Multiple sequence alignment - TraesCS5B01G568300

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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 TraesCS5B01G568300 chr5B 100.000 2441 0 0 1 2441 711436305 711438745 0 4508
1 TraesCS5B01G568300 chrUn 96.206 2451 81 8 1 2441 264303584 264301136 0 4000
2 TraesCS5B01G568300 chr4B 96.129 2428 88 6 1 2425 161612401 161609977 0 3958
3 TraesCS5B01G568300 chr6B 95.513 2429 103 6 1 2425 177552686 177555112 0 3877
4 TraesCS5B01G568300 chr6B 95.150 2433 107 9 1 2425 704385710 704383281 0 3829
5 TraesCS5B01G568300 chr2B 95.158 2437 104 11 1 2425 23097920 23095486 0 3834
6 TraesCS5B01G568300 chr2B 94.862 2433 112 10 1 2425 679046304 679043877 0 3788
7 TraesCS5B01G568300 chr2B 94.733 2430 122 6 1 2425 671383057 671380629 0 3773
8 TraesCS5B01G568300 chr1B 94.611 2431 123 8 1 2425 604136158 604133730 0 3757
9 TraesCS5B01G568300 chr3B 94.533 2433 120 12 2 2425 587980898 587978470 0 3744


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 TraesCS5B01G568300 chr5B 711436305 711438745 2440 False 4508 4508 100.000 1 2441 1 chr5B.!!$F1 2440
1 TraesCS5B01G568300 chrUn 264301136 264303584 2448 True 4000 4000 96.206 1 2441 1 chrUn.!!$R1 2440
2 TraesCS5B01G568300 chr4B 161609977 161612401 2424 True 3958 3958 96.129 1 2425 1 chr4B.!!$R1 2424
3 TraesCS5B01G568300 chr6B 177552686 177555112 2426 False 3877 3877 95.513 1 2425 1 chr6B.!!$F1 2424
4 TraesCS5B01G568300 chr6B 704383281 704385710 2429 True 3829 3829 95.150 1 2425 1 chr6B.!!$R1 2424
5 TraesCS5B01G568300 chr2B 23095486 23097920 2434 True 3834 3834 95.158 1 2425 1 chr2B.!!$R1 2424
6 TraesCS5B01G568300 chr2B 679043877 679046304 2427 True 3788 3788 94.862 1 2425 1 chr2B.!!$R3 2424
7 TraesCS5B01G568300 chr2B 671380629 671383057 2428 True 3773 3773 94.733 1 2425 1 chr2B.!!$R2 2424
8 TraesCS5B01G568300 chr1B 604133730 604136158 2428 True 3757 3757 94.611 1 2425 1 chr1B.!!$R1 2424
9 TraesCS5B01G568300 chr3B 587978470 587980898 2428 True 3744 3744 94.533 2 2425 1 chr3B.!!$R1 2423

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
243 244 1.280133 AGCAAGCACATGAAGGAGCTA 59.720 47.619 0.0 0.0 36.07 3.32 F
438 443 3.256383 CAGAACCAAGGTCATTCAATGCA 59.744 43.478 0.0 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1439 1460 1.903183 GCAGGACAAGTCTACCTTCCT 59.097 52.381 0.0 0.0 29.56 3.36 R
1967 1998 3.461946 AGCGATGAAAAAGAAGAAGCG 57.538 42.857 0.0 0.0 0.00 4.68 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
203 204 4.988540 GCTGTATGATATTGTCAAGCGGTA 59.011 41.667 0.00 0.00 40.97 4.02
213 214 1.742831 GTCAAGCGGTATGGAAATGCA 59.257 47.619 0.00 0.00 0.00 3.96
243 244 1.280133 AGCAAGCACATGAAGGAGCTA 59.720 47.619 0.00 0.00 36.07 3.32
333 334 6.539826 TCTTCGTACTTTCTATACACGATCCA 59.460 38.462 0.00 0.00 40.85 3.41
438 443 3.256383 CAGAACCAAGGTCATTCAATGCA 59.744 43.478 0.00 0.00 0.00 3.96
442 447 3.642848 ACCAAGGTCATTCAATGCAAAGT 59.357 39.130 0.00 0.00 0.00 2.66
611 617 4.776837 TGCAAAATATGGGATGGTGACTTT 59.223 37.500 0.00 0.00 0.00 2.66
647 653 5.047519 CCTGAGGAAGAATTTTGCTCAACAT 60.048 40.000 18.02 0.00 44.29 2.71
984 996 6.657966 TGAACTCTGCTTCTCATTTCATTCAT 59.342 34.615 0.00 0.00 0.00 2.57
1556 1579 3.986006 TCCGGAGCACGCGAGTTT 61.986 61.111 15.93 0.00 46.40 2.66
1619 1642 2.354891 CGTGGCGTTACACACCGA 60.355 61.111 7.57 0.00 41.38 4.69
1967 1998 7.401484 TGTCGTTTTTCATTTTGGCTATTTC 57.599 32.000 0.00 0.00 0.00 2.17
2006 2037 0.179084 TAACTGCACCGGCTAGCATC 60.179 55.000 18.24 0.00 40.42 3.91
2074 2105 4.028026 CGTTACGCTTTTTCCAACTTGTTG 60.028 41.667 6.52 6.52 0.00 3.33
2076 2107 2.266554 CGCTTTTTCCAACTTGTTGCA 58.733 42.857 7.89 0.00 0.00 4.08
2124 2155 3.740321 TGTTACTAAACCGCGTCGATTTT 59.260 39.130 4.92 0.00 34.49 1.82
2264 2296 6.256539 CAGATACAGTACAACTAACATGGCAG 59.743 42.308 0.00 0.00 0.00 4.85
2265 2297 4.617253 ACAGTACAACTAACATGGCAGA 57.383 40.909 0.00 0.00 0.00 4.26
2266 2298 5.165961 ACAGTACAACTAACATGGCAGAT 57.834 39.130 0.00 0.00 0.00 2.90
2267 2299 5.178797 ACAGTACAACTAACATGGCAGATC 58.821 41.667 0.00 0.00 0.00 2.75
2268 2300 4.572389 CAGTACAACTAACATGGCAGATCC 59.428 45.833 0.00 0.00 0.00 3.36
2280 2312 4.202245 TGGCAGATCCAGTACAACTAAC 57.798 45.455 0.00 0.00 40.72 2.34
2281 2313 3.580895 TGGCAGATCCAGTACAACTAACA 59.419 43.478 0.00 0.00 40.72 2.41
2282 2314 4.225042 TGGCAGATCCAGTACAACTAACAT 59.775 41.667 0.00 0.00 40.72 2.71
2283 2315 4.572389 GGCAGATCCAGTACAACTAACATG 59.428 45.833 0.00 0.00 34.01 3.21
2284 2316 4.572389 GCAGATCCAGTACAACTAACATGG 59.428 45.833 0.00 0.00 0.00 3.66
2285 2317 4.572389 CAGATCCAGTACAACTAACATGGC 59.428 45.833 0.00 0.00 0.00 4.40
2286 2318 4.225042 AGATCCAGTACAACTAACATGGCA 59.775 41.667 0.00 0.00 0.00 4.92
2327 2359 3.198872 GGCAGATTCAGTACAACTAGCC 58.801 50.000 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.734137 GGCTCATAGTCTTCCGCGA 59.266 57.895 8.23 0.00 0.00 5.87
203 204 1.619807 GCTGGCCCTTGCATTTCCAT 61.620 55.000 0.00 0.00 40.13 3.41
213 214 4.608774 TGCTTGCTGCTGGCCCTT 62.609 61.111 0.00 0.00 43.37 3.95
243 244 2.295070 GGGTGTGGTCATTTACGCTTTT 59.705 45.455 0.00 0.00 0.00 2.27
438 443 0.947244 AGGTCGACGTACGTCACTTT 59.053 50.000 38.60 24.96 44.77 2.66
442 447 1.165907 ACCAAGGTCGACGTACGTCA 61.166 55.000 38.60 26.24 44.77 4.35
611 617 3.394274 TCTTCCTCAGGATTTTGTGGTGA 59.606 43.478 0.00 0.00 34.23 4.02
647 653 2.880268 CAGTGTGAGCTTGAATTCACCA 59.120 45.455 7.89 1.46 42.30 4.17
984 996 5.512232 GGGGAACATGACCTGCATTTAAAAA 60.512 40.000 0.00 0.00 34.15 1.94
1439 1460 1.903183 GCAGGACAAGTCTACCTTCCT 59.097 52.381 0.00 0.00 29.56 3.36
1488 1510 6.068010 ACCAGTTCCATGTGTAGATTTTTCA 58.932 36.000 0.00 0.00 0.00 2.69
1556 1579 4.287067 ACTTTCTTGATAGCTTCCTCCACA 59.713 41.667 0.00 0.00 0.00 4.17
1967 1998 3.461946 AGCGATGAAAAAGAAGAAGCG 57.538 42.857 0.00 0.00 0.00 4.68
2074 2105 4.558470 GTGTGTTGTGTGCAATATATGTGC 59.442 41.667 10.94 10.94 42.55 4.57
2076 2107 7.336679 ACATAGTGTGTTGTGTGCAATATATGT 59.663 33.333 0.00 0.00 38.01 2.29
2264 2296 4.513442 TGCCATGTTAGTTGTACTGGATC 58.487 43.478 0.00 0.00 0.00 3.36
2265 2297 4.225042 TCTGCCATGTTAGTTGTACTGGAT 59.775 41.667 0.00 0.00 0.00 3.41
2266 2298 3.580895 TCTGCCATGTTAGTTGTACTGGA 59.419 43.478 0.00 0.00 0.00 3.86
2267 2299 3.937814 TCTGCCATGTTAGTTGTACTGG 58.062 45.455 0.00 0.00 0.00 4.00
2268 2300 4.572389 GGATCTGCCATGTTAGTTGTACTG 59.428 45.833 0.00 0.00 36.34 2.74
2269 2301 4.225042 TGGATCTGCCATGTTAGTTGTACT 59.775 41.667 0.00 0.00 43.33 2.73
2270 2302 4.513442 TGGATCTGCCATGTTAGTTGTAC 58.487 43.478 0.00 0.00 43.33 2.90
2271 2303 4.835284 TGGATCTGCCATGTTAGTTGTA 57.165 40.909 0.00 0.00 43.33 2.41
2272 2304 3.719268 TGGATCTGCCATGTTAGTTGT 57.281 42.857 0.00 0.00 43.33 3.32
2282 2314 3.580895 TGTTAGTTGTACTGGATCTGCCA 59.419 43.478 0.00 0.00 46.96 4.92
2283 2315 4.202245 TGTTAGTTGTACTGGATCTGCC 57.798 45.455 0.00 0.00 37.10 4.85
2284 2316 4.572389 CCATGTTAGTTGTACTGGATCTGC 59.428 45.833 0.00 0.00 0.00 4.26
2285 2317 4.572389 GCCATGTTAGTTGTACTGGATCTG 59.428 45.833 0.00 0.00 0.00 2.90
2286 2318 4.225042 TGCCATGTTAGTTGTACTGGATCT 59.775 41.667 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.