Multiple sequence alignment - TraesCS5D01G464100

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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 TraesCS5D01G464100 chr5D 100.000 2937 0 0 1 2937 507519389 507516453 0.000000e+00 5424
1 TraesCS5D01G464100 chr5D 90.802 1870 149 16 870 2737 506739552 506737704 0.000000e+00 2479
2 TraesCS5D01G464100 chr5D 90.855 1334 108 5 1405 2737 506703338 506702018 0.000000e+00 1775
3 TraesCS5D01G464100 chr5D 91.500 1047 73 13 64 1101 506704376 506703337 0.000000e+00 1426
4 TraesCS5D01G464100 chr5D 91.646 814 57 10 64 868 506740336 506739525 0.000000e+00 1116
5 TraesCS5D01G464100 chr5D 93.000 200 8 5 2740 2937 271836440 271836245 1.330000e-73 287
6 TraesCS5D01G464100 chr5D 97.101 69 2 0 1 69 506754118 506754050 1.850000e-22 117
7 TraesCS5D01G464100 chr5D 94.203 69 4 0 1 69 506735901 506735833 4.000000e-19 106
8 TraesCS5D01G464100 chr5A 91.703 2748 209 15 1 2737 634359016 634356277 0.000000e+00 3794
9 TraesCS5D01G464100 chr5A 90.263 2773 200 42 1 2737 635244493 635247231 0.000000e+00 3561
10 TraesCS5D01G464100 chr5A 90.220 2771 196 33 1 2737 634991111 634988382 0.000000e+00 3546
11 TraesCS5D01G464100 chr5A 88.409 1967 192 14 1 1939 638380613 638382571 0.000000e+00 2337
12 TraesCS5D01G464100 chr5A 85.946 555 73 3 2186 2737 638334274 638333722 3.260000e-164 588
13 TraesCS5D01G464100 chr5B 90.398 2739 218 24 5 2737 637216637 637213938 0.000000e+00 3559
14 TraesCS5D01G464100 chr5B 89.774 2748 215 44 1 2737 637805314 637802622 0.000000e+00 3458
15 TraesCS5D01G464100 chr5B 89.651 2754 213 45 1 2737 637784148 637781450 0.000000e+00 3441
16 TraesCS5D01G464100 chr5B 89.959 2201 173 24 189 2382 637729951 637727792 0.000000e+00 2796
17 TraesCS5D01G464100 chr4D 92.233 206 5 7 2740 2937 407438920 407439122 6.200000e-72 281
18 TraesCS5D01G464100 chr4D 90.777 206 8 4 2740 2937 191061460 191061258 6.240000e-67 265
19 TraesCS5D01G464100 chr3B 90.777 206 11 5 2736 2937 316574339 316574138 4.820000e-68 268
20 TraesCS5D01G464100 chr2B 91.133 203 7 8 2740 2937 204761683 204761487 6.240000e-67 265
21 TraesCS5D01G464100 chr4B 89.623 212 10 5 2733 2937 343080584 343080790 2.900000e-65 259
22 TraesCS5D01G464100 chr4B 87.069 232 15 9 2715 2937 271459781 271459556 6.290000e-62 248
23 TraesCS5D01G464100 chr3D 90.148 203 13 4 2740 2937 427167053 427166853 1.040000e-64 257
24 TraesCS5D01G464100 chr3D 89.756 205 14 4 2736 2937 262971562 262971362 3.760000e-64 255


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 TraesCS5D01G464100 chr5D 507516453 507519389 2936 True 5424.000000 5424 100.0000 1 2937 1 chr5D.!!$R3 2936
1 TraesCS5D01G464100 chr5D 506702018 506704376 2358 True 1600.500000 1775 91.1775 64 2737 2 chr5D.!!$R4 2673
2 TraesCS5D01G464100 chr5D 506735833 506740336 4503 True 1233.666667 2479 92.2170 1 2737 3 chr5D.!!$R5 2736
3 TraesCS5D01G464100 chr5A 634356277 634359016 2739 True 3794.000000 3794 91.7030 1 2737 1 chr5A.!!$R1 2736
4 TraesCS5D01G464100 chr5A 635244493 635247231 2738 False 3561.000000 3561 90.2630 1 2737 1 chr5A.!!$F1 2736
5 TraesCS5D01G464100 chr5A 634988382 634991111 2729 True 3546.000000 3546 90.2200 1 2737 1 chr5A.!!$R2 2736
6 TraesCS5D01G464100 chr5A 638380613 638382571 1958 False 2337.000000 2337 88.4090 1 1939 1 chr5A.!!$F2 1938
7 TraesCS5D01G464100 chr5A 638333722 638334274 552 True 588.000000 588 85.9460 2186 2737 1 chr5A.!!$R3 551
8 TraesCS5D01G464100 chr5B 637213938 637216637 2699 True 3559.000000 3559 90.3980 5 2737 1 chr5B.!!$R1 2732
9 TraesCS5D01G464100 chr5B 637802622 637805314 2692 True 3458.000000 3458 89.7740 1 2737 1 chr5B.!!$R4 2736
10 TraesCS5D01G464100 chr5B 637781450 637784148 2698 True 3441.000000 3441 89.6510 1 2737 1 chr5B.!!$R3 2736
11 TraesCS5D01G464100 chr5B 637727792 637729951 2159 True 2796.000000 2796 89.9590 189 2382 1 chr5B.!!$R2 2193

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
512 538 1.002403 TACATCTCCCCTTCGGCCA 59.998 57.895 2.24 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2127 0.25589 AGCTTCGAGCCTCTCTCTCT 59.744 55.0 3.66 0.0 43.77 3.1 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
115 116 5.607939 TGCATAATTCGTAGGAGAAAGGA 57.392 39.130 0.00 0.00 33.43 3.36
116 117 5.984725 TGCATAATTCGTAGGAGAAAGGAA 58.015 37.500 0.00 0.00 33.43 3.36
134 135 8.830741 AGAAAGGAAAGGATCTCTTCAGATTTA 58.169 33.333 8.82 0.00 39.71 1.40
253 277 4.284550 CCACCCACCCACCACTGG 62.285 72.222 0.00 0.00 37.29 4.00
280 305 5.367060 GTCACTCTCCCCCATACTCTATTTT 59.633 44.000 0.00 0.00 0.00 1.82
310 335 1.192146 TTCTTCCTGTCCACCCTCCG 61.192 60.000 0.00 0.00 0.00 4.63
363 388 7.363705 CCCCTCTATCAATATAGAAGCAGACAG 60.364 44.444 0.00 0.00 42.77 3.51
512 538 1.002403 TACATCTCCCCTTCGGCCA 59.998 57.895 2.24 0.00 0.00 5.36
523 550 5.343715 TCCCCTTCGGCCACTATATATAAA 58.656 41.667 2.24 0.00 0.00 1.40
605 632 4.894622 AGATCTCCATTCTCTTCCTCCTT 58.105 43.478 0.00 0.00 0.00 3.36
664 694 3.331120 AGCCTTAGCCTTCATATCCCTT 58.669 45.455 0.00 0.00 41.25 3.95
695 727 9.793252 ATCCTTTGTTTCTCGATATTTTTCATG 57.207 29.630 0.00 0.00 0.00 3.07
788 821 7.511268 TGTGTAGGGTGTAAGTAGTTCATTTT 58.489 34.615 0.00 0.00 0.00 1.82
1114 1158 4.323417 ACAATCTCCTTGCGTGTATTTGA 58.677 39.130 0.00 0.00 38.50 2.69
1118 1162 5.079689 TCTCCTTGCGTGTATTTGACATA 57.920 39.130 0.00 0.00 41.14 2.29
1126 1170 5.107259 TGCGTGTATTTGACATAAGTGTGTC 60.107 40.000 1.55 1.55 46.75 3.67
1195 1265 2.360191 GGCATCCAAGGCCCAAGA 59.640 61.111 0.00 0.00 45.87 3.02
1326 1396 5.390991 GGAAAAGAAGCAGTTGACCTATTCG 60.391 44.000 0.00 0.00 0.00 3.34
1630 1702 1.202510 GGTGCTGATGTTTTTGTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
1653 1726 6.295462 CCAAACCAATCAATGTTCAGGATCTT 60.295 38.462 0.00 0.00 0.00 2.40
1681 1754 9.751542 AGTCTATAATTAAGGAAGTCATCAACG 57.248 33.333 0.00 0.00 0.00 4.10
1746 1819 6.260936 TGAGCGATGGAGGAAATATTTTTCTC 59.739 38.462 17.28 17.28 40.91 2.87
1908 1981 7.912250 GGCATTGATATATTTCTTTATCGGCAG 59.088 37.037 0.00 0.00 0.00 4.85
2041 2123 4.330620 TCGAGGGTATGTTTTGCGTAATTC 59.669 41.667 0.00 0.00 0.00 2.17
2045 2127 5.642919 AGGGTATGTTTTGCGTAATTCGTAA 59.357 36.000 0.00 0.00 41.81 3.18
2046 2128 5.961263 GGGTATGTTTTGCGTAATTCGTAAG 59.039 40.000 0.00 0.00 43.90 2.34
2076 2158 2.283884 GCTCGAAGCTACTTGAGATTGC 59.716 50.000 6.82 0.00 38.45 3.56
2088 2170 8.023128 GCTACTTGAGATTGCTTTAACATTTCA 58.977 33.333 0.00 0.00 0.00 2.69
2117 2199 9.868277 AGACATTGATTTTTAACACAAAACTCA 57.132 25.926 0.00 0.15 0.00 3.41
2142 2224 6.309737 AGAAGTACGTCCTTGCGTTTATAAAG 59.690 38.462 0.00 0.00 43.04 1.85
2143 2225 5.713025 AGTACGTCCTTGCGTTTATAAAGA 58.287 37.500 0.00 0.00 43.04 2.52
2210 2292 0.178918 CCTACTCATCCCTCCCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
2314 2397 1.739929 CGTGCTACCCAACGCATCA 60.740 57.895 0.00 0.00 38.56 3.07
2324 2407 1.002900 CCAACGCATCACTTTGTCGTT 60.003 47.619 0.00 0.00 38.74 3.85
2326 2409 1.577468 ACGCATCACTTTGTCGTTGA 58.423 45.000 0.00 0.00 0.00 3.18
2342 2425 5.295787 TGTCGTTGAATAAGCCACCAATATC 59.704 40.000 0.00 0.00 0.00 1.63
2344 2427 4.272504 CGTTGAATAAGCCACCAATATCGT 59.727 41.667 0.00 0.00 0.00 3.73
2428 2520 6.286758 CCATATTTATGTGAGCAGAGAGTGT 58.713 40.000 0.00 0.00 31.82 3.55
2429 2521 6.202379 CCATATTTATGTGAGCAGAGAGTGTG 59.798 42.308 0.00 0.00 31.82 3.82
2448 2540 3.135348 TGTGGGATTTTTGCATGGTGAAA 59.865 39.130 0.00 0.00 0.00 2.69
2453 2545 2.818130 TTTTGCATGGTGAAAGAGGC 57.182 45.000 0.00 0.00 0.00 4.70
2457 2549 1.660560 GCATGGTGAAAGAGGCGCAT 61.661 55.000 10.83 0.00 0.00 4.73
2503 2595 2.654863 CCCTTTGCCCCTGTATAAGTG 58.345 52.381 0.00 0.00 0.00 3.16
2590 2684 3.121929 TCCATTCTACTCCTCCAGCTT 57.878 47.619 0.00 0.00 0.00 3.74
2689 2783 8.175716 GCTTGTAGTAGTTTTTGTATCCATGTC 58.824 37.037 0.00 0.00 0.00 3.06
2737 2831 5.932303 GTGATGGTATTTGTGTGTAGAGTGT 59.068 40.000 0.00 0.00 0.00 3.55
2738 2832 6.426937 GTGATGGTATTTGTGTGTAGAGTGTT 59.573 38.462 0.00 0.00 0.00 3.32
2739 2833 6.995686 TGATGGTATTTGTGTGTAGAGTGTTT 59.004 34.615 0.00 0.00 0.00 2.83
2740 2834 6.854496 TGGTATTTGTGTGTAGAGTGTTTC 57.146 37.500 0.00 0.00 0.00 2.78
2741 2835 6.350103 TGGTATTTGTGTGTAGAGTGTTTCA 58.650 36.000 0.00 0.00 0.00 2.69
2742 2836 6.259167 TGGTATTTGTGTGTAGAGTGTTTCAC 59.741 38.462 0.00 0.00 34.10 3.18
2744 2838 2.198406 TGTGTGTAGAGTGTTTCACGC 58.802 47.619 0.00 0.00 39.64 5.34
2745 2839 1.525619 GTGTGTAGAGTGTTTCACGCC 59.474 52.381 0.53 0.00 39.64 5.68
2748 2842 1.139256 TGTAGAGTGTTTCACGCCCAA 59.861 47.619 0.53 0.00 39.64 4.12
2750 2844 2.851263 AGAGTGTTTCACGCCCAATA 57.149 45.000 0.53 0.00 39.64 1.90
2753 2847 1.472480 AGTGTTTCACGCCCAATATGC 59.528 47.619 0.00 0.00 39.64 3.14
2763 2857 2.565841 GCCCAATATGCGATCCTATCC 58.434 52.381 0.00 0.00 0.00 2.59
2764 2858 2.826428 CCCAATATGCGATCCTATCCG 58.174 52.381 0.00 0.00 0.00 4.18
2765 2859 2.430694 CCCAATATGCGATCCTATCCGA 59.569 50.000 0.00 0.00 0.00 4.55
2766 2860 3.491619 CCCAATATGCGATCCTATCCGAG 60.492 52.174 0.00 0.00 0.00 4.63
2767 2861 3.381590 CCAATATGCGATCCTATCCGAGA 59.618 47.826 0.00 0.00 0.00 4.04
2768 2862 4.498850 CCAATATGCGATCCTATCCGAGAG 60.499 50.000 0.00 0.00 0.00 3.20
2786 2880 1.295746 GGAACTCGAAGGTCCCACC 59.704 63.158 7.50 0.00 46.52 4.61
2788 2882 0.395312 GAACTCGAAGGTCCCACCAA 59.605 55.000 0.00 0.00 41.95 3.67
2790 2884 1.296715 CTCGAAGGTCCCACCAAGG 59.703 63.158 0.00 0.00 41.95 3.61
2791 2885 1.152204 TCGAAGGTCCCACCAAGGA 60.152 57.895 0.00 0.00 41.95 3.36
2793 2887 1.200519 CGAAGGTCCCACCAAGGATA 58.799 55.000 0.00 0.00 41.95 2.59
2794 2888 1.139058 CGAAGGTCCCACCAAGGATAG 59.861 57.143 0.00 0.00 41.95 2.08
2796 2890 2.182516 AGGTCCCACCAAGGATAGAG 57.817 55.000 0.00 0.00 41.95 2.43
2797 2891 0.470341 GGTCCCACCAAGGATAGAGC 59.530 60.000 0.00 0.00 41.22 4.09
2798 2892 0.470341 GTCCCACCAAGGATAGAGCC 59.530 60.000 0.00 0.00 41.22 4.70
2799 2893 1.048724 TCCCACCAAGGATAGAGCCG 61.049 60.000 0.00 0.00 41.22 5.52
2800 2894 1.227674 CCACCAAGGATAGAGCCGC 60.228 63.158 0.00 0.00 41.22 6.53
2802 2896 0.107456 CACCAAGGATAGAGCCGCAT 59.893 55.000 0.00 0.00 0.00 4.73
2804 2898 2.027745 CACCAAGGATAGAGCCGCATAT 60.028 50.000 0.00 0.00 0.00 1.78
2805 2899 2.639839 ACCAAGGATAGAGCCGCATATT 59.360 45.455 0.00 0.00 0.00 1.28
2807 2901 3.306989 CCAAGGATAGAGCCGCATATTCA 60.307 47.826 0.00 0.00 0.00 2.57
2808 2902 4.318332 CAAGGATAGAGCCGCATATTCAA 58.682 43.478 0.00 0.00 0.00 2.69
2809 2903 4.199432 AGGATAGAGCCGCATATTCAAG 57.801 45.455 0.00 0.00 0.00 3.02
2811 2905 3.929610 GGATAGAGCCGCATATTCAAGAC 59.070 47.826 0.00 0.00 0.00 3.01
2812 2906 2.988010 AGAGCCGCATATTCAAGACA 57.012 45.000 0.00 0.00 0.00 3.41
2813 2907 2.555199 AGAGCCGCATATTCAAGACAC 58.445 47.619 0.00 0.00 0.00 3.67
2814 2908 2.169352 AGAGCCGCATATTCAAGACACT 59.831 45.455 0.00 0.00 0.00 3.55
2816 2910 3.347216 AGCCGCATATTCAAGACACTTT 58.653 40.909 0.00 0.00 0.00 2.66
2818 2912 3.853671 GCCGCATATTCAAGACACTTTTG 59.146 43.478 0.00 0.00 0.00 2.44
2819 2913 3.853671 CCGCATATTCAAGACACTTTTGC 59.146 43.478 0.00 0.00 0.00 3.68
2822 2916 5.060077 CGCATATTCAAGACACTTTTGCAAG 59.940 40.000 0.00 0.00 35.92 4.01
2825 2919 3.781079 TCAAGACACTTTTGCAAGGTG 57.219 42.857 23.72 23.72 33.82 4.00
2826 2920 2.426738 TCAAGACACTTTTGCAAGGTGG 59.573 45.455 26.69 15.48 33.82 4.61
2827 2921 2.426738 CAAGACACTTTTGCAAGGTGGA 59.573 45.455 26.69 2.16 33.82 4.02
2828 2922 2.949447 AGACACTTTTGCAAGGTGGAT 58.051 42.857 26.69 17.24 33.82 3.41
2829 2923 4.098914 AGACACTTTTGCAAGGTGGATA 57.901 40.909 26.69 0.83 33.82 2.59
2830 2924 4.666512 AGACACTTTTGCAAGGTGGATAT 58.333 39.130 26.69 13.71 33.82 1.63
2831 2925 4.702131 AGACACTTTTGCAAGGTGGATATC 59.298 41.667 26.69 18.89 33.82 1.63
2833 2927 5.018809 ACACTTTTGCAAGGTGGATATCAT 58.981 37.500 26.69 10.63 33.82 2.45
2834 2928 5.481473 ACACTTTTGCAAGGTGGATATCATT 59.519 36.000 26.69 10.12 33.82 2.57
2835 2929 6.663093 ACACTTTTGCAAGGTGGATATCATTA 59.337 34.615 26.69 0.00 33.82 1.90
2836 2930 6.974622 CACTTTTGCAAGGTGGATATCATTAC 59.025 38.462 20.05 0.54 33.82 1.89
2837 2931 6.663093 ACTTTTGCAAGGTGGATATCATTACA 59.337 34.615 4.83 0.00 33.82 2.41
2838 2932 7.342799 ACTTTTGCAAGGTGGATATCATTACAT 59.657 33.333 4.83 0.00 33.82 2.29
2839 2933 6.882610 TTGCAAGGTGGATATCATTACATC 57.117 37.500 4.83 0.00 0.00 3.06
2841 2935 4.997395 GCAAGGTGGATATCATTACATCGT 59.003 41.667 4.83 0.00 0.00 3.73
2842 2936 6.163476 GCAAGGTGGATATCATTACATCGTA 58.837 40.000 4.83 0.00 0.00 3.43
2843 2937 6.090898 GCAAGGTGGATATCATTACATCGTAC 59.909 42.308 4.83 0.00 0.00 3.67
2844 2938 6.282199 AGGTGGATATCATTACATCGTACC 57.718 41.667 4.83 0.00 33.04 3.34
2845 2939 5.778241 AGGTGGATATCATTACATCGTACCA 59.222 40.000 4.83 0.00 34.25 3.25
2846 2940 6.440647 AGGTGGATATCATTACATCGTACCAT 59.559 38.462 4.83 0.00 34.25 3.55
2847 2941 7.038302 AGGTGGATATCATTACATCGTACCATT 60.038 37.037 4.83 0.00 34.25 3.16
2848 2942 8.255206 GGTGGATATCATTACATCGTACCATTA 58.745 37.037 4.83 0.00 33.08 1.90
2849 2943 9.084164 GTGGATATCATTACATCGTACCATTAC 57.916 37.037 4.83 0.00 0.00 1.89
2850 2944 8.808092 TGGATATCATTACATCGTACCATTACA 58.192 33.333 4.83 0.00 0.00 2.41
2851 2945 9.817809 GGATATCATTACATCGTACCATTACAT 57.182 33.333 4.83 0.00 0.00 2.29
2861 2955 9.803315 ACATCGTACCATTACATATAATAGCTG 57.197 33.333 0.00 0.00 29.44 4.24
2863 2957 7.778083 TCGTACCATTACATATAATAGCTGGG 58.222 38.462 0.00 0.00 29.44 4.45
2864 2958 6.984474 CGTACCATTACATATAATAGCTGGGG 59.016 42.308 0.00 0.00 29.44 4.96
2865 2959 7.147794 CGTACCATTACATATAATAGCTGGGGA 60.148 40.741 0.00 0.00 29.44 4.81
2866 2960 7.771506 ACCATTACATATAATAGCTGGGGAT 57.228 36.000 0.00 0.00 29.44 3.85
2868 2962 8.714906 ACCATTACATATAATAGCTGGGGATAC 58.285 37.037 0.00 0.00 29.44 2.24
2869 2963 8.713971 CCATTACATATAATAGCTGGGGATACA 58.286 37.037 0.00 0.00 30.60 2.29
2873 2967 8.854237 ACATATAATAGCTGGGGATACATACA 57.146 34.615 0.00 0.00 39.74 2.29
2874 2968 9.279233 ACATATAATAGCTGGGGATACATACAA 57.721 33.333 0.00 0.00 39.74 2.41
2878 2972 2.158608 AGCTGGGGATACATACAAAGGC 60.159 50.000 0.00 0.00 39.74 4.35
2879 2973 2.422803 GCTGGGGATACATACAAAGGCA 60.423 50.000 0.00 0.00 39.74 4.75
2880 2974 3.751893 GCTGGGGATACATACAAAGGCAT 60.752 47.826 0.00 0.00 39.74 4.40
2881 2975 4.506625 GCTGGGGATACATACAAAGGCATA 60.507 45.833 0.00 0.00 39.74 3.14
2882 2976 5.807721 GCTGGGGATACATACAAAGGCATAT 60.808 44.000 0.00 0.00 39.74 1.78
2883 2977 6.578238 GCTGGGGATACATACAAAGGCATATA 60.578 42.308 0.00 0.00 39.74 0.86
2884 2978 7.336475 TGGGGATACATACAAAGGCATATAA 57.664 36.000 0.00 0.00 39.74 0.98
2886 2980 8.397957 TGGGGATACATACAAAGGCATATAAAT 58.602 33.333 0.00 0.00 39.74 1.40
2887 2981 8.686334 GGGGATACATACAAAGGCATATAAATG 58.314 37.037 0.00 0.00 39.74 2.32
2919 3013 8.882736 TGAATACATCATACATGAGAACAACAC 58.117 33.333 0.00 0.00 40.64 3.32
2920 3014 7.792374 ATACATCATACATGAGAACAACACC 57.208 36.000 0.00 0.00 40.64 4.16
2921 3015 4.943705 ACATCATACATGAGAACAACACCC 59.056 41.667 0.00 0.00 40.64 4.61
2923 3017 3.259625 TCATACATGAGAACAACACCCGA 59.740 43.478 0.00 0.00 32.11 5.14
2924 3018 1.878953 ACATGAGAACAACACCCGAC 58.121 50.000 0.00 0.00 0.00 4.79
2925 3019 1.416401 ACATGAGAACAACACCCGACT 59.584 47.619 0.00 0.00 0.00 4.18
2926 3020 2.631062 ACATGAGAACAACACCCGACTA 59.369 45.455 0.00 0.00 0.00 2.59
2927 3021 2.806608 TGAGAACAACACCCGACTAC 57.193 50.000 0.00 0.00 0.00 2.73
2928 3022 2.033372 TGAGAACAACACCCGACTACA 58.967 47.619 0.00 0.00 0.00 2.74
2929 3023 2.035449 TGAGAACAACACCCGACTACAG 59.965 50.000 0.00 0.00 0.00 2.74
2930 3024 2.295349 GAGAACAACACCCGACTACAGA 59.705 50.000 0.00 0.00 0.00 3.41
2931 3025 2.897969 AGAACAACACCCGACTACAGAT 59.102 45.455 0.00 0.00 0.00 2.90
2932 3026 2.743636 ACAACACCCGACTACAGATG 57.256 50.000 0.00 0.00 0.00 2.90
2933 3027 2.244695 ACAACACCCGACTACAGATGA 58.755 47.619 0.00 0.00 0.00 2.92
2934 3028 2.631062 ACAACACCCGACTACAGATGAA 59.369 45.455 0.00 0.00 0.00 2.57
2935 3029 3.070446 ACAACACCCGACTACAGATGAAA 59.930 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 277 0.745468 GTATGGGGGAGAGTGACGAC 59.255 60.000 0.00 0.00 0.00 4.34
280 305 3.149196 GACAGGAAGAAGAACATTGGCA 58.851 45.455 0.00 0.00 0.00 4.92
310 335 1.410882 GGGTAGCATGAGAGAGGTGAC 59.589 57.143 0.00 0.00 0.00 3.67
363 388 7.609146 TGATCCATCTTTCCAGATATGCAATAC 59.391 37.037 0.00 0.00 37.71 1.89
523 550 4.526970 CCTTGTACCCTGATTATGTTGCT 58.473 43.478 0.00 0.00 0.00 3.91
569 596 2.200899 GAGATCTTTCCGCTCTTGCTC 58.799 52.381 0.00 0.00 36.97 4.26
605 632 0.395862 GATGGAGGACGAGGAGGTCA 60.396 60.000 0.00 0.00 38.70 4.02
664 694 7.938140 AATATCGAGAAACAAAGGATGGAAA 57.062 32.000 0.00 0.00 0.00 3.13
695 727 5.784578 ACAAAAACTACAAAGGGTGGATC 57.215 39.130 0.00 0.00 0.00 3.36
875 912 3.944422 AATAGACGCAGCCAAATAACG 57.056 42.857 0.00 0.00 0.00 3.18
955 995 8.406297 CCTTCCGTCATATAGATTGATCGAATA 58.594 37.037 0.00 0.00 0.00 1.75
957 997 6.208797 ACCTTCCGTCATATAGATTGATCGAA 59.791 38.462 0.00 0.00 0.00 3.71
1114 1158 6.374417 AGTTATTCCCTGACACACTTATGT 57.626 37.500 0.00 0.00 40.80 2.29
1118 1162 8.164070 AGAAATTAGTTATTCCCTGACACACTT 58.836 33.333 0.00 0.00 0.00 3.16
1195 1265 3.390639 CAGTGCCTTCATAGAGGAGGATT 59.609 47.826 0.00 0.00 39.25 3.01
1282 1352 2.128035 CATTCACGGCGAGAGTAATCC 58.872 52.381 16.62 0.00 0.00 3.01
1326 1396 3.551846 TGTCAAACTTCTTCCCCTCAAC 58.448 45.455 0.00 0.00 0.00 3.18
1489 1561 4.863152 AGCAACACAACAAAAGAATTGC 57.137 36.364 0.00 0.00 40.92 3.56
1490 1562 7.737395 TGTTAAGCAACACAACAAAAGAATTG 58.263 30.769 0.00 0.00 39.75 2.32
1630 1702 6.494491 TCAAGATCCTGAACATTGATTGGTTT 59.506 34.615 0.00 0.00 0.00 3.27
1681 1754 4.278975 AGACCATGGTGTTCTTCTTCTC 57.721 45.455 25.52 2.51 0.00 2.87
1746 1819 8.511604 ACATAAGAAAACATAGTTCCATGAGG 57.488 34.615 0.00 0.00 0.00 3.86
1864 1937 2.175284 TGCCATGGAATCAAGGATAGCA 59.825 45.455 18.40 0.00 33.85 3.49
1900 1973 5.123227 GCCCTATTTATATTGCTGCCGATA 58.877 41.667 0.00 0.00 0.00 2.92
1908 1981 5.059404 ACATTGCGCCCTATTTATATTGC 57.941 39.130 4.18 0.00 0.00 3.56
2041 2123 1.942677 TCGAGCCTCTCTCTCTTACG 58.057 55.000 0.00 0.00 39.70 3.18
2045 2127 0.255890 AGCTTCGAGCCTCTCTCTCT 59.744 55.000 3.66 0.00 43.77 3.10
2046 2128 1.602377 GTAGCTTCGAGCCTCTCTCTC 59.398 57.143 0.00 0.00 43.77 3.20
2076 2158 8.955061 AATCAATGTCTCGTGAAATGTTAAAG 57.045 30.769 0.00 0.00 0.00 1.85
2088 2170 8.803799 GTTTTGTGTTAAAAATCAATGTCTCGT 58.196 29.630 0.00 0.00 32.02 4.18
2210 2292 1.439644 GAGAGAGGCACTAAGGGCG 59.560 63.158 0.00 0.00 41.55 6.13
2216 2298 1.611006 GATCATGCGAGAGAGGCACTA 59.389 52.381 0.00 0.00 44.23 2.74
2314 2397 3.252458 GGTGGCTTATTCAACGACAAAGT 59.748 43.478 0.00 0.00 0.00 2.66
2324 2407 7.936847 AGAAATACGATATTGGTGGCTTATTCA 59.063 33.333 0.00 0.00 0.00 2.57
2326 2409 7.936847 TCAGAAATACGATATTGGTGGCTTATT 59.063 33.333 0.00 0.00 0.00 1.40
2342 2425 5.723492 TGATGCACATCTTCAGAAATACG 57.277 39.130 11.66 0.00 38.60 3.06
2391 2483 8.575589 TCACATAAATATGGCAAGCGAATATTT 58.424 29.630 19.34 19.34 38.99 1.40
2399 2491 4.276678 TCTGCTCACATAAATATGGCAAGC 59.723 41.667 12.91 12.91 38.00 4.01
2400 2492 5.761726 TCTCTGCTCACATAAATATGGCAAG 59.238 40.000 5.48 6.00 38.00 4.01
2428 2520 3.645212 TCTTTCACCATGCAAAAATCCCA 59.355 39.130 0.00 0.00 0.00 4.37
2429 2521 4.248058 CTCTTTCACCATGCAAAAATCCC 58.752 43.478 0.00 0.00 0.00 3.85
2448 2540 1.242076 GCCAATGAATATGCGCCTCT 58.758 50.000 4.18 0.00 0.00 3.69
2453 2545 1.067425 CCCATGGCCAATGAATATGCG 60.067 52.381 10.96 0.00 38.72 4.73
2457 2549 4.025360 GCATATCCCATGGCCAATGAATA 58.975 43.478 10.96 6.62 38.72 1.75
2503 2595 0.764890 TACCCTGAGTATGCCATGGC 59.235 55.000 30.54 30.54 42.35 4.40
2744 2838 2.430694 TCGGATAGGATCGCATATTGGG 59.569 50.000 0.00 0.00 0.00 4.12
2745 2839 3.381590 TCTCGGATAGGATCGCATATTGG 59.618 47.826 0.00 0.00 0.00 3.16
2748 2842 3.117851 TCCTCTCGGATAGGATCGCATAT 60.118 47.826 7.97 0.00 38.24 1.78
2750 2844 1.004862 TCCTCTCGGATAGGATCGCAT 59.995 52.381 7.97 0.00 38.24 4.73
2753 2847 2.745281 GAGTTCCTCTCGGATAGGATCG 59.255 54.545 12.36 0.00 42.69 3.69
2764 2858 0.818938 GGGACCTTCGAGTTCCTCTC 59.181 60.000 8.46 0.00 39.62 3.20
2765 2859 0.114560 TGGGACCTTCGAGTTCCTCT 59.885 55.000 3.93 0.00 36.24 3.69
2766 2860 0.246910 GTGGGACCTTCGAGTTCCTC 59.753 60.000 3.93 0.00 36.24 3.71
2767 2861 1.192803 GGTGGGACCTTCGAGTTCCT 61.193 60.000 3.93 0.00 36.24 3.36
2768 2862 1.295746 GGTGGGACCTTCGAGTTCC 59.704 63.158 0.00 0.00 35.75 3.62
2769 2863 0.395312 TTGGTGGGACCTTCGAGTTC 59.605 55.000 0.00 0.00 39.58 3.01
2770 2864 0.396811 CTTGGTGGGACCTTCGAGTT 59.603 55.000 0.00 0.00 39.58 3.01
2771 2865 1.481056 CCTTGGTGGGACCTTCGAGT 61.481 60.000 0.00 0.00 39.58 4.18
2774 2868 1.139058 CTATCCTTGGTGGGACCTTCG 59.861 57.143 0.00 0.00 39.58 3.79
2776 2870 2.482494 CTCTATCCTTGGTGGGACCTT 58.518 52.381 0.00 0.00 39.58 3.50
2778 2872 0.470341 GCTCTATCCTTGGTGGGACC 59.530 60.000 0.00 0.00 38.30 4.46
2779 2873 0.470341 GGCTCTATCCTTGGTGGGAC 59.530 60.000 0.00 0.00 38.30 4.46
2780 2874 1.048724 CGGCTCTATCCTTGGTGGGA 61.049 60.000 0.00 0.00 39.95 4.37
2781 2875 1.447643 CGGCTCTATCCTTGGTGGG 59.552 63.158 0.00 0.00 36.20 4.61
2782 2876 1.227674 GCGGCTCTATCCTTGGTGG 60.228 63.158 0.00 0.00 37.10 4.61
2783 2877 0.107456 ATGCGGCTCTATCCTTGGTG 59.893 55.000 0.00 0.00 0.00 4.17
2784 2878 1.717032 TATGCGGCTCTATCCTTGGT 58.283 50.000 0.00 0.00 0.00 3.67
2785 2879 3.265791 GAATATGCGGCTCTATCCTTGG 58.734 50.000 0.00 0.00 0.00 3.61
2786 2880 3.930336 TGAATATGCGGCTCTATCCTTG 58.070 45.455 0.00 0.00 0.00 3.61
2788 2882 3.834813 TCTTGAATATGCGGCTCTATCCT 59.165 43.478 0.00 0.00 0.00 3.24
2790 2884 4.387256 GTGTCTTGAATATGCGGCTCTATC 59.613 45.833 0.00 0.00 0.00 2.08
2791 2885 4.039730 AGTGTCTTGAATATGCGGCTCTAT 59.960 41.667 0.00 0.00 0.00 1.98
2793 2887 2.169352 AGTGTCTTGAATATGCGGCTCT 59.831 45.455 0.00 0.00 0.00 4.09
2794 2888 2.555199 AGTGTCTTGAATATGCGGCTC 58.445 47.619 0.00 0.00 0.00 4.70
2796 2890 3.764885 AAAGTGTCTTGAATATGCGGC 57.235 42.857 0.00 0.00 0.00 6.53
2797 2891 3.853671 GCAAAAGTGTCTTGAATATGCGG 59.146 43.478 0.00 0.00 0.00 5.69
2798 2892 4.475028 TGCAAAAGTGTCTTGAATATGCG 58.525 39.130 0.00 0.00 34.16 4.73
2799 2893 5.346822 CCTTGCAAAAGTGTCTTGAATATGC 59.653 40.000 0.00 0.00 0.00 3.14
2800 2894 6.364165 CACCTTGCAAAAGTGTCTTGAATATG 59.636 38.462 17.23 0.00 0.00 1.78
2802 2896 5.221224 CCACCTTGCAAAAGTGTCTTGAATA 60.221 40.000 21.49 0.00 0.00 1.75
2804 2898 3.119173 CCACCTTGCAAAAGTGTCTTGAA 60.119 43.478 21.49 0.00 0.00 2.69
2805 2899 2.426738 CCACCTTGCAAAAGTGTCTTGA 59.573 45.455 21.49 0.00 0.00 3.02
2807 2901 2.733956 TCCACCTTGCAAAAGTGTCTT 58.266 42.857 21.49 0.00 0.00 3.01
2808 2902 2.435372 TCCACCTTGCAAAAGTGTCT 57.565 45.000 21.49 0.00 0.00 3.41
2809 2903 4.458989 TGATATCCACCTTGCAAAAGTGTC 59.541 41.667 21.49 15.06 0.00 3.67
2811 2905 5.587388 ATGATATCCACCTTGCAAAAGTG 57.413 39.130 18.13 18.13 0.00 3.16
2812 2906 6.663093 TGTAATGATATCCACCTTGCAAAAGT 59.337 34.615 0.00 0.00 0.00 2.66
2813 2907 7.099266 TGTAATGATATCCACCTTGCAAAAG 57.901 36.000 0.00 0.00 0.00 2.27
2814 2908 7.468494 CGATGTAATGATATCCACCTTGCAAAA 60.468 37.037 0.00 0.00 0.00 2.44
2816 2910 5.469760 CGATGTAATGATATCCACCTTGCAA 59.530 40.000 0.00 0.00 0.00 4.08
2818 2912 4.997395 ACGATGTAATGATATCCACCTTGC 59.003 41.667 0.00 0.00 0.00 4.01
2819 2913 6.590292 GGTACGATGTAATGATATCCACCTTG 59.410 42.308 0.00 0.00 29.18 3.61
2822 2916 6.032956 TGGTACGATGTAATGATATCCACC 57.967 41.667 0.00 0.00 30.94 4.61
2825 2919 9.817809 ATGTAATGGTACGATGTAATGATATCC 57.182 33.333 0.00 0.00 32.40 2.59
2835 2929 9.803315 CAGCTATTATATGTAATGGTACGATGT 57.197 33.333 5.06 0.00 32.93 3.06
2836 2930 9.249457 CCAGCTATTATATGTAATGGTACGATG 57.751 37.037 5.06 0.00 32.93 3.84
2837 2931 8.421784 CCCAGCTATTATATGTAATGGTACGAT 58.578 37.037 5.06 0.00 32.93 3.73
2838 2932 7.147794 CCCCAGCTATTATATGTAATGGTACGA 60.148 40.741 5.06 0.00 32.93 3.43
2839 2933 6.984474 CCCCAGCTATTATATGTAATGGTACG 59.016 42.308 5.06 0.00 32.93 3.67
2841 2935 8.869986 ATCCCCAGCTATTATATGTAATGGTA 57.130 34.615 5.06 0.00 32.93 3.25
2842 2936 7.771506 ATCCCCAGCTATTATATGTAATGGT 57.228 36.000 5.06 0.00 32.93 3.55
2843 2937 8.713971 TGTATCCCCAGCTATTATATGTAATGG 58.286 37.037 5.06 3.38 32.84 3.16
2847 2941 9.945633 TGTATGTATCCCCAGCTATTATATGTA 57.054 33.333 0.00 0.00 0.00 2.29
2848 2942 8.854237 TGTATGTATCCCCAGCTATTATATGT 57.146 34.615 0.00 0.00 0.00 2.29
2851 2945 8.768397 CCTTTGTATGTATCCCCAGCTATTATA 58.232 37.037 0.00 0.00 0.00 0.98
2852 2946 7.633789 CCTTTGTATGTATCCCCAGCTATTAT 58.366 38.462 0.00 0.00 0.00 1.28
2853 2947 6.521770 GCCTTTGTATGTATCCCCAGCTATTA 60.522 42.308 0.00 0.00 0.00 0.98
2854 2948 5.749032 GCCTTTGTATGTATCCCCAGCTATT 60.749 44.000 0.00 0.00 0.00 1.73
2855 2949 4.263506 GCCTTTGTATGTATCCCCAGCTAT 60.264 45.833 0.00 0.00 0.00 2.97
2856 2950 3.072476 GCCTTTGTATGTATCCCCAGCTA 59.928 47.826 0.00 0.00 0.00 3.32
2858 2952 2.230660 GCCTTTGTATGTATCCCCAGC 58.769 52.381 0.00 0.00 0.00 4.85
2859 2953 3.576078 TGCCTTTGTATGTATCCCCAG 57.424 47.619 0.00 0.00 0.00 4.45
2860 2954 5.858876 ATATGCCTTTGTATGTATCCCCA 57.141 39.130 0.00 0.00 0.00 4.96
2861 2955 8.686334 CATTTATATGCCTTTGTATGTATCCCC 58.314 37.037 0.00 0.00 0.00 4.81
2881 2975 9.299465 TGTATGATGTATTCATGTGGCATTTAT 57.701 29.630 0.00 0.00 44.90 1.40
2882 2976 8.688747 TGTATGATGTATTCATGTGGCATTTA 57.311 30.769 0.00 0.00 44.90 1.40
2883 2977 7.585579 TGTATGATGTATTCATGTGGCATTT 57.414 32.000 0.00 0.00 44.90 2.32
2884 2978 7.449086 TCATGTATGATGTATTCATGTGGCATT 59.551 33.333 0.00 0.00 44.90 3.56
2886 2980 6.297582 TCATGTATGATGTATTCATGTGGCA 58.702 36.000 0.00 0.00 44.90 4.92
2887 2981 6.652062 TCTCATGTATGATGTATTCATGTGGC 59.348 38.462 0.00 0.00 44.90 5.01
2889 2983 9.048446 TGTTCTCATGTATGATGTATTCATGTG 57.952 33.333 0.00 0.00 44.90 3.21
2890 2984 9.617523 TTGTTCTCATGTATGATGTATTCATGT 57.382 29.630 0.00 0.00 44.90 3.21
2891 2985 9.874215 GTTGTTCTCATGTATGATGTATTCATG 57.126 33.333 0.00 0.00 44.90 3.07
2892 2986 9.617523 TGTTGTTCTCATGTATGATGTATTCAT 57.382 29.630 0.00 0.00 46.86 2.57
2895 2989 7.283127 GGGTGTTGTTCTCATGTATGATGTATT 59.717 37.037 0.00 0.00 36.02 1.89
2896 2990 6.767902 GGGTGTTGTTCTCATGTATGATGTAT 59.232 38.462 0.00 0.00 36.02 2.29
2897 2991 6.112734 GGGTGTTGTTCTCATGTATGATGTA 58.887 40.000 0.00 0.00 36.02 2.29
2898 2992 4.943705 GGGTGTTGTTCTCATGTATGATGT 59.056 41.667 0.00 0.00 36.02 3.06
2899 2993 4.034394 CGGGTGTTGTTCTCATGTATGATG 59.966 45.833 0.00 0.00 36.02 3.07
2900 2994 4.081142 TCGGGTGTTGTTCTCATGTATGAT 60.081 41.667 0.00 0.00 36.02 2.45
2901 2995 3.259625 TCGGGTGTTGTTCTCATGTATGA 59.740 43.478 0.00 0.00 35.16 2.15
2902 2996 3.370978 GTCGGGTGTTGTTCTCATGTATG 59.629 47.826 0.00 0.00 0.00 2.39
2903 2997 3.260884 AGTCGGGTGTTGTTCTCATGTAT 59.739 43.478 0.00 0.00 0.00 2.29
2904 2998 2.631062 AGTCGGGTGTTGTTCTCATGTA 59.369 45.455 0.00 0.00 0.00 2.29
2905 2999 1.416401 AGTCGGGTGTTGTTCTCATGT 59.584 47.619 0.00 0.00 0.00 3.21
2908 3002 2.033372 TGTAGTCGGGTGTTGTTCTCA 58.967 47.619 0.00 0.00 0.00 3.27
2909 3003 2.295349 TCTGTAGTCGGGTGTTGTTCTC 59.705 50.000 0.00 0.00 0.00 2.87
2912 3006 2.631062 TCATCTGTAGTCGGGTGTTGTT 59.369 45.455 0.00 0.00 33.17 2.83
2913 3007 2.244695 TCATCTGTAGTCGGGTGTTGT 58.755 47.619 0.00 0.00 33.17 3.32
2914 3008 3.313012 TTCATCTGTAGTCGGGTGTTG 57.687 47.619 0.00 0.00 33.17 3.33
2915 3009 3.660865 GTTTCATCTGTAGTCGGGTGTT 58.339 45.455 0.00 0.00 33.17 3.32


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

AutoCloner maintained by Alex Coulton.