Multiple sequence alignment - TraesCS2D01G390000

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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 TraesCS2D01G390000 chr2D 100.000 5511 0 0 1 5511 497372315 497366805 0.000000e+00 10178
1 TraesCS2D01G390000 chr2D 76.091 481 93 16 3291 3763 637092093 637092559 1.190000e-56 231
2 TraesCS2D01G390000 chr2A 94.869 5515 189 40 1 5449 641962502 641957016 0.000000e+00 8530
3 TraesCS2D01G390000 chr2B 96.119 3221 93 18 1882 5077 583681916 583678703 0.000000e+00 5227
4 TraesCS2D01G390000 chr2B 89.361 1861 106 45 1 1837 583683708 583681916 0.000000e+00 2255
5 TraesCS2D01G390000 chr2B 78.486 502 101 4 3067 3562 794502341 794501841 6.890000e-84 322
6 TraesCS2D01G390000 chr3D 83.122 237 19 9 5207 5429 460939668 460939897 4.360000e-46 196
7 TraesCS2D01G390000 chr3B 82.278 237 22 8 5207 5429 611179415 611179645 2.620000e-43 187
8 TraesCS2D01G390000 chr3A 82.203 236 20 9 5207 5427 603268174 603268402 3.390000e-42 183


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 TraesCS2D01G390000 chr2D 497366805 497372315 5510 True 10178 10178 100.000 1 5511 1 chr2D.!!$R1 5510
1 TraesCS2D01G390000 chr2A 641957016 641962502 5486 True 8530 8530 94.869 1 5449 1 chr2A.!!$R1 5448
2 TraesCS2D01G390000 chr2B 583678703 583683708 5005 True 3741 5227 92.740 1 5077 2 chr2B.!!$R2 5076
3 TraesCS2D01G390000 chr2B 794501841 794502341 500 True 322 322 78.486 3067 3562 1 chr2B.!!$R1 495

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
972 1019 0.313987 CCGGTTCTTCCTGGTTTTGC 59.686 55.000 0.00 0.00 0.0 3.68 F
1330 1378 0.178964 TTTGGGGGAGAGCTTTGTGG 60.179 55.000 0.00 0.00 0.0 4.17 F
1528 1576 0.649475 GCAACTAGATGCAGCTCACG 59.351 55.000 19.13 0.37 45.7 4.35 F
2267 2315 1.447838 GAAGCCGCCGACATTGAGA 60.448 57.895 0.00 0.00 0.0 3.27 F
3289 3362 5.753921 CGGAGGAAGATCTAATTTACCACAC 59.246 44.000 0.00 0.00 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 1966 0.390340 TCGAGGAATGCAGCACAGAC 60.390 55.000 0.00 0.0 0.00 3.51 R
3289 3362 0.890996 GGAACCCACAGGAGTTGCAG 60.891 60.000 0.00 0.0 34.76 4.41 R
3428 3501 1.151668 CAAACGAAGCAGTCCCTGAG 58.848 55.000 0.00 0.0 32.44 3.35 R
3675 3751 1.145571 ACCCCTGCAAAAGAGGTACA 58.854 50.000 0.00 0.0 0.00 2.90 R
4894 4973 1.061033 AGAGGGGCCTGTTATGGAGAT 60.061 52.381 0.84 0.0 0.00 2.75 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
86 91 4.086706 ACTCCTTTATTTCCTATGCCGG 57.913 45.455 0.00 0.00 0.00 6.13
87 92 2.814336 CTCCTTTATTTCCTATGCCGGC 59.186 50.000 22.73 22.73 0.00 6.13
88 93 2.441750 TCCTTTATTTCCTATGCCGGCT 59.558 45.455 29.70 15.76 0.00 5.52
89 94 3.117663 TCCTTTATTTCCTATGCCGGCTT 60.118 43.478 29.70 24.47 0.00 4.35
90 95 3.636764 CCTTTATTTCCTATGCCGGCTTT 59.363 43.478 29.70 17.74 0.00 3.51
91 96 4.825085 CCTTTATTTCCTATGCCGGCTTTA 59.175 41.667 29.70 17.93 0.00 1.85
129 134 2.546778 CCATTGGATGTGCTTTCATGC 58.453 47.619 0.00 0.00 36.83 4.06
167 172 2.226437 GACGTGCATTGGTGAACAGAAT 59.774 45.455 0.00 0.00 33.05 2.40
325 334 9.996554 CTTAGTCCACACCACATGATTATATAA 57.003 33.333 0.00 0.00 0.00 0.98
411 420 4.520492 CAGAAAAGAAGCTTTGGCCTCTTA 59.480 41.667 3.32 0.00 45.30 2.10
412 421 5.184671 CAGAAAAGAAGCTTTGGCCTCTTAT 59.815 40.000 3.32 0.00 45.30 1.73
413 422 5.417266 AGAAAAGAAGCTTTGGCCTCTTATC 59.583 40.000 3.32 0.00 45.30 1.75
414 423 3.289407 AGAAGCTTTGGCCTCTTATCC 57.711 47.619 3.32 0.00 35.94 2.59
484 495 2.076100 CTTGGCTGCGTCATTACTGAA 58.924 47.619 0.00 0.00 31.85 3.02
562 577 2.422803 CCTTTCACCCAAAGACTCACCA 60.423 50.000 0.00 0.00 44.02 4.17
601 624 2.421399 GCTGCTGCATTCCCTTCCC 61.421 63.158 11.11 0.00 39.41 3.97
602 625 1.305623 CTGCTGCATTCCCTTCCCT 59.694 57.895 1.31 0.00 0.00 4.20
603 626 0.324091 CTGCTGCATTCCCTTCCCTT 60.324 55.000 1.31 0.00 0.00 3.95
604 627 0.323725 TGCTGCATTCCCTTCCCTTC 60.324 55.000 0.00 0.00 0.00 3.46
605 628 1.039785 GCTGCATTCCCTTCCCTTCC 61.040 60.000 0.00 0.00 0.00 3.46
643 666 2.204244 TTTCCCCTCTCCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
840 874 2.691409 ACAGATTCATACACCACCGG 57.309 50.000 0.00 0.00 0.00 5.28
874 908 1.080498 GATTTCCCCCTCCCCCTTTTT 59.920 52.381 0.00 0.00 0.00 1.94
935 982 3.192633 ACTGCTCTGTTTTTCCGTGTTTT 59.807 39.130 0.00 0.00 0.00 2.43
945 992 1.394618 TCCGTGTTTTTCTGGTTGGG 58.605 50.000 0.00 0.00 0.00 4.12
965 1012 2.633488 GAATTCCTCCGGTTCTTCCTG 58.367 52.381 0.00 0.00 0.00 3.86
970 1017 1.202891 CCTCCGGTTCTTCCTGGTTTT 60.203 52.381 0.00 0.00 33.68 2.43
971 1018 1.880027 CTCCGGTTCTTCCTGGTTTTG 59.120 52.381 0.00 0.00 33.68 2.44
972 1019 0.313987 CCGGTTCTTCCTGGTTTTGC 59.686 55.000 0.00 0.00 0.00 3.68
973 1020 1.318576 CGGTTCTTCCTGGTTTTGCT 58.681 50.000 0.00 0.00 0.00 3.91
974 1021 1.681264 CGGTTCTTCCTGGTTTTGCTT 59.319 47.619 0.00 0.00 0.00 3.91
975 1022 2.543653 CGGTTCTTCCTGGTTTTGCTTG 60.544 50.000 0.00 0.00 0.00 4.01
976 1023 2.473816 GTTCTTCCTGGTTTTGCTTGC 58.526 47.619 0.00 0.00 0.00 4.01
1062 1109 1.807573 GCTCCTGTTCTTCGGCTCG 60.808 63.158 0.00 0.00 0.00 5.03
1165 1213 2.290260 TGTCATGGGCGTTGATTTCTCT 60.290 45.455 0.00 0.00 0.00 3.10
1210 1258 3.312709 CGCAAGAAATCTTTCGGCC 57.687 52.632 7.22 0.00 41.92 6.13
1214 1262 0.704664 AAGAAATCTTTCGGCCCCCT 59.295 50.000 0.00 0.00 41.92 4.79
1218 1266 1.506028 AATCTTTCGGCCCCCTTGGA 61.506 55.000 0.00 0.00 35.39 3.53
1220 1268 3.938637 CTTTCGGCCCCCTTGGACC 62.939 68.421 0.00 0.00 40.14 4.46
1238 1286 1.742768 CCGGCTTCCTAATCTCGCT 59.257 57.895 0.00 0.00 0.00 4.93
1240 1288 1.492720 CGGCTTCCTAATCTCGCTTC 58.507 55.000 0.00 0.00 0.00 3.86
1247 1295 5.006261 GCTTCCTAATCTCGCTTCTTCTTTC 59.994 44.000 0.00 0.00 0.00 2.62
1256 1304 3.189287 TCGCTTCTTCTTTCTTGATTGCC 59.811 43.478 0.00 0.00 0.00 4.52
1318 1366 3.261354 ACCTGAGGTGTTTGGGGG 58.739 61.111 1.77 0.00 32.98 5.40
1325 1373 1.068352 AGGTGTTTGGGGGAGAGCTT 61.068 55.000 0.00 0.00 0.00 3.74
1328 1376 0.555769 TGTTTGGGGGAGAGCTTTGT 59.444 50.000 0.00 0.00 0.00 2.83
1330 1378 0.178964 TTTGGGGGAGAGCTTTGTGG 60.179 55.000 0.00 0.00 0.00 4.17
1331 1379 2.080336 TTGGGGGAGAGCTTTGTGGG 62.080 60.000 0.00 0.00 0.00 4.61
1422 1470 5.221682 ACCTCATCTTGGCAGATATTCAGAG 60.222 44.000 0.00 0.00 37.71 3.35
1528 1576 0.649475 GCAACTAGATGCAGCTCACG 59.351 55.000 19.13 0.37 45.70 4.35
1599 1647 2.222227 TAGAGTTCCTGAGCTGCTGA 57.778 50.000 7.01 0.00 0.00 4.26
1832 1880 5.520376 AACCACTGAAAACAAATCTGGAG 57.480 39.130 0.00 0.00 0.00 3.86
1858 1906 4.020662 TGCAGTTGACCATGTATGTGACTA 60.021 41.667 0.00 0.00 0.00 2.59
1860 1908 5.411361 GCAGTTGACCATGTATGTGACTAAA 59.589 40.000 0.00 0.00 0.00 1.85
1877 1925 9.990360 TGTGACTAAATACTAATTGTTGTCTCA 57.010 29.630 0.00 0.00 0.00 3.27
2001 2049 9.907576 GTAAAAATTCTGATACAATCTCGTGAG 57.092 33.333 0.00 0.00 0.00 3.51
2020 2068 1.831736 AGGGACACGCTGCTAATAAGT 59.168 47.619 0.00 0.00 0.00 2.24
2032 2080 5.992217 GCTGCTAATAAGTACCTGCAATACT 59.008 40.000 4.77 4.77 34.25 2.12
2034 2082 6.884832 TGCTAATAAGTACCTGCAATACTGT 58.115 36.000 10.31 5.05 33.11 3.55
2055 2103 6.422100 ACTGTGTACATTCTTGCATATCGATC 59.578 38.462 0.00 0.00 0.00 3.69
2267 2315 1.447838 GAAGCCGCCGACATTGAGA 60.448 57.895 0.00 0.00 0.00 3.27
2617 2668 6.878923 TGGATGGTCAGAAATACACACTTAAG 59.121 38.462 0.00 0.00 0.00 1.85
3000 3068 8.786898 AGCTATAATACTTCGTGATACCGTAAA 58.213 33.333 0.00 0.00 0.00 2.01
3116 3186 6.385033 GTTGTCTGATCTTTTGAATTCAGGG 58.615 40.000 8.41 3.47 36.64 4.45
3247 3317 8.091385 TGTATAATGCATGAAGAGCAGTTATG 57.909 34.615 0.00 0.00 46.36 1.90
3289 3362 5.753921 CGGAGGAAGATCTAATTTACCACAC 59.246 44.000 0.00 0.00 0.00 3.82
3409 3482 8.985315 TCTGTTCCTGCAGATAATAAATCATT 57.015 30.769 17.39 0.00 40.23 2.57
3428 3501 8.738645 AATCATTCCTTACAAGTGAATCCTAC 57.261 34.615 3.94 0.00 0.00 3.18
3644 3720 9.421806 CATTCTATTAGTCAGAGAAGCTATTGG 57.578 37.037 0.00 0.00 32.94 3.16
3740 3816 4.034285 ACCCTGGAAAATGTAGGTTCAG 57.966 45.455 0.00 0.00 0.00 3.02
3851 3927 1.949525 TGGTGCTTTTCTCTTCACTGC 59.050 47.619 0.00 0.00 0.00 4.40
3855 3931 4.397417 GGTGCTTTTCTCTTCACTGCATAT 59.603 41.667 0.00 0.00 0.00 1.78
3863 3939 8.703604 TTTCTCTTCACTGCATATACTGTTAC 57.296 34.615 0.00 0.00 0.00 2.50
3871 3947 6.752351 CACTGCATATACTGTTACGAACTTCT 59.248 38.462 0.00 0.00 0.00 2.85
4333 4410 5.162837 ACCCCCAGATAAAATATCCATGCTT 60.163 40.000 0.00 0.00 0.00 3.91
4460 4537 1.608717 CTCAGTAACCCGCAGCTCCT 61.609 60.000 0.00 0.00 0.00 3.69
4894 4973 1.702401 TCCCACTTGAGCATGTTGGTA 59.298 47.619 0.00 0.00 0.00 3.25
4911 4990 1.351350 GGTATCTCCATAACAGGCCCC 59.649 57.143 0.00 0.00 35.97 5.80
4942 5021 2.653234 ATGGCAGGTCATCTTGATCC 57.347 50.000 0.00 0.00 0.00 3.36
5083 5182 6.877611 ATCACAAAGTTCCAACGTATTCTT 57.122 33.333 0.00 0.00 0.00 2.52
5086 5185 6.970043 TCACAAAGTTCCAACGTATTCTTTTG 59.030 34.615 0.00 0.00 0.00 2.44
5093 5192 6.295039 TCCAACGTATTCTTTTGTGTTCTC 57.705 37.500 0.00 0.00 0.00 2.87
5117 5216 7.722363 TCATCTAATATCCGTTTGTGCTTCTA 58.278 34.615 0.00 0.00 0.00 2.10
5146 5246 9.587772 TTAGTGAGAGTAGTAATTGAAGAATGC 57.412 33.333 0.00 0.00 0.00 3.56
5147 5247 7.615403 AGTGAGAGTAGTAATTGAAGAATGCA 58.385 34.615 0.00 0.00 0.00 3.96
5177 5277 4.946160 ACTGAATTAAGATGTTCCCCCA 57.054 40.909 0.00 0.00 0.00 4.96
5210 5310 1.917303 CGTGTTGCAACAAAAGACACC 59.083 47.619 32.61 16.79 41.21 4.16
5213 5313 3.932089 GTGTTGCAACAAAAGACACCAAT 59.068 39.130 32.61 0.00 41.21 3.16
5229 5329 2.283298 CCAATGAGACTGGTCGAATGG 58.717 52.381 0.00 0.60 34.09 3.16
5240 5340 6.761714 AGACTGGTCGAATGGATTATAAACAC 59.238 38.462 0.00 0.00 34.09 3.32
5242 5342 5.421277 TGGTCGAATGGATTATAAACACGT 58.579 37.500 0.00 0.00 0.00 4.49
5277 5377 5.070313 AGGGATTACATGTTGCAACAAAACT 59.930 36.000 34.06 16.62 43.03 2.66
5289 5389 3.740832 GCAACAAAACTTACCAATGAGGC 59.259 43.478 0.00 0.00 43.14 4.70
5297 5397 0.673333 TACCAATGAGGCTGCACACG 60.673 55.000 0.50 0.00 43.14 4.49
5307 5407 2.048970 TGCACACGCGTACCGATT 60.049 55.556 13.44 0.00 42.97 3.34
5321 5421 0.108585 CCGATTGGGTATCTGTGGGG 59.891 60.000 0.00 0.00 0.00 4.96
5346 5446 3.156293 TGGTGTGTGCATAGAAAATGCT 58.844 40.909 10.95 0.00 44.79 3.79
5416 5516 7.715249 CCAAAGTGGAAGCTATAATACTAGCAA 59.285 37.037 5.94 0.00 42.44 3.91
5421 5521 7.226720 GTGGAAGCTATAATACTAGCAAGCAAA 59.773 37.037 5.94 0.00 45.35 3.68
5431 5531 0.183492 AGCAAGCAAACCACTCCTCA 59.817 50.000 0.00 0.00 0.00 3.86
5432 5532 1.202976 AGCAAGCAAACCACTCCTCAT 60.203 47.619 0.00 0.00 0.00 2.90
5437 5537 1.815003 GCAAACCACTCCTCATGGAAG 59.185 52.381 0.00 0.00 42.66 3.46
5441 5541 1.153289 CACTCCTCATGGAAGCCCG 60.153 63.158 0.00 0.00 42.66 6.13
5449 5549 2.423538 CTCATGGAAGCCCGGTTTTAAG 59.576 50.000 0.00 0.00 34.29 1.85
5450 5550 1.476488 CATGGAAGCCCGGTTTTAAGG 59.524 52.381 0.00 0.00 34.29 2.69
5451 5551 0.772384 TGGAAGCCCGGTTTTAAGGA 59.228 50.000 0.00 0.00 34.29 3.36
5452 5552 1.145325 TGGAAGCCCGGTTTTAAGGAA 59.855 47.619 0.00 0.00 34.29 3.36
5453 5553 1.816835 GGAAGCCCGGTTTTAAGGAAG 59.183 52.381 0.00 0.00 0.00 3.46
5454 5554 1.201647 GAAGCCCGGTTTTAAGGAAGC 59.798 52.381 0.00 0.00 0.00 3.86
5455 5555 0.611062 AGCCCGGTTTTAAGGAAGCC 60.611 55.000 0.00 0.00 35.44 4.35
5456 5556 1.601419 GCCCGGTTTTAAGGAAGCCC 61.601 60.000 0.00 0.00 35.35 5.19
5457 5557 0.251430 CCCGGTTTTAAGGAAGCCCA 60.251 55.000 0.00 0.00 35.35 5.36
5458 5558 1.173913 CCGGTTTTAAGGAAGCCCAG 58.826 55.000 0.00 0.00 35.35 4.45
5459 5559 1.546998 CCGGTTTTAAGGAAGCCCAGT 60.547 52.381 0.00 0.00 35.35 4.00
5460 5560 2.235891 CGGTTTTAAGGAAGCCCAGTT 58.764 47.619 0.00 0.00 35.35 3.16
5461 5561 2.626266 CGGTTTTAAGGAAGCCCAGTTT 59.374 45.455 0.00 0.00 35.35 2.66
5462 5562 3.069016 CGGTTTTAAGGAAGCCCAGTTTT 59.931 43.478 0.00 0.00 35.35 2.43
5463 5563 4.278919 CGGTTTTAAGGAAGCCCAGTTTTA 59.721 41.667 0.00 0.00 35.35 1.52
5464 5564 5.221283 CGGTTTTAAGGAAGCCCAGTTTTAA 60.221 40.000 0.00 0.00 35.35 1.52
5465 5565 6.584488 GGTTTTAAGGAAGCCCAGTTTTAAA 58.416 36.000 0.00 0.00 32.84 1.52
5466 5566 7.221450 GGTTTTAAGGAAGCCCAGTTTTAAAT 58.779 34.615 0.00 0.00 32.84 1.40
5467 5567 7.717875 GGTTTTAAGGAAGCCCAGTTTTAAATT 59.282 33.333 0.00 0.00 32.84 1.82
5468 5568 9.116067 GTTTTAAGGAAGCCCAGTTTTAAATTT 57.884 29.630 0.00 0.00 33.88 1.82
5469 5569 8.896320 TTTAAGGAAGCCCAGTTTTAAATTTC 57.104 30.769 0.00 0.00 33.88 2.17
5470 5570 5.483685 AGGAAGCCCAGTTTTAAATTTCC 57.516 39.130 0.00 0.00 34.48 3.13
5471 5571 4.904853 AGGAAGCCCAGTTTTAAATTTCCA 59.095 37.500 0.00 0.00 36.24 3.53
5472 5572 5.547666 AGGAAGCCCAGTTTTAAATTTCCAT 59.452 36.000 0.00 0.00 36.24 3.41
5473 5573 6.728632 AGGAAGCCCAGTTTTAAATTTCCATA 59.271 34.615 0.00 0.00 36.24 2.74
5474 5574 7.236640 AGGAAGCCCAGTTTTAAATTTCCATAA 59.763 33.333 0.00 0.00 36.24 1.90
5475 5575 7.880713 GGAAGCCCAGTTTTAAATTTCCATAAA 59.119 33.333 0.00 0.00 34.44 1.40
5476 5576 8.615878 AAGCCCAGTTTTAAATTTCCATAAAC 57.384 30.769 0.00 2.47 0.00 2.01
5477 5577 7.165485 AGCCCAGTTTTAAATTTCCATAAACC 58.835 34.615 0.00 0.00 30.93 3.27
5478 5578 6.937465 GCCCAGTTTTAAATTTCCATAAACCA 59.063 34.615 0.00 0.00 30.93 3.67
5479 5579 7.094975 GCCCAGTTTTAAATTTCCATAAACCAC 60.095 37.037 0.00 0.00 30.93 4.16
5480 5580 7.934120 CCCAGTTTTAAATTTCCATAAACCACA 59.066 33.333 0.00 0.00 30.93 4.17
5481 5581 8.769891 CCAGTTTTAAATTTCCATAAACCACAC 58.230 33.333 0.00 0.00 30.93 3.82
5482 5582 8.484008 CAGTTTTAAATTTCCATAAACCACACG 58.516 33.333 0.00 0.00 30.93 4.49
5483 5583 8.414778 AGTTTTAAATTTCCATAAACCACACGA 58.585 29.630 0.00 0.00 30.93 4.35
5484 5584 9.198837 GTTTTAAATTTCCATAAACCACACGAT 57.801 29.630 0.00 0.00 0.00 3.73
5485 5585 9.765795 TTTTAAATTTCCATAAACCACACGATT 57.234 25.926 0.00 0.00 0.00 3.34
5492 5592 8.542497 TTCCATAAACCACACGATTATATAGC 57.458 34.615 0.00 0.00 0.00 2.97
5493 5593 7.101054 TCCATAAACCACACGATTATATAGCC 58.899 38.462 0.00 0.00 0.00 3.93
5494 5594 6.876789 CCATAAACCACACGATTATATAGCCA 59.123 38.462 0.00 0.00 0.00 4.75
5495 5595 7.389330 CCATAAACCACACGATTATATAGCCAA 59.611 37.037 0.00 0.00 0.00 4.52
5496 5596 8.779303 CATAAACCACACGATTATATAGCCAAA 58.221 33.333 0.00 0.00 0.00 3.28
5497 5597 6.861065 AACCACACGATTATATAGCCAAAG 57.139 37.500 0.00 0.00 0.00 2.77
5498 5598 5.305585 ACCACACGATTATATAGCCAAAGG 58.694 41.667 0.00 0.00 0.00 3.11
5499 5599 4.695455 CCACACGATTATATAGCCAAAGGG 59.305 45.833 0.00 0.00 37.18 3.95
5500 5600 4.695455 CACACGATTATATAGCCAAAGGGG 59.305 45.833 0.00 0.00 40.85 4.79
5501 5601 4.261801 CACGATTATATAGCCAAAGGGGG 58.738 47.826 0.00 0.00 37.04 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 68 3.747708 GCCGGCATAGGAAATAAAGGAGT 60.748 47.826 24.80 0.00 0.00 3.85
129 134 3.731216 CACGTCTAGAGCAATGAATACGG 59.269 47.826 0.00 0.00 33.65 4.02
167 172 6.569127 TGCCCCTTTAAGAGATAACACATA 57.431 37.500 0.00 0.00 0.00 2.29
356 365 3.772025 TCTTTCAGCCTTTGGGTTTTTCA 59.228 39.130 0.00 0.00 34.45 2.69
362 371 1.986882 CTGTCTTTCAGCCTTTGGGT 58.013 50.000 0.00 0.00 37.36 4.51
382 391 4.760204 GCCAAAGCTTCTTTTCTGGTAGTA 59.240 41.667 12.91 0.00 35.50 1.82
383 392 3.570125 GCCAAAGCTTCTTTTCTGGTAGT 59.430 43.478 12.91 0.00 35.50 2.73
384 393 3.057245 GGCCAAAGCTTCTTTTCTGGTAG 60.057 47.826 12.91 0.00 39.73 3.18
410 419 2.088355 AGGAGGTAGGGGTAGAGGGATA 60.088 54.545 0.00 0.00 0.00 2.59
411 420 1.168853 GGAGGTAGGGGTAGAGGGAT 58.831 60.000 0.00 0.00 0.00 3.85
412 421 0.049066 AGGAGGTAGGGGTAGAGGGA 59.951 60.000 0.00 0.00 0.00 4.20
413 422 0.483770 GAGGAGGTAGGGGTAGAGGG 59.516 65.000 0.00 0.00 0.00 4.30
414 423 1.426215 GAGAGGAGGTAGGGGTAGAGG 59.574 61.905 0.00 0.00 0.00 3.69
484 495 8.473358 AGTATAGTTTAAAAAGCTGTGGGTTT 57.527 30.769 0.00 0.00 43.80 3.27
562 577 1.847088 GGAAGGGTGAGATTAAGGCCT 59.153 52.381 0.00 0.00 0.00 5.19
601 624 5.772169 GGGATTGGAGAAATAATGGAGGAAG 59.228 44.000 0.00 0.00 0.00 3.46
602 625 5.436374 AGGGATTGGAGAAATAATGGAGGAA 59.564 40.000 0.00 0.00 0.00 3.36
603 626 4.984268 AGGGATTGGAGAAATAATGGAGGA 59.016 41.667 0.00 0.00 0.00 3.71
604 627 5.330648 AGGGATTGGAGAAATAATGGAGG 57.669 43.478 0.00 0.00 0.00 4.30
605 628 6.266330 GGAAAGGGATTGGAGAAATAATGGAG 59.734 42.308 0.00 0.00 0.00 3.86
840 874 1.095600 GAAATCAAGGGGCGGTTCTC 58.904 55.000 0.00 0.00 0.00 2.87
874 908 1.393539 GCAAGTAATTCGCGAGCAGAA 59.606 47.619 9.59 0.00 0.00 3.02
935 982 1.004277 CGGAGGAATTCCCAACCAGAA 59.996 52.381 21.22 0.00 43.63 3.02
1116 1164 1.202818 GCGGAGGAGCAAAGGGATAAT 60.203 52.381 0.00 0.00 37.05 1.28
1165 1213 2.487086 CGGTCCCCAGATGCATAATTCA 60.487 50.000 0.00 0.00 0.00 2.57
1194 1242 0.817654 GGGGGCCGAAAGATTTCTTG 59.182 55.000 0.00 0.00 36.12 3.02
1210 1258 4.426313 GAAGCCGGGTCCAAGGGG 62.426 72.222 6.62 0.00 0.00 4.79
1214 1262 0.544697 GATTAGGAAGCCGGGTCCAA 59.455 55.000 19.76 13.51 37.65 3.53
1218 1266 2.029307 GCGAGATTAGGAAGCCGGGT 62.029 60.000 0.00 0.00 0.00 5.28
1220 1268 0.105039 AAGCGAGATTAGGAAGCCGG 59.895 55.000 0.00 0.00 0.00 6.13
1222 1270 2.900716 AGAAGCGAGATTAGGAAGCC 57.099 50.000 0.00 0.00 0.00 4.35
1224 1272 6.337356 AGAAAGAAGAAGCGAGATTAGGAAG 58.663 40.000 0.00 0.00 0.00 3.46
1238 1286 4.319477 CGAACGGCAATCAAGAAAGAAGAA 60.319 41.667 0.00 0.00 0.00 2.52
1240 1288 3.058914 ACGAACGGCAATCAAGAAAGAAG 60.059 43.478 0.00 0.00 0.00 2.85
1247 1295 1.052287 GCAAACGAACGGCAATCAAG 58.948 50.000 0.00 0.00 0.00 3.02
1256 1304 0.304098 TACCAAACCGCAAACGAACG 59.696 50.000 0.00 0.00 43.93 3.95
1317 1365 2.338785 GCAGCCCACAAAGCTCTCC 61.339 63.158 0.00 0.00 38.95 3.71
1318 1366 0.892814 AAGCAGCCCACAAAGCTCTC 60.893 55.000 0.00 0.00 38.95 3.20
1325 1373 1.186917 CCAATCCAAGCAGCCCACAA 61.187 55.000 0.00 0.00 0.00 3.33
1328 1376 2.037687 CCCAATCCAAGCAGCCCA 59.962 61.111 0.00 0.00 0.00 5.36
1330 1378 1.478105 CTTAACCCAATCCAAGCAGCC 59.522 52.381 0.00 0.00 0.00 4.85
1331 1379 1.478105 CCTTAACCCAATCCAAGCAGC 59.522 52.381 0.00 0.00 0.00 5.25
1528 1576 7.413548 GCTCTTGTCTTCTTGTATAAAAGGAGC 60.414 40.741 6.11 8.55 33.39 4.70
1663 1711 5.994668 ACAGAGGTTAAAGCAAAAGAGAGAG 59.005 40.000 0.00 0.00 0.00 3.20
1758 1806 3.822735 CCATACCAAATGAGGCATACCAG 59.177 47.826 0.00 0.00 39.06 4.00
1832 1880 4.875536 TCACATACATGGTCAACTGCATAC 59.124 41.667 0.00 0.00 0.00 2.39
1918 1966 0.390340 TCGAGGAATGCAGCACAGAC 60.390 55.000 0.00 0.00 0.00 3.51
1977 2025 7.066284 CCCTCACGAGATTGTATCAGAATTTTT 59.934 37.037 0.00 0.00 0.00 1.94
2001 2049 2.311124 ACTTATTAGCAGCGTGTCCC 57.689 50.000 0.00 0.00 0.00 4.46
2020 2068 6.294361 AGAATGTACACAGTATTGCAGGTA 57.706 37.500 0.00 0.00 0.00 3.08
2032 2080 6.515832 AGATCGATATGCAAGAATGTACACA 58.484 36.000 0.00 0.00 0.00 3.72
2034 2082 6.986231 ACAAGATCGATATGCAAGAATGTACA 59.014 34.615 0.00 0.00 0.00 2.90
2089 2137 2.426738 CAAAGTGGAGTGCCTGTTTCAA 59.573 45.455 0.00 0.00 34.31 2.69
2267 2315 0.955919 GCTGCCGCTGTTCCTTTAGT 60.956 55.000 0.00 0.00 0.00 2.24
2288 2336 2.476821 CTGTGGCTTGGCTTTTTCTTG 58.523 47.619 0.00 0.00 0.00 3.02
2617 2668 6.683974 AGATATAACATTGCAGACCAACAC 57.316 37.500 0.00 0.00 35.99 3.32
3095 3163 5.707298 TGACCCTGAATTCAAAAGATCAGAC 59.293 40.000 9.88 0.00 41.38 3.51
3233 3303 6.650807 CAGAAAGGTAACATAACTGCTCTTCA 59.349 38.462 0.00 0.00 41.41 3.02
3247 3317 2.764572 TCCGAGGATCCAGAAAGGTAAC 59.235 50.000 15.82 0.00 39.02 2.50
3289 3362 0.890996 GGAACCCACAGGAGTTGCAG 60.891 60.000 0.00 0.00 34.76 4.41
3329 3402 5.237996 TGAGTTTGAACTTCTCAGAAGCATG 59.762 40.000 14.81 0.00 39.88 4.06
3409 3482 6.531503 CTGAGTAGGATTCACTTGTAAGGA 57.468 41.667 0.00 0.00 0.00 3.36
3428 3501 1.151668 CAAACGAAGCAGTCCCTGAG 58.848 55.000 0.00 0.00 32.44 3.35
3440 3513 4.884458 TTCACTATGCACAACAAACGAA 57.116 36.364 0.00 0.00 0.00 3.85
3555 3628 9.931210 GAAACCAATGCACAATACTACTAATAC 57.069 33.333 0.00 0.00 0.00 1.89
3644 3720 4.767409 ACCTTAGCTTCTTGATTTTCACCC 59.233 41.667 0.00 0.00 0.00 4.61
3675 3751 1.145571 ACCCCTGCAAAAGAGGTACA 58.854 50.000 0.00 0.00 0.00 2.90
3676 3752 3.428413 TTACCCCTGCAAAAGAGGTAC 57.572 47.619 0.00 0.00 32.90 3.34
3740 3816 6.874664 ACCTCTAAAGCTACTGAAACTAAAGC 59.125 38.462 0.00 0.00 0.00 3.51
3851 3927 9.798994 AAGGTTAGAAGTTCGTAACAGTATATG 57.201 33.333 18.59 0.00 31.80 1.78
3855 3931 7.491682 ACAAAGGTTAGAAGTTCGTAACAGTA 58.508 34.615 18.59 0.00 31.80 2.74
3863 3939 5.479716 ACACAACAAAGGTTAGAAGTTCG 57.520 39.130 0.00 0.00 34.87 3.95
3871 3947 9.344772 ACTTAATCATGTACACAACAAAGGTTA 57.655 29.630 0.00 0.00 42.70 2.85
4033 4110 4.534103 AGAGGAACTAAGATTGCTGACCTT 59.466 41.667 0.00 0.00 41.55 3.50
4333 4410 2.687200 ATGTACTGCGGAGGGGCA 60.687 61.111 9.36 4.32 41.45 5.36
4542 4619 5.160386 TCCAGGAAACTAAGGGAAACTACT 58.840 41.667 0.00 0.00 40.21 2.57
4894 4973 1.061033 AGAGGGGCCTGTTATGGAGAT 60.061 52.381 0.84 0.00 0.00 2.75
4911 4990 3.282885 GACCTGCCATTCCCTAAAAGAG 58.717 50.000 0.00 0.00 0.00 2.85
4999 5096 7.400052 TCATGCATACCTGTACATGATACCTAT 59.600 37.037 0.00 0.00 42.86 2.57
5018 5115 4.785346 AGGTCACCTAAAGATCATGCAT 57.215 40.909 0.00 0.00 28.47 3.96
5020 5117 5.858381 TCATAGGTCACCTAAAGATCATGC 58.142 41.667 7.92 0.00 39.77 4.06
5069 5168 6.316640 TGAGAACACAAAAGAATACGTTGGAA 59.683 34.615 0.00 0.00 0.00 3.53
5083 5182 8.664798 CAAACGGATATTAGATGAGAACACAAA 58.335 33.333 0.00 0.00 0.00 2.83
5086 5185 7.621991 CACAAACGGATATTAGATGAGAACAC 58.378 38.462 0.00 0.00 0.00 3.32
5093 5192 6.851222 AGAAGCACAAACGGATATTAGATG 57.149 37.500 0.00 0.00 0.00 2.90
5104 5203 6.093404 TCTCACTAAGATAGAAGCACAAACG 58.907 40.000 0.00 0.00 0.00 3.60
5191 5291 2.953020 TGGTGTCTTTTGTTGCAACAC 58.047 42.857 31.17 19.39 38.92 3.32
5192 5292 3.667497 TTGGTGTCTTTTGTTGCAACA 57.333 38.095 27.96 27.96 37.08 3.33
5193 5293 4.180057 TCATTGGTGTCTTTTGTTGCAAC 58.820 39.130 22.83 22.83 0.00 4.17
5210 5310 3.251479 TCCATTCGACCAGTCTCATTG 57.749 47.619 0.00 0.00 0.00 2.82
5213 5313 6.724893 TTATAATCCATTCGACCAGTCTCA 57.275 37.500 0.00 0.00 0.00 3.27
5229 5329 8.186163 CCTTTTTAGGGGAACGTGTTTATAATC 58.814 37.037 0.00 0.00 0.00 1.75
5256 5356 7.436673 TGGTAAGTTTTGTTGCAACATGTAATC 59.563 33.333 31.48 20.44 38.95 1.75
5277 5377 1.533625 GTGTGCAGCCTCATTGGTAA 58.466 50.000 0.00 0.00 38.35 2.85
5307 5407 1.568597 CCAAATCCCCACAGATACCCA 59.431 52.381 0.00 0.00 0.00 4.51
5321 5421 5.062558 GCATTTTCTATGCACACACCAAATC 59.937 40.000 4.95 0.00 44.00 2.17
5346 5446 8.856153 TGTCAGCTTTTATCTTATGGTTTACA 57.144 30.769 0.00 0.00 0.00 2.41
5416 5516 1.067295 TCCATGAGGAGTGGTTTGCT 58.933 50.000 0.00 0.00 39.61 3.91
5421 5521 1.566298 GGGCTTCCATGAGGAGTGGT 61.566 60.000 0.00 0.00 46.74 4.16
5431 5531 1.356398 TCCTTAAAACCGGGCTTCCAT 59.644 47.619 6.32 0.00 0.00 3.41
5432 5532 0.772384 TCCTTAAAACCGGGCTTCCA 59.228 50.000 6.32 0.00 0.00 3.53
5437 5537 1.601419 GGGCTTCCTTAAAACCGGGC 61.601 60.000 6.32 0.00 0.00 6.13
5441 5541 4.682778 AAAACTGGGCTTCCTTAAAACC 57.317 40.909 0.00 0.00 0.00 3.27
5449 5549 5.222079 TGGAAATTTAAAACTGGGCTTCC 57.778 39.130 0.00 0.00 33.24 3.46
5450 5550 8.717821 GTTTATGGAAATTTAAAACTGGGCTTC 58.282 33.333 0.00 0.00 0.00 3.86
5451 5551 7.663905 GGTTTATGGAAATTTAAAACTGGGCTT 59.336 33.333 13.28 0.00 32.11 4.35
5452 5552 7.165485 GGTTTATGGAAATTTAAAACTGGGCT 58.835 34.615 13.28 0.00 32.11 5.19
5453 5553 6.937465 TGGTTTATGGAAATTTAAAACTGGGC 59.063 34.615 13.28 0.00 32.11 5.36
5454 5554 7.934120 TGTGGTTTATGGAAATTTAAAACTGGG 59.066 33.333 13.28 0.00 32.11 4.45
5455 5555 8.769891 GTGTGGTTTATGGAAATTTAAAACTGG 58.230 33.333 13.28 0.00 32.11 4.00
5456 5556 8.484008 CGTGTGGTTTATGGAAATTTAAAACTG 58.516 33.333 13.28 0.00 32.11 3.16
5457 5557 8.414778 TCGTGTGGTTTATGGAAATTTAAAACT 58.585 29.630 13.28 0.00 32.11 2.66
5458 5558 8.576936 TCGTGTGGTTTATGGAAATTTAAAAC 57.423 30.769 0.00 0.62 0.00 2.43
5459 5559 9.765795 AATCGTGTGGTTTATGGAAATTTAAAA 57.234 25.926 0.00 0.00 0.00 1.52
5466 5566 8.995220 GCTATATAATCGTGTGGTTTATGGAAA 58.005 33.333 0.00 0.00 0.00 3.13
5467 5567 7.604927 GGCTATATAATCGTGTGGTTTATGGAA 59.395 37.037 0.00 0.00 0.00 3.53
5468 5568 7.101054 GGCTATATAATCGTGTGGTTTATGGA 58.899 38.462 0.00 0.00 0.00 3.41
5469 5569 6.876789 TGGCTATATAATCGTGTGGTTTATGG 59.123 38.462 0.00 0.00 0.00 2.74
5470 5570 7.899178 TGGCTATATAATCGTGTGGTTTATG 57.101 36.000 0.00 0.00 0.00 1.90
5471 5571 8.911918 TTTGGCTATATAATCGTGTGGTTTAT 57.088 30.769 0.00 0.00 0.00 1.40
5472 5572 7.442969 CCTTTGGCTATATAATCGTGTGGTTTA 59.557 37.037 0.00 0.00 0.00 2.01
5473 5573 6.262273 CCTTTGGCTATATAATCGTGTGGTTT 59.738 38.462 0.00 0.00 0.00 3.27
5474 5574 5.763204 CCTTTGGCTATATAATCGTGTGGTT 59.237 40.000 0.00 0.00 0.00 3.67
5475 5575 5.305585 CCTTTGGCTATATAATCGTGTGGT 58.694 41.667 0.00 0.00 0.00 4.16
5476 5576 4.695455 CCCTTTGGCTATATAATCGTGTGG 59.305 45.833 0.00 0.00 0.00 4.17
5477 5577 4.695455 CCCCTTTGGCTATATAATCGTGTG 59.305 45.833 0.00 0.00 0.00 3.82
5478 5578 4.263331 CCCCCTTTGGCTATATAATCGTGT 60.263 45.833 0.00 0.00 0.00 4.49
5479 5579 4.261801 CCCCCTTTGGCTATATAATCGTG 58.738 47.826 0.00 0.00 0.00 4.35
5480 5580 4.569719 CCCCCTTTGGCTATATAATCGT 57.430 45.455 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.