Multiple sequence alignment - TraesCS2D01G415500

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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 TraesCS2D01G415500 chr2D 100.000 2354 0 0 1 2354 529178939 529176586 0.000000e+00 4348
1 TraesCS2D01G415500 chr2B 91.600 2000 65 41 1 1950 628806443 628804497 0.000000e+00 2667
2 TraesCS2D01G415500 chr2B 96.817 377 12 0 1978 2354 628804492 628804116 4.270000e-177 630
3 TraesCS2D01G415500 chr2A 88.156 2288 141 56 141 2354 674000792 674003023 0.000000e+00 2604
4 TraesCS2D01G415500 chr2A 97.500 80 2 0 1 80 674000689 674000768 1.130000e-28 137


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 TraesCS2D01G415500 chr2D 529176586 529178939 2353 True 4348.0 4348 100.0000 1 2354 1 chr2D.!!$R1 2353
1 TraesCS2D01G415500 chr2B 628804116 628806443 2327 True 1648.5 2667 94.2085 1 2354 2 chr2B.!!$R1 2353
2 TraesCS2D01G415500 chr2A 674000689 674003023 2334 False 1370.5 2604 92.8280 1 2354 2 chr2A.!!$F1 2353

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
737 768 0.457035 GTGGTCCTATTCGTACGCCA 59.543 55.0 11.24 7.44 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1926 3.181474 GCAGATAAGCGAAGGGTTAGACT 60.181 47.826 0.0 0.0 39.29 3.24 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
124 125 3.614806 CGCAGCTTCCTCTCCTCT 58.385 61.111 0.00 0.00 0.00 3.69
125 126 1.437160 CGCAGCTTCCTCTCCTCTC 59.563 63.158 0.00 0.00 0.00 3.20
126 127 1.822615 GCAGCTTCCTCTCCTCTCC 59.177 63.158 0.00 0.00 0.00 3.71
503 522 3.011595 TGGTCCATCAATCTTTCCATGGT 59.988 43.478 12.58 0.00 37.62 3.55
737 768 0.457035 GTGGTCCTATTCGTACGCCA 59.543 55.000 11.24 7.44 0.00 5.69
797 845 3.749064 TCGGTGACTCAGAGCGCC 61.749 66.667 2.29 12.16 34.37 6.53
1294 1369 3.068691 CCTTCCGCCGTCTCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
1526 1627 1.877443 GAGGCTTCTAGCTAGACTCCG 59.123 57.143 23.17 12.45 41.13 4.63
1640 1742 9.571810 CTATGATGAGATGCTACTGAATTCTAC 57.428 37.037 7.05 0.00 0.00 2.59
1761 1863 5.272283 TCCTCGTGTTAGTTGAGAACTTT 57.728 39.130 0.00 0.00 42.81 2.66
1818 1926 3.029483 TGATATGCATGGCCCAAAGAA 57.971 42.857 10.16 0.00 0.00 2.52
1898 2012 2.811410 TGGGCCTCGATAACCGTATAT 58.189 47.619 4.53 0.00 39.75 0.86
1943 2061 2.170397 ACGATACCCATCACAGAATGCA 59.830 45.455 0.00 0.00 42.53 3.96
1950 2068 5.555017 ACCCATCACAGAATGCATATCTAC 58.445 41.667 0.00 0.00 42.53 2.59
2074 2193 0.174389 CCGTGCATGTAGCTCAGTCT 59.826 55.000 4.96 0.00 45.94 3.24
2098 2230 5.317808 AGTCTAGCTAGTCTCAACAACTCA 58.682 41.667 20.10 0.00 0.00 3.41
2213 2345 0.251916 TGCTTTCTGATGGTACGGGG 59.748 55.000 0.00 0.00 0.00 5.73
2262 2396 5.612725 AATCAAAAGAAAAAGGACCAGCA 57.387 34.783 0.00 0.00 0.00 4.41
2267 2401 4.861102 AAGAAAAAGGACCAGCAATCAG 57.139 40.909 0.00 0.00 0.00 2.90
2339 2475 4.371624 TCCAGGAAGAAAAGATCAGCAA 57.628 40.909 0.00 0.00 0.00 3.91
2342 2478 4.082895 CCAGGAAGAAAAGATCAGCAAGTG 60.083 45.833 0.00 0.00 0.00 3.16
2349 2485 5.645497 AGAAAAGATCAGCAAGTGTATGGTC 59.355 40.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 4.140599 AGGAGAGGAAGCTGCGCG 62.141 66.667 0.00 0.00 0.00 6.86
106 107 2.202864 GAGGAGAGGAAGCTGCGC 60.203 66.667 0.00 0.00 0.00 6.09
107 108 1.437160 GAGAGGAGAGGAAGCTGCG 59.563 63.158 0.00 0.00 0.00 5.18
117 118 4.816984 GTCGCCGGGGAGAGGAGA 62.817 72.222 23.26 0.00 35.23 3.71
168 186 4.742201 CACTGCTCACCCCGTCCG 62.742 72.222 0.00 0.00 0.00 4.79
169 187 4.394712 CCACTGCTCACCCCGTCC 62.395 72.222 0.00 0.00 0.00 4.79
170 188 3.626924 ACCACTGCTCACCCCGTC 61.627 66.667 0.00 0.00 0.00 4.79
171 189 3.941188 CACCACTGCTCACCCCGT 61.941 66.667 0.00 0.00 0.00 5.28
464 482 2.078665 CATGGGTAGGGTGAGGGGG 61.079 68.421 0.00 0.00 0.00 5.40
465 483 2.078665 CCATGGGTAGGGTGAGGGG 61.079 68.421 2.85 0.00 0.00 4.79
466 484 1.307866 ACCATGGGTAGGGTGAGGG 60.308 63.158 18.09 0.00 40.01 4.30
470 488 0.474184 GATGGACCATGGGTAGGGTG 59.526 60.000 18.09 0.00 41.95 4.61
471 489 0.045623 TGATGGACCATGGGTAGGGT 59.954 55.000 18.09 0.00 45.19 4.34
475 494 4.386312 GGAAAGATTGATGGACCATGGGTA 60.386 45.833 18.09 1.58 35.25 3.69
503 522 1.066430 GTGTCAGCCGGATTAACTCCA 60.066 52.381 5.05 0.00 45.24 3.86
522 541 1.263356 TTCCCTCTTCGTGAATCGGT 58.737 50.000 0.00 0.00 40.32 4.69
663 682 2.126307 CTCGAGCTGTGTGGGACG 60.126 66.667 0.00 0.00 0.00 4.79
1526 1627 3.463944 TGAAGAAGAACGAGTCCCAAAC 58.536 45.455 0.00 0.00 0.00 2.93
1640 1742 4.619760 TGAAGATTTGCACGTACTAGTTCG 59.380 41.667 18.88 18.88 0.00 3.95
1761 1863 8.781196 GTCTGATCTAAGTATGTATCGGTGTAA 58.219 37.037 0.00 0.00 0.00 2.41
1818 1926 3.181474 GCAGATAAGCGAAGGGTTAGACT 60.181 47.826 0.00 0.00 39.29 3.24
1943 2061 8.106247 TCCTTTTCTTTTGTTTGCGTAGATAT 57.894 30.769 0.00 0.00 0.00 1.63
1950 2068 5.523013 TGTTTCCTTTTCTTTTGTTTGCG 57.477 34.783 0.00 0.00 0.00 4.85
2074 2193 6.372103 GTGAGTTGTTGAGACTAGCTAGACTA 59.628 42.308 27.45 9.51 0.00 2.59
2237 2369 7.560368 TGCTGGTCCTTTTTCTTTTGATTAAA 58.440 30.769 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.