Multiple sequence alignment - TraesCS4D01G090900

Loading Multiple Alignment...

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 TraesCS4D01G090900 chr4D 100.000 4433 0 0 1 4433 65940493 65936061 0 8187
1 TraesCS4D01G090900 chr4B 97.609 3555 65 6 880 4433 96641764 96638229 0 6076
2 TraesCS4D01G090900 chr4B 95.148 845 21 7 1 825 96642740 96641896 0 1315
3 TraesCS4D01G090900 chr4A 97.417 2710 49 8 1 2693 529625689 529628394 0 4597
4 TraesCS4D01G090900 chr4A 95.849 1855 55 7 2579 4433 529628392 529630224 0 2979


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 TraesCS4D01G090900 chr4D 65936061 65940493 4432 True 8187.0 8187 100.0000 1 4433 1 chr4D.!!$R1 4432
1 TraesCS4D01G090900 chr4B 96638229 96642740 4511 True 3695.5 6076 96.3785 1 4433 2 chr4B.!!$R1 4432
2 TraesCS4D01G090900 chr4A 529625689 529630224 4535 False 3788.0 4597 96.6330 1 4433 2 chr4A.!!$F1 4432

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
317 320 0.179150 CGAAGAGGAGGTGAAGAGCG 60.179 60.000 0.0 0.0 0.00 5.03 F
391 394 0.394352 CCAAACCTAAGATGCCGCCT 60.394 55.000 0.0 0.0 0.00 5.52 F
1483 1588 0.974383 CCGTCACCTACAACTCCCTT 59.026 55.000 0.0 0.0 0.00 3.95 F
2740 2957 7.202526 TGAATTTCAAACATCCAGTTCTTGTC 58.797 34.615 0.0 0.0 40.26 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1134 1239 2.125753 GCTCGCTGTCCAGACCAG 60.126 66.667 0.0 0.0 0.00 4.00 R
2740 2957 2.691409 TCCTTCCTCCAGTTTATGCG 57.309 50.000 0.0 0.0 0.00 4.73 R
2985 3202 1.026182 TCACATCCAAGGTGATGCGC 61.026 55.000 0.0 0.0 44.84 6.09 R
3912 4131 1.302752 TGCTCTGTGTGGGATGTGC 60.303 57.895 0.0 0.0 0.00 4.57 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
280 283 2.693762 GGACGACATCACGGACGGA 61.694 63.158 0.00 0.00 37.61 4.69
317 320 0.179150 CGAAGAGGAGGTGAAGAGCG 60.179 60.000 0.00 0.00 0.00 5.03
391 394 0.394352 CCAAACCTAAGATGCCGCCT 60.394 55.000 0.00 0.00 0.00 5.52
433 436 2.456577 GAAGAGGAGAGGAAGCAGAGT 58.543 52.381 0.00 0.00 0.00 3.24
652 668 2.238521 TGATTTCTTTTTCAGCCGGCT 58.761 42.857 27.08 27.08 0.00 5.52
694 710 2.224523 TGTATGATCCTGCCGATTTCCC 60.225 50.000 0.00 0.00 0.00 3.97
821 844 4.959631 TGTTGTGAATCTTTCGTACGAC 57.040 40.909 19.36 5.88 0.00 4.34
1134 1239 4.135493 GTCGCGAACTCGGCAAGC 62.135 66.667 12.06 0.00 40.23 4.01
1483 1588 0.974383 CCGTCACCTACAACTCCCTT 59.026 55.000 0.00 0.00 0.00 3.95
2740 2957 7.202526 TGAATTTCAAACATCCAGTTCTTGTC 58.797 34.615 0.00 0.00 40.26 3.18
2985 3202 0.036010 AGTGATCTTTGCCTGGTCCG 60.036 55.000 0.00 0.00 0.00 4.79
3121 3338 7.673810 AGTTTTTGTTTAACGCAGTGAATAC 57.326 32.000 0.00 0.00 45.00 1.89
3234 3452 2.617276 CCTGTTGCTCCAGACATGATGT 60.617 50.000 0.00 0.00 34.23 3.06
3314 3532 7.172019 AGTCCATTTGTTCATCATTTTTGCTTC 59.828 33.333 0.00 0.00 0.00 3.86
3397 3615 7.225027 AACAGCATTAAGCCGTTTGAAGAAAG 61.225 38.462 0.00 0.00 40.89 2.62
3563 3782 5.933187 TTGTTGCACAGTATATCGTTTGT 57.067 34.783 0.00 0.00 0.00 2.83
3666 3885 7.329226 GCACATAGCAATGTAACATTCTTGTTT 59.671 33.333 0.00 0.00 44.70 2.83
3764 3983 3.003394 TCACCTGCCTCATATGGTTTG 57.997 47.619 2.13 0.00 0.00 2.93
3787 4006 2.872245 GTTGCTACTCTGTTTGTCAGCA 59.128 45.455 0.00 0.00 43.32 4.41
3854 4073 4.824289 TGGAACCCGAGACACTTTATTAC 58.176 43.478 0.00 0.00 0.00 1.89
3856 4075 5.107824 GGAACCCGAGACACTTTATTACTC 58.892 45.833 0.00 0.00 0.00 2.59
3857 4076 4.732672 ACCCGAGACACTTTATTACTCC 57.267 45.455 0.00 0.00 0.00 3.85
4238 4457 6.486253 AACACTATAAGTTCACAGTGCATG 57.514 37.500 9.98 0.00 41.67 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
280 283 1.065491 TCGGGCATGTATTCAACAGCT 60.065 47.619 0.00 0.00 42.70 4.24
391 394 0.586319 CTTCTTGCTCGGTTTTCGCA 59.414 50.000 0.00 0.00 39.05 5.10
433 436 0.107831 CAAACCCGTCCAACTCCTCA 59.892 55.000 0.00 0.00 0.00 3.86
821 844 5.048083 TCGATGGGATTTCCTTCAAAAACTG 60.048 40.000 0.00 0.00 39.06 3.16
1002 1107 1.685820 GGGAGGGAGTTGGGAGTTG 59.314 63.158 0.00 0.00 0.00 3.16
1080 1185 0.906066 TGTTATGGGGTAAGCGCTCA 59.094 50.000 12.06 3.76 0.00 4.26
1134 1239 2.125753 GCTCGCTGTCCAGACCAG 60.126 66.667 0.00 0.00 0.00 4.00
2740 2957 2.691409 TCCTTCCTCCAGTTTATGCG 57.309 50.000 0.00 0.00 0.00 4.73
2985 3202 1.026182 TCACATCCAAGGTGATGCGC 61.026 55.000 0.00 0.00 44.84 6.09
3121 3338 2.579207 ACTCCATGACAACGATACGG 57.421 50.000 0.00 0.00 0.00 4.02
3254 3472 8.531146 ACTAAGTACCAATATTTGCATTTTGCT 58.469 29.630 0.75 0.00 45.31 3.91
3314 3532 4.378616 CCGCTTCACAAGAATTAAACAACG 59.621 41.667 0.00 0.00 32.31 4.10
3365 3583 3.940303 CGGCTTAATGCTGTTACATGAC 58.060 45.455 0.00 0.00 42.87 3.06
3397 3615 8.931385 AATGTTTCTTTCATTGGCATACATAC 57.069 30.769 0.00 0.00 34.74 2.39
3563 3782 6.211184 ACCATATGCAGTCAATGGAAAAGAAA 59.789 34.615 20.75 0.00 42.36 2.52
3666 3885 7.574592 GCCATTAGCATGCAAATAAACCAAAAA 60.575 33.333 21.98 0.00 42.97 1.94
3787 4006 5.562298 ACCACATACACTACTGGAAACTT 57.438 39.130 0.00 0.00 0.00 2.66
3912 4131 1.302752 TGCTCTGTGTGGGATGTGC 60.303 57.895 0.00 0.00 0.00 4.57
4276 4495 4.156739 GCTACATGGCAAGTTCTTTAGCTT 59.843 41.667 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.