Multiple sequence alignment - TraesCS3A01G304200

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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 TraesCS3A01G304200 chr3A 100.000 3803 0 0 1 3803 539721047 539724849 0 7023
1 TraesCS3A01G304200 chr3A 99.159 3803 30 2 1 3803 609273617 609269817 0 6844
2 TraesCS3A01G304200 chr2B 99.106 3803 34 0 1 3803 105309259 105313061 0 6835
3 TraesCS3A01G304200 chrUn 99.080 3804 34 1 1 3803 65537956 65534153 0 6830
4 TraesCS3A01G304200 chr5A 99.080 3803 35 0 1 3803 34742400 34738598 0 6830
5 TraesCS3A01G304200 chr1B 99.080 3803 35 0 1 3803 496630727 496634529 0 6830
6 TraesCS3A01G304200 chr1B 99.080 3803 35 0 1 3803 533679088 533682890 0 6830
7 TraesCS3A01G304200 chr4A 99.080 3803 34 1 1 3803 246189 242388 0 6828
8 TraesCS3A01G304200 chr7B 99.053 3803 36 0 1 3803 734022740 734018938 0 6824
9 TraesCS3A01G304200 chr7A 99.053 3803 36 0 1 3803 69964825 69961023 0 6824


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 TraesCS3A01G304200 chr3A 539721047 539724849 3802 False 7023 7023 100.000 1 3803 1 chr3A.!!$F1 3802
1 TraesCS3A01G304200 chr3A 609269817 609273617 3800 True 6844 6844 99.159 1 3803 1 chr3A.!!$R1 3802
2 TraesCS3A01G304200 chr2B 105309259 105313061 3802 False 6835 6835 99.106 1 3803 1 chr2B.!!$F1 3802
3 TraesCS3A01G304200 chrUn 65534153 65537956 3803 True 6830 6830 99.080 1 3803 1 chrUn.!!$R1 3802
4 TraesCS3A01G304200 chr5A 34738598 34742400 3802 True 6830 6830 99.080 1 3803 1 chr5A.!!$R1 3802
5 TraesCS3A01G304200 chr1B 496630727 496634529 3802 False 6830 6830 99.080 1 3803 1 chr1B.!!$F1 3802
6 TraesCS3A01G304200 chr1B 533679088 533682890 3802 False 6830 6830 99.080 1 3803 1 chr1B.!!$F2 3802
7 TraesCS3A01G304200 chr4A 242388 246189 3801 True 6828 6828 99.080 1 3803 1 chr4A.!!$R1 3802
8 TraesCS3A01G304200 chr7B 734018938 734022740 3802 True 6824 6824 99.053 1 3803 1 chr7B.!!$R1 3802
9 TraesCS3A01G304200 chr7A 69961023 69964825 3802 True 6824 6824 99.053 1 3803 1 chr7A.!!$R1 3802

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
365 366 0.317854 GGCAAAGGCTTGTCGACAAC 60.318 55.0 26.53 21.06 40.87 3.32 F
793 794 0.382515 GACATTAGCCGAGCTCGACT 59.617 55.0 36.59 32.08 43.02 4.18 F
1817 1818 2.094757 TTGGAGAAGCGGCGTCTCAA 62.095 55.0 35.09 27.39 42.85 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1249 1.135094 CCAGTGGCATAGGGATGTCT 58.865 55.000 0.00 0.00 38.58 3.41 R
2240 2241 2.086510 GTGCAACGTGTGTCACTGT 58.913 52.632 4.27 0.04 33.83 3.55 R
3613 3617 2.267642 GCACTACCCGGTGATGCA 59.732 61.111 18.43 0.00 39.34 3.96 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
255 256 2.750637 GCGGGGTCGACTCAGAGA 60.751 66.667 20.33 0.00 39.00 3.10
365 366 0.317854 GGCAAAGGCTTGTCGACAAC 60.318 55.000 26.53 21.06 40.87 3.32
392 393 2.889045 GGTCATACTATACCGCTGGTGA 59.111 50.000 10.01 0.00 36.19 4.02
793 794 0.382515 GACATTAGCCGAGCTCGACT 59.617 55.000 36.59 32.08 43.02 4.18
1817 1818 2.094757 TTGGAGAAGCGGCGTCTCAA 62.095 55.000 35.09 27.39 42.85 3.02
2341 2342 4.028757 CGAACGTAGACTACACAAATGTCG 59.971 45.833 12.99 6.36 40.48 4.35
2722 2723 3.111853 ACAGTGACATCGACACAATGT 57.888 42.857 12.97 12.97 39.99 2.71
2821 2822 5.411977 CCTTGAGTCGAGTTGTCTAGTTCTA 59.588 44.000 6.64 0.00 0.00 2.10
3323 3325 2.664971 CGAAGACAAACTCGCTACTCGT 60.665 50.000 0.00 0.00 39.67 4.18
3757 3761 3.306780 GCACCCTCGCATATACTAATGGT 60.307 47.826 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
255 256 0.185175 GAGTGGTGTCCCAAGGGTTT 59.815 55.000 4.80 0.00 44.15 3.27
365 366 2.093658 GCGGTATAGTATGACCCCCATG 60.094 54.545 0.00 0.00 36.71 3.66
392 393 1.420138 TGGTCTTTTTCTCCTTCCGCT 59.580 47.619 0.00 0.00 0.00 5.52
486 487 1.537348 CCGAGTCGTTGTTCCACTTGA 60.537 52.381 12.31 0.00 0.00 3.02
793 794 6.704493 GCTTAATTAGTTACCGTGATGATGGA 59.296 38.462 0.00 0.00 31.82 3.41
1248 1249 1.135094 CCAGTGGCATAGGGATGTCT 58.865 55.000 0.00 0.00 38.58 3.41
1817 1818 2.173569 GGGTATGCCACATCCTTCTCTT 59.826 50.000 1.04 0.00 36.17 2.85
2240 2241 2.086510 GTGCAACGTGTGTCACTGT 58.913 52.632 4.27 0.04 33.83 3.55
2341 2342 5.584251 GGAGAACATCATCAAGAACCTTCTC 59.416 44.000 0.00 0.00 36.28 2.87
2603 2604 4.520492 ACTGGATGCGAAAGAATTCTTGTT 59.480 37.500 21.15 6.78 36.12 2.83
2722 2723 3.365868 GCGTTGTCATCCTGCATTTGTAA 60.366 43.478 0.00 0.00 0.00 2.41
2821 2822 4.022068 ACAACATGAGCCAATCGATGTTTT 60.022 37.500 0.00 0.00 37.46 2.43
3182 3183 3.787001 CTCCAACGCTCCCTCCCC 61.787 72.222 0.00 0.00 0.00 4.81
3323 3325 8.234136 ACATTATATTACAAGTCTCGAGACCA 57.766 34.615 35.83 19.41 45.85 4.02
3613 3617 2.267642 GCACTACCCGGTGATGCA 59.732 61.111 18.43 0.00 39.34 3.96


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

AutoCloner maintained by Alex Coulton.