Multiple sequence alignment - TraesCS4D01G183900

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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 TraesCS4D01G183900 chr4D 100.000 2270 0 0 1 2270 321938121 321940390 0 4193
1 TraesCS4D01G183900 chr7D 96.658 2274 67 6 1 2270 572699832 572702100 0 3770
2 TraesCS4D01G183900 chr2D 96.524 2273 66 8 5 2270 460769300 460767034 0 3747
3 TraesCS4D01G183900 chr6D 96.438 2274 70 7 1 2270 323708555 323706289 0 3740
4 TraesCS4D01G183900 chr5D 96.438 2274 68 9 1 2270 11985458 11983194 0 3738
5 TraesCS4D01G183900 chr1D 96.264 2275 78 6 1 2270 27465527 27467799 0 3723
6 TraesCS4D01G183900 chr2A 96.128 2273 78 6 1 2270 766427739 766425474 0 3701
7 TraesCS4D01G183900 chrUn 96.635 2229 66 6 1 2225 108946062 108943839 0 3692
8 TraesCS4D01G183900 chr2B 95.736 2275 91 5 1 2270 691461222 691458949 0 3659
9 TraesCS4D01G183900 chr2B 95.777 2273 87 5 1 2270 383000643 382998377 0 3657


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 TraesCS4D01G183900 chr4D 321938121 321940390 2269 False 4193 4193 100.000 1 2270 1 chr4D.!!$F1 2269
1 TraesCS4D01G183900 chr7D 572699832 572702100 2268 False 3770 3770 96.658 1 2270 1 chr7D.!!$F1 2269
2 TraesCS4D01G183900 chr2D 460767034 460769300 2266 True 3747 3747 96.524 5 2270 1 chr2D.!!$R1 2265
3 TraesCS4D01G183900 chr6D 323706289 323708555 2266 True 3740 3740 96.438 1 2270 1 chr6D.!!$R1 2269
4 TraesCS4D01G183900 chr5D 11983194 11985458 2264 True 3738 3738 96.438 1 2270 1 chr5D.!!$R1 2269
5 TraesCS4D01G183900 chr1D 27465527 27467799 2272 False 3723 3723 96.264 1 2270 1 chr1D.!!$F1 2269
6 TraesCS4D01G183900 chr2A 766425474 766427739 2265 True 3701 3701 96.128 1 2270 1 chr2A.!!$R1 2269
7 TraesCS4D01G183900 chrUn 108943839 108946062 2223 True 3692 3692 96.635 1 2225 1 chrUn.!!$R1 2224
8 TraesCS4D01G183900 chr2B 691458949 691461222 2273 True 3659 3659 95.736 1 2270 1 chr2B.!!$R2 2269
9 TraesCS4D01G183900 chr2B 382998377 383000643 2266 True 3657 3657 95.777 1 2270 1 chr2B.!!$R1 2269

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
552 562 0.178301 GAGACCGAAGAATCCACCCC 59.822 60.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1761 0.395312 ACGTTTGGTCGGTCCTTCAT 59.605 50.0 0.0 0.0 37.07 2.57 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
75 78 3.088194 TCGAAGGTATAACCATGTCGC 57.912 47.619 10.29 0.00 41.95 5.19
76 79 2.427812 TCGAAGGTATAACCATGTCGCA 59.572 45.455 10.29 0.00 41.95 5.10
77 80 2.538449 CGAAGGTATAACCATGTCGCAC 59.462 50.000 0.00 0.00 41.95 5.34
78 81 3.527533 GAAGGTATAACCATGTCGCACA 58.472 45.455 0.00 0.00 41.95 4.57
81 84 4.523083 AGGTATAACCATGTCGCACAAAT 58.477 39.130 0.00 0.00 41.95 2.32
83 86 5.034152 GGTATAACCATGTCGCACAAATTG 58.966 41.667 0.00 0.00 38.42 2.32
333 343 6.800408 GGGTTGATCTTAGCGAGTTTAAAAAC 59.200 38.462 0.00 0.00 39.17 2.43
552 562 0.178301 GAGACCGAAGAATCCACCCC 59.822 60.000 0.00 0.00 0.00 4.95
874 884 5.428253 CGGAGGAACTGGATTCTGAAAATA 58.572 41.667 0.00 0.00 41.55 1.40
906 916 1.138464 GTGGAGGTACCGATTCCTTCC 59.862 57.143 17.22 12.37 42.61 3.46
917 927 0.250467 ATTCCTTCCGCATGGGATCG 60.250 55.000 12.02 0.00 46.62 3.69
926 936 1.339055 CGCATGGGATCGGGACATATT 60.339 52.381 3.11 0.00 0.00 1.28
1124 1138 5.449314 CCGTGAAATGTGTTGAAACAGGTTA 60.449 40.000 0.00 0.00 40.05 2.85
1365 1381 0.045623 TATGGGAAGGCTTGGAGGGA 59.954 55.000 3.46 0.00 0.00 4.20
1397 1413 2.950418 GCTATGGAGGAAAGGTTTGGGG 60.950 54.545 0.00 0.00 0.00 4.96
1546 1562 4.859798 CGAGTGTTCTTCTCTTTCGCTATT 59.140 41.667 0.00 0.00 0.00 1.73
1695 1711 0.615544 ATGGCATTTGTGGAGGGTGG 60.616 55.000 0.00 0.00 0.00 4.61
1877 1893 3.640407 AGAGCCGGTGGTGCATGT 61.640 61.111 1.90 0.00 0.00 3.21
2170 2186 7.015584 AGGGCAATAAAGAATTTTTCTGAGTGT 59.984 33.333 0.00 0.00 40.59 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.790962 CTCAGCAGCACCGGCCAT 62.791 66.667 0.00 0.0 42.56 4.40
14 16 1.458398 CTCCTCTCTTCGACTCAGCA 58.542 55.000 0.00 0.0 0.00 4.41
268 276 5.093849 ACATTACCAGTGCCGTAGTAAAT 57.906 39.130 0.00 0.0 0.00 1.40
874 884 0.252284 ACCTCCACTTCATCCTCGGT 60.252 55.000 0.00 0.0 0.00 4.69
906 916 0.250234 ATATGTCCCGATCCCATGCG 59.750 55.000 0.00 0.0 0.00 4.73
917 927 0.182775 AAGGCCGGTGAATATGTCCC 59.817 55.000 1.90 0.0 0.00 4.46
946 956 2.359981 CATGGAGTCTCATGGCCATT 57.640 50.000 17.92 0.0 39.01 3.16
1124 1138 2.671070 CGTGCACCTTCCCAGGAT 59.329 61.111 12.15 0.0 44.19 3.24
1397 1413 6.363626 ACATTATCATATGAGTCGAAGAACGC 59.636 38.462 11.78 0.0 39.69 4.84
1546 1562 1.922135 GCCGGAAAGCTTCGATGCAA 61.922 55.000 23.42 0.0 34.99 4.08
1745 1761 0.395312 ACGTTTGGTCGGTCCTTCAT 59.605 50.000 0.00 0.0 37.07 2.57
2170 2186 5.130705 TCACTGGAGGCTCTTTCTCTATA 57.869 43.478 15.23 0.0 0.00 1.31


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

AutoCloner maintained by Alex Coulton.