Multiple sequence alignment - TraesCS2A01G102700

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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 TraesCS2A01G102700 chr2A 100.000 3201 0 0 1 3201 55969011 55965811 0.000000e+00 5912.0
1 TraesCS2A01G102700 chr2A 86.944 2673 181 73 16 2632 56102973 56100413 0.000000e+00 2848.0
2 TraesCS2A01G102700 chr2A 81.496 254 19 9 2778 3028 56099532 56099304 1.960000e-42 183.0
3 TraesCS2A01G102700 chr2D 92.129 2668 124 32 6 2632 55238202 55235580 0.000000e+00 3685.0
4 TraesCS2A01G102700 chr2D 89.248 1237 88 17 1241 2463 55256211 55255006 0.000000e+00 1506.0
5 TraesCS2A01G102700 chr2D 88.046 1121 67 26 6 1108 55257283 55256212 0.000000e+00 1266.0
6 TraesCS2A01G102700 chr2D 88.056 427 31 10 2775 3195 55235509 55235097 3.710000e-134 488.0
7 TraesCS2A01G102700 chr2B 89.780 2505 169 35 1 2463 87412530 87410071 0.000000e+00 3127.0
8 TraesCS2A01G102700 chr5D 78.125 160 16 10 2632 2772 8960287 8960446 2.050000e-12 84.2
9 TraesCS2A01G102700 chr1D 84.416 77 3 4 2632 2699 118803469 118803393 2.060000e-07 67.6


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 TraesCS2A01G102700 chr2A 55965811 55969011 3200 True 5912.0 5912 100.0000 1 3201 1 chr2A.!!$R1 3200
1 TraesCS2A01G102700 chr2A 56099304 56102973 3669 True 1515.5 2848 84.2200 16 3028 2 chr2A.!!$R2 3012
2 TraesCS2A01G102700 chr2D 55235097 55238202 3105 True 2086.5 3685 90.0925 6 3195 2 chr2D.!!$R1 3189
3 TraesCS2A01G102700 chr2D 55255006 55257283 2277 True 1386.0 1506 88.6470 6 2463 2 chr2D.!!$R2 2457
4 TraesCS2A01G102700 chr2B 87410071 87412530 2459 True 3127.0 3127 89.7800 1 2463 1 chr2B.!!$R1 2462

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
883 933 0.031043 TGCTGCACTGCAACAATGAC 59.969 50.0 4.59 0.0 40.29 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2708 2870 0.029989 AATCTACTCCCCTCCCACCC 60.03 60.0 0.0 0.0 0.0 4.61 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
43 51 6.183360 TGCACGTTAATCAGTATAGCAAACAG 60.183 38.462 0.00 0.00 0.00 3.16
217 230 1.521457 ATCCATGTGTACGCAGCCG 60.521 57.895 15.35 5.85 41.14 5.52
286 303 2.564721 GGTTGTTGCAGCTCACCCC 61.565 63.158 10.24 1.30 0.00 4.95
287 304 2.203480 TTGTTGCAGCTCACCCCC 60.203 61.111 1.17 0.00 0.00 5.40
288 305 4.641645 TGTTGCAGCTCACCCCCG 62.642 66.667 1.17 0.00 0.00 5.73
314 331 4.344390 ACCGAAACTCTGAAGGATATACCC 59.656 45.833 0.00 0.00 40.05 3.69
554 581 1.416373 CTCATGCTCCGTGATGATCG 58.584 55.000 0.00 0.00 0.00 3.69
715 747 0.181824 GCAATATACGGTGGGTGGGT 59.818 55.000 0.00 0.00 0.00 4.51
716 748 1.961793 CAATATACGGTGGGTGGGTG 58.038 55.000 0.00 0.00 0.00 4.61
717 749 1.210967 CAATATACGGTGGGTGGGTGT 59.789 52.381 0.00 0.00 0.00 4.16
719 751 1.484038 TATACGGTGGGTGGGTGTAC 58.516 55.000 0.00 0.00 0.00 2.90
722 754 2.831043 GGTGGGTGGGTGTACGTT 59.169 61.111 0.00 0.00 0.00 3.99
723 755 1.301953 GGTGGGTGGGTGTACGTTC 60.302 63.158 0.00 0.00 0.00 3.95
725 757 0.968405 GTGGGTGGGTGTACGTTCTA 59.032 55.000 0.00 0.00 0.00 2.10
781 814 6.925610 TGTTATTTCACTAGATGATGGCAC 57.074 37.500 0.00 0.00 37.11 5.01
818 851 2.509336 GTCATGGCGACGGTGGAG 60.509 66.667 0.00 0.00 34.19 3.86
883 933 0.031043 TGCTGCACTGCAACAATGAC 59.969 50.000 4.59 0.00 40.29 3.06
897 947 6.152492 TGCAACAATGACATATTTCTTAGGCA 59.848 34.615 0.00 0.00 0.00 4.75
980 1034 2.754478 CGATTAAACGTTCGTTGGAGC 58.246 47.619 11.24 5.49 0.00 4.70
982 1036 3.481467 CGATTAAACGTTCGTTGGAGCTC 60.481 47.826 4.71 4.71 0.00 4.09
983 1037 1.411394 TAAACGTTCGTTGGAGCTCG 58.589 50.000 7.83 0.00 0.00 5.03
1022 1083 1.298014 CAGAGAAGGTGAGTGCCCC 59.702 63.158 0.00 0.00 0.00 5.80
1032 1093 3.039202 GAGTGCCCCGTTTCATGCG 62.039 63.158 0.00 0.00 0.00 4.73
1049 1114 4.968626 CATGCGTACATGCTTGAGTTAAA 58.031 39.130 6.60 0.00 46.75 1.52
1050 1115 5.572211 CATGCGTACATGCTTGAGTTAAAT 58.428 37.500 6.60 0.00 46.75 1.40
1051 1116 5.621197 TGCGTACATGCTTGAGTTAAATT 57.379 34.783 6.60 0.00 35.36 1.82
1052 1117 6.007936 TGCGTACATGCTTGAGTTAAATTT 57.992 33.333 6.60 0.00 35.36 1.82
1053 1118 6.442952 TGCGTACATGCTTGAGTTAAATTTT 58.557 32.000 6.60 0.00 35.36 1.82
1054 1119 6.362016 TGCGTACATGCTTGAGTTAAATTTTG 59.638 34.615 6.60 0.00 35.36 2.44
1055 1120 6.667386 GCGTACATGCTTGAGTTAAATTTTGC 60.667 38.462 6.60 0.00 0.00 3.68
1056 1121 6.362016 CGTACATGCTTGAGTTAAATTTTGCA 59.638 34.615 6.60 0.00 0.00 4.08
1198 1263 2.860136 TCGAATGCGAGAAATGCTACAG 59.140 45.455 0.00 0.00 42.51 2.74
1263 1333 9.155975 AGTACAATAGTCAAGCACTCAATTTAG 57.844 33.333 0.00 0.00 36.43 1.85
1266 1336 8.292448 ACAATAGTCAAGCACTCAATTTAGTTG 58.708 33.333 0.00 0.00 36.43 3.16
1280 1367 9.743057 CTCAATTTAGTTGTGTCAAATTAACCA 57.257 29.630 0.00 0.00 38.95 3.67
1284 1371 8.864069 TTTAGTTGTGTCAAATTAACCATGTG 57.136 30.769 0.00 0.00 0.00 3.21
1330 1417 4.431894 TTCGCTTATTAACTTCGATGCG 57.568 40.909 0.00 0.00 42.89 4.73
1384 1471 1.002087 AGGACCATCAACTTCGACACC 59.998 52.381 0.00 0.00 0.00 4.16
1484 1571 4.657504 AGGCTATCAAGGACATCAAGATCA 59.342 41.667 0.00 0.00 0.00 2.92
1492 1579 5.604758 AGGACATCAAGATCATCGAAGAA 57.395 39.130 0.00 0.00 43.58 2.52
1600 1702 1.748122 CTGCTGCAAGAAGCCCGAT 60.748 57.895 3.02 0.00 44.83 4.18
1628 1730 1.484240 AGCCGGATGAGAAGAAGAAGG 59.516 52.381 5.05 0.00 0.00 3.46
1648 1750 1.211969 CGACGAGAAGAAGCCGGAA 59.788 57.895 5.05 0.00 0.00 4.30
1669 1774 7.135467 CGGAAGAAAAGAAGGAAGAAAAGAAG 58.865 38.462 0.00 0.00 0.00 2.85
1712 1820 4.159506 AGAAGAAGACGGATGAGAAGAAGG 59.840 45.833 0.00 0.00 0.00 3.46
1961 2099 3.068691 CGACCCCGAAGAGGCAGA 61.069 66.667 0.00 0.00 39.21 4.26
2206 2345 3.069289 GTGCACTGTCATGTGATCTCAA 58.931 45.455 10.32 0.00 40.12 3.02
2257 2402 1.808945 CCACCTCTCTGCATGTTGTTC 59.191 52.381 0.00 0.00 0.00 3.18
2489 2642 8.556194 CAATGTTTTAAATAGCCGTCTATAGCA 58.444 33.333 0.00 0.00 34.53 3.49
2510 2672 2.158900 ACCGCTATAGCAGTTTGAGCAT 60.159 45.455 23.99 0.00 42.21 3.79
2518 2680 1.228245 AGTTTGAGCATGGTGCCGT 60.228 52.632 0.00 0.00 46.52 5.68
2529 2691 3.563808 GCATGGTGCCGTTAAATGATAGA 59.436 43.478 0.00 0.00 37.42 1.98
2535 2697 7.728148 TGGTGCCGTTAAATGATAGACTATAA 58.272 34.615 0.00 0.00 0.00 0.98
2537 2699 7.331193 GGTGCCGTTAAATGATAGACTATAAGG 59.669 40.741 0.00 0.00 0.00 2.69
2577 2739 4.459337 AGAAAAAGTTCTCAAATAGCCGGG 59.541 41.667 2.18 0.00 40.18 5.73
2584 2746 3.853207 TCTCAAATAGCCGGGTATACCT 58.147 45.455 25.66 8.54 36.97 3.08
2602 2764 4.348863 ACCTCTGCTATAGCTGATTTGG 57.651 45.455 28.09 26.22 45.61 3.28
2605 2767 4.282957 CCTCTGCTATAGCTGATTTGGAGA 59.717 45.833 28.09 17.40 45.61 3.71
2608 2770 5.365025 TCTGCTATAGCTGATTTGGAGAACT 59.635 40.000 25.38 0.00 42.71 3.01
2609 2771 6.551227 TCTGCTATAGCTGATTTGGAGAACTA 59.449 38.462 25.38 3.97 42.71 2.24
2611 2773 6.098266 TGCTATAGCTGATTTGGAGAACTACA 59.902 38.462 24.61 0.00 42.66 2.74
2632 2794 1.681264 GCTATTTGGCATAACCCGCTT 59.319 47.619 0.00 0.00 37.83 4.68
2633 2795 2.287608 GCTATTTGGCATAACCCGCTTC 60.288 50.000 0.00 0.00 37.83 3.86
2635 2797 2.791347 TTTGGCATAACCCGCTTCTA 57.209 45.000 0.00 0.00 37.83 2.10
2636 2798 2.032680 TTGGCATAACCCGCTTCTAC 57.967 50.000 0.00 0.00 37.83 2.59
2637 2799 0.179094 TGGCATAACCCGCTTCTACG 60.179 55.000 0.00 0.00 37.83 3.51
2638 2800 0.179092 GGCATAACCCGCTTCTACGT 60.179 55.000 0.00 0.00 0.00 3.57
2640 2802 2.391879 GCATAACCCGCTTCTACGTAG 58.608 52.381 16.73 16.73 0.00 3.51
2642 2804 3.852572 GCATAACCCGCTTCTACGTAGAG 60.853 52.174 23.51 18.19 33.21 2.43
2643 2805 0.455005 AACCCGCTTCTACGTAGAGC 59.545 55.000 23.51 24.34 33.21 4.09
2644 2806 0.394080 ACCCGCTTCTACGTAGAGCT 60.394 55.000 28.35 16.76 33.21 4.09
2646 2808 1.263752 CCCGCTTCTACGTAGAGCTAC 59.736 57.143 28.35 18.54 33.21 3.58
2660 2822 6.707599 GTAGAGCTACGTGAAAACTGATTT 57.292 37.500 0.00 0.00 0.00 2.17
2661 2823 5.597813 AGAGCTACGTGAAAACTGATTTG 57.402 39.130 0.00 0.00 0.00 2.32
2662 2824 4.452455 AGAGCTACGTGAAAACTGATTTGG 59.548 41.667 0.00 0.00 0.00 3.28
2664 2826 3.500680 GCTACGTGAAAACTGATTTGGGA 59.499 43.478 0.00 0.00 0.00 4.37
2665 2827 4.156008 GCTACGTGAAAACTGATTTGGGAT 59.844 41.667 0.00 0.00 0.00 3.85
2666 2828 4.503741 ACGTGAAAACTGATTTGGGATG 57.496 40.909 0.00 0.00 0.00 3.51
2667 2829 4.141287 ACGTGAAAACTGATTTGGGATGA 58.859 39.130 0.00 0.00 0.00 2.92
2668 2830 4.766891 ACGTGAAAACTGATTTGGGATGAT 59.233 37.500 0.00 0.00 0.00 2.45
2669 2831 5.243730 ACGTGAAAACTGATTTGGGATGATT 59.756 36.000 0.00 0.00 0.00 2.57
2670 2832 6.158598 CGTGAAAACTGATTTGGGATGATTT 58.841 36.000 0.00 0.00 0.00 2.17
2675 2837 8.977267 AAAACTGATTTGGGATGATTTGAAAA 57.023 26.923 0.00 0.00 0.00 2.29
2676 2838 8.977267 AAACTGATTTGGGATGATTTGAAAAA 57.023 26.923 0.00 0.00 0.00 1.94
2691 2853 2.937285 AAAAATAGCCCGGGCCCCA 61.937 57.895 41.72 27.27 43.17 4.96
2702 2864 2.121608 GGCCCCACCCCATGAAAA 59.878 61.111 0.00 0.00 0.00 2.29
2703 2865 1.306911 GGCCCCACCCCATGAAAAT 60.307 57.895 0.00 0.00 0.00 1.82
2704 2866 0.913934 GGCCCCACCCCATGAAAATT 60.914 55.000 0.00 0.00 0.00 1.82
2705 2867 0.991146 GCCCCACCCCATGAAAATTT 59.009 50.000 0.00 0.00 0.00 1.82
2706 2868 1.339920 GCCCCACCCCATGAAAATTTG 60.340 52.381 0.00 0.00 0.00 2.32
2707 2869 1.281577 CCCCACCCCATGAAAATTTGG 59.718 52.381 0.00 0.00 0.00 3.28
2713 2875 2.785540 CCATGAAAATTTGGGGGTGG 57.214 50.000 0.00 0.00 0.00 4.61
2714 2876 1.281577 CCATGAAAATTTGGGGGTGGG 59.718 52.381 0.00 0.00 0.00 4.61
2715 2877 2.264455 CATGAAAATTTGGGGGTGGGA 58.736 47.619 0.00 0.00 0.00 4.37
2716 2878 2.022718 TGAAAATTTGGGGGTGGGAG 57.977 50.000 0.00 0.00 0.00 4.30
2717 2879 1.275666 GAAAATTTGGGGGTGGGAGG 58.724 55.000 0.00 0.00 0.00 4.30
2718 2880 0.178876 AAAATTTGGGGGTGGGAGGG 60.179 55.000 0.00 0.00 0.00 4.30
2719 2881 2.118547 AAATTTGGGGGTGGGAGGGG 62.119 60.000 0.00 0.00 0.00 4.79
2720 2882 3.548934 ATTTGGGGGTGGGAGGGGA 62.549 63.158 0.00 0.00 0.00 4.81
2721 2883 4.693915 TTGGGGGTGGGAGGGGAG 62.694 72.222 0.00 0.00 0.00 4.30
2723 2885 3.702623 GGGGGTGGGAGGGGAGTA 61.703 72.222 0.00 0.00 0.00 2.59
2724 2886 2.040779 GGGGTGGGAGGGGAGTAG 60.041 72.222 0.00 0.00 0.00 2.57
2725 2887 2.643808 GGGGTGGGAGGGGAGTAGA 61.644 68.421 0.00 0.00 0.00 2.59
2726 2888 1.632740 GGGTGGGAGGGGAGTAGAT 59.367 63.158 0.00 0.00 0.00 1.98
2727 2889 0.029989 GGGTGGGAGGGGAGTAGATT 60.030 60.000 0.00 0.00 0.00 2.40
2728 2890 1.222298 GGGTGGGAGGGGAGTAGATTA 59.778 57.143 0.00 0.00 0.00 1.75
2729 2891 2.610873 GGTGGGAGGGGAGTAGATTAG 58.389 57.143 0.00 0.00 0.00 1.73
2730 2892 2.610873 GTGGGAGGGGAGTAGATTAGG 58.389 57.143 0.00 0.00 0.00 2.69
2731 2893 2.179424 GTGGGAGGGGAGTAGATTAGGA 59.821 54.545 0.00 0.00 0.00 2.94
2732 2894 2.451273 TGGGAGGGGAGTAGATTAGGAG 59.549 54.545 0.00 0.00 0.00 3.69
2733 2895 2.225420 GGGAGGGGAGTAGATTAGGAGG 60.225 59.091 0.00 0.00 0.00 4.30
2734 2896 2.451659 GGAGGGGAGTAGATTAGGAGGT 59.548 54.545 0.00 0.00 0.00 3.85
2735 2897 3.116668 GGAGGGGAGTAGATTAGGAGGTT 60.117 52.174 0.00 0.00 0.00 3.50
2736 2898 4.558715 GAGGGGAGTAGATTAGGAGGTTT 58.441 47.826 0.00 0.00 0.00 3.27
2737 2899 5.401119 GGAGGGGAGTAGATTAGGAGGTTTA 60.401 48.000 0.00 0.00 0.00 2.01
2738 2900 6.310459 AGGGGAGTAGATTAGGAGGTTTAT 57.690 41.667 0.00 0.00 0.00 1.40
2739 2901 6.704792 AGGGGAGTAGATTAGGAGGTTTATT 58.295 40.000 0.00 0.00 0.00 1.40
2740 2902 7.844566 AGGGGAGTAGATTAGGAGGTTTATTA 58.155 38.462 0.00 0.00 0.00 0.98
2741 2903 7.733955 AGGGGAGTAGATTAGGAGGTTTATTAC 59.266 40.741 0.00 0.00 0.00 1.89
2755 2917 6.410942 GGTTTATTACCTAGATGGGTACGT 57.589 41.667 0.00 0.00 44.10 3.57
2756 2918 7.524717 GGTTTATTACCTAGATGGGTACGTA 57.475 40.000 0.00 0.00 44.10 3.57
2757 2919 7.597386 GGTTTATTACCTAGATGGGTACGTAG 58.403 42.308 0.00 0.00 44.10 3.51
2758 2920 7.309438 GGTTTATTACCTAGATGGGTACGTAGG 60.309 44.444 0.00 0.00 44.10 3.18
2759 2921 4.796110 TTACCTAGATGGGTACGTAGGT 57.204 45.455 7.49 7.49 45.82 3.08
2760 2922 2.941480 ACCTAGATGGGTACGTAGGTG 58.059 52.381 0.00 0.00 43.03 4.00
2761 2923 2.243221 ACCTAGATGGGTACGTAGGTGT 59.757 50.000 0.00 0.00 43.03 4.16
2762 2924 3.459598 ACCTAGATGGGTACGTAGGTGTA 59.540 47.826 0.00 0.00 43.03 2.90
2763 2925 4.070716 CCTAGATGGGTACGTAGGTGTAG 58.929 52.174 0.00 0.00 0.00 2.74
2764 2926 2.941480 AGATGGGTACGTAGGTGTAGG 58.059 52.381 0.00 0.00 0.00 3.18
2765 2927 2.511218 AGATGGGTACGTAGGTGTAGGA 59.489 50.000 0.00 0.00 0.00 2.94
2766 2928 3.139770 AGATGGGTACGTAGGTGTAGGAT 59.860 47.826 0.00 0.00 0.00 3.24
2767 2929 3.386932 TGGGTACGTAGGTGTAGGATT 57.613 47.619 0.00 0.00 0.00 3.01
2768 2930 4.518278 TGGGTACGTAGGTGTAGGATTA 57.482 45.455 0.00 0.00 0.00 1.75
2769 2931 5.065613 TGGGTACGTAGGTGTAGGATTAT 57.934 43.478 0.00 0.00 0.00 1.28
2770 2932 5.457686 TGGGTACGTAGGTGTAGGATTATT 58.542 41.667 0.00 0.00 0.00 1.40
2809 3778 0.458716 GAAGCCACTCACGGTAGAGC 60.459 60.000 7.28 1.18 39.26 4.09
2852 3821 0.391263 GACTACGGGGAAGTTGCCTG 60.391 60.000 19.96 19.96 40.48 4.85
2938 3910 4.455190 TGTCAGTCAATTTCGATGATGCAA 59.545 37.500 0.00 0.00 0.00 4.08
2954 3926 2.083774 TGCAACAGCAGCATAGTAACC 58.916 47.619 0.00 0.00 37.02 2.85
2955 3927 2.083774 GCAACAGCAGCATAGTAACCA 58.916 47.619 0.00 0.00 0.00 3.67
2962 3934 3.056393 AGCAGCATAGTAACCACACGTAA 60.056 43.478 0.00 0.00 0.00 3.18
2972 3944 1.289109 CCACACGTAAGGCAAGACCG 61.289 60.000 0.00 0.00 46.52 4.79
2973 3945 0.319211 CACACGTAAGGCAAGACCGA 60.319 55.000 0.00 0.00 46.52 4.69
2974 3946 0.606604 ACACGTAAGGCAAGACCGAT 59.393 50.000 0.00 0.00 46.52 4.18
2975 3947 0.999406 CACGTAAGGCAAGACCGATG 59.001 55.000 0.00 0.00 46.52 3.84
2976 3948 0.606604 ACGTAAGGCAAGACCGATGT 59.393 50.000 0.00 0.00 46.52 3.06
2977 3949 1.278238 CGTAAGGCAAGACCGATGTC 58.722 55.000 0.00 0.00 46.52 3.06
2978 3950 1.653151 GTAAGGCAAGACCGATGTCC 58.347 55.000 0.00 0.00 46.52 4.02
2979 3951 0.174845 TAAGGCAAGACCGATGTCCG 59.825 55.000 0.00 0.00 46.52 4.79
3000 3972 1.174712 TGGAGCAAAGAAGGCAGCAC 61.175 55.000 0.00 0.00 0.00 4.40
3024 3996 2.046217 GGAGTCGTTCCAAGGCCC 60.046 66.667 0.00 0.00 46.01 5.80
3050 4022 0.895559 GGTTTGGGCTCCACCTTGAG 60.896 60.000 0.00 0.00 39.10 3.02
3051 4023 0.110486 GTTTGGGCTCCACCTTGAGA 59.890 55.000 0.00 0.00 39.10 3.27
3077 4049 3.120105 CAGCTGCTGGGCATGATG 58.880 61.111 21.71 0.00 38.13 3.07
3090 4062 0.458669 CATGATGGAAGCAGCAACCC 59.541 55.000 0.00 0.00 32.93 4.11
3160 4132 9.036671 ACAAAATAAAATCAACAACCCGTTAAG 57.963 29.630 0.00 0.00 35.52 1.85
3168 4142 0.536460 CAACCCGTTAAGCCAGTGGT 60.536 55.000 11.74 0.00 0.00 4.16
3171 4145 2.469952 ACCCGTTAAGCCAGTGGTATA 58.530 47.619 11.74 1.31 0.00 1.47
3173 4147 3.263937 ACCCGTTAAGCCAGTGGTATAAA 59.736 43.478 11.74 0.00 0.00 1.40
3178 4152 7.067251 CCCGTTAAGCCAGTGGTATAAATTTAA 59.933 37.037 11.74 2.88 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 51 1.815003 CATCTTTCTTGTGACCTGGGC 59.185 52.381 0.00 0.00 0.00 5.36
217 230 3.409026 AAATGATCCCGTAGATGGCTC 57.591 47.619 0.00 0.00 34.42 4.70
229 246 5.163581 CCTCATGTCCAAGTGAAAATGATCC 60.164 44.000 0.00 0.00 31.43 3.36
288 305 2.814280 TCCTTCAGAGTTTCGGTGAC 57.186 50.000 0.00 0.00 0.00 3.67
554 581 1.830847 AACAACCTTTCCCCGCCAC 60.831 57.895 0.00 0.00 0.00 5.01
715 747 6.932356 AATCGAATAGGAGTAGAACGTACA 57.068 37.500 0.00 0.00 0.00 2.90
716 748 7.481169 GCATAATCGAATAGGAGTAGAACGTAC 59.519 40.741 0.00 0.00 0.00 3.67
717 749 7.361542 GGCATAATCGAATAGGAGTAGAACGTA 60.362 40.741 0.00 0.00 0.00 3.57
719 751 5.800941 GGCATAATCGAATAGGAGTAGAACG 59.199 44.000 0.00 0.00 0.00 3.95
722 754 6.319152 GCTAGGCATAATCGAATAGGAGTAGA 59.681 42.308 0.00 0.00 0.00 2.59
723 755 6.320164 AGCTAGGCATAATCGAATAGGAGTAG 59.680 42.308 0.00 0.00 0.00 2.57
725 757 5.020132 AGCTAGGCATAATCGAATAGGAGT 58.980 41.667 0.00 0.00 0.00 3.85
757 790 6.037062 CGTGCCATCATCTAGTGAAATAACAA 59.963 38.462 0.00 0.00 40.97 2.83
781 814 0.665068 TCGTCACACACCGAAATCCG 60.665 55.000 0.00 0.00 38.18 4.18
897 947 6.547510 GGGACTCTTACTTAATCATGGCAATT 59.452 38.462 0.00 0.00 0.00 2.32
980 1034 4.869440 CTGGAGCTGAGGCGCGAG 62.869 72.222 12.10 0.00 44.37 5.03
1032 1093 7.636259 TGCAAAATTTAACTCAAGCATGTAC 57.364 32.000 0.00 0.00 0.00 2.90
1198 1263 7.849804 TTACATAGCACTTTCTGAATCTTCC 57.150 36.000 0.00 0.00 0.00 3.46
1263 1333 9.128107 CTTATCACATGGTTAATTTGACACAAC 57.872 33.333 0.00 0.00 27.84 3.32
1266 1336 9.559958 CTTCTTATCACATGGTTAATTTGACAC 57.440 33.333 0.00 0.00 27.84 3.67
1280 1367 7.781324 AAAATGGTTCCACTTCTTATCACAT 57.219 32.000 0.00 0.00 0.00 3.21
1330 1417 6.589523 CCTTCTCTGATCCATCGATGTTAATC 59.410 42.308 23.27 20.45 0.00 1.75
1384 1471 0.859232 CGGTCACCGTGTTCTTCTTG 59.141 55.000 8.54 0.00 42.73 3.02
1465 1552 6.655078 TCGATGATCTTGATGTCCTTGATA 57.345 37.500 0.00 0.00 0.00 2.15
1484 1571 2.762535 TCGGGCTTCTTTTCTTCGAT 57.237 45.000 0.00 0.00 0.00 3.59
1492 1579 0.038166 TCTTGGCATCGGGCTTCTTT 59.962 50.000 0.00 0.00 44.01 2.52
1525 1612 1.406751 GGCTTCTTCTCCTCTGGCTTC 60.407 57.143 0.00 0.00 0.00 3.86
1531 1618 0.686112 CCTCGGGCTTCTTCTCCTCT 60.686 60.000 0.00 0.00 0.00 3.69
1600 1702 1.852633 TCTCATCCGGCTTCTTCTCA 58.147 50.000 0.00 0.00 0.00 3.27
1628 1730 2.881352 CGGCTTCTTCTCGTCGGC 60.881 66.667 0.00 0.00 0.00 5.54
1648 1750 6.775142 CCTCCTTCTTTTCTTCCTTCTTTTCT 59.225 38.462 0.00 0.00 0.00 2.52
1669 1774 6.773200 TCTTCTTTTCTTCCTTCTTTTCCTCC 59.227 38.462 0.00 0.00 0.00 4.30
1712 1820 2.041115 GTTTGGGCTTCTCCTCGCC 61.041 63.158 0.00 0.00 45.55 5.54
2191 2329 1.405933 CCGGCTTGAGATCACATGACA 60.406 52.381 11.51 0.00 0.00 3.58
2257 2402 3.930229 TGGAACATCGAATTACCACGAAG 59.070 43.478 0.00 0.00 41.65 3.79
2421 2574 6.238621 CCAAACTTTTAGTGCCCCAAAAATTC 60.239 38.462 0.00 0.00 0.00 2.17
2510 2672 4.481368 AGTCTATCATTTAACGGCACCA 57.519 40.909 0.00 0.00 0.00 4.17
2566 2728 3.864921 GCAGAGGTATACCCGGCTATTTG 60.865 52.174 18.65 5.62 38.74 2.32
2577 2739 7.038659 CCAAATCAGCTATAGCAGAGGTATAC 58.961 42.308 26.07 0.00 45.16 1.47
2584 2746 5.365025 AGTTCTCCAAATCAGCTATAGCAGA 59.635 40.000 26.07 23.24 45.16 4.26
2602 2764 6.017852 GGTTATGCCAAATAGCTGTAGTTCTC 60.018 42.308 0.00 0.00 37.17 2.87
2605 2767 4.887655 GGGTTATGCCAAATAGCTGTAGTT 59.112 41.667 0.00 0.00 39.65 2.24
2608 2770 3.472652 CGGGTTATGCCAAATAGCTGTA 58.527 45.455 0.00 0.00 39.65 2.74
2609 2771 2.297701 CGGGTTATGCCAAATAGCTGT 58.702 47.619 0.00 0.00 39.65 4.40
2611 2773 1.133792 AGCGGGTTATGCCAAATAGCT 60.134 47.619 0.00 0.00 39.65 3.32
2637 2799 6.401153 CCAAATCAGTTTTCACGTAGCTCTAC 60.401 42.308 0.00 0.00 0.00 2.59
2638 2800 5.637810 CCAAATCAGTTTTCACGTAGCTCTA 59.362 40.000 0.00 0.00 0.00 2.43
2640 2802 4.378459 CCCAAATCAGTTTTCACGTAGCTC 60.378 45.833 0.00 0.00 0.00 4.09
2642 2804 3.500680 TCCCAAATCAGTTTTCACGTAGC 59.499 43.478 0.00 0.00 0.00 3.58
2643 2805 5.411361 TCATCCCAAATCAGTTTTCACGTAG 59.589 40.000 0.00 0.00 0.00 3.51
2644 2806 5.309638 TCATCCCAAATCAGTTTTCACGTA 58.690 37.500 0.00 0.00 0.00 3.57
2646 2808 4.764679 TCATCCCAAATCAGTTTTCACG 57.235 40.909 0.00 0.00 0.00 4.35
2647 2809 7.153985 TCAAATCATCCCAAATCAGTTTTCAC 58.846 34.615 0.00 0.00 0.00 3.18
2650 2812 8.977267 TTTTCAAATCATCCCAAATCAGTTTT 57.023 26.923 0.00 0.00 0.00 2.43
2651 2813 8.977267 TTTTTCAAATCATCCCAAATCAGTTT 57.023 26.923 0.00 0.00 0.00 2.66
2675 2837 4.137615 GTGGGGCCCGGGCTATTT 62.138 66.667 42.70 0.00 41.60 1.40
2685 2847 0.913934 AATTTTCATGGGGTGGGGCC 60.914 55.000 0.00 0.00 0.00 5.80
2686 2848 0.991146 AAATTTTCATGGGGTGGGGC 59.009 50.000 0.00 0.00 0.00 5.80
2687 2849 1.281577 CCAAATTTTCATGGGGTGGGG 59.718 52.381 0.00 0.00 32.87 4.96
2688 2850 2.785540 CCAAATTTTCATGGGGTGGG 57.214 50.000 0.00 0.00 32.87 4.61
2694 2856 1.281577 CCCACCCCCAAATTTTCATGG 59.718 52.381 0.00 0.00 36.42 3.66
2696 2858 2.550175 CTCCCACCCCCAAATTTTCAT 58.450 47.619 0.00 0.00 0.00 2.57
2698 2860 1.275666 CCTCCCACCCCCAAATTTTC 58.724 55.000 0.00 0.00 0.00 2.29
2699 2861 0.178876 CCCTCCCACCCCCAAATTTT 60.179 55.000 0.00 0.00 0.00 1.82
2700 2862 1.473844 CCCTCCCACCCCCAAATTT 59.526 57.895 0.00 0.00 0.00 1.82
2701 2863 2.566903 CCCCTCCCACCCCCAAATT 61.567 63.158 0.00 0.00 0.00 1.82
2702 2864 2.952359 CCCCTCCCACCCCCAAAT 60.952 66.667 0.00 0.00 0.00 2.32
2703 2865 4.224971 TCCCCTCCCACCCCCAAA 62.225 66.667 0.00 0.00 0.00 3.28
2704 2866 4.693915 CTCCCCTCCCACCCCCAA 62.694 72.222 0.00 0.00 0.00 4.12
2706 2868 3.702623 TACTCCCCTCCCACCCCC 61.703 72.222 0.00 0.00 0.00 5.40
2707 2869 1.974551 ATCTACTCCCCTCCCACCCC 61.975 65.000 0.00 0.00 0.00 4.95
2708 2870 0.029989 AATCTACTCCCCTCCCACCC 60.030 60.000 0.00 0.00 0.00 4.61
2709 2871 2.610873 CTAATCTACTCCCCTCCCACC 58.389 57.143 0.00 0.00 0.00 4.61
2710 2872 2.179424 TCCTAATCTACTCCCCTCCCAC 59.821 54.545 0.00 0.00 0.00 4.61
2711 2873 2.451273 CTCCTAATCTACTCCCCTCCCA 59.549 54.545 0.00 0.00 0.00 4.37
2712 2874 2.225420 CCTCCTAATCTACTCCCCTCCC 60.225 59.091 0.00 0.00 0.00 4.30
2713 2875 2.451659 ACCTCCTAATCTACTCCCCTCC 59.548 54.545 0.00 0.00 0.00 4.30
2714 2876 3.907459 ACCTCCTAATCTACTCCCCTC 57.093 52.381 0.00 0.00 0.00 4.30
2715 2877 4.645968 AAACCTCCTAATCTACTCCCCT 57.354 45.455 0.00 0.00 0.00 4.79
2716 2878 7.038445 GGTAATAAACCTCCTAATCTACTCCCC 60.038 44.444 0.00 0.00 45.75 4.81
2717 2879 7.905265 GGTAATAAACCTCCTAATCTACTCCC 58.095 42.308 0.00 0.00 45.75 4.30
2733 2895 7.231519 ACCTACGTACCCATCTAGGTAATAAAC 59.768 40.741 0.52 0.00 43.97 2.01
2734 2896 7.231317 CACCTACGTACCCATCTAGGTAATAAA 59.769 40.741 2.20 0.00 43.97 1.40
2735 2897 6.716628 CACCTACGTACCCATCTAGGTAATAA 59.283 42.308 2.20 0.00 43.97 1.40
2736 2898 6.183361 ACACCTACGTACCCATCTAGGTAATA 60.183 42.308 2.20 0.00 43.97 0.98
2737 2899 5.075493 CACCTACGTACCCATCTAGGTAAT 58.925 45.833 2.20 0.00 43.97 1.89
2738 2900 4.079787 ACACCTACGTACCCATCTAGGTAA 60.080 45.833 2.20 0.00 43.97 2.85
2739 2901 3.459598 ACACCTACGTACCCATCTAGGTA 59.540 47.826 2.20 0.00 41.58 3.08
2740 2902 2.243221 ACACCTACGTACCCATCTAGGT 59.757 50.000 0.00 0.00 44.37 3.08
2741 2903 2.941480 ACACCTACGTACCCATCTAGG 58.059 52.381 0.00 0.00 33.22 3.02
2742 2904 4.070716 CCTACACCTACGTACCCATCTAG 58.929 52.174 0.00 0.00 0.00 2.43
2743 2905 3.716353 TCCTACACCTACGTACCCATCTA 59.284 47.826 0.00 0.00 0.00 1.98
2744 2906 2.511218 TCCTACACCTACGTACCCATCT 59.489 50.000 0.00 0.00 0.00 2.90
2745 2907 2.936202 TCCTACACCTACGTACCCATC 58.064 52.381 0.00 0.00 0.00 3.51
2746 2908 3.607490 ATCCTACACCTACGTACCCAT 57.393 47.619 0.00 0.00 0.00 4.00
2747 2909 3.386932 AATCCTACACCTACGTACCCA 57.613 47.619 0.00 0.00 0.00 4.51
2748 2910 5.302823 ACAATAATCCTACACCTACGTACCC 59.697 44.000 0.00 0.00 0.00 3.69
2749 2911 6.396829 ACAATAATCCTACACCTACGTACC 57.603 41.667 0.00 0.00 0.00 3.34
2750 2912 7.221452 CACAACAATAATCCTACACCTACGTAC 59.779 40.741 0.00 0.00 0.00 3.67
2751 2913 7.259882 CACAACAATAATCCTACACCTACGTA 58.740 38.462 0.00 0.00 0.00 3.57
2752 2914 6.103997 CACAACAATAATCCTACACCTACGT 58.896 40.000 0.00 0.00 0.00 3.57
2753 2915 5.522460 CCACAACAATAATCCTACACCTACG 59.478 44.000 0.00 0.00 0.00 3.51
2754 2916 6.537660 GTCCACAACAATAATCCTACACCTAC 59.462 42.308 0.00 0.00 0.00 3.18
2755 2917 6.213802 TGTCCACAACAATAATCCTACACCTA 59.786 38.462 0.00 0.00 34.03 3.08
2756 2918 5.013704 TGTCCACAACAATAATCCTACACCT 59.986 40.000 0.00 0.00 34.03 4.00
2757 2919 5.123344 GTGTCCACAACAATAATCCTACACC 59.877 44.000 0.00 0.00 40.31 4.16
2758 2920 5.938125 AGTGTCCACAACAATAATCCTACAC 59.062 40.000 0.00 0.00 40.31 2.90
2759 2921 5.937540 CAGTGTCCACAACAATAATCCTACA 59.062 40.000 0.00 0.00 40.31 2.74
2760 2922 5.354234 CCAGTGTCCACAACAATAATCCTAC 59.646 44.000 0.00 0.00 40.31 3.18
2761 2923 5.496556 CCAGTGTCCACAACAATAATCCTA 58.503 41.667 0.00 0.00 40.31 2.94
2762 2924 4.335416 CCAGTGTCCACAACAATAATCCT 58.665 43.478 0.00 0.00 40.31 3.24
2763 2925 3.119495 GCCAGTGTCCACAACAATAATCC 60.119 47.826 0.00 0.00 40.31 3.01
2764 2926 3.505680 TGCCAGTGTCCACAACAATAATC 59.494 43.478 0.00 0.00 40.31 1.75
2765 2927 3.495331 TGCCAGTGTCCACAACAATAAT 58.505 40.909 0.00 0.00 40.31 1.28
2766 2928 2.884012 CTGCCAGTGTCCACAACAATAA 59.116 45.455 0.00 0.00 40.31 1.40
2767 2929 2.503331 CTGCCAGTGTCCACAACAATA 58.497 47.619 0.00 0.00 40.31 1.90
2768 2930 1.321474 CTGCCAGTGTCCACAACAAT 58.679 50.000 0.00 0.00 40.31 2.71
2769 2931 0.751277 CCTGCCAGTGTCCACAACAA 60.751 55.000 0.00 0.00 40.31 2.83
2770 2932 1.152984 CCTGCCAGTGTCCACAACA 60.153 57.895 0.00 0.00 34.78 3.33
2809 3778 1.923204 CTCTTTCTTCTCACCGCATCG 59.077 52.381 0.00 0.00 0.00 3.84
2852 3821 5.975693 TGACTGACCCAAATCATAAAACC 57.024 39.130 0.00 0.00 0.00 3.27
2910 3882 5.244755 TCATCGAAATTGACTGACATTGGA 58.755 37.500 0.00 0.00 0.00 3.53
2938 3910 2.699954 GTGTGGTTACTATGCTGCTGT 58.300 47.619 0.00 0.01 0.00 4.40
2948 3920 2.366266 TCTTGCCTTACGTGTGGTTACT 59.634 45.455 0.00 0.00 0.00 2.24
2949 3921 2.477754 GTCTTGCCTTACGTGTGGTTAC 59.522 50.000 0.00 0.00 0.00 2.50
2952 3924 0.250166 GGTCTTGCCTTACGTGTGGT 60.250 55.000 0.00 0.00 0.00 4.16
2953 3925 1.289109 CGGTCTTGCCTTACGTGTGG 61.289 60.000 0.00 0.56 34.25 4.17
2954 3926 0.319211 TCGGTCTTGCCTTACGTGTG 60.319 55.000 0.00 0.00 34.25 3.82
2955 3927 0.606604 ATCGGTCTTGCCTTACGTGT 59.393 50.000 0.00 0.00 34.25 4.49
2962 3934 1.330655 ATCGGACATCGGTCTTGCCT 61.331 55.000 0.00 0.00 43.77 4.75
2972 3944 2.315925 TCTTTGCTCCATCGGACATC 57.684 50.000 0.00 0.00 0.00 3.06
2973 3945 2.636830 CTTCTTTGCTCCATCGGACAT 58.363 47.619 0.00 0.00 0.00 3.06
2974 3946 1.339055 CCTTCTTTGCTCCATCGGACA 60.339 52.381 0.00 0.00 0.00 4.02
2975 3947 1.373570 CCTTCTTTGCTCCATCGGAC 58.626 55.000 0.00 0.00 0.00 4.79
2976 3948 0.392998 GCCTTCTTTGCTCCATCGGA 60.393 55.000 0.00 0.00 0.00 4.55
2977 3949 0.677731 TGCCTTCTTTGCTCCATCGG 60.678 55.000 0.00 0.00 0.00 4.18
2978 3950 0.731417 CTGCCTTCTTTGCTCCATCG 59.269 55.000 0.00 0.00 0.00 3.84
2979 3951 0.455005 GCTGCCTTCTTTGCTCCATC 59.545 55.000 0.00 0.00 0.00 3.51
3024 3996 1.989508 GGAGCCCAAACCCCCAATG 60.990 63.158 0.00 0.00 0.00 2.82
3035 4007 1.492133 CCTTCTCAAGGTGGAGCCCA 61.492 60.000 0.00 0.00 43.95 5.36
3050 4022 4.357279 AGCAGCTGGGCCACCTTC 62.357 66.667 17.12 0.00 37.76 3.46
3051 4023 4.673375 CAGCAGCTGGGCCACCTT 62.673 66.667 17.12 0.00 37.76 3.50
3060 4032 2.490148 CCATCATGCCCAGCAGCTG 61.490 63.158 16.23 16.23 43.65 4.24
3077 4049 3.376918 GCTGGGGTTGCTGCTTCC 61.377 66.667 0.00 3.15 0.00 3.46
3106 4078 1.163554 GGCTTGAGTGCTCTCTTTGG 58.836 55.000 16.23 5.68 40.98 3.28
3140 4112 4.583489 TGGCTTAACGGGTTGTTGATTTTA 59.417 37.500 0.00 0.00 42.01 1.52


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

AutoCloner maintained by Alex Coulton.