Multiple sequence alignment - TraesCS4A01G415900

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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 TraesCS4A01G415900 chr4A 100.000 3159 0 0 1 3159 685788453 685785295 0.000000e+00 5834.0
1 TraesCS4A01G415900 chr4A 80.000 155 29 2 1439 1592 685770351 685770198 2.580000e-21 113.0
2 TraesCS4A01G415900 chr4D 85.477 2410 137 80 593 2887 479412697 479410386 0.000000e+00 2314.0
3 TraesCS4A01G415900 chr4D 80.000 155 29 2 1439 1592 479380705 479380552 2.580000e-21 113.0
4 TraesCS4A01G415900 chr4B 88.350 1648 104 38 593 2172 606555717 606554090 0.000000e+00 1899.0
5 TraesCS4A01G415900 chr4B 79.970 659 39 46 2261 2866 606553846 606553228 1.770000e-107 399.0
6 TraesCS4A01G415900 chr4B 78.710 155 31 2 1439 1592 606182095 606181942 5.570000e-18 102.0
7 TraesCS4A01G415900 chr6D 88.485 165 9 4 2921 3085 376938970 376939124 1.160000e-44 191.0
8 TraesCS4A01G415900 chr2D 87.578 161 16 2 2925 3085 76872253 76872409 1.940000e-42 183.0
9 TraesCS4A01G415900 chr2D 90.210 143 7 4 2953 3094 423348393 423348529 2.500000e-41 180.0
10 TraesCS4A01G415900 chr2B 86.207 174 17 2 2918 3085 798195984 798196156 6.960000e-42 182.0
11 TraesCS4A01G415900 chr3A 86.310 168 19 4 2921 3086 613347423 613347588 2.500000e-41 180.0
12 TraesCS4A01G415900 chr3B 87.821 156 13 3 2932 3087 823446035 823446184 9.000000e-41 178.0
13 TraesCS4A01G415900 chr5D 86.145 166 16 5 2921 3083 510208459 510208620 4.190000e-39 172.0
14 TraesCS4A01G415900 chr5B 85.542 166 18 5 2921 3082 701984629 701984466 5.420000e-38 169.0
15 TraesCS4A01G415900 chr5B 85.542 166 18 5 2921 3082 702071306 702071143 5.420000e-38 169.0
16 TraesCS4A01G415900 chr7B 80.597 134 26 0 1440 1573 28506272 28506139 1.550000e-18 104.0
17 TraesCS4A01G415900 chr7D 80.451 133 26 0 1440 1572 80979848 80979716 5.570000e-18 102.0
18 TraesCS4A01G415900 chr7A 79.699 133 27 0 1440 1572 83635929 83635797 2.590000e-16 97.1


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 TraesCS4A01G415900 chr4A 685785295 685788453 3158 True 5834 5834 100.000 1 3159 1 chr4A.!!$R2 3158
1 TraesCS4A01G415900 chr4D 479410386 479412697 2311 True 2314 2314 85.477 593 2887 1 chr4D.!!$R2 2294
2 TraesCS4A01G415900 chr4B 606553228 606555717 2489 True 1149 1899 84.160 593 2866 2 chr4B.!!$R2 2273


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
172 173 0.093026 CAATGGTTCGTTCGCTCGAC 59.907 55.0 1.66 0.0 39.58 4.2 F
182 183 0.101579 TTCGCTCGACGGATGCATAA 59.898 50.0 0.00 0.0 43.89 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2048 0.179127 CTCGAGATCGTGTGTGCCAT 60.179 55.0 6.58 0.00 40.80 4.40 R
2172 2265 0.313987 TGGACACACACGAGCTAGTG 59.686 55.0 23.45 23.45 46.83 2.74 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.