Multiple sequence alignment - TraesCS5A01G166900

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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 TraesCS5A01G166900 chr5A 100.000 2414 0 0 1 2414 355847734 355845321 0 4458
1 TraesCS5A01G166900 chr5D 96.358 2416 79 8 1 2414 268480173 268477765 0 3965
2 TraesCS5A01G166900 chr5B 95.998 2424 75 12 1 2414 303914251 303911840 0 3919


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 TraesCS5A01G166900 chr5A 355845321 355847734 2413 True 4458 4458 100.000 1 2414 1 chr5A.!!$R1 2413
1 TraesCS5A01G166900 chr5D 268477765 268480173 2408 True 3965 3965 96.358 1 2414 1 chr5D.!!$R1 2413
2 TraesCS5A01G166900 chr5B 303911840 303914251 2411 True 3919 3919 95.998 1 2414 1 chr5B.!!$R1 2413

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
913 914 0.178975 AAACAATGGAACCCTCGGCA 60.179 50.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2134 0.663153 GCCCCAGCATATCGAAACAC 59.337 55.0 0.0 0.0 39.53 3.32 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
105 106 3.696051 CCTCATTGACCACTACAATTGGG 59.304 47.826 10.83 3.61 38.59 4.12
137 138 3.292460 CACCCCTTGTTTCAGTAACCAA 58.708 45.455 0.00 0.00 35.81 3.67
142 143 6.266786 ACCCCTTGTTTCAGTAACCAATAAAG 59.733 38.462 0.00 0.00 35.81 1.85
150 151 6.614694 TCAGTAACCAATAAAGGTGAGCTA 57.385 37.500 0.00 0.00 42.25 3.32
151 152 6.403878 TCAGTAACCAATAAAGGTGAGCTAC 58.596 40.000 0.00 0.00 42.25 3.58
160 161 8.739972 CCAATAAAGGTGAGCTACATTAAAACT 58.260 33.333 0.00 0.00 30.95 2.66
272 273 7.334090 ACATAAGAGTGCTCATATTGTTGTCT 58.666 34.615 1.82 0.00 0.00 3.41
450 451 8.947115 AGAGCCAATAAAACAGTATAACTTCAC 58.053 33.333 0.00 0.00 0.00 3.18
651 652 0.961753 CCAACCTTCCAGAAGTTGCC 59.038 55.000 6.65 0.00 36.72 4.52
750 751 6.147985 TCTCGTGTATCATATCCTCTTCTTCG 59.852 42.308 0.00 0.00 0.00 3.79
870 871 2.360350 CCAGCCGATGTGCTTGGT 60.360 61.111 0.00 0.00 40.32 3.67
882 883 4.027572 TGTGCTTGGTTTTTCTTCTTCG 57.972 40.909 0.00 0.00 0.00 3.79
913 914 0.178975 AAACAATGGAACCCTCGGCA 60.179 50.000 0.00 0.00 0.00 5.69
1212 1213 0.535335 GTGTGAATACCTCCTCCGCA 59.465 55.000 0.00 0.00 0.00 5.69
1269 1270 0.466189 CAGGAACAGCAAGGGTGTGT 60.466 55.000 1.45 0.00 43.73 3.72
1458 1459 2.741092 GTCACGGAGCCCTTGTGA 59.259 61.111 0.00 0.00 40.12 3.58
2078 2084 0.035458 CCGAGGCTTTCTTGGTGAGT 59.965 55.000 0.00 0.00 41.31 3.41
2082 2088 0.961753 GGCTTTCTTGGTGAGTTGGG 59.038 55.000 0.00 0.00 0.00 4.12
2255 2262 0.108804 TCCTCGCGGAAAGCTTACTG 60.109 55.000 6.13 0.00 45.59 2.74
2285 2294 1.228306 CCAACGTTGGGCCAACCTA 60.228 57.895 36.64 7.77 44.70 3.08
2290 2299 1.376609 CGTTGGGCCAACCTAGCATC 61.377 60.000 36.64 15.31 40.82 3.91
2291 2300 0.034089 GTTGGGCCAACCTAGCATCT 60.034 55.000 34.31 0.00 38.30 2.90
2297 2306 1.475930 GCCAACCTAGCATCTCCCTTC 60.476 57.143 0.00 0.00 0.00 3.46
2315 2324 7.230913 TCTCCCTTCGATCGAGTAATCTATTTT 59.769 37.037 18.54 0.00 0.00 1.82
2386 2397 3.961477 TGTAATATCGGTGTGCAATGC 57.039 42.857 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 6.170506 TGTAGCTCACCTTTATTGGTTACTG 58.829 40.000 0.00 0.00 38.45 2.74
137 138 9.384764 GAGAGTTTTAATGTAGCTCACCTTTAT 57.615 33.333 0.00 0.00 0.00 1.40
142 143 8.950208 ATTAGAGAGTTTTAATGTAGCTCACC 57.050 34.615 0.00 0.00 0.00 4.02
160 161 5.745312 TCTGCACCTTCAAGAATTAGAGA 57.255 39.130 0.00 0.00 0.00 3.10
412 413 2.175878 TTGGCTCTCTGCTGAAGTTC 57.824 50.000 0.00 0.00 42.39 3.01
419 420 4.026356 ACTGTTTTATTGGCTCTCTGCT 57.974 40.909 0.00 0.00 42.39 4.24
651 652 2.579873 AGGAAGGCAATGGATGATTCG 58.420 47.619 0.00 0.00 30.87 3.34
750 751 4.077300 TGACCACATGAATGGAGATAGC 57.923 45.455 9.25 0.00 43.02 2.97
870 871 5.751509 TGATGACGAAGACGAAGAAGAAAAA 59.248 36.000 0.00 0.00 42.66 1.94
882 883 5.147162 GTTCCATTGTTTGATGACGAAGAC 58.853 41.667 0.00 0.00 0.00 3.01
913 914 1.376037 GTGCGCCTGAGCTAAACCT 60.376 57.895 4.18 0.00 38.13 3.50
977 978 6.552445 TTGATGTAATGGGTAAATTTGGGG 57.448 37.500 0.00 0.00 0.00 4.96
1269 1270 2.038813 TGCTGGAGTCCCGATGGA 59.961 61.111 6.74 0.00 38.75 3.41
1284 1285 1.066430 TCGGTGAAGAATACCCTGTGC 60.066 52.381 0.00 0.00 34.66 4.57
1311 1312 1.674322 CGCCCCAACATTCGGTTCT 60.674 57.895 0.00 0.00 37.72 3.01
1323 1324 3.220999 CTTGACTCGTGTCGCCCCA 62.221 63.158 12.54 0.00 45.70 4.96
1446 1447 0.110486 TCAAAGGTCACAAGGGCTCC 59.890 55.000 0.00 0.00 0.00 4.70
1458 1459 1.140312 TCTCCAAGGTGCTCAAAGGT 58.860 50.000 0.00 0.00 0.00 3.50
1674 1678 2.263077 CTGATGCGCGGTATCTTATCC 58.737 52.381 8.83 0.00 0.00 2.59
2078 2084 1.075836 CACGAAATCCCCACCCCAA 59.924 57.895 0.00 0.00 0.00 4.12
2082 2088 2.017049 CAATCTCACGAAATCCCCACC 58.983 52.381 0.00 0.00 0.00 4.61
2126 2132 2.575532 CCCCAGCATATCGAAACACAT 58.424 47.619 0.00 0.00 0.00 3.21
2127 2133 2.016604 GCCCCAGCATATCGAAACACA 61.017 52.381 0.00 0.00 39.53 3.72
2128 2134 0.663153 GCCCCAGCATATCGAAACAC 59.337 55.000 0.00 0.00 39.53 3.32
2280 2289 2.160721 TCGAAGGGAGATGCTAGGTT 57.839 50.000 0.00 0.00 0.00 3.50
2285 2294 0.958091 CTCGATCGAAGGGAGATGCT 59.042 55.000 19.92 0.00 0.00 3.79
2290 2299 6.503589 AATAGATTACTCGATCGAAGGGAG 57.496 41.667 19.92 9.48 0.00 4.30
2291 2300 6.896021 AAATAGATTACTCGATCGAAGGGA 57.104 37.500 19.92 1.69 0.00 4.20
2375 2386 0.890542 TGGTCAGAGCATTGCACACC 60.891 55.000 11.91 9.68 0.00 4.16


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

AutoCloner maintained by Alex Coulton.