Multiple sequence alignment - TraesCS2A01G285600

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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 TraesCS2A01G285600 chr2A 100.000 2405 0 0 1 2405 483602760 483600356 0 4442
1 TraesCS2A01G285600 chr2D 97.174 2406 56 9 1 2401 359398349 359400747 0 4056
2 TraesCS2A01G285600 chr2B 96.400 2417 67 12 1 2405 427247840 427245432 0 3964


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 TraesCS2A01G285600 chr2A 483600356 483602760 2404 True 4442 4442 100.000 1 2405 1 chr2A.!!$R1 2404
1 TraesCS2A01G285600 chr2D 359398349 359400747 2398 False 4056 4056 97.174 1 2401 1 chr2D.!!$F1 2400
2 TraesCS2A01G285600 chr2B 427245432 427247840 2408 True 3964 3964 96.400 1 2405 1 chr2B.!!$R1 2404

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
226 228 1.600636 CAGTCCGCTGCCCTTTCAA 60.601 57.895 0.0 0.0 35.77 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1790 0.622136 TGAAGCCAGCATCTGACCAT 59.378 50.0 0.0 0.0 32.44 3.55 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
103 105 3.493129 CGCTAGCCGCATTAGATGTAAAA 59.507 43.478 9.66 0.00 39.08 1.52
126 128 9.912634 AAAATCAACATTTTCAATAGTCATCGT 57.087 25.926 0.00 0.00 37.63 3.73
226 228 1.600636 CAGTCCGCTGCCCTTTCAA 60.601 57.895 0.00 0.00 35.77 2.69
334 338 4.976540 AGTACCATATTTCTAGGGTGCC 57.023 45.455 0.00 0.00 43.05 5.01
558 566 9.696917 CTAATTTGTGAAATAGGCTTGACTTTT 57.303 29.630 0.00 0.00 0.00 2.27
582 590 2.416431 GCATTGCTGTGGCCTCTTTAAG 60.416 50.000 3.32 0.00 37.74 1.85
595 603 6.126768 TGGCCTCTTTAAGCAGAACATATACT 60.127 38.462 3.32 0.00 0.00 2.12
627 635 3.126514 CGAGCTGCTGAAACAATCAAGAT 59.873 43.478 7.01 0.00 37.67 2.40
628 636 4.413087 GAGCTGCTGAAACAATCAAGATG 58.587 43.478 7.01 0.00 37.67 2.90
720 730 2.996621 GTCTAAAGTTGCATGCGTCTCT 59.003 45.455 14.09 5.60 0.00 3.10
757 767 3.937814 TCGAAAACCTGCATGTACATCT 58.062 40.909 5.07 0.00 0.00 2.90
854 868 2.867855 CGCTGCCCCCGCTCTATAA 61.868 63.158 0.00 0.00 35.36 0.98
989 1003 6.927294 AATTAGCTAGTTAATTTCGCAGCT 57.073 33.333 16.33 8.69 41.87 4.24
1539 1553 0.402504 AGAGAGTGAGAGGTCGGTGT 59.597 55.000 0.00 0.00 0.00 4.16
1540 1554 1.202952 AGAGAGTGAGAGGTCGGTGTT 60.203 52.381 0.00 0.00 0.00 3.32
1579 1594 1.801178 CCTCCGTCTTGTTTGAGCTTC 59.199 52.381 0.00 0.00 0.00 3.86
1725 1741 7.477494 TGCCTTGTTTAAAACTTCTGTTAGTC 58.523 34.615 0.00 0.00 34.96 2.59
1742 1758 2.494059 AGTCGTGTGTTCATCCTTTGG 58.506 47.619 0.00 0.00 0.00 3.28
1760 1777 1.601903 TGGCATTTTGTCTCGTGTGTC 59.398 47.619 0.00 0.00 0.00 3.67
1767 1784 0.031585 TGTCTCGTGTGTCCTTTCGG 59.968 55.000 0.00 0.00 0.00 4.30
1773 1790 1.219646 GTGTGTCCTTTCGGCGTTAA 58.780 50.000 6.85 1.68 0.00 2.01
1884 1901 3.947612 AGAGAGACCGGGATACAACTA 57.052 47.619 6.32 0.00 39.74 2.24
1887 1904 4.411540 AGAGAGACCGGGATACAACTACTA 59.588 45.833 6.32 0.00 39.74 1.82
2347 2364 0.840288 ACTGTGGACCATACTGGCCA 60.840 55.000 4.71 4.71 42.67 5.36
2397 2414 5.163426 GCTTAGTTAACTCTTACTCCCTCCC 60.163 48.000 12.39 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 8.267620 TCACGATGACTATTGAAAATGTTGAT 57.732 30.769 0.00 0.00 0.00 2.57
125 127 7.615403 TGAGTGATTATATTCCTAGGCATCAC 58.385 38.462 2.96 13.20 39.46 3.06
126 128 7.797121 TGAGTGATTATATTCCTAGGCATCA 57.203 36.000 2.96 2.10 0.00 3.07
261 263 4.885325 AGGGAAAACTACGTCATGTTTTGT 59.115 37.500 22.60 8.04 43.61 2.83
334 338 6.037062 TGACATGAAGTGTAACAGTGAAAGTG 59.963 38.462 0.00 0.00 42.36 3.16
558 566 0.329261 AGAGGCCACAGCAATGCTAA 59.671 50.000 7.70 0.00 42.56 3.09
595 603 3.106242 TCAGCAGCTCGAAGTTAAACA 57.894 42.857 0.00 0.00 0.00 2.83
720 730 6.318144 AGGTTTTCGATACTAGACGATCTCAA 59.682 38.462 0.00 0.00 38.30 3.02
757 767 5.628797 AGGAATGCCTTTTTCTTTTCCAA 57.371 34.783 0.00 0.00 43.90 3.53
854 868 2.169352 AGTGAGAAGAGGCGCATGTATT 59.831 45.455 10.83 0.00 0.00 1.89
913 927 2.359975 GCGGGAGGTGGTTTGAGG 60.360 66.667 0.00 0.00 0.00 3.86
989 1003 3.183754 CCGTACTGCATTGTTCGATACA 58.816 45.455 6.68 0.00 33.61 2.29
1160 1174 2.270205 CCATGCCGCAGAAGAGGT 59.730 61.111 0.00 0.00 37.01 3.85
1412 1426 5.288712 CAGTAACGGTGTCACTGACAATATC 59.711 44.000 18.86 1.49 44.49 1.63
1579 1594 2.510238 GCACGCACTAGCTCCCAG 60.510 66.667 0.00 0.00 39.10 4.45
1725 1741 0.950836 TGCCAAAGGATGAACACACG 59.049 50.000 0.00 0.00 0.00 4.49
1742 1758 1.873591 AGGACACACGAGACAAAATGC 59.126 47.619 0.00 0.00 0.00 3.56
1767 1784 1.331756 CCAGCATCTGACCATTAACGC 59.668 52.381 0.00 0.00 32.44 4.84
1773 1790 0.622136 TGAAGCCAGCATCTGACCAT 59.378 50.000 0.00 0.00 32.44 3.55


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

AutoCloner maintained by Alex Coulton.