Multiple sequence alignment - TraesCS7D01G400000

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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 TraesCS7D01G400000 chr7D 100.000 3128 0 0 1 3128 516971125 516974252 0 5777
1 TraesCS7D01G400000 chr7B 95.549 3190 65 26 1 3128 549349478 549352652 0 5033
2 TraesCS7D01G400000 chr7A 93.750 3184 110 48 1 3126 591551920 591555072 0 4695


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 TraesCS7D01G400000 chr7D 516971125 516974252 3127 False 5777 5777 100.000 1 3128 1 chr7D.!!$F1 3127
1 TraesCS7D01G400000 chr7B 549349478 549352652 3174 False 5033 5033 95.549 1 3128 1 chr7B.!!$F1 3127
2 TraesCS7D01G400000 chr7A 591551920 591555072 3152 False 4695 4695 93.750 1 3126 1 chr7A.!!$F1 3125

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
387 391 0.047802 TCATCCCTCCCCCAATCCTT 59.952 55.0 0.0 0.0 0.0 3.36 F
389 393 0.351998 ATCCCTCCCCCAATCCTTCT 59.648 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1919 1.152881 GCGCAGGATCCCCTTGAAT 60.153 57.895 8.55 0.0 42.02 2.57 R
2410 2460 3.923017 ACGATTTCAAAAGGAAGCAGG 57.077 42.857 0.00 0.0 36.72 4.85 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
106 107 3.848975 ACACATTCTCTCTCCATTCCCTT 59.151 43.478 0.00 0.00 0.00 3.95
387 391 0.047802 TCATCCCTCCCCCAATCCTT 59.952 55.000 0.00 0.00 0.00 3.36
388 392 0.480252 CATCCCTCCCCCAATCCTTC 59.520 60.000 0.00 0.00 0.00 3.46
389 393 0.351998 ATCCCTCCCCCAATCCTTCT 59.648 55.000 0.00 0.00 0.00 2.85
594 609 2.494073 AGAGGCGAAGAAAGGTGAGTAG 59.506 50.000 0.00 0.00 0.00 2.57
623 647 5.485620 GTTGGGGTAGTAACTAGTTTCCTG 58.514 45.833 14.49 0.00 0.00 3.86
794 820 3.954904 TCTGTCTAATCTACTGGTGAGCC 59.045 47.826 0.00 0.00 0.00 4.70
941 969 4.202792 TGAGAGGGAAGGAAGGAGAAAGTA 60.203 45.833 0.00 0.00 0.00 2.24
1455 1483 1.525995 CAACTGCTCCACCCACGTT 60.526 57.895 0.00 0.00 0.00 3.99
1677 1705 4.645136 TCAGGTATGTGGTAGCTACTCAAG 59.355 45.833 22.74 11.22 39.05 3.02
1695 1723 6.968250 ACTCAAGTACAGTCTACAGTACAAC 58.032 40.000 15.43 0.00 40.10 3.32
1699 1727 3.662247 ACAGTCTACAGTACAACCAGC 57.338 47.619 0.00 0.00 0.00 4.85
1812 1856 4.201679 CGGTGCGTGCGGATAGGA 62.202 66.667 0.00 0.00 0.00 2.94
1959 2003 2.184579 GCGGAGTACCACCAGCTC 59.815 66.667 7.34 0.00 35.59 4.09
2447 2498 8.746922 TGAAATCGTTTACTACTACATTTCGT 57.253 30.769 0.00 0.00 33.39 3.85
2838 2903 5.412594 TCTTTGGCTAATCTTTGCACTACTG 59.587 40.000 0.00 0.00 0.00 2.74
2847 2912 3.508012 TCTTTGCACTACTGTCTCTCTCC 59.492 47.826 0.00 0.00 0.00 3.71
3044 3132 9.462174 TGTGCATGATTTACTTTTAAGAAACTG 57.538 29.630 0.00 0.00 0.00 3.16
3071 3159 4.273724 GCAAACTTATCTAAGCCTAGCCAC 59.726 45.833 0.00 0.00 36.79 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 6.068498 AGAGAGGAGAGAGGAAATAAAGGAGA 60.068 42.308 0.00 0.00 0.00 3.71
387 391 5.336531 GCGTGGCTAGGCTATATAAAGAAGA 60.337 44.000 18.18 0.00 34.94 2.87
388 392 4.865365 GCGTGGCTAGGCTATATAAAGAAG 59.135 45.833 18.18 0.00 34.94 2.85
389 393 4.282449 TGCGTGGCTAGGCTATATAAAGAA 59.718 41.667 18.18 0.00 38.47 2.52
594 609 4.529769 ACTAGTTACTACCCCAACCACTTC 59.470 45.833 0.00 0.00 0.00 3.01
623 647 1.362406 GCGAGCCTGCCTAACAAGTC 61.362 60.000 0.00 0.00 0.00 3.01
794 820 5.359009 ACCCATAGCTCAGATTTTCAACATG 59.641 40.000 0.00 0.00 0.00 3.21
897 923 1.877443 CCTCCTACAAACACAAACGGG 59.123 52.381 0.00 0.00 0.00 5.28
899 925 3.199677 TCACCTCCTACAAACACAAACG 58.800 45.455 0.00 0.00 0.00 3.60
941 969 2.320587 CGCGCTCACTTCCTTGCTT 61.321 57.895 5.56 0.00 0.00 3.91
1098 1126 2.769617 CGCGCGTACAGAAACAGG 59.230 61.111 24.19 0.00 0.00 4.00
1455 1483 4.147135 GGGACCCAGGTGCTCTTA 57.853 61.111 5.33 0.00 36.67 2.10
1677 1705 4.483311 GCTGGTTGTACTGTAGACTGTAC 58.517 47.826 17.99 17.99 45.57 2.90
1695 1723 1.592400 CTGAATGGTGCAGTGGCTGG 61.592 60.000 0.00 0.00 41.91 4.85
1699 1727 1.300971 CGTCCTGAATGGTGCAGTGG 61.301 60.000 0.00 0.00 37.07 4.00
1761 1805 2.187946 CTCAGCTCCGGCGGAAAT 59.812 61.111 30.59 18.25 41.62 2.17
1875 1919 1.152881 GCGCAGGATCCCCTTGAAT 60.153 57.895 8.55 0.00 42.02 2.57
2410 2460 3.923017 ACGATTTCAAAAGGAAGCAGG 57.077 42.857 0.00 0.00 36.72 4.85
2447 2498 1.819928 AACCAATCACGTGCTGCATA 58.180 45.000 11.67 0.00 0.00 3.14
2838 2903 4.608948 CTCTAGAGAGAGGGAGAGAGAC 57.391 54.545 15.05 0.00 44.92 3.36
2921 3005 5.164233 ACACTGATCTATGTCACTTCAACG 58.836 41.667 0.00 0.00 0.00 4.10
3044 3132 4.907879 AGGCTTAGATAAGTTTGCATGC 57.092 40.909 11.82 11.82 35.75 4.06


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

AutoCloner maintained by Alex Coulton.