Multiple sequence alignment - TraesCS5A01G110800

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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 TraesCS5A01G110800 chr5A 100.000 4261 0 0 1 4261 210978699 210982959 0 7869
1 TraesCS5A01G110800 chr5A 98.498 4262 63 1 1 4261 194027276 194023015 0 7515
2 TraesCS5A01G110800 chr5A 98.217 4263 73 3 1 4261 369464927 369469188 0 7448
3 TraesCS5A01G110800 chr2B 98.498 4262 61 2 1 4261 69244642 69240383 0 7513
4 TraesCS5A01G110800 chr2B 98.381 4263 66 3 1 4261 720558812 720554551 0 7487
5 TraesCS5A01G110800 chr5B 98.382 4264 66 3 1 4261 493189634 493185371 0 7489
6 TraesCS5A01G110800 chr5B 98.100 4263 79 2 1 4261 657803455 657799193 0 7422
7 TraesCS5A01G110800 chr4B 98.147 4264 75 4 1 4261 242088313 242084051 0 7433
8 TraesCS5A01G110800 chr3B 98.123 4262 79 1 1 4261 617526575 617530836 0 7426


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 TraesCS5A01G110800 chr5A 210978699 210982959 4260 False 7869 7869 100.000 1 4261 1 chr5A.!!$F1 4260
1 TraesCS5A01G110800 chr5A 194023015 194027276 4261 True 7515 7515 98.498 1 4261 1 chr5A.!!$R1 4260
2 TraesCS5A01G110800 chr5A 369464927 369469188 4261 False 7448 7448 98.217 1 4261 1 chr5A.!!$F2 4260
3 TraesCS5A01G110800 chr2B 69240383 69244642 4259 True 7513 7513 98.498 1 4261 1 chr2B.!!$R1 4260
4 TraesCS5A01G110800 chr2B 720554551 720558812 4261 True 7487 7487 98.381 1 4261 1 chr2B.!!$R2 4260
5 TraesCS5A01G110800 chr5B 493185371 493189634 4263 True 7489 7489 98.382 1 4261 1 chr5B.!!$R1 4260
6 TraesCS5A01G110800 chr5B 657799193 657803455 4262 True 7422 7422 98.100 1 4261 1 chr5B.!!$R2 4260
7 TraesCS5A01G110800 chr4B 242084051 242088313 4262 True 7433 7433 98.147 1 4261 1 chr4B.!!$R1 4260
8 TraesCS5A01G110800 chr3B 617526575 617530836 4261 False 7426 7426 98.123 1 4261 1 chr3B.!!$F1 4260

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
698 701 0.971386 TCCGTTCCGCCTTACTCTTT 59.029 50.000 0.00 0.0 0.0 2.52 F
1039 1042 2.229784 GAGTGCAATTGGGTTCCTTCTG 59.770 50.000 7.72 0.0 0.0 3.02 F
1973 1976 1.625315 CTGATCCAGGGCGATAATCCA 59.375 52.381 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1750 0.034896 GTGTGTCGGAGTGGGTCATT 59.965 55.000 0.0 0.0 0.0 2.57 R
2712 2717 0.325296 TGGGCTACATCCTCTTCGGT 60.325 55.000 0.0 0.0 0.0 4.69 R
3807 3815 3.792401 CGGTCATGGAGTGTATTTGCTA 58.208 45.455 0.0 0.0 0.0 3.49 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
414 417 1.294780 CTCTGCTTCGTCTTGGGCT 59.705 57.895 0.00 0.00 0.00 5.19
481 484 2.885616 TCTTCTCCGTTCCCAGTAAGT 58.114 47.619 0.00 0.00 0.00 2.24
698 701 0.971386 TCCGTTCCGCCTTACTCTTT 59.029 50.000 0.00 0.00 0.00 2.52
726 729 9.860898 GAATATTTCCTATTTTTGTGAGCTTGT 57.139 29.630 0.00 0.00 29.93 3.16
1039 1042 2.229784 GAGTGCAATTGGGTTCCTTCTG 59.770 50.000 7.72 0.00 0.00 3.02
1367 1370 5.001874 AGACCTCTTTCATTTAAACCGTCC 58.998 41.667 0.00 0.00 0.00 4.79
1533 1536 2.566724 TGACAATGAAAATCCCTTGCCC 59.433 45.455 0.00 0.00 0.00 5.36
1747 1750 6.524101 TGTGCAAGTATACTGATAGTGTCA 57.476 37.500 6.06 1.14 35.05 3.58
1782 1785 4.394729 GACACACTAAAATCCAACTCCCA 58.605 43.478 0.00 0.00 0.00 4.37
1973 1976 1.625315 CTGATCCAGGGCGATAATCCA 59.375 52.381 0.00 0.00 0.00 3.41
2657 2662 3.715628 TGCTTTTCCTTGACTCTTTGC 57.284 42.857 0.00 0.00 0.00 3.68
2791 2796 4.223700 TCCTGAGGATATTCCCAATGATCG 59.776 45.833 0.00 0.00 37.19 3.69
2817 2822 4.746535 TTACAAGACGATGCTATTCCCA 57.253 40.909 0.00 0.00 0.00 4.37
3176 3182 8.613922 AAATGATGAGGGATAAATTTGAGGTT 57.386 30.769 0.00 0.00 0.00 3.50
3550 3558 5.506649 GGACCGTTTGTTGAAAGCTAAATGA 60.507 40.000 0.00 0.00 0.00 2.57
3807 3815 2.818130 TGAACTTACGGCCGTAAAGT 57.182 45.000 40.88 35.10 39.69 2.66
3972 3981 1.346395 TGCGGAAGAAACTGAAGGCTA 59.654 47.619 0.00 0.00 0.00 3.93
4091 4100 0.396435 ACAGGTTGTCGATGCTTCCA 59.604 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
388 391 1.909141 GACGAAGCAGAGGTCGACGA 61.909 60.000 9.92 0.00 39.64 4.20
414 417 2.036571 CGCTCAGGTTGATGCAGCA 61.037 57.895 0.00 0.00 0.00 4.41
481 484 6.957020 AGATCTAGGTCAAGAAGAGGAGAAAA 59.043 38.462 5.64 0.00 0.00 2.29
711 714 6.568462 CGGATCTACAACAAGCTCACAAAAAT 60.568 38.462 0.00 0.00 0.00 1.82
724 727 0.973632 ACAGCCACGGATCTACAACA 59.026 50.000 0.00 0.00 0.00 3.33
726 729 5.361571 TCTTATTACAGCCACGGATCTACAA 59.638 40.000 0.00 0.00 0.00 2.41
854 857 4.232091 CCAGGGGACTAATGGTATACACT 58.768 47.826 5.01 0.00 40.21 3.55
1039 1042 0.949105 AACTGTGATTCCGTGACGCC 60.949 55.000 0.00 0.00 0.00 5.68
1195 1198 2.282407 GTAAAATTTAGAGCCGGGCGA 58.718 47.619 14.39 0.00 0.00 5.54
1367 1370 1.635663 GCCGTCGGTGAATTCAGTGG 61.636 60.000 13.94 7.59 0.00 4.00
1747 1750 0.034896 GTGTGTCGGAGTGGGTCATT 59.965 55.000 0.00 0.00 0.00 2.57
1782 1785 4.219507 ACAGATTCTGTGACTTCGTCATCT 59.780 41.667 18.35 0.00 44.63 2.90
1973 1976 4.895297 TGAGGAAGTTTCTTGCTCCAAAAT 59.105 37.500 21.61 0.00 36.25 1.82
2541 2546 1.669760 GTGGCCGACGATTCACCAA 60.670 57.895 0.00 0.00 31.10 3.67
2657 2662 2.700371 AGGTTTGGCCCTGAAAGAAAAG 59.300 45.455 0.00 0.00 38.26 2.27
2701 2706 1.478137 CTCTTCGGTCGCTTTATCCG 58.522 55.000 0.00 0.00 44.76 4.18
2712 2717 0.325296 TGGGCTACATCCTCTTCGGT 60.325 55.000 0.00 0.00 0.00 4.69
2791 2796 5.234543 GGAATAGCATCGTCTTGTAAAGGAC 59.765 44.000 0.00 0.00 46.24 3.85
2817 2822 8.325477 ACTGAAGTATTAATAGGCCTCTCTTT 57.675 34.615 9.68 1.51 0.00 2.52
3176 3182 4.530946 AGGCAGGCAGTAAAGAAGTAAGTA 59.469 41.667 0.00 0.00 0.00 2.24
3807 3815 3.792401 CGGTCATGGAGTGTATTTGCTA 58.208 45.455 0.00 0.00 0.00 3.49
3972 3981 5.578157 AATTGTTCCACTAAGGTGTAGGT 57.422 39.130 0.00 0.00 41.53 3.08
4091 4100 4.488911 AGCTCCTCCATCCGGGCT 62.489 66.667 0.00 0.00 36.21 5.19


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

AutoCloner maintained by Alex Coulton.