Multiple sequence alignment - TraesCS2B01G560800

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 TraesCS2B01G560800 chr2B 100.000 2267 0 0 1 2267 753949057 753951323 0.000000e+00 4187.0
1 TraesCS2B01G560800 chr2B 87.410 278 33 2 991 1268 754342798 754343073 3.630000e-83 318.0
2 TraesCS2B01G560800 chr2B 85.965 285 34 2 990 1268 708863278 708862994 1.320000e-77 300.0
3 TraesCS2B01G560800 chr2D 81.086 571 69 22 992 1544 617992148 617992697 9.680000e-114 420.0
4 TraesCS2B01G560800 chr2D 85.938 384 31 10 77 441 617940940 617941319 2.730000e-104 388.0
5 TraesCS2B01G560800 chr2D 86.944 337 20 7 1320 1653 617955725 617956040 7.700000e-95 357.0
6 TraesCS2B01G560800 chr2D 88.489 278 31 1 1000 1277 618060726 618061002 3.610000e-88 335.0
7 TraesCS2B01G560800 chr2D 85.870 276 33 4 992 1267 617995183 617995452 2.850000e-74 289.0
8 TraesCS2B01G560800 chr2D 85.211 284 36 2 990 1267 617973041 617973324 1.020000e-73 287.0
9 TraesCS2B01G560800 chr2D 91.346 104 5 3 1823 1922 617956030 617956133 3.040000e-29 139.0
10 TraesCS2B01G560800 chr2D 79.381 194 31 8 713 904 617991828 617992014 6.570000e-26 128.0
11 TraesCS2B01G560800 chr2A 86.486 333 26 10 1266 1596 748536031 748536346 4.630000e-92 348.0
12 TraesCS2B01G560800 chr2A 85.666 293 33 5 982 1268 748776005 748776294 1.320000e-77 300.0
13 TraesCS2B01G560800 chr2A 85.563 284 35 2 990 1267 748537847 748538130 2.200000e-75 292.0
14 TraesCS2B01G560800 chr2A 85.766 274 33 2 992 1259 748528067 748528340 3.690000e-73 285.0
15 TraesCS2B01G560800 chr7D 75.000 172 31 9 1977 2143 2256760 2256924 4.040000e-08 69.4
16 TraesCS2B01G560800 chr7B 85.075 67 10 0 2163 2229 710438546 710438612 4.040000e-08 69.4


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 TraesCS2B01G560800 chr2B 753949057 753951323 2266 False 4187 4187 100.000000 1 2267 1 chr2B.!!$F1 2266
1 TraesCS2B01G560800 chr2D 617991828 617995452 3624 False 279 420 82.112333 713 1544 3 chr2D.!!$F5 831
2 TraesCS2B01G560800 chr2A 748536031 748538130 2099 False 320 348 86.024500 990 1596 2 chr2A.!!$F3 606


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
327 328 0.031178 CTGCTGGCAGTGGACAAAAC 59.969 55.0 17.16 0.0 39.1 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 5327 0.035881 ATCGGGCTATGCTCATGGTG 59.964 55.0 0.0 0.0 0.0 4.17 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.