Multiple sequence alignment - TraesCS3A01G172400

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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 TraesCS3A01G172400 chr3A 100.000 3219 0 0 1 3219 187252817 187249599 0 5945
1 TraesCS3A01G172400 chr3D 96.530 2738 41 8 1 2697 160703640 160700916 0 4481
2 TraesCS3A01G172400 chr3D 93.690 523 27 3 2695 3216 160700801 160700284 0 778
3 TraesCS3A01G172400 chr3B 89.609 2791 166 56 1 2697 237337342 237334582 0 3434
4 TraesCS3A01G172400 chr3B 91.028 535 32 8 2695 3219 237334453 237333925 0 708


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 TraesCS3A01G172400 chr3A 187249599 187252817 3218 True 5945.0 5945 100.0000 1 3219 1 chr3A.!!$R1 3218
1 TraesCS3A01G172400 chr3D 160700284 160703640 3356 True 2629.5 4481 95.1100 1 3216 2 chr3D.!!$R1 3215
2 TraesCS3A01G172400 chr3B 237333925 237337342 3417 True 2071.0 3434 90.3185 1 3219 2 chr3B.!!$R1 3218


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
603 677 1.072806 TCTGATGTGCATATGGCCCTC 59.927 52.381 0.0 0.0 43.89 4.30 F
615 689 2.031465 GCCCTCGTCGGAAACCAA 59.969 61.111 0.0 0.0 33.16 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1640 1.593196 CGGTTCAGGAACAAAGCTCA 58.407 50.0 13.62 0.0 42.85 4.26 R
2479 2618 2.887152 GGGTCCAAATCCATGTGATAGC 59.113 50.0 0.00 0.0 31.83 2.97 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)



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AutoCloner maintained by Alex Coulton.