Multiple sequence alignment - TraesCS7A01G238100

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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 TraesCS7A01G238100 chr7A 100.000 2340 0 0 1 2340 211366272 211363933 0 4322
1 TraesCS7A01G238100 chr7A 97.703 2351 42 6 1 2340 638509520 638507171 0 4032
2 TraesCS7A01G238100 chr7D 97.655 2345 50 3 1 2340 382087949 382090293 0 4021
3 TraesCS7A01G238100 chrUn 97.448 2351 49 5 1 2340 171006431 171008781 0 3999
4 TraesCS7A01G238100 chr6B 97.448 2351 49 5 1 2340 596603714 596601364 0 3999
5 TraesCS7A01G238100 chr1A 97.142 2344 58 5 1 2340 94665786 94663448 0 3949
6 TraesCS7A01G238100 chr1B 97.021 2350 58 6 1 2340 672539369 672541716 0 3941


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 TraesCS7A01G238100 chr7A 211363933 211366272 2339 True 4322 4322 100.000 1 2340 1 chr7A.!!$R1 2339
1 TraesCS7A01G238100 chr7A 638507171 638509520 2349 True 4032 4032 97.703 1 2340 1 chr7A.!!$R2 2339
2 TraesCS7A01G238100 chr7D 382087949 382090293 2344 False 4021 4021 97.655 1 2340 1 chr7D.!!$F1 2339
3 TraesCS7A01G238100 chrUn 171006431 171008781 2350 False 3999 3999 97.448 1 2340 1 chrUn.!!$F1 2339
4 TraesCS7A01G238100 chr6B 596601364 596603714 2350 True 3999 3999 97.448 1 2340 1 chr6B.!!$R1 2339
5 TraesCS7A01G238100 chr1A 94663448 94665786 2338 True 3949 3949 97.142 1 2340 1 chr1A.!!$R1 2339
6 TraesCS7A01G238100 chr1B 672539369 672541716 2347 False 3941 3941 97.021 1 2340 1 chr1B.!!$F1 2339

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
546 555 0.11734 AAGCCCACAGACTCCCTAGT 59.883 55.0 0.0 0.0 39.21 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1484 2.423898 CCCGGTCGCCTGTCTATGT 61.424 63.158 0.0 0.0 0.0 2.29 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
451 460 2.703536 TGTGGGACTGCTTTTGTCTCTA 59.296 45.455 0.00 0.0 36.01 2.43
546 555 0.117340 AAGCCCACAGACTCCCTAGT 59.883 55.000 0.00 0.0 39.21 2.57
698 707 6.613271 TCCATGACTTCTAGAGGAAAGCTAAT 59.387 38.462 9.14 0.0 33.07 1.73
792 801 2.291209 TGTTGTACCTCACTCCCGTA 57.709 50.000 0.00 0.0 0.00 4.02
872 882 1.820519 GGGCTTTGCATCTGACATTCA 59.179 47.619 0.00 0.0 0.00 2.57
887 897 4.018506 TGACATTCATTGGGCTTTCCTCTA 60.019 41.667 0.00 0.0 36.20 2.43
1097 1108 9.869667 ACTCTTCCACTGACTTATATATGTACT 57.130 33.333 1.48 0.0 0.00 2.73
1304 1316 0.404040 GGGCGGGGATAATCATTCCA 59.596 55.000 0.00 0.0 34.77 3.53
1364 1376 1.630369 AGCCAGCCAATTGAGTCACTA 59.370 47.619 7.12 0.0 0.00 2.74
1479 1491 3.187211 GCTGCTCGCCTACATAGAC 57.813 57.895 0.00 0.0 0.00 2.59
1689 1702 1.320344 CCGAACCTCTGATCGACCCA 61.320 60.000 1.01 0.0 41.43 4.51
1788 1801 3.028366 GCGTCGGCTTGGAAGAAGC 62.028 63.158 0.00 0.0 42.30 3.86
1838 1851 5.463392 GCTGTAATAGATCGACTTGAATGCA 59.537 40.000 0.00 0.0 0.00 3.96
1883 1896 1.003118 CCATTTCAAGGGAGGACGACA 59.997 52.381 0.00 0.0 29.54 4.35
1890 1903 1.705873 AGGGAGGACGACATACCATC 58.294 55.000 3.17 0.0 0.00 3.51
1965 1978 4.331717 CGTGCTAAAAATCCGGTACATTCT 59.668 41.667 0.00 0.0 0.00 2.40
2072 2087 7.179338 CCCAGTAGTTCATATAGGAGCTATTGT 59.821 40.741 22.65 8.2 36.94 2.71
2074 2089 8.797438 CAGTAGTTCATATAGGAGCTATTGTCA 58.203 37.037 18.95 0.0 35.26 3.58
2156 2171 4.809426 AGTATTGCGCTATTTACCAGTGAC 59.191 41.667 10.14 0.0 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 1.003476 GCGTTTCCGGTAAAGGGGA 60.003 57.895 0.00 0.0 34.28 4.81
296 305 6.330178 AGCCTCTAAAGACTCTACTCCTAA 57.670 41.667 0.00 0.0 0.00 2.69
451 460 2.905415 TCAAGGGGCATTTGACATCT 57.095 45.000 0.00 0.0 30.03 2.90
546 555 4.438336 CGCATTTTAGGTCGAGTAGAGACA 60.438 45.833 0.00 0.0 40.20 3.41
698 707 2.282674 CTCCCAGCCAGCAAGCAA 60.283 61.111 0.55 0.0 34.23 3.91
741 750 2.583441 CCACCTTCTCACGGAGCCA 61.583 63.158 0.00 0.0 0.00 4.75
792 801 3.463048 AAAGAGCAGACCCCATTGAAT 57.537 42.857 0.00 0.0 0.00 2.57
872 882 0.546598 CCCGTAGAGGAAAGCCCAAT 59.453 55.000 0.00 0.0 45.00 3.16
898 908 1.561643 TGCACAAAAAGGTTGGGACA 58.438 45.000 0.00 0.0 0.00 4.02
904 914 4.165180 AGGGGTTTATTGCACAAAAAGGTT 59.835 37.500 0.00 0.0 0.00 3.50
905 915 3.714280 AGGGGTTTATTGCACAAAAAGGT 59.286 39.130 0.00 0.0 0.00 3.50
1097 1108 5.072040 TCACTTTCTCGTATGAGCATTCA 57.928 39.130 7.11 0.0 42.26 2.57
1111 1122 2.370189 CAGACCCAGGAGTTCACTTTCT 59.630 50.000 0.00 0.0 0.00 2.52
1205 1217 2.898612 TGTAACCGTCACCTGTAATCCA 59.101 45.455 0.00 0.0 0.00 3.41
1364 1376 2.668550 GCCTCCTGCGGTCGTTTT 60.669 61.111 0.00 0.0 0.00 2.43
1472 1484 2.423898 CCCGGTCGCCTGTCTATGT 61.424 63.158 0.00 0.0 0.00 2.29
1712 1725 5.713792 ACTGAATCTCGTCTTTCTCTCAA 57.286 39.130 0.00 0.0 0.00 3.02
1713 1726 6.431543 ACTTACTGAATCTCGTCTTTCTCTCA 59.568 38.462 0.00 0.0 0.00 3.27
1788 1801 3.296943 CGCGGTTGTTCGTATTTCATTTG 59.703 43.478 0.00 0.0 0.00 2.32
1815 1828 7.598118 AGATGCATTCAAGTCGATCTATTACAG 59.402 37.037 0.00 0.0 0.00 2.74
1883 1896 7.822334 TCGACAAAACAGAAAGTATGATGGTAT 59.178 33.333 0.00 0.0 0.00 2.73
1890 1903 4.378459 GGGCTCGACAAAACAGAAAGTATG 60.378 45.833 0.00 0.0 0.00 2.39
1965 1978 5.319043 AGACTAGGATGGGAAACAAAACA 57.681 39.130 0.00 0.0 0.00 2.83
2025 2039 4.219115 GGGAGATCATAGTGGAGAAGTCA 58.781 47.826 0.00 0.0 0.00 3.41
2035 2049 5.144159 TGAACTACTGGGGAGATCATAGT 57.856 43.478 0.00 0.0 0.00 2.12
2072 2087 7.990314 TCATAACCACGAATAGGAATGAAATGA 59.010 33.333 0.00 0.0 32.88 2.57
2074 2089 8.786898 CATCATAACCACGAATAGGAATGAAAT 58.213 33.333 0.00 0.0 36.45 2.17
2156 2171 7.557719 ACCAAAAGATCAGTCCAATAATACCAG 59.442 37.037 0.00 0.0 0.00 4.00


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

AutoCloner maintained by Alex Coulton.