Multiple sequence alignment - TraesCS7B01G284000

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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 TraesCS7B01G284000 chr7B 100.000 2369 0 0 1 2369 518289908 518287540 0 4375
1 TraesCS7B01G284000 chr7B 99.620 2369 9 0 1 2369 518305917 518303549 0 4325
2 TraesCS7B01G284000 chr4B 96.380 2376 76 6 3 2369 485379952 485382326 0 3903
3 TraesCS7B01G284000 chr4B 93.924 2370 135 8 3 2369 165971548 165969185 0 3570
4 TraesCS7B01G284000 chr3A 88.791 2382 239 22 1 2369 46666767 46664401 0 2894
5 TraesCS7B01G284000 chr3A 88.146 2379 242 22 1 2369 167683344 167680996 0 2795
6 TraesCS7B01G284000 chr2A 88.445 2380 232 25 1 2369 82414415 82412068 0 2832
7 TraesCS7B01G284000 chr2A 86.993 2391 258 36 1 2369 266908213 266905854 0 2643
8 TraesCS7B01G284000 chr2A 84.719 1996 262 32 1 1983 140707849 140709814 0 1956
9 TraesCS7B01G284000 chr2A 87.163 1223 148 8 1 1219 100908406 100907189 0 1380
10 TraesCS7B01G284000 chr1A 87.516 2275 255 25 1 2265 313569434 313567179 0 2601
11 TraesCS7B01G284000 chr7A 86.783 2285 265 25 1 2261 592894921 592897192 0 2512
12 TraesCS7B01G284000 chr1B 88.927 2023 188 31 364 2369 260841935 260839932 0 2462


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 TraesCS7B01G284000 chr7B 518287540 518289908 2368 True 4375 4375 100.000 1 2369 1 chr7B.!!$R1 2368
1 TraesCS7B01G284000 chr7B 518303549 518305917 2368 True 4325 4325 99.620 1 2369 1 chr7B.!!$R2 2368
2 TraesCS7B01G284000 chr4B 485379952 485382326 2374 False 3903 3903 96.380 3 2369 1 chr4B.!!$F1 2366
3 TraesCS7B01G284000 chr4B 165969185 165971548 2363 True 3570 3570 93.924 3 2369 1 chr4B.!!$R1 2366
4 TraesCS7B01G284000 chr3A 46664401 46666767 2366 True 2894 2894 88.791 1 2369 1 chr3A.!!$R1 2368
5 TraesCS7B01G284000 chr3A 167680996 167683344 2348 True 2795 2795 88.146 1 2369 1 chr3A.!!$R2 2368
6 TraesCS7B01G284000 chr2A 82412068 82414415 2347 True 2832 2832 88.445 1 2369 1 chr2A.!!$R1 2368
7 TraesCS7B01G284000 chr2A 266905854 266908213 2359 True 2643 2643 86.993 1 2369 1 chr2A.!!$R3 2368
8 TraesCS7B01G284000 chr2A 140707849 140709814 1965 False 1956 1956 84.719 1 1983 1 chr2A.!!$F1 1982
9 TraesCS7B01G284000 chr2A 100907189 100908406 1217 True 1380 1380 87.163 1 1219 1 chr2A.!!$R2 1218
10 TraesCS7B01G284000 chr1A 313567179 313569434 2255 True 2601 2601 87.516 1 2265 1 chr1A.!!$R1 2264
11 TraesCS7B01G284000 chr7A 592894921 592897192 2271 False 2512 2512 86.783 1 2261 1 chr7A.!!$F1 2260
12 TraesCS7B01G284000 chr1B 260839932 260841935 2003 True 2462 2462 88.927 364 2369 1 chr1B.!!$R1 2005


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
694 706 6.111669 ACGCTGGTAGTACTATCTCATCTA 57.888 41.667 14.21 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1852 9.31906 ACACTTGATGATCTAGGTGTATCATAT 57.681 33.333 8.65 0.0 41.7 1.78 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
694 706 6.111669 ACGCTGGTAGTACTATCTCATCTA 57.888 41.667 14.21 0.0 0.0 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.891183 AATCGATGGGAAATCTTACTTATCG 57.109 36.000 0.00 0.0 37.94 2.92
1813 1852 9.319060 ACACTTGATGATCTAGGTGTATCATAT 57.681 33.333 8.65 0.0 41.70 1.78



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AutoCloner maintained by Alex Coulton.