Multiple sequence alignment - TraesCS6A01G091600

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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 TraesCS6A01G091600 chr6A 100.000 2488 0 0 1 2488 60180894 60183381 0 4595
1 TraesCS6A01G091600 chr2A 96.746 2489 74 4 1 2488 651452687 651455169 0 4141
2 TraesCS6A01G091600 chr2A 96.342 2488 86 4 1 2488 643207787 643210269 0 4085
3 TraesCS6A01G091600 chr3A 96.505 2489 80 6 1 2488 178144728 178142246 0 4108
4 TraesCS6A01G091600 chr3A 96.466 2490 81 5 3 2488 597896003 597893517 0 4104
5 TraesCS6A01G091600 chr3A 96.223 2489 90 4 1 2488 679680139 679682624 0 4072
6 TraesCS6A01G091600 chr3A 96.154 2496 85 8 1 2488 446308445 446310937 0 4067
7 TraesCS6A01G091600 chr5A 96.194 2496 84 6 1 2488 610715561 610718053 0 4072
8 TraesCS6A01G091600 chr5A 96.145 2490 90 5 1 2488 650259661 650257176 0 4061
9 TraesCS6A01G091600 chr5A 96.106 2491 89 6 1 2488 538783221 538780736 0 4056


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 TraesCS6A01G091600 chr6A 60180894 60183381 2487 False 4595 4595 100.000 1 2488 1 chr6A.!!$F1 2487
1 TraesCS6A01G091600 chr2A 651452687 651455169 2482 False 4141 4141 96.746 1 2488 1 chr2A.!!$F2 2487
2 TraesCS6A01G091600 chr2A 643207787 643210269 2482 False 4085 4085 96.342 1 2488 1 chr2A.!!$F1 2487
3 TraesCS6A01G091600 chr3A 178142246 178144728 2482 True 4108 4108 96.505 1 2488 1 chr3A.!!$R1 2487
4 TraesCS6A01G091600 chr3A 597893517 597896003 2486 True 4104 4104 96.466 3 2488 1 chr3A.!!$R2 2485
5 TraesCS6A01G091600 chr3A 679680139 679682624 2485 False 4072 4072 96.223 1 2488 1 chr3A.!!$F2 2487
6 TraesCS6A01G091600 chr3A 446308445 446310937 2492 False 4067 4067 96.154 1 2488 1 chr3A.!!$F1 2487
7 TraesCS6A01G091600 chr5A 610715561 610718053 2492 False 4072 4072 96.194 1 2488 1 chr5A.!!$F1 2487
8 TraesCS6A01G091600 chr5A 650257176 650259661 2485 True 4061 4061 96.145 1 2488 1 chr5A.!!$R2 2487
9 TraesCS6A01G091600 chr5A 538780736 538783221 2485 True 4056 4056 96.106 1 2488 1 chr5A.!!$R1 2487

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
128 133 0.838987 GGTAGTTCACCCACCTCCCA 60.839 60.0 0.00 0.0 42.07 4.37 F
169 174 1.440618 TCAGGGCCACTAAGGAACAA 58.559 50.0 6.18 0.0 41.22 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1468 0.108186 CGTTGCAGCTGTGATAGGGA 60.108 55.000 16.64 0.0 0.00 4.20 R
1736 1751 1.536766 CAAATGTCGCTCACACACCAT 59.463 47.619 0.00 0.0 38.04 3.55 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
95 100 1.203187 AGAGTGCCACTCCTGGTTCTA 60.203 52.381 20.90 0.00 46.18 2.10
128 133 0.838987 GGTAGTTCACCCACCTCCCA 60.839 60.000 0.00 0.00 42.07 4.37
169 174 1.440618 TCAGGGCCACTAAGGAACAA 58.559 50.000 6.18 0.00 41.22 2.83
334 341 5.066893 ACTTTCTATACACGATCCGCTTACA 59.933 40.000 0.00 0.00 0.00 2.41
390 402 9.836864 GTAGGCATGATTATTCCATGTCATATA 57.163 33.333 9.86 0.00 46.03 0.86
506 518 6.675971 GCCAAACGGTAAAATGTCGATGAATA 60.676 38.462 0.00 0.00 0.00 1.75
547 559 5.578336 CGACTACATCAACAATCACACTGAT 59.422 40.000 0.00 0.00 39.09 2.90
548 560 6.454715 CGACTACATCAACAATCACACTGATG 60.455 42.308 8.88 8.88 46.88 3.07
640 652 7.147497 ACCACAAAATCCTGAGGAAGAATTTTT 60.147 33.333 4.76 4.52 34.34 1.94
647 659 5.470098 TCCTGAGGAAGAATTTTTCTCAACG 59.530 40.000 0.00 4.71 39.61 4.10
653 665 2.031157 AGAATTTTTCTCAACGCGGTGG 60.031 45.455 26.21 15.32 34.07 4.61
1224 1239 3.463048 AAGGTCCAGATCAGGCATTTT 57.537 42.857 0.00 0.00 0.00 1.82
1453 1468 1.000396 GGGCAGGCAGAATTGTCCT 60.000 57.895 0.00 0.00 36.16 3.85
1487 1502 2.038690 AACGGTCGTTGAGCTCTGA 58.961 52.632 16.19 7.52 36.91 3.27
1500 1515 6.366630 GTTGAGCTCTGAAAAATCTACACAC 58.633 40.000 16.19 0.00 0.00 3.82
1518 1533 2.036217 ACACGGAACTGGTTGACGAATA 59.964 45.455 11.96 0.00 0.00 1.75
1666 1681 9.064706 CGAGGAATGTAAGGTACTATCTCTTTA 57.935 37.037 0.00 0.00 38.49 1.85
1825 1840 7.373441 GCGTTACAGCAGATATGTTTTTATGTC 59.627 37.037 0.00 0.00 37.05 3.06
1929 1944 6.318648 GGCAAATGTAGTTCATTAGACATGGA 59.681 38.462 0.00 0.00 44.85 3.41
2184 2201 8.532186 AATACCATGGCATATTTTCAGTACAA 57.468 30.769 13.04 0.00 0.00 2.41
2263 2303 6.106673 GCAGATACAGTACAACTAACATGGT 58.893 40.000 0.00 0.00 0.00 3.55
2308 2348 4.442052 GCAGATCCAGTACAACTAGCATGA 60.442 45.833 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.044946 ATTGCCCTTGCCCTCGTC 60.045 61.111 0.00 0.00 36.33 4.20
95 100 0.326048 ACTACCCTCTGCTGCCTCAT 60.326 55.000 0.00 0.00 0.00 2.90
128 133 0.395311 TCGGGCTCGTAGTCTTCCAT 60.395 55.000 5.57 0.00 37.69 3.41
169 174 2.795175 CGATATCGTACAGCTGGGTT 57.205 50.000 19.93 0.00 34.11 4.11
232 237 3.003480 GGTCATTTACGCTTTCAGCTCT 58.997 45.455 0.00 0.00 39.60 4.09
360 372 8.217111 TGACATGGAATAATCATGCCTACTAAA 58.783 33.333 0.00 0.00 44.09 1.85
390 402 6.813152 GTCCAAACATAAGCTGTATGCAAATT 59.187 34.615 12.84 4.62 45.94 1.82
395 407 4.635765 TCTGTCCAAACATAAGCTGTATGC 59.364 41.667 12.84 0.00 36.98 3.14
506 518 0.392706 TCGATCCCGCATGCAACTAT 59.607 50.000 19.57 4.99 35.37 2.12
547 559 0.179059 ATCTTGTCGGCACACACACA 60.179 50.000 0.00 0.00 29.76 3.72
548 560 1.790755 TATCTTGTCGGCACACACAC 58.209 50.000 0.00 0.00 29.76 3.82
640 652 0.034198 TTGAATCCACCGCGTTGAGA 59.966 50.000 4.75 0.78 0.00 3.27
647 659 0.955428 TGTGAGCTTGAATCCACCGC 60.955 55.000 0.00 0.00 0.00 5.68
653 665 5.679734 TTTCTTCAGTGTGAGCTTGAATC 57.320 39.130 0.00 0.00 0.00 2.52
686 698 1.425066 ACATTGCAGACAGGGAAGGAA 59.575 47.619 0.00 0.00 0.00 3.36
738 751 2.627221 TGCCACATAAACACAAGTGCAT 59.373 40.909 0.00 0.00 0.00 3.96
786 800 5.779529 AAAATCAAGAAGTCAGTGTGCAT 57.220 34.783 0.00 0.00 0.00 3.96
1224 1239 2.760650 AGTCGCCACATACTCAATCAGA 59.239 45.455 0.00 0.00 0.00 3.27
1229 1244 0.735978 CGCAGTCGCCACATACTCAA 60.736 55.000 0.00 0.00 33.11 3.02
1259 1274 4.454504 TGAAGGAAGGAAGAAATTACGTGC 59.545 41.667 0.00 0.00 0.00 5.34
1345 1360 3.059188 CACGCAAAAAGGACAGTCGTAAT 60.059 43.478 0.00 0.00 0.00 1.89
1438 1453 3.181526 GGGAGGACAATTCTGCCTG 57.818 57.895 0.00 0.00 39.30 4.85
1453 1468 0.108186 CGTTGCAGCTGTGATAGGGA 60.108 55.000 16.64 0.00 0.00 4.20
1485 1500 4.513692 CCAGTTCCGTGTGTAGATTTTTCA 59.486 41.667 0.00 0.00 0.00 2.69
1487 1502 4.457466 ACCAGTTCCGTGTGTAGATTTTT 58.543 39.130 0.00 0.00 0.00 1.94
1500 1515 3.991773 TCTTTATTCGTCAACCAGTTCCG 59.008 43.478 0.00 0.00 0.00 4.30
1518 1533 2.031157 CGGACCGCTTGTTGAAATCTTT 60.031 45.455 0.00 0.00 0.00 2.52
1666 1681 8.188139 ACACAAACATAGTTTTCAACGAGAAAT 58.812 29.630 8.22 0.00 45.15 2.17
1736 1751 1.536766 CAAATGTCGCTCACACACCAT 59.463 47.619 0.00 0.00 38.04 3.55
1920 1935 6.321435 ACGATGACTTTCACTATCCATGTCTA 59.679 38.462 0.00 0.00 0.00 2.59
1929 1944 6.422701 TGAAAAACGACGATGACTTTCACTAT 59.577 34.615 0.00 0.00 30.13 2.12
2184 2201 5.932619 TGTACTGTATCTGCCATGTTAGT 57.067 39.130 0.00 0.00 0.00 2.24
2263 2303 6.953101 TGCCATTTTAGTTGTACTGGATCTA 58.047 36.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.