Multiple sequence alignment - TraesCS7B01G312800

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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 TraesCS7B01G312800 chr7B 100.000 2285 0 0 1 2285 558761203 558758919 0.000000e+00 4220.0
1 TraesCS7B01G312800 chr7B 89.027 565 37 17 892 1433 558992684 558992122 0.000000e+00 676.0
2 TraesCS7B01G312800 chr7B 85.389 527 41 21 746 1239 558981796 558981273 4.350000e-142 514.0
3 TraesCS7B01G312800 chr7B 97.015 268 7 1 1 267 680672088 680672355 1.240000e-122 449.0
4 TraesCS7B01G312800 chr7B 96.947 262 7 1 4 264 540066646 540066385 2.690000e-119 438.0
5 TraesCS7B01G312800 chr7B 96.591 264 9 0 1 264 730187659 730187922 2.690000e-119 438.0
6 TraesCS7B01G312800 chr7B 84.270 445 21 14 1108 1551 558929769 558930165 2.750000e-104 388.0
7 TraesCS7B01G312800 chr7B 88.182 330 33 4 572 899 558993176 558992851 2.750000e-104 388.0
8 TraesCS7B01G312800 chr7B 87.755 294 21 4 759 1042 558929495 558929783 1.690000e-86 329.0
9 TraesCS7B01G312800 chr7B 87.500 224 15 7 265 487 558927480 558927691 1.750000e-61 246.0
10 TraesCS7B01G312800 chr7B 91.250 160 10 3 372 531 558993232 558993077 4.940000e-52 215.0
11 TraesCS7B01G312800 chr7B 93.103 116 7 1 1666 1780 558930312 558930427 3.900000e-38 169.0
12 TraesCS7B01G312800 chr7B 88.889 90 4 4 1465 1552 558990644 558990559 3.100000e-19 106.0
13 TraesCS7B01G312800 chr7B 96.491 57 2 0 501 557 558927832 558927888 6.720000e-16 95.3
14 TraesCS7B01G312800 chr7B 84.337 83 8 5 2182 2262 624445653 624445732 2.430000e-10 76.8
15 TraesCS7B01G312800 chr7D 88.115 833 47 18 745 1552 523392406 523393211 0.000000e+00 942.0
16 TraesCS7B01G312800 chr6B 97.348 264 7 0 1 264 78707086 78707349 1.240000e-122 449.0
17 TraesCS7B01G312800 chr6B 96.604 265 8 1 1 264 658594909 658595173 2.690000e-119 438.0
18 TraesCS7B01G312800 chr5B 97.004 267 8 0 1 267 591124851 591124585 1.240000e-122 449.0
19 TraesCS7B01G312800 chr2B 97.348 264 7 0 1 264 794607247 794606984 1.240000e-122 449.0
20 TraesCS7B01G312800 chr2B 84.337 83 8 5 2182 2262 48038523 48038444 2.430000e-10 76.8
21 TraesCS7B01G312800 chr4A 96.604 265 8 1 1 264 726413783 726414047 2.690000e-119 438.0
22 TraesCS7B01G312800 chr3B 96.935 261 8 0 1 261 224680007 224680267 2.690000e-119 438.0
23 TraesCS7B01G312800 chr7A 82.759 145 24 1 269 413 566027900 566027757 6.630000e-26 128.0
24 TraesCS7B01G312800 chr2A 91.304 46 4 0 1782 1827 605183037 605182992 1.900000e-06 63.9
25 TraesCS7B01G312800 chr4D 80.000 100 7 5 2166 2262 23217570 23217481 6.820000e-06 62.1
26 TraesCS7B01G312800 chr3D 80.000 100 7 5 2166 2262 208582376 208582287 6.820000e-06 62.1
27 TraesCS7B01G312800 chr2D 79.612 103 7 5 2164 2262 37230838 37230746 6.820000e-06 62.1


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 TraesCS7B01G312800 chr7B 558758919 558761203 2284 True 4220.00 4220 100.0000 1 2285 1 chr7B.!!$R2 2284
1 TraesCS7B01G312800 chr7B 558981273 558981796 523 True 514.00 514 85.3890 746 1239 1 chr7B.!!$R3 493
2 TraesCS7B01G312800 chr7B 558990559 558993232 2673 True 346.25 676 89.3370 372 1552 4 chr7B.!!$R4 1180
3 TraesCS7B01G312800 chr7B 558927480 558930427 2947 False 245.46 388 89.8238 265 1780 5 chr7B.!!$F4 1515
4 TraesCS7B01G312800 chr7D 523392406 523393211 805 False 942.00 942 88.1150 745 1552 1 chr7D.!!$F1 807


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
225 226 0.034863 TTGAACCGGGACTAATGGGC 60.035 55.0 6.32 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 5490 0.0293 CGCCCATAATTGCTGGAACG 59.971 55.0 9.77 9.14 35.7 3.95 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.