Multiple sequence alignment - TraesCS5A01G181500

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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 TraesCS5A01G181500 chr5A 100.000 3371 0 0 1 3371 380226819 380223449 0.000000e+00 6226.0
1 TraesCS5A01G181500 chr5B 93.680 3054 98 26 1 3000 326919267 326916255 0.000000e+00 4482.0
2 TraesCS5A01G181500 chr5D 94.383 2368 82 26 657 3000 287809216 287806876 0.000000e+00 3589.0
3 TraesCS5A01G181500 chr5D 87.108 574 34 20 7 573 287809760 287809220 6.180000e-172 614.0
4 TraesCS5A01G181500 chr5D 85.714 161 14 5 2844 3000 270200643 270200798 9.680000e-36 161.0
5 TraesCS5A01G181500 chr5D 96.875 32 1 0 2994 3025 353691713 353691744 2.000000e-03 54.7
6 TraesCS5A01G181500 chr1B 90.102 394 21 2 2996 3371 612933321 612933714 2.340000e-136 496.0
7 TraesCS5A01G181500 chr4A 89.340 394 24 4 2996 3371 655628673 655629066 2.350000e-131 479.0
8 TraesCS5A01G181500 chr3D 90.133 375 25 4 3007 3371 599168197 599167825 8.460000e-131 477.0
9 TraesCS5A01G181500 chr1D 85.535 159 17 5 2843 3000 443815793 443815640 9.680000e-36 161.0
10 TraesCS5A01G181500 chr1D 100.000 28 0 0 2998 3025 229408622 229408595 6.000000e-03 52.8
11 TraesCS5A01G181500 chr7D 85.276 163 14 6 2841 3000 544656442 544656597 3.480000e-35 159.0
12 TraesCS5A01G181500 chr4B 88.281 128 8 3 2855 2980 581308322 581308444 2.710000e-31 147.0
13 TraesCS5A01G181500 chr2D 85.517 145 15 3 2855 2998 579765615 579765476 2.710000e-31 147.0
14 TraesCS5A01G181500 chr7A 83.230 161 21 2 2841 3000 626415124 626415279 3.510000e-30 143.0
15 TraesCS5A01G181500 chr2A 83.448 145 18 2 2855 2998 717391896 717391757 2.730000e-26 130.0
16 TraesCS5A01G181500 chr2B 100.000 28 0 0 2996 3023 261968327 261968300 6.000000e-03 52.8


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 TraesCS5A01G181500 chr5A 380223449 380226819 3370 True 6226.0 6226 100.0000 1 3371 1 chr5A.!!$R1 3370
1 TraesCS5A01G181500 chr5B 326916255 326919267 3012 True 4482.0 4482 93.6800 1 3000 1 chr5B.!!$R1 2999
2 TraesCS5A01G181500 chr5D 287806876 287809760 2884 True 2101.5 3589 90.7455 7 3000 2 chr5D.!!$R1 2993


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
144 148 0.739112 GAGAAGCCAAGACCTCGCAG 60.739 60.0 0.00 0.0 0.00 5.18 F
2030 2077 1.327303 TTGGTTTGGTTAGCCTGCTG 58.673 50.0 0.97 0.0 35.27 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2148 0.251916 TTCCTCCGATGCCGTTTCAT 59.748 50.0 0.00 0.0 0.0 2.57 R
3198 3270 0.033228 CTTGGCAGGCTATCTCGAGG 59.967 60.0 13.56 0.0 0.0 4.63 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.