Multiple sequence alignment - TraesCS2B01G283800

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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 TraesCS2B01G283800 chr2B 100.000 2646 0 0 1 2646 391167714 391165069 0 4887
1 TraesCS2B01G283800 chr2B 97.921 2646 52 2 1 2646 112847905 112845263 0 4578
2 TraesCS2B01G283800 chr1A 98.488 2646 37 2 1 2646 498684525 498687167 0 4662
3 TraesCS2B01G283800 chrUn 98.487 2643 40 0 1 2643 186201715 186204357 0 4660
4 TraesCS2B01G283800 chr7B 98.413 2646 42 0 1 2646 742996151 742993506 0 4654
5 TraesCS2B01G283800 chr7B 98.375 2646 42 1 1 2646 716872076 716874720 0 4647
6 TraesCS2B01G283800 chr5A 98.035 2646 52 0 1 2646 492862433 492859788 0 4599
7 TraesCS2B01G283800 chr4B 97.808 2646 56 2 1 2646 209306366 209303723 0 4564
8 TraesCS2B01G283800 chr4A 97.771 2647 57 2 1 2646 67603672 67601027 0 4560
9 TraesCS2B01G283800 chr3A 97.732 2646 60 0 1 2646 725803458 725800813 0 4554


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 TraesCS2B01G283800 chr2B 391165069 391167714 2645 True 4887 4887 100.000 1 2646 1 chr2B.!!$R2 2645
1 TraesCS2B01G283800 chr2B 112845263 112847905 2642 True 4578 4578 97.921 1 2646 1 chr2B.!!$R1 2645
2 TraesCS2B01G283800 chr1A 498684525 498687167 2642 False 4662 4662 98.488 1 2646 1 chr1A.!!$F1 2645
3 TraesCS2B01G283800 chrUn 186201715 186204357 2642 False 4660 4660 98.487 1 2643 1 chrUn.!!$F1 2642
4 TraesCS2B01G283800 chr7B 742993506 742996151 2645 True 4654 4654 98.413 1 2646 1 chr7B.!!$R1 2645
5 TraesCS2B01G283800 chr7B 716872076 716874720 2644 False 4647 4647 98.375 1 2646 1 chr7B.!!$F1 2645
6 TraesCS2B01G283800 chr5A 492859788 492862433 2645 True 4599 4599 98.035 1 2646 1 chr5A.!!$R1 2645
7 TraesCS2B01G283800 chr4B 209303723 209306366 2643 True 4564 4564 97.808 1 2646 1 chr4B.!!$R1 2645
8 TraesCS2B01G283800 chr4A 67601027 67603672 2645 True 4560 4560 97.771 1 2646 1 chr4A.!!$R1 2645
9 TraesCS2B01G283800 chr3A 725800813 725803458 2645 True 4554 4554 97.732 1 2646 1 chr3A.!!$R1 2645

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
116 117 0.179089 AGCAGCAAGGCTATGTCTCG 60.179 55.0 0.0 0.0 43.7 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1696 0.109342 GCATGTCCCGATGATTCCCT 59.891 55.0 0.0 0.0 0.0 4.2 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
67 68 4.515191 GCACTACATGAACAAGAAGGACAA 59.485 41.667 0.00 0.00 0.00 3.18
95 96 1.271840 ATTAGAAGTCGGCTGCCCCA 61.272 55.000 14.12 0.00 0.00 4.96
116 117 0.179089 AGCAGCAAGGCTATGTCTCG 60.179 55.000 0.00 0.00 43.70 4.04
174 176 7.285629 TGTCCTAATAGAAGTTCATGTCGATCT 59.714 37.037 5.50 0.00 0.00 2.75
203 205 4.080356 AGCCAGTGCCATCATTAGAAAGTA 60.080 41.667 0.00 0.00 38.69 2.24
526 529 1.639298 GAGCGCCGCAAGACAAGATT 61.639 55.000 13.36 0.00 43.02 2.40
1211 1215 8.732531 CGATTGTAAACTATTCCCACCTAAAAA 58.267 33.333 0.00 0.00 0.00 1.94
1355 1360 5.892348 ACCCAAGAAAGACCATATCAACTT 58.108 37.500 0.00 0.00 0.00 2.66
1444 1449 2.214376 TGGCCAAACGAATCCAAGAT 57.786 45.000 0.61 0.00 0.00 2.40
1482 1487 6.772716 AGCCAGAAAAGAATAACAAGAGAACA 59.227 34.615 0.00 0.00 0.00 3.18
1507 1512 3.713764 AGCAACTCCATATTCTACTGGCT 59.286 43.478 0.00 0.00 32.30 4.75
1532 1537 4.830046 GCCTCTCTGATCTACTATCCAACA 59.170 45.833 0.00 0.00 0.00 3.33
1577 1582 0.983467 TAGGCTCACATTCTGGCACA 59.017 50.000 0.00 0.00 0.00 4.57
1587 1592 0.602638 TTCTGGCACATCGTTCGCTT 60.603 50.000 0.00 0.00 38.20 4.68
1691 1696 0.030705 AGCTGGCCTTCTCCTATCCA 60.031 55.000 3.32 0.00 0.00 3.41
1965 1970 2.054799 GGCATAACCAGTATCTCCCCA 58.945 52.381 0.00 0.00 38.86 4.96
1966 1971 2.441750 GGCATAACCAGTATCTCCCCAA 59.558 50.000 0.00 0.00 38.86 4.12
2157 2162 3.643237 TCCCTACCAATGTCCTAGACTG 58.357 50.000 0.00 0.00 33.15 3.51
2208 2213 3.135895 AGGATACAAAGTTACCCGGGATG 59.864 47.826 32.02 17.28 41.41 3.51
2228 2234 1.300963 GCTTGCCCTCTGGATCACA 59.699 57.895 0.00 0.00 0.00 3.58
2320 2326 9.540538 AGCAGATACAACTATTACAGATCCTAT 57.459 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 6.217294 GCAGCCGACTTCTAATTCTAGTTAT 58.783 40.000 0.00 0.00 0.00 1.89
95 96 0.617413 AGACATAGCCTTGCTGCTGT 59.383 50.000 0.00 2.62 42.77 4.40
116 117 1.746171 GCCCCCTATCGAACTTTGACC 60.746 57.143 0.00 0.00 0.00 4.02
174 176 1.077501 GATGGCACTGGCTTGGCTA 60.078 57.895 12.96 0.00 42.50 3.93
203 205 1.544246 GGCTGAAACTAAAATGGCCGT 59.456 47.619 0.00 0.00 0.00 5.68
421 423 2.631062 TCTCCTTGGTCGTAAAGCTTCA 59.369 45.455 0.00 0.00 0.00 3.02
526 529 4.104579 TCATAGCCTTCCCTTCAATATGCA 59.895 41.667 0.00 0.00 0.00 3.96
1161 1165 6.183359 CGAGTTTGAAAGCATTAATGAAGTGC 60.183 38.462 19.73 4.69 39.10 4.40
1355 1360 7.220030 GTGATTTATCCTGCTATTTGGAGAGA 58.780 38.462 0.00 0.00 36.08 3.10
1482 1487 5.358160 GCCAGTAGAATATGGAGTTGCTTTT 59.642 40.000 0.00 0.00 39.02 2.27
1486 1491 4.078639 AGCCAGTAGAATATGGAGTTGC 57.921 45.455 0.00 0.00 39.02 4.17
1507 1512 5.066913 TGGATAGTAGATCAGAGAGGCAA 57.933 43.478 0.00 0.00 0.00 4.52
1587 1592 4.523083 ACAAGCAAGTCCTTTGAGTACAA 58.477 39.130 0.00 0.00 39.21 2.41
1691 1696 0.109342 GCATGTCCCGATGATTCCCT 59.891 55.000 0.00 0.00 0.00 4.20
1965 1970 4.229582 TGGGTATCCATGCCTCTTAGTTTT 59.770 41.667 0.00 0.00 38.32 2.43
1966 1971 3.785887 TGGGTATCCATGCCTCTTAGTTT 59.214 43.478 0.00 0.00 38.32 2.66
2228 2234 0.178990 GGAACAAGCAAGGACCCAGT 60.179 55.000 0.00 0.00 0.00 4.00
2320 2326 7.779798 CCCTTATGTTCTGATGGGAAATAAGAA 59.220 37.037 0.00 0.00 36.90 2.52
2323 2329 7.091993 ACTCCCTTATGTTCTGATGGGAAATAA 60.092 37.037 0.00 0.00 42.41 1.40


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

AutoCloner maintained by Alex Coulton.