Multiple sequence alignment - TraesCS2B01G436400

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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 TraesCS2B01G436400 chr2B 100.000 2483 0 0 1 2483 627150357 627152839 0.000000e+00 4586.0
1 TraesCS2B01G436400 chr2B 100.000 76 0 0 1937 2012 627152217 627152292 9.260000e-30 141.0
2 TraesCS2B01G436400 chr2B 100.000 76 0 0 1861 1936 627152293 627152368 9.260000e-30 141.0
3 TraesCS2B01G436400 chr2B 90.909 55 2 3 2399 2450 627152698 627152752 1.230000e-08 71.3
4 TraesCS2B01G436400 chr2B 90.909 55 2 3 2342 2396 627152755 627152806 1.230000e-08 71.3
5 TraesCS2B01G436400 chr2D 94.659 1292 47 13 584 1861 528806853 528808136 0.000000e+00 1984.0
6 TraesCS2B01G436400 chr2D 89.318 337 31 3 1965 2297 528808198 528808533 3.820000e-113 418.0
7 TraesCS2B01G436400 chr2D 88.293 205 12 5 2291 2483 528808593 528808797 4.130000e-58 235.0
8 TraesCS2B01G436400 chr2A 91.574 1258 76 16 700 1936 673369932 673371180 0.000000e+00 1709.0
9 TraesCS2B01G436400 chr2A 91.270 252 11 6 2243 2483 673371368 673371619 1.420000e-87 333.0
10 TraesCS2B01G436400 chr2A 85.393 267 21 12 1940 2203 673371108 673371359 6.810000e-66 261.0
11 TraesCS2B01G436400 chr5B 83.607 122 12 4 4 117 165121349 165121228 9.390000e-20 108.0
12 TraesCS2B01G436400 chr5B 84.821 112 7 5 1 103 294747986 294747876 1.210000e-18 104.0
13 TraesCS2B01G436400 chr5B 85.417 96 11 1 25 117 515989399 515989494 2.030000e-16 97.1
14 TraesCS2B01G436400 chr7D 82.540 126 13 4 1 117 367861583 367861458 4.370000e-18 102.0
15 TraesCS2B01G436400 chr4D 81.600 125 15 3 1 117 393106628 393106504 2.030000e-16 97.1
16 TraesCS2B01G436400 chr4D 81.481 108 15 1 13 115 486800020 486799913 1.580000e-12 84.2
17 TraesCS2B01G436400 chr7A 80.800 125 16 4 1 117 462116722 462116598 9.460000e-15 91.6
18 TraesCS2B01G436400 chr6A 81.301 123 14 3 4 117 358409222 358409100 9.460000e-15 91.6
19 TraesCS2B01G436400 chr6D 79.528 127 15 5 1 117 353042305 353042180 2.050000e-11 80.5


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 TraesCS2B01G436400 chr2B 627150357 627152839 2482 False 1002.120000 4586 96.363600 1 2483 5 chr2B.!!$F1 2482
1 TraesCS2B01G436400 chr2D 528806853 528808797 1944 False 879.000000 1984 90.756667 584 2483 3 chr2D.!!$F1 1899
2 TraesCS2B01G436400 chr2A 673369932 673371619 1687 False 767.666667 1709 89.412333 700 2483 3 chr2A.!!$F1 1783


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
99 100 0.032130 TGAACACAGGAGCAGACGTC 59.968 55.0 7.70 7.70 0.0 4.34 F
103 104 0.170116 CACAGGAGCAGACGTCTCTC 59.830 60.0 24.81 24.81 0.0 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1339 0.243907 ACATCCACGAGAACACGGAG 59.756 55.000 0.0 0.0 37.61 4.63 R
1788 1802 1.893808 CAGTTGCACACTTCGCCCT 60.894 57.895 0.0 0.0 30.92 5.19 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.