Multiple sequence alignment - TraesCS5D01G150700

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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 TraesCS5D01G150700 chr5D 100.000 4068 0 0 1 4068 239939217 239943284 0.000000e+00 7513
1 TraesCS5D01G150700 chr5B 97.560 1844 44 1 53 1896 263547788 263545946 0.000000e+00 3155
2 TraesCS5D01G150700 chr5B 96.392 776 18 8 1914 2680 263545961 263545187 0.000000e+00 1269
3 TraesCS5D01G150700 chr5B 91.558 616 36 6 2728 3342 263545192 263544592 0.000000e+00 835
4 TraesCS5D01G150700 chr5B 88.030 401 24 11 3412 3805 263544568 263544185 1.720000e-123 453
5 TraesCS5D01G150700 chr5B 89.879 247 20 4 3800 4045 263544105 263543863 3.050000e-81 313
6 TraesCS5D01G150700 chr5A 95.833 1896 56 6 1 1896 313907614 313905742 0.000000e+00 3042
7 TraesCS5D01G150700 chr5A 93.698 1444 64 17 1914 3342 313905757 313904326 0.000000e+00 2137
8 TraesCS5D01G150700 chr5A 93.167 600 16 8 3476 4066 313904271 313903688 0.000000e+00 857
9 TraesCS5D01G150700 chr1A 83.117 154 16 4 86 230 281893471 281893623 9.170000e-27 132


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 TraesCS5D01G150700 chr5D 239939217 239943284 4067 False 7513 7513 100.000000 1 4068 1 chr5D.!!$F1 4067
1 TraesCS5D01G150700 chr5B 263543863 263547788 3925 True 1205 3155 92.683800 53 4045 5 chr5B.!!$R1 3992
2 TraesCS5D01G150700 chr5A 313903688 313907614 3926 True 2012 3042 94.232667 1 4066 3 chr5A.!!$R1 4065


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
427 428 0.798776 AGTTATTCGTGCAGCACAGC 59.201 50.000 25.19 7.78 33.4 4.40 F
1437 1438 1.066929 CAAAGGGCTGGCATTGTTACC 60.067 52.381 0.82 0.00 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 1954 0.253044 GCTAACTGGACCATGCTCCA 59.747 55.0 9.43 9.43 38.05 3.86 R
3422 3440 0.034896 TTCCCACCGAAAGACTCTGC 59.965 55.0 0.00 0.00 0.00 4.26 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.