Multiple sequence alignment - TraesCS4A01G039900

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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 TraesCS4A01G039900 chr4A 100.000 2916 0 0 1 2916 32652568 32655483 0.000000e+00 5385.0
1 TraesCS4A01G039900 chr4D 88.150 1941 135 39 994 2885 431232046 431233940 0.000000e+00 2222.0
2 TraesCS4A01G039900 chr4D 86.548 394 26 13 463 843 431231436 431231815 2.700000e-110 409.0
3 TraesCS4A01G039900 chr4D 93.827 162 7 1 833 994 431231844 431232002 1.040000e-59 241.0
4 TraesCS4A01G039900 chr4B 87.584 1047 65 27 1463 2484 529677254 529678260 0.000000e+00 1153.0
5 TraesCS4A01G039900 chr4B 86.196 623 40 23 838 1420 529676547 529677163 1.470000e-177 632.0
6 TraesCS4A01G039900 chr4B 80.000 420 36 27 453 838 529676103 529676508 1.720000e-67 267.0
7 TraesCS4A01G039900 chr4B 85.408 233 15 9 2688 2916 529678481 529678698 1.050000e-54 224.0
8 TraesCS4A01G039900 chr4B 85.586 111 16 0 2518 2628 115527070 115527180 1.840000e-22 117.0
9 TraesCS4A01G039900 chr4B 93.443 61 4 0 453 513 529653174 529653234 1.110000e-14 91.6
10 TraesCS4A01G039900 chrUn 89.706 68 6 1 278 345 65665374 65665440 5.180000e-13 86.1
11 TraesCS4A01G039900 chr2D 90.196 51 5 0 1039 1089 345519514 345519464 1.880000e-07 67.6
12 TraesCS4A01G039900 chr2B 90.196 51 5 0 1039 1089 411001501 411001451 1.880000e-07 67.6
13 TraesCS4A01G039900 chr2A 88.889 54 6 0 1036 1089 458670108 458670161 1.880000e-07 67.6
14 TraesCS4A01G039900 chr3A 100.000 28 0 0 277 304 602223888 602223861 5.000000e-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 TraesCS4A01G039900 chr4A 32652568 32655483 2915 False 5385.000000 5385 100.000000 1 2916 1 chr4A.!!$F1 2915
1 TraesCS4A01G039900 chr4D 431231436 431233940 2504 False 957.333333 2222 89.508333 463 2885 3 chr4D.!!$F1 2422
2 TraesCS4A01G039900 chr4B 529676103 529678698 2595 False 569.000000 1153 84.797000 453 2916 4 chr4B.!!$F3 2463


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
417 418 0.031178 ACACTTAACGAAGTCGCGGT 59.969 50.0 6.13 0.00 45.00 5.68 F
998 1094 0.387367 ATTAGATAGCGAGCGCACGG 60.387 55.0 27.65 10.49 44.88 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1981 0.108138 GGGAGAATGGTCACCTGTCG 60.108 60.0 0.0 0.0 35.03 4.35 R
2887 3304 0.107081 GATCTCTCTCCTCCCGTCGA 59.893 60.0 0.0 0.0 0.00 4.20 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.