Multiple sequence alignment - TraesCS5A01G436600

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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 TraesCS5A01G436600 chr5A 100.000 2549 0 0 1 2549 619264486 619267034 0.000000e+00 4708
1 TraesCS5A01G436600 chrUn 97.757 2541 51 6 12 2549 93411504 93408967 0.000000e+00 4372
2 TraesCS5A01G436600 chrUn 97.696 2344 50 4 208 2549 216520280 216517939 0.000000e+00 4026
3 TraesCS5A01G436600 chr5D 97.559 2540 58 4 12 2549 503216345 503218882 0.000000e+00 4344
4 TraesCS5A01G436600 chr2D 97.560 2541 57 5 12 2549 272795767 272793229 0.000000e+00 4344
5 TraesCS5A01G436600 chr3B 97.403 2541 60 6 12 2549 201525151 201527688 0.000000e+00 4322
6 TraesCS5A01G436600 chr3A 97.047 2540 72 3 12 2549 672911882 672909344 0.000000e+00 4272
7 TraesCS5A01G436600 chr6A 96.657 2543 77 5 12 2549 260118156 260115617 0.000000e+00 4218
8 TraesCS5A01G436600 chr6D 97.783 2345 47 5 208 2549 168253248 168255590 0.000000e+00 4037
9 TraesCS5A01G436600 chr6D 97.546 2119 47 4 12 2129 168249667 168251781 0.000000e+00 3620
10 TraesCS5A01G436600 chr2B 97.506 401 10 0 2073 2473 771170504 771170104 0.000000e+00 686
11 TraesCS5A01G436600 chr2B 96.053 76 2 1 2475 2549 83488228 83488303 3.440000e-24 122


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 TraesCS5A01G436600 chr5A 619264486 619267034 2548 False 4708.0 4708 100.0000 1 2549 1 chr5A.!!$F1 2548
1 TraesCS5A01G436600 chrUn 93408967 93411504 2537 True 4372.0 4372 97.7570 12 2549 1 chrUn.!!$R1 2537
2 TraesCS5A01G436600 chrUn 216517939 216520280 2341 True 4026.0 4026 97.6960 208 2549 1 chrUn.!!$R2 2341
3 TraesCS5A01G436600 chr5D 503216345 503218882 2537 False 4344.0 4344 97.5590 12 2549 1 chr5D.!!$F1 2537
4 TraesCS5A01G436600 chr2D 272793229 272795767 2538 True 4344.0 4344 97.5600 12 2549 1 chr2D.!!$R1 2537
5 TraesCS5A01G436600 chr3B 201525151 201527688 2537 False 4322.0 4322 97.4030 12 2549 1 chr3B.!!$F1 2537
6 TraesCS5A01G436600 chr3A 672909344 672911882 2538 True 4272.0 4272 97.0470 12 2549 1 chr3A.!!$R1 2537
7 TraesCS5A01G436600 chr6A 260115617 260118156 2539 True 4218.0 4218 96.6570 12 2549 1 chr6A.!!$R1 2537
8 TraesCS5A01G436600 chr6D 168249667 168255590 5923 False 3828.5 4037 97.6645 12 2549 2 chr6D.!!$F1 2537

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
571 3963 0.923358 TCCCCCAATTTGCGACCTAT 59.077 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2340 5737 0.759436 GAGGGGGAGGTCATAAGCGA 60.759 60.0 0.0 0.0 0.0 4.93 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
178 182 6.774656 CACCTTTAAGATGGGATAAGATGCTT 59.225 38.462 0.00 0.00 0.00 3.91
195 199 3.634504 TGCTTGATAGGGCATGATGTTT 58.365 40.909 0.00 0.00 33.23 2.83
264 268 6.272822 AGAACTCTTTGTGCTTTGAAAACT 57.727 33.333 0.00 0.00 27.44 2.66
431 435 1.587066 AAGGTTATTCCCCGCCTACA 58.413 50.000 0.00 0.00 36.75 2.74
571 3963 0.923358 TCCCCCAATTTGCGACCTAT 59.077 50.000 0.00 0.00 0.00 2.57
612 4004 9.841295 TGTAAATAGGTATATGTTCCTTTCCAC 57.159 33.333 0.00 0.00 35.51 4.02
663 4055 2.370189 GTGGGTAGAATGCTAGATGCCT 59.630 50.000 0.00 0.00 42.00 4.75
672 4064 1.626356 GCTAGATGCCTGGGACCACA 61.626 60.000 0.00 0.00 35.15 4.17
725 4117 5.705609 TGACCTTTTCTATCTTTGCCAAC 57.294 39.130 0.00 0.00 0.00 3.77
1246 4643 1.807814 AGATCCGGCTCTACCCAAAT 58.192 50.000 5.89 0.00 33.26 2.32
1280 4677 2.225017 CCCCAACATTACCCACTTGTCT 60.225 50.000 0.00 0.00 0.00 3.41
1285 4682 5.512404 CCAACATTACCCACTTGTCTGACTA 60.512 44.000 9.51 0.09 0.00 2.59
1376 4773 5.392380 CCTCTTTTGCAATGAGTTTCGCTAT 60.392 40.000 21.02 0.00 32.43 2.97
1407 4804 1.141858 GCTCTAGCTAATTGCCCACCT 59.858 52.381 0.00 0.00 44.23 4.00
1700 5097 5.759059 TCCATCATCTGGCTTATGTTCTTT 58.241 37.500 0.00 0.00 45.52 2.52
1721 5118 9.981114 TTCTTTATGTAGCATTCAGATCGAATA 57.019 29.630 10.91 0.00 42.70 1.75
1780 5177 4.807783 GGGTAACGTAGGAGACATCCCTG 61.808 56.522 0.00 0.00 42.56 4.45
2008 5405 6.588719 TGCTGCCATTACTCAATAGTTTTT 57.411 33.333 0.00 0.00 37.15 1.94
2054 5451 6.070021 AGGTAGTCAAATTGGATCAGTGATCA 60.070 38.462 29.56 14.32 40.50 2.92
2318 5715 6.316140 CCAGATATGTCTTTTTGATTCCGTCA 59.684 38.462 0.00 0.00 30.42 4.35
2340 5737 8.437742 CGTCAAAAATCTGTTTTACGGTATAGT 58.562 33.333 0.00 0.00 36.42 2.12
2383 5780 2.024414 GCCTTGCGGTAATGATTCCTT 58.976 47.619 0.00 0.00 0.00 3.36
2462 5859 4.574674 TGGATTTCACTTGCCTGTCTAT 57.425 40.909 0.00 0.00 0.00 1.98
2473 5870 1.282157 GCCTGTCTATGGTTCCCTTGT 59.718 52.381 0.00 0.00 0.00 3.16
2485 5882 2.669569 CCTTGTGTGTGCTCGGGG 60.670 66.667 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.549078 GTAGTTTCCCCATAAAAATGTTGAAAA 57.451 29.630 0.00 0.00 0.00 2.29
3 4 7.868415 CGTAGTTTCCCCATAAAAATGTTGAAA 59.132 33.333 0.00 0.00 0.00 2.69
4 5 7.014422 ACGTAGTTTCCCCATAAAAATGTTGAA 59.986 33.333 0.00 0.00 37.78 2.69
5 6 6.490721 ACGTAGTTTCCCCATAAAAATGTTGA 59.509 34.615 0.00 0.00 37.78 3.18
6 7 6.683715 ACGTAGTTTCCCCATAAAAATGTTG 58.316 36.000 0.00 0.00 37.78 3.33
7 8 6.904463 ACGTAGTTTCCCCATAAAAATGTT 57.096 33.333 0.00 0.00 37.78 2.71
155 159 7.000472 TCAAGCATCTTATCCCATCTTAAAGG 59.000 38.462 0.00 0.00 0.00 3.11
178 182 7.315066 TGATACTAAACATCATGCCCTATCA 57.685 36.000 0.00 0.00 0.00 2.15
191 195 8.308931 ACGAGGAAACTGTTATGATACTAAACA 58.691 33.333 0.00 0.00 44.43 2.83
195 199 8.743085 ACTACGAGGAAACTGTTATGATACTA 57.257 34.615 0.00 0.00 44.43 1.82
264 268 4.393680 GCACAAAAACGTATCCCTATGTCA 59.606 41.667 0.00 0.00 0.00 3.58
338 342 3.876309 AAAGTGGGCTAAGGAAACTCA 57.124 42.857 0.00 0.00 42.68 3.41
410 414 2.435437 TGTAGGCGGGGAATAACCTTAC 59.565 50.000 0.00 0.00 38.98 2.34
547 3939 1.548269 GTCGCAAATTGGGGGAATTCA 59.452 47.619 10.15 0.00 32.76 2.57
612 4004 4.996758 TGGCCATACAATCGTGATTCATAG 59.003 41.667 0.00 0.00 0.00 2.23
663 4055 6.134535 AGAAACAATAGTAATGTGGTCCCA 57.865 37.500 0.00 0.00 0.00 4.37
672 4064 9.674068 GAAGGAGGAGAAAGAAACAATAGTAAT 57.326 33.333 0.00 0.00 0.00 1.89
725 4117 6.690098 CGAATCCTTTTGTAGCTCATCATTTG 59.310 38.462 0.00 0.00 0.00 2.32
787 4180 9.034800 ACATAGAATGCCAATCTTTAAAAAGGA 57.965 29.630 2.77 0.00 36.67 3.36
800 4193 5.934043 CGAGATATTGGACATAGAATGCCAA 59.066 40.000 14.05 14.05 44.45 4.52
1280 4677 4.458989 CCCAAAACTGCTTAGCAATAGTCA 59.541 41.667 8.68 0.00 38.41 3.41
1285 4682 5.264395 AGTATCCCAAAACTGCTTAGCAAT 58.736 37.500 8.68 0.00 38.41 3.56
1407 4804 5.147330 ACATAGAAATCACACGTGGAAGA 57.853 39.130 21.57 14.78 0.00 2.87
1700 5097 8.797438 AGAGTTATTCGATCTGAATGCTACATA 58.203 33.333 17.47 0.36 46.72 2.29
1721 5118 9.448294 GAAGTATCGACGTAATTTCATAGAGTT 57.552 33.333 0.00 0.00 0.00 3.01
2008 5405 4.901849 CCTCTATGGGATAGACCTCAACAA 59.098 45.833 0.00 0.00 36.98 2.83
2025 5422 7.345653 TCACTGATCCAATTTGACTACCTCTAT 59.654 37.037 0.00 0.00 0.00 1.98
2318 5715 7.332678 AGCGACTATACCGTAAAACAGATTTTT 59.667 33.333 0.00 0.00 38.91 1.94
2326 5723 6.142958 GGTCATAAGCGACTATACCGTAAAAC 59.857 42.308 0.00 0.00 36.12 2.43
2340 5737 0.759436 GAGGGGGAGGTCATAAGCGA 60.759 60.000 0.00 0.00 0.00 4.93
2383 5780 6.459848 CGTTGTGGTAAAGGTTGTAATTCCAA 60.460 38.462 0.00 0.00 0.00 3.53
2473 5870 2.203728 ACCTACCCCGAGCACACA 60.204 61.111 0.00 0.00 0.00 3.72
2485 5882 7.271868 GGCGAAACATTTATACAAAACACCTAC 59.728 37.037 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.