Multiple sequence alignment - TraesCS5A01G436900

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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 TraesCS5A01G436900 chr5A 100.000 2269 0 0 1 2269 619268298 619266030 0 4191
1 TraesCS5A01G436900 chr1A 97.888 2273 43 5 1 2269 554514178 554511907 0 3927
2 TraesCS5A01G436900 chr5D 97.844 2273 44 5 1 2269 503220148 503217877 0 3921
3 TraesCS5A01G436900 chr5D 97.668 2273 48 5 1 2269 503276296 503278567 0 3899
4 TraesCS5A01G436900 chr5D 97.580 2273 50 5 1 2269 6190870 6188599 0 3888
5 TraesCS5A01G436900 chr3B 97.800 2273 45 5 1 2269 201528954 201526683 0 3916
6 TraesCS5A01G436900 chr6D 97.756 2273 46 5 1 2269 168256856 168254585 0 3910
7 TraesCS5A01G436900 chrUn 97.667 2272 48 5 1 2268 346594564 346596834 0 3897
8 TraesCS5A01G436900 chr3D 97.624 2273 46 7 1 2269 589277615 589279883 0 3892
9 TraesCS5A01G436900 chr3A 97.447 2272 53 5 1 2269 672908079 672910348 0 3869


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 TraesCS5A01G436900 chr5A 619266030 619268298 2268 True 4191 4191 100.000 1 2269 1 chr5A.!!$R1 2268
1 TraesCS5A01G436900 chr1A 554511907 554514178 2271 True 3927 3927 97.888 1 2269 1 chr1A.!!$R1 2268
2 TraesCS5A01G436900 chr5D 503217877 503220148 2271 True 3921 3921 97.844 1 2269 1 chr5D.!!$R2 2268
3 TraesCS5A01G436900 chr5D 503276296 503278567 2271 False 3899 3899 97.668 1 2269 1 chr5D.!!$F1 2268
4 TraesCS5A01G436900 chr5D 6188599 6190870 2271 True 3888 3888 97.580 1 2269 1 chr5D.!!$R1 2268
5 TraesCS5A01G436900 chr3B 201526683 201528954 2271 True 3916 3916 97.800 1 2269 1 chr3B.!!$R1 2268
6 TraesCS5A01G436900 chr6D 168254585 168256856 2271 True 3910 3910 97.756 1 2269 1 chr6D.!!$R1 2268
7 TraesCS5A01G436900 chrUn 346594564 346596834 2270 False 3897 3897 97.667 1 2268 1 chrUn.!!$F1 2267
8 TraesCS5A01G436900 chr3D 589277615 589279883 2268 False 3892 3892 97.624 1 2269 1 chr3D.!!$F1 2268
9 TraesCS5A01G436900 chr3A 672908079 672910348 2269 False 3869 3869 97.447 1 2269 1 chr3A.!!$F1 2268

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
764 767 2.158623 CCCTGTTAAGCATCCATGGCTA 60.159 50.0 6.96 0.0 41.66 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2139 2.992847 TCCTAGGTCTCTGTGTTCCA 57.007 50.0 9.08 0.0 0.0 3.53 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
368 370 4.438744 CGAGGTTTGGGAATAAGTGATTGC 60.439 45.833 0.00 0.00 35.21 3.56
625 628 7.334090 TCAATCTCTCTTTCAATTCGAGGATT 58.666 34.615 0.00 0.00 31.22 3.01
649 652 7.718334 TCAGAGAGGTGTTTTCATAGTCATA 57.282 36.000 0.00 0.00 0.00 2.15
764 767 2.158623 CCCTGTTAAGCATCCATGGCTA 60.159 50.000 6.96 0.00 41.66 3.93
863 866 6.636454 TTCCATAAGTCTATTGGAACTGGT 57.364 37.500 10.84 0.00 34.16 4.00
884 887 5.070981 TGGTTCTCTATCCATGGAATCTCAC 59.929 44.000 20.67 11.21 0.00 3.51
1218 1222 3.828451 GGGCCATACAATGCATTACAGAT 59.172 43.478 12.53 0.33 0.00 2.90
1255 1259 5.932455 CCCTTCAACCGGGTTATTCTATTA 58.068 41.667 12.95 0.00 36.91 0.98
1327 1332 7.271868 GGCGAAACATTTATACAAAACACCTAC 59.728 37.037 0.00 0.00 0.00 3.18
1400 1405 5.820423 ACGAAATAATTTGATCCATGGACGA 59.180 36.000 18.99 8.35 0.00 4.20
1429 1434 6.459848 CGTTGTGGTAAAGGTTGTAATTCCAA 60.460 38.462 0.00 0.00 0.00 3.53
1472 1477 0.759436 GAGGGGGAGGTCATAAGCGA 60.759 60.000 0.00 0.00 0.00 4.93
1486 1491 6.142958 GGTCATAAGCGACTATACCGTAAAAC 59.857 42.308 0.00 0.00 36.12 2.43
1804 1811 4.901849 CCTCTATGGGATAGACCTCAACAA 59.098 45.833 0.00 0.00 36.98 2.83
2091 2098 9.448294 GAAGTATCGACGTAATTTCATAGAGTT 57.552 33.333 0.00 0.00 0.00 3.01
2112 2119 8.797438 AGAGTTATTCGATCTGAATGCTACATA 58.203 33.333 17.47 0.36 46.72 2.29
2132 2139 9.499479 CTACATAAAGAACATAAGCCAGATGAT 57.501 33.333 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 161 7.364144 GGGCTTCTTATTCCACAAGAATGAAAT 60.364 37.037 0.00 0.00 45.11 2.17
368 370 9.107177 GATGTATATTCCTTGCTCATTATCAGG 57.893 37.037 0.00 0.00 0.00 3.86
625 628 6.611613 ATGACTATGAAAACACCTCTCTGA 57.388 37.500 0.00 0.00 0.00 3.27
736 739 3.459227 TGGATGCTTAACAGGGATCATCA 59.541 43.478 0.00 0.00 34.04 3.07
764 767 1.967779 AGTTGGGCGCTTTAACCATTT 59.032 42.857 7.64 0.00 33.63 2.32
863 866 4.594920 GGGTGAGATTCCATGGATAGAGAA 59.405 45.833 17.06 0.00 0.00 2.87
884 887 6.127925 CCAATTCGTTATGTATGGATGATGGG 60.128 42.308 0.00 0.00 0.00 4.00
1218 1222 5.607477 GGTTGAAGGGTAATGATCATACGA 58.393 41.667 9.04 0.00 0.00 3.43
1327 1332 2.669569 CCTTGTGTGTGCTCGGGG 60.670 66.667 0.00 0.00 0.00 5.73
1350 1355 4.574674 TGGATTTCACTTGCCTGTCTAT 57.425 40.909 0.00 0.00 0.00 1.98
1429 1434 2.024414 GCCTTGCGGTAATGATTCCTT 58.976 47.619 0.00 0.00 0.00 3.36
1472 1477 8.437742 CGTCAAAAATCTGTTTTACGGTATAGT 58.562 33.333 0.00 0.00 36.42 2.12
1758 1765 6.070021 AGGTAGTCAAATTGGATCAGTGATCA 60.070 38.462 29.56 14.32 40.50 2.92
1804 1811 6.588719 TGCTGCCATTACTCAATAGTTTTT 57.411 33.333 0.00 0.00 37.15 1.94
1811 1818 3.689347 TCACTTGCTGCCATTACTCAAT 58.311 40.909 0.00 0.00 0.00 2.57
2032 2039 4.807783 GGGTAACGTAGGAGACATCCCTG 61.808 56.522 0.00 0.00 42.56 4.45
2091 2098 9.981114 TTCTTTATGTAGCATTCAGATCGAATA 57.019 29.630 10.91 0.00 42.70 1.75
2112 2119 5.759059 TCCATCATCTGGCTTATGTTCTTT 58.241 37.500 0.00 0.00 45.52 2.52
2132 2139 2.992847 TCCTAGGTCTCTGTGTTCCA 57.007 50.000 9.08 0.00 0.00 3.53
2138 2145 5.718801 TCTTCTACATCCTAGGTCTCTGT 57.281 43.478 9.08 10.77 0.00 3.41


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

AutoCloner maintained by Alex Coulton.