2735 2946 1.745890 CCTCCAACATATCGGCCGA 59.254 57.895 33.12 33.12 0.00 5.54
2736 2947 1.301716 CCCTCCAACATATCGGCCG 60.302 63.158 22.12 22.12 0.00 6.13
2737 2948 1.600916 GCCCTCCAACATATCGGCC 60.601 63.158 0.00 0.00 0.00 6.13
2738 2949 0.465460 TTGCCCTCCAACATATCGGC 60.465 55.000 0.00 0.00 36.91 5.54
2739 2950 1.881973 CATTGCCCTCCAACATATCGG 59.118 52.381 0.00 0.00 35.99 4.18
2740 2951 1.881973 CCATTGCCCTCCAACATATCG 59.118 52.381 0.00 0.00 35.99 2.92
2741 2952 2.242043 CCCATTGCCCTCCAACATATC 58.758 52.381 0.00 0.00 35.99 1.63
2742 2953 1.758841 GCCCATTGCCCTCCAACATAT 60.759 52.381 0.00 0.00 35.99 1.78
2743 2954 0.396974 GCCCATTGCCCTCCAACATA 60.397 55.000 0.00 0.00 35.99 2.29
2744 2955 1.686800 GCCCATTGCCCTCCAACAT 60.687 57.895 0.00 0.00 35.99 2.71
2745 2956 2.283821 GCCCATTGCCCTCCAACA 60.284 61.111 0.00 0.00 35.99 3.33
2746 2957 3.451894 CGCCCATTGCCCTCCAAC 61.452 66.667 0.00 0.00 35.99 3.77
2747 2958 4.757355 CCGCCCATTGCCCTCCAA 62.757 66.667 0.00 0.00 37.94 3.53
2750 2961 3.721370 ATGTCCGCCCATTGCCCTC 62.721 63.158 0.00 0.00 36.24 4.30
2751 2962 3.743017 ATGTCCGCCCATTGCCCT 61.743 61.111 0.00 0.00 36.24 5.19
2752 2963 2.902423 TACATGTCCGCCCATTGCCC 62.902 60.000 0.00 0.00 36.24 5.36
2753 2964 0.823356 ATACATGTCCGCCCATTGCC 60.823 55.000 0.00 0.00 36.24 4.52
2754 2965 0.593128 GATACATGTCCGCCCATTGC 59.407 55.000 0.00 0.00 0.00 3.56
2755 2966 0.867746 CGATACATGTCCGCCCATTG 59.132 55.000 0.00 0.00 0.00 2.82
2756 2967 0.884704 GCGATACATGTCCGCCCATT 60.885 55.000 25.79 0.00 42.77 3.16
2757 2968 1.301716 GCGATACATGTCCGCCCAT 60.302 57.895 25.79 5.40 42.77 4.00
2758 2969 2.108157 GCGATACATGTCCGCCCA 59.892 61.111 25.79 0.52 42.77 5.36
2775 2986 3.548587 GCTTGATATGTAACGCAGCATG 58.451 45.455 0.00 0.00 40.87 4.06
2776 2987 2.221749 CGCTTGATATGTAACGCAGCAT 59.778 45.455 0.00 0.00 0.00 3.79
2777 2988 1.592543 CGCTTGATATGTAACGCAGCA 59.407 47.619 0.00 0.00 0.00 4.41
2778 2989 1.070577 CCGCTTGATATGTAACGCAGC 60.071 52.381 0.00 0.00 0.00 5.25
2779 2990 2.201732 ACCGCTTGATATGTAACGCAG 58.798 47.619 0.00 0.00 0.00 5.18
2780 2991 2.198406 GACCGCTTGATATGTAACGCA 58.802 47.619 0.00 0.00 0.00 5.24
2781 2992 1.189446 CGACCGCTTGATATGTAACGC 59.811 52.381 0.00 0.00 0.00 4.84
2782 2993 1.189446 GCGACCGCTTGATATGTAACG 59.811 52.381 7.19 0.00 38.26 3.18
2783 2994 1.525619 GGCGACCGCTTGATATGTAAC 59.474 52.381 14.25 0.00 41.60 2.50
2784 2995 1.411246 AGGCGACCGCTTGATATGTAA 59.589 47.619 14.25 0.00 41.60 2.41
2785 2996 1.037493 AGGCGACCGCTTGATATGTA 58.963 50.000 14.25 0.00 41.60 2.29
2786 2997 1.037493 TAGGCGACCGCTTGATATGT 58.963 50.000 14.25 0.00 41.60 2.29
2787 2998 1.269569 TGTAGGCGACCGCTTGATATG 60.270 52.381 14.25 0.00 41.60 1.78
2788 2999 1.000163 CTGTAGGCGACCGCTTGATAT 60.000 52.381 14.25 0.00 41.60 1.63
2789 3000 0.384309 CTGTAGGCGACCGCTTGATA 59.616 55.000 14.25 0.58 41.60 2.15
2790 3001 1.141881 CTGTAGGCGACCGCTTGAT 59.858 57.895 14.25 1.46 41.60 2.57
2791 3002 1.974875 TCTGTAGGCGACCGCTTGA 60.975 57.895 14.25 0.00 41.60 3.02
2792 3003 1.805945 GTCTGTAGGCGACCGCTTG 60.806 63.158 14.25 0.00 41.60 4.01
2793 3004 2.572284 GTCTGTAGGCGACCGCTT 59.428 61.111 14.25 9.33 41.60 4.68
2794 3005 3.450115 GGTCTGTAGGCGACCGCT 61.450 66.667 14.25 3.32 41.29 5.52
2798 3009 1.716826 CGAGGAGGTCTGTAGGCGAC 61.717 65.000 0.00 0.00 0.00 5.19
2799 3010 1.451567 CGAGGAGGTCTGTAGGCGA 60.452 63.158 0.00 0.00 0.00 5.54
2800 3011 1.716826 GACGAGGAGGTCTGTAGGCG 61.717 65.000 0.00 0.00 34.09 5.52
2801 3012 1.716826 CGACGAGGAGGTCTGTAGGC 61.717 65.000 0.00 0.00 34.75 3.93
2802 3013 1.716826 GCGACGAGGAGGTCTGTAGG 61.717 65.000 0.00 0.00 34.75 3.18
2803 3014 0.745128 AGCGACGAGGAGGTCTGTAG 60.745 60.000 0.00 0.00 34.75 2.74
2804 3015 0.538584 TAGCGACGAGGAGGTCTGTA 59.461 55.000 0.00 0.00 34.75 2.74
2805 3016 0.745128 CTAGCGACGAGGAGGTCTGT 60.745 60.000 0.00 0.00 34.75 3.41
2806 3017 2.018544 CTAGCGACGAGGAGGTCTG 58.981 63.158 0.00 0.00 34.75 3.51
2807 3018 1.820481 GCTAGCGACGAGGAGGTCT 60.820 63.158 0.00 0.00 34.75 3.85
2808 3019 1.448922 ATGCTAGCGACGAGGAGGTC 61.449 60.000 10.77 0.00 0.00 3.85
2809 3020 1.454111 ATGCTAGCGACGAGGAGGT 60.454 57.895 10.77 0.00 0.00 3.85
2810 3021 1.007964 CATGCTAGCGACGAGGAGG 60.008 63.158 10.77 0.00 0.00 4.30
2811 3022 1.007964 CCATGCTAGCGACGAGGAG 60.008 63.158 10.77 0.00 0.00 3.69
2812 3023 1.753078 ACCATGCTAGCGACGAGGA 60.753 57.895 10.77 0.00 0.00 3.71
2813 3024 1.589993 CACCATGCTAGCGACGAGG 60.590 63.158 10.77 9.45 0.00 4.63
2814 3025 1.589993 CCACCATGCTAGCGACGAG 60.590 63.158 10.77 0.00 0.00 4.18
2815 3026 2.494445 CCACCATGCTAGCGACGA 59.506 61.111 10.77 0.00 0.00 4.20
2816 3027 2.586079 CCCACCATGCTAGCGACG 60.586 66.667 10.77 1.53 0.00 5.12
2817 3028 2.203070 CCCCACCATGCTAGCGAC 60.203 66.667 10.77 0.00 0.00 5.19
2818 3029 2.687200 ACCCCACCATGCTAGCGA 60.687 61.111 10.77 0.00 0.00 4.93
2819 3030 2.514592 CACCCCACCATGCTAGCG 60.515 66.667 10.77 0.00 0.00 4.26
2820 3031 2.124151 CCACCCCACCATGCTAGC 60.124 66.667 8.10 8.10 0.00 3.42
2821 3032 1.224592 GTCCACCCCACCATGCTAG 59.775 63.158 0.00 0.00 0.00 3.42
2822 3033 2.305607 GGTCCACCCCACCATGCTA 61.306 63.158 0.00 0.00 33.63 3.49
2823 3034 3.661648 GGTCCACCCCACCATGCT 61.662 66.667 0.00 0.00 33.63 3.79
2825 3036 4.424711 CCGGTCCACCCCACCATG 62.425 72.222 0.00 0.00 32.89 3.66
2833 3044 2.192175 CTAATGGGCCGGTCCACC 59.808 66.667 34.46 14.92 39.97 4.61
2834 3045 2.516225 GCTAATGGGCCGGTCCAC 60.516 66.667 34.46 14.90 39.97 4.02
2835 3046 4.169696 CGCTAATGGGCCGGTCCA 62.170 66.667 33.79 33.79 41.60 4.02
2843 3054 2.114670 CCAGGTGTGCGCTAATGGG 61.115 63.158 9.73 0.00 0.00 4.00
2844 3055 2.114670 CCCAGGTGTGCGCTAATGG 61.115 63.158 9.73 9.71 0.00 3.16
2845 3056 0.464373 ATCCCAGGTGTGCGCTAATG 60.464 55.000 9.73 0.03 0.00 1.90
2846 3057 0.179045 GATCCCAGGTGTGCGCTAAT 60.179 55.000 9.73 0.00 0.00 1.73
2847 3058 1.220749 GATCCCAGGTGTGCGCTAA 59.779 57.895 9.73 0.00 0.00 3.09
2848 3059 2.900273 GATCCCAGGTGTGCGCTA 59.100 61.111 9.73 0.00 0.00 4.26
2849 3060 4.457496 CGATCCCAGGTGTGCGCT 62.457 66.667 9.73 0.00 0.00 5.92
2851 3062 4.457496 AGCGATCCCAGGTGTGCG 62.457 66.667 0.00 0.00 0.00 5.34
2852 3063 2.512515 GAGCGATCCCAGGTGTGC 60.513 66.667 0.00 0.00 0.00 4.57
2853 3064 2.202797 CGAGCGATCCCAGGTGTG 60.203 66.667 0.00 0.00 0.00 3.82
2854 3065 4.148825 GCGAGCGATCCCAGGTGT 62.149 66.667 0.00 0.00 0.00 4.16
2855 3066 3.781770 GAGCGAGCGATCCCAGGTG 62.782 68.421 0.00 0.00 0.00 4.00
2856 3067 3.532155 GAGCGAGCGATCCCAGGT 61.532 66.667 0.00 0.00 0.00 4.00
2857 3068 4.292178 GGAGCGAGCGATCCCAGG 62.292 72.222 15.69 0.00 44.27 4.45
2862 3073 1.166129 TATACTGGGAGCGAGCGATC 58.834 55.000 0.00 0.00 0.00 3.69
2863 3074 1.840737 ATATACTGGGAGCGAGCGAT 58.159 50.000 0.00 0.00 0.00 4.58
2864 3075 2.484742 TATATACTGGGAGCGAGCGA 57.515 50.000 0.00 0.00 0.00 4.93
2865 3076 2.423892 ACATATATACTGGGAGCGAGCG 59.576 50.000 0.00 0.00 0.00 5.03
2866 3077 5.508153 CCATACATATATACTGGGAGCGAGC 60.508 48.000 0.00 0.00 0.00 5.03
2867 3078 5.594725 ACCATACATATATACTGGGAGCGAG 59.405 44.000 10.51 0.00 0.00 5.03
2868 3079 5.359860 CACCATACATATATACTGGGAGCGA 59.640 44.000 10.51 0.00 0.00 4.93
2869 3080 5.127194 ACACCATACATATATACTGGGAGCG 59.873 44.000 10.51 0.00 0.00 5.03
2870 3081 6.546428 ACACCATACATATATACTGGGAGC 57.454 41.667 10.51 0.00 0.00 4.70
2871 3082 7.180229 TGGAACACCATACATATATACTGGGAG 59.820 40.741 10.51 6.50 0.00 4.30
2872 3083 7.020009 TGGAACACCATACATATATACTGGGA 58.980 38.462 10.51 0.00 0.00 4.37
2873 3084 7.252612 TGGAACACCATACATATATACTGGG 57.747 40.000 10.51 2.98 0.00 4.45
2902 3113 5.050363 CACACAGACAGTACGTATGCTTTTT 60.050 40.000 0.00 0.00 40.66 1.94
2903 3114 4.447724 CACACAGACAGTACGTATGCTTTT 59.552 41.667 0.00 0.00 40.66 2.27
2904 3115 3.987868 CACACAGACAGTACGTATGCTTT 59.012 43.478 0.00 0.00 40.66 3.51
2905 3116 3.575630 CACACAGACAGTACGTATGCTT 58.424 45.455 0.00 0.00 40.66 3.91
2906 3117 2.094700 CCACACAGACAGTACGTATGCT 60.095 50.000 0.00 0.00 40.66 3.79
2907 3118 2.259618 CCACACAGACAGTACGTATGC 58.740 52.381 0.00 0.00 40.66 3.14
2908 3119 3.570926 ACCACACAGACAGTACGTATG 57.429 47.619 0.00 9.77 42.75 2.39
2909 3120 4.595762 AAACCACACAGACAGTACGTAT 57.404 40.909 0.00 0.00 0.00 3.06
2910 3121 4.389890 AAAACCACACAGACAGTACGTA 57.610 40.909 0.00 0.00 0.00 3.57
2911 3122 2.973694 AAACCACACAGACAGTACGT 57.026 45.000 0.00 0.00 0.00 3.57
2934 3145 8.079809 CGTATGTAGTGGGAAAAACAAGAAAAT 58.920 33.333 0.00 0.00 0.00 1.82
2935 3146 7.282675 TCGTATGTAGTGGGAAAAACAAGAAAA 59.717 33.333 0.00 0.00 0.00 2.29
2936 3147 6.766944 TCGTATGTAGTGGGAAAAACAAGAAA 59.233 34.615 0.00 0.00 0.00 2.52
2937 3148 6.289834 TCGTATGTAGTGGGAAAAACAAGAA 58.710 36.000 0.00 0.00 0.00 2.52
2938 3149 5.856156 TCGTATGTAGTGGGAAAAACAAGA 58.144 37.500 0.00 0.00 0.00 3.02
2939 3150 6.737254 ATCGTATGTAGTGGGAAAAACAAG 57.263 37.500 0.00 0.00 0.00 3.16
2940 3151 7.513371 AAATCGTATGTAGTGGGAAAAACAA 57.487 32.000 0.00 0.00 0.00 2.83
2941 3152 7.513371 AAAATCGTATGTAGTGGGAAAAACA 57.487 32.000 0.00 0.00 0.00 2.83
2942 3153 9.896263 TTTAAAATCGTATGTAGTGGGAAAAAC 57.104 29.630 0.00 0.00 0.00 2.43
2983 3194 9.626045 GAAGATGACTTTAATCCGTGAATTTTT 57.374 29.630 0.00 0.00 36.39 1.94
2984 3195 8.792633 TGAAGATGACTTTAATCCGTGAATTTT 58.207 29.630 0.00 0.00 36.39 1.82
2985 3196 8.335532 TGAAGATGACTTTAATCCGTGAATTT 57.664 30.769 0.00 0.00 36.39 1.82
2986 3197 7.921786 TGAAGATGACTTTAATCCGTGAATT 57.078 32.000 0.00 0.00 36.39 2.17
2987 3198 7.921786 TTGAAGATGACTTTAATCCGTGAAT 57.078 32.000 0.00 0.00 36.39 2.57
2988 3199 7.390440 ACATTGAAGATGACTTTAATCCGTGAA 59.610 33.333 0.00 0.00 39.28 3.18
2989 3200 6.878923 ACATTGAAGATGACTTTAATCCGTGA 59.121 34.615 0.00 0.00 39.28 4.35
2990 3201 7.076842 ACATTGAAGATGACTTTAATCCGTG 57.923 36.000 0.00 0.00 39.28 4.94
2991 3202 7.687941 AACATTGAAGATGACTTTAATCCGT 57.312 32.000 0.00 0.00 39.28 4.69
2992 3203 8.970691 AAAACATTGAAGATGACTTTAATCCG 57.029 30.769 0.00 0.00 39.28 4.18
2998 3209 9.447157 TTTTCCAAAAACATTGAAGATGACTTT 57.553 25.926 0.00 0.00 36.39 2.66
2999 3210 9.447157 TTTTTCCAAAAACATTGAAGATGACTT 57.553 25.926 0.00 0.00 34.71 3.01
3048 3259 8.253810 TGTAACCTTGTTTTGAATTCACATTCA 58.746 29.630 7.89 2.92 45.96 2.57
3049 3260 8.641499 TGTAACCTTGTTTTGAATTCACATTC 57.359 30.769 7.89 0.25 39.58 2.67
3050 3261 9.442047 TTTGTAACCTTGTTTTGAATTCACATT 57.558 25.926 7.89 0.00 0.00 2.71
3051 3262 9.612066 ATTTGTAACCTTGTTTTGAATTCACAT 57.388 25.926 7.89 0.00 0.00 3.21
3052 3263 9.442047 AATTTGTAACCTTGTTTTGAATTCACA 57.558 25.926 7.89 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.