Multiple sequence alignment - TraesCS1B01G385600

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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 TraesCS1B01G385600 chr1B 100.000 4240 0 0 1 4240 619189737 619185498 0.000000e+00 7830
1 TraesCS1B01G385600 chr2B 98.587 4246 53 4 1 4240 449213739 449209495 0.000000e+00 7502
2 TraesCS1B01G385600 chr2B 98.562 4243 52 3 1 4240 234535563 234531327 0.000000e+00 7489
3 TraesCS1B01G385600 chr3B 98.491 4242 60 4 1 4240 6005172 6000933 0.000000e+00 7476
4 TraesCS1B01G385600 chr3B 98.397 4241 67 1 1 4240 92291150 92286910 0.000000e+00 7454
5 TraesCS1B01G385600 chr6D 97.718 4250 83 6 1 4240 458922767 458918522 0.000000e+00 7299
6 TraesCS1B01G385600 chr7A 97.484 4252 92 6 1 4240 563516503 563512255 0.000000e+00 7245
7 TraesCS1B01G385600 chr7D 97.270 4249 91 11 1 4240 307045651 307049883 0.000000e+00 7180
8 TraesCS1B01G385600 chr4B 98.194 4041 65 3 208 4240 495582454 495578414 0.000000e+00 7051
9 TraesCS1B01G385600 chr6A 98.710 3722 45 2 1 3719 84403953 84400232 0.000000e+00 6604
10 TraesCS1B01G385600 chr3A 92.500 240 6 1 3571 3810 107583601 107583828 2.440000e-87 333
11 TraesCS1B01G385600 chr3A 97.619 168 4 0 3809 3976 108767961 108767794 5.360000e-74 289
12 TraesCS1B01G385600 chr2A 98.095 105 1 1 4104 4207 24355093 24354989 9.370000e-42 182


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 TraesCS1B01G385600 chr1B 619185498 619189737 4239 True 7830 7830 100.000 1 4240 1 chr1B.!!$R1 4239
1 TraesCS1B01G385600 chr2B 449209495 449213739 4244 True 7502 7502 98.587 1 4240 1 chr2B.!!$R2 4239
2 TraesCS1B01G385600 chr2B 234531327 234535563 4236 True 7489 7489 98.562 1 4240 1 chr2B.!!$R1 4239
3 TraesCS1B01G385600 chr3B 6000933 6005172 4239 True 7476 7476 98.491 1 4240 1 chr3B.!!$R1 4239
4 TraesCS1B01G385600 chr3B 92286910 92291150 4240 True 7454 7454 98.397 1 4240 1 chr3B.!!$R2 4239
5 TraesCS1B01G385600 chr6D 458918522 458922767 4245 True 7299 7299 97.718 1 4240 1 chr6D.!!$R1 4239
6 TraesCS1B01G385600 chr7A 563512255 563516503 4248 True 7245 7245 97.484 1 4240 1 chr7A.!!$R1 4239
7 TraesCS1B01G385600 chr7D 307045651 307049883 4232 False 7180 7180 97.270 1 4240 1 chr7D.!!$F1 4239
8 TraesCS1B01G385600 chr4B 495578414 495582454 4040 True 7051 7051 98.194 208 4240 1 chr4B.!!$R1 4032
9 TraesCS1B01G385600 chr6A 84400232 84403953 3721 True 6604 6604 98.710 1 3719 1 chr6A.!!$R1 3718

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
568 573 0.539438 AAGCATCCCAAAAGCGTCCA 60.539 50.000 0.0 0.0 0.00 4.02 F
1755 1771 1.134610 CCAGCCCCTTTTCATCAATGC 60.135 52.381 0.0 0.0 0.00 3.56 F
1760 1776 3.094572 CCCCTTTTCATCAATGCACTCT 58.905 45.455 0.0 0.0 0.00 3.24 F
1874 1890 3.200605 TGCAGAAGAGAAATGCTATCCCA 59.799 43.478 0.0 0.0 40.62 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1786 1.537348 CGAACGAACCACACTCCTTCA 60.537 52.381 0.00 0.0 0.00 3.02 R
2584 2605 1.332997 CCAGAAGAAGATGCCATTCGC 59.667 52.381 0.00 0.0 38.31 4.70 R
3224 3245 4.345257 CCTAGCAGCTAAAAGAGGGTATCA 59.655 45.833 3.09 0.0 0.00 2.15 R
3542 3565 7.339466 GCATATGGTACCCAAATAAGAATAGGG 59.661 40.741 10.07 0.0 45.20 3.53 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
380 385 5.175859 TCTATCGAGCCGTGAAAAAGATTT 58.824 37.500 0.00 0.00 0.00 2.17
568 573 0.539438 AAGCATCCCAAAAGCGTCCA 60.539 50.000 0.00 0.00 0.00 4.02
586 591 3.065371 GTCCAGGTCGAAATATGGCTTTG 59.935 47.826 0.00 0.00 32.63 2.77
712 717 7.083858 CACATTTTCGTTAATCCATGAACAGT 58.916 34.615 0.00 0.00 0.00 3.55
794 799 5.379732 AGAATCGGACGATATCTTTCTCC 57.620 43.478 7.72 0.00 33.97 3.71
1755 1771 1.134610 CCAGCCCCTTTTCATCAATGC 60.135 52.381 0.00 0.00 0.00 3.56
1760 1776 3.094572 CCCCTTTTCATCAATGCACTCT 58.905 45.455 0.00 0.00 0.00 3.24
1770 1786 4.456280 TCAATGCACTCTTGACGTCTAT 57.544 40.909 17.92 0.00 0.00 1.98
1874 1890 3.200605 TGCAGAAGAGAAATGCTATCCCA 59.799 43.478 0.00 0.00 40.62 4.37
1898 1915 7.335924 CCAATCCGACCAAGATAGAACTTTTAA 59.664 37.037 0.00 0.00 0.00 1.52
1954 1971 3.806949 ATTAAGGTGAAGCAGGGTCAA 57.193 42.857 0.00 0.00 0.00 3.18
2295 2316 8.495260 AGGATTCCTCGAAAAGTTAAGGATTAT 58.505 33.333 0.00 0.00 37.74 1.28
2754 2775 5.411977 GGAGACTCAAATGATGGATATGCAG 59.588 44.000 2.55 0.00 0.00 4.41
2882 2903 5.163353 TGCAGGATTATACACGAAAGATCCA 60.163 40.000 0.00 0.00 36.39 3.41
3083 3104 8.251750 TCAAGTTATTAATGACTGGACGAAAG 57.748 34.615 13.14 0.00 0.00 2.62
3224 3245 2.169769 CCCCATTCTTGCAATTGCTCAT 59.830 45.455 29.37 13.76 42.66 2.90
3542 3565 6.341316 TCAGACCTGCTTTTGACATATCTAC 58.659 40.000 0.00 0.00 0.00 2.59
3691 3714 5.724328 TCGAAGCTATTTGATGTCTGACTT 58.276 37.500 9.51 2.27 0.00 3.01
3828 3851 5.185635 TCCCTCGGACTCGAAAAGTAATAAA 59.814 40.000 0.00 0.00 45.47 1.40
3889 3912 6.272318 CACTGTTGGAACTAATGAAGCAAAA 58.728 36.000 0.00 0.00 0.00 2.44
3890 3913 6.925165 CACTGTTGGAACTAATGAAGCAAAAT 59.075 34.615 0.00 0.00 0.00 1.82
3905 3928 7.715657 TGAAGCAAAATATTGACCCATCATAC 58.284 34.615 0.00 0.00 38.94 2.39
4032 4055 6.661304 TCCCCGAATACCTAAAATAGAGAC 57.339 41.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 176 9.841880 CTTTTTCTAAGGGCTAAAATCACTTAC 57.158 33.333 0.00 0.00 0.00 2.34
380 385 8.062065 AGTGGATTTGTTTCTGTCTTTTGTTA 57.938 30.769 0.00 0.00 0.00 2.41
486 491 7.569240 AGATCCTATTTCAATCGGAACTTTCT 58.431 34.615 0.00 0.00 31.99 2.52
568 573 6.530019 AATTTCAAAGCCATATTTCGACCT 57.470 33.333 0.00 0.00 0.00 3.85
586 591 9.865484 GCATCTACTAATTCGGAACTTAATTTC 57.135 33.333 0.00 0.00 0.00 2.17
712 717 9.190317 GGATCCATGTGTCTACATACATAGATA 57.810 37.037 6.95 0.00 45.53 1.98
794 799 9.597999 CTCTTTCTTTTCCTTTTTGTTTGTTTG 57.402 29.630 0.00 0.00 0.00 2.93
1522 1531 7.618019 ATTTCATAGTAGCCTCATTAGACCA 57.382 36.000 0.00 0.00 0.00 4.02
1755 1771 4.156922 ACTCCTTCATAGACGTCAAGAGTG 59.843 45.833 19.50 8.62 0.00 3.51
1760 1776 3.056821 CCACACTCCTTCATAGACGTCAA 60.057 47.826 19.50 1.80 0.00 3.18
1770 1786 1.537348 CGAACGAACCACACTCCTTCA 60.537 52.381 0.00 0.00 0.00 3.02
1874 1890 7.881232 TGTTAAAAGTTCTATCTTGGTCGGATT 59.119 33.333 0.00 0.00 0.00 3.01
2154 2171 3.576078 TTCGTTCCCAATAGCCATGAT 57.424 42.857 0.00 0.00 0.00 2.45
2584 2605 1.332997 CCAGAAGAAGATGCCATTCGC 59.667 52.381 0.00 0.00 38.31 4.70
3083 3104 4.402474 AGCACATAAGGGGTTATTTCTTGC 59.598 41.667 0.00 0.00 0.00 4.01
3224 3245 4.345257 CCTAGCAGCTAAAAGAGGGTATCA 59.655 45.833 3.09 0.00 0.00 2.15
3542 3565 7.339466 GCATATGGTACCCAAATAAGAATAGGG 59.661 40.741 10.07 0.00 45.20 3.53
3691 3714 8.519799 TCTCTTCTTTCTTTTCTTTTTGCCTA 57.480 30.769 0.00 0.00 0.00 3.93
3889 3912 6.467490 TTGGATGGTATGATGGGTCAATAT 57.533 37.500 0.00 0.00 38.01 1.28
3890 3913 5.921153 TTGGATGGTATGATGGGTCAATA 57.079 39.130 0.00 0.00 38.01 1.90
3905 3928 5.047660 TGGTATTTTCCGTTTCTTTGGATGG 60.048 40.000 0.00 0.00 33.42 3.51
4071 4094 4.916041 TCTCTGACATTCCATGTTTCCT 57.084 40.909 0.00 0.00 45.03 3.36


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

AutoCloner maintained by Alex Coulton.