Multiple sequence alignment - TraesCS1A01G216300

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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 TraesCS1A01G216300 chr1A 100.000 2239 0 0 722 2960 382253426 382251188 0.000000e+00 4135
1 TraesCS1A01G216300 chr1A 100.000 433 0 0 1 433 382254147 382253715 0.000000e+00 800
2 TraesCS1A01G216300 chr1D 95.219 2280 55 11 722 2960 305230255 305227989 0.000000e+00 3557
3 TraesCS1A01G216300 chr1D 91.532 248 15 3 186 433 305230718 305230477 1.310000e-88 337
4 TraesCS1A01G216300 chr1B 93.621 2273 67 31 722 2951 412242772 412245009 0.000000e+00 3323
5 TraesCS1A01G216300 chr1B 92.800 250 11 4 186 433 412242305 412242549 3.630000e-94 355


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 TraesCS1A01G216300 chr1A 382251188 382254147 2959 True 2467.5 4135 100.0000 1 2960 2 chr1A.!!$R1 2959
1 TraesCS1A01G216300 chr1D 305227989 305230718 2729 True 1947.0 3557 93.3755 186 2960 2 chr1D.!!$R1 2774
2 TraesCS1A01G216300 chr1B 412242305 412245009 2704 False 1839.0 3323 93.2105 186 2951 2 chr1B.!!$F1 2765


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
121 122 0.251073 GAAACCCTAACCCTAGCGCA 59.749 55.0 11.47 0.00 0.0 6.09 F
122 123 0.252197 AAACCCTAACCCTAGCGCAG 59.748 55.0 11.47 4.88 0.0 5.18 F
1017 1026 0.396417 CCATGTCCTCCTCCTCGTCT 60.396 60.0 0.00 0.00 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1500 1.063417 CCCCTGGGCTTGATCTTGATT 60.063 52.381 7.39 0.0 0.0 2.57 R
1830 1839 1.220206 CTGGGTGCGCTTCATCTCT 59.780 57.895 9.73 0.0 0.0 3.10 R
2860 2922 0.613853 CACCCTCCTCAAGTCCGGTA 60.614 60.000 0.00 0.0 0.0 4.02 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)



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

AutoCloner maintained by Alex Coulton.