Multiple sequence alignment - TraesCS1D01G232000

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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 TraesCS1D01G232000 chr1D 100.000 3101 0 0 1 3101 320397250 320394150 0 5727
1 TraesCS1D01G232000 chr1B 96.811 3104 94 4 1 3101 433433503 433430402 0 5179
2 TraesCS1D01G232000 chr1A 96.750 2277 54 8 3 2271 402805774 402808038 0 3777
3 TraesCS1D01G232000 chr1A 94.768 841 36 1 2269 3101 402808344 402809184 0 1303


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 TraesCS1D01G232000 chr1D 320394150 320397250 3100 True 5727 5727 100.000 1 3101 1 chr1D.!!$R1 3100
1 TraesCS1D01G232000 chr1B 433430402 433433503 3101 True 5179 5179 96.811 1 3101 1 chr1B.!!$R1 3100
2 TraesCS1D01G232000 chr1A 402805774 402809184 3410 False 2540 3777 95.759 3 3101 2 chr1A.!!$F1 3098

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
368 374 0.82501 ACAGGCCCAAAGCAGAACAG 60.825 55.0 0.0 0.0 46.5 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2640 2.826674 TATTTCCCCAAGGGCTGAAG 57.173 50.0 0.0 0.0 43.94 3.02 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
86 87 3.282885 GGTTCCTCTAGCCCAAATTCTG 58.717 50.000 0.00 0.00 0.00 3.02
368 374 0.825010 ACAGGCCCAAAGCAGAACAG 60.825 55.000 0.00 0.00 46.50 3.16
530 536 4.090090 AGGTTGAGCTATGTACTGTGTCT 58.910 43.478 0.00 0.00 0.00 3.41
543 549 3.081061 ACTGTGTCTGTTGCTTGTTTGA 58.919 40.909 0.00 0.00 0.00 2.69
609 615 4.327087 GCGATGTTTGATCAATGGGTTTTC 59.673 41.667 9.40 0.00 0.00 2.29
669 676 6.345961 CGCTCAACGTATGTAGTTTGTTTGTA 60.346 38.462 0.00 0.00 36.87 2.41
903 910 9.836076 AGTTTGTTAGTCACACTAAAAACTTTC 57.164 29.630 18.63 6.49 41.84 2.62
978 985 4.565652 CGCCCTGCCTATATTTAATCCAGT 60.566 45.833 0.00 0.00 0.00 4.00
1104 1111 6.757947 CAGACAAATTTATTCGAATTGCCCAT 59.242 34.615 17.19 0.00 30.06 4.00
1604 1611 6.096001 AGGCAAACAAGAAATGGCTTCTATAG 59.904 38.462 0.00 0.00 46.42 1.31
1682 1689 2.280708 GTGATAATTCGTTCCGTGGTCG 59.719 50.000 0.00 0.00 0.00 4.79
1788 1795 3.701205 ACAGTATTGATGCACCTGTCA 57.299 42.857 0.00 0.00 30.94 3.58
2230 2240 8.935844 TGGTCGCATCATATATTCTGATTTAAC 58.064 33.333 0.00 0.00 31.00 2.01
2322 2640 8.583810 AAATGTGCTATTTTATGACATGATGC 57.416 30.769 0.00 0.00 0.00 3.91
2328 2646 6.581542 GCTATTTTATGACATGATGCTTCAGC 59.418 38.462 8.40 0.00 42.50 4.26
2336 2654 3.773149 ATGATGCTTCAGCCCTTGGGG 62.773 57.143 7.91 1.39 38.77 4.96
2737 3055 3.624410 GGTGCCCTACCTTTTATAACGTG 59.376 47.826 0.00 0.00 46.51 4.49
2740 3058 4.020396 TGCCCTACCTTTTATAACGTGTCA 60.020 41.667 0.00 0.00 0.00 3.58
2861 3187 4.134379 TCATCAGCCTGTCATTCTTCTC 57.866 45.455 0.00 0.00 0.00 2.87
3082 3408 5.534654 TCTGAACAATTGTAAACCCCTTGAG 59.465 40.000 12.39 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 5.998363 AGACCACTTAAATTCTGTCTGTTCC 59.002 40.000 0.00 0.00 32.22 3.62
154 156 4.148825 CCGGCCGAGAAGGTCCAG 62.149 72.222 30.73 0.44 43.19 3.86
235 237 4.560856 CTCCGCTCGAGCCTTCCG 62.561 72.222 30.66 16.39 37.91 4.30
330 336 6.327934 GCCTGTAGTAATCGTAAACTGAGAA 58.672 40.000 0.00 0.00 0.00 2.87
368 374 4.574421 CCCCCTTGATTTGTTGTTTGTTTC 59.426 41.667 0.00 0.00 0.00 2.78
473 479 1.644786 GATCCCAAGGACGCAAACCG 61.645 60.000 0.00 0.00 44.21 4.44
506 512 5.715279 AGACACAGTACATAGCTCAACCTTA 59.285 40.000 0.00 0.00 0.00 2.69
530 536 3.703556 TGGAAGGAATCAAACAAGCAACA 59.296 39.130 0.00 0.00 0.00 3.33
543 549 3.312736 ACACAAACTGGTGGAAGGAAT 57.687 42.857 0.00 0.00 43.08 3.01
609 615 7.980662 TGATGTCATAAACAAATTTAGCATGGG 59.019 33.333 0.00 0.00 42.37 4.00
669 676 4.060900 AGATTGTCGCGCTCATCAATTAT 58.939 39.130 5.56 2.10 31.87 1.28
1104 1111 2.057922 GGAAGGCTGGGATCCAATCTA 58.942 52.381 15.23 0.00 30.80 1.98
1682 1689 5.390356 GCTTCTCTTGTTCTGTAGACATTGC 60.390 44.000 0.00 0.00 0.00 3.56
1788 1795 7.642586 GCAAACAAGACAAAAAGTAATACGACT 59.357 33.333 0.00 0.00 0.00 4.18
2230 2240 6.263168 AGAAACAGGGAAATGTCAACTTACAG 59.737 38.462 0.00 0.00 31.70 2.74
2322 2640 2.826674 TATTTCCCCAAGGGCTGAAG 57.173 50.000 0.00 0.00 43.94 3.02
2328 2646 5.598417 CCTTGAACTATTATTTCCCCAAGGG 59.402 44.000 0.00 0.00 43.24 3.95
2666 2984 6.284891 TCCTTTTCCATAAAATCTTGCCAG 57.715 37.500 0.00 0.00 34.18 4.85
2861 3187 4.271049 CAGGTGTAGAATGGTAATTGCTCG 59.729 45.833 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.