Multiple sequence alignment - TraesCS5B01G054500

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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 TraesCS5B01G054500 chr5B 100.000 2339 0 0 1 2339 59780959 59778621 0 4320
1 TraesCS5B01G054500 chr5B 97.287 1364 37 0 1 1364 547493213 547491850 0 2314
2 TraesCS5B01G054500 chr5B 93.347 977 65 0 1363 2339 406395906 406394930 0 1445
3 TraesCS5B01G054500 chr2B 97.659 1367 30 2 1 1367 390803527 390802163 0 2346
4 TraesCS5B01G054500 chr1B 97.579 1363 32 1 1 1363 92336397 92337758 0 2333
5 TraesCS5B01G054500 chr1B 97.212 1363 36 2 2 1364 482480375 482481735 0 2305
6 TraesCS5B01G054500 chr1B 93.552 977 63 0 1363 2339 246792146 246793122 0 1456
7 TraesCS5B01G054500 chr1B 92.988 984 69 0 1356 2339 418098043 418097060 0 1435
8 TraesCS5B01G054500 chr3B 97.507 1364 34 0 1 1364 161678845 161677482 0 2331
9 TraesCS5B01G054500 chr3B 97.283 1362 37 0 1 1362 772414831 772413470 0 2311
10 TraesCS5B01G054500 chr3B 97.141 1364 38 1 1 1364 571263362 571262000 0 2302
11 TraesCS5B01G054500 chr3B 93.449 977 64 0 1363 2339 344962261 344963237 0 1450
12 TraesCS5B01G054500 chr7B 97.214 1364 32 2 1 1364 729023353 729024710 0 2303
13 TraesCS5B01G054500 chr6B 96.928 1367 40 2 1 1367 257594373 257595737 0 2290
14 TraesCS5B01G054500 chr6B 93.859 977 59 1 1363 2339 494806209 494805234 0 1471
15 TraesCS5B01G054500 chr6B 93.654 977 62 0 1363 2339 404401681 404400705 0 1461
16 TraesCS5B01G054500 chr6B 93.347 977 65 0 1363 2339 68616786 68617762 0 1445
17 TraesCS5B01G054500 chrUn 93.347 977 65 0 1363 2339 318209186 318208210 0 1445
18 TraesCS5B01G054500 chr4B 93.347 977 62 1 1363 2339 576410895 576411868 0 1441


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 TraesCS5B01G054500 chr5B 59778621 59780959 2338 True 4320 4320 100.000 1 2339 1 chr5B.!!$R1 2338
1 TraesCS5B01G054500 chr5B 547491850 547493213 1363 True 2314 2314 97.287 1 1364 1 chr5B.!!$R3 1363
2 TraesCS5B01G054500 chr5B 406394930 406395906 976 True 1445 1445 93.347 1363 2339 1 chr5B.!!$R2 976
3 TraesCS5B01G054500 chr2B 390802163 390803527 1364 True 2346 2346 97.659 1 1367 1 chr2B.!!$R1 1366
4 TraesCS5B01G054500 chr1B 92336397 92337758 1361 False 2333 2333 97.579 1 1363 1 chr1B.!!$F1 1362
5 TraesCS5B01G054500 chr1B 482480375 482481735 1360 False 2305 2305 97.212 2 1364 1 chr1B.!!$F3 1362
6 TraesCS5B01G054500 chr1B 246792146 246793122 976 False 1456 1456 93.552 1363 2339 1 chr1B.!!$F2 976
7 TraesCS5B01G054500 chr1B 418097060 418098043 983 True 1435 1435 92.988 1356 2339 1 chr1B.!!$R1 983
8 TraesCS5B01G054500 chr3B 161677482 161678845 1363 True 2331 2331 97.507 1 1364 1 chr3B.!!$R1 1363
9 TraesCS5B01G054500 chr3B 772413470 772414831 1361 True 2311 2311 97.283 1 1362 1 chr3B.!!$R3 1361
10 TraesCS5B01G054500 chr3B 571262000 571263362 1362 True 2302 2302 97.141 1 1364 1 chr3B.!!$R2 1363
11 TraesCS5B01G054500 chr3B 344962261 344963237 976 False 1450 1450 93.449 1363 2339 1 chr3B.!!$F1 976
12 TraesCS5B01G054500 chr7B 729023353 729024710 1357 False 2303 2303 97.214 1 1364 1 chr7B.!!$F1 1363
13 TraesCS5B01G054500 chr6B 257594373 257595737 1364 False 2290 2290 96.928 1 1367 1 chr6B.!!$F2 1366
14 TraesCS5B01G054500 chr6B 494805234 494806209 975 True 1471 1471 93.859 1363 2339 1 chr6B.!!$R2 976
15 TraesCS5B01G054500 chr6B 404400705 404401681 976 True 1461 1461 93.654 1363 2339 1 chr6B.!!$R1 976
16 TraesCS5B01G054500 chr6B 68616786 68617762 976 False 1445 1445 93.347 1363 2339 1 chr6B.!!$F1 976
17 TraesCS5B01G054500 chrUn 318208210 318209186 976 True 1445 1445 93.347 1363 2339 1 chrUn.!!$R1 976
18 TraesCS5B01G054500 chr4B 576410895 576411868 973 False 1441 1441 93.347 1363 2339 1 chr4B.!!$F1 976

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
359 360 2.092646 CCACGGTCAATCCTATTTGGGA 60.093 50.0 0.0 0.0 39.95 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2054 0.385974 CGCGGCTTGAAGTTTCTTGG 60.386 55.0 0.0 0.0 0.0 3.61 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
59 60 3.135348 TGGATTCCAAATTGTGCAAACCA 59.865 39.130 1.94 0.00 0.00 3.67
330 331 4.957296 AGTTACGACATACCAATGGGATC 58.043 43.478 3.55 0.00 37.43 3.36
359 360 2.092646 CCACGGTCAATCCTATTTGGGA 60.093 50.000 0.00 0.00 39.95 4.37
463 464 9.367444 GTGTTAACTTAGCTAATAGACATGTGT 57.633 33.333 1.15 0.22 0.00 3.72
700 702 3.189910 GCGTGACATGATTGCCATATCAT 59.810 43.478 0.00 0.00 40.43 2.45
1016 1018 1.615392 GTTGATGGCTGAAGCTTTGGT 59.385 47.619 0.00 0.00 41.70 3.67
1038 1040 5.066764 GGTGTTAAAATTTGGCCTATCGCTA 59.933 40.000 3.32 0.00 37.74 4.26
1122 1124 1.541379 TGAACGAAGGAGGACGATCA 58.459 50.000 0.00 0.00 38.52 2.92
1381 1384 5.897377 AAAAAGAGCAACGCTATGGTAAT 57.103 34.783 0.00 0.00 39.88 1.89
1483 1486 5.743026 TCTTTCGTTTGCACAACTATGAA 57.257 34.783 9.17 4.42 0.00 2.57
1495 1498 6.992123 TGCACAACTATGAAGAAGAGAAGAAA 59.008 34.615 0.00 0.00 0.00 2.52
1678 1681 5.305644 TCTCTTCAAGAAGCTACAACTCCTT 59.694 40.000 4.95 0.00 38.28 3.36
1792 1795 3.071479 GGCACGTTTCTTGAATGGACTA 58.929 45.455 0.00 0.00 0.00 2.59
1847 1850 3.107601 CCCTACTCCAACCTCATTGAGA 58.892 50.000 15.36 0.00 41.23 3.27
1890 1893 2.096069 CAGAACGTCAAGTGCAAGATGG 60.096 50.000 0.00 0.00 0.00 3.51
1892 1895 1.133253 CGTCAAGTGCAAGATGGCG 59.867 57.895 7.16 7.16 35.74 5.69
1935 1938 2.612221 CCAAGACCTACGGTTTCTCCAC 60.612 54.545 0.00 0.00 35.25 4.02
1936 1939 2.299297 CAAGACCTACGGTTTCTCCACT 59.701 50.000 0.00 0.00 35.25 4.00
2018 2021 6.345920 ACGACAAGTCAAGTTACAAGAAAG 57.654 37.500 0.72 0.00 0.00 2.62
2051 2054 3.888930 CTCAAGTCATCCTCTCCCTACTC 59.111 52.174 0.00 0.00 0.00 2.59
2243 2246 1.995542 AGGAAATGGAAGCCCTTGAGA 59.004 47.619 0.00 0.00 0.00 3.27
2282 2285 3.775202 CGAGTGAACGAGGATGAAGATT 58.225 45.455 0.00 0.00 35.09 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
267 268 4.837860 TCCCATTCCACAAAATAAGCAGTT 59.162 37.500 0.00 0.0 0.00 3.16
268 269 4.220602 GTCCCATTCCACAAAATAAGCAGT 59.779 41.667 0.00 0.0 0.00 4.40
330 331 0.799534 GATTGACCGTGGTACGTCCG 60.800 60.000 0.00 0.0 40.58 4.79
359 360 4.218312 ACAAGCAAGTTTCCAAATCCTCT 58.782 39.130 0.00 0.0 0.00 3.69
463 464 2.753452 CAGGACACTTAGGCGAGACTTA 59.247 50.000 0.00 0.0 0.00 2.24
700 702 0.104882 TCCCACCACAAGTACCAGGA 60.105 55.000 0.00 0.0 0.00 3.86
1016 1018 5.220970 GCTAGCGATAGGCCAAATTTTAACA 60.221 40.000 10.15 0.0 45.17 2.41
1038 1040 2.386064 TACAACCCGTCCTTTGCGCT 62.386 55.000 9.73 0.0 0.00 5.92
1378 1381 6.211184 ACTTGGGCATTGTGAATTTGAGATTA 59.789 34.615 0.00 0.0 0.00 1.75
1381 1384 3.896888 ACTTGGGCATTGTGAATTTGAGA 59.103 39.130 0.00 0.0 0.00 3.27
1483 1486 4.813697 GCCATAGCGATTTTCTTCTCTTCT 59.186 41.667 0.00 0.0 0.00 2.85
1495 1498 3.136763 CTCAAGTGATGCCATAGCGATT 58.863 45.455 0.00 0.0 44.31 3.34
1695 1698 8.960591 CCATTTCCTTGTAGTATTCTTCAACAT 58.039 33.333 0.00 0.0 30.16 2.71
1792 1795 5.070047 GGCAATCTTCTTGATGGGATGATTT 59.930 40.000 0.00 0.0 36.27 2.17
1847 1850 2.283298 CTTGGTAGCTTGATGCACGAT 58.717 47.619 0.00 0.0 45.94 3.73
1935 1938 2.737252 GGAGTCGTTGAAGCTTGGTTAG 59.263 50.000 2.10 0.0 0.00 2.34
1936 1939 2.367567 AGGAGTCGTTGAAGCTTGGTTA 59.632 45.455 2.10 0.0 0.00 2.85
2051 2054 0.385974 CGCGGCTTGAAGTTTCTTGG 60.386 55.000 0.00 0.0 0.00 3.61
2243 2246 2.576832 GCTGGTGCATGGCCACTTT 61.577 57.895 8.16 0.0 39.41 2.66
2282 2285 5.227569 TCCTCATCACAAAAGACTTGCTA 57.772 39.130 0.00 0.0 0.00 3.49


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

AutoCloner maintained by Alex Coulton.