Multiple sequence alignment - TraesCS1B01G141800

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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 TraesCS1B01G141800 chr1B 100.000 2639 0 0 1 2639 189587240 189589878 0 4874
1 TraesCS1B01G141800 chr7B 90.841 2653 217 19 1 2639 151132760 151130120 0 3530
2 TraesCS1B01G141800 chr7B 89.444 2662 228 22 1 2639 396280760 396278129 0 3310
3 TraesCS1B01G141800 chr7B 87.851 1745 194 14 904 2639 506241333 506239598 0 2032
4 TraesCS1B01G141800 chr7B 83.271 1327 197 24 649 1964 361254992 361256304 0 1197
5 TraesCS1B01G141800 chr1D 90.762 2652 218 26 1 2639 307650904 307648267 0 3515
6 TraesCS1B01G141800 chr1D 82.850 2105 313 38 1 2079 69098931 69101013 0 1844
7 TraesCS1B01G141800 chr1D 82.938 2110 295 53 1 2079 397992003 397994078 0 1842
8 TraesCS1B01G141800 chr6D 88.075 2675 270 35 1 2639 333794254 333791593 0 3127
9 TraesCS1B01G141800 chr6D 91.085 1346 98 11 147 1488 364247743 364246416 0 1801
10 TraesCS1B01G141800 chr6D 82.312 2024 313 32 1 2003 321241398 321239399 0 1712
11 TraesCS1B01G141800 chr2B 86.882 2668 288 31 1 2639 263700354 263702988 0 2931
12 TraesCS1B01G141800 chr4D 89.228 2358 220 26 301 2639 393474112 393471770 0 2916
13 TraesCS1B01G141800 chr4A 85.732 2432 298 35 165 2579 48884550 48882151 0 2523
14 TraesCS1B01G141800 chr2D 91.338 1293 89 19 1 1274 162338479 162337191 0 1746
15 TraesCS1B01G141800 chr2D 85.142 1622 204 31 1 1606 260490827 260489227 0 1626
16 TraesCS1B01G141800 chr2D 87.993 1166 119 15 1488 2639 162321159 162320001 0 1358


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 TraesCS1B01G141800 chr1B 189587240 189589878 2638 False 4874 4874 100.000 1 2639 1 chr1B.!!$F1 2638
1 TraesCS1B01G141800 chr7B 151130120 151132760 2640 True 3530 3530 90.841 1 2639 1 chr7B.!!$R1 2638
2 TraesCS1B01G141800 chr7B 396278129 396280760 2631 True 3310 3310 89.444 1 2639 1 chr7B.!!$R2 2638
3 TraesCS1B01G141800 chr7B 506239598 506241333 1735 True 2032 2032 87.851 904 2639 1 chr7B.!!$R3 1735
4 TraesCS1B01G141800 chr7B 361254992 361256304 1312 False 1197 1197 83.271 649 1964 1 chr7B.!!$F1 1315
5 TraesCS1B01G141800 chr1D 307648267 307650904 2637 True 3515 3515 90.762 1 2639 1 chr1D.!!$R1 2638
6 TraesCS1B01G141800 chr1D 69098931 69101013 2082 False 1844 1844 82.850 1 2079 1 chr1D.!!$F1 2078
7 TraesCS1B01G141800 chr1D 397992003 397994078 2075 False 1842 1842 82.938 1 2079 1 chr1D.!!$F2 2078
8 TraesCS1B01G141800 chr6D 333791593 333794254 2661 True 3127 3127 88.075 1 2639 1 chr6D.!!$R2 2638
9 TraesCS1B01G141800 chr6D 364246416 364247743 1327 True 1801 1801 91.085 147 1488 1 chr6D.!!$R3 1341
10 TraesCS1B01G141800 chr6D 321239399 321241398 1999 True 1712 1712 82.312 1 2003 1 chr6D.!!$R1 2002
11 TraesCS1B01G141800 chr2B 263700354 263702988 2634 False 2931 2931 86.882 1 2639 1 chr2B.!!$F1 2638
12 TraesCS1B01G141800 chr4D 393471770 393474112 2342 True 2916 2916 89.228 301 2639 1 chr4D.!!$R1 2338
13 TraesCS1B01G141800 chr4A 48882151 48884550 2399 True 2523 2523 85.732 165 2579 1 chr4A.!!$R1 2414
14 TraesCS1B01G141800 chr2D 162337191 162338479 1288 True 1746 1746 91.338 1 1274 1 chr2D.!!$R2 1273
15 TraesCS1B01G141800 chr2D 260489227 260490827 1600 True 1626 1626 85.142 1 1606 1 chr2D.!!$R3 1605
16 TraesCS1B01G141800 chr2D 162320001 162321159 1158 True 1358 1358 87.993 1488 2639 1 chr2D.!!$R1 1151


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
195 198 0.690762 AGTACTGCGGGTTGTGGATT 59.309 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1815 0.598065 ATTCCACCAAGAAAGTGCGC 59.402 50.0 0.0 0.0 33.75 6.09 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.