Multiple sequence alignment - TraesCS4B01G207200

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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 TraesCS4B01G207200 chr4B 100.000 3917 0 0 1 3917 441669983 441673899 0.000000e+00 7234.0
1 TraesCS4B01G207200 chr4D 94.706 3797 95 46 162 3917 358468215 358471946 0.000000e+00 5801.0
2 TraesCS4B01G207200 chr4A 94.718 3275 104 39 676 3915 106912164 106908924 0.000000e+00 5025.0
3 TraesCS4B01G207200 chr4A 83.075 644 46 22 3 630 106912861 106912265 9.640000e-146 527.0
4 TraesCS4B01G207200 chr6B 95.122 41 2 0 3668 3708 289179293 289179333 9.080000e-07 65.8
5 TraesCS4B01G207200 chr5D 89.362 47 5 0 3665 3711 563397318 563397272 4.230000e-05 60.2


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 TraesCS4B01G207200 chr4B 441669983 441673899 3916 False 7234 7234 100.0000 1 3917 1 chr4B.!!$F1 3916
1 TraesCS4B01G207200 chr4D 358468215 358471946 3731 False 5801 5801 94.7060 162 3917 1 chr4D.!!$F1 3755
2 TraesCS4B01G207200 chr4A 106908924 106912861 3937 True 2776 5025 88.8965 3 3915 2 chr4A.!!$R1 3912


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
934 1017 0.108472 CTCAGATCTGCAAGCGACCA 60.108 55.000 18.36 0.0 0.00 4.02 F
1836 1922 1.537638 CAGCTCTACGCCGATATCTGT 59.462 52.381 0.34 0.0 40.39 3.41 F
2388 2474 0.937304 GCAACGAAGTGACTTCTGCA 59.063 50.000 25.42 0.0 45.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2234 0.472734 AGTCCTCTGGTGCAGGAAGT 60.473 55.000 0.00 0.0 41.94 3.01 R
2842 2928 0.687098 TATGGCATGGCTGGGTTTGG 60.687 55.000 21.08 0.0 0.00 3.28 R
3895 4021 1.682344 GGGCGGGCTCCTTTGATTT 60.682 57.895 0.26 0.0 0.00 2.17 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.