Multiple sequence alignment - TraesCS2A01G435200

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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 TraesCS2A01G435200 chr2A 100.000 6847 0 0 1 6847 687279599 687272753 0 12645
1 TraesCS2A01G435200 chr5A 98.642 6848 78 8 1 6847 294227002 294233835 0 12116
2 TraesCS2A01G435200 chr5A 98.367 6859 89 16 1 6847 9618909 9625756 0 12024
3 TraesCS2A01G435200 chr4B 98.482 6850 89 12 1 6847 261499258 261492421 0 12059
4 TraesCS2A01G435200 chr4B 98.468 6855 77 16 1 6847 14719143 14712309 0 12052
5 TraesCS2A01G435200 chr7A 98.397 6861 81 22 1 6847 23298658 23291813 0 12033
6 TraesCS2A01G435200 chr2B 98.381 6857 85 17 1 6847 741902559 741909399 0 12024
7 TraesCS2A01G435200 chr1A 98.322 6854 97 11 1 6847 255464232 255471074 0 12004
8 TraesCS2A01G435200 chr1A 98.280 6860 91 17 1 6847 127080744 127087589 0 11989
9 TraesCS2A01G435200 chr3B 98.074 6853 110 18 1 6847 462506625 462499789 0 11904


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 TraesCS2A01G435200 chr2A 687272753 687279599 6846 True 12645 12645 100.000 1 6847 1 chr2A.!!$R1 6846
1 TraesCS2A01G435200 chr5A 294227002 294233835 6833 False 12116 12116 98.642 1 6847 1 chr5A.!!$F2 6846
2 TraesCS2A01G435200 chr5A 9618909 9625756 6847 False 12024 12024 98.367 1 6847 1 chr5A.!!$F1 6846
3 TraesCS2A01G435200 chr4B 261492421 261499258 6837 True 12059 12059 98.482 1 6847 1 chr4B.!!$R2 6846
4 TraesCS2A01G435200 chr4B 14712309 14719143 6834 True 12052 12052 98.468 1 6847 1 chr4B.!!$R1 6846
5 TraesCS2A01G435200 chr7A 23291813 23298658 6845 True 12033 12033 98.397 1 6847 1 chr7A.!!$R1 6846
6 TraesCS2A01G435200 chr2B 741902559 741909399 6840 False 12024 12024 98.381 1 6847 1 chr2B.!!$F1 6846
7 TraesCS2A01G435200 chr1A 255464232 255471074 6842 False 12004 12004 98.322 1 6847 1 chr1A.!!$F2 6846
8 TraesCS2A01G435200 chr1A 127080744 127087589 6845 False 11989 11989 98.280 1 6847 1 chr1A.!!$F1 6846
9 TraesCS2A01G435200 chr3B 462499789 462506625 6836 True 11904 11904 98.074 1 6847 1 chr3B.!!$R1 6846

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
146 150 1.843992 CAGCAGTTGTTTTGGTCAGC 58.156 50.000 0.0 0.0 0.0 4.26 F
1011 1020 4.507388 CGCAGGGCAAAAATGGTTATAATG 59.493 41.667 0.0 0.0 0.0 1.90 F
2085 2105 5.324409 TCATTTTCTAATCAACAGGGCAGT 58.676 37.500 0.0 0.0 0.0 4.40 F
2105 2125 2.367567 GTGGTGAAGGAGTTGAGGTGTA 59.632 50.000 0.0 0.0 0.0 2.90 F
3354 3380 6.072508 CCAGTATCTTGTTTGTAGTTGCACAT 60.073 38.462 0.0 0.0 0.0 3.21 F
4202 4236 1.202698 AGGAAATGGGAGCAGCGATAC 60.203 52.381 0.0 0.0 0.0 2.24 F
4335 4375 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.0 0.0 0.0 3.71 F
5034 5078 1.573108 CTCCCAGACCTAAGCTCCAA 58.427 55.000 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2105 1.507140 ACACCTCAACTCCTTCACCA 58.493 50.000 0.0 0.0 0.00 4.17 R
2105 2125 1.516110 CTCCACATCTTCCCCTGGAT 58.484 55.000 0.0 0.0 32.27 3.41 R
4040 4074 4.656112 AGGATCAATATCTGGTTCCTCGTT 59.344 41.667 0.0 0.0 34.69 3.85 R
4202 4236 0.101219 TCCTCATCGTCGTCAGCATG 59.899 55.000 0.0 0.0 37.54 4.06 R
4240 4274 0.749649 CATCCTTGTCCTCCTCCTCG 59.250 60.000 0.0 0.0 0.00 4.63 R
5034 5078 0.964358 GGATGCTGCCTTGCTCTTGT 60.964 55.000 0.0 0.0 0.00 3.16 R
5343 5387 2.037251 CTCTCGTCTCTGAACCCCAAAA 59.963 50.000 0.0 0.0 0.00 2.44 R
5960 6005 2.167075 GAGCTATTGCCTTGCCAACATT 59.833 45.455 0.0 0.0 40.80 2.71 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
20 21 2.884894 TGTTGTGTGCAATGCATTGA 57.115 40.000 37.36 21.76 41.91 2.57
29 30 4.239304 GTGCAATGCATTGACTGATTTCA 58.761 39.130 37.36 21.93 41.91 2.69
146 150 1.843992 CAGCAGTTGTTTTGGTCAGC 58.156 50.000 0.00 0.00 0.00 4.26
403 407 8.946085 CATCACTTTTACTAAGTTGGCTATTCA 58.054 33.333 0.00 0.00 0.00 2.57
404 408 9.686683 ATCACTTTTACTAAGTTGGCTATTCAT 57.313 29.630 0.00 0.00 0.00 2.57
1011 1020 4.507388 CGCAGGGCAAAAATGGTTATAATG 59.493 41.667 0.00 0.00 0.00 1.90
2085 2105 5.324409 TCATTTTCTAATCAACAGGGCAGT 58.676 37.500 0.00 0.00 0.00 4.40
2105 2125 2.367567 GTGGTGAAGGAGTTGAGGTGTA 59.632 50.000 0.00 0.00 0.00 2.90
3175 3198 8.659925 TCTGCACACATGTTCATTTTAAATTT 57.340 26.923 0.00 0.00 0.00 1.82
3222 3246 6.863126 GCACAGTTTTACTAATCTTGTTGCAT 59.137 34.615 0.00 0.00 0.00 3.96
3354 3380 6.072508 CCAGTATCTTGTTTGTAGTTGCACAT 60.073 38.462 0.00 0.00 0.00 3.21
4040 4074 7.394077 TCATTGAAGAAGTTGCCAAGATTGATA 59.606 33.333 0.00 0.00 0.00 2.15
4202 4236 1.202698 AGGAAATGGGAGCAGCGATAC 60.203 52.381 0.00 0.00 0.00 2.24
4240 4274 2.411904 GAGACAGATGCGGATGAATCC 58.588 52.381 0.00 0.00 43.65 3.01
4333 4373 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
4334 4374 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
4335 4375 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
4909 4953 2.877097 TTGCCATTGACAAGAGCCTA 57.123 45.000 9.13 0.00 0.00 3.93
4949 4993 7.435305 TGCTGAAAAGAATCAAATTGACATGA 58.565 30.769 0.00 0.00 0.00 3.07
5034 5078 1.573108 CTCCCAGACCTAAGCTCCAA 58.427 55.000 0.00 0.00 0.00 3.53
5089 5133 1.798813 GTGGTCCAGAAGTGTAAAGCG 59.201 52.381 0.00 0.00 0.00 4.68
5285 5329 2.038659 CAACAGTCCCACCAAAACCAT 58.961 47.619 0.00 0.00 0.00 3.55
5342 5386 1.051556 GGGGGAACAGGCCACAAAAA 61.052 55.000 5.01 0.00 31.00 1.94
5343 5387 1.055849 GGGGAACAGGCCACAAAAAT 58.944 50.000 5.01 0.00 0.00 1.82
5654 5699 4.713553 TCAGCAACCATTAACACAAGAGA 58.286 39.130 0.00 0.00 0.00 3.10
5796 5841 5.617252 TGAACCCTTACGAAGATCAAACTT 58.383 37.500 0.00 0.00 0.00 2.66
5960 6005 3.851458 ATGAAGGATGTGATGCTGCTA 57.149 42.857 0.00 0.00 0.00 3.49
6029 6074 2.191908 GCCACACCCCGATATGCA 59.808 61.111 0.00 0.00 0.00 3.96
6351 6396 2.887152 CAGAACAGGGCTTTTAGTTGCT 59.113 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.533730 TCTGAACACCAACTATGAAATCAGT 58.466 36.000 0.00 0.0 0.00 3.41
29 30 7.607991 CCACTTAAATCTCTGAACACCAACTAT 59.392 37.037 0.00 0.0 0.00 2.12
146 150 2.801063 CACACAAAAACAGTGAGCCAG 58.199 47.619 0.00 0.0 40.16 4.85
375 379 4.154195 AGCCAACTTAGTAAAAGTGATGCG 59.846 41.667 0.00 0.0 0.00 4.73
403 407 9.056005 CAACTGGCACAAGTGTATAACATATAT 57.944 33.333 1.79 0.0 38.70 0.86
404 408 7.011950 GCAACTGGCACAAGTGTATAACATATA 59.988 37.037 1.79 0.0 43.97 0.86
1011 1020 3.866582 CCACCCGCATCTCCTCCC 61.867 72.222 0.00 0.0 0.00 4.30
2085 2105 1.507140 ACACCTCAACTCCTTCACCA 58.493 50.000 0.00 0.0 0.00 4.17
2105 2125 1.516110 CTCCACATCTTCCCCTGGAT 58.484 55.000 0.00 0.0 32.27 3.41
2652 2672 2.878406 GTGTTCTGCTACAAAGAGGCAA 59.122 45.455 0.00 0.0 35.49 4.52
2921 2942 6.994421 TTAGAGTACTATCCCATGCATTCA 57.006 37.500 0.00 0.0 0.00 2.57
3354 3380 6.456795 TGAATGAAACCACACATTACAACA 57.543 33.333 0.00 0.0 36.94 3.33
4040 4074 4.656112 AGGATCAATATCTGGTTCCTCGTT 59.344 41.667 0.00 0.0 34.69 3.85
4202 4236 0.101219 TCCTCATCGTCGTCAGCATG 59.899 55.000 0.00 0.0 37.54 4.06
4240 4274 0.749649 CATCCTTGTCCTCCTCCTCG 59.250 60.000 0.00 0.0 0.00 4.63
4333 4373 3.181454 TGTCCTCTTCTTGTTTGTCCTCC 60.181 47.826 0.00 0.0 0.00 4.30
4334 4374 4.073293 TGTCCTCTTCTTGTTTGTCCTC 57.927 45.455 0.00 0.0 0.00 3.71
4335 4375 4.503714 TTGTCCTCTTCTTGTTTGTCCT 57.496 40.909 0.00 0.0 0.00 3.85
4909 4953 8.571461 TCTTTTCAGCATCAGTTGATAAGAAT 57.429 30.769 10.81 0.0 43.95 2.40
4949 4993 1.450360 AGACCCTTTCCTGCTTCCTT 58.550 50.000 0.00 0.0 0.00 3.36
5034 5078 0.964358 GGATGCTGCCTTGCTCTTGT 60.964 55.000 0.00 0.0 0.00 3.16
5089 5133 6.017400 TGCAGATTCTTCTTCATTGAAACC 57.983 37.500 0.01 0.0 0.00 3.27
5285 5329 6.293626 GCAAACTTGACAATCTTCTGCTTAGA 60.294 38.462 0.00 0.0 0.00 2.10
5342 5386 2.637872 TCTCGTCTCTGAACCCCAAAAT 59.362 45.455 0.00 0.0 0.00 1.82
5343 5387 2.037251 CTCTCGTCTCTGAACCCCAAAA 59.963 50.000 0.00 0.0 0.00 2.44
5654 5699 7.039882 CACCTACTTATAATGTCGAACACCTT 58.960 38.462 0.00 0.0 0.00 3.50
5796 5841 3.605634 CAGAACCCGTCACCATGATAAA 58.394 45.455 0.00 0.0 0.00 1.40
5960 6005 2.167075 GAGCTATTGCCTTGCCAACATT 59.833 45.455 0.00 0.0 40.80 2.71
6584 6635 2.489329 CCTCAGTGGCATAACAACCTTG 59.511 50.000 0.00 0.0 0.00 3.61


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

AutoCloner maintained by Alex Coulton.