Multiple sequence alignment - TraesCS4D01G193600

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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 TraesCS4D01G193600 chr4D 100.000 5646 0 0 1 5646 336848300 336842655 0.000000e+00 10427
1 TraesCS4D01G193600 chr4A 92.583 5595 233 72 3 5482 136610581 136616108 0.000000e+00 7866
2 TraesCS4D01G193600 chr4A 96.970 66 1 1 5582 5646 136616159 136616224 5.980000e-20 110
3 TraesCS4D01G193600 chr4B 94.849 3339 121 24 3 3301 415129312 415125985 0.000000e+00 5166
4 TraesCS4D01G193600 chr4B 92.659 2016 85 22 3345 5314 415125976 415123978 0.000000e+00 2844


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 TraesCS4D01G193600 chr4D 336842655 336848300 5645 True 10427 10427 100.0000 1 5646 1 chr4D.!!$R1 5645
1 TraesCS4D01G193600 chr4A 136610581 136616224 5643 False 3988 7866 94.7765 3 5646 2 chr4A.!!$F1 5643
2 TraesCS4D01G193600 chr4B 415123978 415129312 5334 True 4005 5166 93.7540 3 5314 2 chr4B.!!$R1 5311

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
852 892 0.731174 GCATTAACCAACCAACCGCG 60.731 55.000 0.0 0.0 0.00 6.46 F
1305 1350 2.046314 CTTCGCCCCGTTGACCAT 60.046 61.111 0.0 0.0 0.00 3.55 F
1977 2031 1.221840 CTTCCCTCCGGACACCATG 59.778 63.158 0.0 0.0 38.14 3.66 F
2787 2841 0.034896 CGTGGTTCTACCTTGTGGCT 59.965 55.000 0.0 0.0 39.58 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1800 3.328931 ACCACAAGTCATTGGTCTCATCT 59.671 43.478 0.00 0.00 42.86 2.90 R
2787 2841 3.706373 GCAGCCTCGAAGTCCCCA 61.706 66.667 0.00 0.00 0.00 4.96 R
3602 3680 0.099082 CGACGTCAAGGCTAGAGTCC 59.901 60.000 17.16 0.00 0.00 3.85 R
4766 4883 1.143481 TGTCTATACCCATCGGTCCGA 59.857 52.381 18.01 18.01 43.29 4.55 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
47 48 1.500474 TGCATTTGGGGGTCAAACAA 58.500 45.000 0.00 0.00 46.72 2.83
56 57 3.141272 TGGGGGTCAAACAATTTCCTAGT 59.859 43.478 0.00 0.00 0.00 2.57
93 95 3.429547 CCTCGACTCATTCTTTGACCGAT 60.430 47.826 0.00 0.00 35.27 4.18
167 170 5.775813 CCCCCAATCTATCTGATCAGATT 57.224 43.478 36.46 20.78 45.31 2.40
168 171 5.743117 CCCCCAATCTATCTGATCAGATTC 58.257 45.833 36.46 0.00 45.31 2.52
171 174 5.417811 CCAATCTATCTGATCAGATTCGGG 58.582 45.833 36.46 26.20 45.31 5.14
184 187 2.092914 AGATTCGGGGTTGTCTTCCATC 60.093 50.000 0.00 0.00 0.00 3.51
207 210 1.071605 CTTCACCGCCTTCTTCTTCG 58.928 55.000 0.00 0.00 0.00 3.79
208 211 0.949105 TTCACCGCCTTCTTCTTCGC 60.949 55.000 0.00 0.00 0.00 4.70
217 221 1.725164 CTTCTTCTTCGCGGTGGTTAC 59.275 52.381 6.13 0.00 0.00 2.50
281 286 2.459644 TGGCAAATTTCAGGCTGCTAT 58.540 42.857 10.34 2.32 35.13 2.97
292 297 5.722021 TCAGGCTGCTATATCGACAATAA 57.278 39.130 10.34 0.00 0.00 1.40
293 298 5.714047 TCAGGCTGCTATATCGACAATAAG 58.286 41.667 10.34 0.00 0.00 1.73
323 329 0.796312 CGATGGTGTTTCGGAGGTTG 59.204 55.000 0.00 0.00 33.05 3.77
338 344 1.070786 GTTGAGAGGTGGCACCGAA 59.929 57.895 29.76 18.10 44.90 4.30
343 349 2.027625 GAGGTGGCACCGAACTTCG 61.028 63.158 29.76 4.07 44.90 3.79
372 378 1.227556 GTTGTCGGTGAGTGCAGGT 60.228 57.895 0.00 0.00 0.00 4.00
415 426 4.069304 TCAAGGAAGGGTGTGTAATTTCG 58.931 43.478 0.00 0.00 0.00 3.46
544 559 1.202770 ACACCAGTCAACAGCCCTAAC 60.203 52.381 0.00 0.00 0.00 2.34
549 565 3.004734 CCAGTCAACAGCCCTAACAAAAG 59.995 47.826 0.00 0.00 0.00 2.27
577 593 6.798476 CACTAACACAGCACAATAATCACAAG 59.202 38.462 0.00 0.00 0.00 3.16
597 613 7.449827 CACAAGCTGTGCATTAATAACAAATG 58.550 34.615 0.00 6.49 41.89 2.32
598 614 6.591062 ACAAGCTGTGCATTAATAACAAATGG 59.409 34.615 0.00 0.00 35.34 3.16
682 700 3.546002 TTAAACGCGAAGGTCCAATTG 57.454 42.857 15.93 0.00 0.00 2.32
852 892 0.731174 GCATTAACCAACCAACCGCG 60.731 55.000 0.00 0.00 0.00 6.46
1227 1272 2.736826 GGGGGCCTTCTCTTCCGAG 61.737 68.421 0.84 0.00 38.67 4.63
1305 1350 2.046314 CTTCGCCCCGTTGACCAT 60.046 61.111 0.00 0.00 0.00 3.55
1662 1707 2.681778 CGCACTCCACCTCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
1746 1800 3.157881 TGAGAGCGAGGAAGAAGAAGAA 58.842 45.455 0.00 0.00 0.00 2.52
1977 2031 1.221840 CTTCCCTCCGGACACCATG 59.778 63.158 0.00 0.00 38.14 3.66
2787 2841 0.034896 CGTGGTTCTACCTTGTGGCT 59.965 55.000 0.00 0.00 39.58 4.75
3149 3203 4.227864 AGAACATCCCATCAAGTCCTTC 57.772 45.455 0.00 0.00 0.00 3.46
3155 3209 2.242196 TCCCATCAAGTCCTTCCATTCC 59.758 50.000 0.00 0.00 0.00 3.01
3156 3210 2.243221 CCCATCAAGTCCTTCCATTCCT 59.757 50.000 0.00 0.00 0.00 3.36
3157 3211 3.549794 CCATCAAGTCCTTCCATTCCTC 58.450 50.000 0.00 0.00 0.00 3.71
3179 3233 9.613428 TCCTCCATAATTACTTGTATCAAGTTG 57.387 33.333 18.02 10.89 0.00 3.16
3180 3234 8.345565 CCTCCATAATTACTTGTATCAAGTTGC 58.654 37.037 18.02 0.00 0.00 4.17
3183 3237 8.677300 CCATAATTACTTGTATCAAGTTGCTGT 58.323 33.333 18.02 5.34 0.00 4.40
3184 3238 9.708222 CATAATTACTTGTATCAAGTTGCTGTC 57.292 33.333 18.02 0.00 0.00 3.51
3185 3239 7.986085 AATTACTTGTATCAAGTTGCTGTCT 57.014 32.000 18.02 0.00 0.00 3.41
3200 3254 8.704849 AGTTGCTGTCTACTAGATCTTCATAT 57.295 34.615 0.00 0.00 0.00 1.78
3201 3255 9.800572 AGTTGCTGTCTACTAGATCTTCATATA 57.199 33.333 0.00 0.00 0.00 0.86
3203 3257 8.275015 TGCTGTCTACTAGATCTTCATATAGC 57.725 38.462 0.00 4.67 28.09 2.97
3204 3258 7.338196 TGCTGTCTACTAGATCTTCATATAGCC 59.662 40.741 0.00 0.00 28.09 3.93
3205 3259 7.556275 GCTGTCTACTAGATCTTCATATAGCCT 59.444 40.741 0.00 0.00 28.09 4.58
3241 3297 7.398024 ACATGTAAGAGCAGGAATTTTAGTCT 58.602 34.615 0.00 0.00 0.00 3.24
3245 3301 8.251721 TGTAAGAGCAGGAATTTTAGTCTACTC 58.748 37.037 0.00 0.00 0.00 2.59
3279 3335 5.764131 TCACAAAAACGACAACAGTTTCTT 58.236 33.333 0.00 0.00 40.49 2.52
3306 3383 7.753309 ACTGTCTAGTATGCTATCTTGGTAG 57.247 40.000 0.00 0.00 34.74 3.18
3307 3384 7.291566 ACTGTCTAGTATGCTATCTTGGTAGT 58.708 38.462 0.00 0.00 34.74 2.73
3308 3385 8.438373 ACTGTCTAGTATGCTATCTTGGTAGTA 58.562 37.037 0.00 0.00 34.74 1.82
3309 3386 9.456147 CTGTCTAGTATGCTATCTTGGTAGTAT 57.544 37.037 0.00 0.00 32.76 2.12
3316 3393 9.640963 GTATGCTATCTTGGTAGTATAGTTTGG 57.359 37.037 0.12 0.00 32.36 3.28
3317 3394 7.907841 TGCTATCTTGGTAGTATAGTTTGGA 57.092 36.000 0.00 0.00 0.00 3.53
3318 3395 8.313944 TGCTATCTTGGTAGTATAGTTTGGAA 57.686 34.615 0.00 0.00 0.00 3.53
3319 3396 8.764558 TGCTATCTTGGTAGTATAGTTTGGAAA 58.235 33.333 0.00 0.00 0.00 3.13
3320 3397 9.609346 GCTATCTTGGTAGTATAGTTTGGAAAA 57.391 33.333 0.00 0.00 0.00 2.29
3323 3400 9.802039 ATCTTGGTAGTATAGTTTGGAAAACAA 57.198 29.630 5.72 0.00 37.28 2.83
3324 3401 9.059260 TCTTGGTAGTATAGTTTGGAAAACAAC 57.941 33.333 5.72 1.57 39.19 3.32
3325 3402 8.983702 TTGGTAGTATAGTTTGGAAAACAACT 57.016 30.769 5.72 7.78 39.19 3.16
3326 3403 8.385898 TGGTAGTATAGTTTGGAAAACAACTG 57.614 34.615 5.72 0.00 39.19 3.16
3327 3404 7.994334 TGGTAGTATAGTTTGGAAAACAACTGT 59.006 33.333 5.72 0.00 39.19 3.55
3328 3405 8.287503 GGTAGTATAGTTTGGAAAACAACTGTG 58.712 37.037 5.72 0.00 39.19 3.66
3329 3406 9.048446 GTAGTATAGTTTGGAAAACAACTGTGA 57.952 33.333 5.72 0.00 39.19 3.58
3330 3407 8.691661 AGTATAGTTTGGAAAACAACTGTGAT 57.308 30.769 5.72 0.00 39.19 3.06
3331 3408 9.787435 AGTATAGTTTGGAAAACAACTGTGATA 57.213 29.630 5.72 0.00 39.19 2.15
3333 3410 8.918202 ATAGTTTGGAAAACAACTGTGATAGA 57.082 30.769 5.72 0.00 39.19 1.98
3334 3411 7.823745 AGTTTGGAAAACAACTGTGATAGAT 57.176 32.000 5.72 0.00 39.19 1.98
3335 3412 7.651808 AGTTTGGAAAACAACTGTGATAGATG 58.348 34.615 5.72 0.00 39.19 2.90
3336 3413 7.285401 AGTTTGGAAAACAACTGTGATAGATGT 59.715 33.333 5.72 0.00 43.40 3.06
3353 3430 9.286170 TGATAGATGTTGTATACTGGAGTAGTC 57.714 37.037 4.17 0.00 40.89 2.59
3370 3447 7.822822 TGGAGTAGTCTTTAAAGTTCATAAGCC 59.177 37.037 14.74 8.78 0.00 4.35
3392 3470 8.814038 AGCCTAACATATTTCTTGTCTTTCAT 57.186 30.769 0.00 0.00 0.00 2.57
3602 3680 3.904339 TCCTAAAGGCTTATGCTCTAGGG 59.096 47.826 16.54 0.00 36.41 3.53
3723 3801 1.293924 CATCCATCACCGCTTCTCAC 58.706 55.000 0.00 0.00 0.00 3.51
3917 3995 6.663523 GGGTCCATTTCTTGAAGAATAGGAAA 59.336 38.462 22.38 4.30 38.44 3.13
4040 4118 3.393089 AGTGATCTCAATATGGCGACC 57.607 47.619 0.00 0.00 0.00 4.79
4209 4292 6.198966 GTCAACTTTCAACACCAAATGCTAAG 59.801 38.462 0.00 0.00 0.00 2.18
4317 4408 8.210946 TCTGGAGACGATAATGGATTGTTAAAT 58.789 33.333 0.00 0.00 31.71 1.40
4318 4409 8.746052 TGGAGACGATAATGGATTGTTAAATT 57.254 30.769 0.00 0.00 31.71 1.82
4319 4410 9.184523 TGGAGACGATAATGGATTGTTAAATTT 57.815 29.630 0.00 0.00 31.71 1.82
4347 4440 8.908786 TGATAGCTATTTTTCCAATAGTGAGG 57.091 34.615 7.87 0.00 33.79 3.86
4408 4506 5.937187 TGATAACATGTTTGTTGTGATCCG 58.063 37.500 17.78 0.00 45.56 4.18
4409 4507 5.471797 TGATAACATGTTTGTTGTGATCCGT 59.528 36.000 17.78 0.00 45.56 4.69
4450 4548 2.203365 GAGGAGGAGGCGATCGGA 60.203 66.667 18.30 0.00 0.00 4.55
4699 4816 4.032104 GCTGAATGATGAAACGATTTTGGC 59.968 41.667 0.00 0.00 0.00 4.52
4734 4851 2.419324 CAGCAAGGAGAGAAGAATGCAC 59.581 50.000 0.00 0.00 36.30 4.57
4764 4881 1.876664 CAGAAGAGAGCACGGACGA 59.123 57.895 0.00 0.00 0.00 4.20
4765 4882 0.179176 CAGAAGAGAGCACGGACGAG 60.179 60.000 0.00 0.00 0.00 4.18
4766 4883 0.606944 AGAAGAGAGCACGGACGAGT 60.607 55.000 0.00 0.00 0.00 4.18
4767 4884 0.179184 GAAGAGAGCACGGACGAGTC 60.179 60.000 0.00 0.00 0.00 3.36
4768 4885 1.913451 AAGAGAGCACGGACGAGTCG 61.913 60.000 11.85 11.85 0.00 4.18
4954 5094 2.936032 GACAAGGGGCTCCAGGGT 60.936 66.667 4.79 0.00 34.83 4.34
5002 5142 2.982488 TGAAAAGAGAGGAAGAGGGCTT 59.018 45.455 0.00 0.00 36.96 4.35
5140 5293 1.068610 CCTGTTGGTGGCGTGTTATTG 60.069 52.381 0.00 0.00 0.00 1.90
5197 5350 1.067974 CACGACCCAGCCAATACGATA 59.932 52.381 0.00 0.00 0.00 2.92
5198 5351 1.068127 ACGACCCAGCCAATACGATAC 59.932 52.381 0.00 0.00 0.00 2.24
5199 5352 1.779569 GACCCAGCCAATACGATACG 58.220 55.000 0.00 0.00 0.00 3.06
5200 5353 1.338973 GACCCAGCCAATACGATACGA 59.661 52.381 0.00 0.00 0.00 3.43
5201 5354 1.968493 ACCCAGCCAATACGATACGAT 59.032 47.619 0.00 0.00 0.00 3.73
5202 5355 2.367567 ACCCAGCCAATACGATACGATT 59.632 45.455 0.00 0.00 0.00 3.34
5203 5356 2.736721 CCCAGCCAATACGATACGATTG 59.263 50.000 0.00 0.00 33.63 2.67
5204 5357 2.157668 CCAGCCAATACGATACGATTGC 59.842 50.000 0.00 0.00 32.69 3.56
5208 5361 3.363970 GCCAATACGATACGATTGCTTGG 60.364 47.826 0.00 0.00 35.97 3.61
5260 5440 2.608988 CTCCCCACCCAGCTCAGT 60.609 66.667 0.00 0.00 0.00 3.41
5266 5446 3.314331 ACCCAGCTCAGTCCACCG 61.314 66.667 0.00 0.00 0.00 4.94
5268 5448 2.575993 CCAGCTCAGTCCACCGAG 59.424 66.667 0.00 0.00 0.00 4.63
5274 5454 0.668706 CTCAGTCCACCGAGCTGTTG 60.669 60.000 0.00 0.00 0.00 3.33
5289 5474 2.094854 GCTGTTGCATTCCCAAAGAGAG 60.095 50.000 0.00 0.00 39.41 3.20
5292 5477 3.072915 TGTTGCATTCCCAAAGAGAGAGA 59.927 43.478 0.00 0.00 0.00 3.10
5293 5478 4.074970 GTTGCATTCCCAAAGAGAGAGAA 58.925 43.478 0.00 0.00 0.00 2.87
5310 5495 7.986889 AGAGAGAGAATTCTGGCTTTTCTTATC 59.013 37.037 14.00 5.02 32.53 1.75
5360 5550 4.370049 TCGTCTTCATAAAAACCACGACA 58.630 39.130 0.00 0.00 30.28 4.35
5365 5555 7.305474 GTCTTCATAAAAACCACGACAATCAT 58.695 34.615 0.00 0.00 0.00 2.45
5377 5567 4.977963 CACGACAATCATCTGTTTTTGCTT 59.022 37.500 0.00 0.00 0.00 3.91
5382 5572 7.095940 CGACAATCATCTGTTTTTGCTTCATTT 60.096 33.333 0.00 0.00 0.00 2.32
5388 5578 7.650504 TCATCTGTTTTTGCTTCATTTCTTCTG 59.349 33.333 0.00 0.00 0.00 3.02
5399 5589 6.800892 GCTTCATTTCTTCTGTTCTCAACATC 59.199 38.462 0.00 0.00 41.26 3.06
5408 5598 7.500227 TCTTCTGTTCTCAACATCTTTGTCAAT 59.500 33.333 0.00 0.00 41.26 2.57
5418 5608 8.871862 TCAACATCTTTGTCAATCTTGTTTTTG 58.128 29.630 5.33 0.00 34.06 2.44
5475 5665 0.106619 CCCGCTGGGTAGAGACTACT 60.107 60.000 5.56 0.00 38.25 2.57
5476 5666 1.310904 CCGCTGGGTAGAGACTACTC 58.689 60.000 8.48 5.54 42.90 2.59
5477 5667 1.310904 CGCTGGGTAGAGACTACTCC 58.689 60.000 6.38 7.57 43.53 3.85
5478 5668 1.694844 GCTGGGTAGAGACTACTCCC 58.305 60.000 6.38 2.80 43.53 4.30
5479 5669 1.215924 GCTGGGTAGAGACTACTCCCT 59.784 57.143 6.38 0.00 43.53 4.20
5480 5670 2.358405 GCTGGGTAGAGACTACTCCCTT 60.358 54.545 6.38 0.00 43.53 3.95
5481 5671 3.882515 GCTGGGTAGAGACTACTCCCTTT 60.883 52.174 6.38 0.00 43.53 3.11
5482 5672 4.354662 CTGGGTAGAGACTACTCCCTTTT 58.645 47.826 6.38 0.00 43.53 2.27
5483 5673 4.759953 TGGGTAGAGACTACTCCCTTTTT 58.240 43.478 6.38 0.00 43.53 1.94
5484 5674 4.776308 TGGGTAGAGACTACTCCCTTTTTC 59.224 45.833 6.38 0.00 43.53 2.29
5485 5675 5.024785 GGGTAGAGACTACTCCCTTTTTCT 58.975 45.833 8.48 0.00 43.53 2.52
5486 5676 5.484644 GGGTAGAGACTACTCCCTTTTTCTT 59.515 44.000 8.48 0.00 43.53 2.52
5487 5677 6.013553 GGGTAGAGACTACTCCCTTTTTCTTT 60.014 42.308 8.48 0.00 43.53 2.52
5488 5678 7.451732 GGTAGAGACTACTCCCTTTTTCTTTT 58.548 38.462 8.48 0.00 43.53 2.27
5489 5679 7.603404 GGTAGAGACTACTCCCTTTTTCTTTTC 59.397 40.741 8.48 0.00 43.53 2.29
5490 5680 7.381789 AGAGACTACTCCCTTTTTCTTTTCT 57.618 36.000 0.00 0.00 43.53 2.52
5491 5681 7.807198 AGAGACTACTCCCTTTTTCTTTTCTT 58.193 34.615 0.00 0.00 43.53 2.52
5492 5682 8.275758 AGAGACTACTCCCTTTTTCTTTTCTTT 58.724 33.333 0.00 0.00 43.53 2.52
5493 5683 8.824756 AGACTACTCCCTTTTTCTTTTCTTTT 57.175 30.769 0.00 0.00 0.00 2.27
5494 5684 9.256228 AGACTACTCCCTTTTTCTTTTCTTTTT 57.744 29.630 0.00 0.00 0.00 1.94
5522 5712 5.395611 ACAGGTAGAGACTACTCCTTTGTT 58.604 41.667 8.48 0.00 43.53 2.83
5533 5723 8.383175 AGACTACTCCTTTGTTATTGATTTGGA 58.617 33.333 0.00 0.00 0.00 3.53
5538 5728 3.859411 TTGTTATTGATTTGGACCGCC 57.141 42.857 0.00 0.00 0.00 6.13
5540 5730 3.360867 TGTTATTGATTTGGACCGCCAT 58.639 40.909 0.00 0.00 45.46 4.40
5541 5731 3.380004 TGTTATTGATTTGGACCGCCATC 59.620 43.478 0.00 0.00 45.46 3.51
5542 5732 1.402787 ATTGATTTGGACCGCCATCC 58.597 50.000 0.00 0.00 45.46 3.51
5543 5733 0.682855 TTGATTTGGACCGCCATCCC 60.683 55.000 0.00 0.00 45.46 3.85
5544 5734 2.124320 ATTTGGACCGCCATCCCG 60.124 61.111 0.00 0.00 45.46 5.14
5545 5735 2.602746 GATTTGGACCGCCATCCCGA 62.603 60.000 0.00 0.00 45.46 5.14
5546 5736 1.994885 ATTTGGACCGCCATCCCGAT 61.995 55.000 0.00 0.00 45.46 4.18
5569 5778 0.825840 CAAAACTCTTTGGGCCCGGA 60.826 55.000 19.37 14.25 38.64 5.14
5570 5779 0.539669 AAAACTCTTTGGGCCCGGAG 60.540 55.000 27.20 27.20 0.00 4.63
5571 5780 1.423794 AAACTCTTTGGGCCCGGAGA 61.424 55.000 32.30 27.45 0.00 3.71
5572 5781 1.208165 AACTCTTTGGGCCCGGAGAT 61.208 55.000 32.30 23.44 0.00 2.75
5573 5782 1.208165 ACTCTTTGGGCCCGGAGATT 61.208 55.000 32.30 22.35 0.00 2.40
5574 5783 0.464554 CTCTTTGGGCCCGGAGATTC 60.465 60.000 25.77 0.00 0.00 2.52
5575 5784 0.914417 TCTTTGGGCCCGGAGATTCT 60.914 55.000 19.37 0.00 0.00 2.40
5576 5785 0.837272 CTTTGGGCCCGGAGATTCTA 59.163 55.000 19.37 0.00 0.00 2.10
5577 5786 1.211949 CTTTGGGCCCGGAGATTCTAA 59.788 52.381 19.37 0.00 0.00 2.10
5578 5787 1.291109 TTGGGCCCGGAGATTCTAAA 58.709 50.000 19.37 0.00 0.00 1.85
5579 5788 1.291109 TGGGCCCGGAGATTCTAAAA 58.709 50.000 19.37 0.00 0.00 1.52
5580 5789 1.636519 TGGGCCCGGAGATTCTAAAAA 59.363 47.619 19.37 0.00 0.00 1.94
5611 5820 0.865111 GCCCGGTTGATTGCAAAAAC 59.135 50.000 16.23 16.23 35.42 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.279981 GGGTTTGTAGAAAGCAACAATTTCTTT 59.720 33.333 15.42 0.00 42.86 2.52
1 2 6.761242 GGGTTTGTAGAAAGCAACAATTTCTT 59.239 34.615 15.42 0.00 42.86 2.52
47 48 5.825593 TTGTGTCCTCTCAACTAGGAAAT 57.174 39.130 0.00 0.00 44.67 2.17
93 95 3.210227 ACACCAATGTTGTCGAATGTCA 58.790 40.909 0.00 0.00 34.46 3.58
167 170 1.988015 GGATGGAAGACAACCCCGA 59.012 57.895 0.00 0.00 36.09 5.14
168 171 4.637771 GGATGGAAGACAACCCCG 57.362 61.111 0.00 0.00 36.09 5.73
171 174 2.305927 TGAAGAGGGATGGAAGACAACC 59.694 50.000 0.00 0.00 41.07 3.77
184 187 0.391793 GAAGAAGGCGGTGAAGAGGG 60.392 60.000 0.00 0.00 0.00 4.30
207 210 1.199097 CTGGAAACATGTAACCACCGC 59.801 52.381 16.61 0.00 41.51 5.68
208 211 2.742053 CTCTGGAAACATGTAACCACCG 59.258 50.000 16.61 10.42 41.51 4.94
217 221 4.232221 GACAACAATGCTCTGGAAACATG 58.768 43.478 0.00 0.00 41.51 3.21
260 265 1.050204 AGCAGCCTGAAATTTGCCAA 58.950 45.000 0.00 0.00 37.26 4.52
261 266 1.921982 TAGCAGCCTGAAATTTGCCA 58.078 45.000 0.00 0.00 37.26 4.92
265 270 5.368145 TGTCGATATAGCAGCCTGAAATTT 58.632 37.500 0.00 0.00 0.00 1.82
267 272 4.607293 TGTCGATATAGCAGCCTGAAAT 57.393 40.909 0.00 0.00 0.00 2.17
281 286 4.873827 GCAACTGGGAACTTATTGTCGATA 59.126 41.667 0.00 0.00 0.00 2.92
292 297 0.606401 CACCATCGCAACTGGGAACT 60.606 55.000 0.17 0.00 40.44 3.01
293 298 0.889186 ACACCATCGCAACTGGGAAC 60.889 55.000 0.17 0.00 40.44 3.62
323 329 0.670854 GAAGTTCGGTGCCACCTCTC 60.671 60.000 12.94 1.75 35.66 3.20
353 359 1.069765 CCTGCACTCACCGACAACT 59.930 57.895 0.00 0.00 0.00 3.16
372 378 5.404096 TGATGAATTAACGTTCGTGCTCTA 58.596 37.500 2.82 0.00 0.00 2.43
486 501 3.541632 TGCTTCCTTTCGAAAGACAGTT 58.458 40.909 34.00 0.00 41.84 3.16
544 559 4.980590 TGTGCTGTGTTAGTGTTCTTTTG 58.019 39.130 0.00 0.00 0.00 2.44
549 565 6.797033 GTGATTATTGTGCTGTGTTAGTGTTC 59.203 38.462 0.00 0.00 0.00 3.18
577 593 5.519927 GGACCATTTGTTATTAATGCACAGC 59.480 40.000 0.00 0.00 32.82 4.40
585 601 7.923344 CACAAACAGTGGACCATTTGTTATTAA 59.077 33.333 20.98 0.00 41.98 1.40
625 641 3.371168 TGCTTTGCTTGAAATGTTCGAC 58.629 40.909 0.00 0.00 0.00 4.20
626 642 3.706802 TGCTTTGCTTGAAATGTTCGA 57.293 38.095 0.00 0.00 0.00 3.71
1352 1397 1.801913 CAGAGGTCGTCGCCTTTCG 60.802 63.158 9.18 0.00 39.34 3.46
1746 1800 3.328931 ACCACAAGTCATTGGTCTCATCT 59.671 43.478 0.00 0.00 42.86 2.90
2787 2841 3.706373 GCAGCCTCGAAGTCCCCA 61.706 66.667 0.00 0.00 0.00 4.96
3149 3203 9.573166 TTGATACAAGTAATTATGGAGGAATGG 57.427 33.333 0.00 0.00 0.00 3.16
3155 3209 9.113838 AGCAACTTGATACAAGTAATTATGGAG 57.886 33.333 15.77 2.40 0.00 3.86
3156 3210 8.892723 CAGCAACTTGATACAAGTAATTATGGA 58.107 33.333 15.77 0.00 0.00 3.41
3157 3211 8.677300 ACAGCAACTTGATACAAGTAATTATGG 58.323 33.333 15.77 6.73 0.00 2.74
3179 3233 7.556275 AGGCTATATGAAGATCTAGTAGACAGC 59.444 40.741 0.85 0.18 0.00 4.40
3213 3268 9.167311 ACTAAAATTCCTGCTCTTACATGTAAG 57.833 33.333 31.44 31.44 42.86 2.34
3219 3274 8.135382 AGTAGACTAAAATTCCTGCTCTTACA 57.865 34.615 0.00 0.00 0.00 2.41
3220 3275 8.251721 TGAGTAGACTAAAATTCCTGCTCTTAC 58.748 37.037 0.00 0.00 38.58 2.34
3241 3297 8.237949 TCGTTTTTGTGAATTTGTTTCTGAGTA 58.762 29.630 0.00 0.00 35.23 2.59
3245 3301 7.043454 TGTCGTTTTTGTGAATTTGTTTCTG 57.957 32.000 0.00 0.00 35.23 3.02
3301 3378 7.994334 ACAGTTGTTTTCCAAACTATACTACCA 59.006 33.333 1.33 0.00 34.07 3.25
3302 3379 8.287503 CACAGTTGTTTTCCAAACTATACTACC 58.712 37.037 1.33 0.00 34.07 3.18
3303 3380 9.048446 TCACAGTTGTTTTCCAAACTATACTAC 57.952 33.333 1.33 0.00 34.07 2.73
3308 3385 8.918202 TCTATCACAGTTGTTTTCCAAACTAT 57.082 30.769 1.33 0.00 34.07 2.12
3309 3386 8.783093 CATCTATCACAGTTGTTTTCCAAACTA 58.217 33.333 1.33 0.00 34.07 2.24
3310 3387 7.285401 ACATCTATCACAGTTGTTTTCCAAACT 59.715 33.333 1.33 0.00 34.18 2.66
3311 3388 7.425606 ACATCTATCACAGTTGTTTTCCAAAC 58.574 34.615 0.00 0.00 34.18 2.93
3312 3389 7.581213 ACATCTATCACAGTTGTTTTCCAAA 57.419 32.000 0.00 0.00 34.18 3.28
3313 3390 7.424803 CAACATCTATCACAGTTGTTTTCCAA 58.575 34.615 0.00 0.00 42.11 3.53
3314 3391 6.969366 CAACATCTATCACAGTTGTTTTCCA 58.031 36.000 0.00 0.00 42.11 3.53
3321 3398 8.197439 TCCAGTATACAACATCTATCACAGTTG 58.803 37.037 5.50 0.00 45.02 3.16
3322 3399 8.306313 TCCAGTATACAACATCTATCACAGTT 57.694 34.615 5.50 0.00 0.00 3.16
3323 3400 7.561722 ACTCCAGTATACAACATCTATCACAGT 59.438 37.037 5.50 0.00 0.00 3.55
3324 3401 7.946207 ACTCCAGTATACAACATCTATCACAG 58.054 38.462 5.50 0.00 0.00 3.66
3325 3402 7.898014 ACTCCAGTATACAACATCTATCACA 57.102 36.000 5.50 0.00 0.00 3.58
3326 3403 9.069082 ACTACTCCAGTATACAACATCTATCAC 57.931 37.037 5.50 0.00 34.98 3.06
3327 3404 9.286170 GACTACTCCAGTATACAACATCTATCA 57.714 37.037 5.50 0.00 37.72 2.15
3328 3405 9.509956 AGACTACTCCAGTATACAACATCTATC 57.490 37.037 5.50 0.00 37.72 2.08
3329 3406 9.869667 AAGACTACTCCAGTATACAACATCTAT 57.130 33.333 5.50 0.00 37.72 1.98
3330 3407 9.696572 AAAGACTACTCCAGTATACAACATCTA 57.303 33.333 5.50 0.00 37.72 1.98
3331 3408 8.596781 AAAGACTACTCCAGTATACAACATCT 57.403 34.615 5.50 0.00 37.72 2.90
3342 3419 9.930693 CTTATGAACTTTAAAGACTACTCCAGT 57.069 33.333 21.92 0.00 41.47 4.00
3343 3420 8.874816 GCTTATGAACTTTAAAGACTACTCCAG 58.125 37.037 21.92 8.46 0.00 3.86
3389 3467 7.501892 TGACAATTTAGCCTACAATGCATATGA 59.498 33.333 6.97 0.00 0.00 2.15
3392 3470 7.053498 TCTGACAATTTAGCCTACAATGCATA 58.947 34.615 0.00 0.00 0.00 3.14
3440 3518 4.802039 TGAATCGAACTATTCCGTGCTAAC 59.198 41.667 0.00 0.00 35.40 2.34
3602 3680 0.099082 CGACGTCAAGGCTAGAGTCC 59.901 60.000 17.16 0.00 0.00 3.85
3917 3995 4.021229 TCATCTCATCAAATGCAGCCTTT 58.979 39.130 0.00 0.00 0.00 3.11
4286 4377 3.767131 TCCATTATCGTCTCCAGACAACA 59.233 43.478 7.48 0.00 44.99 3.33
4323 4416 9.561069 TTCCTCACTATTGGAAAAATAGCTATC 57.439 33.333 6.72 0.00 39.15 2.08
4336 4429 5.033589 AGCTCTGAATTCCTCACTATTGG 57.966 43.478 2.27 0.00 0.00 3.16
4338 4431 7.856415 ACTTTAGCTCTGAATTCCTCACTATT 58.144 34.615 2.27 0.00 0.00 1.73
4339 4432 7.344352 AGACTTTAGCTCTGAATTCCTCACTAT 59.656 37.037 2.27 0.00 0.00 2.12
4340 4433 6.665680 AGACTTTAGCTCTGAATTCCTCACTA 59.334 38.462 2.27 0.00 0.00 2.74
4341 4434 5.483583 AGACTTTAGCTCTGAATTCCTCACT 59.516 40.000 2.27 0.00 0.00 3.41
4342 4435 5.580297 CAGACTTTAGCTCTGAATTCCTCAC 59.420 44.000 2.27 0.00 37.90 3.51
4343 4436 5.481824 TCAGACTTTAGCTCTGAATTCCTCA 59.518 40.000 2.27 0.00 40.98 3.86
4408 4506 3.246619 GTTCTCGTCCATCAGAACTGAC 58.753 50.000 6.67 0.00 43.54 3.51
4409 4507 2.890945 TGTTCTCGTCCATCAGAACTGA 59.109 45.455 6.98 6.98 45.97 3.41
4450 4548 4.370066 AGCGCTTGCGTCAGCTCT 62.370 61.111 16.38 1.08 45.69 4.09
4699 4816 4.803908 GCTGCGGAAGGGAAGGGG 62.804 72.222 0.00 0.00 0.00 4.79
4764 4881 1.422781 TCTATACCCATCGGTCCGACT 59.577 52.381 18.08 3.11 43.29 4.18
4765 4882 1.538950 GTCTATACCCATCGGTCCGAC 59.461 57.143 18.08 0.00 43.29 4.79
4766 4883 1.143481 TGTCTATACCCATCGGTCCGA 59.857 52.381 18.01 18.01 43.29 4.55
4767 4884 1.612676 TGTCTATACCCATCGGTCCG 58.387 55.000 4.39 4.39 43.29 4.79
4768 4885 3.802675 GCTTTGTCTATACCCATCGGTCC 60.803 52.174 0.00 0.00 43.29 4.46
4954 5094 3.099905 CTCTCATCAGACCAACCCAGTA 58.900 50.000 0.00 0.00 0.00 2.74
5002 5142 2.670905 CTGTTCTGTTGTGTTGTGTCGA 59.329 45.455 0.00 0.00 0.00 4.20
5197 5350 0.673437 CCAACCAACCAAGCAATCGT 59.327 50.000 0.00 0.00 0.00 3.73
5198 5351 0.673437 ACCAACCAACCAAGCAATCG 59.327 50.000 0.00 0.00 0.00 3.34
5199 5352 2.158971 ACAACCAACCAACCAAGCAATC 60.159 45.455 0.00 0.00 0.00 2.67
5200 5353 1.836802 ACAACCAACCAACCAAGCAAT 59.163 42.857 0.00 0.00 0.00 3.56
5201 5354 1.205893 GACAACCAACCAACCAAGCAA 59.794 47.619 0.00 0.00 0.00 3.91
5202 5355 0.820871 GACAACCAACCAACCAAGCA 59.179 50.000 0.00 0.00 0.00 3.91
5203 5356 0.248866 CGACAACCAACCAACCAAGC 60.249 55.000 0.00 0.00 0.00 4.01
5204 5357 0.248866 GCGACAACCAACCAACCAAG 60.249 55.000 0.00 0.00 0.00 3.61
5208 5361 2.330041 CGGCGACAACCAACCAAC 59.670 61.111 0.00 0.00 0.00 3.77
5260 5440 0.955428 GAATGCAACAGCTCGGTGGA 60.955 55.000 0.00 1.31 0.00 4.02
5266 5446 1.888512 TCTTTGGGAATGCAACAGCTC 59.111 47.619 0.00 0.00 0.00 4.09
5268 5448 1.888512 TCTCTTTGGGAATGCAACAGC 59.111 47.619 0.00 0.00 0.00 4.40
5274 5454 5.066246 CAGAATTCTCTCTCTTTGGGAATGC 59.934 44.000 4.57 0.00 0.00 3.56
5289 5474 6.459435 GCAGGATAAGAAAAGCCAGAATTCTC 60.459 42.308 4.57 0.00 32.45 2.87
5292 5477 5.267587 AGCAGGATAAGAAAAGCCAGAATT 58.732 37.500 0.00 0.00 0.00 2.17
5293 5478 4.864726 AGCAGGATAAGAAAAGCCAGAAT 58.135 39.130 0.00 0.00 0.00 2.40
5310 5495 3.801997 CCTGGCCTGGGTAGCAGG 61.802 72.222 20.77 3.75 42.56 4.85
5360 5550 8.897872 AAGAAATGAAGCAAAAACAGATGATT 57.102 26.923 0.00 0.00 0.00 2.57
5365 5555 6.866480 ACAGAAGAAATGAAGCAAAAACAGA 58.134 32.000 0.00 0.00 0.00 3.41
5377 5567 8.347771 CAAAGATGTTGAGAACAGAAGAAATGA 58.652 33.333 0.00 0.00 45.95 2.57
5382 5572 6.348498 TGACAAAGATGTTGAGAACAGAAGA 58.652 36.000 0.00 0.00 45.95 2.87
5388 5578 7.420800 ACAAGATTGACAAAGATGTTGAGAAC 58.579 34.615 0.00 0.00 40.74 3.01
5399 5589 5.811613 TGGAGCAAAAACAAGATTGACAAAG 59.188 36.000 0.00 0.00 0.00 2.77
5408 5598 4.947388 ACTTACAGTGGAGCAAAAACAAGA 59.053 37.500 0.00 0.00 0.00 3.02
5418 5608 6.256757 GTGATTGATTAGACTTACAGTGGAGC 59.743 42.308 0.00 0.00 0.00 4.70
5433 5623 1.934589 CGGCGACCTGTGATTGATTA 58.065 50.000 0.00 0.00 0.00 1.75
5434 5624 1.369091 GCGGCGACCTGTGATTGATT 61.369 55.000 12.98 0.00 0.00 2.57
5491 5681 6.208994 GGAGTAGTCTCTACCTGTCTCAAAAA 59.791 42.308 0.00 0.00 40.29 1.94
5492 5682 5.711036 GGAGTAGTCTCTACCTGTCTCAAAA 59.289 44.000 0.00 0.00 40.29 2.44
5493 5683 5.014333 AGGAGTAGTCTCTACCTGTCTCAAA 59.986 44.000 0.00 0.00 40.29 2.69
5494 5684 4.536888 AGGAGTAGTCTCTACCTGTCTCAA 59.463 45.833 0.00 0.00 40.29 3.02
5495 5685 4.105577 AGGAGTAGTCTCTACCTGTCTCA 58.894 47.826 0.00 0.00 40.29 3.27
5496 5686 4.765813 AGGAGTAGTCTCTACCTGTCTC 57.234 50.000 0.00 0.00 40.29 3.36
5497 5687 5.222171 ACAAAGGAGTAGTCTCTACCTGTCT 60.222 44.000 0.00 0.00 40.29 3.41
5498 5688 5.011586 ACAAAGGAGTAGTCTCTACCTGTC 58.988 45.833 0.00 0.00 40.29 3.51
5499 5689 5.000570 ACAAAGGAGTAGTCTCTACCTGT 57.999 43.478 0.00 0.00 40.29 4.00
5500 5690 5.986501 AACAAAGGAGTAGTCTCTACCTG 57.013 43.478 0.00 0.00 40.29 4.00
5501 5691 7.894364 TCAATAACAAAGGAGTAGTCTCTACCT 59.106 37.037 0.00 0.00 40.29 3.08
5502 5692 8.064336 TCAATAACAAAGGAGTAGTCTCTACC 57.936 38.462 0.00 0.00 40.29 3.18
5505 5695 9.442047 CAAATCAATAACAAAGGAGTAGTCTCT 57.558 33.333 0.00 0.00 40.29 3.10
5506 5696 8.669243 CCAAATCAATAACAAAGGAGTAGTCTC 58.331 37.037 0.00 0.00 39.76 3.36
5507 5697 8.383175 TCCAAATCAATAACAAAGGAGTAGTCT 58.617 33.333 0.00 0.00 0.00 3.24
5508 5698 8.451748 GTCCAAATCAATAACAAAGGAGTAGTC 58.548 37.037 0.00 0.00 0.00 2.59
5509 5699 7.393515 GGTCCAAATCAATAACAAAGGAGTAGT 59.606 37.037 0.00 0.00 0.00 2.73
5510 5700 7.414098 CGGTCCAAATCAATAACAAAGGAGTAG 60.414 40.741 0.00 0.00 0.00 2.57
5511 5701 6.373216 CGGTCCAAATCAATAACAAAGGAGTA 59.627 38.462 0.00 0.00 0.00 2.59
5512 5702 5.183140 CGGTCCAAATCAATAACAAAGGAGT 59.817 40.000 0.00 0.00 0.00 3.85
5513 5703 5.640732 CGGTCCAAATCAATAACAAAGGAG 58.359 41.667 0.00 0.00 0.00 3.69
5538 5728 0.657840 GAGTTTTGCGGATCGGGATG 59.342 55.000 2.13 0.00 0.00 3.51
5540 5730 0.323629 AAGAGTTTTGCGGATCGGGA 59.676 50.000 2.13 0.00 0.00 5.14
5541 5731 1.135689 CAAAGAGTTTTGCGGATCGGG 60.136 52.381 2.13 0.00 37.47 5.14
5542 5732 1.135689 CCAAAGAGTTTTGCGGATCGG 60.136 52.381 0.00 0.00 41.87 4.18
5543 5733 1.135689 CCCAAAGAGTTTTGCGGATCG 60.136 52.381 0.00 0.00 41.87 3.69
5544 5734 1.402852 GCCCAAAGAGTTTTGCGGATC 60.403 52.381 9.98 0.00 41.87 3.36
5545 5735 0.603065 GCCCAAAGAGTTTTGCGGAT 59.397 50.000 9.98 0.00 41.87 4.18
5546 5736 1.460273 GGCCCAAAGAGTTTTGCGGA 61.460 55.000 0.00 0.00 41.87 5.54
5580 5789 1.138069 CAACCGGGCCAAAGAGTTTTT 59.862 47.619 6.32 0.00 0.00 1.94
5581 5790 0.750249 CAACCGGGCCAAAGAGTTTT 59.250 50.000 6.32 0.00 0.00 2.43
5582 5791 0.106419 TCAACCGGGCCAAAGAGTTT 60.106 50.000 6.32 0.00 0.00 2.66
5583 5792 0.112412 ATCAACCGGGCCAAAGAGTT 59.888 50.000 6.32 0.00 0.00 3.01
5584 5793 0.112412 AATCAACCGGGCCAAAGAGT 59.888 50.000 6.32 0.00 0.00 3.24
5585 5794 0.527565 CAATCAACCGGGCCAAAGAG 59.472 55.000 6.32 0.00 0.00 2.85
5586 5795 1.531739 GCAATCAACCGGGCCAAAGA 61.532 55.000 6.32 0.00 0.00 2.52
5587 5796 1.079888 GCAATCAACCGGGCCAAAG 60.080 57.895 6.32 0.00 0.00 2.77
5588 5797 1.402896 TTGCAATCAACCGGGCCAAA 61.403 50.000 6.32 0.00 0.00 3.28
5589 5798 1.402896 TTTGCAATCAACCGGGCCAA 61.403 50.000 6.32 0.00 30.75 4.52
5590 5799 1.402896 TTTTGCAATCAACCGGGCCA 61.403 50.000 6.32 0.00 30.75 5.36
5591 5800 0.250081 TTTTTGCAATCAACCGGGCC 60.250 50.000 6.32 0.00 30.75 5.80
5592 5801 0.865111 GTTTTTGCAATCAACCGGGC 59.135 50.000 6.32 0.00 30.75 6.13
5593 5802 1.135867 CGTTTTTGCAATCAACCGGG 58.864 50.000 6.32 0.00 30.75 5.73
5594 5803 2.126914 TCGTTTTTGCAATCAACCGG 57.873 45.000 0.00 0.00 30.75 5.28
5595 5804 3.367607 TCTTCGTTTTTGCAATCAACCG 58.632 40.909 0.00 0.00 30.75 4.44
5596 5805 5.040635 TCTTCTTCGTTTTTGCAATCAACC 58.959 37.500 0.00 0.00 30.75 3.77
5597 5806 5.743872 ACTCTTCTTCGTTTTTGCAATCAAC 59.256 36.000 0.00 5.96 30.75 3.18
5611 5820 3.198872 GGGCCTAAATCACTCTTCTTCG 58.801 50.000 0.84 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.