Multiple sequence alignment - TraesCS2B01G013400

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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 TraesCS2B01G013400 chr2B 100.000 2198 0 0 1 2198 6425314 6427511 0.000000e+00 4060
1 TraesCS2B01G013400 chr2B 97.044 2199 32 4 1 2198 6411258 6413424 0.000000e+00 3670
2 TraesCS2B01G013400 chr2B 92.641 1753 110 9 7 1758 6381858 6383592 0.000000e+00 2505
3 TraesCS2B01G013400 chr2B 89.552 201 17 3 1751 1948 6385493 6385692 3.620000e-63 252
4 TraesCS2B01G013400 chr2D 90.549 1767 142 14 7 1771 4706878 4705135 0.000000e+00 2314
5 TraesCS2B01G013400 chr2D 90.498 1768 142 14 7 1771 4686604 4684860 0.000000e+00 2311
6 TraesCS2B01G013400 chr2D 94.549 587 30 1 7 593 4668488 4667904 0.000000e+00 905
7 TraesCS2B01G013400 chr2D 81.882 287 46 4 918 1201 3453991 3454274 1.010000e-58 237
8 TraesCS2B01G013400 chrUn 94.878 410 17 2 812 1221 477374847 477375252 2.380000e-179 638


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 TraesCS2B01G013400 chr2B 6425314 6427511 2197 False 4060.0 4060 100.0000 1 2198 1 chr2B.!!$F2 2197
1 TraesCS2B01G013400 chr2B 6411258 6413424 2166 False 3670.0 3670 97.0440 1 2198 1 chr2B.!!$F1 2197
2 TraesCS2B01G013400 chr2B 6381858 6385692 3834 False 1378.5 2505 91.0965 7 1948 2 chr2B.!!$F3 1941
3 TraesCS2B01G013400 chr2D 4705135 4706878 1743 True 2314.0 2314 90.5490 7 1771 1 chr2D.!!$R3 1764
4 TraesCS2B01G013400 chr2D 4684860 4686604 1744 True 2311.0 2311 90.4980 7 1771 1 chr2D.!!$R2 1764
5 TraesCS2B01G013400 chr2D 4667904 4668488 584 True 905.0 905 94.5490 7 593 1 chr2D.!!$R1 586

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
708 710 4.17329 AGACCTCATAGTGGAGAGTACC 57.827 50.0 0.0 0.0 37.05 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 1617 1.657181 GGCTTGTGCGGTGAAAACG 60.657 57.895 0.0 0.0 40.82 3.6 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
609 611 6.072064 TGGCATGGCAAAATTTAAAGATTTGG 60.072 34.615 21.13 7.5 35.21 3.28
708 710 4.173290 AGACCTCATAGTGGAGAGTACC 57.827 50.000 0.00 0.0 37.05 3.34
765 767 8.885693 ATACTCTATATATTCTGCCACAGACA 57.114 34.615 0.00 0.0 40.46 3.41
766 768 7.603180 ACTCTATATATTCTGCCACAGACAA 57.397 36.000 0.00 0.0 40.46 3.18
767 769 8.200024 ACTCTATATATTCTGCCACAGACAAT 57.800 34.615 0.00 0.0 40.46 2.71
768 770 8.093307 ACTCTATATATTCTGCCACAGACAATG 58.907 37.037 0.00 0.0 40.46 2.82
769 771 8.193953 TCTATATATTCTGCCACAGACAATGA 57.806 34.615 0.00 0.0 40.46 2.57
770 772 8.650490 TCTATATATTCTGCCACAGACAATGAA 58.350 33.333 0.00 0.0 40.46 2.57
771 773 9.445878 CTATATATTCTGCCACAGACAATGAAT 57.554 33.333 0.00 0.0 40.46 2.57
1105 1116 1.079127 TTTAGTCTCAGCCTGCCGC 60.079 57.895 0.00 0.0 37.98 6.53
1506 1517 2.610374 TGGTGCGTTTTTCTCACTGTAC 59.390 45.455 0.00 0.0 32.94 2.90
1737 1749 4.202182 ACGTTTGTGCTTCCTAGAGTAACA 60.202 41.667 0.00 0.0 0.00 2.41
1738 1750 4.386049 CGTTTGTGCTTCCTAGAGTAACAG 59.614 45.833 0.00 0.0 0.00 3.16
1797 3717 3.684908 TGGGTGATGTACTTTCCATGTG 58.315 45.455 0.00 0.0 0.00 3.21
1957 3880 4.110036 TCTGTGTGACATAATCGGACAG 57.890 45.455 0.00 0.0 39.17 3.51
1959 3882 4.108336 CTGTGTGACATAATCGGACAGAG 58.892 47.826 0.00 0.0 39.75 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 4.722526 AAATGCATGCCCATACCTAGTA 57.277 40.909 16.68 0.00 0.00 1.82
493 495 4.018779 CACTTCCCCATTGGTCTTTAGGTA 60.019 45.833 1.20 0.00 34.77 3.08
1105 1116 6.870965 GCATCTTTCCTATCACCATAGTACAG 59.129 42.308 0.00 0.00 31.28 2.74
1506 1517 2.238144 ACATGACTGACCATTCTCCTGG 59.762 50.000 0.00 0.00 42.35 4.45
1519 1530 3.885484 AAAAACTCGCAGACATGACTG 57.115 42.857 19.11 19.11 40.43 3.51
1605 1617 1.657181 GGCTTGTGCGGTGAAAACG 60.657 57.895 0.00 0.00 40.82 3.60
1715 1727 4.304110 TGTTACTCTAGGAAGCACAAACG 58.696 43.478 0.00 0.00 0.00 3.60
1717 1729 5.801531 TCTGTTACTCTAGGAAGCACAAA 57.198 39.130 0.00 0.00 0.00 2.83
1797 3717 1.926510 GCAGAAAACACAAGTTGCACC 59.073 47.619 1.81 0.00 38.17 5.01
1957 3880 1.987770 CATGTTGCGCAAAATGACCTC 59.012 47.619 38.73 19.59 38.08 3.85
1959 3882 1.782044 ACATGTTGCGCAAAATGACC 58.218 45.000 44.51 25.31 38.08 4.02


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

AutoCloner maintained by Alex Coulton.