Multiple sequence alignment - TraesCS6A01G114400

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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 TraesCS6A01G114400 chr6A 100.000 2471 0 0 1 2471 84404721 84402251 0 4564
1 TraesCS6A01G114400 chr3A 98.896 2446 25 1 26 2471 495099908 495097465 0 4366
2 TraesCS6A01G114400 chr2B 98.692 2446 30 1 26 2471 449214482 449212039 0 4338
3 TraesCS6A01G114400 chr2B 98.693 2448 22 3 26 2471 234536306 234533867 0 4335
4 TraesCS6A01G114400 chr1B 98.651 2446 31 1 26 2471 619190480 619188037 0 4333
5 TraesCS6A01G114400 chr3B 98.283 2446 39 1 26 2471 6005915 6003473 0 4281
6 TraesCS6A01G114400 chr1A 98.160 2446 43 1 26 2471 278526044 278528487 0 4266
7 TraesCS6A01G114400 chr6D 98.038 2446 45 2 26 2471 458923510 458921068 0 4248
8 TraesCS6A01G114400 chr7A 97.673 2449 51 3 26 2471 563517246 563514801 0 4202
9 TraesCS6A01G114400 chr3D 97.507 2447 56 4 26 2471 501833529 501831087 0 4176


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 TraesCS6A01G114400 chr6A 84402251 84404721 2470 True 4564 4564 100.000 1 2471 1 chr6A.!!$R1 2470
1 TraesCS6A01G114400 chr3A 495097465 495099908 2443 True 4366 4366 98.896 26 2471 1 chr3A.!!$R1 2445
2 TraesCS6A01G114400 chr2B 449212039 449214482 2443 True 4338 4338 98.692 26 2471 1 chr2B.!!$R2 2445
3 TraesCS6A01G114400 chr2B 234533867 234536306 2439 True 4335 4335 98.693 26 2471 1 chr2B.!!$R1 2445
4 TraesCS6A01G114400 chr1B 619188037 619190480 2443 True 4333 4333 98.651 26 2471 1 chr1B.!!$R1 2445
5 TraesCS6A01G114400 chr3B 6003473 6005915 2442 True 4281 4281 98.283 26 2471 1 chr3B.!!$R1 2445
6 TraesCS6A01G114400 chr1A 278526044 278528487 2443 False 4266 4266 98.160 26 2471 1 chr1A.!!$F1 2445
7 TraesCS6A01G114400 chr6D 458921068 458923510 2442 True 4248 4248 98.038 26 2471 1 chr6D.!!$R1 2445
8 TraesCS6A01G114400 chr7A 563514801 563517246 2445 True 4202 4202 97.673 26 2471 1 chr7A.!!$R1 2445
9 TraesCS6A01G114400 chr3D 501831087 501833529 2442 True 4176 4176 97.507 26 2471 1 chr3D.!!$R1 2445

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
21 22 1.136891 TGCCGTGATACACTCAGGATG 59.863 52.381 0.0 0.0 41.32 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1527 8.897752 CCGATTCTCCTTCTATTGATTCTTTTT 58.102 33.333 0.0 0.0 0.0 1.94 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
19 20 1.485124 ATGCCGTGATACACTCAGGA 58.515 50.000 0.00 0.00 41.32 3.86
20 21 1.485124 TGCCGTGATACACTCAGGAT 58.515 50.000 0.00 0.00 41.32 3.24
21 22 1.136891 TGCCGTGATACACTCAGGATG 59.863 52.381 0.00 0.00 41.32 3.51
22 23 1.137086 GCCGTGATACACTCAGGATGT 59.863 52.381 0.00 0.00 41.32 3.06
23 24 2.361119 GCCGTGATACACTCAGGATGTA 59.639 50.000 0.00 0.00 41.32 2.29
24 25 3.005897 GCCGTGATACACTCAGGATGTAT 59.994 47.826 0.00 0.00 44.19 2.29
113 114 7.054751 ACCATGAAATTAAGTAGCTAAGGTCC 58.945 38.462 0.00 0.00 0.00 4.46
301 302 5.149239 AGTATTAGTAAGAGGAGGAAGGGC 58.851 45.833 0.00 0.00 0.00 5.19
409 410 5.918608 AGTGCGTTGTAGATTCTTATCCAT 58.081 37.500 0.00 0.00 0.00 3.41
453 454 3.366679 CCATGTGAATCAAGCAACAGGAC 60.367 47.826 0.00 0.00 0.00 3.85
1300 1304 5.707764 GGATCTAAACAAGGAAGAGCACTTT 59.292 40.000 0.00 0.00 36.39 2.66
1523 1527 2.074576 GGATCCGTACATCTCGATCGA 58.925 52.381 18.32 18.32 0.00 3.59
1926 1931 6.603599 TCTTCTTCTGATCGATTCAACCTCTA 59.396 38.462 0.00 0.00 32.78 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.485124 TCCTGAGTGTATCACGGCAT 58.515 50.000 0.00 0.00 39.64 4.40
1 2 1.136891 CATCCTGAGTGTATCACGGCA 59.863 52.381 0.00 0.00 39.64 5.69
2 3 1.137086 ACATCCTGAGTGTATCACGGC 59.863 52.381 0.00 0.00 39.64 5.68
3 4 4.855715 ATACATCCTGAGTGTATCACGG 57.144 45.455 0.00 0.00 38.10 4.94
8 9 6.368805 TGAGAGTGATACATCCTGAGTGTAT 58.631 40.000 0.00 0.00 43.47 2.29
9 10 5.755849 TGAGAGTGATACATCCTGAGTGTA 58.244 41.667 0.00 0.00 36.58 2.90
10 11 4.604156 TGAGAGTGATACATCCTGAGTGT 58.396 43.478 0.00 0.00 0.00 3.55
11 12 5.787953 ATGAGAGTGATACATCCTGAGTG 57.212 43.478 0.00 0.00 0.00 3.51
12 13 6.382282 TGAAATGAGAGTGATACATCCTGAGT 59.618 38.462 0.00 0.00 0.00 3.41
13 14 6.814043 TGAAATGAGAGTGATACATCCTGAG 58.186 40.000 0.00 0.00 0.00 3.35
14 15 6.796785 TGAAATGAGAGTGATACATCCTGA 57.203 37.500 0.00 0.00 0.00 3.86
15 16 7.520131 GCATTGAAATGAGAGTGATACATCCTG 60.520 40.741 7.21 0.00 38.70 3.86
16 17 6.485984 GCATTGAAATGAGAGTGATACATCCT 59.514 38.462 7.21 0.00 38.70 3.24
17 18 6.565435 CGCATTGAAATGAGAGTGATACATCC 60.565 42.308 7.21 0.00 38.30 3.51
18 19 6.361114 CGCATTGAAATGAGAGTGATACATC 58.639 40.000 7.21 0.00 38.30 3.06
19 20 5.237996 CCGCATTGAAATGAGAGTGATACAT 59.762 40.000 7.21 0.00 38.30 2.29
20 21 4.571984 CCGCATTGAAATGAGAGTGATACA 59.428 41.667 7.21 0.00 38.30 2.29
21 22 4.553547 GCCGCATTGAAATGAGAGTGATAC 60.554 45.833 7.21 0.00 38.30 2.24
22 23 3.561310 GCCGCATTGAAATGAGAGTGATA 59.439 43.478 7.21 0.00 38.30 2.15
23 24 2.357009 GCCGCATTGAAATGAGAGTGAT 59.643 45.455 7.21 0.00 38.30 3.06
24 25 1.739466 GCCGCATTGAAATGAGAGTGA 59.261 47.619 7.21 0.00 38.30 3.41
113 114 8.840321 CATATCCTTGTTTAAATAGGTCCACTG 58.160 37.037 15.16 7.13 0.00 3.66
301 302 6.387465 TCACACCGAGTTCAAAGATACTTAG 58.613 40.000 0.00 0.00 0.00 2.18
453 454 5.447624 AAACTTTCGTTATTGGGTCCTTG 57.552 39.130 0.00 0.00 31.86 3.61
745 746 0.750850 CCTTTTCCCGCTAGGATCGA 59.249 55.000 0.00 0.00 46.94 3.59
1523 1527 8.897752 CCGATTCTCCTTCTATTGATTCTTTTT 58.102 33.333 0.00 0.00 0.00 1.94
1926 1931 9.981460 ATAGAACCAAGGTCTATCTTTTTGATT 57.019 29.630 0.00 0.00 36.65 2.57
2166 2171 6.034442 TCCCCCTAGAGTAGCTGTTAATAA 57.966 41.667 0.00 0.00 0.00 1.40
2286 2291 4.762765 AGTAGCCTCATTAGACCGTAGATG 59.237 45.833 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.