Multiple sequence alignment - TraesCS6B01G093800

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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 TraesCS6B01G093800 chr6B 100.000 4723 0 0 1 4723 69705566 69700844 0 8722
1 TraesCS6B01G093800 chr3A 98.583 4729 58 9 1 4723 212717365 212712640 0 8353
2 TraesCS6B01G093800 chr2A 98.498 4728 65 6 1 4723 306631056 306626330 0 8333
3 TraesCS6B01G093800 chr2A 98.287 4728 74 7 1 4723 740477620 740472895 0 8275
4 TraesCS6B01G093800 chr3B 98.435 4727 68 6 1 4723 193965014 193969738 0 8314
5 TraesCS6B01G093800 chr3B 98.308 4728 73 7 1 4723 542902183 542906908 0 8281
6 TraesCS6B01G093800 chr3B 98.287 4728 73 8 1 4723 798434504 798429780 0 8275
7 TraesCS6B01G093800 chr7B 98.371 4728 70 7 1 4723 147718769 147714044 0 8298
8 TraesCS6B01G093800 chr7A 98.287 4729 73 8 1 4723 457566305 457561579 0 8277
9 TraesCS6B01G093800 chr5B 98.267 4732 71 11 1 4723 158895547 158890818 0 8274


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 TraesCS6B01G093800 chr6B 69700844 69705566 4722 True 8722 8722 100.000 1 4723 1 chr6B.!!$R1 4722
1 TraesCS6B01G093800 chr3A 212712640 212717365 4725 True 8353 8353 98.583 1 4723 1 chr3A.!!$R1 4722
2 TraesCS6B01G093800 chr2A 306626330 306631056 4726 True 8333 8333 98.498 1 4723 1 chr2A.!!$R1 4722
3 TraesCS6B01G093800 chr2A 740472895 740477620 4725 True 8275 8275 98.287 1 4723 1 chr2A.!!$R2 4722
4 TraesCS6B01G093800 chr3B 193965014 193969738 4724 False 8314 8314 98.435 1 4723 1 chr3B.!!$F1 4722
5 TraesCS6B01G093800 chr3B 542902183 542906908 4725 False 8281 8281 98.308 1 4723 1 chr3B.!!$F2 4722
6 TraesCS6B01G093800 chr3B 798429780 798434504 4724 True 8275 8275 98.287 1 4723 1 chr3B.!!$R1 4722
7 TraesCS6B01G093800 chr7B 147714044 147718769 4725 True 8298 8298 98.371 1 4723 1 chr7B.!!$R1 4722
8 TraesCS6B01G093800 chr7A 457561579 457566305 4726 True 8277 8277 98.287 1 4723 1 chr7A.!!$R1 4722
9 TraesCS6B01G093800 chr5B 158890818 158895547 4729 True 8274 8274 98.267 1 4723 1 chr5B.!!$R1 4722

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
151 152 0.034198 TGCCGTGCTAGCACAAACTA 59.966 50.000 38.95 21.5 46.47 2.24 F
1054 1057 0.380378 GAAAGGTGTTGCGCTTGTCA 59.620 50.000 9.73 0.0 0.00 3.58 F
1935 1938 1.489230 ACGGTGGAGGAGTTTGAAAGT 59.511 47.619 0.00 0.0 0.00 2.66 F
2375 2379 0.245539 GTTGCCATGACATGCAGCTT 59.754 50.000 10.10 0.0 38.95 3.74 F
3034 3043 1.503542 CCAGCATGTTCACGGCTTC 59.496 57.895 0.00 0.0 35.27 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1677 0.322187 ACAGCCAAACGTACCCATCC 60.322 55.000 0.0 0.0 0.00 3.51 R
1981 1984 0.324943 TCCCACAGGCTAACAAGAGC 59.675 55.000 0.0 0.0 42.05 4.09 R
3166 3175 0.872388 GTCCCGTTCGAATTTGCAGT 59.128 50.000 0.0 0.0 0.00 4.40 R
3303 3312 1.009675 CCAGAACTGCGTGTGTTGC 60.010 57.895 0.0 0.0 0.00 4.17 R
4446 4463 3.810941 TGGTTTCGTCGTTTCTAGCATTT 59.189 39.130 0.0 0.0 0.00 2.32 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
151 152 0.034198 TGCCGTGCTAGCACAAACTA 59.966 50.000 38.95 21.50 46.47 2.24
168 169 7.117523 GCACAAACTACAAATTGCCATGAATTA 59.882 33.333 0.00 0.00 0.00 1.40
296 297 3.088532 GACCACACAAGATGGCCAAATA 58.911 45.455 10.96 0.00 41.31 1.40
397 398 7.254590 GCAAAACAATAGTTGCCATGTTTGTTA 60.255 33.333 3.78 0.00 43.16 2.41
656 658 4.555709 ACGCGTTCCACCAGCCAA 62.556 61.111 5.58 0.00 0.00 4.52
921 924 5.073691 AGCAAAGGAATACTACCAGGCATAT 59.926 40.000 0.00 0.00 0.00 1.78
1049 1052 2.597510 GGGGAAAGGTGTTGCGCT 60.598 61.111 9.73 0.00 0.00 5.92
1054 1057 0.380378 GAAAGGTGTTGCGCTTGTCA 59.620 50.000 9.73 0.00 0.00 3.58
1754 1757 5.050363 CGATGAACATAATAACGGACCAAGG 60.050 44.000 0.00 0.00 0.00 3.61
1760 1763 6.005198 ACATAATAACGGACCAAGGTTTCAA 58.995 36.000 0.00 0.00 0.00 2.69
1935 1938 1.489230 ACGGTGGAGGAGTTTGAAAGT 59.511 47.619 0.00 0.00 0.00 2.66
1981 1984 0.679505 TCAAGTCCAGGACAACGAGG 59.320 55.000 22.31 4.34 34.60 4.63
2375 2379 0.245539 GTTGCCATGACATGCAGCTT 59.754 50.000 10.10 0.00 38.95 3.74
2490 2494 5.739935 GCATTTCCCTTGTTGAATGAAGTGT 60.740 40.000 0.00 0.00 32.61 3.55
2772 2779 7.103641 ACGATATCCAGTTGAAAATGTACTGT 58.896 34.615 0.00 0.00 38.04 3.55
2938 2947 9.699410 ATTTCTATTTCCATGACAACATAAGGA 57.301 29.630 0.00 0.00 35.09 3.36
3034 3043 1.503542 CCAGCATGTTCACGGCTTC 59.496 57.895 0.00 0.00 35.27 3.86
3166 3175 2.662866 AGGCGAGTACTACTGCCAATA 58.337 47.619 26.27 0.00 41.60 1.90
3467 3476 1.610522 CACAGGAAGGCACTGAAAAGG 59.389 52.381 10.22 0.00 40.86 3.11
3521 3530 1.131928 AAGCCTTACACCGGTTCCCT 61.132 55.000 2.97 0.00 0.00 4.20
4079 4093 2.386661 AAGTTGTACTGGATCTGCCG 57.613 50.000 0.00 0.00 40.66 5.69
4180 4194 3.924114 TCCCCATGACAAATACGATGT 57.076 42.857 0.00 0.00 0.00 3.06
4665 4684 9.482175 AGAACAGAGAGATAGTACCTTACATTT 57.518 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 5.704978 GGTTGGTTAATTCATGGCAATTTGT 59.295 36.000 0.00 0.00 0.00 2.83
168 169 5.488341 CTGTAAGCATAGTAGTGGTTGGTT 58.512 41.667 1.98 0.00 39.84 3.67
221 222 1.675641 GTGAAGCTTGCCACGGGAT 60.676 57.895 2.10 0.00 0.00 3.85
296 297 3.290948 TTCCTTACCTTGTTGTGCTGT 57.709 42.857 0.00 0.00 0.00 4.40
656 658 0.534877 TTTGCGGCATGACAGTCTGT 60.535 50.000 4.81 4.81 0.00 3.41
921 924 2.609984 CGCAAATCCATGGAACTTTGCA 60.610 45.455 39.24 15.03 44.10 4.08
1049 1052 3.064207 CTCTTTCGTTCCGGAATGACAA 58.936 45.455 33.68 26.64 36.19 3.18
1054 1057 2.561419 TGTCTCTCTTTCGTTCCGGAAT 59.439 45.455 22.04 0.00 0.00 3.01
1073 1076 1.909302 ACCCCGTCTTGAGAATGATGT 59.091 47.619 0.00 0.00 0.00 3.06
1425 1428 5.928602 GGATCTTCCTTTGCTTTCGCATCA 61.929 45.833 0.00 0.00 38.72 3.07
1674 1677 0.322187 ACAGCCAAACGTACCCATCC 60.322 55.000 0.00 0.00 0.00 3.51
1981 1984 0.324943 TCCCACAGGCTAACAAGAGC 59.675 55.000 0.00 0.00 42.05 4.09
2375 2379 7.816995 GGCAAACAGTATTTCATTAAACATGGA 59.183 33.333 0.00 0.00 0.00 3.41
2490 2494 2.752354 AGCGCATAAAACATGGCAACTA 59.248 40.909 11.47 0.00 37.61 2.24
2772 2779 5.184671 TGCAATACAACAGACATGGCAATTA 59.815 36.000 0.00 0.00 0.00 1.40
2938 2947 4.688879 TCGTGCGATCTTTTTCTTGTACAT 59.311 37.500 0.00 0.00 0.00 2.29
3034 3043 1.153509 GTATGTTCGTCCACCCGGG 60.154 63.158 22.25 22.25 38.37 5.73
3166 3175 0.872388 GTCCCGTTCGAATTTGCAGT 59.128 50.000 0.00 0.00 0.00 4.40
3227 3236 2.551006 GGGCATGCGTGTCACAACA 61.551 57.895 13.47 0.81 0.00 3.33
3229 3238 2.983030 GGGGCATGCGTGTCACAA 60.983 61.111 13.47 0.00 32.21 3.33
3303 3312 1.009675 CCAGAACTGCGTGTGTTGC 60.010 57.895 0.00 0.00 0.00 4.17
3822 3835 9.003658 TCAATGAATTTTCCTTCTACTTCTGTC 57.996 33.333 0.00 0.00 0.00 3.51
4007 4021 5.626809 GCAGATCCAGTACAACTAACATGGA 60.627 44.000 0.00 0.00 40.86 3.41
4079 4093 8.786898 ACATGGCAGATACATCATAAATAACAC 58.213 33.333 0.00 0.00 0.00 3.32
4446 4463 3.810941 TGGTTTCGTCGTTTCTAGCATTT 59.189 39.130 0.00 0.00 0.00 2.32
4665 4684 5.527214 CACACCTTACATTCTGTTGTTGAGA 59.473 40.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.