Multiple sequence alignment - TraesCS6D01G285700

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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 TraesCS6D01G285700 chr6D 100.000 2435 0 0 1 2435 394542389 394539955 0 4497
1 TraesCS6D01G285700 chr6D 95.160 2438 109 5 1 2435 383813753 383811322 0 3840
2 TraesCS6D01G285700 chr6D 94.922 2442 117 5 1 2435 285225760 285223319 0 3816
3 TraesCS6D01G285700 chr6D 94.914 2438 121 3 1 2435 92313170 92315607 0 3812
4 TraesCS6D01G285700 chr5D 95.691 2437 103 2 1 2435 348915083 348912647 0 3917
5 TraesCS6D01G285700 chr1D 95.201 2438 112 4 1 2433 274896819 274894382 0 3849
6 TraesCS6D01G285700 chr1D 94.715 2441 121 5 1 2435 217507448 217505010 0 3786
7 TraesCS6D01G285700 chr3D 94.992 2436 120 2 1 2435 355949511 355947077 0 3821
8 TraesCS6D01G285700 chr3D 94.825 2435 124 2 1 2433 442727816 442725382 0 3797
9 TraesCS6D01G285700 chr7D 94.791 2438 122 5 1 2435 239723420 239720985 0 3794


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 TraesCS6D01G285700 chr6D 394539955 394542389 2434 True 4497 4497 100.000 1 2435 1 chr6D.!!$R3 2434
1 TraesCS6D01G285700 chr6D 383811322 383813753 2431 True 3840 3840 95.160 1 2435 1 chr6D.!!$R2 2434
2 TraesCS6D01G285700 chr6D 285223319 285225760 2441 True 3816 3816 94.922 1 2435 1 chr6D.!!$R1 2434
3 TraesCS6D01G285700 chr6D 92313170 92315607 2437 False 3812 3812 94.914 1 2435 1 chr6D.!!$F1 2434
4 TraesCS6D01G285700 chr5D 348912647 348915083 2436 True 3917 3917 95.691 1 2435 1 chr5D.!!$R1 2434
5 TraesCS6D01G285700 chr1D 274894382 274896819 2437 True 3849 3849 95.201 1 2433 1 chr1D.!!$R2 2432
6 TraesCS6D01G285700 chr1D 217505010 217507448 2438 True 3786 3786 94.715 1 2435 1 chr1D.!!$R1 2434
7 TraesCS6D01G285700 chr3D 355947077 355949511 2434 True 3821 3821 94.992 1 2435 1 chr3D.!!$R1 2434
8 TraesCS6D01G285700 chr3D 442725382 442727816 2434 True 3797 3797 94.825 1 2433 1 chr3D.!!$R2 2432
9 TraesCS6D01G285700 chr7D 239720985 239723420 2435 True 3794 3794 94.791 1 2435 1 chr7D.!!$R1 2434

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
813 816 0.108041 CGTGTGCTTACCCGGGTTAT 60.108 55.0 35.42 9.98 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1703 1.152963 GCATGCGTACCCAGGGAAT 60.153 57.895 14.54 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
69 70 2.333926 CGTCGCAGAGGTATGAAACAA 58.666 47.619 0.00 0.00 36.95 2.83
72 73 4.319190 CGTCGCAGAGGTATGAAACAAAAA 60.319 41.667 0.00 0.00 36.95 1.94
221 223 3.071602 ACATAGAGGCGGATGCTAACATT 59.928 43.478 0.00 0.00 42.25 2.71
226 228 1.383456 GCGGATGCTAACATTGGGCA 61.383 55.000 4.29 4.29 36.35 5.36
371 373 0.361184 CGTTCGACGCCTTTAACTCG 59.639 55.000 0.00 0.00 33.65 4.18
399 401 1.565305 GTACATCCGAGCTGCTCAAG 58.435 55.000 27.46 18.39 0.00 3.02
408 410 2.709213 GAGCTGCTCAAGATGGTCTTT 58.291 47.619 24.02 0.00 33.78 2.52
420 422 1.285950 GGTCTTTCCAAAGCCACGC 59.714 57.895 7.32 0.00 35.99 5.34
492 495 2.093764 CAGTAGCCCCTGAGACTTGAAG 60.094 54.545 0.00 0.00 34.23 3.02
500 503 2.486191 CCTGAGACTTGAAGCAGTTGGT 60.486 50.000 0.00 0.00 0.00 3.67
553 556 5.270794 AGGTTCTTACGGAGAAGAATACCT 58.729 41.667 11.16 11.40 44.92 3.08
778 781 1.507630 GCCGCATGCTCAATGACAA 59.492 52.632 17.13 0.00 38.72 3.18
790 793 4.702131 GCTCAATGACAACTAAAGGATGGT 59.298 41.667 0.00 0.00 0.00 3.55
813 816 0.108041 CGTGTGCTTACCCGGGTTAT 60.108 55.000 35.42 9.98 0.00 1.89
975 980 3.729862 AAGAGTTCGACGAAGAAACCT 57.270 42.857 11.25 3.82 0.00 3.50
979 984 1.192534 GTTCGACGAAGAAACCTGCTG 59.807 52.381 11.25 0.00 0.00 4.41
1391 1397 4.141620 CCAACAGGATTGTAGGCTAGACAT 60.142 45.833 0.00 0.00 36.23 3.06
1394 1400 3.007398 CAGGATTGTAGGCTAGACATCCC 59.993 52.174 19.66 11.89 30.78 3.85
1395 1401 3.116551 AGGATTGTAGGCTAGACATCCCT 60.117 47.826 19.66 13.34 30.78 4.20
1426 1432 9.771534 ATGGTATAGAAGAAGAATTTAGTCAGC 57.228 33.333 0.00 0.00 0.00 4.26
1460 1466 7.715249 ACTGTGTACTTCAAGTGACATGTATTT 59.285 33.333 0.00 0.00 0.00 1.40
1499 1505 0.679640 TCATTTGTCATGGCGGACCC 60.680 55.000 6.65 0.00 36.97 4.46
1695 1703 4.533311 AGAATAGTTCCGTTAAGGGTTCCA 59.467 41.667 13.68 0.00 41.52 3.53
1747 1756 0.667487 CCGAGCTGCGAAAAGAGACA 60.667 55.000 0.00 0.00 44.57 3.41
1750 1759 2.072298 GAGCTGCGAAAAGAGACACAT 58.928 47.619 0.00 0.00 0.00 3.21
1754 1763 3.484886 GCTGCGAAAAGAGACACATGATC 60.485 47.826 0.00 0.00 0.00 2.92
1841 1850 3.251571 CTTAAGAACGCTAGCTTTCGGT 58.748 45.455 23.53 18.70 30.78 4.69
1848 1857 1.809684 GCTAGCTTTCGGTTTCACCT 58.190 50.000 7.70 0.00 35.66 4.00
1930 1939 3.562182 CCCTAGCCAAATTAACGGGAAT 58.438 45.455 0.00 0.00 31.85 3.01
2003 2012 6.585416 AGTCATATCGATGCATATAATGGCA 58.415 36.000 8.54 0.00 45.23 4.92
2202 2218 9.827411 AAGAAAGAAATAAAAGACAGATAACGC 57.173 29.630 0.00 0.00 0.00 4.84
2266 2285 2.381725 GCACTAGGCGTAGAACCTTT 57.618 50.000 19.82 0.00 38.81 3.11
2319 2338 1.410517 AGTCGATTGTCCGATGCATCT 59.589 47.619 23.73 4.28 40.91 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.275573 GTCTCAGTCCTAACCGCCTTT 59.724 52.381 0.00 0.00 0.00 3.11
35 36 2.104859 CGACGGCGTCTCAGTCCTA 61.105 63.158 33.90 0.00 36.69 2.94
69 70 2.190841 CAACCACGGAGCGGGTTTT 61.191 57.895 0.00 0.00 44.78 2.43
72 73 4.309950 GACAACCACGGAGCGGGT 62.310 66.667 0.00 0.00 39.65 5.28
109 111 2.840511 TCCTACTAGGAAACATGGGCA 58.159 47.619 1.90 0.00 42.51 5.36
226 228 1.376812 GGAGGAACATCCGGCGTTT 60.377 57.895 6.01 0.00 42.75 3.60
321 323 2.029290 AGAAACAAGCGTCACGGAGTAT 60.029 45.455 0.00 0.00 41.61 2.12
371 373 2.025727 CGGATGTACGCGTCTCCC 59.974 66.667 18.63 12.42 0.00 4.30
408 410 2.046009 TACTGGTGCGTGGCTTTGGA 62.046 55.000 0.00 0.00 0.00 3.53
420 422 6.014840 ACCCGTATATCCTTTACATACTGGTG 60.015 42.308 6.34 0.00 39.68 4.17
492 495 6.919721 TCCTTAAATCAATTGTACCAACTGC 58.080 36.000 5.13 0.00 0.00 4.40
505 508 9.806203 CTATGCAAACAATGATCCTTAAATCAA 57.194 29.630 0.00 0.00 39.04 2.57
553 556 2.828520 CCTCCAGCTCTTGAGACAACTA 59.171 50.000 1.30 0.00 0.00 2.24
644 647 9.859427 CCTGTCATTCTTTGCAATAGAAATAAA 57.141 29.630 20.38 10.77 35.43 1.40
745 748 1.758440 GCGGCTCATCCCCTATCACA 61.758 60.000 0.00 0.00 0.00 3.58
778 781 1.623811 ACACGCTCACCATCCTTTAGT 59.376 47.619 0.00 0.00 0.00 2.24
964 969 1.412710 TCTGTCAGCAGGTTTCTTCGT 59.587 47.619 0.00 0.00 42.78 3.85
990 995 1.964223 CCCGTCAGCATACCTACAGAT 59.036 52.381 0.00 0.00 0.00 2.90
995 1000 0.394762 ACGACCCGTCAGCATACCTA 60.395 55.000 0.00 0.00 33.69 3.08
1426 1432 5.692204 CACTTGAAGTACACAGTCACTTAGG 59.308 44.000 0.00 0.00 35.17 2.69
1460 1466 3.456644 TGATTTACAATCCGGCTAGGGAA 59.543 43.478 0.00 0.00 40.09 3.97
1499 1505 0.243907 TCCAGAGGTCGAAGCGAAAG 59.756 55.000 0.00 0.00 37.72 2.62
1695 1703 1.152963 GCATGCGTACCCAGGGAAT 60.153 57.895 14.54 0.00 0.00 3.01
1719 1727 3.857854 GCAGCTCGGACATGCACG 61.858 66.667 3.46 3.46 39.75 5.34
1747 1756 3.435601 GCCCCCAGATGTTTAGATCATGT 60.436 47.826 0.00 0.00 0.00 3.21
1750 1759 2.204463 TGCCCCCAGATGTTTAGATCA 58.796 47.619 0.00 0.00 0.00 2.92
1754 1763 2.442236 ACATGCCCCCAGATGTTTAG 57.558 50.000 0.00 0.00 27.94 1.85
1795 1804 2.249844 ACTCGGTCGGTGAACAAAAT 57.750 45.000 0.00 0.00 0.00 1.82
1848 1857 2.651455 CCGGATGTGTACCTCAGACTA 58.349 52.381 0.00 0.00 0.00 2.59
1930 1939 3.343617 GCTCTTGTGTTTATGCCCTACA 58.656 45.455 0.00 0.00 0.00 2.74
2024 2034 1.543607 TGCCCCACACATGTGTTATG 58.456 50.000 28.64 19.02 42.83 1.90
2156 2166 4.101119 TCTTTCTTCCCTTCTTCTTCACGT 59.899 41.667 0.00 0.00 0.00 4.49
2158 2168 6.768381 TCTTTCTTTCTTCCCTTCTTCTTCAC 59.232 38.462 0.00 0.00 0.00 3.18
2266 2285 2.343758 GAACGCAGCCAGACTCCA 59.656 61.111 0.00 0.00 0.00 3.86
2319 2338 3.807538 GGAGCGTACCGTCTGCGA 61.808 66.667 0.00 0.00 41.33 5.10


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

AutoCloner maintained by Alex Coulton.