Multiple sequence alignment - TraesCS1B01G462000

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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 TraesCS1B01G462000 chr1B 100.000 6932 0 0 1 6932 674627094 674634025 0.000000e+00 12802
1 TraesCS1B01G462000 chr1A 90.983 6599 343 111 28 6509 581579748 581586211 0.000000e+00 8658
2 TraesCS1B01G462000 chr1A 88.915 424 45 2 6509 6931 29998060 29997638 7.970000e-144 521
3 TraesCS1B01G462000 chr1D 91.884 6173 312 78 312 6398 484398348 484404417 0.000000e+00 8449
4 TraesCS1B01G462000 chr1D 95.536 112 5 0 6398 6509 484404457 484404568 5.520000e-41 180
5 TraesCS1B01G462000 chr2B 98.349 424 7 0 6509 6932 390967293 390967716 0.000000e+00 745
6 TraesCS1B01G462000 chr2B 96.471 425 15 0 6508 6932 10676329 10675905 0.000000e+00 702
7 TraesCS1B01G462000 chr5A 95.765 425 18 0 6508 6932 109310734 109310310 0.000000e+00 686
8 TraesCS1B01G462000 chr5A 92.925 424 29 1 6509 6932 552313232 552312810 3.550000e-172 616
9 TraesCS1B01G462000 chr7A 94.340 424 24 0 6509 6932 24852108 24852531 0.000000e+00 651
10 TraesCS1B01G462000 chr7A 85.450 433 56 4 6505 6932 736610384 736610814 1.770000e-120 444
11 TraesCS1B01G462000 chr7A 82.405 449 54 13 4270 4710 80851430 80850999 1.100000e-97 368
12 TraesCS1B01G462000 chr6B 90.118 425 37 5 6509 6932 490338135 490338555 1.310000e-151 547
13 TraesCS1B01G462000 chr4A 86.052 423 56 2 6509 6930 702515864 702516284 1.060000e-122 451
14 TraesCS1B01G462000 chr3D 87.712 236 29 0 4624 4859 315482790 315483025 6.850000e-70 276
15 TraesCS1B01G462000 chr3D 92.683 123 9 0 1000 1122 328378024 328378146 1.990000e-40 178
16 TraesCS1B01G462000 chr3B 87.288 236 30 0 4624 4859 404828094 404827859 3.190000e-68 270
17 TraesCS1B01G462000 chr3B 92.683 123 9 0 1000 1122 421675506 421675384 1.990000e-40 178
18 TraesCS1B01G462000 chr7B 93.443 122 7 1 4345 4466 23439857 23439737 5.520000e-41 180
19 TraesCS1B01G462000 chr3A 91.935 124 10 0 1000 1123 442756860 442756983 2.570000e-39 174


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 TraesCS1B01G462000 chr1B 674627094 674634025 6931 False 12802.0 12802 100.000 1 6932 1 chr1B.!!$F1 6931
1 TraesCS1B01G462000 chr1A 581579748 581586211 6463 False 8658.0 8658 90.983 28 6509 1 chr1A.!!$F1 6481
2 TraesCS1B01G462000 chr1D 484398348 484404568 6220 False 4314.5 8449 93.710 312 6509 2 chr1D.!!$F1 6197


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
130 131 0.036875 AAGGAAAAGAGGACGCAGGG 59.963 55.0 0.0 0.0 0.00 4.45 F
1308 1361 0.252197 CCGGTTTTCGAGGGGATTCT 59.748 55.0 0.0 0.0 42.43 2.40 F
2204 2289 0.978146 AGGTGGACTTGGATCTCGGG 60.978 60.0 0.0 0.0 0.00 5.14 F
4063 4173 0.108424 CTCAGGAGCCGAAGTTGGAG 60.108 60.0 0.0 0.0 0.00 3.86 F
4898 5010 0.034477 CACCACCTCCACCCATAACC 60.034 60.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1637 0.034089 ACTTATCCTGGCCACCTTGC 60.034 55.000 0.00 0.0 0.00 4.01 R
2299 2387 0.754472 CATTGCCATTAAGCAGGGGG 59.246 55.000 0.00 0.0 45.13 5.40 R
4177 4287 1.003545 CTCACCTGAAACAACAGTGCG 60.004 52.381 0.00 0.0 36.30 5.34 R
5832 5961 0.175073 CGTTCTGGTGTACTAGGGGC 59.825 60.000 0.00 0.0 0.00 5.80 R
6207 6338 0.315251 CAGGCTCTGTCTCGACAACA 59.685 55.000 1.02 0.0 41.33 3.33 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.