Multiple sequence alignment - TraesCS7A01G397000

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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 TraesCS7A01G397000 chr7A 100.000 2369 0 0 1 2369 575291120 575293488 0 4375
1 TraesCS7A01G397000 chr7A 97.766 2372 50 3 1 2369 60120927 60118556 0 4084
2 TraesCS7A01G397000 chr7A 97.386 2372 58 4 1 2369 63429290 63431660 0 4034
3 TraesCS7A01G397000 chr7D 98.018 2371 45 2 1 2369 203518117 203520487 0 4117
4 TraesCS7A01G397000 chr7B 97.976 2372 45 3 1 2369 644470082 644472453 0 4111
5 TraesCS7A01G397000 chr3A 97.680 2371 52 3 1 2369 633113889 633116258 0 4071
6 TraesCS7A01G397000 chr3A 96.922 2372 70 3 1 2369 51869813 51872184 0 3973
7 TraesCS7A01G397000 chr6B 97.426 2370 60 1 1 2369 306993349 306990980 0 4037
8 TraesCS7A01G397000 chr2B 96.963 2371 64 4 1 2369 391110201 391107837 0 3973
9 TraesCS7A01G397000 chr3B 95.485 2370 99 3 1 2369 368854326 368851964 0 3777


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 TraesCS7A01G397000 chr7A 575291120 575293488 2368 False 4375 4375 100.000 1 2369 1 chr7A.!!$F2 2368
1 TraesCS7A01G397000 chr7A 60118556 60120927 2371 True 4084 4084 97.766 1 2369 1 chr7A.!!$R1 2368
2 TraesCS7A01G397000 chr7A 63429290 63431660 2370 False 4034 4034 97.386 1 2369 1 chr7A.!!$F1 2368
3 TraesCS7A01G397000 chr7D 203518117 203520487 2370 False 4117 4117 98.018 1 2369 1 chr7D.!!$F1 2368
4 TraesCS7A01G397000 chr7B 644470082 644472453 2371 False 4111 4111 97.976 1 2369 1 chr7B.!!$F1 2368
5 TraesCS7A01G397000 chr3A 633113889 633116258 2369 False 4071 4071 97.680 1 2369 1 chr3A.!!$F2 2368
6 TraesCS7A01G397000 chr3A 51869813 51872184 2371 False 3973 3973 96.922 1 2369 1 chr3A.!!$F1 2368
7 TraesCS7A01G397000 chr6B 306990980 306993349 2369 True 4037 4037 97.426 1 2369 1 chr6B.!!$R1 2368
8 TraesCS7A01G397000 chr2B 391107837 391110201 2364 True 3973 3973 96.963 1 2369 1 chr2B.!!$R1 2368
9 TraesCS7A01G397000 chr3B 368851964 368854326 2362 True 3777 3777 95.485 1 2369 1 chr3B.!!$R1 2368

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
575 576 0.105658 TCTAGAATAGGGCTGCGGGT 60.106 55.0 0.0 0.0 39.78 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2246 0.885879 CCTTCCTTTTTACGCCACCC 59.114 55.0 0.0 0.0 0.0 4.61 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
406 407 0.108019 AGTCCCCGTTTCAGGTGTTC 59.892 55.000 0.00 0.00 0.00 3.18
575 576 0.105658 TCTAGAATAGGGCTGCGGGT 60.106 55.000 0.00 0.00 39.78 5.28
598 599 2.298729 GGAGGGCTTTGTTTGTGCAATA 59.701 45.455 0.00 0.00 0.00 1.90
601 602 4.971939 AGGGCTTTGTTTGTGCAATATTT 58.028 34.783 0.00 0.00 0.00 1.40
735 736 1.711375 TCCCTAGAGGAGCCGTATGAT 59.289 52.381 0.00 0.00 40.93 2.45
755 756 2.070861 CGGAAGCTTCACGTACAGC 58.929 57.895 27.02 9.63 36.16 4.40
1033 1034 2.552315 GGTGAAGCCAAGTCAATTTCGA 59.448 45.455 0.00 0.00 37.17 3.71
1062 1063 1.215423 ACCCTGCAACTGAGGAAAAGT 59.785 47.619 0.00 0.00 31.48 2.66
1098 1099 1.484356 GAAGCGTGTACGTTGTCACT 58.516 50.000 6.27 0.00 42.22 3.41
1192 1193 2.607750 GCAGGGGGACAGGAGACA 60.608 66.667 0.00 0.00 0.00 3.41
1234 1235 1.736645 CTACAGGCAACACCGACGG 60.737 63.158 13.61 13.61 46.52 4.79
1239 1240 4.309950 GCAACACCGACGGGACCT 62.310 66.667 20.00 0.00 36.97 3.85
1289 1290 0.689745 TCCATAGTACCCGCAGCCTT 60.690 55.000 0.00 0.00 0.00 4.35
1412 1418 5.869344 ACGATACATCCAATACCAATGATCG 59.131 40.000 0.00 0.00 36.98 3.69
1413 1419 5.869344 CGATACATCCAATACCAATGATCGT 59.131 40.000 0.00 0.00 32.34 3.73
1418 1424 2.034558 CCAATACCAATGATCGTTGCCC 59.965 50.000 20.29 0.00 0.00 5.36
1482 1488 7.334671 AGAGCTAGTGTCAATAAAAAGGCTAAC 59.665 37.037 0.00 0.00 0.00 2.34
1570 1576 2.111878 GCGCCCATGCCTACTCAT 59.888 61.111 0.00 0.00 0.00 2.90
2006 2013 1.539388 ACTTTCAATGCGCGAAATCCA 59.461 42.857 12.10 0.00 32.21 3.41
2037 2044 1.599542 GAGTGCGAAACTTCTTGCTGT 59.400 47.619 0.00 0.00 40.07 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
575 576 1.133637 TGCACAAACAAAGCCCTCCTA 60.134 47.619 0.00 0.00 0.00 2.94
598 599 1.339151 GGAGAGGGTGTTGCGAGAAAT 60.339 52.381 0.00 0.00 0.00 2.17
601 602 1.228894 AGGAGAGGGTGTTGCGAGA 60.229 57.895 0.00 0.00 0.00 4.04
735 736 0.666274 CTGTACGTGAAGCTTCCGCA 60.666 55.000 26.77 19.47 39.10 5.69
755 756 0.523519 GGAAAGGCTCGGCTTCAAAG 59.476 55.000 6.18 0.00 0.00 2.77
989 990 1.904440 AGGCCTCATCTCCAAATCCT 58.096 50.000 0.00 0.00 0.00 3.24
992 993 3.102204 CCAAAAGGCCTCATCTCCAAAT 58.898 45.455 5.23 0.00 0.00 2.32
1033 1034 2.133641 GTTGCAGGGTTTGGTGGCT 61.134 57.895 0.00 0.00 0.00 4.75
1098 1099 3.009115 CTTTGGAGGGCGGGGAGA 61.009 66.667 0.00 0.00 0.00 3.71
1289 1290 7.282585 AGAAAATGATGAATATGAAGTCCGGA 58.717 34.615 0.00 0.00 0.00 5.14
1412 1418 1.068127 AGTATCGTATCGGTGGGCAAC 59.932 52.381 0.00 0.00 0.00 4.17
1413 1419 1.338973 GAGTATCGTATCGGTGGGCAA 59.661 52.381 0.00 0.00 0.00 4.52
1418 1424 2.501261 TGGAGGAGTATCGTATCGGTG 58.499 52.381 0.00 0.00 34.37 4.94
1482 1488 3.694072 AGGAGATTGACTCTTCTCTGTCG 59.306 47.826 0.00 0.00 34.39 4.35
1570 1576 1.340017 GCCATGGTAGAAGTTGCTCCA 60.340 52.381 14.67 0.00 0.00 3.86
1864 1871 2.508526 GGCTTCATTGCCCCTAGTATG 58.491 52.381 0.00 0.00 46.82 2.39
2037 2044 2.018542 AGCAGCGAATAAAACGGCTA 57.981 45.000 0.00 0.00 0.00 3.93
2129 2137 4.223923 GTGGATCGAGGGAATGGAATCTAT 59.776 45.833 0.00 0.00 0.00 1.98
2218 2226 2.158549 CCCCTCCCAATCCTTGAAGATC 60.159 54.545 0.00 0.00 0.00 2.75
2238 2246 0.885879 CCTTCCTTTTTACGCCACCC 59.114 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.