Multiple sequence alignment - TraesCS5A01G421000

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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 TraesCS5A01G421000 chr5A 100.000 2216 0 0 1 2216 607274215 607272000 0 4093
1 TraesCS5A01G421000 chr1D 97.296 2219 55 5 1 2216 254398294 254400510 0 3760
2 TraesCS5A01G421000 chr5D 97.250 2218 56 5 1 2216 503278411 503280625 0 3753
3 TraesCS5A01G421000 chr5D 97.206 2219 56 6 1 2216 6188755 6186540 0 3749
4 TraesCS5A01G421000 chr5D 96.407 2199 71 8 1 2196 432403682 432405875 0 3616
5 TraesCS5A01G421000 chr5D 97.946 1266 23 3 1 1265 503218033 503216770 0 2191
6 TraesCS5A01G421000 chr3D 97.250 2218 55 6 1 2216 589279727 589281940 0 3753
7 TraesCS5A01G421000 chr1A 96.964 2174 53 6 1 2171 554512063 554509900 0 3637
8 TraesCS5A01G421000 chr4A 95.502 2223 90 7 3 2216 309514944 309512723 0 3542
9 TraesCS5A01G421000 chr4A 95.482 2169 86 11 54 2216 310738341 310736179 0 3452
10 TraesCS5A01G421000 chr4B 95.002 2221 89 10 1 2216 308696285 308694082 0 3467
11 TraesCS5A01G421000 chr6D 96.417 1870 58 8 353 2216 45519037 45517171 0 3073


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 TraesCS5A01G421000 chr5A 607272000 607274215 2215 True 4093 4093 100.000 1 2216 1 chr5A.!!$R1 2215
1 TraesCS5A01G421000 chr1D 254398294 254400510 2216 False 3760 3760 97.296 1 2216 1 chr1D.!!$F1 2215
2 TraesCS5A01G421000 chr5D 503278411 503280625 2214 False 3753 3753 97.250 1 2216 1 chr5D.!!$F2 2215
3 TraesCS5A01G421000 chr5D 6186540 6188755 2215 True 3749 3749 97.206 1 2216 1 chr5D.!!$R1 2215
4 TraesCS5A01G421000 chr5D 432403682 432405875 2193 False 3616 3616 96.407 1 2196 1 chr5D.!!$F1 2195
5 TraesCS5A01G421000 chr5D 503216770 503218033 1263 True 2191 2191 97.946 1 1265 1 chr5D.!!$R2 1264
6 TraesCS5A01G421000 chr3D 589279727 589281940 2213 False 3753 3753 97.250 1 2216 1 chr3D.!!$F1 2215
7 TraesCS5A01G421000 chr1A 554509900 554512063 2163 True 3637 3637 96.964 1 2171 1 chr1A.!!$R1 2170
8 TraesCS5A01G421000 chr4A 309512723 309514944 2221 True 3542 3542 95.502 3 2216 1 chr4A.!!$R1 2213
9 TraesCS5A01G421000 chr4A 310736179 310738341 2162 True 3452 3452 95.482 54 2216 1 chr4A.!!$R2 2162
10 TraesCS5A01G421000 chr4B 308694082 308696285 2203 True 3467 3467 95.002 1 2216 1 chr4B.!!$R1 2215
11 TraesCS5A01G421000 chr6D 45517171 45519037 1866 True 3073 3073 96.417 353 2216 1 chr6D.!!$R1 1863

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
441 443 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1594 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.0 20.48 20.48 41.62 3.58 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
25 26 4.949856 AGAACATAAGCCAAATGACGGAAT 59.050 37.500 0.00 0.00 0.00 3.01
153 154 5.630121 AGATCCATCTGTCTAGAGATCGTT 58.370 41.667 10.21 0.00 38.60 3.85
441 443 1.544246 GACAAGTGGGTAATGTTGGGC 59.456 52.381 0.00 0.00 0.00 5.36
560 562 2.282180 GGCGGTGAAGGGAAAGCA 60.282 61.111 0.00 0.00 0.00 3.91
593 598 1.959710 AAAAACCCACAACCCCTTGT 58.040 45.000 0.00 0.00 41.61 3.16
634 639 7.837187 TGGAAGAAGAACTAGGAAAAGGAAAAA 59.163 33.333 0.00 0.00 0.00 1.94
880 889 3.877559 TCTAACCTCCGTACTTCGATCA 58.122 45.455 0.00 0.00 42.86 2.92
889 898 6.387041 TCCGTACTTCGATCAAGATATTGT 57.613 37.500 10.61 0.00 42.86 2.71
1036 1049 5.479124 AGAAACAATAGTAACGTGGTCCT 57.521 39.130 0.00 0.00 0.00 3.85
1104 1117 7.752239 GCGATTCATAATGGAAAGGAACATATG 59.248 37.037 0.00 0.00 0.00 1.78
1611 1634 5.048434 GCAGCCAAGAAGAAGTGTAAAGAAT 60.048 40.000 0.00 0.00 0.00 2.40
1672 1695 3.133362 CCAAAATAACCATGAGCAGCCAT 59.867 43.478 0.00 0.00 0.00 4.40
1735 1758 6.207213 CCTCATTAGCAGATTCATTTTCAGC 58.793 40.000 0.00 0.00 0.00 4.26
1795 1818 3.455910 TGCATAGCACTGAATAGGGAACT 59.544 43.478 0.00 0.00 37.94 3.01
1804 1827 4.163458 ACTGAATAGGGAACTGCCGAATAA 59.837 41.667 0.00 0.00 43.88 1.40
1839 1863 5.771666 CCTAACATGTGGAAGGATGCATAAT 59.228 40.000 14.22 0.00 0.00 1.28
1848 1872 6.262944 GTGGAAGGATGCATAATGATGTTGTA 59.737 38.462 0.00 0.00 35.30 2.41
1921 1945 3.696051 GCATACCATCAGAAAAGCTTCCA 59.304 43.478 0.00 0.00 31.28 3.53
1924 1948 3.094572 ACCATCAGAAAAGCTTCCATGG 58.905 45.455 4.97 4.97 42.90 3.66
1997 2022 6.154877 TGAATATGCAACAACAATCCAAGGAT 59.845 34.615 0.00 0.00 36.23 3.24
2010 2035 1.212688 CCAAGGATGCATACCCAGACA 59.787 52.381 4.93 0.00 0.00 3.41
2011 2036 2.357050 CCAAGGATGCATACCCAGACAA 60.357 50.000 4.93 0.00 0.00 3.18
2178 2205 4.021894 CGCAGAAGTAGGGATAATAGCACT 60.022 45.833 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.556911 AGGTCTCTGCATTCCGTCATT 59.443 47.619 0.00 0.00 0.00 2.57
25 26 3.953542 TCTACATCCTAGGTCTCTGCA 57.046 47.619 9.08 0.00 0.00 4.41
318 320 5.491070 TGCAATGAGTTTCACTATAGCACT 58.509 37.500 0.00 0.00 0.00 4.40
328 330 3.960102 ACCCTCTTTTGCAATGAGTTTCA 59.040 39.130 21.02 0.00 32.43 2.69
593 598 0.326595 TTCCAAGCGCAGGATAACCA 59.673 50.000 20.31 4.53 38.94 3.67
862 871 3.087031 TCTTGATCGAAGTACGGAGGTT 58.913 45.455 0.00 0.00 42.82 3.50
880 889 8.256356 AGAGTGGCTTCTATGTACAATATCTT 57.744 34.615 0.00 0.00 0.00 2.40
889 898 8.380099 TCCTTTTTAAAGAGTGGCTTCTATGTA 58.620 33.333 5.15 0.00 38.28 2.29
1036 1049 1.699634 GGGTAGAATGCTAGATGCCCA 59.300 52.381 0.00 0.00 42.00 5.36
1104 1117 9.297037 ACCATAGGATTTGTTATGTAAATAGGC 57.703 33.333 0.00 0.00 0.00 3.93
1359 1375 7.828717 TGCTGTTGAAGTTCCATCTATTAATGA 59.171 33.333 0.00 0.00 0.00 2.57
1572 1594 1.092345 GCTGCTTGGCCTGTAGTAGC 61.092 60.000 20.48 20.48 41.62 3.58
1611 1634 7.119699 CCAATATGCTAGTTTCAACAACTCTCA 59.880 37.037 0.00 0.00 0.00 3.27
1701 1724 7.283127 TGAATCTGCTAATGAGGGTTACAAATC 59.717 37.037 0.00 0.00 0.00 2.17
1735 1758 6.745474 AACCTCTAGTTTGATCAGGGAAACTG 60.745 42.308 17.11 9.54 41.43 3.16
1795 1818 2.352388 GTGTAGCTGGTTTATTCGGCA 58.648 47.619 0.00 0.00 38.87 5.69
1804 1827 3.559171 CCACATGTTAGGTGTAGCTGGTT 60.559 47.826 0.00 0.00 34.46 3.67
1839 1863 2.256306 TCCAGGCAGAGTACAACATCA 58.744 47.619 0.00 0.00 0.00 3.07
1848 1872 4.785346 ATGATTGTATTCCAGGCAGAGT 57.215 40.909 0.00 0.00 0.00 3.24
1921 1945 5.402054 TCTTGATTTACCCTATTGGCCAT 57.598 39.130 6.09 0.00 37.83 4.40
1924 1948 6.930731 TGTTTTCTTGATTTACCCTATTGGC 58.069 36.000 0.00 0.00 37.83 4.52
1997 2022 5.381757 ACTTAGTTTTTGTCTGGGTATGCA 58.618 37.500 0.00 0.00 0.00 3.96
2010 2035 4.573607 GTCGTGAGTGGGAACTTAGTTTTT 59.426 41.667 0.00 0.00 0.00 1.94
2011 2036 4.124970 GTCGTGAGTGGGAACTTAGTTTT 58.875 43.478 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.