Multiple sequence alignment - TraesCS4D01G317700

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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 TraesCS4D01G317700 chr4D 100.000 3266 0 0 1 3266 482669893 482666628 0 6032
1 TraesCS4D01G317700 chr6D 97.521 3267 76 4 1 3266 437005285 437008547 0 5579
2 TraesCS4D01G317700 chr7D 97.277 3269 83 6 1 3266 614566401 614569666 0 5539
3 TraesCS4D01G317700 chr2D 97.184 3267 85 6 1 3266 139702888 139699628 0 5517
4 TraesCS4D01G317700 chr2D 97.062 3267 89 5 1 3266 522778923 522782183 0 5494
5 TraesCS4D01G317700 chr3D 97.000 3267 92 5 1 3266 483312751 483309490 0 5485
6 TraesCS4D01G317700 chr7A 95.751 3271 130 6 1 3266 493726524 493729790 0 5262
7 TraesCS4D01G317700 chr7A 94.521 3267 172 6 2 3266 536365325 536368586 0 5035
8 TraesCS4D01G317700 chr7A 93.823 3270 162 12 1 3266 93310883 93314116 0 4883
9 TraesCS4D01G317700 chr5A 93.786 3267 164 11 1 3266 689846360 689843132 0 4872
10 TraesCS4D01G317700 chr3A 93.752 3105 155 11 165 3266 535603338 535606406 0 4623


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 TraesCS4D01G317700 chr4D 482666628 482669893 3265 True 6032 6032 100.000 1 3266 1 chr4D.!!$R1 3265
1 TraesCS4D01G317700 chr6D 437005285 437008547 3262 False 5579 5579 97.521 1 3266 1 chr6D.!!$F1 3265
2 TraesCS4D01G317700 chr7D 614566401 614569666 3265 False 5539 5539 97.277 1 3266 1 chr7D.!!$F1 3265
3 TraesCS4D01G317700 chr2D 139699628 139702888 3260 True 5517 5517 97.184 1 3266 1 chr2D.!!$R1 3265
4 TraesCS4D01G317700 chr2D 522778923 522782183 3260 False 5494 5494 97.062 1 3266 1 chr2D.!!$F1 3265
5 TraesCS4D01G317700 chr3D 483309490 483312751 3261 True 5485 5485 97.000 1 3266 1 chr3D.!!$R1 3265
6 TraesCS4D01G317700 chr7A 493726524 493729790 3266 False 5262 5262 95.751 1 3266 1 chr7A.!!$F2 3265
7 TraesCS4D01G317700 chr7A 536365325 536368586 3261 False 5035 5035 94.521 2 3266 1 chr7A.!!$F3 3264
8 TraesCS4D01G317700 chr7A 93310883 93314116 3233 False 4883 4883 93.823 1 3266 1 chr7A.!!$F1 3265
9 TraesCS4D01G317700 chr5A 689843132 689846360 3228 True 4872 4872 93.786 1 3266 1 chr5A.!!$R1 3265
10 TraesCS4D01G317700 chr3A 535603338 535606406 3068 False 4623 4623 93.752 165 3266 1 chr3A.!!$F1 3101

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
578 586 0.387239 CACGTGAGAGTGATGCGTCA 60.387 55.0 10.9 3.97 44.43 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2308 1.967319 AACACAAGCAACTCCACGAT 58.033 45.0 0.0 0.0 0.0 3.73 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
270 278 3.447229 GGAAGAGAGGAAGGAAGAGAGTG 59.553 52.174 0.00 0.00 0.00 3.51
501 509 0.394762 GGGGCATGCATCTGAAGACA 60.395 55.000 21.36 0.00 0.00 3.41
578 586 0.387239 CACGTGAGAGTGATGCGTCA 60.387 55.000 10.90 3.97 44.43 4.35
616 624 3.605634 AGGCATTTGTGCGAATAGTACA 58.394 40.909 0.00 0.00 43.67 2.90
874 882 3.083997 GCCTCCTCCACGACCCAT 61.084 66.667 0.00 0.00 0.00 4.00
1729 1744 8.606040 AACATGCTGTGCTTGTATTTTATTTT 57.394 26.923 10.64 0.00 44.18 1.82
1895 1912 6.206042 AGGAGGATAGATTCTACACCTTTGT 58.794 40.000 17.06 7.28 40.02 2.83
2140 2157 4.277476 CCCACTGCCAAATTACCTCATTA 58.723 43.478 0.00 0.00 0.00 1.90
2290 2308 7.441157 AGTGATGACGAAAACATAGAAAACTGA 59.559 33.333 0.00 0.00 0.00 3.41
2329 2347 8.177119 TGTGTTTATGCTTGTCCTTTCTATTT 57.823 30.769 0.00 0.00 0.00 1.40
2366 2384 5.695363 AGTTTACTTCTGTTAGAACGAAGCC 59.305 40.000 18.41 9.94 40.16 4.35
2454 2472 7.885297 TGTGATTGAGCAAGTTATTTAGCTTT 58.115 30.769 0.00 0.00 37.48 3.51
2539 2558 7.239972 TCTAAAAACAACAAAATGCAAAGCAC 58.760 30.769 0.00 0.00 43.04 4.40
2598 2617 1.975327 CGGCTTCTTGAGGAGTGGA 59.025 57.895 0.00 0.00 0.00 4.02
2684 2703 0.688487 GTGTGTTACTACAGGGGCCA 59.312 55.000 4.39 0.00 34.24 5.36
2854 2878 3.372730 GCAAGGCACGGGATTGCA 61.373 61.111 19.51 0.00 46.64 4.08
2863 2887 1.068333 CACGGGATTGCAACTTCTTGG 60.068 52.381 0.00 0.00 0.00 3.61
2993 3017 2.898612 TGGTACCGTGACCATGTAAGAA 59.101 45.455 7.57 0.00 44.79 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 31 1.440938 CTTCAACACCACCGGCGAAA 61.441 55.000 9.30 0.00 0.00 3.46
30 33 2.280524 CTTCAACACCACCGGCGA 60.281 61.111 9.30 0.00 0.00 5.54
270 278 1.341156 CCATCTCTCCCACCTCCACC 61.341 65.000 0.00 0.00 0.00 4.61
501 509 3.191581 CACAACCGTGACTCTCTGAGTAT 59.808 47.826 4.32 0.00 46.80 2.12
578 586 3.517612 TGCCTCTACTACCAAACTTCCT 58.482 45.455 0.00 0.00 0.00 3.36
616 624 2.370849 ACCCACAACCGATACTCTTTGT 59.629 45.455 0.00 0.00 32.34 2.83
619 627 1.553704 GGACCCACAACCGATACTCTT 59.446 52.381 0.00 0.00 0.00 2.85
874 882 3.117436 AGTTACCCTTTTGTGCCAAGGTA 60.117 43.478 0.00 0.00 39.50 3.08
1274 1288 0.107945 CTGTAGAACTGCTGCCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
1284 1298 3.119101 CCTCCACGCATAACTGTAGAACT 60.119 47.826 0.00 0.00 0.00 3.01
1878 1895 3.767673 AGCCGACAAAGGTGTAGAATCTA 59.232 43.478 0.00 0.00 38.41 1.98
1881 1898 3.244422 TGAAGCCGACAAAGGTGTAGAAT 60.244 43.478 0.00 0.00 38.41 2.40
2140 2157 2.288457 ACGCATCTATCGCTGCATACTT 60.288 45.455 0.00 0.00 38.30 2.24
2290 2308 1.967319 AACACAAGCAACTCCACGAT 58.033 45.000 0.00 0.00 0.00 3.73
2329 2347 7.889469 ACAGAAGTAAACTACGAACCTGATAA 58.111 34.615 0.00 0.00 0.00 1.75
2366 2384 6.980978 ACCTGATACAGATGACATTAGAAACG 59.019 38.462 0.00 0.00 32.44 3.60
2539 2558 4.795970 ACTGTACTCAACGCAAAAAGAG 57.204 40.909 0.00 0.00 0.00 2.85
2598 2617 0.042131 TCCGACCCATACCACTCCTT 59.958 55.000 0.00 0.00 0.00 3.36
2684 2703 2.759641 TACTCCGTCCACGTGCCTCT 62.760 60.000 10.91 0.00 37.74 3.69
2854 2878 0.470766 TACCCGTGCACCAAGAAGTT 59.529 50.000 12.15 0.00 0.00 2.66
2863 2887 0.165079 CAACGTTGATACCCGTGCAC 59.835 55.000 23.90 6.82 37.38 4.57


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

AutoCloner maintained by Alex Coulton.