Multiple sequence alignment - TraesCS2A01G422000

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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 TraesCS2A01G422000 chr2A 100.000 2513 0 0 1 2513 677262023 677264535 0 4641
1 TraesCS2A01G422000 chr4A 96.824 2519 69 11 1 2513 45631395 45633908 0 4198
2 TraesCS2A01G422000 chr4A 95.772 615 17 4 1901 2513 9468754 9469361 0 983
3 TraesCS2A01G422000 chr4A 95.772 615 15 5 1901 2513 246821249 246820644 0 981
4 TraesCS2A01G422000 chr7D 95.943 2539 74 9 1 2513 421675283 421677818 0 4091
5 TraesCS2A01G422000 chr5A 95.952 2520 79 13 1 2513 13143402 13140899 0 4067
6 TraesCS2A01G422000 chr6A 95.833 2520 90 15 1 2513 484784652 484782141 0 4058
7 TraesCS2A01G422000 chr6A 95.631 2518 94 9 1 2513 176534600 176532094 0 4026
8 TraesCS2A01G422000 chr6A 95.610 615 17 5 1901 2513 357524783 357524177 0 977
9 TraesCS2A01G422000 chr6D 95.903 2514 74 10 1 2491 459129171 459131678 0 4045
10 TraesCS2A01G422000 chr6D 95.356 2541 74 13 1 2513 397854471 397851947 0 3999
11 TraesCS2A01G422000 chr1A 95.711 2518 80 10 1 2513 519376702 519374208 0 4026
12 TraesCS2A01G422000 chr1A 95.935 615 15 5 1901 2513 517445084 517444478 0 989
13 TraesCS2A01G422000 chr5D 95.667 2377 74 10 1 2353 58009616 58007245 0 3792


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 TraesCS2A01G422000 chr2A 677262023 677264535 2512 False 4641 4641 100.000 1 2513 1 chr2A.!!$F1 2512
1 TraesCS2A01G422000 chr4A 45631395 45633908 2513 False 4198 4198 96.824 1 2513 1 chr4A.!!$F2 2512
2 TraesCS2A01G422000 chr4A 9468754 9469361 607 False 983 983 95.772 1901 2513 1 chr4A.!!$F1 612
3 TraesCS2A01G422000 chr4A 246820644 246821249 605 True 981 981 95.772 1901 2513 1 chr4A.!!$R1 612
4 TraesCS2A01G422000 chr7D 421675283 421677818 2535 False 4091 4091 95.943 1 2513 1 chr7D.!!$F1 2512
5 TraesCS2A01G422000 chr5A 13140899 13143402 2503 True 4067 4067 95.952 1 2513 1 chr5A.!!$R1 2512
6 TraesCS2A01G422000 chr6A 484782141 484784652 2511 True 4058 4058 95.833 1 2513 1 chr6A.!!$R3 2512
7 TraesCS2A01G422000 chr6A 176532094 176534600 2506 True 4026 4026 95.631 1 2513 1 chr6A.!!$R1 2512
8 TraesCS2A01G422000 chr6A 357524177 357524783 606 True 977 977 95.610 1901 2513 1 chr6A.!!$R2 612
9 TraesCS2A01G422000 chr6D 459129171 459131678 2507 False 4045 4045 95.903 1 2491 1 chr6D.!!$F1 2490
10 TraesCS2A01G422000 chr6D 397851947 397854471 2524 True 3999 3999 95.356 1 2513 1 chr6D.!!$R1 2512
11 TraesCS2A01G422000 chr1A 519374208 519376702 2494 True 4026 4026 95.711 1 2513 1 chr1A.!!$R2 2512
12 TraesCS2A01G422000 chr1A 517444478 517445084 606 True 989 989 95.935 1901 2513 1 chr1A.!!$R1 612
13 TraesCS2A01G422000 chr5D 58007245 58009616 2371 True 3792 3792 95.667 1 2353 1 chr5D.!!$R1 2352

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
834 852 2.046447 TCCCCTTCTCCTCTTCTCCATT 59.954 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 1825 0.875728 ACTGACGAACTCGAGGACAG 59.124 55.0 18.41 15.99 43.02 3.51 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
93 95 6.301169 AGTTCGGATCCTTCTTATTCACTT 57.699 37.500 10.75 0.0 0.00 3.16
119 122 8.924691 TCAAAATGAAGCTATGGAAATTTTTCG 58.075 29.630 0.00 0.0 38.06 3.46
183 188 5.134661 CCTCTCTCCCTATTCTACGAACTT 58.865 45.833 0.00 0.0 0.00 2.66
444 462 5.126061 GGTAACTAGGTCTCATAAACGGACA 59.874 44.000 0.00 0.0 0.00 4.02
534 552 2.502538 CCCTAATAACCCCGTTGACTCA 59.497 50.000 0.00 0.0 0.00 3.41
800 818 6.630444 TTGCAAAATACAATGTGGCAAATT 57.370 29.167 0.00 0.0 36.90 1.82
834 852 2.046447 TCCCCTTCTCCTCTTCTCCATT 59.954 50.000 0.00 0.0 0.00 3.16
840 858 5.513788 CCTTCTCCTCTTCTCCATTTGACAA 60.514 44.000 0.00 0.0 0.00 3.18
930 948 5.047306 TCTCGAGCAATTCCTCTGTTTCTTA 60.047 40.000 7.81 0.0 0.00 2.10
940 958 2.231478 CTCTGTTTCTTACTCTCGGGCA 59.769 50.000 0.00 0.0 0.00 5.36
1010 1028 2.107366 TCCAGTGCCGATGACTCAATA 58.893 47.619 0.00 0.0 0.00 1.90
1013 1031 3.461061 CAGTGCCGATGACTCAATACAT 58.539 45.455 0.00 0.0 0.00 2.29
1332 1351 1.855441 ATCTGCCCCATGACAGTGCA 61.855 55.000 0.00 0.0 35.37 4.57
1660 1679 3.807622 CAGTTTCGGCAGAAGACAACTAA 59.192 43.478 0.00 0.0 37.70 2.24
1756 1775 2.486472 AAGCAGTACTTGAGCAGCAT 57.514 45.000 6.47 0.0 37.17 3.79
1806 1825 0.944386 TCTCGCACTTGCCAAACTTC 59.056 50.000 0.00 0.0 37.91 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 69 7.848128 AGTGAATAAGAAGGATCCGAACTTAA 58.152 34.615 22.18 10.84 0.00 1.85
75 77 8.960591 TCATTTTGAAGTGAATAAGAAGGATCC 58.039 33.333 2.48 2.48 0.00 3.36
93 95 8.924691 CGAAAAATTTCCATAGCTTCATTTTGA 58.075 29.630 0.00 0.00 33.68 2.69
183 188 5.069119 AGCTATCACCTATGAACATGTTCGA 59.931 40.000 28.55 20.04 42.28 3.71
534 552 2.643551 CATTTCTGCGGGGTTATGAGT 58.356 47.619 0.00 0.00 0.00 3.41
777 795 6.039047 ACAATTTGCCACATTGTATTTTGCAA 59.961 30.769 7.42 0.00 41.99 4.08
800 818 4.348168 GGAGAAGGGGAAGCTATATTGACA 59.652 45.833 0.00 0.00 0.00 3.58
834 852 2.287547 GCTCGATGCCTTTGTTTGTCAA 60.288 45.455 0.00 0.00 35.15 3.18
840 858 2.012673 GATCTGCTCGATGCCTTTGTT 58.987 47.619 4.73 0.00 42.00 2.83
867 885 1.705186 TGGGGGAAAGAAACAGAGGAG 59.295 52.381 0.00 0.00 0.00 3.69
930 948 1.067212 GTCGACATATTGCCCGAGAGT 59.933 52.381 11.55 0.00 0.00 3.24
1010 1028 1.302511 GTCCGTGGGCAGTCAATGT 60.303 57.895 0.00 0.00 0.00 2.71
1013 1031 2.425592 CAGTCCGTGGGCAGTCAA 59.574 61.111 0.00 0.00 0.00 3.18
1044 1062 3.508012 TCTTCTCCTCCTTCGAAGTCAAG 59.492 47.826 23.03 16.13 36.44 3.02
1111 1129 1.415659 CTCAGATCTAACCTGCCCCTG 59.584 57.143 0.00 0.00 0.00 4.45
1660 1679 9.520515 AACAAAATAATCCTATCACTGAACTGT 57.479 29.630 0.00 0.00 0.00 3.55
1756 1775 9.607333 AGAGATGAACTTGATGTATATCCCTTA 57.393 33.333 0.00 0.00 32.09 2.69
1806 1825 0.875728 ACTGACGAACTCGAGGACAG 59.124 55.000 18.41 15.99 43.02 3.51
1843 1865 2.239654 TCTCTTTGGGCCCATGAACTAG 59.760 50.000 29.23 16.96 0.00 2.57


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

AutoCloner maintained by Alex Coulton.