Multiple sequence alignment - TraesCS3B01G162200

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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 TraesCS3B01G162200 chr3B 100.000 2822 0 0 1 2822 159513755 159516576 0 5212
1 TraesCS3B01G162200 chr3B 97.656 2773 62 3 1 2771 284646182 284643411 0 4758
2 TraesCS3B01G162200 chr3B 96.887 2827 82 6 1 2822 86366006 86363181 0 4728
3 TraesCS3B01G162200 chr5B 97.913 2827 54 3 1 2822 387193364 387196190 0 4889
4 TraesCS3B01G162200 chr5B 97.207 2828 72 7 1 2822 356262574 356259748 0 4778
5 TraesCS3B01G162200 chr5B 97.098 2826 77 5 1 2822 102071551 102074375 0 4759
6 TraesCS3B01G162200 chrUn 97.413 2822 67 6 5 2822 266213962 266211143 0 4802
7 TraesCS3B01G162200 chr7B 96.675 2827 88 6 1 2822 746907053 746904228 0 4695
8 TraesCS3B01G162200 chr7B 94.981 2829 132 9 1 2822 464876825 464879650 0 4429
9 TraesCS3B01G162200 chr2B 95.549 2831 116 7 1 2822 162963563 162960734 0 4521


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 TraesCS3B01G162200 chr3B 159513755 159516576 2821 False 5212 5212 100.000 1 2822 1 chr3B.!!$F1 2821
1 TraesCS3B01G162200 chr3B 284643411 284646182 2771 True 4758 4758 97.656 1 2771 1 chr3B.!!$R2 2770
2 TraesCS3B01G162200 chr3B 86363181 86366006 2825 True 4728 4728 96.887 1 2822 1 chr3B.!!$R1 2821
3 TraesCS3B01G162200 chr5B 387193364 387196190 2826 False 4889 4889 97.913 1 2822 1 chr5B.!!$F2 2821
4 TraesCS3B01G162200 chr5B 356259748 356262574 2826 True 4778 4778 97.207 1 2822 1 chr5B.!!$R1 2821
5 TraesCS3B01G162200 chr5B 102071551 102074375 2824 False 4759 4759 97.098 1 2822 1 chr5B.!!$F1 2821
6 TraesCS3B01G162200 chrUn 266211143 266213962 2819 True 4802 4802 97.413 5 2822 1 chrUn.!!$R1 2817
7 TraesCS3B01G162200 chr7B 746904228 746907053 2825 True 4695 4695 96.675 1 2822 1 chr7B.!!$R1 2821
8 TraesCS3B01G162200 chr7B 464876825 464879650 2825 False 4429 4429 94.981 1 2822 1 chr7B.!!$F1 2821
9 TraesCS3B01G162200 chr2B 162960734 162963563 2829 True 4521 4521 95.549 1 2822 1 chr2B.!!$R1 2821

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
100 101 0.53578 TGGCTTGCACTTGGTCTCAG 60.536 55.000 0.00 0.0 0.0 3.35 F
943 948 1.33624 GGCGCAAATATGAGGATTGGC 60.336 52.381 10.83 0.0 33.1 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 1417 1.879380 TCGGCTGTGATTCTGTTTTGG 59.121 47.619 0.00 0.0 0.0 3.28 R
1960 1968 3.313012 CGGCCATGATCGGATAGTTTA 57.687 47.619 2.24 0.0 0.0 2.01 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
100 101 0.535780 TGGCTTGCACTTGGTCTCAG 60.536 55.000 0.00 0.00 0.00 3.35
157 158 8.880878 TCAGAAATTTAAAGCCAAGGTTAAAC 57.119 30.769 0.00 0.00 33.31 2.01
221 222 4.339814 AGACATCGGAGATAGAGTGGAAAC 59.660 45.833 0.00 0.00 45.12 2.78
643 644 2.224744 TGTAAAAGCTGCAGGTGATGGA 60.225 45.455 20.97 0.89 0.00 3.41
795 799 5.411053 CAGCAAACCAAAAGAAAACAAAGGA 59.589 36.000 0.00 0.00 0.00 3.36
943 948 1.336240 GGCGCAAATATGAGGATTGGC 60.336 52.381 10.83 0.00 33.10 4.52
1226 1231 4.079958 AGAGGTGGTCAAACAAGTTTACCT 60.080 41.667 14.51 14.51 39.31 3.08
1441 1446 1.703014 ATCACAGCCGAGATGCCCAT 61.703 55.000 0.00 0.00 0.00 4.00
1608 1613 5.309282 AGTGAAGAAAGAGAAGGATGGAAGT 59.691 40.000 0.00 0.00 0.00 3.01
1730 1735 5.624159 GAATTCATCCACAGGTATGATCCA 58.376 41.667 0.00 0.00 32.40 3.41
1777 1783 7.566569 TGATCCATGGATGCAACATAATTTTT 58.433 30.769 32.05 2.07 34.60 1.94
1960 1968 5.066246 GCCGATACTTAGCTATCGTCCTAAT 59.934 44.000 13.90 0.00 42.63 1.73
2015 2023 7.608153 TCTAACATCGTCCTTAGTTCAATTGA 58.392 34.615 3.38 3.38 0.00 2.57
2070 2078 6.255294 AGCCTTGTCTCTCTAGTACTATGA 57.745 41.667 2.33 4.53 0.00 2.15
2267 2277 7.442364 GCTATACATATTGAGGCTTTCAGTGAA 59.558 37.037 0.08 0.08 37.07 3.18
2338 2348 9.031360 TGACGAATCACTTATAGTTTATCTTGC 57.969 33.333 0.00 0.00 0.00 4.01
2452 2462 6.398095 CATCCGGCTACTATGTTAATCATGA 58.602 40.000 0.00 0.00 37.91 3.07
2582 2592 9.807921 AAAGTGAGGATTGGAGAAAGTTTATTA 57.192 29.630 0.00 0.00 0.00 0.98
2766 2787 4.634012 TCGCCCTAAGCATATAAATGGT 57.366 40.909 0.00 0.00 45.63 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 9.703892 AGATATTTAGAACATACATGTCTCAGC 57.296 33.333 0.00 0.00 40.80 4.26
221 222 1.001048 CCATTCGGCTATGCATTGTGG 60.001 52.381 3.54 2.21 0.00 4.17
591 592 1.451028 GGATCGGCTTGAAGCAGCT 60.451 57.895 19.89 6.43 44.75 4.24
795 799 6.270815 TCTCTTATACTTGCGCTTATTTCGT 58.729 36.000 9.73 0.00 0.00 3.85
943 948 8.666573 TGCATTAAAATTATCACTTTGCCAATG 58.333 29.630 0.00 0.00 0.00 2.82
1226 1231 7.759886 CACTCTTACGACCATCTCTTTTAATGA 59.240 37.037 0.00 0.00 0.00 2.57
1412 1417 1.879380 TCGGCTGTGATTCTGTTTTGG 59.121 47.619 0.00 0.00 0.00 3.28
1441 1446 5.592282 TCTTTTGCCAATATGATAAGCCGAA 59.408 36.000 0.00 0.00 0.00 4.30
1608 1613 5.299782 ACACCTTCGGCTTAATTGTTTGTTA 59.700 36.000 0.00 0.00 0.00 2.41
1730 1735 3.136641 AGTAAGTCCATGGAGGGTGAT 57.863 47.619 16.81 0.36 38.24 3.06
1826 1832 4.808895 CCCCTTTGTCTTAGCAACAAAAAC 59.191 41.667 3.38 0.00 43.78 2.43
1960 1968 3.313012 CGGCCATGATCGGATAGTTTA 57.687 47.619 2.24 0.00 0.00 2.01
2015 2023 3.764237 ACATGTACCTTGTCTCGGTTT 57.236 42.857 0.00 0.00 35.98 3.27
2070 2078 8.739039 TGAATTCAACCATCGAAACATAATCTT 58.261 29.630 5.45 0.00 0.00 2.40
2267 2277 6.985188 ATTTGTTGCACTACTCATAACGAT 57.015 33.333 0.00 0.00 0.00 3.73
2452 2462 6.513884 CGGCTATTGATAGAAATGCAACACAT 60.514 38.462 0.00 0.00 34.71 3.21
2582 2592 8.579850 TTGTTAGGACTTTGCAGATAATCAAT 57.420 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.