Multiple sequence alignment - TraesCS4A01G069600

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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 TraesCS4A01G069600 chr4A 100.000 2381 0 0 1 2381 67552538 67550158 0 4397
1 TraesCS4A01G069600 chr4A 97.690 2381 50 3 1 2381 432422037 432424412 0 4087
2 TraesCS4A01G069600 chr7D 98.531 2382 33 2 1 2381 382011794 382009414 0 4204
3 TraesCS4A01G069600 chr3D 98.321 2383 37 2 1 2381 202614316 202616697 0 4176
4 TraesCS4A01G069600 chr5A 98.279 2382 40 1 1 2381 16620901 16618520 0 4170
5 TraesCS4A01G069600 chr7B 98.111 2382 42 3 1 2381 743111071 743108692 0 4146
6 TraesCS4A01G069600 chr7B 97.860 2383 45 6 1 2381 743068677 743071055 0 4113
7 TraesCS4A01G069600 chr2D 98.027 2382 43 4 1 2381 635039630 635042008 0 4135
8 TraesCS4A01G069600 chr2A 97.649 2382 52 4 1 2381 735175171 735177549 0 4085
9 TraesCS4A01G069600 chr7A 97.606 2381 55 2 1 2381 120826481 120824103 0 4080


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 TraesCS4A01G069600 chr4A 67550158 67552538 2380 True 4397 4397 100.000 1 2381 1 chr4A.!!$R1 2380
1 TraesCS4A01G069600 chr4A 432422037 432424412 2375 False 4087 4087 97.690 1 2381 1 chr4A.!!$F1 2380
2 TraesCS4A01G069600 chr7D 382009414 382011794 2380 True 4204 4204 98.531 1 2381 1 chr7D.!!$R1 2380
3 TraesCS4A01G069600 chr3D 202614316 202616697 2381 False 4176 4176 98.321 1 2381 1 chr3D.!!$F1 2380
4 TraesCS4A01G069600 chr5A 16618520 16620901 2381 True 4170 4170 98.279 1 2381 1 chr5A.!!$R1 2380
5 TraesCS4A01G069600 chr7B 743108692 743111071 2379 True 4146 4146 98.111 1 2381 1 chr7B.!!$R1 2380
6 TraesCS4A01G069600 chr7B 743068677 743071055 2378 False 4113 4113 97.860 1 2381 1 chr7B.!!$F1 2380
7 TraesCS4A01G069600 chr2D 635039630 635042008 2378 False 4135 4135 98.027 1 2381 1 chr2D.!!$F1 2380
8 TraesCS4A01G069600 chr2A 735175171 735177549 2378 False 4085 4085 97.649 1 2381 1 chr2A.!!$F1 2380
9 TraesCS4A01G069600 chr7A 120824103 120826481 2378 True 4080 4080 97.606 1 2381 1 chr7A.!!$R1 2380

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
698 700 1.028905 CCAAAACATGTGTGTCGGGT 58.971 50.0 0.0 0.0 37.67 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 1549 0.119155 TGAGTGATCCCTTCCCCTGT 59.881 55.0 0.0 0.0 0.0 4.0 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
63 64 1.133809 TGGCTACCCACTGGAGCTTT 61.134 55.000 8.32 0.00 35.79 3.51
87 88 2.290071 CCAACTACCACCGGTCAATTCT 60.290 50.000 2.59 0.00 37.09 2.40
97 98 1.886222 CGGTCAATTCTGCTTTGGGGA 60.886 52.381 0.00 0.00 0.00 4.81
698 700 1.028905 CCAAAACATGTGTGTCGGGT 58.971 50.000 0.00 0.00 37.67 5.28
809 811 4.337274 CCGTCTGTTCCTAAAACAAAACCT 59.663 41.667 0.00 0.00 0.00 3.50
864 866 2.668889 GCAGACAGCAGCAGCACT 60.669 61.111 3.17 0.00 45.49 4.40
968 970 2.878406 AGCTGTTTCGCTTGCTTCTTTA 59.122 40.909 0.00 0.00 36.74 1.85
1028 1030 5.122239 ACGAAAAGCGAGATGATTCAAATCA 59.878 36.000 7.82 7.82 45.41 2.57
1313 1315 2.264480 CCGCCTCGACACATTCCA 59.736 61.111 0.00 0.00 0.00 3.53
1785 1789 4.293671 CAGTTTTGGGGCGGGGGA 62.294 66.667 0.00 0.00 0.00 4.81
2072 2077 0.036858 AGAAGCAAGACGAGGAAGCC 60.037 55.000 0.00 0.00 0.00 4.35
2140 2145 6.374333 ACAACAGTAGCGACCATGAATAAAAT 59.626 34.615 0.00 0.00 0.00 1.82
2158 2164 5.381174 AAAATAGCCCCTTGTTTAACGAC 57.619 39.130 0.00 0.00 0.00 4.34
2332 2338 5.365619 CCAATAGTTTAGTAGTCGGCCAAT 58.634 41.667 2.24 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 4.299009 ACCGGTGGTAGTTGGTCA 57.701 55.556 6.12 0.0 32.11 4.02
97 98 1.078823 TGATGGTAGAGTCAGGGGTGT 59.921 52.381 0.00 0.0 0.00 4.16
581 583 4.899352 ATTCATATGGGCTACTGAGGAC 57.101 45.455 2.13 0.0 0.00 3.85
638 640 7.827236 CCATAACTCAAAATAGGTGACCTAACA 59.173 37.037 16.38 0.0 39.77 2.41
698 700 0.036765 GTAGGTTGATGGGTCGCACA 60.037 55.000 0.00 0.0 0.00 4.57
864 866 1.404391 GATTCGGACTTCGTAGAGCCA 59.596 52.381 0.00 0.0 38.43 4.75
968 970 3.443681 GCCATAATAGCCGCCACAATAAT 59.556 43.478 0.00 0.0 0.00 1.28
1028 1030 5.579753 ACAGATCAGGCCATCTATCAATT 57.420 39.130 5.01 0.0 31.47 2.32
1547 1549 0.119155 TGAGTGATCCCTTCCCCTGT 59.881 55.000 0.00 0.0 0.00 4.00
1654 1656 5.627040 CGAAGTTCCTTACCTTAGCTGGATT 60.627 44.000 0.00 0.0 0.00 3.01
1686 1688 4.385405 GCAGCGGAGTGGAGCAGT 62.385 66.667 0.00 0.0 35.48 4.40
1785 1789 4.671831 TCATTCTTCTGGTCTCTCTCTGT 58.328 43.478 0.00 0.0 0.00 3.41
2072 2077 0.169230 ACTGCTTCTACGACAGCTCG 59.831 55.000 0.00 0.0 46.06 5.03
2140 2145 3.775261 AAGTCGTTAAACAAGGGGCTA 57.225 42.857 0.00 0.0 0.00 3.93
2158 2164 0.320160 GCCTGGGAAAAGCAGCAAAG 60.320 55.000 0.00 0.0 0.00 2.77
2332 2338 1.995066 ATGTCGTGAGCATGGGGGA 60.995 57.895 0.00 0.0 0.00 4.81


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

AutoCloner maintained by Alex Coulton.