Multiple sequence alignment - TraesCS3B01G424900

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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 TraesCS3B01G424900 chr3B 100.000 4737 0 0 1 4737 662974762 662979498 0.000000e+00 8748
1 TraesCS3B01G424900 chr3B 87.654 243 23 5 1986 2226 662976808 662977045 4.670000e-70 276
2 TraesCS3B01G424900 chr3D 92.319 2721 150 33 1989 4678 501299385 501302077 0.000000e+00 3812
3 TraesCS3B01G424900 chr3D 85.951 2356 171 79 19 2284 501297337 501299622 0.000000e+00 2370
4 TraesCS3B01G424900 chr3D 88.462 286 23 5 2011 2287 501299284 501299568 2.110000e-88 337
5 TraesCS3B01G424900 chr3A 93.328 2518 131 24 1980 4484 640766636 640769129 0.000000e+00 3685
6 TraesCS3B01G424900 chr3A 86.839 2363 171 70 20 2287 640764388 640766705 0.000000e+00 2512
7 TraesCS3B01G424900 chr3A 89.308 318 23 6 1980 2287 640766451 640766767 5.750000e-104 388
8 TraesCS3B01G424900 chr3A 88.387 310 24 7 1989 2287 640766521 640766829 3.480000e-96 363
9 TraesCS3B01G424900 chr3A 87.179 312 31 7 1980 2284 640766574 640766883 3.510000e-91 346


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 TraesCS3B01G424900 chr3B 662974762 662979498 4736 False 4512.0 8748 93.827000 1 4737 2 chr3B.!!$F1 4736
1 TraesCS3B01G424900 chr3D 501297337 501302077 4740 False 2173.0 3812 88.910667 19 4678 3 chr3D.!!$F1 4659
2 TraesCS3B01G424900 chr3A 640764388 640769129 4741 False 1458.8 3685 89.008200 20 4484 5 chr3A.!!$F1 4464


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
475 491 0.110486 AAACCCAGGCAAGTCGTGAT 59.890 50.0 0.0 0.0 32.56 3.06 F
719 820 0.178861 TCCTTCCTCCCCTTGCTTCT 60.179 55.0 0.0 0.0 0.00 2.85 F
1805 1957 0.383949 TGTGAAGTTGCCGAAAAGCC 59.616 50.0 0.0 0.0 0.00 4.35 F
3190 3596 0.109723 TCACCCGTCTTTTCCTTGGG 59.890 55.0 0.0 0.0 45.70 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2658 0.686789 TGAGCTCTAAACCTGCTGCA 59.313 50.0 16.19 0.88 37.16 4.41 R
2371 2772 0.865769 CGAAAAGCTAAGGTGCACGT 59.134 50.0 11.45 8.83 34.99 4.49 R
3505 3911 0.719465 GTTCCGCAACGATCGTCAAT 59.281 50.0 22.98 2.55 0.00 2.57 R
4607 5048 0.322975 CCCGATATTGGCTCCAGGAG 59.677 60.0 12.81 12.81 0.00 3.69 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.