Multiple sequence alignment - TraesCS1A01G093900

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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 TraesCS1A01G093900 chr1A 100.000 6629 0 0 1 6629 86650058 86643430 0.000000e+00 12242.0
1 TraesCS1A01G093900 chr1D 96.559 5929 151 21 564 6453 90650461 90644547 0.000000e+00 9769.0
2 TraesCS1A01G093900 chr1D 91.484 364 27 4 207 570 90651208 90650849 1.280000e-136 497.0
3 TraesCS1A01G093900 chr1D 94.286 70 4 0 2117 2186 90648843 90648774 2.530000e-19 108.0
4 TraesCS1A01G093900 chr1B 96.714 5478 134 10 564 6006 145458187 145452721 0.000000e+00 9077.0
5 TraesCS1A01G093900 chr1B 90.211 521 47 4 50 570 145458940 145458424 0.000000e+00 676.0
6 TraesCS1A01G093900 chr1B 89.159 535 27 10 5937 6441 145452754 145452221 7.250000e-179 638.0
7 TraesCS1A01G093900 chr1B 95.000 100 4 1 6530 6629 145451769 145451671 8.900000e-34 156.0
8 TraesCS1A01G093900 chr1B 95.714 70 3 0 2117 2186 145456569 145456500 5.430000e-21 113.0
9 TraesCS1A01G093900 chr2D 93.182 44 2 1 6004 6047 506776633 506776591 5.550000e-06 63.9
10 TraesCS1A01G093900 chr2A 93.182 44 2 1 6004 6047 651599229 651599187 5.550000e-06 63.9


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 TraesCS1A01G093900 chr1A 86643430 86650058 6628 True 12242 12242 100.000000 1 6629 1 chr1A.!!$R1 6628
1 TraesCS1A01G093900 chr1D 90644547 90651208 6661 True 3458 9769 94.109667 207 6453 3 chr1D.!!$R1 6246
2 TraesCS1A01G093900 chr1B 145451671 145458940 7269 True 2132 9077 93.359600 50 6629 5 chr1B.!!$R1 6579

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
287 288 0.240945 CTGTCCGGGTGTGAATTTGC 59.759 55.000 0.00 0.0 0.00 3.68 F
1498 1897 0.035458 CGAACCAGAGGAAAGTGCCT 59.965 55.000 0.00 0.0 42.17 4.75 F
2705 3106 0.318955 GTTGTTGCTGGTGGTGATGC 60.319 55.000 0.00 0.0 0.00 3.91 F
2840 3241 1.625315 TGAGATAGTTGTGGCTGCAGT 59.375 47.619 16.64 0.0 0.00 4.40 F
3258 3689 2.884639 GGGTTTTGACTCTGCTGCTTTA 59.115 45.455 0.00 0.0 0.00 1.85 F
4464 4895 1.372683 GCAGTCAAGAGCTCACCCA 59.627 57.895 17.77 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 2105 0.467290 TTCAGCCTCACCACCCAAAC 60.467 55.000 0.00 0.0 0.00 2.93 R
3258 3689 0.107654 CCGCTTTTAGTAGGGCAGCT 60.108 55.000 0.00 0.0 0.00 4.24 R
3564 3995 0.514691 GCACTTGTGCTGCTACTGTC 59.485 55.000 17.36 0.0 0.00 3.51 R
3648 4079 1.201965 GCTTTCTTCCGTGCATTCTCG 60.202 52.381 0.00 0.0 0.00 4.04 R
5220 5651 1.073897 GACCTTCAGCCCAGTTGCT 59.926 57.895 0.00 0.0 44.00 3.91 R
5848 6279 0.238289 GATGGACAGCAACAACGGTG 59.762 55.000 0.00 0.0 40.25 4.94 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
17 18 3.640407 AGGAGGCCGCAGAGCAAA 61.640 61.111 9.31 0.00 0.00 3.68
18 19 3.130160 GGAGGCCGCAGAGCAAAG 61.130 66.667 9.31 0.00 0.00 2.77
19 20 3.808656 GAGGCCGCAGAGCAAAGC 61.809 66.667 0.00 0.00 0.00 3.51
22 23 2.436646 GCCGCAGAGCAAAGCCTA 60.437 61.111 0.00 0.00 0.00 3.93
23 24 2.754995 GCCGCAGAGCAAAGCCTAC 61.755 63.158 0.00 0.00 0.00 3.18
24 25 1.375908 CCGCAGAGCAAAGCCTACA 60.376 57.895 0.00 0.00 0.00 2.74
25 26 1.639298 CCGCAGAGCAAAGCCTACAC 61.639 60.000 0.00 0.00 0.00 2.90
26 27 1.790387 GCAGAGCAAAGCCTACACG 59.210 57.895 0.00 0.00 0.00 4.49
27 28 0.670546 GCAGAGCAAAGCCTACACGA 60.671 55.000 0.00 0.00 0.00 4.35
28 29 1.071605 CAGAGCAAAGCCTACACGAC 58.928 55.000 0.00 0.00 0.00 4.34
29 30 0.679505 AGAGCAAAGCCTACACGACA 59.320 50.000 0.00 0.00 0.00 4.35
30 31 1.276421 AGAGCAAAGCCTACACGACAT 59.724 47.619 0.00 0.00 0.00 3.06
31 32 1.394917 GAGCAAAGCCTACACGACATG 59.605 52.381 0.00 0.00 0.00 3.21
32 33 0.447801 GCAAAGCCTACACGACATGG 59.552 55.000 0.00 0.00 0.00 3.66
33 34 1.808411 CAAAGCCTACACGACATGGT 58.192 50.000 0.00 0.00 0.00 3.55
34 35 1.732259 CAAAGCCTACACGACATGGTC 59.268 52.381 0.00 0.00 0.00 4.02
35 36 0.973632 AAGCCTACACGACATGGTCA 59.026 50.000 0.00 0.00 32.09 4.02
36 37 0.973632 AGCCTACACGACATGGTCAA 59.026 50.000 0.00 0.00 32.09 3.18
37 38 1.555075 AGCCTACACGACATGGTCAAT 59.445 47.619 0.00 0.00 32.09 2.57
38 39 2.027192 AGCCTACACGACATGGTCAATT 60.027 45.455 0.00 0.00 32.09 2.32
39 40 2.351726 GCCTACACGACATGGTCAATTC 59.648 50.000 0.00 0.00 32.09 2.17
40 41 3.861840 CCTACACGACATGGTCAATTCT 58.138 45.455 0.00 0.00 32.09 2.40
41 42 3.618594 CCTACACGACATGGTCAATTCTG 59.381 47.826 0.00 0.00 32.09 3.02
42 43 1.806542 ACACGACATGGTCAATTCTGC 59.193 47.619 0.00 0.00 32.09 4.26
43 44 2.079158 CACGACATGGTCAATTCTGCT 58.921 47.619 0.00 0.00 32.09 4.24
44 45 2.094894 CACGACATGGTCAATTCTGCTC 59.905 50.000 0.00 0.00 32.09 4.26
45 46 1.325640 CGACATGGTCAATTCTGCTCG 59.674 52.381 0.00 0.00 32.09 5.03
46 47 2.350522 GACATGGTCAATTCTGCTCGT 58.649 47.619 0.00 0.00 32.09 4.18
47 48 2.744202 GACATGGTCAATTCTGCTCGTT 59.256 45.455 0.00 0.00 32.09 3.85
48 49 3.149196 ACATGGTCAATTCTGCTCGTTT 58.851 40.909 0.00 0.00 0.00 3.60
54 55 2.162208 TCAATTCTGCTCGTTTCATGGC 59.838 45.455 0.00 0.00 0.00 4.40
98 99 0.397564 TGTGAGAGTGGCAGATGCAA 59.602 50.000 7.19 0.00 44.36 4.08
146 147 2.259917 AGGTGAGACATGGTGATGTGA 58.740 47.619 0.00 0.00 43.22 3.58
155 156 3.827876 ACATGGTGATGTGAAGAATTGCA 59.172 39.130 0.00 0.00 41.52 4.08
183 184 2.216148 CCTTGAGGGAGCTACTGGG 58.784 63.158 0.00 0.00 37.23 4.45
184 185 0.618968 CCTTGAGGGAGCTACTGGGT 60.619 60.000 0.00 0.00 37.23 4.51
195 196 1.202770 GCTACTGGGTGTGTGGAAGTT 60.203 52.381 0.00 0.00 0.00 2.66
199 200 2.441750 ACTGGGTGTGTGGAAGTTACAT 59.558 45.455 0.00 0.00 0.00 2.29
205 206 6.213802 TGGGTGTGTGGAAGTTACATATCTAA 59.786 38.462 0.00 0.00 0.00 2.10
206 207 7.107542 GGGTGTGTGGAAGTTACATATCTAAA 58.892 38.462 0.00 0.00 0.00 1.85
207 208 7.773690 GGGTGTGTGGAAGTTACATATCTAAAT 59.226 37.037 0.00 0.00 0.00 1.40
222 223 8.270744 ACATATCTAAATGAGGAGCTCAAGTTT 58.729 33.333 17.19 12.43 44.04 2.66
250 251 1.207791 GGAGAGGAATCCTGGCTTGA 58.792 55.000 6.50 0.00 36.35 3.02
285 286 3.339547 CCTGTCCGGGTGTGAATTT 57.660 52.632 0.00 0.00 0.00 1.82
286 287 0.881118 CCTGTCCGGGTGTGAATTTG 59.119 55.000 0.00 0.00 0.00 2.32
287 288 0.240945 CTGTCCGGGTGTGAATTTGC 59.759 55.000 0.00 0.00 0.00 3.68
289 290 1.969064 TCCGGGTGTGAATTTGCGG 60.969 57.895 0.00 0.00 0.00 5.69
290 291 2.265182 CCGGGTGTGAATTTGCGGT 61.265 57.895 0.00 0.00 0.00 5.68
292 293 1.584495 GGGTGTGAATTTGCGGTCC 59.416 57.895 0.00 0.00 0.00 4.46
293 294 0.893727 GGGTGTGAATTTGCGGTCCT 60.894 55.000 0.00 0.00 0.00 3.85
294 295 0.240945 GGTGTGAATTTGCGGTCCTG 59.759 55.000 0.00 0.00 0.00 3.86
295 296 1.234821 GTGTGAATTTGCGGTCCTGA 58.765 50.000 0.00 0.00 0.00 3.86
296 297 1.812571 GTGTGAATTTGCGGTCCTGAT 59.187 47.619 0.00 0.00 0.00 2.90
297 298 3.006940 GTGTGAATTTGCGGTCCTGATA 58.993 45.455 0.00 0.00 0.00 2.15
300 301 2.238646 TGAATTTGCGGTCCTGATAGGT 59.761 45.455 0.00 0.00 36.53 3.08
426 427 8.999431 TGTTTGTATGATTTCTAGTCCTGTTTC 58.001 33.333 0.00 0.00 0.00 2.78
461 462 0.674895 AACTGATGCTCCTTCCACGC 60.675 55.000 0.00 0.00 0.00 5.34
481 482 5.850128 CACGCCTACTATATCTCGTTGTTAC 59.150 44.000 0.00 0.00 0.00 2.50
484 485 5.618640 GCCTACTATATCTCGTTGTTACCGG 60.619 48.000 0.00 0.00 0.00 5.28
488 489 2.358939 ATCTCGTTGTTACCGGTGAC 57.641 50.000 21.91 21.91 0.00 3.67
540 541 2.425668 GTGTAGGTGTTTGCAGGTGTTT 59.574 45.455 0.00 0.00 0.00 2.83
552 553 3.010420 GCAGGTGTTTCCATCTCTTACC 58.990 50.000 0.00 0.00 39.02 2.85
559 560 5.125097 GTGTTTCCATCTCTTACCGTCTAGA 59.875 44.000 0.00 0.00 0.00 2.43
594 989 1.493772 TACAGGTCGTTTTGCGTCTG 58.506 50.000 0.00 0.00 42.99 3.51
600 995 0.653636 TCGTTTTGCGTCTGGTTGTC 59.346 50.000 0.00 0.00 42.13 3.18
612 1007 4.260784 CGTCTGGTTGTCCTTCTTCTTTTG 60.261 45.833 0.00 0.00 34.23 2.44
708 1104 9.305925 CACAAAAATAGAAAAGGAATATGGAGC 57.694 33.333 0.00 0.00 0.00 4.70
715 1111 9.881773 ATAGAAAAGGAATATGGAGCCAATAAA 57.118 29.630 0.00 0.00 0.00 1.40
716 1112 8.608185 AGAAAAGGAATATGGAGCCAATAAAA 57.392 30.769 0.00 0.00 0.00 1.52
1098 1494 3.650950 GAGGGGGCCAAGAGTGCA 61.651 66.667 4.39 0.00 0.00 4.57
1158 1554 2.472029 GAGGAGGTGAGATTTGAGGGA 58.528 52.381 0.00 0.00 0.00 4.20
1272 1668 1.504275 AAGATGCAAGTGAGGGGGCT 61.504 55.000 0.00 0.00 0.00 5.19
1438 1837 1.895707 GATGCTTCCCTGCCATCCG 60.896 63.158 0.00 0.00 0.00 4.18
1498 1897 0.035458 CGAACCAGAGGAAAGTGCCT 59.965 55.000 0.00 0.00 42.17 4.75
1620 2019 4.630644 AGATGATGGTGAGTTTGACAGT 57.369 40.909 0.00 0.00 0.00 3.55
1745 2144 2.113986 GCCTGCTGAGTTGGTGGT 59.886 61.111 0.00 0.00 0.00 4.16
1866 2265 2.239907 GGTAAGTGGGCCTCTTCAATCT 59.760 50.000 23.11 2.37 0.00 2.40
1871 2270 3.782523 AGTGGGCCTCTTCAATCTGATAA 59.217 43.478 4.53 0.00 0.00 1.75
1938 2337 3.164268 TCAAATGACCCAATCCAGGTTG 58.836 45.455 0.00 0.00 37.88 3.77
1946 2345 1.679944 CCAATCCAGGTTGCTGACGAT 60.680 52.381 0.00 0.00 0.00 3.73
1955 2354 1.017177 TTGCTGACGATGGTAACCGC 61.017 55.000 0.00 0.00 0.00 5.68
2021 2420 1.882352 GCAACTCCAGTGGTAAGTGGG 60.882 57.143 9.54 4.10 45.77 4.61
2032 2431 3.311596 GTGGTAAGTGGGCATATTCGTTC 59.688 47.826 0.00 0.00 0.00 3.95
2102 2503 4.808558 TCAAATGTAATGAAGCAGGTTGC 58.191 39.130 0.00 0.00 45.46 4.17
2206 2607 4.016444 GGAGAACCATGCTAATGTGGAAA 58.984 43.478 0.00 0.00 38.86 3.13
2248 2649 1.031571 GGTGAATGATGCAAGCCCGA 61.032 55.000 0.00 0.00 0.00 5.14
2359 2760 3.632145 CCAGGTTATTGACAATGGTAGCC 59.368 47.826 11.05 2.84 33.93 3.93
2390 2791 4.141528 CCAGGCTAATGAGAAAGATGAGGT 60.142 45.833 0.00 0.00 0.00 3.85
2391 2792 5.435291 CAGGCTAATGAGAAAGATGAGGTT 58.565 41.667 0.00 0.00 0.00 3.50
2446 2847 5.129485 CCTGAGGTAAGTGGTCATGTTCTAT 59.871 44.000 0.00 0.00 0.00 1.98
2451 2852 8.375493 AGGTAAGTGGTCATGTTCTATCTAAA 57.625 34.615 0.00 0.00 0.00 1.85
2484 2885 9.326413 GCTAGTAGTGTTAACATTAATGTGGAT 57.674 33.333 21.46 9.00 41.61 3.41
2538 2939 5.215252 ACCAGGTTATCGATGACATTAGG 57.785 43.478 20.44 14.37 0.00 2.69
2705 3106 0.318955 GTTGTTGCTGGTGGTGATGC 60.319 55.000 0.00 0.00 0.00 3.91
2840 3241 1.625315 TGAGATAGTTGTGGCTGCAGT 59.375 47.619 16.64 0.00 0.00 4.40
3201 3632 5.105187 TGTTCTTGATGATTCTGAGGACGAT 60.105 40.000 0.00 0.00 0.00 3.73
3240 3671 3.662078 TGAGGATGATGATGAGAAGGGT 58.338 45.455 0.00 0.00 0.00 4.34
3243 3674 5.044624 TGAGGATGATGATGAGAAGGGTTTT 60.045 40.000 0.00 0.00 0.00 2.43
3246 3677 5.067023 GGATGATGATGAGAAGGGTTTTGAC 59.933 44.000 0.00 0.00 0.00 3.18
3258 3689 2.884639 GGGTTTTGACTCTGCTGCTTTA 59.115 45.455 0.00 0.00 0.00 1.85
3369 3800 4.106925 CCTGCTGGTCTGGGCTCC 62.107 72.222 0.51 0.00 0.00 4.70
3648 4079 2.225255 GACAAACAGAGCTTTCAGCCTC 59.775 50.000 0.00 0.00 43.77 4.70
3654 4085 1.830477 AGAGCTTTCAGCCTCGAGAAT 59.170 47.619 15.71 0.00 43.77 2.40
4140 4571 1.729586 ACGGTGCCCCTATGACATAT 58.270 50.000 0.00 0.00 0.00 1.78
4404 4835 3.195041 GAAGCTTTTTGGGTTCCGC 57.805 52.632 0.00 0.00 37.64 5.54
4464 4895 1.372683 GCAGTCAAGAGCTCACCCA 59.627 57.895 17.77 0.00 0.00 4.51
4662 5093 7.194112 TGATGAGTATGATTACAGGGTCAAA 57.806 36.000 0.00 0.00 0.00 2.69
4749 5180 4.841422 AGTCTGATATGGATGCTTATGGC 58.159 43.478 0.00 0.00 42.22 4.40
4767 5198 1.546476 GGCTATGCTAGTATCGCAGGT 59.454 52.381 17.02 0.00 41.22 4.00
4773 5204 4.137116 TGCTAGTATCGCAGGTGAAAAT 57.863 40.909 0.00 0.00 32.80 1.82
4869 5300 1.392589 ATCCGACATACCGTTACCGT 58.607 50.000 0.00 0.00 0.00 4.83
4950 5381 2.773661 TCATGACTGTGGCTATGATGGT 59.226 45.455 0.00 0.00 0.00 3.55
5163 5594 3.839051 GGTGAGACCAAATTCAAGAGC 57.161 47.619 0.00 0.00 38.42 4.09
5220 5651 4.819630 GTGACTTTCTTGGGTGACATTGTA 59.180 41.667 0.00 0.00 0.00 2.41
5313 5744 0.975556 TGCGAGCTCAAGGGGATACA 60.976 55.000 15.40 0.00 39.74 2.29
5337 5768 1.792757 ATGGAGCCAACCTGGAAGCA 61.793 55.000 0.00 0.00 40.96 3.91
5556 5987 3.120105 CAGGTCCAGATCGCGCTA 58.880 61.111 5.56 0.00 0.00 4.26
5565 5996 0.179026 AGATCGCGCTACTGGGTCTA 60.179 55.000 5.56 0.00 0.00 2.59
5590 6021 3.234353 CCAGTGATAGCCTCCATCTACA 58.766 50.000 0.00 0.00 0.00 2.74
5910 6341 5.505324 GCATGATGAGGAAATAAGCACTGTC 60.505 44.000 0.00 0.00 0.00 3.51
5984 6451 2.152016 GAGTACCAACCCAGAACTTGC 58.848 52.381 0.00 0.00 0.00 4.01
6030 6499 6.816136 TCACTCTCTTCACAAATGTAAGACA 58.184 36.000 0.00 0.00 0.00 3.41
6106 6584 5.479306 TGAATCTCAGGTAGTGTTACTTGC 58.521 41.667 0.00 0.00 36.95 4.01
6109 6587 5.640189 TCTCAGGTAGTGTTACTTGCTAC 57.360 43.478 0.00 0.00 36.95 3.58
6151 6629 0.736636 TCCACTATACCGACTGTGCG 59.263 55.000 0.00 0.00 0.00 5.34
6174 6652 7.389330 TGCGGTTTTTGAGTATGAGAAAATAGA 59.611 33.333 0.00 0.00 0.00 1.98
6176 6654 8.717821 CGGTTTTTGAGTATGAGAAAATAGACA 58.282 33.333 0.00 0.00 0.00 3.41
6229 6730 1.186200 CAGGTGGATCCTCGTCTGAA 58.814 55.000 14.23 0.00 46.24 3.02
6233 6734 2.338500 GTGGATCCTCGTCTGAACAAC 58.662 52.381 14.23 0.00 0.00 3.32
6251 6752 5.543507 ACAACAAAAGATGCAAACCCATA 57.456 34.783 0.00 0.00 0.00 2.74
6338 6840 5.366752 GTCTGACGAAGAAATTTCAGTTCG 58.633 41.667 27.56 27.56 45.66 3.95
6339 6841 4.447724 TCTGACGAAGAAATTTCAGTTCGG 59.552 41.667 30.16 20.57 44.72 4.30
6373 6875 6.591935 TGGATTTGGATTACTGATACCTGTC 58.408 40.000 0.00 0.00 0.00 3.51
6380 6882 5.010820 GGATTACTGATACCTGTCACCCTAC 59.989 48.000 0.00 0.00 0.00 3.18
6404 6906 3.065786 TGTTTCTGCAGTTCTGCTTTCTG 59.934 43.478 22.44 9.88 35.49 3.02
6417 6919 4.397103 TCTGCTTTCTGCTGGTGATTATTG 59.603 41.667 0.00 0.00 43.37 1.90
6435 6937 6.824958 TTATTGACTATTACCTGGCTCCTT 57.175 37.500 0.00 0.00 0.00 3.36
6463 6965 2.281140 TGCATTGCATTTCGATGGTG 57.719 45.000 7.38 0.00 37.11 4.17
6464 6966 1.817447 TGCATTGCATTTCGATGGTGA 59.183 42.857 7.38 0.00 37.11 4.02
6465 6967 2.427812 TGCATTGCATTTCGATGGTGAT 59.572 40.909 7.38 0.00 37.11 3.06
6466 6968 3.119065 TGCATTGCATTTCGATGGTGATT 60.119 39.130 7.38 0.00 37.11 2.57
6467 6969 3.866910 GCATTGCATTTCGATGGTGATTT 59.133 39.130 3.15 0.00 37.11 2.17
6468 6970 4.330620 GCATTGCATTTCGATGGTGATTTT 59.669 37.500 3.15 0.00 37.11 1.82
6469 6971 5.163834 GCATTGCATTTCGATGGTGATTTTT 60.164 36.000 3.15 0.00 37.11 1.94
6470 6972 6.471839 CATTGCATTTCGATGGTGATTTTTC 58.528 36.000 0.00 0.00 33.72 2.29
6471 6973 5.389859 TGCATTTCGATGGTGATTTTTCT 57.610 34.783 0.00 0.00 0.00 2.52
6472 6974 5.162794 TGCATTTCGATGGTGATTTTTCTG 58.837 37.500 0.00 0.00 0.00 3.02
6473 6975 5.163513 GCATTTCGATGGTGATTTTTCTGT 58.836 37.500 0.00 0.00 0.00 3.41
6475 6977 6.974622 GCATTTCGATGGTGATTTTTCTGTAT 59.025 34.615 0.00 0.00 0.00 2.29
6476 6978 7.043854 GCATTTCGATGGTGATTTTTCTGTATG 60.044 37.037 0.00 0.00 0.00 2.39
6477 6979 7.447374 TTTCGATGGTGATTTTTCTGTATGT 57.553 32.000 0.00 0.00 0.00 2.29
6478 6980 7.447374 TTCGATGGTGATTTTTCTGTATGTT 57.553 32.000 0.00 0.00 0.00 2.71
6479 6981 6.841119 TCGATGGTGATTTTTCTGTATGTTG 58.159 36.000 0.00 0.00 0.00 3.33
6480 6982 6.652900 TCGATGGTGATTTTTCTGTATGTTGA 59.347 34.615 0.00 0.00 0.00 3.18
6481 6983 7.174080 TCGATGGTGATTTTTCTGTATGTTGAA 59.826 33.333 0.00 0.00 0.00 2.69
6482 6984 7.271223 CGATGGTGATTTTTCTGTATGTTGAAC 59.729 37.037 0.00 0.00 0.00 3.18
6483 6985 6.434596 TGGTGATTTTTCTGTATGTTGAACG 58.565 36.000 0.00 0.00 0.00 3.95
6485 6987 6.577427 GGTGATTTTTCTGTATGTTGAACGTC 59.423 38.462 0.00 0.00 0.00 4.34
6549 7414 2.548057 TGTGGATTCAGTTTGAAGTCGC 59.452 45.455 0.00 0.76 40.05 5.19
6560 7425 2.432206 TGAAGTCGCGTGAGAATTGA 57.568 45.000 5.77 0.00 0.00 2.57
6573 7438 5.174761 CGTGAGAATTGAGAATCCGATCTTC 59.825 44.000 0.00 0.00 0.00 2.87
6574 7439 6.279882 GTGAGAATTGAGAATCCGATCTTCT 58.720 40.000 0.00 0.00 35.69 2.85
6626 7491 8.129840 AGTTAGTACTGATAGTATGCTGAAACG 58.870 37.037 5.39 0.00 32.65 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.130160 CTTTGCTCTGCGGCCTCC 61.130 66.667 0.00 0.00 0.00 4.30
4 5 3.976701 TAGGCTTTGCTCTGCGGCC 62.977 63.158 0.00 0.00 39.89 6.13
5 6 2.436646 TAGGCTTTGCTCTGCGGC 60.437 61.111 0.00 0.00 0.00 6.53
6 7 1.375908 TGTAGGCTTTGCTCTGCGG 60.376 57.895 0.00 0.00 0.00 5.69
7 8 1.790387 GTGTAGGCTTTGCTCTGCG 59.210 57.895 0.00 0.00 0.00 5.18
8 9 0.670546 TCGTGTAGGCTTTGCTCTGC 60.671 55.000 0.00 0.00 0.00 4.26
9 10 1.071605 GTCGTGTAGGCTTTGCTCTG 58.928 55.000 0.00 0.00 0.00 3.35
10 11 0.679505 TGTCGTGTAGGCTTTGCTCT 59.320 50.000 0.00 0.00 0.00 4.09
11 12 1.394917 CATGTCGTGTAGGCTTTGCTC 59.605 52.381 0.00 0.00 0.00 4.26
12 13 1.442769 CATGTCGTGTAGGCTTTGCT 58.557 50.000 0.00 0.00 0.00 3.91
13 14 0.447801 CCATGTCGTGTAGGCTTTGC 59.552 55.000 0.00 0.00 0.00 3.68
14 15 1.732259 GACCATGTCGTGTAGGCTTTG 59.268 52.381 0.00 0.00 0.00 2.77
15 16 1.346395 TGACCATGTCGTGTAGGCTTT 59.654 47.619 0.00 0.00 34.95 3.51
16 17 0.973632 TGACCATGTCGTGTAGGCTT 59.026 50.000 0.00 0.00 34.95 4.35
17 18 0.973632 TTGACCATGTCGTGTAGGCT 59.026 50.000 0.00 0.00 34.95 4.58
18 19 2.024176 ATTGACCATGTCGTGTAGGC 57.976 50.000 0.00 0.00 34.95 3.93
19 20 3.618594 CAGAATTGACCATGTCGTGTAGG 59.381 47.826 0.00 0.00 34.95 3.18
20 21 3.062639 GCAGAATTGACCATGTCGTGTAG 59.937 47.826 0.00 0.00 34.95 2.74
21 22 3.000041 GCAGAATTGACCATGTCGTGTA 59.000 45.455 0.00 0.00 34.95 2.90
22 23 1.806542 GCAGAATTGACCATGTCGTGT 59.193 47.619 0.00 0.00 34.95 4.49
23 24 2.079158 AGCAGAATTGACCATGTCGTG 58.921 47.619 0.00 0.00 34.95 4.35
24 25 2.350522 GAGCAGAATTGACCATGTCGT 58.649 47.619 0.00 0.00 34.95 4.34
25 26 1.325640 CGAGCAGAATTGACCATGTCG 59.674 52.381 0.00 0.00 34.95 4.35
26 27 2.350522 ACGAGCAGAATTGACCATGTC 58.649 47.619 0.00 0.00 0.00 3.06
27 28 2.479566 ACGAGCAGAATTGACCATGT 57.520 45.000 0.00 0.00 0.00 3.21
28 29 3.189080 TGAAACGAGCAGAATTGACCATG 59.811 43.478 0.00 0.00 0.00 3.66
29 30 3.411446 TGAAACGAGCAGAATTGACCAT 58.589 40.909 0.00 0.00 0.00 3.55
30 31 2.844946 TGAAACGAGCAGAATTGACCA 58.155 42.857 0.00 0.00 0.00 4.02
31 32 3.426695 CCATGAAACGAGCAGAATTGACC 60.427 47.826 0.00 0.00 0.00 4.02
32 33 3.751621 CCATGAAACGAGCAGAATTGAC 58.248 45.455 0.00 0.00 0.00 3.18
33 34 2.162208 GCCATGAAACGAGCAGAATTGA 59.838 45.455 0.00 0.00 0.00 2.57
34 35 2.523015 GCCATGAAACGAGCAGAATTG 58.477 47.619 0.00 0.00 0.00 2.32
35 36 1.131126 CGCCATGAAACGAGCAGAATT 59.869 47.619 0.00 0.00 0.00 2.17
36 37 0.729116 CGCCATGAAACGAGCAGAAT 59.271 50.000 0.00 0.00 0.00 2.40
37 38 0.320334 TCGCCATGAAACGAGCAGAA 60.320 50.000 0.00 0.00 33.69 3.02
38 39 0.320334 TTCGCCATGAAACGAGCAGA 60.320 50.000 0.00 0.00 39.81 4.26
39 40 0.179215 GTTCGCCATGAAACGAGCAG 60.179 55.000 12.27 0.00 39.81 4.24
40 41 1.866237 GTTCGCCATGAAACGAGCA 59.134 52.632 12.27 0.00 39.81 4.26
41 42 1.225745 CGTTCGCCATGAAACGAGC 60.226 57.895 17.55 13.16 39.81 5.03
42 43 0.999406 ATCGTTCGCCATGAAACGAG 59.001 50.000 24.41 9.69 40.64 4.18
43 44 0.718904 CATCGTTCGCCATGAAACGA 59.281 50.000 23.34 23.34 41.13 3.85
44 45 0.247655 CCATCGTTCGCCATGAAACG 60.248 55.000 16.78 16.78 38.60 3.60
45 46 0.802494 ACCATCGTTCGCCATGAAAC 59.198 50.000 0.00 0.00 38.60 2.78
46 47 0.801872 CACCATCGTTCGCCATGAAA 59.198 50.000 0.00 0.00 38.60 2.69
47 48 1.024046 CCACCATCGTTCGCCATGAA 61.024 55.000 0.00 0.00 0.00 2.57
48 49 1.449423 CCACCATCGTTCGCCATGA 60.449 57.895 0.00 0.00 0.00 3.07
54 55 3.039202 GCAAGCCCACCATCGTTCG 62.039 63.158 0.00 0.00 0.00 3.95
98 99 4.681978 GCACCTCGTCGCACCCTT 62.682 66.667 0.00 0.00 0.00 3.95
109 110 4.517285 TCACCTTCAAATCATAGCACCTC 58.483 43.478 0.00 0.00 0.00 3.85
168 169 0.904865 CACACCCAGTAGCTCCCTCA 60.905 60.000 0.00 0.00 0.00 3.86
179 180 2.631160 TGTAACTTCCACACACCCAG 57.369 50.000 0.00 0.00 0.00 4.45
183 184 9.378551 TCATTTAGATATGTAACTTCCACACAC 57.621 33.333 0.00 0.00 0.00 3.82
184 185 9.599866 CTCATTTAGATATGTAACTTCCACACA 57.400 33.333 0.00 0.00 0.00 3.72
195 196 8.484214 ACTTGAGCTCCTCATTTAGATATGTA 57.516 34.615 12.15 0.00 40.39 2.29
199 200 9.823647 CTTAAACTTGAGCTCCTCATTTAGATA 57.176 33.333 12.15 0.00 40.39 1.98
205 206 4.013050 GCCTTAAACTTGAGCTCCTCATT 58.987 43.478 12.15 4.30 40.39 2.57
206 207 3.615155 GCCTTAAACTTGAGCTCCTCAT 58.385 45.455 12.15 0.00 40.39 2.90
207 208 2.290323 GGCCTTAAACTTGAGCTCCTCA 60.290 50.000 12.15 0.00 38.87 3.86
222 223 1.705873 GATTCCTCTCCTCGGCCTTA 58.294 55.000 0.00 0.00 0.00 2.69
243 244 2.844451 GCAACACGCCTTCAAGCCA 61.844 57.895 0.00 0.00 32.94 4.75
269 270 1.511318 CGCAAATTCACACCCGGACA 61.511 55.000 0.73 0.00 0.00 4.02
271 272 1.969064 CCGCAAATTCACACCCGGA 60.969 57.895 0.73 0.00 38.04 5.14
285 286 3.521605 CGACCTATCAGGACCGCA 58.478 61.111 0.00 0.00 37.67 5.69
286 287 2.027751 GCGACCTATCAGGACCGC 59.972 66.667 16.17 16.17 46.32 5.68
287 288 1.360551 CAGCGACCTATCAGGACCG 59.639 63.158 0.00 3.66 37.67 4.79
289 290 1.742768 CCCAGCGACCTATCAGGAC 59.257 63.158 0.00 0.00 37.67 3.85
290 291 2.134287 GCCCAGCGACCTATCAGGA 61.134 63.158 0.00 0.00 37.67 3.86
414 415 9.449719 ACCAATTTATAACAGAAACAGGACTAG 57.550 33.333 0.00 0.00 0.00 2.57
415 416 9.444600 GACCAATTTATAACAGAAACAGGACTA 57.555 33.333 0.00 0.00 0.00 2.59
426 427 7.765307 AGCATCAGTTGACCAATTTATAACAG 58.235 34.615 0.00 0.00 0.00 3.16
461 462 5.471456 ACCGGTAACAACGAGATATAGTAGG 59.529 44.000 4.49 0.00 0.00 3.18
481 482 2.173669 CGCAATAGCCAGTCACCGG 61.174 63.158 0.00 0.00 37.52 5.28
484 485 0.108138 AGACCGCAATAGCCAGTCAC 60.108 55.000 7.68 0.00 40.93 3.67
488 489 1.737838 TTGAAGACCGCAATAGCCAG 58.262 50.000 0.00 0.00 37.52 4.85
540 541 3.884091 GCTTCTAGACGGTAAGAGATGGA 59.116 47.826 0.00 0.00 0.00 3.41
594 989 5.469084 ACGATACAAAAGAAGAAGGACAACC 59.531 40.000 0.00 0.00 0.00 3.77
600 995 6.204882 ACAGGAAACGATACAAAAGAAGAAGG 59.795 38.462 0.00 0.00 0.00 3.46
631 1026 9.836864 TGTAGAAAGTGCATCAGATATTTATGT 57.163 29.630 0.00 0.00 0.00 2.29
669 1065 7.164230 TCTATTTTTGTGTTCTGTGTTTGGT 57.836 32.000 0.00 0.00 0.00 3.67
684 1080 8.477256 TGGCTCCATATTCCTTTTCTATTTTTG 58.523 33.333 0.00 0.00 0.00 2.44
685 1081 8.608185 TGGCTCCATATTCCTTTTCTATTTTT 57.392 30.769 0.00 0.00 0.00 1.94
1158 1554 2.105993 ACCAGTAAAGCTCCGGTCTTTT 59.894 45.455 22.49 14.31 35.58 2.27
1272 1668 2.003830 TCCTCCTCCTTCTCTTCTCCA 58.996 52.381 0.00 0.00 0.00 3.86
1438 1837 2.176273 CACCTACCAGCGCATCAGC 61.176 63.158 11.47 0.00 37.42 4.26
1498 1897 2.106511 CCACTTCCTTCACCTCCAAAGA 59.893 50.000 0.00 0.00 0.00 2.52
1508 1907 0.817634 CACGTTGCCCACTTCCTTCA 60.818 55.000 0.00 0.00 0.00 3.02
1536 1935 1.266178 TCTCCTCGGACAATTCAGCA 58.734 50.000 0.00 0.00 0.00 4.41
1620 2019 2.263540 GCCGTAACCGCCTTCTCA 59.736 61.111 0.00 0.00 0.00 3.27
1706 2105 0.467290 TTCAGCCTCACCACCCAAAC 60.467 55.000 0.00 0.00 0.00 2.93
1745 2144 0.768221 AGCTTCTTCACCTCCCACCA 60.768 55.000 0.00 0.00 0.00 4.17
1820 2219 1.129437 GACTTGCATCGCTTTCAGGTC 59.871 52.381 0.00 0.00 31.46 3.85
1938 2337 2.514013 CGCGGTTACCATCGTCAGC 61.514 63.158 1.13 0.00 0.00 4.26
1946 2345 1.004320 AACATCAGCGCGGTTACCA 60.004 52.632 8.73 0.00 0.00 3.25
1955 2354 0.994995 CCTCGTCTTCAACATCAGCG 59.005 55.000 0.00 0.00 0.00 5.18
2021 2420 7.988904 AGTAACAGAACTAGAACGAATATGC 57.011 36.000 0.00 0.00 0.00 3.14
2032 2431 8.350722 TGTCAAGACAACTAGTAACAGAACTAG 58.649 37.037 9.02 9.02 43.72 2.57
2248 2649 3.719268 TTGAGCATGTCCACTTACCAT 57.281 42.857 0.00 0.00 0.00 3.55
2390 2791 3.063704 CTGGCTCGGGCATTGCAA 61.064 61.111 10.74 0.00 40.87 4.08
2391 2792 3.565961 TTCTGGCTCGGGCATTGCA 62.566 57.895 10.74 0.00 40.87 4.08
2424 2825 5.958380 AGATAGAACATGACCACTTACCTCA 59.042 40.000 0.00 0.00 0.00 3.86
2484 2885 9.026121 TCGTTTGAATTCTTTATATCCCCAAAA 57.974 29.630 7.05 0.00 0.00 2.44
2485 2886 8.582657 TCGTTTGAATTCTTTATATCCCCAAA 57.417 30.769 7.05 0.00 0.00 3.28
2508 2909 4.157840 TCATCGATAACCTGGTATGGATCG 59.842 45.833 19.23 19.23 36.07 3.69
2538 2939 1.149148 GCTTCACCAAACTCTCCGAC 58.851 55.000 0.00 0.00 0.00 4.79
2574 2975 1.664151 CTTTCGGTAAGCGGAACATCC 59.336 52.381 0.00 0.00 34.38 3.51
2705 3106 4.177026 CAACTCCCGAGACAAGATAACAG 58.823 47.826 0.00 0.00 0.00 3.16
2977 3408 3.203040 CCCTCATTACCACTCCCATCTTT 59.797 47.826 0.00 0.00 0.00 2.52
3045 3476 6.041423 TCAGAGTTCTCTATGATTGCAACA 57.959 37.500 0.00 2.38 37.06 3.33
3201 3632 4.518970 TCCTCATTATCGTCGTCATCATCA 59.481 41.667 0.00 0.00 0.00 3.07
3258 3689 0.107654 CCGCTTTTAGTAGGGCAGCT 60.108 55.000 0.00 0.00 0.00 4.24
3324 3755 3.129287 CCATGGAAAAGATTCTGGAACCG 59.871 47.826 5.56 0.00 34.39 4.44
3369 3800 3.506108 CGCAAAGATGGGGCTGAG 58.494 61.111 0.00 0.00 35.94 3.35
3564 3995 0.514691 GCACTTGTGCTGCTACTGTC 59.485 55.000 17.36 0.00 0.00 3.51
3648 4079 1.201965 GCTTTCTTCCGTGCATTCTCG 60.202 52.381 0.00 0.00 0.00 4.04
3654 4085 2.330254 CAAGGCTTTCTTCCGTGCA 58.670 52.632 0.00 0.00 32.41 4.57
4140 4571 1.743431 CGCTGTGCCATCAATACCTCA 60.743 52.381 0.00 0.00 0.00 3.86
4641 5072 6.620877 AGTTTGACCCTGTAATCATACTCA 57.379 37.500 0.00 0.00 33.50 3.41
4749 5180 4.505313 TTCACCTGCGATACTAGCATAG 57.495 45.455 0.00 0.00 44.26 2.23
4869 5300 4.165372 ACAGTAGAGGTTGGTTCCAGAAAA 59.835 41.667 0.00 0.00 0.00 2.29
5163 5594 4.214971 CCAGTGGTCTTGTTCTTCTTGATG 59.785 45.833 0.00 0.00 0.00 3.07
5220 5651 1.073897 GACCTTCAGCCCAGTTGCT 59.926 57.895 0.00 0.00 44.00 3.91
5337 5768 7.681939 TGGATAATCTTTGTCTTTTAAGCGT 57.318 32.000 0.00 0.00 0.00 5.07
5436 5867 1.550524 CCAATCGAGAACTGGGACTGA 59.449 52.381 0.00 0.00 0.00 3.41
5565 5996 0.339859 TGGAGGCTATCACTGGGACT 59.660 55.000 0.00 0.00 0.00 3.85
5657 6088 6.330004 TGCTAACACAACACATTGATGATT 57.670 33.333 0.00 0.00 39.30 2.57
5658 6089 5.963176 TGCTAACACAACACATTGATGAT 57.037 34.783 0.00 0.00 39.30 2.45
5664 6095 6.581712 AGGAAAATTGCTAACACAACACATT 58.418 32.000 0.00 0.00 31.03 2.71
5848 6279 0.238289 GATGGACAGCAACAACGGTG 59.762 55.000 0.00 0.00 40.25 4.94
5984 6451 6.374613 GTGAGTACCTCCCTTCCAAAATAAAG 59.625 42.308 0.00 0.00 0.00 1.85
6030 6499 6.418946 TCCCTTTGTTTAAAACTGCCAAAAT 58.581 32.000 0.00 0.00 0.00 1.82
6084 6562 5.725362 AGCAAGTAACACTACCTGAGATTC 58.275 41.667 0.00 0.00 0.00 2.52
6106 6584 4.614555 TTAAGCATGATTGTTGCCGTAG 57.385 40.909 6.43 0.00 41.06 3.51
6109 6587 6.005583 AGATATTAAGCATGATTGTTGCCG 57.994 37.500 6.43 0.00 41.06 5.69
6229 6730 3.902881 TGGGTTTGCATCTTTTGTTGT 57.097 38.095 0.00 0.00 0.00 3.32
6233 6734 6.480981 GGATCATTATGGGTTTGCATCTTTTG 59.519 38.462 0.00 0.00 0.00 2.44
6251 6752 9.656323 TTATAGAACTACTGTACCAGGATCATT 57.344 33.333 0.00 0.00 35.51 2.57
6338 6840 7.384932 CAGTAATCCAAATCCAAAGTTTGAACC 59.615 37.037 17.33 0.00 38.51 3.62
6339 6841 8.141268 TCAGTAATCCAAATCCAAAGTTTGAAC 58.859 33.333 17.33 0.39 38.51 3.18
6373 6875 2.783135 ACTGCAGAAACATGTAGGGTG 58.217 47.619 23.35 0.00 37.24 4.61
6404 6906 6.428159 CCAGGTAATAGTCAATAATCACCAGC 59.572 42.308 0.00 0.00 0.00 4.85
6417 6919 6.231951 GGATTTAAGGAGCCAGGTAATAGTC 58.768 44.000 0.00 0.00 0.00 2.59
6453 6955 7.447374 ACATACAGAAAAATCACCATCGAAA 57.553 32.000 0.00 0.00 0.00 3.46
6455 6957 6.652900 TCAACATACAGAAAAATCACCATCGA 59.347 34.615 0.00 0.00 0.00 3.59
6456 6958 6.841119 TCAACATACAGAAAAATCACCATCG 58.159 36.000 0.00 0.00 0.00 3.84
6457 6959 7.271223 CGTTCAACATACAGAAAAATCACCATC 59.729 37.037 0.00 0.00 0.00 3.51
6458 6960 7.083858 CGTTCAACATACAGAAAAATCACCAT 58.916 34.615 0.00 0.00 0.00 3.55
6459 6961 6.038825 ACGTTCAACATACAGAAAAATCACCA 59.961 34.615 0.00 0.00 0.00 4.17
6460 6962 6.435428 ACGTTCAACATACAGAAAAATCACC 58.565 36.000 0.00 0.00 0.00 4.02
6461 6963 7.129622 TGACGTTCAACATACAGAAAAATCAC 58.870 34.615 0.00 0.00 0.00 3.06
6462 6964 7.252965 TGACGTTCAACATACAGAAAAATCA 57.747 32.000 0.00 0.00 0.00 2.57
6477 6979 9.932699 TTCGAATAAATTTTAGTTGACGTTCAA 57.067 25.926 6.14 0.00 33.32 2.69
6478 6980 9.932699 TTTCGAATAAATTTTAGTTGACGTTCA 57.067 25.926 0.00 0.00 0.00 3.18
6505 7096 8.973378 CACACGGTTTCAACATATTTACAAAAT 58.027 29.630 0.00 0.00 0.00 1.82
6506 7097 7.435488 CCACACGGTTTCAACATATTTACAAAA 59.565 33.333 0.00 0.00 0.00 2.44
6510 7101 6.243811 TCCACACGGTTTCAACATATTTAC 57.756 37.500 0.00 0.00 0.00 2.01
6517 7108 2.616376 CTGAATCCACACGGTTTCAACA 59.384 45.455 6.48 0.00 45.89 3.33
6521 7112 3.314080 TCAAACTGAATCCACACGGTTTC 59.686 43.478 0.00 0.00 41.62 2.78
6522 7113 3.283751 TCAAACTGAATCCACACGGTTT 58.716 40.909 0.00 0.00 43.45 3.27
6523 7114 2.925724 TCAAACTGAATCCACACGGTT 58.074 42.857 0.00 0.00 37.22 4.44
6524 7115 2.631160 TCAAACTGAATCCACACGGT 57.369 45.000 0.00 0.00 0.00 4.83
6525 7116 2.878406 ACTTCAAACTGAATCCACACGG 59.122 45.455 0.00 0.00 35.59 4.94
6526 7117 3.362986 CGACTTCAAACTGAATCCACACG 60.363 47.826 0.00 0.00 35.59 4.49
6527 7118 3.607078 GCGACTTCAAACTGAATCCACAC 60.607 47.826 0.00 0.00 35.59 3.82
6528 7119 2.548057 GCGACTTCAAACTGAATCCACA 59.452 45.455 0.00 0.00 35.59 4.17
6549 7414 4.615949 AGATCGGATTCTCAATTCTCACG 58.384 43.478 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.