Multiple sequence alignment - TraesCS5A01G354400

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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 TraesCS5A01G354400 chr5A 100.000 2808 0 0 1 2808 557069427 557066620 0.000000e+00 5186
1 TraesCS5A01G354400 chr2A 79.294 821 154 14 982 1796 705945436 705946246 6.790000e-156 560
2 TraesCS5A01G354400 chr2A 72.928 543 116 27 725 1251 36883795 36884322 2.900000e-35 159
3 TraesCS5A01G354400 chr6A 77.695 937 179 24 873 1796 60395869 60396788 1.900000e-151 545
4 TraesCS5A01G354400 chr7A 77.186 938 190 21 873 1799 419044538 419043614 2.480000e-145 525
5 TraesCS5A01G354400 chr5B 88.854 314 15 12 64 371 536382823 536382524 4.420000e-98 368
6 TraesCS5A01G354400 chr5B 79.487 312 29 15 71 379 536423578 536423299 3.690000e-44 189
7 TraesCS5A01G354400 chr5B 88.889 117 5 2 397 513 536382256 536382148 1.360000e-28 137
8 TraesCS5A01G354400 chr5D 82.564 390 21 19 155 513 440935871 440935498 1.630000e-77 300
9 TraesCS5A01G354400 chr5D 94.241 191 9 2 2619 2808 301966557 301966368 9.840000e-75 291
10 TraesCS5A01G354400 chr5D 90.511 137 9 3 266 399 440941135 440941000 7.990000e-41 178
11 TraesCS5A01G354400 chr5D 92.308 52 4 0 1 52 440937131 440937080 1.080000e-09 75
12 TraesCS5A01G354400 chr3D 95.213 188 8 1 2622 2808 316981139 316980952 2.110000e-76 296
13 TraesCS5A01G354400 chr3D 95.628 183 8 0 2626 2808 66396218 66396036 7.610000e-76 294
14 TraesCS5A01G354400 chr3D 93.035 201 12 2 2609 2808 19003779 19003580 2.740000e-75 292
15 TraesCS5A01G354400 chr6D 95.628 183 8 0 2626 2808 300476561 300476379 7.610000e-76 294
16 TraesCS5A01G354400 chr4D 94.681 188 9 1 2622 2808 15391686 15391499 9.840000e-75 291
17 TraesCS5A01G354400 chr4D 94.681 188 9 1 2622 2808 360424997 360425184 9.840000e-75 291
18 TraesCS5A01G354400 chr1D 94.681 188 9 1 2622 2808 300892150 300892337 9.840000e-75 291
19 TraesCS5A01G354400 chr1D 94.681 188 9 1 2622 2808 369989948 369989761 9.840000e-75 291


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 TraesCS5A01G354400 chr5A 557066620 557069427 2807 True 5186.0 5186 100.0000 1 2808 1 chr5A.!!$R1 2807
1 TraesCS5A01G354400 chr2A 705945436 705946246 810 False 560.0 560 79.2940 982 1796 1 chr2A.!!$F2 814
2 TraesCS5A01G354400 chr6A 60395869 60396788 919 False 545.0 545 77.6950 873 1796 1 chr6A.!!$F1 923
3 TraesCS5A01G354400 chr7A 419043614 419044538 924 True 525.0 525 77.1860 873 1799 1 chr7A.!!$R1 926
4 TraesCS5A01G354400 chr5B 536382148 536382823 675 True 252.5 368 88.8715 64 513 2 chr5B.!!$R2 449


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
594 843 0.033228 TGGCACCGGCTTGATTTTTG 59.967 50.0 0.0 0.0 40.87 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 2689 0.036732 ACACCTGTGACATCGGCAAT 59.963 50.0 3.94 0.0 0.0 3.56 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.