Multiple sequence alignment - TraesCS5A01G314100

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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 TraesCS5A01G314100 chr5A 100.000 2808 0 0 1 2808 524682984 524680177 0 5186
1 TraesCS5A01G314100 chr5A 96.656 2811 86 8 1 2808 33912289 33909484 0 4663
2 TraesCS5A01G314100 chr5A 95.348 2816 110 18 1 2808 169176807 169179609 0 4455
3 TraesCS5A01G314100 chr2A 96.946 2816 76 8 1 2808 733077697 733074884 0 4715
4 TraesCS5A01G314100 chr4A 96.732 2815 83 8 1 2808 37336002 37333190 0 4680
5 TraesCS5A01G314100 chr3A 96.478 2811 93 6 1 2808 711570929 711573736 0 4638


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 TraesCS5A01G314100 chr5A 524680177 524682984 2807 True 5186 5186 100.000 1 2808 1 chr5A.!!$R2 2807
1 TraesCS5A01G314100 chr5A 33909484 33912289 2805 True 4663 4663 96.656 1 2808 1 chr5A.!!$R1 2807
2 TraesCS5A01G314100 chr5A 169176807 169179609 2802 False 4455 4455 95.348 1 2808 1 chr5A.!!$F1 2807
3 TraesCS5A01G314100 chr2A 733074884 733077697 2813 True 4715 4715 96.946 1 2808 1 chr2A.!!$R1 2807
4 TraesCS5A01G314100 chr4A 37333190 37336002 2812 True 4680 4680 96.732 1 2808 1 chr4A.!!$R1 2807
5 TraesCS5A01G314100 chr3A 711570929 711573736 2807 False 4638 4638 96.478 1 2808 1 chr3A.!!$F1 2807

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
899 905 4.756642 CACATGACACATCTGTTAGTTGGT 59.243 41.667 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2117 2.430546 TTTTAGCAATGTTGGCACCG 57.569 45.0 0.0 0.0 0.0 4.94 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
102 104 4.991024 GGGTAATAAGGCCCGCAA 57.009 55.556 0.00 0.00 34.90 4.85
139 141 5.410924 TCCATTCATCGACTACAACAAGAG 58.589 41.667 0.00 0.00 0.00 2.85
287 289 8.579850 ACATATCTTTTTCAGTTGCATAGGAA 57.420 30.769 0.00 0.00 0.00 3.36
290 292 6.707440 TCTTTTTCAGTTGCATAGGAACAA 57.293 33.333 4.29 0.00 0.00 2.83
427 429 8.694394 GCTAACTTGTCTTTTTATTGCTTTCAG 58.306 33.333 0.00 0.00 0.00 3.02
899 905 4.756642 CACATGACACATCTGTTAGTTGGT 59.243 41.667 0.00 0.00 0.00 3.67
1099 1107 0.942884 GGACGGACGCTTCGAAGTTT 60.943 55.000 25.24 13.14 0.00 2.66
1116 1124 3.620488 AGTTTTTGACTCAAGCAGGACA 58.380 40.909 0.00 0.00 31.20 4.02
1443 1455 2.927477 GCGCATAAGTAGTTGCACACTA 59.073 45.455 0.30 0.00 38.80 2.74
1569 1583 4.194640 CAGTAGGACATAAGCAGTTGCAT 58.805 43.478 6.90 0.00 45.16 3.96
1750 1766 2.761786 AGCTGGCATATGATTGGGTT 57.238 45.000 6.97 0.00 0.00 4.11
1752 1768 4.393239 AGCTGGCATATGATTGGGTTAT 57.607 40.909 6.97 0.00 0.00 1.89
1756 1772 5.319453 CTGGCATATGATTGGGTTATCAGT 58.681 41.667 6.97 0.00 37.91 3.41
2095 2117 2.983229 AGATGCTGAATGTGTCCACTC 58.017 47.619 0.00 0.00 0.00 3.51
2099 2122 1.432514 CTGAATGTGTCCACTCGGTG 58.567 55.000 0.00 0.00 0.00 4.94
2162 2186 8.017418 TGTTCCAAAGTTACAAATGAGGAAAT 57.983 30.769 0.00 0.00 35.86 2.17
2190 2214 0.764369 AGGAGCCTGAGTGGACACAA 60.764 55.000 5.14 0.00 38.35 3.33
2225 2249 3.041211 TCTATAGATTGGCACTGGCTGT 58.959 45.455 0.00 0.00 40.87 4.40
2802 2828 3.399181 CTAGTTGGGCCTGGCGGA 61.399 66.667 13.40 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 1.118965 TGGTCCCGAAGAACTGCTCA 61.119 55.000 0.00 0.00 31.28 4.26
102 104 4.916041 TGAATGGAGACCTTTGAGATGT 57.084 40.909 0.00 0.00 0.00 3.06
139 141 3.149196 TCATTGGTGCTGAAAGTCTTCC 58.851 45.455 0.00 0.00 35.30 3.46
287 289 3.275617 TCTGTGCAACTAAGTGGTTGT 57.724 42.857 9.00 0.00 45.69 3.32
290 292 2.618709 GCTTTCTGTGCAACTAAGTGGT 59.381 45.455 0.00 0.00 38.04 4.16
325 327 3.818773 GTGCAACTAAAAGCCCTGTTCTA 59.181 43.478 0.00 0.00 0.00 2.10
387 389 2.180276 AGTTAGCTCGAAGGGTCACAT 58.820 47.619 0.00 0.00 0.00 3.21
427 429 8.627208 TGATTATCTCAGGGCTGATTATTTTC 57.373 34.615 0.00 0.00 39.13 2.29
740 746 4.824479 TCACATTGTGGATCTCTTGCTA 57.176 40.909 16.46 0.00 33.87 3.49
747 753 7.830697 TGTTTATCTCATTCACATTGTGGATCT 59.169 33.333 16.46 1.52 27.74 2.75
857 863 0.890542 GCAACTGGACATGCTGTGGA 60.891 55.000 0.00 0.00 39.46 4.02
899 905 6.952773 AAAACAGGTTGCAACAAGTATCTA 57.047 33.333 29.55 0.00 0.00 1.98
1099 1107 2.564771 CAGTGTCCTGCTTGAGTCAAA 58.435 47.619 7.06 0.00 0.00 2.69
1116 1124 2.936919 TCAGCTCAATGTTGTCCAGT 57.063 45.000 0.00 0.00 0.00 4.00
1443 1455 0.813610 TGTGCAACTGCTTACGTGCT 60.814 50.000 0.00 0.00 42.66 4.40
1569 1583 8.644374 AAACCAAATAAAGGTAATGCACTCTA 57.356 30.769 0.00 0.00 38.76 2.43
2095 2117 2.430546 TTTTAGCAATGTTGGCACCG 57.569 45.000 0.00 0.00 0.00 4.94
2162 2186 2.762887 CACTCAGGCTCCTGTGATTCTA 59.237 50.000 20.88 0.00 43.96 2.10
2207 2231 4.443978 AATACAGCCAGTGCCAATCTAT 57.556 40.909 0.00 0.00 38.69 1.98
2225 2249 7.923878 GCTACACCCAAAGAAGAAAAACAAATA 59.076 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.