Multiple sequence alignment - TraesCS6A01G185000

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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 TraesCS6A01G185000 chr6A 100.000 2402 0 0 1 2402 216102133 216099732 0 4436
1 TraesCS6A01G185000 chr6A 94.230 2409 128 10 1 2402 212812045 212814449 0 3668
2 TraesCS6A01G185000 chr3A 93.835 2417 131 8 1 2402 167000031 166997618 0 3622
3 TraesCS6A01G185000 chr2A 93.846 2405 134 12 3 2402 237660361 237662756 0 3609
4 TraesCS6A01G185000 chr2A 93.671 2386 141 9 3 2382 591964859 591967240 0 3561
5 TraesCS6A01G185000 chr2A 93.512 2389 143 11 1 2382 694874191 694876574 0 3542
6 TraesCS6A01G185000 chr1A 93.920 2385 135 8 1 2380 542335709 542338088 0 3592
7 TraesCS6A01G185000 chr1A 93.641 2406 142 9 3 2402 505829269 505831669 0 3585
8 TraesCS6A01G185000 chr4A 93.602 2407 142 11 3 2402 150178865 150181266 0 3581
9 TraesCS6A01G185000 chr4A 93.475 2406 146 8 3 2402 30386787 30384387 0 3563


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 TraesCS6A01G185000 chr6A 216099732 216102133 2401 True 4436 4436 100.000 1 2402 1 chr6A.!!$R1 2401
1 TraesCS6A01G185000 chr6A 212812045 212814449 2404 False 3668 3668 94.230 1 2402 1 chr6A.!!$F1 2401
2 TraesCS6A01G185000 chr3A 166997618 167000031 2413 True 3622 3622 93.835 1 2402 1 chr3A.!!$R1 2401
3 TraesCS6A01G185000 chr2A 237660361 237662756 2395 False 3609 3609 93.846 3 2402 1 chr2A.!!$F1 2399
4 TraesCS6A01G185000 chr2A 591964859 591967240 2381 False 3561 3561 93.671 3 2382 1 chr2A.!!$F2 2379
5 TraesCS6A01G185000 chr2A 694874191 694876574 2383 False 3542 3542 93.512 1 2382 1 chr2A.!!$F3 2381
6 TraesCS6A01G185000 chr1A 542335709 542338088 2379 False 3592 3592 93.920 1 2380 1 chr1A.!!$F2 2379
7 TraesCS6A01G185000 chr1A 505829269 505831669 2400 False 3585 3585 93.641 3 2402 1 chr1A.!!$F1 2399
8 TraesCS6A01G185000 chr4A 150178865 150181266 2401 False 3581 3581 93.602 3 2402 1 chr4A.!!$F1 2399
9 TraesCS6A01G185000 chr4A 30384387 30386787 2400 True 3563 3563 93.475 3 2402 1 chr4A.!!$R1 2399

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
783 787 0.17691 TTTAGGCGCGTGATCATCCA 59.823 50.0 13.84 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1879 1.068741 GTGGAGTTGGACGACTGAAGT 59.931 52.381 0.0 0.0 0.0 3.01 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
227 229 1.663379 CTCGCCACCCACGTAGATCA 61.663 60.000 0.00 0.00 0.00 2.92
250 252 3.754172 CGGATTCTCACTACCTCCCCATA 60.754 52.174 0.00 0.00 0.00 2.74
260 262 2.929301 ACCTCCCCATACTTTCTTCCA 58.071 47.619 0.00 0.00 0.00 3.53
325 328 7.123383 TCACTCCAAACACCATAGTCTATCTA 58.877 38.462 0.00 0.00 0.00 1.98
415 418 2.037367 ACCTGCCGCTCCTAGTCA 59.963 61.111 0.00 0.00 0.00 3.41
520 523 3.010200 ACTTTCCCAGCCATGATTCTC 57.990 47.619 0.00 0.00 0.00 2.87
682 685 1.529244 GCAGGTCAAGGTGCTGGTT 60.529 57.895 0.00 0.00 36.71 3.67
746 750 0.891373 CTGCTGGAGGTCTTTCTCGA 59.109 55.000 0.00 0.00 34.74 4.04
783 787 0.176910 TTTAGGCGCGTGATCATCCA 59.823 50.000 13.84 0.00 0.00 3.41
922 926 3.711704 GTCTAGGAGGGTGATTCCATTCA 59.288 47.826 0.00 0.00 37.18 2.57
1009 1013 6.533723 GTGTGATATCTTGTTTATGGTCGACA 59.466 38.462 18.91 3.91 0.00 4.35
1195 1199 0.603569 GAAGTCAACTCGCCTCCTCA 59.396 55.000 0.00 0.00 0.00 3.86
1445 1459 6.713450 GGTAACCATCTAACTTGTCCTTTTCA 59.287 38.462 0.00 0.00 0.00 2.69
1455 1469 4.511826 ACTTGTCCTTTTCATCGACTCAAC 59.488 41.667 0.00 0.00 0.00 3.18
1550 1564 2.420687 GGACGAGGAAATGGAAGATGCT 60.421 50.000 0.00 0.00 0.00 3.79
1638 1653 2.232941 GTGACTCACTTGGGGTCGAATA 59.767 50.000 1.58 0.00 33.21 1.75
1728 1743 2.235898 CAGGAAGAGCAAGAAGGTAGCT 59.764 50.000 0.00 0.00 42.17 3.32
1864 1879 0.391130 GCCGACTGCACCTGTGATTA 60.391 55.000 0.51 0.00 40.77 1.75
1919 1934 3.900892 CGCCGCACCTAGGTCGAT 61.901 66.667 25.72 0.00 32.73 3.59
2018 2033 0.533755 GATGATGGAGCGGGTGAAGG 60.534 60.000 0.00 0.00 0.00 3.46
2038 2053 1.460504 CAGTGCATGAGAACAGCCAT 58.539 50.000 0.00 0.00 0.00 4.40
2040 2055 1.171308 GTGCATGAGAACAGCCATGT 58.829 50.000 0.00 0.00 41.49 3.21
2078 2093 2.824041 CCCTTCGGGCCAATGTCG 60.824 66.667 4.39 0.00 35.35 4.35
2364 2384 6.712095 TCTTTTGTACTCCTTACACTCGACTA 59.288 38.462 0.00 0.00 40.60 2.59
2395 2415 3.364764 CGGTCGAGTAGTTTCGTTCTTCT 60.365 47.826 0.00 0.00 41.22 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.034878 CCAGATCTCGACAAGGATCCA 58.965 52.381 15.82 0.00 39.12 3.41
39 40 2.725312 GGCAGGCCAGATCTCGACA 61.725 63.158 5.01 0.00 35.81 4.35
87 88 0.608640 GTCCTGGGTGATTGTCGAGT 59.391 55.000 0.00 0.00 0.00 4.18
227 229 1.688627 GGGGAGGTAGTGAGAATCCGT 60.689 57.143 0.00 0.00 0.00 4.69
325 328 2.094659 CATCGACACGAAAGCGGCT 61.095 57.895 0.00 0.00 39.99 5.52
415 418 2.222027 CTCGACTTGGCCTTTTTGACT 58.778 47.619 3.32 0.00 0.00 3.41
602 605 0.765510 ACTCGAGCCAAGGAAAAGGT 59.234 50.000 13.61 0.00 0.00 3.50
746 750 0.537188 AAGAGGTTGGATGCGTCGAT 59.463 50.000 0.00 0.00 0.00 3.59
783 787 2.171448 GAGCCCAGAGTACATCCACATT 59.829 50.000 0.00 0.00 0.00 2.71
922 926 2.972505 CGGCTGGTGCGAGTTGTT 60.973 61.111 0.00 0.00 40.82 2.83
1009 1013 5.316987 AGGACAACGATCAAAGGAAATTCT 58.683 37.500 0.00 0.00 0.00 2.40
1182 1186 2.286523 CCCTGTGAGGAGGCGAGTT 61.287 63.158 0.00 0.00 37.67 3.01
1195 1199 1.700186 GTTTGGTTCTCCTCTCCCTGT 59.300 52.381 0.00 0.00 34.23 4.00
1209 1213 1.885850 GGTCGTGAGCGTGTTTGGT 60.886 57.895 0.00 0.00 39.49 3.67
1236 1240 2.355115 GGCCACCAAGTCCGGAAT 59.645 61.111 5.23 0.00 0.00 3.01
1237 1241 4.323477 CGGCCACCAAGTCCGGAA 62.323 66.667 5.23 0.00 39.52 4.30
1348 1361 1.614241 GGAGGAGGTAGCTTTCGGCA 61.614 60.000 0.00 0.00 44.79 5.69
1431 1444 4.703897 TGAGTCGATGAAAAGGACAAGTT 58.296 39.130 0.00 0.00 33.18 2.66
1445 1459 1.131883 CGTCCGGTTAGTTGAGTCGAT 59.868 52.381 0.00 0.00 0.00 3.59
1550 1564 0.104882 TACCTGGGTTGGAGGTCACA 60.105 55.000 0.00 0.00 43.15 3.58
1728 1743 1.676678 GCCGAGACATCCTACCAGCA 61.677 60.000 0.00 0.00 0.00 4.41
1864 1879 1.068741 GTGGAGTTGGACGACTGAAGT 59.931 52.381 0.00 0.00 0.00 3.01
1912 1927 3.251004 GTGAAAAAGTGAGCAATCGACCT 59.749 43.478 0.00 0.00 0.00 3.85
1919 1934 2.378038 AGCTGGTGAAAAAGTGAGCAA 58.622 42.857 0.00 0.00 0.00 3.91
1990 2005 1.808891 CGCTCCATCATCATGTCAGCA 60.809 52.381 0.00 0.00 35.22 4.41
2018 2033 1.239296 TGGCTGTTCTCATGCACTGC 61.239 55.000 10.81 10.81 37.19 4.40
2038 2053 2.048597 CTGGCGTCGTAGGCAACA 60.049 61.111 9.82 0.00 46.12 3.33
2040 2055 2.048597 CACTGGCGTCGTAGGCAA 60.049 61.111 9.82 0.00 46.12 4.52
2078 2093 2.702261 ACAGTCGAGTCTACTCACCTC 58.298 52.381 10.55 0.00 43.00 3.85
2302 2322 3.314331 CCCCAGTCGACTGCCAGT 61.314 66.667 35.09 0.00 42.47 4.00
2364 2384 3.925630 TACTCGACCGGTCCGCCTT 62.926 63.158 28.52 11.09 0.00 4.35


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

AutoCloner maintained by Alex Coulton.