Multiple sequence alignment - TraesCS4B01G319700

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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 TraesCS4B01G319700 chr4B 100.000 3170 0 0 1 3170 610436485 610433316 0.000000e+00 5854.0
1 TraesCS4B01G319700 chr4B 75.598 209 40 11 1617 1820 531094081 531094283 3.370000e-15 93.5
2 TraesCS4B01G319700 chr4D 89.449 2360 119 53 559 2891 481448896 481446640 0.000000e+00 2859.0
3 TraesCS4B01G319700 chr4D 89.236 576 23 13 1 551 481449498 481448937 0.000000e+00 684.0
4 TraesCS4B01G319700 chr4D 91.071 280 25 0 2891 3170 481440496 481440217 2.310000e-101 379.0
5 TraesCS4B01G319700 chr5A 87.466 1827 127 56 259 2033 661220799 661222575 0.000000e+00 2012.0
6 TraesCS4B01G319700 chr5A 90.395 531 40 3 2647 3169 661223280 661223807 0.000000e+00 688.0
7 TraesCS4B01G319700 chr5A 89.474 456 25 14 2192 2642 661222805 661223242 3.570000e-154 555.0
8 TraesCS4B01G319700 chr5A 91.000 100 6 1 2101 2197 661222603 661222702 7.130000e-27 132.0
9 TraesCS4B01G319700 chr5A 98.246 57 1 0 1 57 661220613 661220669 2.010000e-17 100.0
10 TraesCS4B01G319700 chr4A 75.641 234 43 14 1617 1843 34294923 34295149 1.560000e-18 104.0


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 TraesCS4B01G319700 chr4B 610433316 610436485 3169 True 5854.0 5854 100.0000 1 3170 1 chr4B.!!$R1 3169
1 TraesCS4B01G319700 chr4D 481446640 481449498 2858 True 1771.5 2859 89.3425 1 2891 2 chr4D.!!$R2 2890
2 TraesCS4B01G319700 chr5A 661220613 661223807 3194 False 697.4 2012 91.3162 1 3169 5 chr5A.!!$F1 3168


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
620 695 0.320421 TTGCTTGCGTGGACTAGGAC 60.32 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2520 0.977627 ACTCGGCCTCATGATGGTCA 60.978 55.0 13.82 3.55 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.