Multiple sequence alignment - TraesCS7A01G017000

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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 TraesCS7A01G017000 chr7A 100.000 2264 0 0 1 2264 7487849 7485586 0 4181
1 TraesCS7A01G017000 chr7A 98.718 546 7 0 1719 2264 2106503 2105958 0 970
2 TraesCS7A01G017000 chr7A 98.535 546 8 0 1719 2264 7479287 7478742 0 965
3 TraesCS7A01G017000 chr7A 98.535 546 6 1 1719 2264 728967168 728967711 0 963
4 TraesCS7A01G017000 chr7A 98.182 550 8 1 1715 2264 393845625 393846172 0 959
5 TraesCS7A01G017000 chr5B 97.673 1719 39 1 1 1718 464634106 464635824 0 2952
6 TraesCS7A01G017000 chr5B 97.151 1720 46 3 1 1718 530940831 530939113 0 2902
7 TraesCS7A01G017000 chr2B 97.266 1719 45 2 1 1718 563917140 563915423 0 2913
8 TraesCS7A01G017000 chr7B 97.263 1717 46 1 1 1716 687040622 687042338 0 2909
9 TraesCS7A01G017000 chr7B 97.150 1719 48 1 1 1718 235458094 235456376 0 2902
10 TraesCS7A01G017000 chr4B 97.150 1719 48 1 1 1718 402787203 402785485 0 2902
11 TraesCS7A01G017000 chr3B 97.091 1719 48 2 1 1718 16124436 16122719 0 2896
12 TraesCS7A01G017000 chr1B 96.917 1719 52 1 1 1718 38183391 38185109 0 2880
13 TraesCS7A01G017000 chr4A 96.859 1719 53 1 1 1718 712877478 712879196 0 2874
14 TraesCS7A01G017000 chr4A 98.182 550 8 1 1715 2264 22896821 22896274 0 959
15 TraesCS7A01G017000 chr1A 98.537 547 8 0 1718 2264 6120712 6121258 0 966
16 TraesCS7A01G017000 chr6A 98.535 546 6 2 1719 2264 72966520 72967063 0 963
17 TraesCS7A01G017000 chr6A 98.358 548 7 1 1717 2264 402922483 402923028 0 961
18 TraesCS7A01G017000 chr6A 98.358 548 7 2 1717 2264 504018258 504018803 0 961


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 TraesCS7A01G017000 chr7A 7485586 7487849 2263 True 4181 4181 100.000 1 2264 1 chr7A.!!$R3 2263
1 TraesCS7A01G017000 chr7A 2105958 2106503 545 True 970 970 98.718 1719 2264 1 chr7A.!!$R1 545
2 TraesCS7A01G017000 chr7A 7478742 7479287 545 True 965 965 98.535 1719 2264 1 chr7A.!!$R2 545
3 TraesCS7A01G017000 chr7A 728967168 728967711 543 False 963 963 98.535 1719 2264 1 chr7A.!!$F2 545
4 TraesCS7A01G017000 chr7A 393845625 393846172 547 False 959 959 98.182 1715 2264 1 chr7A.!!$F1 549
5 TraesCS7A01G017000 chr5B 464634106 464635824 1718 False 2952 2952 97.673 1 1718 1 chr5B.!!$F1 1717
6 TraesCS7A01G017000 chr5B 530939113 530940831 1718 True 2902 2902 97.151 1 1718 1 chr5B.!!$R1 1717
7 TraesCS7A01G017000 chr2B 563915423 563917140 1717 True 2913 2913 97.266 1 1718 1 chr2B.!!$R1 1717
8 TraesCS7A01G017000 chr7B 687040622 687042338 1716 False 2909 2909 97.263 1 1716 1 chr7B.!!$F1 1715
9 TraesCS7A01G017000 chr7B 235456376 235458094 1718 True 2902 2902 97.150 1 1718 1 chr7B.!!$R1 1717
10 TraesCS7A01G017000 chr4B 402785485 402787203 1718 True 2902 2902 97.150 1 1718 1 chr4B.!!$R1 1717
11 TraesCS7A01G017000 chr3B 16122719 16124436 1717 True 2896 2896 97.091 1 1718 1 chr3B.!!$R1 1717
12 TraesCS7A01G017000 chr1B 38183391 38185109 1718 False 2880 2880 96.917 1 1718 1 chr1B.!!$F1 1717
13 TraesCS7A01G017000 chr4A 712877478 712879196 1718 False 2874 2874 96.859 1 1718 1 chr4A.!!$F1 1717
14 TraesCS7A01G017000 chr4A 22896274 22896821 547 True 959 959 98.182 1715 2264 1 chr4A.!!$R1 549
15 TraesCS7A01G017000 chr1A 6120712 6121258 546 False 966 966 98.537 1718 2264 1 chr1A.!!$F1 546
16 TraesCS7A01G017000 chr6A 72966520 72967063 543 False 963 963 98.535 1719 2264 1 chr6A.!!$F1 545
17 TraesCS7A01G017000 chr6A 402922483 402923028 545 False 961 961 98.358 1717 2264 1 chr6A.!!$F2 547
18 TraesCS7A01G017000 chr6A 504018258 504018803 545 False 961 961 98.358 1717 2264 1 chr6A.!!$F3 547

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
102 103 0.538118 ATTGGCCATGCTCGCATTTT 59.462 45.0 6.09 0.0 33.90 1.82 F
672 673 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.0 16.64 0.0 33.17 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1195 1.141858 TGTGCATAGTTGGGACACACA 59.858 47.619 0.00 0.0 39.29 3.72 R
1988 1990 2.889045 ACGATCGGGTGCTAAGCTAATA 59.111 45.455 20.98 0.0 0.00 0.98 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
102 103 0.538118 ATTGGCCATGCTCGCATTTT 59.462 45.000 6.09 0.00 33.90 1.82
136 137 4.565166 CGAAGGCGAGAAACATACATGTTA 59.435 41.667 2.30 0.00 44.47 2.41
137 138 5.062934 CGAAGGCGAGAAACATACATGTTAA 59.937 40.000 2.30 0.00 44.47 2.01
154 155 6.015856 ACATGTTAATGATGGAAAAACCGTGA 60.016 34.615 0.00 0.00 38.12 4.35
172 173 2.681848 GTGAGGATGCAAGAGTTCCATG 59.318 50.000 6.09 0.00 31.65 3.66
202 203 2.813226 TAGGTTGACATGGGCGCCAC 62.813 60.000 30.85 18.39 35.80 5.01
349 350 2.543037 TGACCTGGCTGGATACACTA 57.457 50.000 18.12 0.00 46.17 2.74
395 396 1.588239 TTCATGGAGGCTCCTGACAT 58.412 50.000 32.28 16.07 37.46 3.06
435 436 1.203001 GGTGAAGGGGGACACAATGAA 60.203 52.381 0.00 0.00 38.57 2.57
672 673 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
701 702 1.668101 GCTAGAGGTGGTGGTCGAGG 61.668 65.000 0.00 0.00 0.00 4.63
732 733 0.965866 CTAGAGGTGGTGGTCGAGCA 60.966 60.000 14.39 14.39 0.00 4.26
733 734 0.965866 TAGAGGTGGTGGTCGAGCAG 60.966 60.000 19.24 0.00 30.97 4.24
740 741 2.031012 TGGTCGAGCAGGCACAAG 59.969 61.111 14.39 0.00 0.00 3.16
1114 1115 1.228552 AAGGATGTGCCCACACCAC 60.229 57.895 16.64 6.71 46.86 4.16
1180 1181 2.290367 CGCAACAAGTCATGGACAGAAA 59.710 45.455 0.00 0.00 34.60 2.52
1313 1315 9.507329 AGTTGTCACTCATATGTCTAACAAAAT 57.493 29.630 13.82 7.15 0.00 1.82
1654 1656 4.922206 TCAGTAGACAAATGGAAAGGCAT 58.078 39.130 0.00 0.00 0.00 4.40
1677 1679 2.604855 GGCGTCGATGATGAACTATCGT 60.605 50.000 9.31 0.00 44.68 3.73
1987 1989 5.512298 TGATCTGATTGACATGACCCATTT 58.488 37.500 0.00 0.00 0.00 2.32
1988 1990 5.953548 TGATCTGATTGACATGACCCATTTT 59.046 36.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 2.279650 GCCTTCGCCGCCGTTATA 60.280 61.111 0.00 0.00 35.54 0.98
136 137 3.761897 TCCTCACGGTTTTTCCATCATT 58.238 40.909 0.00 0.00 35.57 2.57
137 138 3.433306 TCCTCACGGTTTTTCCATCAT 57.567 42.857 0.00 0.00 35.57 2.45
154 155 2.619849 CCACATGGAACTCTTGCATCCT 60.620 50.000 4.96 0.00 39.89 3.24
172 173 3.955650 TGTCAACCTAGTAGCTTCCAC 57.044 47.619 0.00 0.00 0.00 4.02
202 203 2.488153 GGTCCAAGAAAGGGTGAAATCG 59.512 50.000 0.00 0.00 0.00 3.34
349 350 3.367292 CCGCTACCAAATTGTTTCATGCT 60.367 43.478 0.00 0.00 0.00 3.79
395 396 1.880221 CGCACACCCCACAGTTGATAA 60.880 52.381 0.00 0.00 0.00 1.75
435 436 5.335661 GGTTTTCTTATTCTTGCATGTCCGT 60.336 40.000 0.00 0.00 0.00 4.69
672 673 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
687 688 1.982938 GCTACCTCGACCACCACCT 60.983 63.158 0.00 0.00 0.00 4.00
701 702 2.611518 CACCTCTAGCACTTGTGCTAC 58.388 52.381 25.81 0.74 44.28 3.58
732 733 0.322975 CACCTCTAGCACTTGTGCCT 59.677 55.000 20.39 11.33 34.90 4.75
733 734 0.674895 CCACCTCTAGCACTTGTGCC 60.675 60.000 20.39 4.86 34.90 5.01
740 741 1.215647 CGACCACCACCTCTAGCAC 59.784 63.158 0.00 0.00 0.00 4.40
950 951 6.650807 CACAAGACCTAAAGAGAGTAAATGCA 59.349 38.462 0.00 0.00 0.00 3.96
967 968 5.438761 AGAACAATTGTTAGCACAAGACC 57.561 39.130 23.33 7.42 46.25 3.85
1114 1115 1.619654 ACATCACCACACCAACATGG 58.380 50.000 0.00 0.00 45.02 3.66
1127 1128 2.035066 ACCTTCAGCTTGCAAACATCAC 59.965 45.455 0.00 0.00 0.00 3.06
1194 1195 1.141858 TGTGCATAGTTGGGACACACA 59.858 47.619 0.00 0.00 39.29 3.72
1313 1315 5.546499 GGAGGGGACTACATATAAACCATGA 59.454 44.000 0.00 0.00 42.76 3.07
1987 1989 3.319972 ACGATCGGGTGCTAAGCTAATAA 59.680 43.478 20.98 0.00 0.00 1.40
1988 1990 2.889045 ACGATCGGGTGCTAAGCTAATA 59.111 45.455 20.98 0.00 0.00 0.98
2058 2060 5.290493 ACGGGAGTTGCATAATCTCATAA 57.710 39.130 0.00 0.00 43.33 1.90


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

AutoCloner maintained by Alex Coulton.