Multiple sequence alignment - TraesCS6A01G178300

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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 TraesCS6A01G178300 chr6A 100.000 2549 0 0 1 2549 200077628 200080176 0 4708
1 TraesCS6A01G178300 chr6A 95.447 571 26 0 1 571 88294692 88295262 0 911
2 TraesCS6A01G178300 chr7A 97.475 1980 46 4 572 2549 689996369 689994392 0 3376
3 TraesCS6A01G178300 chr7A 97.379 1984 50 2 567 2549 150203043 150201061 0 3374
4 TraesCS6A01G178300 chr7A 96.142 1996 69 8 559 2549 701581927 701583919 0 3253
5 TraesCS6A01G178300 chr4A 97.026 1984 53 5 568 2549 626934250 626932271 0 3332
6 TraesCS6A01G178300 chr5A 96.737 1992 57 5 561 2549 90997646 90999632 0 3312
7 TraesCS6A01G178300 chr5A 96.524 1985 59 8 572 2549 14186781 14184800 0 3275
8 TraesCS6A01G178300 chr5A 96.192 1996 63 7 561 2549 91049235 91051224 0 3253
9 TraesCS6A01G178300 chr6B 96.517 1981 62 6 572 2549 660437743 660435767 0 3269
10 TraesCS6A01G178300 chr3A 96.466 1981 64 5 571 2549 735555340 735557316 0 3265
11 TraesCS6A01G178300 chr6D 96.147 571 22 0 1 571 261691433 261692003 0 933
12 TraesCS6A01G178300 chr6D 95.271 571 26 1 1 571 390708918 390709487 0 904
13 TraesCS6A01G178300 chr2A 95.797 571 24 0 1 571 733379659 733380229 0 922
14 TraesCS6A01G178300 chr1D 95.944 567 23 0 5 571 176517812 176517246 0 920
15 TraesCS6A01G178300 chr5D 95.447 571 26 0 1 571 389602605 389602035 0 911
16 TraesCS6A01G178300 chr5B 95.113 573 25 3 1 571 629092905 629093476 0 900
17 TraesCS6A01G178300 chr4D 95.096 571 28 0 1 571 112379970 112380540 0 900
18 TraesCS6A01G178300 chr1B 91.088 662 58 1 1 662 581708620 581709280 0 894


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 TraesCS6A01G178300 chr6A 200077628 200080176 2548 False 4708 4708 100.000 1 2549 1 chr6A.!!$F2 2548
1 TraesCS6A01G178300 chr6A 88294692 88295262 570 False 911 911 95.447 1 571 1 chr6A.!!$F1 570
2 TraesCS6A01G178300 chr7A 689994392 689996369 1977 True 3376 3376 97.475 572 2549 1 chr7A.!!$R2 1977
3 TraesCS6A01G178300 chr7A 150201061 150203043 1982 True 3374 3374 97.379 567 2549 1 chr7A.!!$R1 1982
4 TraesCS6A01G178300 chr7A 701581927 701583919 1992 False 3253 3253 96.142 559 2549 1 chr7A.!!$F1 1990
5 TraesCS6A01G178300 chr4A 626932271 626934250 1979 True 3332 3332 97.026 568 2549 1 chr4A.!!$R1 1981
6 TraesCS6A01G178300 chr5A 90997646 90999632 1986 False 3312 3312 96.737 561 2549 1 chr5A.!!$F1 1988
7 TraesCS6A01G178300 chr5A 14184800 14186781 1981 True 3275 3275 96.524 572 2549 1 chr5A.!!$R1 1977
8 TraesCS6A01G178300 chr5A 91049235 91051224 1989 False 3253 3253 96.192 561 2549 1 chr5A.!!$F2 1988
9 TraesCS6A01G178300 chr6B 660435767 660437743 1976 True 3269 3269 96.517 572 2549 1 chr6B.!!$R1 1977
10 TraesCS6A01G178300 chr3A 735555340 735557316 1976 False 3265 3265 96.466 571 2549 1 chr3A.!!$F1 1978
11 TraesCS6A01G178300 chr6D 261691433 261692003 570 False 933 933 96.147 1 571 1 chr6D.!!$F1 570
12 TraesCS6A01G178300 chr6D 390708918 390709487 569 False 904 904 95.271 1 571 1 chr6D.!!$F2 570
13 TraesCS6A01G178300 chr2A 733379659 733380229 570 False 922 922 95.797 1 571 1 chr2A.!!$F1 570
14 TraesCS6A01G178300 chr1D 176517246 176517812 566 True 920 920 95.944 5 571 1 chr1D.!!$R1 566
15 TraesCS6A01G178300 chr5D 389602035 389602605 570 True 911 911 95.447 1 571 1 chr5D.!!$R1 570
16 TraesCS6A01G178300 chr5B 629092905 629093476 571 False 900 900 95.113 1 571 1 chr5B.!!$F1 570
17 TraesCS6A01G178300 chr4D 112379970 112380540 570 False 900 900 95.096 1 571 1 chr4D.!!$F1 570
18 TraesCS6A01G178300 chr1B 581708620 581709280 660 False 894 894 91.088 1 662 1 chr1B.!!$F1 661

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
329 331 0.395311 AGAGCATGCATCAACCCCTG 60.395 55.0 21.98 0.0 0.00 4.45 F
1119 1126 1.056660 GGAGGGTTTCTCAGACACCA 58.943 55.0 12.23 0.0 44.19 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1355 1362 0.543749 CATCCCTTCTTCCGGAGCTT 59.456 55.000 3.34 0.0 0.00 3.74 R
2514 2529 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.0 43.38 2.43 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
43 44 4.002906 TCATATAACCATCCCTCAACGC 57.997 45.455 0.00 0.0 0.00 4.84
61 62 1.071605 GCGCAACGAAGAATCACTCT 58.928 50.000 0.30 0.0 35.13 3.24
69 70 6.073765 GCAACGAAGAATCACTCTAAAGTTCA 60.074 38.462 0.00 0.0 31.71 3.18
313 315 6.395629 TCTACCGGAGAAACAAATACAAGAG 58.604 40.000 9.46 0.0 0.00 2.85
315 317 3.751175 CCGGAGAAACAAATACAAGAGCA 59.249 43.478 0.00 0.0 0.00 4.26
329 331 0.395311 AGAGCATGCATCAACCCCTG 60.395 55.000 21.98 0.0 0.00 4.45
330 332 2.012902 GAGCATGCATCAACCCCTGC 62.013 60.000 21.98 0.0 38.87 4.85
384 386 1.859998 GCGAGTTGAGTGCCAAAACAC 60.860 52.381 0.00 0.0 41.02 3.32
414 416 5.794894 AGTGAATCAATACGATACCCCATC 58.205 41.667 0.00 0.0 32.51 3.51
821 823 2.100916 GCCATTGAGTAGAGAGCCGTTA 59.899 50.000 0.00 0.0 0.00 3.18
851 853 2.864882 GCTATATAAGCGGGCGACAACA 60.865 50.000 0.00 0.0 42.53 3.33
937 943 3.775654 GCTAGCTGTGGAGGGCGT 61.776 66.667 7.70 0.0 0.00 5.68
1119 1126 1.056660 GGAGGGTTTCTCAGACACCA 58.943 55.000 12.23 0.0 44.19 4.17
1397 1404 3.318875 CGAAGCACGCACTGACAA 58.681 55.556 0.00 0.0 34.51 3.18
1821 1832 1.259840 ATGGGCCAACTGCATCCAAC 61.260 55.000 11.89 0.0 43.89 3.77
1933 1944 8.537728 TGTGGAAGCTAATTGAATTATTCCAT 57.462 30.769 24.58 0.0 41.87 3.41
2417 2432 3.894427 TGCACTACCACATGATTTTGGTT 59.106 39.130 10.67 0.0 44.06 3.67
2543 2558 0.462047 CTCACCCCCTCCGATTTTCG 60.462 60.000 0.00 0.0 40.07 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.386049 ACTTTAGAGTGATTCTTCGTTGCG 59.614 41.667 0.00 0.00 37.36 4.85
61 62 7.342769 TGTTCTCCGCTAGATATGAACTTTA 57.657 36.000 15.11 0.35 35.99 1.85
69 70 6.943146 TCTGTCTTATGTTCTCCGCTAGATAT 59.057 38.462 0.00 0.00 33.05 1.63
313 315 2.497770 GCAGGGGTTGATGCATGC 59.502 61.111 11.82 11.82 42.11 4.06
315 317 3.142838 GCGCAGGGGTTGATGCAT 61.143 61.111 0.30 0.00 42.68 3.96
329 331 2.484264 GACATTGGGGTAATCTATGCGC 59.516 50.000 0.00 0.00 0.00 6.09
330 332 3.498397 GTGACATTGGGGTAATCTATGCG 59.502 47.826 0.00 0.00 0.00 4.73
384 386 8.873830 GGGTATCGTATTGATTCACTTGATATG 58.126 37.037 0.00 0.00 38.57 1.78
414 416 4.094739 TGCAATTGAATACTCATGGTGACG 59.905 41.667 10.34 0.00 0.00 4.35
468 470 5.119588 TCGTTGTTGTCGGATTGAATACTTC 59.880 40.000 0.00 0.00 0.00 3.01
484 486 4.829064 TCCCTTTGAGATTTCGTTGTTG 57.171 40.909 0.00 0.00 0.00 3.33
937 943 4.096003 GCTAGCTTCCCACCGCCA 62.096 66.667 7.70 0.00 0.00 5.69
998 1005 1.556911 GGGAGCTTGAGGAAGACATGA 59.443 52.381 0.00 0.00 0.00 3.07
1099 1106 1.056660 GGTGTCTGAGAAACCCTCCA 58.943 55.000 10.88 0.00 41.25 3.86
1119 1126 0.974383 ACGGACGATTCTGGTTCCTT 59.026 50.000 0.00 0.00 31.53 3.36
1355 1362 0.543749 CATCCCTTCTTCCGGAGCTT 59.456 55.000 3.34 0.00 0.00 3.74
2417 2432 2.304761 CCCTAAACCAAGTGCCACTCTA 59.695 50.000 0.00 0.00 0.00 2.43
2514 2529 1.003051 GGGGGTGAGAAGCCCTCTA 59.997 63.158 12.46 0.00 43.38 2.43


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

AutoCloner maintained by Alex Coulton.