Multiple sequence alignment - TraesCS3A01G039800

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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 TraesCS3A01G039800 chr3A 100.000 2918 0 0 1 2918 20967270 20964353 0.000000e+00 5389
1 TraesCS3A01G039800 chr3A 95.656 1013 38 3 888 1895 21066275 21065264 0.000000e+00 1622
2 TraesCS3A01G039800 chr3A 97.406 771 18 2 118 887 739375308 739376077 0.000000e+00 1312
3 TraesCS3A01G039800 chr3A 97.269 769 18 3 121 888 714405194 714404428 0.000000e+00 1301
4 TraesCS3A01G039800 chr3A 97.132 767 20 2 124 889 738857716 738856951 0.000000e+00 1293
5 TraesCS3A01G039800 chr3A 96.263 669 22 1 888 1553 20989907 20989239 0.000000e+00 1094
6 TraesCS3A01G039800 chr3A 86.726 904 94 18 1893 2778 21065171 21064276 0.000000e+00 981
7 TraesCS3A01G039800 chr3A 88.739 444 33 6 1545 1977 20973501 20973064 7.160000e-146 527
8 TraesCS3A01G039800 chr3A 100.000 119 0 0 1 119 714405214 714405096 1.360000e-53 220
9 TraesCS3A01G039800 chr3D 90.782 1790 140 19 888 2663 15331409 15333187 0.000000e+00 2368
10 TraesCS3A01G039800 chr1A 97.399 769 17 2 124 890 403617854 403617087 0.000000e+00 1306
11 TraesCS3A01G039800 chr1A 97.255 765 19 2 124 887 20441061 20440298 0.000000e+00 1295
12 TraesCS3A01G039800 chr1A 99.160 119 1 0 1 119 403617877 403617759 6.330000e-52 215
13 TraesCS3A01G039800 chr1A 99.160 119 1 0 1 119 583547097 583546979 6.330000e-52 215
14 TraesCS3A01G039800 chr5A 97.143 770 20 2 118 886 483389319 483390087 0.000000e+00 1299
15 TraesCS3A01G039800 chr5A 99.160 119 1 0 1 119 483389302 483389420 6.330000e-52 215
16 TraesCS3A01G039800 chr7A 97.379 763 18 2 124 885 3277287 3276526 0.000000e+00 1297
17 TraesCS3A01G039800 chr7A 96.887 771 21 3 118 887 624936026 624936794 0.000000e+00 1288
18 TraesCS3A01G039800 chr7A 96.762 772 23 2 124 894 686012769 686011999 0.000000e+00 1286
19 TraesCS3A01G039800 chr7A 99.160 119 1 0 1 119 3277310 3277192 6.330000e-52 215
20 TraesCS3A01G039800 chr7A 99.160 119 1 0 1 119 13118964 13118846 6.330000e-52 215
21 TraesCS3A01G039800 chr3B 90.127 790 52 12 1474 2237 22449585 22450374 0.000000e+00 1003
22 TraesCS3A01G039800 chr3B 91.414 594 38 4 888 1478 22443685 22444268 0.000000e+00 802
23 TraesCS3A01G039800 chr3B 79.545 924 169 13 998 1916 22831273 22832181 2.450000e-180 641
24 TraesCS3A01G039800 chr3B 78.533 941 167 28 1032 1952 22784747 22785672 1.170000e-163 586
25 TraesCS3A01G039800 chr3B 78.326 932 168 24 991 1915 22802683 22803587 3.260000e-159 571
26 TraesCS3A01G039800 chr3B 92.035 339 24 1 998 1333 22246477 22246815 9.460000e-130 473
27 TraesCS3A01G039800 chr3B 81.298 524 65 21 2274 2778 22450371 22450880 7.580000e-106 394
28 TraesCS3A01G039800 chr6B 84.394 487 74 1 1000 1486 707804075 707804559 7.320000e-131 477
29 TraesCS3A01G039800 chr7B 99.160 119 1 0 1 119 741000800 741000682 6.330000e-52 215
30 TraesCS3A01G039800 chr6A 99.160 119 1 0 1 119 26809672 26809790 6.330000e-52 215
31 TraesCS3A01G039800 chr6A 99.160 119 1 0 1 119 609412251 609412369 6.330000e-52 215
32 TraesCS3A01G039800 chr5D 94.074 135 5 2 888 1019 398786107 398785973 4.930000e-48 202


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 TraesCS3A01G039800 chr3A 20964353 20967270 2917 True 5389.0 5389 100.0000 1 2918 1 chr3A.!!$R1 2917
1 TraesCS3A01G039800 chr3A 739375308 739376077 769 False 1312.0 1312 97.4060 118 887 1 chr3A.!!$F1 769
2 TraesCS3A01G039800 chr3A 21064276 21066275 1999 True 1301.5 1622 91.1910 888 2778 2 chr3A.!!$R5 1890
3 TraesCS3A01G039800 chr3A 738856951 738857716 765 True 1293.0 1293 97.1320 124 889 1 chr3A.!!$R4 765
4 TraesCS3A01G039800 chr3A 20989239 20989907 668 True 1094.0 1094 96.2630 888 1553 1 chr3A.!!$R3 665
5 TraesCS3A01G039800 chr3A 714404428 714405214 786 True 760.5 1301 98.6345 1 888 2 chr3A.!!$R6 887
6 TraesCS3A01G039800 chr3D 15331409 15333187 1778 False 2368.0 2368 90.7820 888 2663 1 chr3D.!!$F1 1775
7 TraesCS3A01G039800 chr1A 20440298 20441061 763 True 1295.0 1295 97.2550 124 887 1 chr1A.!!$R1 763
8 TraesCS3A01G039800 chr1A 403617087 403617877 790 True 760.5 1306 98.2795 1 890 2 chr1A.!!$R3 889
9 TraesCS3A01G039800 chr5A 483389302 483390087 785 False 757.0 1299 98.1515 1 886 2 chr5A.!!$F1 885
10 TraesCS3A01G039800 chr7A 624936026 624936794 768 False 1288.0 1288 96.8870 118 887 1 chr7A.!!$F1 769
11 TraesCS3A01G039800 chr7A 686011999 686012769 770 True 1286.0 1286 96.7620 124 894 1 chr7A.!!$R2 770
12 TraesCS3A01G039800 chr7A 3276526 3277310 784 True 756.0 1297 98.2695 1 885 2 chr7A.!!$R3 884
13 TraesCS3A01G039800 chr3B 22443685 22444268 583 False 802.0 802 91.4140 888 1478 1 chr3B.!!$F2 590
14 TraesCS3A01G039800 chr3B 22449585 22450880 1295 False 698.5 1003 85.7125 1474 2778 2 chr3B.!!$F6 1304
15 TraesCS3A01G039800 chr3B 22831273 22832181 908 False 641.0 641 79.5450 998 1916 1 chr3B.!!$F5 918
16 TraesCS3A01G039800 chr3B 22784747 22785672 925 False 586.0 586 78.5330 1032 1952 1 chr3B.!!$F3 920
17 TraesCS3A01G039800 chr3B 22802683 22803587 904 False 571.0 571 78.3260 991 1915 1 chr3B.!!$F4 924

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
799 800 1.623811 GCTGGAGACTGTGGAACCTTA 59.376 52.381 0.00 0.0 34.36 2.69 F
1085 1099 0.544697 ACCCATGGTGACGATAACCC 59.455 55.000 11.73 0.0 36.83 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1697 0.589708 ATGCATCGCACCAATCATCG 59.410 50.0 0.00 0.0 43.04 3.84 R
2852 3052 0.104671 GGAGCTGGCAGCAAAACAAA 59.895 50.0 38.09 0.0 45.56 2.83 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
233 234 5.415701 ACTTGATTAATCGCAATTGGACAGT 59.584 36.000 7.72 0.00 0.00 3.55
470 471 7.938715 ACTATCTGGAATTGCAGAAATGATTC 58.061 34.615 30.01 0.00 35.70 2.52
529 530 4.117685 GGTTATTTTCCGAGCTACGACAT 58.882 43.478 7.07 0.00 45.77 3.06
682 683 8.926092 AGGCAATTAGTTTCCCTATCTATTTC 57.074 34.615 0.00 0.00 0.00 2.17
799 800 1.623811 GCTGGAGACTGTGGAACCTTA 59.376 52.381 0.00 0.00 34.36 2.69
827 828 7.873505 TGGCACCTTTTGTTATTTGGTTAATAC 59.126 33.333 0.00 0.00 0.00 1.89
833 834 9.849166 CTTTTGTTATTTGGTTAATACGATGGT 57.151 29.630 0.00 0.00 0.00 3.55
979 983 5.650543 TGCTTGTTTTCTCAAAAGGAAGAC 58.349 37.500 0.00 0.00 0.00 3.01
1049 1057 3.976169 TCTTTCTTGCAATGTTTTCGGG 58.024 40.909 0.00 0.00 0.00 5.14
1063 1074 3.155167 CGGGACTAGCCACCTCCC 61.155 72.222 5.45 5.45 40.49 4.30
1085 1099 0.544697 ACCCATGGTGACGATAACCC 59.455 55.000 11.73 0.00 36.83 4.11
1539 1580 2.123769 GGCCATGGCACCAGCATA 60.124 61.111 36.56 0.00 44.61 3.14
1563 1604 2.498481 TGGCGTTACTAGTTGGCTATGT 59.502 45.455 0.00 0.00 0.00 2.29
1564 1605 3.055675 TGGCGTTACTAGTTGGCTATGTT 60.056 43.478 0.00 0.00 0.00 2.71
1653 1697 0.679505 TGGATATGTCTACCAGCGCC 59.320 55.000 2.29 0.00 0.00 6.53
1900 2045 2.037144 GCGGGTTCCCTAGTAGAATCA 58.963 52.381 6.31 0.00 0.00 2.57
2088 2249 7.496591 ACTTCTGAAGTTAACATTTGTTCCGTA 59.503 33.333 17.00 0.00 39.04 4.02
2134 2298 1.170442 TCATGTCTGCCTTACGACGA 58.830 50.000 0.00 0.00 32.93 4.20
2198 2373 6.183360 TGGATGTACTAGCTCTGGAACATAAC 60.183 42.308 0.00 0.00 38.20 1.89
2231 2406 8.964420 ATGTAATTCGTTAATTGTTTCAGGTG 57.036 30.769 0.00 0.00 36.02 4.00
2294 2469 8.543774 GTTGTTATTTCTCTGTCCTTCATATCG 58.456 37.037 0.00 0.00 0.00 2.92
2319 2494 4.248058 GCAAAAATGAAACCAGCATAGCT 58.752 39.130 0.00 0.00 40.77 3.32
2338 2513 3.190744 AGCTGATGCAGAGTTGTGAATTG 59.809 43.478 0.00 0.00 42.74 2.32
2375 2550 2.813754 GCTGACAAACCTGAATGCTGTA 59.186 45.455 0.00 0.00 0.00 2.74
2379 2554 1.135689 CAAACCTGAATGCTGTACGGC 60.136 52.381 20.17 20.17 0.00 5.68
2380 2555 1.019278 AACCTGAATGCTGTACGGCG 61.019 55.000 21.37 4.80 34.52 6.46
2381 2556 2.173669 CCTGAATGCTGTACGGCGG 61.174 63.158 21.37 12.18 34.52 6.13
2382 2557 2.125310 TGAATGCTGTACGGCGGG 60.125 61.111 21.37 0.00 34.52 6.13
2409 2584 3.884774 AGTGCGTCCTGGGGCAAA 61.885 61.111 13.57 0.00 41.46 3.68
2489 2665 3.894759 CTGGAAGATGGTGTGGATGATT 58.105 45.455 0.00 0.00 34.07 2.57
2525 2701 4.099170 CTGCCTTGCGCTGACAGC 62.099 66.667 17.84 17.84 38.65 4.40
2542 2718 4.457496 CCGTGTCAGCCCAGCGAT 62.457 66.667 0.00 0.00 0.00 4.58
2553 2729 1.656818 CCCAGCGATGGAAATTGCGT 61.657 55.000 24.05 0.00 36.10 5.24
2566 2742 2.787473 ATTGCGTCATGAGGGAGAAA 57.213 45.000 16.66 0.05 0.00 2.52
2588 2766 1.927487 TGAATCCACATTTGCCTGCT 58.073 45.000 0.00 0.00 0.00 4.24
2654 2838 2.900273 GCTCCGTGATAGCCACCA 59.100 61.111 0.00 0.00 42.76 4.17
2655 2839 1.220749 GCTCCGTGATAGCCACCAA 59.779 57.895 0.00 0.00 42.76 3.67
2663 2847 3.919804 CGTGATAGCCACCAATTTGTTTG 59.080 43.478 0.00 0.00 42.76 2.93
2676 2860 1.265236 TTGTTTGGGATGGGTCATGC 58.735 50.000 0.00 0.00 0.00 4.06
2694 2878 1.343142 TGCGTGTCATGTGTAGGAACT 59.657 47.619 0.00 0.00 46.37 3.01
2697 2881 3.770666 CGTGTCATGTGTAGGAACTAGG 58.229 50.000 0.00 0.00 44.14 3.02
2698 2882 3.442625 CGTGTCATGTGTAGGAACTAGGA 59.557 47.826 0.00 0.00 44.14 2.94
2700 2884 5.169295 GTGTCATGTGTAGGAACTAGGAAC 58.831 45.833 0.00 0.00 44.14 3.62
2704 2888 3.853207 TGTGTAGGAACTAGGAACCAGT 58.147 45.455 0.00 0.00 44.14 4.00
2711 2910 3.181458 GGAACTAGGAACCAGTGTGTTCA 60.181 47.826 19.59 5.92 45.12 3.18
2720 2919 3.631250 ACCAGTGTGTTCAGTTCCATTT 58.369 40.909 0.00 0.00 0.00 2.32
2778 2978 2.438021 ACCTTCCCTAATTGCTGCGATA 59.562 45.455 2.13 0.00 0.00 2.92
2779 2979 3.070018 CCTTCCCTAATTGCTGCGATAG 58.930 50.000 2.13 1.31 0.00 2.08
2811 3011 6.317789 TGTATAGCAGCATCTAAATTTGCC 57.682 37.500 0.00 0.00 39.72 4.52
2812 3012 6.064060 TGTATAGCAGCATCTAAATTTGCCT 58.936 36.000 0.00 0.00 39.72 4.75
2813 3013 3.795623 AGCAGCATCTAAATTTGCCTG 57.204 42.857 0.00 1.68 39.72 4.85
2814 3014 3.359033 AGCAGCATCTAAATTTGCCTGA 58.641 40.909 0.00 0.00 39.72 3.86
2815 3015 3.765511 AGCAGCATCTAAATTTGCCTGAA 59.234 39.130 0.00 0.00 39.72 3.02
2816 3016 4.110482 GCAGCATCTAAATTTGCCTGAAG 58.890 43.478 0.00 0.00 39.72 3.02
2817 3017 4.381292 GCAGCATCTAAATTTGCCTGAAGT 60.381 41.667 0.00 0.00 39.72 3.01
2818 3018 5.163622 GCAGCATCTAAATTTGCCTGAAGTA 60.164 40.000 0.00 0.00 39.72 2.24
2819 3019 6.625740 GCAGCATCTAAATTTGCCTGAAGTAA 60.626 38.462 0.00 0.00 39.72 2.24
2820 3020 7.315142 CAGCATCTAAATTTGCCTGAAGTAAA 58.685 34.615 0.00 0.00 39.72 2.01
2821 3021 7.814107 CAGCATCTAAATTTGCCTGAAGTAAAA 59.186 33.333 0.00 0.00 39.72 1.52
2822 3022 8.534496 AGCATCTAAATTTGCCTGAAGTAAAAT 58.466 29.630 0.00 0.00 39.72 1.82
2823 3023 8.598075 GCATCTAAATTTGCCTGAAGTAAAATG 58.402 33.333 0.00 0.00 33.51 2.32
2824 3024 8.598075 CATCTAAATTTGCCTGAAGTAAAATGC 58.402 33.333 0.00 0.00 33.51 3.56
2825 3025 7.895759 TCTAAATTTGCCTGAAGTAAAATGCT 58.104 30.769 0.00 0.00 33.51 3.79
2826 3026 6.790285 AAATTTGCCTGAAGTAAAATGCTG 57.210 33.333 0.00 0.00 33.51 4.41
2827 3027 5.726980 ATTTGCCTGAAGTAAAATGCTGA 57.273 34.783 0.00 0.00 33.51 4.26
2828 3028 5.726980 TTTGCCTGAAGTAAAATGCTGAT 57.273 34.783 0.00 0.00 0.00 2.90
2829 3029 6.832520 TTTGCCTGAAGTAAAATGCTGATA 57.167 33.333 0.00 0.00 0.00 2.15
2830 3030 6.832520 TTGCCTGAAGTAAAATGCTGATAA 57.167 33.333 0.00 0.00 0.00 1.75
2831 3031 6.832520 TGCCTGAAGTAAAATGCTGATAAA 57.167 33.333 0.00 0.00 0.00 1.40
2832 3032 7.408756 TGCCTGAAGTAAAATGCTGATAAAT 57.591 32.000 0.00 0.00 0.00 1.40
2833 3033 7.483307 TGCCTGAAGTAAAATGCTGATAAATC 58.517 34.615 0.00 0.00 0.00 2.17
2834 3034 7.122501 TGCCTGAAGTAAAATGCTGATAAATCA 59.877 33.333 0.00 0.00 35.16 2.57
2835 3035 7.433425 GCCTGAAGTAAAATGCTGATAAATCAC 59.567 37.037 0.00 0.00 32.50 3.06
2836 3036 7.641411 CCTGAAGTAAAATGCTGATAAATCACG 59.359 37.037 0.00 0.00 32.50 4.35
2837 3037 8.039603 TGAAGTAAAATGCTGATAAATCACGT 57.960 30.769 0.00 0.00 32.50 4.49
2838 3038 7.962373 TGAAGTAAAATGCTGATAAATCACGTG 59.038 33.333 9.94 9.94 32.50 4.49
2839 3039 7.609760 AGTAAAATGCTGATAAATCACGTGA 57.390 32.000 22.48 22.48 32.50 4.35
2840 3040 7.688372 AGTAAAATGCTGATAAATCACGTGAG 58.312 34.615 24.41 9.31 32.50 3.51
2855 3055 4.732285 ACGTGAGTAGTGCATTTCTTTG 57.268 40.909 0.00 0.00 46.88 2.77
2856 3056 4.127171 ACGTGAGTAGTGCATTTCTTTGT 58.873 39.130 0.00 0.00 46.88 2.83
2857 3057 4.574828 ACGTGAGTAGTGCATTTCTTTGTT 59.425 37.500 0.00 0.00 46.88 2.83
2858 3058 5.065988 ACGTGAGTAGTGCATTTCTTTGTTT 59.934 36.000 0.00 0.00 46.88 2.83
2859 3059 5.971202 CGTGAGTAGTGCATTTCTTTGTTTT 59.029 36.000 0.00 0.00 0.00 2.43
2860 3060 6.075415 CGTGAGTAGTGCATTTCTTTGTTTTG 60.075 38.462 0.00 0.00 0.00 2.44
2861 3061 5.748152 TGAGTAGTGCATTTCTTTGTTTTGC 59.252 36.000 0.00 0.00 0.00 3.68
2862 3062 5.906073 AGTAGTGCATTTCTTTGTTTTGCT 58.094 33.333 0.00 0.00 34.47 3.91
2863 3063 5.750067 AGTAGTGCATTTCTTTGTTTTGCTG 59.250 36.000 0.00 0.00 34.47 4.41
2864 3064 3.310501 AGTGCATTTCTTTGTTTTGCTGC 59.689 39.130 0.00 0.00 34.47 5.25
2865 3065 2.613133 TGCATTTCTTTGTTTTGCTGCC 59.387 40.909 0.00 0.00 34.47 4.85
2866 3066 2.613133 GCATTTCTTTGTTTTGCTGCCA 59.387 40.909 0.00 0.00 0.00 4.92
2867 3067 3.303526 GCATTTCTTTGTTTTGCTGCCAG 60.304 43.478 0.00 0.00 0.00 4.85
2868 3068 1.938625 TTCTTTGTTTTGCTGCCAGC 58.061 45.000 10.45 10.45 42.82 4.85
2869 3069 1.113788 TCTTTGTTTTGCTGCCAGCT 58.886 45.000 18.96 0.00 42.97 4.24
2870 3070 1.067516 TCTTTGTTTTGCTGCCAGCTC 59.932 47.619 18.96 6.54 42.97 4.09
2871 3071 0.104671 TTTGTTTTGCTGCCAGCTCC 59.895 50.000 18.96 3.55 42.97 4.70
2872 3072 2.074230 TTGTTTTGCTGCCAGCTCCG 62.074 55.000 18.96 0.00 42.97 4.63
2873 3073 3.673484 TTTTGCTGCCAGCTCCGC 61.673 61.111 18.96 0.00 42.97 5.54
2878 3078 4.749310 CTGCCAGCTCCGCGTCTT 62.749 66.667 4.92 0.00 0.00 3.01
2880 3080 4.742201 GCCAGCTCCGCGTCTTGA 62.742 66.667 4.92 0.00 0.00 3.02
2881 3081 2.507992 CCAGCTCCGCGTCTTGAG 60.508 66.667 4.92 5.46 0.00 3.02
2885 3085 2.507992 CTCCGCGTCTTGAGCTGG 60.508 66.667 4.92 0.00 0.00 4.85
2886 3086 3.288308 CTCCGCGTCTTGAGCTGGT 62.288 63.158 4.92 0.00 32.79 4.00
2887 3087 3.114616 CCGCGTCTTGAGCTGGTG 61.115 66.667 4.92 0.00 0.00 4.17
2888 3088 3.782244 CGCGTCTTGAGCTGGTGC 61.782 66.667 0.00 0.00 40.05 5.01
2899 3099 3.473147 GCTGGTGCTCATGATGAGT 57.527 52.632 22.23 0.00 45.94 3.41
2900 3100 1.747709 GCTGGTGCTCATGATGAGTT 58.252 50.000 22.23 0.00 45.94 3.01
2901 3101 2.089980 GCTGGTGCTCATGATGAGTTT 58.910 47.619 22.23 0.00 45.94 2.66
2902 3102 2.490903 GCTGGTGCTCATGATGAGTTTT 59.509 45.455 22.23 0.00 45.94 2.43
2903 3103 3.427233 GCTGGTGCTCATGATGAGTTTTC 60.427 47.826 22.23 7.47 45.94 2.29
2904 3104 4.008330 CTGGTGCTCATGATGAGTTTTCT 58.992 43.478 22.23 0.00 45.94 2.52
2905 3105 4.005650 TGGTGCTCATGATGAGTTTTCTC 58.994 43.478 22.23 6.45 45.94 2.87
2906 3106 4.260170 GGTGCTCATGATGAGTTTTCTCT 58.740 43.478 22.23 0.00 45.94 3.10
2907 3107 5.046376 TGGTGCTCATGATGAGTTTTCTCTA 60.046 40.000 22.23 3.61 45.94 2.43
2908 3108 5.293079 GGTGCTCATGATGAGTTTTCTCTAC 59.707 44.000 22.23 9.44 45.94 2.59
2909 3109 5.293079 GTGCTCATGATGAGTTTTCTCTACC 59.707 44.000 22.23 3.76 45.94 3.18
2910 3110 5.188555 TGCTCATGATGAGTTTTCTCTACCT 59.811 40.000 22.23 0.00 45.94 3.08
2911 3111 5.523188 GCTCATGATGAGTTTTCTCTACCTG 59.477 44.000 22.23 0.00 45.94 4.00
2912 3112 5.423015 TCATGATGAGTTTTCTCTACCTGC 58.577 41.667 0.00 0.00 46.30 4.85
2913 3113 4.890158 TGATGAGTTTTCTCTACCTGCA 57.110 40.909 0.00 0.00 46.30 4.41
2914 3114 4.825422 TGATGAGTTTTCTCTACCTGCAG 58.175 43.478 6.78 6.78 46.30 4.41
2915 3115 4.528206 TGATGAGTTTTCTCTACCTGCAGA 59.472 41.667 17.39 0.00 46.30 4.26
2916 3116 5.188555 TGATGAGTTTTCTCTACCTGCAGAT 59.811 40.000 17.39 0.00 46.30 2.90
2917 3117 5.489792 TGAGTTTTCTCTACCTGCAGATT 57.510 39.130 17.39 3.91 46.30 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.646945 TGACAGCCCAAACATACTTGAAAA 59.353 37.500 0.00 0.00 0.00 2.29
122 123 3.500448 TGACAGCCCAAACATACTTGA 57.500 42.857 0.00 0.00 0.00 3.02
219 220 2.829720 AGTAGGTACTGTCCAATTGCGA 59.170 45.455 0.00 0.00 41.52 5.10
470 471 4.024725 TCCGTGATGTTCTGTTAAAAACCG 60.025 41.667 0.00 0.00 0.00 4.44
529 530 1.735198 GCGACCACGAACGGATCAA 60.735 57.895 0.00 0.00 42.66 2.57
682 683 2.436646 CCACAACCGGCTGGCTAG 60.437 66.667 12.89 3.99 39.70 3.42
799 800 5.303259 ACCAAATAACAAAAGGTGCCAAT 57.697 34.783 0.00 0.00 0.00 3.16
827 828 3.122445 CAGAATGATGCATACGACCATCG 59.878 47.826 0.00 0.00 42.67 3.84
931 935 6.778559 AGGAGTACAGTTAGGCTTTATAGAGG 59.221 42.308 0.00 0.00 0.00 3.69
979 983 6.640907 GCCATTTGGTTCTAACTAGTTGTTTG 59.359 38.462 18.56 5.98 37.53 2.93
1049 1057 1.597461 GTGTGGGAGGTGGCTAGTC 59.403 63.158 0.00 0.00 0.00 2.59
1085 1099 1.070445 GGATGGCATCGGAGAGTGG 59.930 63.158 20.50 0.00 43.63 4.00
1143 1157 0.545787 TGGGGTAGCGGAAGAAGGAA 60.546 55.000 0.00 0.00 0.00 3.36
1194 1208 1.064017 ACACCTTCCCAAAGACAGCAA 60.064 47.619 0.00 0.00 34.14 3.91
1539 1580 0.036671 GCCAACTAGTAACGCCAGGT 60.037 55.000 0.00 0.00 0.00 4.00
1563 1604 2.430332 CTGAAAGTTGGGTTCCTGCAAA 59.570 45.455 0.00 0.00 0.00 3.68
1564 1605 2.031120 CTGAAAGTTGGGTTCCTGCAA 58.969 47.619 0.00 0.00 0.00 4.08
1653 1697 0.589708 ATGCATCGCACCAATCATCG 59.410 50.000 0.00 0.00 43.04 3.84
1900 2045 7.947890 TGAAGGACCTTAGTTTTTGTATTGGAT 59.052 33.333 6.75 0.00 0.00 3.41
1983 2132 2.238521 TCCAGGAAAACATGCAGTTCC 58.761 47.619 12.57 12.57 40.26 3.62
2009 2158 4.417183 ACATCTCAGTACCTCAGGGATAGA 59.583 45.833 0.00 0.00 36.25 1.98
2074 2235 6.595794 CGTTCTACAATACGGAACAAATGTT 58.404 36.000 0.00 0.00 39.18 2.71
2079 2240 3.651206 TGCGTTCTACAATACGGAACAA 58.349 40.909 0.00 0.00 39.18 2.83
2109 2270 5.533482 GTCGTAAGGCAGACATGATAGAAT 58.467 41.667 0.00 0.00 45.31 2.40
2198 2373 9.734620 AACAATTAACGAATTACATCATCATGG 57.265 29.630 0.00 0.00 33.33 3.66
2231 2406 2.761392 TGCATTCATGTCGCAATAGC 57.239 45.000 4.38 0.00 31.46 2.97
2253 2428 9.236006 AGAAATAACAACTCTGCAATATGACTT 57.764 29.630 0.00 0.00 0.00 3.01
2277 2452 3.447229 TGCAACGATATGAAGGACAGAGA 59.553 43.478 0.00 0.00 0.00 3.10
2294 2469 4.816786 ATGCTGGTTTCATTTTTGCAAC 57.183 36.364 0.00 0.00 32.66 4.17
2319 2494 4.136051 TCACAATTCACAACTCTGCATCA 58.864 39.130 0.00 0.00 0.00 3.07
2409 2584 0.610232 GGCAGTTGGATCACAGGCTT 60.610 55.000 0.00 0.00 0.00 4.35
2465 2640 1.133181 TCCACACCATCTTCCAGCCA 61.133 55.000 0.00 0.00 0.00 4.75
2489 2665 1.003118 AGAGGGATTGCGCAACTGTTA 59.997 47.619 27.64 1.15 0.00 2.41
2525 2701 4.457496 ATCGCTGGGCTGACACGG 62.457 66.667 0.00 0.00 0.00 4.94
2542 2718 1.004161 TCCCTCATGACGCAATTTCCA 59.996 47.619 0.00 0.00 0.00 3.53
2553 2729 4.227982 TGGATTCATGTTTCTCCCTCATGA 59.772 41.667 0.00 0.00 43.71 3.07
2566 2742 2.093869 GCAGGCAAATGTGGATTCATGT 60.094 45.455 0.00 0.00 0.00 3.21
2610 2794 3.062763 CTGGATACCAGCAACGATCATC 58.937 50.000 4.84 0.00 45.13 2.92
2611 2795 3.117491 CTGGATACCAGCAACGATCAT 57.883 47.619 4.84 0.00 45.13 2.45
2654 2838 3.307621 GCATGACCCATCCCAAACAAATT 60.308 43.478 0.00 0.00 0.00 1.82
2655 2839 2.236893 GCATGACCCATCCCAAACAAAT 59.763 45.455 0.00 0.00 0.00 2.32
2663 2847 1.819632 GACACGCATGACCCATCCC 60.820 63.158 0.00 0.00 0.00 3.85
2676 2860 3.442625 TCCTAGTTCCTACACATGACACG 59.557 47.826 0.00 0.00 0.00 4.49
2694 2878 4.067972 GAACTGAACACACTGGTTCCTA 57.932 45.455 3.85 0.00 45.12 2.94
2697 2881 2.639065 TGGAACTGAACACACTGGTTC 58.361 47.619 0.00 0.00 45.75 3.62
2698 2882 2.799126 TGGAACTGAACACACTGGTT 57.201 45.000 0.00 0.00 0.00 3.67
2700 2884 5.964958 ATAAATGGAACTGAACACACTGG 57.035 39.130 0.00 0.00 0.00 4.00
2704 2888 8.303156 CCAATGTAATAAATGGAACTGAACACA 58.697 33.333 0.00 0.00 34.82 3.72
2711 2910 7.122650 CACACCTCCAATGTAATAAATGGAACT 59.877 37.037 0.00 0.00 41.20 3.01
2720 2919 5.506730 TTCCACACACCTCCAATGTAATA 57.493 39.130 0.00 0.00 0.00 0.98
2788 2988 6.016860 CAGGCAAATTTAGATGCTGCTATACA 60.017 38.462 0.00 0.00 42.20 2.29
2789 2989 6.205464 TCAGGCAAATTTAGATGCTGCTATAC 59.795 38.462 0.00 0.00 42.20 1.47
2790 2990 6.298361 TCAGGCAAATTTAGATGCTGCTATA 58.702 36.000 0.00 0.00 42.20 1.31
2791 2991 5.135383 TCAGGCAAATTTAGATGCTGCTAT 58.865 37.500 0.00 0.00 42.20 2.97
2792 2992 4.525996 TCAGGCAAATTTAGATGCTGCTA 58.474 39.130 0.00 0.00 42.20 3.49
2793 2993 3.359033 TCAGGCAAATTTAGATGCTGCT 58.641 40.909 0.00 0.00 42.20 4.24
2794 2994 3.788333 TCAGGCAAATTTAGATGCTGC 57.212 42.857 0.00 0.00 42.20 5.25
2795 2995 5.320549 ACTTCAGGCAAATTTAGATGCTG 57.679 39.130 0.22 0.00 42.20 4.41
2796 2996 7.466746 TTTACTTCAGGCAAATTTAGATGCT 57.533 32.000 0.22 0.00 42.20 3.79
2797 2997 8.598075 CATTTTACTTCAGGCAAATTTAGATGC 58.402 33.333 0.00 0.00 41.82 3.91
2798 2998 8.598075 GCATTTTACTTCAGGCAAATTTAGATG 58.402 33.333 0.00 0.00 0.00 2.90
2799 2999 8.534496 AGCATTTTACTTCAGGCAAATTTAGAT 58.466 29.630 0.00 0.00 0.00 1.98
2800 3000 7.814107 CAGCATTTTACTTCAGGCAAATTTAGA 59.186 33.333 0.00 0.00 0.00 2.10
2801 3001 7.814107 TCAGCATTTTACTTCAGGCAAATTTAG 59.186 33.333 0.00 0.00 0.00 1.85
2802 3002 7.665690 TCAGCATTTTACTTCAGGCAAATTTA 58.334 30.769 0.00 0.00 0.00 1.40
2803 3003 6.523840 TCAGCATTTTACTTCAGGCAAATTT 58.476 32.000 0.00 0.00 0.00 1.82
2804 3004 6.100404 TCAGCATTTTACTTCAGGCAAATT 57.900 33.333 0.00 0.00 0.00 1.82
2805 3005 5.726980 TCAGCATTTTACTTCAGGCAAAT 57.273 34.783 0.00 0.00 0.00 2.32
2806 3006 5.726980 ATCAGCATTTTACTTCAGGCAAA 57.273 34.783 0.00 0.00 0.00 3.68
2807 3007 6.832520 TTATCAGCATTTTACTTCAGGCAA 57.167 33.333 0.00 0.00 0.00 4.52
2808 3008 6.832520 TTTATCAGCATTTTACTTCAGGCA 57.167 33.333 0.00 0.00 0.00 4.75
2809 3009 7.433425 GTGATTTATCAGCATTTTACTTCAGGC 59.567 37.037 0.00 0.00 37.51 4.85
2810 3010 7.641411 CGTGATTTATCAGCATTTTACTTCAGG 59.359 37.037 0.00 0.00 37.51 3.86
2811 3011 8.177663 ACGTGATTTATCAGCATTTTACTTCAG 58.822 33.333 0.00 0.00 37.51 3.02
2812 3012 7.962373 CACGTGATTTATCAGCATTTTACTTCA 59.038 33.333 10.90 0.00 37.51 3.02
2813 3013 8.175069 TCACGTGATTTATCAGCATTTTACTTC 58.825 33.333 15.76 0.00 37.51 3.01
2814 3014 8.039603 TCACGTGATTTATCAGCATTTTACTT 57.960 30.769 15.76 0.00 37.51 2.24
2815 3015 7.334421 ACTCACGTGATTTATCAGCATTTTACT 59.666 33.333 20.40 0.00 37.51 2.24
2816 3016 7.464358 ACTCACGTGATTTATCAGCATTTTAC 58.536 34.615 20.40 0.00 37.51 2.01
2817 3017 7.609760 ACTCACGTGATTTATCAGCATTTTA 57.390 32.000 20.40 0.00 37.51 1.52
2818 3018 6.500684 ACTCACGTGATTTATCAGCATTTT 57.499 33.333 20.40 0.00 37.51 1.82
2819 3019 6.818644 ACTACTCACGTGATTTATCAGCATTT 59.181 34.615 20.40 0.00 37.51 2.32
2820 3020 6.256539 CACTACTCACGTGATTTATCAGCATT 59.743 38.462 20.40 0.00 37.51 3.56
2821 3021 5.750547 CACTACTCACGTGATTTATCAGCAT 59.249 40.000 20.40 0.00 37.51 3.79
2822 3022 5.102313 CACTACTCACGTGATTTATCAGCA 58.898 41.667 20.40 0.00 37.51 4.41
2823 3023 4.026475 GCACTACTCACGTGATTTATCAGC 60.026 45.833 20.40 13.31 37.51 4.26
2824 3024 5.102313 TGCACTACTCACGTGATTTATCAG 58.898 41.667 20.40 10.08 37.51 2.90
2825 3025 5.066968 TGCACTACTCACGTGATTTATCA 57.933 39.130 20.40 10.19 34.35 2.15
2826 3026 6.589830 AATGCACTACTCACGTGATTTATC 57.410 37.500 20.40 7.70 34.35 1.75
2827 3027 6.818644 AGAAATGCACTACTCACGTGATTTAT 59.181 34.615 20.40 8.42 34.35 1.40
2828 3028 6.163476 AGAAATGCACTACTCACGTGATTTA 58.837 36.000 20.40 12.31 34.35 1.40
2829 3029 4.997395 AGAAATGCACTACTCACGTGATTT 59.003 37.500 20.40 13.62 34.35 2.17
2830 3030 4.569943 AGAAATGCACTACTCACGTGATT 58.430 39.130 20.40 16.54 34.35 2.57
2831 3031 4.193826 AGAAATGCACTACTCACGTGAT 57.806 40.909 20.40 11.80 34.35 3.06
2832 3032 3.660501 AGAAATGCACTACTCACGTGA 57.339 42.857 18.88 18.88 34.35 4.35
2833 3033 4.024893 ACAAAGAAATGCACTACTCACGTG 60.025 41.667 9.94 9.94 35.53 4.49
2834 3034 4.127171 ACAAAGAAATGCACTACTCACGT 58.873 39.130 0.00 0.00 0.00 4.49
2835 3035 4.732285 ACAAAGAAATGCACTACTCACG 57.268 40.909 0.00 0.00 0.00 4.35
2836 3036 6.291796 GCAAAACAAAGAAATGCACTACTCAC 60.292 38.462 0.00 0.00 37.00 3.51
2837 3037 5.748152 GCAAAACAAAGAAATGCACTACTCA 59.252 36.000 0.00 0.00 37.00 3.41
2838 3038 5.979517 AGCAAAACAAAGAAATGCACTACTC 59.020 36.000 0.00 0.00 39.42 2.59
2839 3039 5.750067 CAGCAAAACAAAGAAATGCACTACT 59.250 36.000 0.00 0.00 39.42 2.57
2840 3040 5.556947 GCAGCAAAACAAAGAAATGCACTAC 60.557 40.000 0.00 0.00 39.42 2.73
2841 3041 4.507388 GCAGCAAAACAAAGAAATGCACTA 59.493 37.500 0.00 0.00 39.42 2.74
2842 3042 3.310501 GCAGCAAAACAAAGAAATGCACT 59.689 39.130 0.00 0.00 39.42 4.40
2843 3043 3.546616 GGCAGCAAAACAAAGAAATGCAC 60.547 43.478 0.00 0.00 39.42 4.57
2844 3044 2.613133 GGCAGCAAAACAAAGAAATGCA 59.387 40.909 0.00 0.00 39.42 3.96
2845 3045 2.613133 TGGCAGCAAAACAAAGAAATGC 59.387 40.909 0.00 0.00 37.28 3.56
2846 3046 3.303526 GCTGGCAGCAAAACAAAGAAATG 60.304 43.478 33.33 0.00 41.89 2.32
2847 3047 2.874086 GCTGGCAGCAAAACAAAGAAAT 59.126 40.909 33.33 0.00 41.89 2.17
2848 3048 2.093553 AGCTGGCAGCAAAACAAAGAAA 60.094 40.909 38.09 0.00 45.56 2.52
2849 3049 1.481772 AGCTGGCAGCAAAACAAAGAA 59.518 42.857 38.09 0.00 45.56 2.52
2850 3050 1.067516 GAGCTGGCAGCAAAACAAAGA 59.932 47.619 38.09 0.00 45.56 2.52
2851 3051 1.494824 GAGCTGGCAGCAAAACAAAG 58.505 50.000 38.09 0.00 45.56 2.77
2852 3052 0.104671 GGAGCTGGCAGCAAAACAAA 59.895 50.000 38.09 0.00 45.56 2.83
2853 3053 1.741525 GGAGCTGGCAGCAAAACAA 59.258 52.632 38.09 0.00 45.56 2.83
2854 3054 2.554636 CGGAGCTGGCAGCAAAACA 61.555 57.895 38.09 0.00 45.56 2.83
2855 3055 2.256461 CGGAGCTGGCAGCAAAAC 59.744 61.111 38.09 24.81 45.56 2.43
2868 3068 2.507992 CCAGCTCAAGACGCGGAG 60.508 66.667 12.47 8.53 0.00 4.63
2869 3069 3.303135 ACCAGCTCAAGACGCGGA 61.303 61.111 12.47 0.00 0.00 5.54
2870 3070 3.114616 CACCAGCTCAAGACGCGG 61.115 66.667 12.47 0.00 0.00 6.46
2871 3071 3.782244 GCACCAGCTCAAGACGCG 61.782 66.667 3.53 3.53 37.91 6.01
2889 3089 5.046376 TGCAGGTAGAGAAAACTCATCATGA 60.046 40.000 0.00 0.00 0.00 3.07
2890 3090 5.181009 TGCAGGTAGAGAAAACTCATCATG 58.819 41.667 0.00 0.00 0.00 3.07
2891 3091 5.188555 TCTGCAGGTAGAGAAAACTCATCAT 59.811 40.000 15.13 0.00 0.00 2.45
2892 3092 4.528206 TCTGCAGGTAGAGAAAACTCATCA 59.472 41.667 15.13 0.00 0.00 3.07
2893 3093 5.078411 TCTGCAGGTAGAGAAAACTCATC 57.922 43.478 15.13 0.00 0.00 2.92
2894 3094 5.690464 ATCTGCAGGTAGAGAAAACTCAT 57.310 39.130 15.13 0.00 0.00 2.90
2895 3095 5.489792 AATCTGCAGGTAGAGAAAACTCA 57.510 39.130 15.13 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.