Multiple sequence alignment - TraesCS3A01G532900

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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 TraesCS3A01G532900 chr3A 100.000 3062 0 0 1 3062 745752102 745755163 0 5655
1 TraesCS3A01G532900 chr3A 97.453 3063 76 2 1 3062 450958828 450961889 0 5223
2 TraesCS3A01G532900 chr1A 97.421 3063 75 4 1 3062 21071775 21068716 0 5216
3 TraesCS3A01G532900 chr7A 97.356 3063 76 4 1 3062 722694216 722691158 0 5203
4 TraesCS3A01G532900 chr6A 97.290 3063 81 2 1 3062 494427072 494430133 0 5195
5 TraesCS3A01G532900 chr4A 97.194 3065 82 4 1 3062 592481273 592484336 0 5180
6 TraesCS3A01G532900 chr4A 97.129 3065 84 4 1 3062 592760079 592763142 0 5169
7 TraesCS3A01G532900 chr4A 97.096 3065 85 4 1 3062 593048157 593051220 0 5164
8 TraesCS3A01G532900 chr2A 97.191 3062 82 3 1 3062 733072361 733075418 0 5175


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 TraesCS3A01G532900 chr3A 745752102 745755163 3061 False 5655 5655 100.000 1 3062 1 chr3A.!!$F2 3061
1 TraesCS3A01G532900 chr3A 450958828 450961889 3061 False 5223 5223 97.453 1 3062 1 chr3A.!!$F1 3061
2 TraesCS3A01G532900 chr1A 21068716 21071775 3059 True 5216 5216 97.421 1 3062 1 chr1A.!!$R1 3061
3 TraesCS3A01G532900 chr7A 722691158 722694216 3058 True 5203 5203 97.356 1 3062 1 chr7A.!!$R1 3061
4 TraesCS3A01G532900 chr6A 494427072 494430133 3061 False 5195 5195 97.290 1 3062 1 chr6A.!!$F1 3061
5 TraesCS3A01G532900 chr4A 592481273 592484336 3063 False 5180 5180 97.194 1 3062 1 chr4A.!!$F1 3061
6 TraesCS3A01G532900 chr4A 592760079 592763142 3063 False 5169 5169 97.129 1 3062 1 chr4A.!!$F2 3061
7 TraesCS3A01G532900 chr4A 593048157 593051220 3063 False 5164 5164 97.096 1 3062 1 chr4A.!!$F3 3061
8 TraesCS3A01G532900 chr2A 733072361 733075418 3057 False 5175 5175 97.191 1 3062 1 chr2A.!!$F1 3061

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
531 535 3.004944 TCGGACCAAAGGCAATAACAAAC 59.995 43.478 0.0 0.0 0.0 2.93 F
1040 1044 0.749649 GTTGGTTGGATGTTGTGCCA 59.250 50.000 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1473 1.734465 CGTCCAATCAGCTCAAACTCC 59.266 52.381 0.0 0.0 0.00 3.85 R
2094 2100 2.422231 GGTGTGTGCAACTGGGCAA 61.422 57.895 0.0 0.0 46.93 4.52 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
70 71 5.694995 TCACCTGATGAAAAGGAGTTTCTT 58.305 37.500 0.00 0.00 45.14 2.52
149 150 7.808279 TGAAGAATTAAGTTTCCCTCTAGGA 57.192 36.000 0.00 0.00 45.68 2.94
312 313 6.264292 ACACAATGTCCTGTATGCAAAAACTA 59.736 34.615 0.00 0.00 0.00 2.24
531 535 3.004944 TCGGACCAAAGGCAATAACAAAC 59.995 43.478 0.00 0.00 0.00 2.93
771 775 6.939730 ACATGACCAACTTGTACAATATGTCA 59.060 34.615 21.94 21.94 35.57 3.58
1030 1034 2.944129 CTCAGGAAAAGGTTGGTTGGA 58.056 47.619 0.00 0.00 0.00 3.53
1033 1037 2.965147 CAGGAAAAGGTTGGTTGGATGT 59.035 45.455 0.00 0.00 0.00 3.06
1040 1044 0.749649 GTTGGTTGGATGTTGTGCCA 59.250 50.000 0.00 0.00 0.00 4.92
1128 1134 3.052944 AGCAGAATTGGGCTGGGTTAATA 60.053 43.478 0.00 0.00 39.30 0.98
1247 1253 1.816835 CCTCCAGTCTACACAGCGTAA 59.183 52.381 0.00 0.00 0.00 3.18
1467 1473 6.760291 AGACCTTTACCACAAGTTTAGAGAG 58.240 40.000 0.00 0.00 0.00 3.20
1659 1665 1.951209 TCCTCTGTTGCCACATCCTA 58.049 50.000 0.00 0.00 30.39 2.94
1776 1782 4.819630 GGTTATGAGCAACCGGATGAAATA 59.180 41.667 17.00 6.61 38.74 1.40
2007 2013 2.366167 CCTCCTCCACCTCCAGGG 60.366 72.222 0.00 0.00 40.27 4.45
2077 2083 7.453752 TCCTGATCTAACTAGGTGTGTAACTTT 59.546 37.037 0.00 0.00 38.04 2.66
2094 2100 7.711846 TGTAACTTTAGTTGCACACATCATTT 58.288 30.769 8.97 0.00 43.77 2.32
2259 2265 0.120377 TCCCCCTCCTGGTTGTACAT 59.880 55.000 0.00 0.00 0.00 2.29
2302 2308 2.045926 GCGTGCTCCTCCCAATGT 60.046 61.111 0.00 0.00 0.00 2.71
2318 2324 1.915078 ATGTCCCTACAGGCAGCACC 61.915 60.000 0.00 0.00 39.49 5.01
2364 2371 2.006415 CTGCCCCCAACTCCCCATA 61.006 63.158 0.00 0.00 0.00 2.74
2709 2718 2.224621 ACAGAACATGCTGCCTAGTTGT 60.225 45.455 0.00 0.00 39.51 3.32
2714 2723 0.250858 ATGCTGCCTAGTTGTGTGCA 60.251 50.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 4.503910 AGTTGCAGTTATACAAGATGCGA 58.496 39.130 0.00 0.00 39.74 5.10
149 150 4.997395 CCATAACAGTTGCACACTAGACTT 59.003 41.667 0.00 0.00 32.76 3.01
312 313 6.348132 GCTGCACCTTTTTAAAAACACTTTGT 60.348 34.615 9.31 0.00 0.00 2.83
531 535 5.535333 TCTCTACGGAAACTTGTACAAAGG 58.465 41.667 10.03 1.39 0.00 3.11
708 712 1.153628 GCAATCGTGGTACGCCTCT 60.154 57.895 0.00 0.00 42.21 3.69
771 775 0.468226 TTCCTATGAAGGGCGCGAAT 59.532 50.000 12.10 0.00 43.84 3.34
1030 1034 1.355381 TCCTGGATTCTGGCACAACAT 59.645 47.619 0.00 0.00 38.70 2.71
1033 1037 1.003580 GAGTCCTGGATTCTGGCACAA 59.996 52.381 11.60 0.00 38.70 3.33
1040 1044 4.262891 TCATCAGAGAGTCCTGGATTCT 57.737 45.455 20.30 20.30 34.99 2.40
1128 1134 6.051717 GTGTGTCATAGCCTCATACTTCATT 58.948 40.000 0.00 0.00 0.00 2.57
1247 1253 2.046314 CGGCGTTGAACCCCTCAT 60.046 61.111 0.00 0.00 32.78 2.90
1467 1473 1.734465 CGTCCAATCAGCTCAAACTCC 59.266 52.381 0.00 0.00 0.00 3.85
1776 1782 3.328931 TCTGCTTCTTTGATTGAGGAGGT 59.671 43.478 0.00 0.00 0.00 3.85
1945 1951 4.988598 CCCCGTTGCAGCAGTCGT 62.989 66.667 16.86 0.00 0.00 4.34
2077 2083 3.305950 GGGCAAAATGATGTGTGCAACTA 60.306 43.478 0.00 0.00 38.78 2.24
2094 2100 2.422231 GGTGTGTGCAACTGGGCAA 61.422 57.895 0.00 0.00 46.93 4.52
2302 2308 3.009115 GGGTGCTGCCTGTAGGGA 61.009 66.667 0.00 0.00 37.23 4.20
2364 2371 6.289064 CAACTGGAGTTACAGACCTAGTTTT 58.711 40.000 0.00 0.00 40.97 2.43
2642 2649 4.262506 GCAACTAAAGTCACTCACCCTAGT 60.263 45.833 0.00 0.00 0.00 2.57
2709 2718 2.942376 CCTCAAACTAACACAGTGCACA 59.058 45.455 21.04 0.00 37.63 4.57
2714 2723 4.757149 GCTTGATCCTCAAACTAACACAGT 59.243 41.667 0.00 0.00 35.73 3.55
2946 2955 2.690497 CAGTAGGACCATCACGATCACT 59.310 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.