Multiple sequence alignment - TraesCS4A01G360300

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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 TraesCS4A01G360300 chr4A 100.000 2328 0 0 1 2328 633425072 633427399 0 4300
1 TraesCS4A01G360300 chr4A 97.851 2327 43 2 2 2328 633467261 633469580 0 4013
2 TraesCS4A01G360300 chr4A 97.808 2327 42 3 2 2328 633533380 633535697 0 4006
3 TraesCS4A01G360300 chr4A 97.679 2327 51 2 2 2328 633508735 633511058 0 3995
4 TraesCS4A01G360300 chr4A 97.379 2327 53 2 2 2328 633685854 633688172 0 3952
5 TraesCS4A01G360300 chr4A 95.966 2330 86 6 2 2328 67576684 67574360 0 3775
6 TraesCS4A01G360300 chr4A 97.888 2178 44 2 2 2179 633740082 633742257 0 3766
7 TraesCS4A01G360300 chr4A 97.929 2173 42 1 2 2174 633580838 633583007 0 3760
8 TraesCS4A01G360300 chr2B 96.139 2331 73 10 2 2328 30670611 30668294 0 3790
9 TraesCS4A01G360300 chr6A 95.883 2332 85 8 2 2328 84434144 84436469 0 3764
10 TraesCS4A01G360300 chr1A 95.285 2333 95 10 2 2328 94783307 94785630 0 3685
11 TraesCS4A01G360300 chr5B 95.111 2332 93 11 2 2328 567270595 567268280 0 3655


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 TraesCS4A01G360300 chr4A 633425072 633427399 2327 False 4300 4300 100.000 1 2328 1 chr4A.!!$F1 2327
1 TraesCS4A01G360300 chr4A 633467261 633469580 2319 False 4013 4013 97.851 2 2328 1 chr4A.!!$F2 2326
2 TraesCS4A01G360300 chr4A 633533380 633535697 2317 False 4006 4006 97.808 2 2328 1 chr4A.!!$F4 2326
3 TraesCS4A01G360300 chr4A 633508735 633511058 2323 False 3995 3995 97.679 2 2328 1 chr4A.!!$F3 2326
4 TraesCS4A01G360300 chr4A 633685854 633688172 2318 False 3952 3952 97.379 2 2328 1 chr4A.!!$F6 2326
5 TraesCS4A01G360300 chr4A 67574360 67576684 2324 True 3775 3775 95.966 2 2328 1 chr4A.!!$R1 2326
6 TraesCS4A01G360300 chr4A 633740082 633742257 2175 False 3766 3766 97.888 2 2179 1 chr4A.!!$F7 2177
7 TraesCS4A01G360300 chr4A 633580838 633583007 2169 False 3760 3760 97.929 2 2174 1 chr4A.!!$F5 2172
8 TraesCS4A01G360300 chr2B 30668294 30670611 2317 True 3790 3790 96.139 2 2328 1 chr2B.!!$R1 2326
9 TraesCS4A01G360300 chr6A 84434144 84436469 2325 False 3764 3764 95.883 2 2328 1 chr6A.!!$F1 2326
10 TraesCS4A01G360300 chr1A 94783307 94785630 2323 False 3685 3685 95.285 2 2328 1 chr1A.!!$F1 2326
11 TraesCS4A01G360300 chr5B 567268280 567270595 2315 True 3655 3655 95.111 2 2328 1 chr5B.!!$R1 2326

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
207 209 1.340088 TTGACCACTACCGCCAAGTA 58.660 50.0 0.0 0.0 0.0 2.24 F
948 952 6.848451 TCCAGCGGAAATACTTTGTTTAATC 58.152 36.0 0.0 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1045 0.163146 GCTGTAACAAGCCGAACGAC 59.837 55.000 0.00 0.0 37.2 4.34 R
2303 2318 4.070552 AGTCCGCGGCAGAGAACC 62.071 66.667 23.51 0.0 0.0 3.62 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
71 72 4.899352 AGAACATGCCTCAGTAGAAAGT 57.101 40.909 0.00 0.00 0.00 2.66
89 91 5.407387 AGAAAGTGAGCTTTTTCGCGTATAA 59.593 36.000 5.77 0.00 44.25 0.98
207 209 1.340088 TTGACCACTACCGCCAAGTA 58.660 50.000 0.00 0.00 0.00 2.24
277 279 7.223387 GCCGATTACGAAATCTACCTTTTTAGA 59.777 37.037 0.00 0.00 39.56 2.10
868 871 7.827236 TCATAAGTGAAATAGTTTGATCGGGTT 59.173 33.333 0.00 0.00 0.00 4.11
948 952 6.848451 TCCAGCGGAAATACTTTGTTTAATC 58.152 36.000 0.00 0.00 0.00 1.75
1041 1045 2.166907 AGAGTCCTGATGTAGTGGGG 57.833 55.000 0.00 0.00 0.00 4.96
1050 1054 2.125793 GTAGTGGGGTCGTTCGGC 60.126 66.667 0.00 0.00 0.00 5.54
1059 1063 0.788391 GGTCGTTCGGCTTGTTACAG 59.212 55.000 0.00 0.00 0.00 2.74
1360 1366 4.769345 ATTGGTCAAAATGGGTTTGTGT 57.231 36.364 0.00 0.00 45.83 3.72
1362 1368 3.099905 TGGTCAAAATGGGTTTGTGTCA 58.900 40.909 0.00 0.00 45.83 3.58
1406 1412 1.351017 CACAGGTGTGGGATTACAGGT 59.649 52.381 1.90 0.00 42.10 4.00
1725 1733 2.224314 GTCAGCAGTTGAGTTTGCCTAC 59.776 50.000 0.00 0.00 41.17 3.18
1729 1737 2.863809 CAGTTGAGTTTGCCTACCCTT 58.136 47.619 0.00 0.00 0.00 3.95
2052 2061 1.292061 CCCGCGAATCCGTAAATCAA 58.708 50.000 8.23 0.00 38.24 2.57
2231 2246 4.394939 GGAGTTTCCTTAGGTAGCCACCT 61.395 52.174 9.37 9.37 45.06 4.00
2303 2318 0.649475 GTATGCTCGCTTGCTGTCTG 59.351 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.123959 GTGGTTATACGCGAAAAAGCTCA 59.876 43.478 15.93 0.00 34.40 4.26
89 91 0.988832 TAATTGGGCTTCGAGGTGGT 59.011 50.000 0.00 0.00 0.00 4.16
207 209 8.805175 TGGACTTCATCAATTTGTGAATTATGT 58.195 29.630 11.94 8.34 40.50 2.29
868 871 3.924013 ATCGGGCCTGACCTGGTCA 62.924 63.158 26.79 26.79 46.01 4.02
1041 1045 0.163146 GCTGTAACAAGCCGAACGAC 59.837 55.000 0.00 0.00 37.20 4.34
1050 1054 3.876274 TCTGCTAGAGGCTGTAACAAG 57.124 47.619 0.00 0.00 42.39 3.16
1059 1063 2.991250 TCAAAACCATCTGCTAGAGGC 58.009 47.619 0.00 0.00 42.22 4.70
1360 1366 5.886474 AGAGTAGATCGTTCAACACCTATGA 59.114 40.000 0.00 0.00 0.00 2.15
1362 1368 6.827251 TGTAGAGTAGATCGTTCAACACCTAT 59.173 38.462 0.00 0.00 0.00 2.57
1398 1404 5.071923 GGTTTATGAGCCCTAGACCTGTAAT 59.928 44.000 0.00 0.00 0.00 1.89
1725 1733 5.567138 CTACAAAAATGAGTAGGCAAGGG 57.433 43.478 0.00 0.00 35.27 3.95
2231 2246 7.508296 ACAGAAGTTTAAGGAGAACTGTAGGTA 59.492 37.037 0.00 0.00 37.41 3.08
2303 2318 4.070552 AGTCCGCGGCAGAGAACC 62.071 66.667 23.51 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.