Multiple sequence alignment - TraesCS3A01G490300

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 TraesCS3A01G490300 chr3A 100.000 4265 0 0 1 4265 717906664 717902400 0.000000e+00 7877.0
1 TraesCS3A01G490300 chr3A 94.872 39 2 0 79 117 647801283 647801321 1.280000e-05 62.1
2 TraesCS3A01G490300 chr3B 83.014 1772 202 59 1813 3545 786142782 786141071 0.000000e+00 1513.0
3 TraesCS3A01G490300 chr3B 92.617 745 38 9 3533 4263 786141058 786140317 0.000000e+00 1055.0
4 TraesCS3A01G490300 chr3B 84.530 808 85 26 955 1730 786143726 786142927 0.000000e+00 763.0
5 TraesCS3A01G490300 chr3D 85.092 1355 125 43 2752 4087 588026897 588025601 0.000000e+00 1312.0
6 TraesCS3A01G490300 chr3D 87.246 886 85 17 818 1686 588028784 588027910 0.000000e+00 985.0
7 TraesCS3A01G490300 chr3D 85.080 563 52 18 3094 3651 588019809 588019274 2.900000e-151 545.0
8 TraesCS3A01G490300 chr3D 87.135 342 31 9 259 591 588029526 588029189 4.030000e-100 375.0
9 TraesCS3A01G490300 chr3D 82.609 414 63 8 2127 2534 588024758 588024348 1.460000e-94 357.0
10 TraesCS3A01G490300 chr3D 84.729 203 11 9 2906 3099 588024033 588023842 7.280000e-43 185.0
11 TraesCS3A01G490300 chr6A 76.550 371 58 24 1009 1367 16462132 16462485 4.380000e-40 176.0
12 TraesCS3A01G490300 chr6D 85.057 174 23 2 1194 1367 16198681 16198851 1.580000e-39 174.0
13 TraesCS3A01G490300 chr6B 83.249 197 26 5 1173 1367 27946494 27946685 1.580000e-39 174.0
14 TraesCS3A01G490300 chr2B 81.910 199 29 4 1173 1367 46603760 46603955 1.230000e-35 161.0
15 TraesCS3A01G490300 chr2B 97.436 39 0 1 258 295 589882590 589882552 9.900000e-07 65.8
16 TraesCS3A01G490300 chr2A 100.000 29 0 0 191 219 38365123 38365095 2.000000e-03 54.7


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 TraesCS3A01G490300 chr3A 717902400 717906664 4264 True 7877.000000 7877 100.000000 1 4265 1 chr3A.!!$R1 4264
1 TraesCS3A01G490300 chr3B 786140317 786143726 3409 True 1110.333333 1513 86.720333 955 4263 3 chr3B.!!$R1 3308
2 TraesCS3A01G490300 chr3D 588023842 588029526 5684 True 642.800000 1312 85.362200 259 4087 5 chr3D.!!$R2 3828
3 TraesCS3A01G490300 chr3D 588019274 588019809 535 True 545.000000 545 85.080000 3094 3651 1 chr3D.!!$R1 557


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
192 193 0.034283 GACGAGGGTCAGGGTAGACT 60.034 60.0 0.00 0.0 42.91 3.24 F
843 1033 0.036164 TACATTGACCGCTGCAGGTT 59.964 50.0 17.12 0.0 46.09 3.50 F
1546 1776 0.107410 ATCGGCCAGCGTAATTTGGA 60.107 50.0 2.24 0.0 36.55 3.53 F
1980 2282 0.041312 CACAGCTGAAAAACGACCCG 60.041 55.0 23.35 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 1699 0.032403 TCAATTTGTGTGGCAGCAGC 59.968 50.0 0.00 0.0 41.10 5.25 R
1961 2263 0.041312 CGGGTCGTTTTTCAGCTGTG 60.041 55.0 14.67 0.0 0.00 3.66 R
2945 3378 0.178953 AGGGGCTGCAGTTGAAACAT 60.179 50.0 16.64 0.0 0.00 2.71 R
3959 4434 0.039527 AACTTCGCAACCAATTCGGC 60.040 50.0 0.00 0.0 39.03 5.54 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)



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

AutoCloner maintained by Alex Coulton.