Multiple sequence alignment - TraesCS2A01G242200

Loading Multiple Alignment...

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 TraesCS2A01G242200 chr2A 100.000 2177 0 0 1 2177 335845066 335842890 0 4021
1 TraesCS2A01G242200 chr6D 98.530 2177 32 0 1 2177 389254923 389252747 0 3843
2 TraesCS2A01G242200 chr3A 98.530 2177 31 1 1 2177 66007378 66009553 0 3842
3 TraesCS2A01G242200 chr3A 97.887 2177 46 0 1 2177 672899767 672901943 0 3766
4 TraesCS2A01G242200 chr5D 98.392 2177 34 1 1 2177 503238780 503236605 0 3825
5 TraesCS2A01G242200 chr5D 98.477 2167 32 1 11 2177 503243019 503240854 0 3818
6 TraesCS2A01G242200 chrUn 98.072 2178 38 2 1 2177 216508364 216510538 0 3786
7 TraesCS2A01G242200 chr3B 97.887 2177 45 1 1 2177 201537274 201535099 0 3764
8 TraesCS2A01G242200 chr2B 97.382 2177 57 0 1 2177 474918684 474916508 0 3705
9 TraesCS2A01G242200 chr1B 97.244 2177 54 1 1 2177 633743659 633745829 0 3683


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 TraesCS2A01G242200 chr2A 335842890 335845066 2176 True 4021.0 4021 100.0000 1 2177 1 chr2A.!!$R1 2176
1 TraesCS2A01G242200 chr6D 389252747 389254923 2176 True 3843.0 3843 98.5300 1 2177 1 chr6D.!!$R1 2176
2 TraesCS2A01G242200 chr3A 66007378 66009553 2175 False 3842.0 3842 98.5300 1 2177 1 chr3A.!!$F1 2176
3 TraesCS2A01G242200 chr3A 672899767 672901943 2176 False 3766.0 3766 97.8870 1 2177 1 chr3A.!!$F2 2176
4 TraesCS2A01G242200 chr5D 503236605 503243019 6414 True 3821.5 3825 98.4345 1 2177 2 chr5D.!!$R1 2176
5 TraesCS2A01G242200 chrUn 216508364 216510538 2174 False 3786.0 3786 98.0720 1 2177 1 chrUn.!!$F1 2176
6 TraesCS2A01G242200 chr3B 201535099 201537274 2175 True 3764.0 3764 97.8870 1 2177 1 chr3B.!!$R1 2176
7 TraesCS2A01G242200 chr2B 474916508 474918684 2176 True 3705.0 3705 97.3820 1 2177 1 chr2B.!!$R1 2176
8 TraesCS2A01G242200 chr1B 633743659 633745829 2170 False 3683.0 3683 97.2440 1 2177 1 chr1B.!!$F1 2176

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
780 5021 0.693049 GAGGGGAAGCAGAACCAAGA 59.307 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 6264 0.252057 TCCACTCCATCCCGAAGACA 60.252 55.0 0.0 0.0 0.0 3.41 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 4420 9.845740 TTGCATTACTTATAGCTTCCTTATTCA 57.154 29.630 0.00 0.00 0.00 2.57
205 4445 5.245531 AGACAAAGCAGATTCGGAATTGTA 58.754 37.500 4.47 0.00 30.37 2.41
315 4555 1.815003 GTCAATCCCACAAGCCTCTTG 59.185 52.381 5.13 5.13 0.00 3.02
323 4563 1.466167 CACAAGCCTCTTGTCCATTCG 59.534 52.381 9.05 0.00 0.00 3.34
453 4693 2.900546 CGCTGAGTTATATCCCTTCCCT 59.099 50.000 0.00 0.00 0.00 4.20
477 4717 6.889198 TGTCCCATCGAGAAAGAGAATTAAT 58.111 36.000 0.00 0.00 0.00 1.40
673 4913 7.270047 TCTGTACGATTTTCCCGATCTAAATT 58.730 34.615 0.00 0.00 0.00 1.82
734 4974 7.558807 TGTTCTATTCGATACTGGTAGGAGAAA 59.441 37.037 0.00 0.00 0.00 2.52
780 5021 0.693049 GAGGGGAAGCAGAACCAAGA 59.307 55.000 0.00 0.00 0.00 3.02
832 5073 3.378427 GCGCCAAAGATCTTACCATTTCT 59.622 43.478 8.75 0.00 0.00 2.52
1101 5342 8.307483 CAAAGATTGACCTCTGTAGAAAGACTA 58.693 37.037 0.00 0.00 0.00 2.59
1110 5351 8.816894 ACCTCTGTAGAAAGACTAATTCATTCA 58.183 33.333 0.00 0.00 34.86 2.57
1184 5425 0.670854 GAAGCGGGTTGACCTCTGTC 60.671 60.000 0.00 0.00 42.12 3.51
1521 5762 3.610242 CGAAAAGATCTTGGACGACTCAG 59.390 47.826 9.17 0.00 0.00 3.35
1586 5827 1.488812 TGCCTAACCGCATGGATAAGT 59.511 47.619 0.00 0.00 39.21 2.24
1705 5946 7.398332 AGGAAAAGGTTCTCTATTGATGCAAAT 59.602 33.333 0.00 0.00 33.92 2.32
1879 6122 1.713078 GAGGGGCAAGGGGATTGATAT 59.287 52.381 0.00 0.00 41.83 1.63
2018 6264 5.365619 ACGTGACTCAATTGGTCTTAGTTT 58.634 37.500 20.58 4.64 35.04 2.66
2029 6275 3.581332 TGGTCTTAGTTTGTCTTCGGGAT 59.419 43.478 0.00 0.00 0.00 3.85
2059 6305 0.684805 AAGGGCGGAGACTCTCGAAT 60.685 55.000 14.93 0.59 32.70 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 4420 5.882557 ACAATTCCGAATCTGCTTTGTCTAT 59.117 36.000 0.00 0.0 0.00 1.98
236 4476 6.567602 AACTCCAGGCTAATAATCTGAAGT 57.432 37.500 0.00 0.0 27.26 3.01
477 4717 1.341976 GCCCCTTTGCCTTAGGATTCA 60.342 52.381 0.69 0.0 34.56 2.57
673 4913 3.072915 TCTTCTTCATGGAAACCTGCTCA 59.927 43.478 0.00 0.0 0.00 4.26
780 5021 2.550830 GGCGACCCATATCATCTTGT 57.449 50.000 0.00 0.0 0.00 3.16
832 5073 1.668826 ATGTAGCCCCAGTTCCTTCA 58.331 50.000 0.00 0.0 0.00 3.02
1101 5342 7.102346 GGTCCTCATATCGATCTGAATGAATT 58.898 38.462 13.72 0.0 0.00 2.17
1110 5351 3.829601 GAGTTGGGTCCTCATATCGATCT 59.170 47.826 0.00 0.0 0.00 2.75
1184 5425 4.653341 AGAGGATTGTACCATGAGAGAAGG 59.347 45.833 0.00 0.0 0.00 3.46
1521 5762 0.249031 AACTGGCTTTCGTGCTTTGC 60.249 50.000 0.00 0.0 0.00 3.68
1586 5827 5.302059 TCCAAAATTGACGGGTTAATGTGAA 59.698 36.000 0.00 0.0 0.00 3.18
1705 5946 3.061369 TCCCTATCCTCTAGGTACAGCA 58.939 50.000 0.00 0.0 36.34 4.41
2018 6264 0.252057 TCCACTCCATCCCGAAGACA 60.252 55.000 0.00 0.0 0.00 3.41
2029 6275 2.592993 CCGCCCTTCTTCCACTCCA 61.593 63.158 0.00 0.0 0.00 3.86
2059 6305 2.546899 TCGAAGGGATCCTTTTCCTCA 58.453 47.619 10.91 0.0 44.82 3.86


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

AutoCloner maintained by Alex Coulton.