Multiple sequence alignment - TraesCS5B01G376600

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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 TraesCS5B01G376600 chr5B 100.000 3482 0 0 1 3482 554525202 554521721 0.000000e+00 6431
1 TraesCS5B01G376600 chr5B 78.894 597 107 11 1 588 55091429 55090843 1.520000e-103 387
2 TraesCS5B01G376600 chr5D 94.535 2141 84 13 478 2594 453827141 453825010 0.000000e+00 3275
3 TraesCS5B01G376600 chr5D 92.604 338 25 0 1 338 453827555 453827218 1.450000e-133 486
4 TraesCS5B01G376600 chr5D 77.032 566 98 13 10 557 501084976 501084425 2.630000e-76 296
5 TraesCS5B01G376600 chr5A 94.748 1847 60 8 699 2530 572865754 572863930 0.000000e+00 2839
6 TraesCS5B01G376600 chr5A 76.708 571 104 16 3 552 393601280 393601842 1.220000e-74 291
7 TraesCS5B01G376600 chr6B 79.679 561 99 11 19 566 508828917 508829475 1.170000e-104 390
8 TraesCS5B01G376600 chr3D 78.283 594 109 10 6 580 571920774 571920182 7.100000e-97 364
9 TraesCS5B01G376600 chr3D 82.192 219 29 4 3268 3482 546651051 546651263 2.760000e-41 180
10 TraesCS5B01G376600 chr7B 77.897 561 88 18 8 552 424040910 424041450 2.020000e-82 316
11 TraesCS5B01G376600 chr7B 79.781 366 74 0 19 384 4239063 4238698 2.060000e-67 267
12 TraesCS5B01G376600 chr2D 78.632 468 83 13 87 552 156497942 156498394 9.450000e-76 294
13 TraesCS5B01G376600 chr6D 76.882 558 95 24 7 552 315978410 315977875 5.690000e-73 285
14 TraesCS5B01G376600 chr6D 79.688 256 32 15 2902 3137 445156485 445156740 2.150000e-37 167
15 TraesCS5B01G376600 chr3B 80.811 370 66 2 108 472 759122531 759122162 5.690000e-73 285
16 TraesCS5B01G376600 chr3B 76.471 221 34 13 2925 3127 112453190 112452970 1.710000e-18 104
17 TraesCS5B01G376600 chr2A 80.184 217 32 5 3268 3480 765858511 765858720 6.020000e-33 152
18 TraesCS5B01G376600 chr4A 77.692 260 46 5 341 588 590605196 590604937 7.790000e-32 148


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 TraesCS5B01G376600 chr5B 554521721 554525202 3481 True 6431.0 6431 100.0000 1 3482 1 chr5B.!!$R2 3481
1 TraesCS5B01G376600 chr5B 55090843 55091429 586 True 387.0 387 78.8940 1 588 1 chr5B.!!$R1 587
2 TraesCS5B01G376600 chr5D 453825010 453827555 2545 True 1880.5 3275 93.5695 1 2594 2 chr5D.!!$R2 2593
3 TraesCS5B01G376600 chr5D 501084425 501084976 551 True 296.0 296 77.0320 10 557 1 chr5D.!!$R1 547
4 TraesCS5B01G376600 chr5A 572863930 572865754 1824 True 2839.0 2839 94.7480 699 2530 1 chr5A.!!$R1 1831
5 TraesCS5B01G376600 chr5A 393601280 393601842 562 False 291.0 291 76.7080 3 552 1 chr5A.!!$F1 549
6 TraesCS5B01G376600 chr6B 508828917 508829475 558 False 390.0 390 79.6790 19 566 1 chr6B.!!$F1 547
7 TraesCS5B01G376600 chr3D 571920182 571920774 592 True 364.0 364 78.2830 6 580 1 chr3D.!!$R1 574
8 TraesCS5B01G376600 chr7B 424040910 424041450 540 False 316.0 316 77.8970 8 552 1 chr7B.!!$F1 544
9 TraesCS5B01G376600 chr6D 315977875 315978410 535 True 285.0 285 76.8820 7 552 1 chr6D.!!$R1 545


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
437 449 0.385473 GAAACGGTCAACCACGCATG 60.385 55.0 0.0 0.0 35.14 4.06 F
447 459 0.602638 ACCACGCATGACACAACGAT 60.603 50.0 0.0 0.0 0.00 3.73 F
1665 1731 1.006832 CGCCCTTAACTTCGTCATGG 58.993 55.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1731 0.316442 CGAATCACGGCATGCACATC 60.316 55.0 21.36 7.47 38.46 3.06 R
1893 1959 0.322008 GGAACACCAGCTCCTTCAGG 60.322 60.0 0.00 0.00 0.00 3.86 R
2813 2879 0.031111 CATGTCACCCCCTCCTAGGA 60.031 60.0 11.98 11.98 37.67 2.94 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)



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AutoCloner maintained by Alex Coulton.