Multiple sequence alignment - TraesCS2A01G296300

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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 TraesCS2A01G296300 chr2A 100.000 5424 0 0 1 5424 509596707 509591284 0 10017
1 TraesCS2A01G296300 chr1B 98.397 5426 82 5 1 5424 630412273 630417695 0 9533
2 TraesCS2A01G296300 chr1B 98.360 5426 80 7 1 5424 245469032 245463614 0 9518
3 TraesCS2A01G296300 chr1B 98.267 5425 91 3 1 5424 259400917 259406339 0 9494
4 TraesCS2A01G296300 chr1B 98.268 5426 89 5 1 5424 630396549 630401971 0 9494
5 TraesCS2A01G296300 chr5A 98.286 5425 91 2 1 5424 99056233 99050810 0 9502
6 TraesCS2A01G296300 chr6B 98.230 5425 85 4 1 5424 655034678 655040092 0 9476
7 TraesCS2A01G296300 chr5B 98.120 5426 98 4 1 5424 349334323 349328900 0 9452
8 TraesCS2A01G296300 chr7B 97.972 5424 107 3 1 5423 157298663 157293242 0 9404
9 TraesCS2A01G296300 chr3B 97.862 5425 114 2 1 5424 354102807 354108230 0 9374


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 TraesCS2A01G296300 chr2A 509591284 509596707 5423 True 10017 10017 100.000 1 5424 1 chr2A.!!$R1 5423
1 TraesCS2A01G296300 chr1B 630412273 630417695 5422 False 9533 9533 98.397 1 5424 1 chr1B.!!$F3 5423
2 TraesCS2A01G296300 chr1B 245463614 245469032 5418 True 9518 9518 98.360 1 5424 1 chr1B.!!$R1 5423
3 TraesCS2A01G296300 chr1B 259400917 259406339 5422 False 9494 9494 98.267 1 5424 1 chr1B.!!$F1 5423
4 TraesCS2A01G296300 chr1B 630396549 630401971 5422 False 9494 9494 98.268 1 5424 1 chr1B.!!$F2 5423
5 TraesCS2A01G296300 chr5A 99050810 99056233 5423 True 9502 9502 98.286 1 5424 1 chr5A.!!$R1 5423
6 TraesCS2A01G296300 chr6B 655034678 655040092 5414 False 9476 9476 98.230 1 5424 1 chr6B.!!$F1 5423
7 TraesCS2A01G296300 chr5B 349328900 349334323 5423 True 9452 9452 98.120 1 5424 1 chr5B.!!$R1 5423
8 TraesCS2A01G296300 chr7B 157293242 157298663 5421 True 9404 9404 97.972 1 5423 1 chr7B.!!$R1 5422
9 TraesCS2A01G296300 chr3B 354102807 354108230 5423 False 9374 9374 97.862 1 5424 1 chr3B.!!$F1 5423

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
431 433 2.592102 AACCTGGAATGCATCTGTGT 57.408 45.000 0.0 0.0 0.0 3.72 F
1635 1639 0.683179 TCGATGACCCACTCCGACAT 60.683 55.000 0.0 0.0 0.0 3.06 F
2232 2236 1.152963 ACCCAGCAACACGAAGCTT 60.153 52.632 0.0 0.0 39.5 3.74 F
2851 2856 1.381928 CGTAGGCCGCTCTGAACCTA 61.382 60.000 0.0 0.0 33.6 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1774 1.398390 CCGGTTCAGCAATAGAGCAAC 59.602 52.381 0.00 0.0 36.85 4.17 R
3446 3453 0.462759 CGGCAATCTGGTCCTCCTTC 60.463 60.000 0.00 0.0 34.23 3.46 R
3904 3911 4.397832 GAGGGCGCCGGGTTGTTA 62.398 66.667 22.54 0.0 0.00 2.41 R
4682 4689 6.206395 TCAAACATGGCAGGTATTTATGTG 57.794 37.500 4.75 0.0 32.75 3.21 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 5.391950 GCATGACGTCATCAGTTTTGGTTAT 60.392 40.000 27.79 0.00 41.91 1.89
431 433 2.592102 AACCTGGAATGCATCTGTGT 57.408 45.000 0.00 0.00 0.00 3.72
937 940 3.999001 TCACAGAATCACAGCTGAATGAC 59.001 43.478 23.35 8.67 36.07 3.06
1203 1207 2.548920 CCTTCAAGACGAGCCTTCAGTT 60.549 50.000 0.00 0.00 0.00 3.16
1635 1639 0.683179 TCGATGACCCACTCCGACAT 60.683 55.000 0.00 0.00 0.00 3.06
1782 1786 7.534239 GCGGTAATATTTTAGTTGCTCTATTGC 59.466 37.037 0.00 0.00 0.00 3.56
2025 2029 4.464008 AGAACTTGATTCACTTGGCTTGA 58.536 39.130 0.00 0.00 40.09 3.02
2147 2151 2.482864 CTGCCTTTGCCAAAATTTCGT 58.517 42.857 0.00 0.00 36.33 3.85
2232 2236 1.152963 ACCCAGCAACACGAAGCTT 60.153 52.632 0.00 0.00 39.50 3.74
2498 2503 5.551305 ACATATGCTTCCAGTATACTGCA 57.449 39.130 24.85 19.92 42.47 4.41
2851 2856 1.381928 CGTAGGCCGCTCTGAACCTA 61.382 60.000 0.00 0.00 33.60 3.08
3446 3453 3.587797 ATGCAGGCTGAAGTGAAAATG 57.412 42.857 20.86 0.00 0.00 2.32
3904 3911 3.072184 GGATCATCACCACAGCTTCCTAT 59.928 47.826 0.00 0.00 0.00 2.57
4132 4139 5.770162 CGAAGAGGATTTAAGGGCCATAAAT 59.230 40.000 22.85 22.85 36.06 1.40
4905 4912 3.571828 TCAAAAATCATTGGCTGAACCGA 59.428 39.130 0.00 0.00 43.94 4.69
5030 5037 7.041508 GCAAAGATATGCTATACTGAGCTGTTT 60.042 37.037 0.00 0.00 43.27 2.83
5080 5087 0.253630 AGGCCCCCAATAGGAGTGAA 60.254 55.000 0.00 0.00 38.24 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.149987 GACGTCATGCCGGTTTACAA 58.850 50.000 11.55 0.00 0.00 2.41
812 815 4.337145 ACATGCCGGATAAAAAGGTGTTA 58.663 39.130 5.05 0.00 0.00 2.41
937 940 1.739338 AAGCGCCGATCAGGACTAGG 61.739 60.000 2.29 0.00 45.00 3.02
1191 1195 6.100004 TCTAAATAACTCAACTGAAGGCTCG 58.900 40.000 0.00 0.00 0.00 5.03
1635 1639 4.968719 TCATCAGGGAGCTGGATTTTAGTA 59.031 41.667 0.00 0.00 0.00 1.82
1770 1774 1.398390 CCGGTTCAGCAATAGAGCAAC 59.602 52.381 0.00 0.00 36.85 4.17
1782 1786 8.603242 AGCATATAAAATAGTAACCGGTTCAG 57.397 34.615 26.16 1.04 0.00 3.02
2498 2503 4.892934 TCAAGGAAAAGTGTAAGCCATTGT 59.107 37.500 0.00 0.00 0.00 2.71
2851 2856 0.919710 GTAAGGGTGGCAGGATTCCT 59.080 55.000 0.00 0.00 0.00 3.36
3446 3453 0.462759 CGGCAATCTGGTCCTCCTTC 60.463 60.000 0.00 0.00 34.23 3.46
3904 3911 4.397832 GAGGGCGCCGGGTTGTTA 62.398 66.667 22.54 0.00 0.00 2.41
4197 4204 9.107367 GCACTCGCTTGTTTTGATTATTATATC 57.893 33.333 0.00 0.00 34.30 1.63
4495 4502 9.969001 AAGTTTTAACTATCCTATTACAAGGCA 57.031 29.630 0.00 0.00 38.57 4.75
4682 4689 6.206395 TCAAACATGGCAGGTATTTATGTG 57.794 37.500 4.75 0.00 32.75 3.21
5009 5016 9.299963 CATCTAAACAGCTCAGTATAGCATATC 57.700 37.037 0.00 0.00 45.30 1.63
5080 5087 3.760684 GACCTGGCTGACTTGAATCATTT 59.239 43.478 0.00 0.00 0.00 2.32
5133 5140 0.827507 AACCATTGCCACGCCTCTTT 60.828 50.000 0.00 0.00 0.00 2.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.