Multiple sequence alignment - TraesCS3A01G093200

Loading Multiple Alignment...

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 TraesCS3A01G093200 chr3A 100.000 2774 0 0 1 2774 59531166 59533939 0.000000e+00 5123
1 TraesCS3A01G093200 chr3A 82.895 304 48 4 1069 1370 647755512 647755211 1.270000e-68 270
2 TraesCS3A01G093200 chr3B 98.382 2781 34 7 1 2774 74293158 74295934 0.000000e+00 4876
3 TraesCS3A01G093200 chr3B 81.849 292 51 2 1079 1370 674063371 674063082 7.670000e-61 244
4 TraesCS3A01G093200 chr3D 97.948 2778 49 7 1 2774 47492515 47495288 0.000000e+00 4807
5 TraesCS3A01G093200 chr3D 82.895 304 48 4 1069 1370 511726696 511726395 1.270000e-68 270
6 TraesCS3A01G093200 chr1B 84.014 294 45 2 1077 1370 475470110 475469819 5.850000e-72 281
7 TraesCS3A01G093200 chr1A 83.673 294 46 2 1077 1370 453523511 453523220 2.720000e-70 276
8 TraesCS3A01G093200 chr4B 85.938 256 34 2 1077 1331 77651298 77651552 3.520000e-69 272
9 TraesCS3A01G093200 chr4D 85.156 256 36 2 1077 1331 52763828 52764082 7.620000e-66 261


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 TraesCS3A01G093200 chr3A 59531166 59533939 2773 False 5123 5123 100.000 1 2774 1 chr3A.!!$F1 2773
1 TraesCS3A01G093200 chr3B 74293158 74295934 2776 False 4876 4876 98.382 1 2774 1 chr3B.!!$F1 2773
2 TraesCS3A01G093200 chr3D 47492515 47495288 2773 False 4807 4807 97.948 1 2774 1 chr3D.!!$F1 2773

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
517 521 0.676151 CAGCCTGTCCTTCTCTTGCC 60.676 60.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 1789 0.106719 CCACTCACTGTTGGTTGGGT 60.107 55.0 0.0 0.0 0.0 4.51 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
44 45 5.139435 ACTGGCTTGCTTTTCTATTTTCC 57.861 39.130 0.00 0.00 0.00 3.13
335 338 1.676967 GCTGCAACAAGGGGAGAGG 60.677 63.158 0.00 0.00 0.00 3.69
364 367 4.159506 TCTCCCAAATATTTTCTTTGCCCG 59.840 41.667 0.00 0.00 33.27 6.13
517 521 0.676151 CAGCCTGTCCTTCTCTTGCC 60.676 60.000 0.00 0.00 0.00 4.52
713 717 4.514441 GTCAAATCATCCCACTGCTATGAG 59.486 45.833 0.00 0.00 33.40 2.90
878 884 1.195115 CCTTCCCAGAACGATCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
884 890 1.135915 CCAGAACGATCCTCACTCCAG 59.864 57.143 0.00 0.00 0.00 3.86
954 961 3.732048 TCTGGGGAAAATGACTAACCC 57.268 47.619 0.00 0.00 39.79 4.11
977 984 5.474876 CCTTTGACAGCTCTCTTAAATTGGT 59.525 40.000 0.00 0.00 0.00 3.67
1592 1599 1.079405 CTCTTTCCGCCGGTTGCTA 60.079 57.895 1.63 0.00 38.05 3.49
1782 1789 2.281692 AGCATGTGAACTGGCGCA 60.282 55.556 10.83 0.00 0.00 6.09
1944 1953 4.533707 ACCGATGGATGTGGAGAATGATAT 59.466 41.667 0.00 0.00 0.00 1.63
1945 1954 4.874396 CCGATGGATGTGGAGAATGATATG 59.126 45.833 0.00 0.00 0.00 1.78
2093 2102 8.048534 AGCCAACATGAATTATATATGTCAGC 57.951 34.615 0.00 0.00 34.18 4.26
2279 2289 3.507162 TGCTCATGAGAAAAGAACCCA 57.493 42.857 27.04 8.27 0.00 4.51
2391 2401 3.012388 AGCTAATGTGGGTTAATTGGGGT 59.988 43.478 0.00 0.00 0.00 4.95
2504 2514 7.727181 TCTTGAGATGCTTAATAGTAAGGGAC 58.273 38.462 11.62 0.00 37.74 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.058817 GGAAAGTTGAGGTGTGTAGACAG 58.941 47.826 0.00 0.00 30.74 3.51
349 352 2.099098 CGAAGGCGGGCAAAGAAAATAT 59.901 45.455 3.78 0.00 0.00 1.28
351 354 0.243636 CGAAGGCGGGCAAAGAAAAT 59.756 50.000 3.78 0.00 0.00 1.82
364 367 2.879002 TCTGATGATCTGACGAAGGC 57.121 50.000 0.00 0.00 0.00 4.35
394 398 0.683504 GGGGTCAACTAGCGGAGAGA 60.684 60.000 0.00 0.00 0.00 3.10
678 682 5.005740 GGATGATTTGACATATGGCTGCTA 58.994 41.667 10.60 0.00 0.00 3.49
778 782 3.447229 ACGCAAGAAATGGGGAAAATAGG 59.553 43.478 0.00 0.00 45.78 2.57
884 890 4.923516 AGTTCTAGGGTTAGGGTTTTCC 57.076 45.455 0.00 0.00 39.75 3.13
954 961 6.016777 ACACCAATTTAAGAGAGCTGTCAAAG 60.017 38.462 14.08 0.00 0.00 2.77
977 984 2.035449 GCCAGCGACCTGTGTATATACA 59.965 50.000 11.62 11.62 37.38 2.29
1592 1599 1.138859 TGCTGCTCCGCATATTGTAGT 59.861 47.619 0.00 0.00 38.13 2.73
1782 1789 0.106719 CCACTCACTGTTGGTTGGGT 60.107 55.000 0.00 0.00 0.00 4.51
2093 2102 1.466167 CAACATGCAGAAAGGGAGACG 59.534 52.381 0.00 0.00 0.00 4.18
2279 2289 2.494471 GTTTATTTGGCCGCCTAAAGGT 59.506 45.455 11.61 0.00 37.57 3.50
2391 2401 7.508687 TGCAGATCATGTAGCCTTTAATTAGA 58.491 34.615 0.00 0.00 0.00 2.10
2528 2538 6.289834 TCAAAACAAATGATGTGATGCCTTT 58.710 32.000 0.00 0.00 42.99 3.11


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

AutoCloner maintained by Alex Coulton.