Multiple sequence alignment - TraesCS3D01G285200

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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 TraesCS3D01G285200 chr3D 100.000 2234 0 0 1 2234 394753129 394750896 0.000000e+00 4126
1 TraesCS3D01G285200 chr3B 98.254 2234 35 1 1 2234 513994773 513992544 0.000000e+00 3906
2 TraesCS3D01G285200 chr3A 96.288 2236 75 3 1 2234 514109643 514107414 0.000000e+00 3663
3 TraesCS3D01G285200 chr7A 85.000 220 31 1 2010 2229 216340846 216341063 2.890000e-54 222


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 TraesCS3D01G285200 chr3D 394750896 394753129 2233 True 4126 4126 100.000 1 2234 1 chr3D.!!$R1 2233
1 TraesCS3D01G285200 chr3B 513992544 513994773 2229 True 3906 3906 98.254 1 2234 1 chr3B.!!$R1 2233
2 TraesCS3D01G285200 chr3A 514107414 514109643 2229 True 3663 3663 96.288 1 2234 1 chr3A.!!$R1 2233

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
897 898 2.138542 ACAGCAATGGATACCAGGGAT 58.861 47.619 0.0 0.0 36.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2208 0.392998 GTGTGCCCCAGATCAACGAT 60.393 55.0 0.0 0.0 0.0 3.73 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
348 349 2.236146 TGATAAGAATGTGAGGCACGGT 59.764 45.455 0.00 0.00 37.14 4.83
681 682 2.224606 CAGGCTGTTTGAAGAAGCAGA 58.775 47.619 6.28 0.00 41.64 4.26
804 805 5.249393 TGCCTCAAAGGTTAAGATCTTCTCT 59.751 40.000 12.24 5.33 37.80 3.10
897 898 2.138542 ACAGCAATGGATACCAGGGAT 58.861 47.619 0.00 0.00 36.75 3.85
1212 1213 2.669849 CTTGCTGCTGAGGAGGCT 59.330 61.111 2.44 0.00 0.00 4.58
1312 1313 4.190001 GTTGATCAGCTCATCATGTGTCT 58.810 43.478 0.00 0.00 32.69 3.41
1368 1369 4.621068 GATTTGATCGGCATTCTTCACA 57.379 40.909 0.00 0.00 0.00 3.58
1371 1372 2.349590 TGATCGGCATTCTTCACAGTG 58.650 47.619 0.00 0.00 0.00 3.66
1403 1404 2.025155 AGCTACGACCTGGTCAGTATG 58.975 52.381 25.42 18.85 32.09 2.39
1515 1518 2.586425 ACCAGTGTTGTTCTTCCCATG 58.414 47.619 0.00 0.00 0.00 3.66
1584 1587 1.600356 TGCGCTTGTGGCTTCATCA 60.600 52.632 9.73 0.00 39.13 3.07
1729 1732 2.434702 AGGGAGACAGGTTATTAAGGCG 59.565 50.000 0.00 0.00 0.00 5.52
1740 1747 4.497507 GGTTATTAAGGCGCCTGAATGTTC 60.498 45.833 39.03 28.44 30.26 3.18
1741 1748 2.489938 TTAAGGCGCCTGAATGTTCT 57.510 45.000 33.60 14.67 0.00 3.01
1742 1749 1.737838 TAAGGCGCCTGAATGTTCTG 58.262 50.000 33.60 0.00 0.00 3.02
1743 1750 0.250901 AAGGCGCCTGAATGTTCTGT 60.251 50.000 33.60 6.99 0.00 3.41
2126 2133 3.244249 GGACTGTCATATTAGGCCTGGAC 60.244 52.174 17.99 14.88 39.13 4.02
2139 2146 0.953960 CCTGGACGGGTACACAAAGC 60.954 60.000 0.00 0.00 0.00 3.51
2150 2157 1.086696 ACACAAAGCGGATGGATTCG 58.913 50.000 0.00 0.00 0.00 3.34
2156 2163 0.824109 AGCGGATGGATTCGAACTCA 59.176 50.000 0.00 1.93 0.00 3.41
2166 2173 4.406972 TGGATTCGAACTCAATCTCTCCAT 59.593 41.667 0.00 0.00 31.82 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
348 349 0.618458 GGATAACCACAGGGCTGTCA 59.382 55.000 0.00 0.00 42.83 3.58
441 442 4.701651 GTGACCTCATTTGGATGTTCATCA 59.298 41.667 13.64 0.00 34.77 3.07
804 805 1.674441 CGTATCCGAGTCCAAGTGCTA 59.326 52.381 0.00 0.00 35.63 3.49
897 898 6.238566 GCTATGCATTGATCTTTTGCTCACTA 60.239 38.462 12.54 0.00 37.28 2.74
1143 1144 1.003355 AAGTCCCATGCCACTCACG 60.003 57.895 0.00 0.00 0.00 4.35
1329 1330 4.603946 GCGGTAGTCGATGGGGGC 62.604 72.222 0.00 0.00 42.43 5.80
1403 1404 9.765795 ACTGTAGCACTCATTATTTATACCTTC 57.234 33.333 0.00 0.00 0.00 3.46
1515 1518 2.798499 GCATGCACTTGATCAAGCATCC 60.798 50.000 30.95 18.90 45.14 3.51
1584 1587 4.923415 AGAACCCTGCTATACTTTTGCTT 58.077 39.130 0.00 0.00 0.00 3.91
1729 1732 5.415701 TCATAAGGAAACAGAACATTCAGGC 59.584 40.000 0.00 0.00 0.00 4.85
1740 1747 8.511604 AAGGTATGTTCATCATAAGGAAACAG 57.488 34.615 0.00 0.00 40.21 3.16
1741 1748 9.613428 CTAAGGTATGTTCATCATAAGGAAACA 57.387 33.333 0.00 0.00 40.21 2.83
1742 1749 9.614792 ACTAAGGTATGTTCATCATAAGGAAAC 57.385 33.333 0.00 0.00 40.21 2.78
1743 1750 9.832445 GACTAAGGTATGTTCATCATAAGGAAA 57.168 33.333 0.00 0.00 40.21 3.13
2108 2115 1.691976 CCGTCCAGGCCTAATATGACA 59.308 52.381 3.98 0.00 0.00 3.58
2126 2133 1.366111 CCATCCGCTTTGTGTACCCG 61.366 60.000 0.00 0.00 0.00 5.28
2139 2146 3.722147 AGATTGAGTTCGAATCCATCCG 58.278 45.455 0.00 0.00 31.22 4.18
2150 2157 4.751767 AGTCCATGGAGAGATTGAGTTC 57.248 45.455 16.81 0.00 0.00 3.01
2156 2163 4.703379 GGATCAAGTCCATGGAGAGATT 57.297 45.455 16.81 5.12 46.96 2.40
2201 2208 0.392998 GTGTGCCCCAGATCAACGAT 60.393 55.000 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.