Multiple sequence alignment - TraesCS7B01G457200

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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 TraesCS7B01G457200 chr7B 100.000 2558 0 0 1 2558 716802610 716800053 0 4724
1 TraesCS7B01G457200 chr7B 98.788 2558 31 0 1 2558 698133376 698130819 0 4553
2 TraesCS7B01G457200 chr7B 98.749 2558 32 0 1 2558 742930720 742933277 0 4547
3 TraesCS7B01G457200 chrUn 98.906 2559 27 1 1 2558 246703761 246701203 0 4569
4 TraesCS7B01G457200 chr6B 98.905 2558 28 0 1 2558 128896748 128894191 0 4569
5 TraesCS7B01G457200 chr5B 98.280 2558 42 2 1 2558 127825763 127823208 0 4479
6 TraesCS7B01G457200 chr5B 98.202 2558 45 1 1 2558 713088996 713091552 0 4468
7 TraesCS7B01G457200 chr5B 98.006 2558 50 1 1 2558 713119730 713117174 0 4440
8 TraesCS7B01G457200 chr3D 98.241 2558 44 1 1 2558 202630985 202628429 0 4473
9 TraesCS7B01G457200 chr2B 97.928 2558 53 0 1 2558 760900738 760898181 0 4431


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 TraesCS7B01G457200 chr7B 716800053 716802610 2557 True 4724 4724 100.000 1 2558 1 chr7B.!!$R2 2557
1 TraesCS7B01G457200 chr7B 698130819 698133376 2557 True 4553 4553 98.788 1 2558 1 chr7B.!!$R1 2557
2 TraesCS7B01G457200 chr7B 742930720 742933277 2557 False 4547 4547 98.749 1 2558 1 chr7B.!!$F1 2557
3 TraesCS7B01G457200 chrUn 246701203 246703761 2558 True 4569 4569 98.906 1 2558 1 chrUn.!!$R1 2557
4 TraesCS7B01G457200 chr6B 128894191 128896748 2557 True 4569 4569 98.905 1 2558 1 chr6B.!!$R1 2557
5 TraesCS7B01G457200 chr5B 127823208 127825763 2555 True 4479 4479 98.280 1 2558 1 chr5B.!!$R1 2557
6 TraesCS7B01G457200 chr5B 713088996 713091552 2556 False 4468 4468 98.202 1 2558 1 chr5B.!!$F1 2557
7 TraesCS7B01G457200 chr5B 713117174 713119730 2556 True 4440 4440 98.006 1 2558 1 chr5B.!!$R2 2557
8 TraesCS7B01G457200 chr3D 202628429 202630985 2556 True 4473 4473 98.241 1 2558 1 chr3D.!!$R1 2557
9 TraesCS7B01G457200 chr2B 760898181 760900738 2557 True 4431 4431 97.928 1 2558 1 chr2B.!!$R1 2557

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
431 434 0.923403 CGAATGATCTTCGCTTCGCA 59.077 50.0 12.24 0.0 34.78 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2083 0.471617 AGCAGCTTGAACCACAGAGT 59.528 50.0 0.0 0.0 0.0 3.24 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
154 155 2.143231 ACTAAAAAGGACCCTCCCCA 57.857 50.000 0.00 0.0 37.19 4.96
192 193 7.448161 TCCTTGAATTATTCGGTCATGCAATAT 59.552 33.333 0.00 0.0 0.00 1.28
229 231 4.709397 AGAATAAAATGCATTTCGACCCCA 59.291 37.500 24.28 5.4 32.27 4.96
326 328 6.712998 AGCTTAGATAAGAGAATACGCTCTCA 59.287 38.462 11.15 0.0 44.18 3.27
431 434 0.923403 CGAATGATCTTCGCTTCGCA 59.077 50.000 12.24 0.0 34.78 5.10
729 732 6.596703 GGGTACAACTCTTATTTGAACGAAC 58.403 40.000 0.00 0.0 0.00 3.95
954 957 6.407299 GGAGGGGATACGTATTTGTTGTTCTA 60.407 42.308 9.92 0.0 37.60 2.10
1093 1096 3.068024 GGAATTTCAGGTGTCAAAGTGCA 59.932 43.478 0.00 0.0 0.00 4.57
1421 1424 4.527944 GGAAGAGGAAAAGGAAATCCGAT 58.472 43.478 0.00 0.0 40.78 4.18
1514 1517 1.831736 ACAAGCCACTAGATTAGCGGT 59.168 47.619 0.00 0.0 30.65 5.68
1607 1610 2.890945 CCGGGACTCAAAAGAATTTGGT 59.109 45.455 0.00 0.0 44.88 3.67
1675 1678 2.761071 GAGCTCGCCTCCTTCTTTG 58.239 57.895 0.00 0.0 34.35 2.77
1808 1811 8.035394 AGAATAAGAAAGAGAAGCGTGATGTTA 58.965 33.333 0.00 0.0 0.00 2.41
1818 1821 2.411748 AGCGTGATGTTATCGTGTTGTG 59.588 45.455 0.00 0.0 0.00 3.33
2073 2076 0.180406 ACCTCGTGCTTGGTTTGAGT 59.820 50.000 0.00 0.0 31.62 3.41
2080 2083 2.165437 GTGCTTGGTTTGAGTGGTTCAA 59.835 45.455 0.00 0.0 43.92 2.69
2276 2279 8.859236 TCAAGATGTCAGATTGATTTTCTCTT 57.141 30.769 0.00 0.0 0.00 2.85
2277 2280 9.293404 TCAAGATGTCAGATTGATTTTCTCTTT 57.707 29.630 0.00 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 4.335647 CAAGGAGGGGCGCACAGT 62.336 66.667 13.89 0.00 0.00 3.55
229 231 6.051717 CCACGAAATGATTGAGAACTAGGAT 58.948 40.000 0.00 0.00 0.00 3.24
445 448 3.914426 AAGGAAAGAGCGATATGGTGT 57.086 42.857 0.00 0.00 0.00 4.16
683 686 5.452917 CCCGTACGGAATTATCCTCTTTCTT 60.453 44.000 35.41 0.00 44.17 2.52
954 957 2.432300 CCGCACCCCCTAATCGACT 61.432 63.158 0.00 0.00 0.00 4.18
1421 1424 0.888736 CACACGAGCAATCCAACCCA 60.889 55.000 0.00 0.00 0.00 4.51
1501 1504 4.141801 TGGTTTATGCACCGCTAATCTAGT 60.142 41.667 0.00 0.00 40.09 2.57
1514 1517 3.057876 GGTTGACGAACATGGTTTATGCA 60.058 43.478 0.00 0.00 40.59 3.96
1607 1610 3.601435 TCGTTCAGGAACAAACACTTCA 58.399 40.909 12.22 0.00 41.20 3.02
1675 1678 4.017271 CGTACAATTTCGGCGATTACAAC 58.983 43.478 11.76 4.62 0.00 3.32
1808 1811 4.771590 ATTTGATTGCTCACAACACGAT 57.228 36.364 0.00 0.00 38.99 3.73
2073 2076 3.278574 CTTGAACCACAGAGTTGAACCA 58.721 45.455 0.00 0.00 0.00 3.67
2080 2083 0.471617 AGCAGCTTGAACCACAGAGT 59.528 50.000 0.00 0.00 0.00 3.24
2276 2279 7.288852 TCAACCTCAATTCCCAGAAAATAACAA 59.711 33.333 0.00 0.00 0.00 2.83
2277 2280 6.780031 TCAACCTCAATTCCCAGAAAATAACA 59.220 34.615 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.