Multiple sequence alignment - TraesCS7B01G323500

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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 TraesCS7B01G323500 chr7B 100.000 2911 0 0 1 2911 574510873 574513783 0.000000e+00 5376
1 TraesCS7B01G323500 chr1A 97.582 2730 58 6 1 2725 184936442 184933716 0.000000e+00 4669
2 TraesCS7B01G323500 chr6B 97.328 2732 60 8 1 2726 610805862 610808586 0.000000e+00 4628
3 TraesCS7B01G323500 chr6B 82.432 1332 196 27 824 2131 103963362 103964679 0.000000e+00 1129
4 TraesCS7B01G323500 chr7A 94.489 2377 106 10 362 2727 32589644 32587282 0.000000e+00 3640
5 TraesCS7B01G323500 chr7A 96.394 1969 66 4 1 1965 255889375 255887408 0.000000e+00 3238
6 TraesCS7B01G323500 chr7A 86.200 1942 246 17 1 1925 88959666 88957730 0.000000e+00 2082
7 TraesCS7B01G323500 chr7A 86.155 1943 245 19 1 1925 722320044 722318108 0.000000e+00 2076
8 TraesCS7B01G323500 chr7A 85.877 963 117 6 1097 2042 171878764 171877804 0.000000e+00 1007
9 TraesCS7B01G323500 chr5A 87.367 2066 229 22 1 2042 663074072 663076129 0.000000e+00 2340
10 TraesCS7B01G323500 chr5A 88.079 713 81 4 1 711 167892428 167891718 0.000000e+00 843
11 TraesCS7B01G323500 chr5A 90.977 133 10 2 2595 2726 36865968 36866099 8.290000e-41 178
12 TraesCS7B01G323500 chrUn 97.377 1258 28 3 1479 2734 259654538 259653284 0.000000e+00 2135
13 TraesCS7B01G323500 chrUn 97.746 976 19 3 1 973 445250994 445251969 0.000000e+00 1677
14 TraesCS7B01G323500 chrUn 85.599 1111 137 17 824 1917 98277487 98276383 0.000000e+00 1144
15 TraesCS7B01G323500 chrUn 85.774 963 118 6 1097 2042 386814551 386813591 0.000000e+00 1002
16 TraesCS7B01G323500 chrUn 97.080 411 12 0 2050 2460 477615150 477614740 0.000000e+00 693
17 TraesCS7B01G323500 chr6A 82.468 1329 197 24 824 2131 53257554 53256241 0.000000e+00 1131
18 TraesCS7B01G323500 chr7D 86.824 850 107 5 6 853 299800632 299799786 0.000000e+00 944


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 TraesCS7B01G323500 chr7B 574510873 574513783 2910 False 5376 5376 100.000 1 2911 1 chr7B.!!$F1 2910
1 TraesCS7B01G323500 chr1A 184933716 184936442 2726 True 4669 4669 97.582 1 2725 1 chr1A.!!$R1 2724
2 TraesCS7B01G323500 chr6B 610805862 610808586 2724 False 4628 4628 97.328 1 2726 1 chr6B.!!$F2 2725
3 TraesCS7B01G323500 chr6B 103963362 103964679 1317 False 1129 1129 82.432 824 2131 1 chr6B.!!$F1 1307
4 TraesCS7B01G323500 chr7A 32587282 32589644 2362 True 3640 3640 94.489 362 2727 1 chr7A.!!$R1 2365
5 TraesCS7B01G323500 chr7A 255887408 255889375 1967 True 3238 3238 96.394 1 1965 1 chr7A.!!$R4 1964
6 TraesCS7B01G323500 chr7A 88957730 88959666 1936 True 2082 2082 86.200 1 1925 1 chr7A.!!$R2 1924
7 TraesCS7B01G323500 chr7A 722318108 722320044 1936 True 2076 2076 86.155 1 1925 1 chr7A.!!$R5 1924
8 TraesCS7B01G323500 chr7A 171877804 171878764 960 True 1007 1007 85.877 1097 2042 1 chr7A.!!$R3 945
9 TraesCS7B01G323500 chr5A 663074072 663076129 2057 False 2340 2340 87.367 1 2042 1 chr5A.!!$F2 2041
10 TraesCS7B01G323500 chr5A 167891718 167892428 710 True 843 843 88.079 1 711 1 chr5A.!!$R1 710
11 TraesCS7B01G323500 chrUn 259653284 259654538 1254 True 2135 2135 97.377 1479 2734 1 chrUn.!!$R2 1255
12 TraesCS7B01G323500 chrUn 445250994 445251969 975 False 1677 1677 97.746 1 973 1 chrUn.!!$F1 972
13 TraesCS7B01G323500 chrUn 98276383 98277487 1104 True 1144 1144 85.599 824 1917 1 chrUn.!!$R1 1093
14 TraesCS7B01G323500 chrUn 386813591 386814551 960 True 1002 1002 85.774 1097 2042 1 chrUn.!!$R3 945
15 TraesCS7B01G323500 chr6A 53256241 53257554 1313 True 1131 1131 82.468 824 2131 1 chr6A.!!$R1 1307
16 TraesCS7B01G323500 chr7D 299799786 299800632 846 True 944 944 86.824 6 853 1 chr7D.!!$R1 847

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
571 577 0.034186 GGATGCCATTCTGTCCACCA 60.034 55.000 0.0 0.0 0.0 4.17 F
1448 1477 1.221021 GAGTGCTAAAGGTCCGGGG 59.779 63.158 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1678 0.545646 ATTCTCCTGCTCAGCTTCCC 59.454 55.0 0.0 0.00 0.00 3.97 R
2818 2870 0.032217 TGAATCATGGGCCCTTTCCC 60.032 55.0 25.7 8.48 46.73 3.97 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
101 102 8.821686 TTTATCAAGATCAAATGGCCTTAAGA 57.178 30.769 3.32 0.00 0.00 2.10
571 577 0.034186 GGATGCCATTCTGTCCACCA 60.034 55.000 0.00 0.00 0.00 4.17
678 684 7.837923 CGTTGATACACGCTAGTACATTTTTAC 59.162 37.037 0.00 0.00 32.43 2.01
932 942 4.886579 GTCAAAGAGGCCAAATTGACATT 58.113 39.130 28.32 0.00 46.75 2.71
962 973 3.900601 AGAGACAAGAGAACATGGACAGT 59.099 43.478 0.00 0.00 0.00 3.55
1182 1193 6.572519 TCTGGAAATTATGCAAAATGGTAGC 58.427 36.000 0.00 0.00 0.00 3.58
1198 1209 1.418637 GTAGCGGGTTTGGATGGGATA 59.581 52.381 0.00 0.00 0.00 2.59
1241 1252 6.220609 ACTGGAGATAGGGAGACATATATGGA 59.779 42.308 16.96 0.00 37.46 3.41
1448 1477 1.221021 GAGTGCTAAAGGTCCGGGG 59.779 63.158 0.00 0.00 0.00 5.73
1522 1552 2.273619 ACCAGCCAAGGAGAATCTTCT 58.726 47.619 0.00 0.00 41.00 2.85
1624 1657 2.017049 GTCAGGTCTTGCAAGTGTGTT 58.983 47.619 25.19 6.17 0.00 3.32
1645 1678 7.222417 TGTGTTGAATACAATTGCAAAGTTCTG 59.778 33.333 1.71 0.00 38.80 3.02
1700 1733 6.667414 TGAATGGTTTACAGAGGGCATTTATT 59.333 34.615 0.00 0.00 0.00 1.40
2111 2154 4.937620 TGCTAGTGCTGTAAGAAAAGGATG 59.062 41.667 0.00 0.00 40.48 3.51
2133 2176 6.331369 TGTTTTCATCTCTTTCATCAACCC 57.669 37.500 0.00 0.00 0.00 4.11
2163 2209 2.252976 TGCTGTGTCATGTGTTGCTA 57.747 45.000 0.00 0.00 0.00 3.49
2170 2216 6.330004 TGTGTCATGTGTTGCTATCATTTT 57.670 33.333 0.00 0.00 0.00 1.82
2178 2224 5.580691 TGTGTTGCTATCATTTTCTCCTACG 59.419 40.000 0.00 0.00 0.00 3.51
2353 2400 1.490490 GGGTCAGCACCTGGATAATCA 59.510 52.381 0.00 0.00 43.22 2.57
2507 2559 0.475044 TACTTGGCCTTGGTCGGTTT 59.525 50.000 3.32 0.00 0.00 3.27
2624 2676 3.845109 AATTCCCACCCTACACCAAAT 57.155 42.857 0.00 0.00 0.00 2.32
2641 2693 3.081804 CAAATGTGGGACTGGGACTAAC 58.918 50.000 0.00 0.00 0.00 2.34
2643 2695 1.053424 TGTGGGACTGGGACTAACAC 58.947 55.000 0.00 0.00 0.00 3.32
2727 2779 4.382291 TCAAACTACCAAACACGCTGTAT 58.618 39.130 0.00 0.00 0.00 2.29
2731 2783 4.491676 ACTACCAAACACGCTGTATGTAG 58.508 43.478 13.53 13.53 34.65 2.74
2732 2784 3.671008 ACCAAACACGCTGTATGTAGA 57.329 42.857 0.00 0.00 0.00 2.59
2733 2785 3.585862 ACCAAACACGCTGTATGTAGAG 58.414 45.455 0.00 0.00 0.00 2.43
2734 2786 2.348666 CCAAACACGCTGTATGTAGAGC 59.651 50.000 0.00 0.00 39.03 4.09
2735 2787 3.254060 CAAACACGCTGTATGTAGAGCT 58.746 45.455 7.46 0.00 40.13 4.09
2736 2788 2.568696 ACACGCTGTATGTAGAGCTG 57.431 50.000 0.00 7.14 40.13 4.24
2737 2789 1.135139 ACACGCTGTATGTAGAGCTGG 59.865 52.381 0.00 2.59 40.13 4.85
2738 2790 0.747255 ACGCTGTATGTAGAGCTGGG 59.253 55.000 0.00 0.00 40.13 4.45
2739 2791 0.747255 CGCTGTATGTAGAGCTGGGT 59.253 55.000 0.00 0.00 40.13 4.51
2740 2792 1.137086 CGCTGTATGTAGAGCTGGGTT 59.863 52.381 0.00 0.00 40.13 4.11
2741 2793 2.555199 GCTGTATGTAGAGCTGGGTTG 58.445 52.381 0.00 0.00 39.29 3.77
2742 2794 2.168521 GCTGTATGTAGAGCTGGGTTGA 59.831 50.000 0.00 0.00 39.29 3.18
2743 2795 3.739519 GCTGTATGTAGAGCTGGGTTGAG 60.740 52.174 0.00 0.00 39.29 3.02
2744 2796 2.766263 TGTATGTAGAGCTGGGTTGAGG 59.234 50.000 0.00 0.00 0.00 3.86
2745 2797 1.207791 ATGTAGAGCTGGGTTGAGGG 58.792 55.000 0.00 0.00 0.00 4.30
2746 2798 0.178903 TGTAGAGCTGGGTTGAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
2747 2799 0.537653 GTAGAGCTGGGTTGAGGGTC 59.462 60.000 0.00 0.00 0.00 4.46
2748 2800 0.617820 TAGAGCTGGGTTGAGGGTCC 60.618 60.000 0.00 0.00 0.00 4.46
2749 2801 2.121963 AGCTGGGTTGAGGGTCCA 60.122 61.111 0.00 0.00 0.00 4.02
2751 2803 3.081554 CTGGGTTGAGGGTCCAGG 58.918 66.667 0.00 0.00 43.09 4.45
2752 2804 1.538876 CTGGGTTGAGGGTCCAGGA 60.539 63.158 0.00 0.00 43.09 3.86
2753 2805 0.916358 CTGGGTTGAGGGTCCAGGAT 60.916 60.000 0.00 0.00 43.09 3.24
2754 2806 0.419865 TGGGTTGAGGGTCCAGGATA 59.580 55.000 0.00 0.00 0.00 2.59
2755 2807 1.203505 TGGGTTGAGGGTCCAGGATAA 60.204 52.381 0.00 0.00 0.00 1.75
2756 2808 1.490910 GGGTTGAGGGTCCAGGATAAG 59.509 57.143 0.00 0.00 0.00 1.73
2757 2809 2.478292 GGTTGAGGGTCCAGGATAAGA 58.522 52.381 0.00 0.00 0.00 2.10
2758 2810 2.436173 GGTTGAGGGTCCAGGATAAGAG 59.564 54.545 0.00 0.00 0.00 2.85
2759 2811 2.436173 GTTGAGGGTCCAGGATAAGAGG 59.564 54.545 0.00 0.00 0.00 3.69
2760 2812 1.937350 TGAGGGTCCAGGATAAGAGGA 59.063 52.381 0.00 0.00 0.00 3.71
2764 2816 1.777941 GTCCAGGATAAGAGGACGGT 58.222 55.000 0.00 0.00 42.02 4.83
2765 2817 1.409427 GTCCAGGATAAGAGGACGGTG 59.591 57.143 0.00 0.00 42.02 4.94
2766 2818 0.753262 CCAGGATAAGAGGACGGTGG 59.247 60.000 0.00 0.00 0.00 4.61
2767 2819 0.105039 CAGGATAAGAGGACGGTGGC 59.895 60.000 0.00 0.00 0.00 5.01
2768 2820 0.325296 AGGATAAGAGGACGGTGGCA 60.325 55.000 0.00 0.00 0.00 4.92
2769 2821 0.105039 GGATAAGAGGACGGTGGCAG 59.895 60.000 0.00 0.00 0.00 4.85
2770 2822 0.530870 GATAAGAGGACGGTGGCAGC 60.531 60.000 6.62 6.62 0.00 5.25
2771 2823 2.298158 ATAAGAGGACGGTGGCAGCG 62.298 60.000 34.40 34.40 45.69 5.18
2779 2831 3.818787 GGTGGCAGCGGCATGAAG 61.819 66.667 11.88 0.00 43.71 3.02
2780 2832 2.747460 GTGGCAGCGGCATGAAGA 60.747 61.111 11.88 0.00 43.71 2.87
2781 2833 2.437180 TGGCAGCGGCATGAAGAG 60.437 61.111 11.88 0.00 43.71 2.85
2782 2834 3.207669 GGCAGCGGCATGAAGAGG 61.208 66.667 11.88 0.00 43.71 3.69
2783 2835 3.885521 GCAGCGGCATGAAGAGGC 61.886 66.667 3.18 0.00 40.72 4.70
2788 2840 4.434685 GGCATGAAGAGGCGAGAG 57.565 61.111 0.00 0.00 0.00 3.20
2789 2841 1.227497 GGCATGAAGAGGCGAGAGG 60.227 63.158 0.00 0.00 0.00 3.69
2790 2842 1.519719 GCATGAAGAGGCGAGAGGT 59.480 57.895 0.00 0.00 0.00 3.85
2791 2843 0.107945 GCATGAAGAGGCGAGAGGTT 60.108 55.000 0.00 0.00 0.00 3.50
2792 2844 1.933247 CATGAAGAGGCGAGAGGTTC 58.067 55.000 0.00 0.00 0.00 3.62
2793 2845 1.205655 CATGAAGAGGCGAGAGGTTCA 59.794 52.381 0.00 0.00 0.00 3.18
2794 2846 1.338107 TGAAGAGGCGAGAGGTTCAA 58.662 50.000 0.00 0.00 0.00 2.69
2795 2847 1.902508 TGAAGAGGCGAGAGGTTCAAT 59.097 47.619 0.00 0.00 0.00 2.57
2796 2848 3.096852 TGAAGAGGCGAGAGGTTCAATA 58.903 45.455 0.00 0.00 0.00 1.90
2797 2849 3.513912 TGAAGAGGCGAGAGGTTCAATAA 59.486 43.478 0.00 0.00 0.00 1.40
2798 2850 3.810310 AGAGGCGAGAGGTTCAATAAG 57.190 47.619 0.00 0.00 0.00 1.73
2799 2851 2.432510 AGAGGCGAGAGGTTCAATAAGG 59.567 50.000 0.00 0.00 0.00 2.69
2800 2852 1.134371 AGGCGAGAGGTTCAATAAGGC 60.134 52.381 0.00 0.00 0.00 4.35
2801 2853 1.134371 GGCGAGAGGTTCAATAAGGCT 60.134 52.381 0.00 0.00 0.00 4.58
2802 2854 2.205911 GCGAGAGGTTCAATAAGGCTC 58.794 52.381 0.00 0.00 0.00 4.70
2803 2855 2.464865 CGAGAGGTTCAATAAGGCTCG 58.535 52.381 0.00 0.00 37.93 5.03
2804 2856 2.159226 CGAGAGGTTCAATAAGGCTCGT 60.159 50.000 0.00 0.00 38.97 4.18
2805 2857 3.190874 GAGAGGTTCAATAAGGCTCGTG 58.809 50.000 0.00 0.00 0.00 4.35
2806 2858 2.832129 AGAGGTTCAATAAGGCTCGTGA 59.168 45.455 0.00 0.00 0.00 4.35
2807 2859 3.260884 AGAGGTTCAATAAGGCTCGTGAA 59.739 43.478 4.00 4.00 0.00 3.18
2808 2860 4.080863 AGAGGTTCAATAAGGCTCGTGAAT 60.081 41.667 9.73 0.00 32.93 2.57
2809 2861 4.589908 AGGTTCAATAAGGCTCGTGAATT 58.410 39.130 9.73 0.00 32.93 2.17
2810 2862 5.010282 AGGTTCAATAAGGCTCGTGAATTT 58.990 37.500 9.73 1.54 32.93 1.82
2811 2863 5.476945 AGGTTCAATAAGGCTCGTGAATTTT 59.523 36.000 9.73 0.00 32.93 1.82
2812 2864 5.572896 GGTTCAATAAGGCTCGTGAATTTTG 59.427 40.000 9.73 0.00 32.93 2.44
2813 2865 5.957842 TCAATAAGGCTCGTGAATTTTGT 57.042 34.783 0.00 0.00 0.00 2.83
2814 2866 7.302524 GTTCAATAAGGCTCGTGAATTTTGTA 58.697 34.615 9.73 0.00 32.93 2.41
2815 2867 7.624360 TCAATAAGGCTCGTGAATTTTGTAT 57.376 32.000 0.00 0.00 0.00 2.29
2816 2868 7.471721 TCAATAAGGCTCGTGAATTTTGTATG 58.528 34.615 0.00 0.00 0.00 2.39
2817 2869 7.335673 TCAATAAGGCTCGTGAATTTTGTATGA 59.664 33.333 0.00 0.00 0.00 2.15
2818 2870 5.551760 AAGGCTCGTGAATTTTGTATGAG 57.448 39.130 0.00 0.00 0.00 2.90
2819 2871 3.941483 AGGCTCGTGAATTTTGTATGAGG 59.059 43.478 0.00 0.00 0.00 3.86
2820 2872 3.065371 GGCTCGTGAATTTTGTATGAGGG 59.935 47.826 0.00 0.00 0.00 4.30
2821 2873 3.938963 GCTCGTGAATTTTGTATGAGGGA 59.061 43.478 0.00 0.00 0.00 4.20
2822 2874 4.394920 GCTCGTGAATTTTGTATGAGGGAA 59.605 41.667 0.00 0.00 0.00 3.97
2823 2875 5.106317 GCTCGTGAATTTTGTATGAGGGAAA 60.106 40.000 0.00 0.00 0.00 3.13
2824 2876 6.494893 TCGTGAATTTTGTATGAGGGAAAG 57.505 37.500 0.00 0.00 0.00 2.62
2825 2877 5.414454 TCGTGAATTTTGTATGAGGGAAAGG 59.586 40.000 0.00 0.00 0.00 3.11
2826 2878 5.393027 CGTGAATTTTGTATGAGGGAAAGGG 60.393 44.000 0.00 0.00 0.00 3.95
2827 2879 4.466015 TGAATTTTGTATGAGGGAAAGGGC 59.534 41.667 0.00 0.00 0.00 5.19
2828 2880 2.525105 TTTGTATGAGGGAAAGGGCC 57.475 50.000 0.00 0.00 0.00 5.80
2837 2889 3.613661 GGAAAGGGCCCATGATTCA 57.386 52.632 27.56 0.00 0.00 2.57
2838 2890 2.092598 GGAAAGGGCCCATGATTCAT 57.907 50.000 27.56 0.00 0.00 2.57
2839 2891 2.401568 GGAAAGGGCCCATGATTCATT 58.598 47.619 27.56 3.12 0.00 2.57
2840 2892 2.773661 GGAAAGGGCCCATGATTCATTT 59.226 45.455 27.56 13.20 0.00 2.32
2841 2893 3.200605 GGAAAGGGCCCATGATTCATTTT 59.799 43.478 27.56 12.38 0.00 1.82
2842 2894 4.324486 GGAAAGGGCCCATGATTCATTTTT 60.324 41.667 27.56 11.55 0.00 1.94
2843 2895 5.104569 GGAAAGGGCCCATGATTCATTTTTA 60.105 40.000 27.56 0.00 0.00 1.52
2844 2896 5.619132 AAGGGCCCATGATTCATTTTTAG 57.381 39.130 27.56 0.00 0.00 1.85
2845 2897 3.969312 AGGGCCCATGATTCATTTTTAGG 59.031 43.478 27.56 0.00 0.00 2.69
2846 2898 3.071457 GGGCCCATGATTCATTTTTAGGG 59.929 47.826 19.95 12.57 38.10 3.53
2847 2899 3.071457 GGCCCATGATTCATTTTTAGGGG 59.929 47.826 16.68 14.14 35.58 4.79
2848 2900 3.711190 GCCCATGATTCATTTTTAGGGGT 59.289 43.478 16.68 0.00 35.58 4.95
2849 2901 4.898861 GCCCATGATTCATTTTTAGGGGTA 59.101 41.667 16.68 0.00 35.58 3.69
2850 2902 5.011023 GCCCATGATTCATTTTTAGGGGTAG 59.989 44.000 16.68 0.00 35.58 3.18
2851 2903 5.539955 CCCATGATTCATTTTTAGGGGTAGG 59.460 44.000 10.01 0.00 0.00 3.18
2852 2904 5.011023 CCATGATTCATTTTTAGGGGTAGGC 59.989 44.000 0.00 0.00 0.00 3.93
2853 2905 5.199982 TGATTCATTTTTAGGGGTAGGCA 57.800 39.130 0.00 0.00 0.00 4.75
2854 2906 5.776358 TGATTCATTTTTAGGGGTAGGCAT 58.224 37.500 0.00 0.00 0.00 4.40
2855 2907 5.833131 TGATTCATTTTTAGGGGTAGGCATC 59.167 40.000 0.00 0.00 0.00 3.91
2856 2908 3.815809 TCATTTTTAGGGGTAGGCATCG 58.184 45.455 0.00 0.00 0.00 3.84
2857 2909 3.201266 TCATTTTTAGGGGTAGGCATCGT 59.799 43.478 0.00 0.00 0.00 3.73
2858 2910 2.702592 TTTTAGGGGTAGGCATCGTG 57.297 50.000 0.00 0.00 0.00 4.35
2859 2911 1.575419 TTTAGGGGTAGGCATCGTGT 58.425 50.000 0.00 0.00 0.00 4.49
2860 2912 1.575419 TTAGGGGTAGGCATCGTGTT 58.425 50.000 0.00 0.00 0.00 3.32
2861 2913 1.575419 TAGGGGTAGGCATCGTGTTT 58.425 50.000 0.00 0.00 0.00 2.83
2862 2914 0.696501 AGGGGTAGGCATCGTGTTTT 59.303 50.000 0.00 0.00 0.00 2.43
2863 2915 1.074889 AGGGGTAGGCATCGTGTTTTT 59.925 47.619 0.00 0.00 0.00 1.94
2902 2954 6.934048 GGATACATCCAAAAAGAGGAAGAG 57.066 41.667 3.26 0.00 46.38 2.85
2903 2955 6.653989 GGATACATCCAAAAAGAGGAAGAGA 58.346 40.000 3.26 0.00 46.38 3.10
2904 2956 7.112779 GGATACATCCAAAAAGAGGAAGAGAA 58.887 38.462 3.26 0.00 46.38 2.87
2905 2957 7.611855 GGATACATCCAAAAAGAGGAAGAGAAA 59.388 37.037 3.26 0.00 46.38 2.52
2906 2958 9.183368 GATACATCCAAAAAGAGGAAGAGAAAT 57.817 33.333 0.00 0.00 38.93 2.17
2909 2961 9.183368 ACATCCAAAAAGAGGAAGAGAAATATC 57.817 33.333 0.00 0.00 38.93 1.63
2910 2962 7.849804 TCCAAAAAGAGGAAGAGAAATATCG 57.150 36.000 0.00 0.00 30.71 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 3.385115 ACAATCTCTTACCCCGAGGAAT 58.615 45.455 0.00 0.00 36.73 3.01
571 577 3.007940 TCAGTCCACTCGGATGATGTTTT 59.992 43.478 0.00 0.00 45.33 2.43
678 684 8.322906 TGAACAAACATCTAATGTCCTACAAG 57.677 34.615 0.00 0.00 44.07 3.16
932 942 6.484643 CCATGTTCTCTTGTCTCTCTTTTTCA 59.515 38.462 0.00 0.00 0.00 2.69
962 973 0.178891 AAGCAACCTCTCCTCCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
1182 1193 3.149196 CTCATTATCCCATCCAAACCCG 58.851 50.000 0.00 0.00 0.00 5.28
1198 1209 6.441924 TCTCCAGTTACCATCTTCTTCTCATT 59.558 38.462 0.00 0.00 0.00 2.57
1241 1252 4.316025 ACATATTGTACCTTTGCCCAGT 57.684 40.909 0.00 0.00 0.00 4.00
1448 1477 9.705290 GATCCATCTTCTACTATTTCTTCTTCC 57.295 37.037 0.00 0.00 0.00 3.46
1522 1552 6.894654 TGGGCTTGTATCCTCATTTAATTCAA 59.105 34.615 0.00 0.00 0.00 2.69
1624 1657 5.538053 TCCCAGAACTTTGCAATTGTATTCA 59.462 36.000 7.40 0.00 0.00 2.57
1645 1678 0.545646 ATTCTCCTGCTCAGCTTCCC 59.454 55.000 0.00 0.00 0.00 3.97
2111 2154 6.331369 TGGGTTGATGAAAGAGATGAAAAC 57.669 37.500 0.00 0.00 0.00 2.43
2133 2176 2.435422 TGACACAGCAATACCCACATG 58.565 47.619 0.00 0.00 0.00 3.21
2163 2209 7.822334 TCATTGTTGTACGTAGGAGAAAATGAT 59.178 33.333 0.00 0.00 0.00 2.45
2170 2216 6.525578 AAGATCATTGTTGTACGTAGGAGA 57.474 37.500 0.00 0.00 0.00 3.71
2353 2400 5.652452 TGTACACTATCTCTACACATGCTGT 59.348 40.000 0.00 0.00 36.82 4.40
2624 2676 1.053424 GTGTTAGTCCCAGTCCCACA 58.947 55.000 0.00 0.00 0.00 4.17
2641 2693 3.981071 TTAGACATGGGAAGTGGAGTG 57.019 47.619 0.00 0.00 0.00 3.51
2643 2695 3.181450 GGGATTAGACATGGGAAGTGGAG 60.181 52.174 0.00 0.00 0.00 3.86
2727 2779 0.178903 ACCCTCAACCCAGCTCTACA 60.179 55.000 0.00 0.00 0.00 2.74
2731 2783 2.190488 CTGGACCCTCAACCCAGCTC 62.190 65.000 0.00 0.00 40.69 4.09
2732 2784 2.121963 TGGACCCTCAACCCAGCT 60.122 61.111 0.00 0.00 0.00 4.24
2733 2785 2.352805 CTGGACCCTCAACCCAGC 59.647 66.667 0.00 0.00 40.69 4.85
2734 2786 0.916358 ATCCTGGACCCTCAACCCAG 60.916 60.000 0.00 0.00 45.28 4.45
2735 2787 0.419865 TATCCTGGACCCTCAACCCA 59.580 55.000 0.00 0.00 0.00 4.51
2736 2788 1.490910 CTTATCCTGGACCCTCAACCC 59.509 57.143 0.00 0.00 0.00 4.11
2737 2789 2.436173 CTCTTATCCTGGACCCTCAACC 59.564 54.545 0.00 0.00 0.00 3.77
2738 2790 2.436173 CCTCTTATCCTGGACCCTCAAC 59.564 54.545 0.00 0.00 0.00 3.18
2739 2791 2.317900 TCCTCTTATCCTGGACCCTCAA 59.682 50.000 0.00 0.00 0.00 3.02
2740 2792 1.937350 TCCTCTTATCCTGGACCCTCA 59.063 52.381 0.00 0.00 0.00 3.86
2741 2793 2.321719 GTCCTCTTATCCTGGACCCTC 58.678 57.143 0.00 0.00 43.10 4.30
2742 2794 1.411787 CGTCCTCTTATCCTGGACCCT 60.412 57.143 0.00 0.00 45.31 4.34
2743 2795 1.041437 CGTCCTCTTATCCTGGACCC 58.959 60.000 0.00 0.00 45.31 4.46
2744 2796 1.041437 CCGTCCTCTTATCCTGGACC 58.959 60.000 0.00 0.00 45.31 4.46
2745 2797 1.409427 CACCGTCCTCTTATCCTGGAC 59.591 57.143 0.00 0.00 44.82 4.02
2746 2798 1.688311 CCACCGTCCTCTTATCCTGGA 60.688 57.143 0.00 0.00 0.00 3.86
2747 2799 0.753262 CCACCGTCCTCTTATCCTGG 59.247 60.000 0.00 0.00 0.00 4.45
2748 2800 0.105039 GCCACCGTCCTCTTATCCTG 59.895 60.000 0.00 0.00 0.00 3.86
2749 2801 0.325296 TGCCACCGTCCTCTTATCCT 60.325 55.000 0.00 0.00 0.00 3.24
2750 2802 0.105039 CTGCCACCGTCCTCTTATCC 59.895 60.000 0.00 0.00 0.00 2.59
2751 2803 0.530870 GCTGCCACCGTCCTCTTATC 60.531 60.000 0.00 0.00 0.00 1.75
2752 2804 1.522569 GCTGCCACCGTCCTCTTAT 59.477 57.895 0.00 0.00 0.00 1.73
2753 2805 2.978824 GCTGCCACCGTCCTCTTA 59.021 61.111 0.00 0.00 0.00 2.10
2754 2806 4.379243 CGCTGCCACCGTCCTCTT 62.379 66.667 0.00 0.00 0.00 2.85
2762 2814 3.818787 CTTCATGCCGCTGCCACC 61.819 66.667 0.00 0.00 36.33 4.61
2763 2815 2.747460 TCTTCATGCCGCTGCCAC 60.747 61.111 0.00 0.00 36.33 5.01
2764 2816 2.437180 CTCTTCATGCCGCTGCCA 60.437 61.111 0.00 0.00 36.33 4.92
2765 2817 3.207669 CCTCTTCATGCCGCTGCC 61.208 66.667 0.00 0.00 36.33 4.85
2766 2818 3.885521 GCCTCTTCATGCCGCTGC 61.886 66.667 0.00 0.00 38.26 5.25
2767 2819 3.570638 CGCCTCTTCATGCCGCTG 61.571 66.667 0.00 0.00 0.00 5.18
2768 2820 3.729965 CTCGCCTCTTCATGCCGCT 62.730 63.158 0.00 0.00 0.00 5.52
2769 2821 3.267860 CTCGCCTCTTCATGCCGC 61.268 66.667 0.00 0.00 0.00 6.53
2770 2822 1.591059 CTCTCGCCTCTTCATGCCG 60.591 63.158 0.00 0.00 0.00 5.69
2771 2823 1.227497 CCTCTCGCCTCTTCATGCC 60.227 63.158 0.00 0.00 0.00 4.40
2772 2824 0.107945 AACCTCTCGCCTCTTCATGC 60.108 55.000 0.00 0.00 0.00 4.06
2773 2825 1.205655 TGAACCTCTCGCCTCTTCATG 59.794 52.381 0.00 0.00 0.00 3.07
2774 2826 1.561643 TGAACCTCTCGCCTCTTCAT 58.438 50.000 0.00 0.00 0.00 2.57
2775 2827 1.338107 TTGAACCTCTCGCCTCTTCA 58.662 50.000 0.00 0.00 0.00 3.02
2776 2828 2.682155 ATTGAACCTCTCGCCTCTTC 57.318 50.000 0.00 0.00 0.00 2.87
2777 2829 3.118592 CCTTATTGAACCTCTCGCCTCTT 60.119 47.826 0.00 0.00 0.00 2.85
2778 2830 2.432510 CCTTATTGAACCTCTCGCCTCT 59.567 50.000 0.00 0.00 0.00 3.69
2779 2831 2.827652 CCTTATTGAACCTCTCGCCTC 58.172 52.381 0.00 0.00 0.00 4.70
2780 2832 1.134371 GCCTTATTGAACCTCTCGCCT 60.134 52.381 0.00 0.00 0.00 5.52
2781 2833 1.134371 AGCCTTATTGAACCTCTCGCC 60.134 52.381 0.00 0.00 0.00 5.54
2782 2834 2.205911 GAGCCTTATTGAACCTCTCGC 58.794 52.381 0.00 0.00 0.00 5.03
2783 2835 2.159226 ACGAGCCTTATTGAACCTCTCG 60.159 50.000 7.12 7.12 44.95 4.04
2784 2836 3.119101 TCACGAGCCTTATTGAACCTCTC 60.119 47.826 0.00 0.00 0.00 3.20
2785 2837 2.832129 TCACGAGCCTTATTGAACCTCT 59.168 45.455 0.00 0.00 0.00 3.69
2786 2838 3.247006 TCACGAGCCTTATTGAACCTC 57.753 47.619 0.00 0.00 0.00 3.85
2787 2839 3.695830 TTCACGAGCCTTATTGAACCT 57.304 42.857 0.00 0.00 0.00 3.50
2788 2840 4.965119 AATTCACGAGCCTTATTGAACC 57.035 40.909 0.00 0.00 30.99 3.62
2789 2841 6.149633 ACAAAATTCACGAGCCTTATTGAAC 58.850 36.000 0.00 0.00 30.99 3.18
2790 2842 6.325919 ACAAAATTCACGAGCCTTATTGAA 57.674 33.333 0.00 0.00 32.71 2.69
2791 2843 5.957842 ACAAAATTCACGAGCCTTATTGA 57.042 34.783 0.00 0.00 0.00 2.57
2792 2844 7.471721 TCATACAAAATTCACGAGCCTTATTG 58.528 34.615 0.00 0.00 0.00 1.90
2793 2845 7.201732 CCTCATACAAAATTCACGAGCCTTATT 60.202 37.037 0.00 0.00 0.00 1.40
2794 2846 6.260936 CCTCATACAAAATTCACGAGCCTTAT 59.739 38.462 0.00 0.00 0.00 1.73
2795 2847 5.584649 CCTCATACAAAATTCACGAGCCTTA 59.415 40.000 0.00 0.00 0.00 2.69
2796 2848 4.396166 CCTCATACAAAATTCACGAGCCTT 59.604 41.667 0.00 0.00 0.00 4.35
2797 2849 3.941483 CCTCATACAAAATTCACGAGCCT 59.059 43.478 0.00 0.00 0.00 4.58
2798 2850 3.065371 CCCTCATACAAAATTCACGAGCC 59.935 47.826 0.00 0.00 0.00 4.70
2799 2851 3.938963 TCCCTCATACAAAATTCACGAGC 59.061 43.478 0.00 0.00 0.00 5.03
2800 2852 6.403636 CCTTTCCCTCATACAAAATTCACGAG 60.404 42.308 0.00 0.00 0.00 4.18
2801 2853 5.414454 CCTTTCCCTCATACAAAATTCACGA 59.586 40.000 0.00 0.00 0.00 4.35
2802 2854 5.393027 CCCTTTCCCTCATACAAAATTCACG 60.393 44.000 0.00 0.00 0.00 4.35
2803 2855 5.624509 GCCCTTTCCCTCATACAAAATTCAC 60.625 44.000 0.00 0.00 0.00 3.18
2804 2856 4.466015 GCCCTTTCCCTCATACAAAATTCA 59.534 41.667 0.00 0.00 0.00 2.57
2805 2857 4.141937 GGCCCTTTCCCTCATACAAAATTC 60.142 45.833 0.00 0.00 0.00 2.17
2806 2858 3.774766 GGCCCTTTCCCTCATACAAAATT 59.225 43.478 0.00 0.00 0.00 1.82
2807 2859 3.374764 GGCCCTTTCCCTCATACAAAAT 58.625 45.455 0.00 0.00 0.00 1.82
2808 2860 2.558800 GGGCCCTTTCCCTCATACAAAA 60.559 50.000 17.04 0.00 43.13 2.44
2809 2861 1.006639 GGGCCCTTTCCCTCATACAAA 59.993 52.381 17.04 0.00 43.13 2.83
2810 2862 0.629058 GGGCCCTTTCCCTCATACAA 59.371 55.000 17.04 0.00 43.13 2.41
2811 2863 0.551377 TGGGCCCTTTCCCTCATACA 60.551 55.000 25.70 0.00 46.67 2.29
2812 2864 0.853530 ATGGGCCCTTTCCCTCATAC 59.146 55.000 25.70 0.00 46.67 2.39
2813 2865 0.852842 CATGGGCCCTTTCCCTCATA 59.147 55.000 25.70 0.00 46.67 2.15
2814 2866 0.925720 TCATGGGCCCTTTCCCTCAT 60.926 55.000 25.70 1.42 46.67 2.90
2815 2867 0.925720 ATCATGGGCCCTTTCCCTCA 60.926 55.000 25.70 0.00 46.67 3.86
2816 2868 0.262876 AATCATGGGCCCTTTCCCTC 59.737 55.000 25.70 0.00 46.67 4.30
2817 2869 0.262876 GAATCATGGGCCCTTTCCCT 59.737 55.000 25.70 2.52 46.67 4.20
2818 2870 0.032217 TGAATCATGGGCCCTTTCCC 60.032 55.000 25.70 8.48 46.73 3.97
2819 2871 2.092598 ATGAATCATGGGCCCTTTCC 57.907 50.000 25.70 7.90 0.00 3.13
2820 2872 4.492494 AAAATGAATCATGGGCCCTTTC 57.508 40.909 25.70 19.59 0.00 2.62
2821 2873 4.932911 AAAAATGAATCATGGGCCCTTT 57.067 36.364 25.70 9.61 0.00 3.11
2822 2874 4.409901 CCTAAAAATGAATCATGGGCCCTT 59.590 41.667 25.70 15.22 0.00 3.95
2823 2875 3.969312 CCTAAAAATGAATCATGGGCCCT 59.031 43.478 25.70 5.48 0.00 5.19
2824 2876 3.071457 CCCTAAAAATGAATCATGGGCCC 59.929 47.826 17.59 17.59 0.00 5.80
2825 2877 3.071457 CCCCTAAAAATGAATCATGGGCC 59.929 47.826 9.42 0.00 32.48 5.80
2826 2878 3.711190 ACCCCTAAAAATGAATCATGGGC 59.289 43.478 12.40 0.00 33.69 5.36
2827 2879 5.539955 CCTACCCCTAAAAATGAATCATGGG 59.460 44.000 11.26 11.26 36.56 4.00
2828 2880 5.011023 GCCTACCCCTAAAAATGAATCATGG 59.989 44.000 0.00 0.00 0.00 3.66
2829 2881 5.598005 TGCCTACCCCTAAAAATGAATCATG 59.402 40.000 0.00 0.00 0.00 3.07
2830 2882 5.776358 TGCCTACCCCTAAAAATGAATCAT 58.224 37.500 0.00 0.00 0.00 2.45
2831 2883 5.199982 TGCCTACCCCTAAAAATGAATCA 57.800 39.130 0.00 0.00 0.00 2.57
2832 2884 5.048713 CGATGCCTACCCCTAAAAATGAATC 60.049 44.000 0.00 0.00 0.00 2.52
2833 2885 4.827284 CGATGCCTACCCCTAAAAATGAAT 59.173 41.667 0.00 0.00 0.00 2.57
2834 2886 4.204012 CGATGCCTACCCCTAAAAATGAA 58.796 43.478 0.00 0.00 0.00 2.57
2835 2887 3.201266 ACGATGCCTACCCCTAAAAATGA 59.799 43.478 0.00 0.00 0.00 2.57
2836 2888 3.315191 CACGATGCCTACCCCTAAAAATG 59.685 47.826 0.00 0.00 0.00 2.32
2837 2889 3.053917 ACACGATGCCTACCCCTAAAAAT 60.054 43.478 0.00 0.00 0.00 1.82
2838 2890 2.306512 ACACGATGCCTACCCCTAAAAA 59.693 45.455 0.00 0.00 0.00 1.94
2839 2891 1.910671 ACACGATGCCTACCCCTAAAA 59.089 47.619 0.00 0.00 0.00 1.52
2840 2892 1.575419 ACACGATGCCTACCCCTAAA 58.425 50.000 0.00 0.00 0.00 1.85
2841 2893 1.575419 AACACGATGCCTACCCCTAA 58.425 50.000 0.00 0.00 0.00 2.69
2842 2894 1.575419 AAACACGATGCCTACCCCTA 58.425 50.000 0.00 0.00 0.00 3.53
2843 2895 0.696501 AAAACACGATGCCTACCCCT 59.303 50.000 0.00 0.00 0.00 4.79
2844 2896 1.541379 AAAAACACGATGCCTACCCC 58.459 50.000 0.00 0.00 0.00 4.95
2880 2932 8.567285 TTTCTCTTCCTCTTTTTGGATGTATC 57.433 34.615 0.00 0.00 33.09 2.24
2883 2935 9.183368 GATATTTCTCTTCCTCTTTTTGGATGT 57.817 33.333 0.00 0.00 33.09 3.06
2884 2936 8.341173 CGATATTTCTCTTCCTCTTTTTGGATG 58.659 37.037 0.00 0.00 33.09 3.51
2885 2937 8.443953 CGATATTTCTCTTCCTCTTTTTGGAT 57.556 34.615 0.00 0.00 33.09 3.41
2886 2938 7.849804 CGATATTTCTCTTCCTCTTTTTGGA 57.150 36.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.