Multiple sequence alignment - TraesCS5A01G033000

Loading Multiple Alignment...

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 TraesCS5A01G033000 chr5A 100.000 2320 0 0 1 2320 30143743 30146062 0 4285
1 TraesCS5A01G033000 chr7A 97.805 2323 48 1 1 2320 94445668 94443346 0 4004
2 TraesCS5A01G033000 chr7A 97.335 2289 56 3 34 2320 665977683 665979968 0 3884
3 TraesCS5A01G033000 chr3A 97.241 2320 63 1 1 2320 740090420 740088102 0 3928
4 TraesCS5A01G033000 chr3A 97.290 2288 61 1 34 2320 60827737 60825450 0 3880
5 TraesCS5A01G033000 chr2A 97.552 2288 55 1 34 2320 690342196 690344483 0 3914
6 TraesCS5A01G033000 chr2D 96.692 2328 68 3 1 2320 63681704 63684030 0 3864
7 TraesCS5A01G033000 chr6D 95.857 2317 86 4 1 2309 80673022 80670708 0 3738
8 TraesCS5A01G033000 chr1A 95.484 2325 96 4 1 2320 72584820 72587140 0 3703
9 TraesCS5A01G033000 chr4D 96.752 2217 63 3 112 2320 496006351 496008566 0 3687
10 TraesCS5A01G033000 chr1B 94.548 2311 115 7 1 2302 122762315 122764623 0 3559
11 TraesCS5A01G033000 chr3D 95.883 1433 49 4 896 2320 448309993 448308563 0 2311


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 TraesCS5A01G033000 chr5A 30143743 30146062 2319 False 4285 4285 100.000 1 2320 1 chr5A.!!$F1 2319
1 TraesCS5A01G033000 chr7A 94443346 94445668 2322 True 4004 4004 97.805 1 2320 1 chr7A.!!$R1 2319
2 TraesCS5A01G033000 chr7A 665977683 665979968 2285 False 3884 3884 97.335 34 2320 1 chr7A.!!$F1 2286
3 TraesCS5A01G033000 chr3A 740088102 740090420 2318 True 3928 3928 97.241 1 2320 1 chr3A.!!$R2 2319
4 TraesCS5A01G033000 chr3A 60825450 60827737 2287 True 3880 3880 97.290 34 2320 1 chr3A.!!$R1 2286
5 TraesCS5A01G033000 chr2A 690342196 690344483 2287 False 3914 3914 97.552 34 2320 1 chr2A.!!$F1 2286
6 TraesCS5A01G033000 chr2D 63681704 63684030 2326 False 3864 3864 96.692 1 2320 1 chr2D.!!$F1 2319
7 TraesCS5A01G033000 chr6D 80670708 80673022 2314 True 3738 3738 95.857 1 2309 1 chr6D.!!$R1 2308
8 TraesCS5A01G033000 chr1A 72584820 72587140 2320 False 3703 3703 95.484 1 2320 1 chr1A.!!$F1 2319
9 TraesCS5A01G033000 chr4D 496006351 496008566 2215 False 3687 3687 96.752 112 2320 1 chr4D.!!$F1 2208
10 TraesCS5A01G033000 chr1B 122762315 122764623 2308 False 3559 3559 94.548 1 2302 1 chr1B.!!$F1 2301
11 TraesCS5A01G033000 chr3D 448308563 448309993 1430 True 2311 2311 95.883 896 2320 1 chr3D.!!$R1 1424

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
762 775 0.830444 TGTGAAGAGGTACGCCAGGT 60.83 55.0 0.0 0.0 37.19 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2091 5.508567 GGTCCTCTAACCTGTAGAGTACTT 58.491 45.833 0.0 0.0 39.42 2.24 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
23 28 6.723298 AAAGAATTGGTGTTGGTAATGTCA 57.277 33.333 0.00 0.00 0.00 3.58
358 370 2.832129 GTGAGTCCTTGAGGTATGACCA 59.168 50.000 0.00 0.00 41.95 4.02
379 391 4.150098 CCATCGCTACGAGCCTTATTTTAC 59.850 45.833 0.00 0.00 39.91 2.01
461 474 1.225148 GGCCATTACCGCCCTTACA 59.775 57.895 0.00 0.00 40.78 2.41
747 760 2.425592 CCAGTCCGGCTGTTGTGA 59.574 61.111 19.93 0.00 43.55 3.58
762 775 0.830444 TGTGAAGAGGTACGCCAGGT 60.830 55.000 0.00 0.00 37.19 4.00
839 852 1.407437 GCCTCGTGGATGTTCTTGGAT 60.407 52.381 7.92 0.00 34.57 3.41
1091 1104 0.035439 CCTGTGGGCCGTAACTTCAT 60.035 55.000 0.00 0.00 0.00 2.57
1228 1241 3.819564 ACAAGGCATACATAAGCGAGA 57.180 42.857 0.00 0.00 0.00 4.04
1242 1255 2.196749 AGCGAGATTGACATGCTTACG 58.803 47.619 0.00 0.00 30.27 3.18
1463 1480 1.790755 TCTTCCACATCGTGTTTCGG 58.209 50.000 0.00 0.00 40.32 4.30
1547 1564 4.338379 AGGTGAGAGTTTCTTGTACCAC 57.662 45.455 0.00 0.00 31.77 4.16
2095 2112 6.639590 AGAAGTACTCTACAGGTTAGAGGA 57.360 41.667 11.94 1.63 43.93 3.71
2216 2250 2.487762 CCGCTTTACTTTCTTGCCATGA 59.512 45.455 0.00 0.00 0.00 3.07
2229 2263 0.676466 GCCATGACGGTTCATCCACA 60.676 55.000 0.00 0.00 40.79 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 28 8.746052 TTATCCCAAAGATACAAATCACGAAT 57.254 30.769 0.00 0.00 37.18 3.34
358 370 4.940463 TGTAAAATAAGGCTCGTAGCGAT 58.060 39.130 0.00 0.00 43.62 4.58
747 760 1.823610 GTAAGACCTGGCGTACCTCTT 59.176 52.381 0.00 0.00 33.71 2.85
762 775 7.695055 TGGGTCAAAAGATTCCATAAGTAAGA 58.305 34.615 0.00 0.00 0.00 2.10
839 852 2.758979 GACATCCCAGTTACGAAGAGGA 59.241 50.000 0.00 0.00 0.00 3.71
1091 1104 0.984230 AGGTTCTTCCGGAGCAATGA 59.016 50.000 3.34 0.00 41.99 2.57
1149 1162 1.001048 GCCCACGTGTATGCGATAGTA 60.001 52.381 15.65 0.00 39.35 1.82
1228 1241 4.320023 TGGTTGTACGTAAGCATGTCAAT 58.680 39.130 0.00 0.00 45.62 2.57
1242 1255 7.778382 AGGGATTTGATAATTACCTGGTTGTAC 59.222 37.037 3.84 0.00 33.05 2.90
1463 1480 4.219033 CGTTGTTGTACTCCAAATTGCTC 58.781 43.478 0.00 0.00 34.07 4.26
1914 1931 5.924475 AAGAGACAAAAAGACATACCACG 57.076 39.130 0.00 0.00 0.00 4.94
2074 2091 5.508567 GGTCCTCTAACCTGTAGAGTACTT 58.491 45.833 0.00 0.00 39.42 2.24
2095 2112 8.049117 ACATGACACATGTTCATATTAAGAGGT 58.951 33.333 17.49 9.85 0.00 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.