Multiple sequence alignment - TraesCS2A01G576700

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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 TraesCS2A01G576700 chr2A 100.000 2525 0 0 1 2525 770907546 770910070 0 4663
1 TraesCS2A01G576700 chr5A 97.121 2536 60 9 1 2525 12294456 12296989 0 4266
2 TraesCS2A01G576700 chr3D 97.083 2537 60 10 1 2525 572954885 572957419 0 4263
3 TraesCS2A01G576700 chr4D 96.921 2533 67 7 1 2524 407144127 407141597 0 4235
4 TraesCS2A01G576700 chr1A 96.923 2535 62 11 1 2525 58012950 58015478 0 4235
5 TraesCS2A01G576700 chr7A 96.884 2535 67 8 1 2525 231223684 231226216 0 4233
6 TraesCS2A01G576700 chr1D 96.923 2535 59 11 1 2525 259691628 259689103 0 4231
7 TraesCS2A01G576700 chr7D 96.843 2534 69 7 2 2525 69728275 69725743 0 4226
8 TraesCS2A01G576700 chr7D 96.805 2535 67 9 1 2525 108538007 108535477 0 4220
9 TraesCS2A01G576700 chr3A 96.803 2534 67 9 1 2525 15659322 15661850 0 4218


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 TraesCS2A01G576700 chr2A 770907546 770910070 2524 False 4663 4663 100.000 1 2525 1 chr2A.!!$F1 2524
1 TraesCS2A01G576700 chr5A 12294456 12296989 2533 False 4266 4266 97.121 1 2525 1 chr5A.!!$F1 2524
2 TraesCS2A01G576700 chr3D 572954885 572957419 2534 False 4263 4263 97.083 1 2525 1 chr3D.!!$F1 2524
3 TraesCS2A01G576700 chr4D 407141597 407144127 2530 True 4235 4235 96.921 1 2524 1 chr4D.!!$R1 2523
4 TraesCS2A01G576700 chr1A 58012950 58015478 2528 False 4235 4235 96.923 1 2525 1 chr1A.!!$F1 2524
5 TraesCS2A01G576700 chr7A 231223684 231226216 2532 False 4233 4233 96.884 1 2525 1 chr7A.!!$F1 2524
6 TraesCS2A01G576700 chr1D 259689103 259691628 2525 True 4231 4231 96.923 1 2525 1 chr1D.!!$R1 2524
7 TraesCS2A01G576700 chr7D 69725743 69728275 2532 True 4226 4226 96.843 2 2525 1 chr7D.!!$R1 2523
8 TraesCS2A01G576700 chr7D 108535477 108538007 2530 True 4220 4220 96.805 1 2525 1 chr7D.!!$R2 2524
9 TraesCS2A01G576700 chr3A 15659322 15661850 2528 False 4218 4218 96.803 1 2525 1 chr3A.!!$F1 2524

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
243 250 1.529152 TAGTTCGTCCTTCTGCGCCA 61.529 55.0 4.18 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1680 1.032114 ATCAGCGGCCTTAACCTTGC 61.032 55.0 0.0 0.0 0.0 4.01 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
243 250 1.529152 TAGTTCGTCCTTCTGCGCCA 61.529 55.000 4.18 0.00 0.00 5.69
653 660 7.914427 TTCCATACTACTGACCATGATTAGT 57.086 36.000 0.00 0.00 0.00 2.24
839 849 2.311463 ACCTCATGCAGTAGCGTAGAT 58.689 47.619 0.00 0.00 46.23 1.98
851 861 6.900299 GCAGTAGCGTAGATCACAATTTTTAC 59.100 38.462 0.00 0.00 0.00 2.01
1068 1078 9.113838 CCTAGCATCAAAATTAGACATGTACTT 57.886 33.333 0.00 0.00 0.00 2.24
1071 1081 8.796475 AGCATCAAAATTAGACATGTACTTTGT 58.204 29.630 0.00 2.23 0.00 2.83
1312 1325 3.130340 AGTCGACAGCACACCAAATTTTT 59.870 39.130 19.50 0.00 0.00 1.94
1543 1557 8.962111 GCAGGTAATTCGTAGTAGTACAATTAC 58.038 37.037 25.37 25.37 39.22 1.89
1666 1680 4.517075 TGGACTCTAGCATCTCGTATGAAG 59.483 45.833 4.96 2.31 0.00 3.02
2157 2176 1.407936 CTCACGGAGGACCTCATCAT 58.592 55.000 23.06 2.16 31.08 2.45
2172 2191 7.993183 GGACCTCATCATAGAATTGAAGGTAAA 59.007 37.037 0.00 0.00 37.11 2.01
2360 2380 0.038744 CTTCACACCCAATGGAGGCT 59.961 55.000 0.00 0.00 34.81 4.58
2413 2433 3.834231 CAGGGGAAACAAAAGGATGTCAT 59.166 43.478 0.00 0.00 31.81 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 250 0.550914 TCTGTCTTGCTGGTTTGGGT 59.449 50.000 0.00 0.00 0.00 4.51
653 660 1.077169 TGGTCTCCTCAACTCTAGGCA 59.923 52.381 0.00 0.00 33.84 4.75
1016 1026 0.899019 GAGAAGTCCACCCAGTCCTC 59.101 60.000 0.00 0.00 0.00 3.71
1068 1078 2.288666 GAATTAGCGATGGCCAGACAA 58.711 47.619 13.05 0.69 41.24 3.18
1071 1081 2.936919 ATGAATTAGCGATGGCCAGA 57.063 45.000 13.05 0.00 41.24 3.86
1312 1325 3.291584 TGTACAACACAAATGGCCTGAA 58.708 40.909 3.32 0.00 32.95 3.02
1472 1485 5.865552 CAGATTGCCTCACCATTTACAAAAG 59.134 40.000 0.00 0.00 0.00 2.27
1590 1604 3.360249 GTCTGCATGACAACAAAAGCT 57.640 42.857 0.00 0.00 44.73 3.74
1666 1680 1.032114 ATCAGCGGCCTTAACCTTGC 61.032 55.000 0.00 0.00 0.00 4.01
2063 2082 4.262420 GGTGCACATCCTATGGTTTTGTTT 60.262 41.667 20.43 0.00 33.60 2.83
2360 2380 3.072211 CTGCTCAGCATTCTCAACAGAA 58.928 45.455 0.00 0.00 43.06 3.02
2413 2433 2.579201 GCTTAGCAGCGACCTCCA 59.421 61.111 0.00 0.00 35.91 3.86


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

AutoCloner maintained by Alex Coulton.