Multiple sequence alignment - TraesCS6A01G297600

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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 TraesCS6A01G297600 chr6A 100.000 2909 0 0 1 2909 531051971 531054879 0 5373
1 TraesCS6A01G297600 chr6A 96.123 2915 105 6 1 2909 554915083 554917995 0 4750
2 TraesCS6A01G297600 chr6A 96.054 2914 108 5 1 2909 494425295 494428206 0 4737
3 TraesCS6A01G297600 chr7A 97.218 2912 74 5 1 2909 675357143 675354236 0 4922
4 TraesCS6A01G297600 chr5A 96.397 2914 98 5 1 2909 33905182 33908093 0 4793
5 TraesCS6A01G297600 chr3A 96.259 2914 101 8 1 2909 745750325 745753235 0 4771
6 TraesCS6A01G297600 chr2A 96.191 2914 95 9 1 2909 58510417 58507515 0 4752
7 TraesCS6A01G297600 chr2A 95.813 2914 112 9 1 2909 733070584 733073492 0 4697
8 TraesCS6A01G297600 chr1A 96.022 2916 107 6 1 2909 365631553 365634466 0 4734
9 TraesCS6A01G297600 chr1A 96.183 2882 104 5 1 2878 10682130 10685009 0 4708


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 TraesCS6A01G297600 chr6A 531051971 531054879 2908 False 5373 5373 100.000 1 2909 1 chr6A.!!$F2 2908
1 TraesCS6A01G297600 chr6A 554915083 554917995 2912 False 4750 4750 96.123 1 2909 1 chr6A.!!$F3 2908
2 TraesCS6A01G297600 chr6A 494425295 494428206 2911 False 4737 4737 96.054 1 2909 1 chr6A.!!$F1 2908
3 TraesCS6A01G297600 chr7A 675354236 675357143 2907 True 4922 4922 97.218 1 2909 1 chr7A.!!$R1 2908
4 TraesCS6A01G297600 chr5A 33905182 33908093 2911 False 4793 4793 96.397 1 2909 1 chr5A.!!$F1 2908
5 TraesCS6A01G297600 chr3A 745750325 745753235 2910 False 4771 4771 96.259 1 2909 1 chr3A.!!$F1 2908
6 TraesCS6A01G297600 chr2A 58507515 58510417 2902 True 4752 4752 96.191 1 2909 1 chr2A.!!$R1 2908
7 TraesCS6A01G297600 chr2A 733070584 733073492 2908 False 4697 4697 95.813 1 2909 1 chr2A.!!$F1 2908
8 TraesCS6A01G297600 chr1A 365631553 365634466 2913 False 4734 4734 96.022 1 2909 1 chr1A.!!$F2 2908
9 TraesCS6A01G297600 chr1A 10682130 10685009 2879 False 4708 4708 96.183 1 2878 1 chr1A.!!$F1 2877

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
343 349 0.379669 CATCCTGGCAATTGAGACGC 59.62 55.0 10.34 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 1987 0.814457 GTTGGACACCAGTTGCACAA 59.186 50.0 0.0 0.0 33.81 3.33 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
58 60 5.278463 GGCAATACATGTTTGTGAGTGAACT 60.278 40.000 2.30 0.00 36.53 3.01
266 272 4.222588 GGCCAGCTGAGACATCTATTCTAT 59.777 45.833 17.39 0.00 0.00 1.98
343 349 0.379669 CATCCTGGCAATTGAGACGC 59.620 55.000 10.34 0.00 0.00 5.19
379 385 3.067106 ACCAGAAATCTGTAGTGCAACG 58.933 45.455 9.43 0.00 41.82 4.10
402 408 5.407084 CGGGAAAAACACAAGAACTTTTGTT 59.593 36.000 11.64 11.64 43.00 2.83
752 762 6.538742 GTCATGCTCTTGCCAGTTATTTACTA 59.461 38.462 0.00 0.00 38.71 1.82
911 922 8.896320 AAGTTTTTAGGTTGTTTGAAACACTT 57.104 26.923 10.72 4.78 41.97 3.16
1130 1144 1.254026 TACTACACGCAGGCAAGTCT 58.746 50.000 0.00 0.00 0.00 3.24
1139 1153 2.012673 GCAGGCAAGTCTTGATGGTAG 58.987 52.381 16.99 0.92 0.00 3.18
1577 1591 5.674496 TGGACCCTATTCCAGATCCAAAATA 59.326 40.000 0.00 0.00 41.00 1.40
1631 1645 3.887716 CCTCCAATATTTGCTGAAGAGGG 59.112 47.826 0.00 0.00 36.76 4.30
1738 1752 3.482232 GATGGGCGATGGGAGGTGG 62.482 68.421 0.00 0.00 0.00 4.61
1844 1858 3.822735 CCTGATGAAAAGGAGTTTCTGCA 59.177 43.478 0.99 0.00 45.14 4.41
1885 1899 3.637911 TGACTACAGGTGTGGTGTTTT 57.362 42.857 3.58 0.00 39.92 2.43
1973 1987 4.281688 ACTGTGCAACTGAAATGGCTTAAT 59.718 37.500 0.00 0.00 39.30 1.40
2058 2072 7.573843 GCAACTAGATTGTCTTTACTGTGCAAT 60.574 37.037 0.00 0.00 40.77 3.56
2180 2194 3.052082 GTGCAGCTGGATGTGCGT 61.052 61.111 17.12 0.00 42.96 5.24
2441 2456 4.263018 TGATGAAGAGGACAGAGTTGTG 57.737 45.455 0.00 0.00 37.76 3.33
2571 2586 4.163458 TCGCACCCTTCATAGGAATAAACT 59.837 41.667 0.00 0.00 45.05 2.66
2840 2857 5.972327 ATCCAGGACTCTCTGATGATTTT 57.028 39.130 0.00 0.00 36.93 1.82
2896 2913 1.888512 GTTTGAGCAGAATTGGGCTGA 59.111 47.619 5.24 0.00 41.22 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
266 272 7.353414 TGGACATTCAATGTTTTTAGTTGGA 57.647 32.000 4.04 0.00 45.03 3.53
343 349 6.763610 AGATTTCTGGTTTTCGCTAGAATAGG 59.236 38.462 0.00 0.00 39.70 2.57
379 385 6.425417 TGAACAAAAGTTCTTGTGTTTTTCCC 59.575 34.615 18.33 8.94 39.47 3.97
658 664 5.657474 TGTAATGATCTGTAGGTTTCCGTC 58.343 41.667 0.00 0.00 0.00 4.79
693 701 7.336931 TGCTACAGAGTTTTTCAGACTTTTTCT 59.663 33.333 0.00 0.00 33.33 2.52
752 762 6.443934 TGTTATGTTAGTTGCACAGTTTGT 57.556 33.333 0.00 0.00 0.00 2.83
1577 1591 4.382040 CCATCTCCTCGTCACTGTTAACAT 60.382 45.833 9.13 0.00 0.00 2.71
1631 1645 4.954826 TCTTCTTCTTACTAGTACCAGCCC 59.045 45.833 0.91 0.00 0.00 5.19
1738 1752 1.368850 GGTCACGAACAAAGTGCGC 60.369 57.895 0.00 0.00 38.28 6.09
1844 1858 6.936900 AGTCAAGTTGCAGTTATACAAGATGT 59.063 34.615 0.00 0.00 0.00 3.06
1973 1987 0.814457 GTTGGACACCAGTTGCACAA 59.186 50.000 0.00 0.00 33.81 3.33
2058 2072 6.641169 TTTTGCATACAGGACATTGTGTAA 57.359 33.333 0.00 0.00 32.98 2.41
2323 2338 3.772025 ACCCTCCTTTGTGTCATCTCTAG 59.228 47.826 0.00 0.00 0.00 2.43
2441 2456 3.706086 AGCCATCCACCCAAAATATGTTC 59.294 43.478 0.00 0.00 0.00 3.18
2484 2499 0.392461 ATGCAATCGTGGTACGCCTT 60.392 50.000 0.00 0.00 42.21 4.35
2545 2560 1.271856 TCCTATGAAGGGTGCGAACA 58.728 50.000 0.00 0.00 43.84 3.18
2552 2567 6.636454 TGTCAGTTTATTCCTATGAAGGGT 57.364 37.500 0.00 0.00 43.84 4.34
2571 2586 2.166870 GCATGAAAGATTGGCCATGTCA 59.833 45.455 6.09 2.47 38.78 3.58
2707 2722 2.158914 TGTATTGACTGCCTCATCGCAT 60.159 45.455 0.00 0.00 38.30 4.73
2840 2857 4.513442 AGCTGAAGTCAACACACTTGTTA 58.487 39.130 0.00 0.00 44.57 2.41


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

AutoCloner maintained by Alex Coulton.