Multiple sequence alignment - TraesCS4D01G179200

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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 TraesCS4D01G179200 chr4D 100.000 2300 0 0 1 2300 310456526 310458825 0 4248
1 TraesCS4D01G179200 chr4A 95.616 2304 82 7 1 2300 164510787 164508499 0 3677
2 TraesCS4D01G179200 chr4B 95.135 2302 82 5 1 2300 387880948 387883221 0 3603


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 TraesCS4D01G179200 chr4D 310456526 310458825 2299 False 4248 4248 100.000 1 2300 1 chr4D.!!$F1 2299
1 TraesCS4D01G179200 chr4A 164508499 164510787 2288 True 3677 3677 95.616 1 2300 1 chr4A.!!$R1 2299
2 TraesCS4D01G179200 chr4B 387880948 387883221 2273 False 3603 3603 95.135 1 2300 1 chr4B.!!$F1 2299

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
661 664 1.253593 TGCACGTCTCTGAGGAGCAT 61.254 55.0 4.59 0.0 38.57 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1671 1.073284 ACAGGTCCAATTAGGCGTGTT 59.927 47.619 0.0 0.0 38.47 3.32 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
24 25 6.376978 GCATCAGAATACATACAAATCAGCC 58.623 40.000 0.00 0.00 0.00 4.85
26 27 5.912892 TCAGAATACATACAAATCAGCCGA 58.087 37.500 0.00 0.00 0.00 5.54
36 37 2.141535 AATCAGCCGACGCTAGAATC 57.858 50.000 0.00 0.00 46.25 2.52
153 156 1.455217 GCCCCAGTAGTAGCCTCGA 60.455 63.158 0.00 0.00 0.00 4.04
258 261 1.413118 TCAGCCACTTCACTGTCAGA 58.587 50.000 6.91 0.00 35.37 3.27
308 311 2.203640 TGTCCCGTGACAGCTCCT 60.204 61.111 0.00 0.00 46.40 3.69
423 426 2.615869 GAGTGCACTCTCAAGATGGAC 58.384 52.381 34.54 8.70 39.81 4.02
558 561 1.452651 ATGCTGTCCTTCCATGCCG 60.453 57.895 0.00 0.00 0.00 5.69
561 564 4.776322 TGTCCTTCCATGCCGCCG 62.776 66.667 0.00 0.00 0.00 6.46
661 664 1.253593 TGCACGTCTCTGAGGAGCAT 61.254 55.000 4.59 0.00 38.57 3.79
676 679 2.354259 GAGCATCCTGTCCTTGAGTTG 58.646 52.381 0.00 0.00 0.00 3.16
711 714 2.263153 GCCCTTGCCTTTTTCGCTA 58.737 52.632 0.00 0.00 0.00 4.26
735 738 5.656416 ACTCTTCCAGTTAGAGATCTTCCAG 59.344 44.000 0.00 0.00 41.32 3.86
859 862 3.056107 TCCTTCAGGACTATTTGGTGACG 60.056 47.826 0.00 0.00 39.78 4.35
945 948 2.434331 CTTGGAACGGGGCCAGAA 59.566 61.111 11.67 0.00 36.64 3.02
1217 1220 4.649674 AGTCTGTACAGGAAGAACTGACAA 59.350 41.667 22.48 0.00 41.70 3.18
1263 1266 0.035630 CAGAACTGGGAAGAGGCAGG 60.036 60.000 0.00 0.00 0.00 4.85
1471 1474 4.706962 GCCTCAAAAATTGGGTAGTCTGAT 59.293 41.667 0.00 0.00 0.00 2.90
1491 1494 0.958876 CGGGCCAGGTTCCTGTTAAC 60.959 60.000 16.33 0.00 32.56 2.01
1633 1636 2.861147 AGTTCCCTGAAGGCTGTTAC 57.139 50.000 0.00 0.00 34.51 2.50
1729 1732 8.316640 AGATAAAATTAGAGGCAATCGACATC 57.683 34.615 0.00 0.00 0.00 3.06
1730 1733 7.933577 AGATAAAATTAGAGGCAATCGACATCA 59.066 33.333 0.00 0.00 0.00 3.07
1787 1790 8.896744 CAAACATAGTATGGATTGATTCAGTGT 58.103 33.333 18.83 0.00 34.89 3.55
1901 1905 5.231265 GCATAAGGCAAAAGTGGTACTAC 57.769 43.478 0.19 0.19 43.97 2.73
1943 1947 9.121517 GTTTAATAAGGGAAAGCTTAAAACGAC 57.878 33.333 0.00 0.00 0.00 4.34
2005 2011 3.618690 AATCTACCTGTGAGCTGGTTC 57.381 47.619 0.00 0.00 43.21 3.62
2209 2215 2.849966 CGTCGGATCGCTCGCAAAG 61.850 63.158 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.550180 TCTCCATCAGATTCTAGCGTCG 59.450 50.000 0.00 0.00 0.00 5.12
26 27 3.820467 CTCTCTCCATCAGATTCTAGCGT 59.180 47.826 0.00 0.00 0.00 5.07
36 37 2.934887 TCTCAGCTCTCTCTCCATCAG 58.065 52.381 0.00 0.00 0.00 2.90
153 156 2.975489 ACATCCCAGTCTTGTCTCACTT 59.025 45.455 0.00 0.00 0.00 3.16
162 165 1.072331 AGCGTCAAACATCCCAGTCTT 59.928 47.619 0.00 0.00 0.00 3.01
258 261 5.186198 GCTACTCTTGACAATGGGTATGTT 58.814 41.667 0.00 0.00 0.00 2.71
423 426 3.190849 CGCTCGCACCACCATCAG 61.191 66.667 0.00 0.00 0.00 2.90
661 664 1.423584 TCTGCAACTCAAGGACAGGA 58.576 50.000 0.00 0.00 0.00 3.86
673 676 4.631377 GGGCCAAAATAAGAATTCTGCAAC 59.369 41.667 9.17 0.00 0.00 4.17
676 679 4.743057 AGGGCCAAAATAAGAATTCTGC 57.257 40.909 9.17 5.94 0.00 4.26
711 714 5.584913 TGGAAGATCTCTAACTGGAAGAGT 58.415 41.667 0.00 0.00 41.11 3.24
735 738 6.349363 GGATCATTGTCCTTTTACTTGTCCAC 60.349 42.308 0.00 0.00 35.32 4.02
859 862 1.301677 CTTGTTCTTCCCCGCTCTGC 61.302 60.000 0.00 0.00 0.00 4.26
930 933 0.178947 ATTTTTCTGGCCCCGTTCCA 60.179 50.000 0.00 0.00 0.00 3.53
1011 1014 4.734398 TGACTTGTCAAGCAACCATTTT 57.266 36.364 12.66 0.00 32.90 1.82
1263 1266 2.296190 AGGAAACAATTTCGCAGGAACC 59.704 45.455 0.00 0.00 40.57 3.62
1633 1636 5.970592 TCTGAAGTACCTGAATCTGTCATG 58.029 41.667 0.00 0.00 35.07 3.07
1668 1671 1.073284 ACAGGTCCAATTAGGCGTGTT 59.927 47.619 0.00 0.00 38.47 3.32
1729 1732 6.947258 TGATGTGTTGCGATTACTAATCATG 58.053 36.000 9.08 0.00 37.78 3.07
1730 1733 7.442062 TGATGATGTGTTGCGATTACTAATCAT 59.558 33.333 9.08 0.00 37.78 2.45
1783 1786 8.491134 TGTTGCCATAATAACCTCTATAACACT 58.509 33.333 0.00 0.00 0.00 3.55
1787 1790 9.688091 TTGTTGTTGCCATAATAACCTCTATAA 57.312 29.630 0.00 0.00 0.00 0.98
1896 1900 4.982999 ACTCGTCGTTCGTACTAGTAGTA 58.017 43.478 5.90 5.90 40.80 1.82
1897 1901 3.839293 ACTCGTCGTTCGTACTAGTAGT 58.161 45.455 8.14 8.14 40.80 2.73
1898 1902 4.831741 AACTCGTCGTTCGTACTAGTAG 57.168 45.455 1.87 0.00 40.80 2.57
1899 1903 6.699895 TTAAACTCGTCGTTCGTACTAGTA 57.300 37.500 0.00 0.00 40.80 1.82
1900 1904 5.591643 TTAAACTCGTCGTTCGTACTAGT 57.408 39.130 0.00 0.00 40.80 2.57
1901 1905 7.371875 CCTTATTAAACTCGTCGTTCGTACTAG 59.628 40.741 0.00 0.00 40.80 2.57
1915 1919 9.338291 CGTTTTAAGCTTTCCCTTATTAAACTC 57.662 33.333 3.20 0.00 31.80 3.01
2005 2011 3.244215 TGACTCAACTTGACCTTAGCTGG 60.244 47.826 0.00 0.00 0.00 4.85
2140 2146 2.095466 TGCAAGTTACAATGCGCTTACC 60.095 45.455 9.73 0.00 45.47 2.85
2209 2215 2.359230 GTGCTGTCAGGGCCAGTC 60.359 66.667 6.18 0.00 32.41 3.51


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

AutoCloner maintained by Alex Coulton.