Multiple sequence alignment - TraesCS4D01G263900

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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 TraesCS4D01G263900 chr4D 100.000 2441 0 0 1 2441 434821514 434823954 0 4508
1 TraesCS4D01G263900 chr4A 91.050 2525 113 45 5 2439 36313042 36315543 0 3306
2 TraesCS4D01G263900 chr4B 90.352 2498 115 62 2 2437 534720867 534723300 0 3162


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 TraesCS4D01G263900 chr4D 434821514 434823954 2440 False 4508 4508 100.000 1 2441 1 chr4D.!!$F1 2440
1 TraesCS4D01G263900 chr4A 36313042 36315543 2501 False 3306 3306 91.050 5 2439 1 chr4A.!!$F1 2434
2 TraesCS4D01G263900 chr4B 534720867 534723300 2433 False 3162 3162 90.352 2 2437 1 chr4B.!!$F1 2435

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
395 416 0.179234 CACCAAACCAAACCCAACCC 59.821 55.0 0.0 0.0 0.0 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2375 3.050275 GCCAGTTCCACTGTCCGC 61.05 66.667 3.3 0.0 44.5 5.54 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
89 91 1.624479 ATGAGCAGCTCCTGTCCCAG 61.624 60.000 20.16 0.00 33.43 4.45
204 218 3.136009 ACCAACCCTTCCGAGTTTAAG 57.864 47.619 0.00 0.00 0.00 1.85
395 416 0.179234 CACCAAACCAAACCCAACCC 59.821 55.000 0.00 0.00 0.00 4.11
453 495 2.114670 GCCACACCATCCATGTCCG 61.115 63.158 0.00 0.00 0.00 4.79
675 721 2.067013 CGCATCATCATGAGTAGCCAG 58.933 52.381 0.09 0.00 30.57 4.85
713 762 5.105716 TGAGAGTATTAGTGCAAGAGGACAC 60.106 44.000 0.00 0.00 38.75 3.67
716 765 2.148916 TTAGTGCAAGAGGACACACG 57.851 50.000 0.00 0.00 38.75 4.49
753 802 2.599032 CCCATGCCTGATGCCTCA 59.401 61.111 0.00 0.00 40.16 3.86
758 808 4.512914 GCCTGATGCCTCACCCCC 62.513 72.222 0.00 0.00 0.00 5.40
800 850 3.268032 CCTGCCCCCTCCAACCTT 61.268 66.667 0.00 0.00 0.00 3.50
1113 1170 2.770048 AAGGAGATGCGGGAGGGG 60.770 66.667 0.00 0.00 0.00 4.79
1633 1710 6.599638 ACTTTACATATCTGAACCTTCAAGGC 59.400 38.462 2.20 0.00 39.63 4.35
1652 1729 2.290789 GCGCGCATATGCTTGCTTG 61.291 57.895 29.10 9.64 40.54 4.01
1735 1815 8.186178 TGCGACTTTCAATACTAATTTCTCTC 57.814 34.615 0.00 0.00 0.00 3.20
1750 1832 4.485024 TTCTCTCTATCGGAATACACGC 57.515 45.455 0.00 0.00 0.00 5.34
1783 1865 3.776969 AGCCAGACAAGATCATGACCTTA 59.223 43.478 0.77 0.00 0.00 2.69
1784 1866 4.225942 AGCCAGACAAGATCATGACCTTAA 59.774 41.667 0.77 0.00 0.00 1.85
1786 1868 6.100279 AGCCAGACAAGATCATGACCTTAATA 59.900 38.462 0.77 0.00 0.00 0.98
1858 1951 7.125755 TCCTACGTACGTCGATATAAAAACAG 58.874 38.462 26.53 11.40 42.86 3.16
1871 1964 7.754924 CGATATAAAAACAGAACATTGTTGGCT 59.245 33.333 6.80 0.00 40.24 4.75
1881 1974 2.549754 ACATTGTTGGCTGAAGTTCTCG 59.450 45.455 4.17 0.00 0.00 4.04
1922 2015 7.327975 CAACTTACATATACACTTGGTCAGGA 58.672 38.462 0.00 0.00 0.00 3.86
1925 2018 8.380099 ACTTACATATACACTTGGTCAGGAAAA 58.620 33.333 0.00 0.00 0.00 2.29
1926 2019 8.786826 TTACATATACACTTGGTCAGGAAAAG 57.213 34.615 0.00 0.00 0.00 2.27
1927 2020 6.779860 ACATATACACTTGGTCAGGAAAAGT 58.220 36.000 0.00 0.00 34.52 2.66
1928 2021 7.231467 ACATATACACTTGGTCAGGAAAAGTT 58.769 34.615 0.00 0.00 31.88 2.66
1951 2049 9.036980 AGTTAAATCCTAACAGAGACACTACAT 57.963 33.333 0.00 0.00 0.00 2.29
1993 2109 5.249420 ACTCCTGCAGAGAGGAAATAAAAC 58.751 41.667 26.12 0.00 46.50 2.43
2156 2285 2.351336 ATCACGCACGGGCTACTAGC 62.351 60.000 8.62 0.00 41.46 3.42
2157 2286 3.066190 ACGCACGGGCTACTAGCA 61.066 61.111 8.62 0.00 44.75 3.49
2158 2287 2.278857 CGCACGGGCTACTAGCAG 60.279 66.667 8.62 5.91 44.75 4.24
2276 2407 3.577805 ACTGGCCAGGGTATTCAATAC 57.422 47.619 35.42 0.00 35.00 1.89
2359 2501 6.828273 TGAATTGAATACATACAGGGTGAAGG 59.172 38.462 0.00 0.00 0.00 3.46
2420 2563 0.889994 ATGCAAAAGCATCCGAAGCA 59.110 45.000 0.00 0.00 34.78 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.093973 GGCCCATCGATCCATGTAGTAG 60.094 54.545 0.00 0.00 0.00 2.57
2 3 1.899814 GGCCCATCGATCCATGTAGTA 59.100 52.381 0.00 0.00 0.00 1.82
3 4 0.687354 GGCCCATCGATCCATGTAGT 59.313 55.000 0.00 0.00 0.00 2.73
4 5 0.686789 TGGCCCATCGATCCATGTAG 59.313 55.000 0.00 0.00 0.00 2.74
5 6 0.686789 CTGGCCCATCGATCCATGTA 59.313 55.000 0.00 0.00 0.00 2.29
6 7 1.453235 CTGGCCCATCGATCCATGT 59.547 57.895 0.00 0.00 0.00 3.21
89 91 4.176851 GACGACCCTCGGCTCGAC 62.177 72.222 7.60 0.00 46.20 4.20
204 218 5.910166 GCCTCTCTTCTTTTTCGTTTTTCTC 59.090 40.000 0.00 0.00 0.00 2.87
395 416 0.391597 AGTGTAGTGGTCGTGGGTTG 59.608 55.000 0.00 0.00 0.00 3.77
453 495 2.355756 GTGTATGCATGGACATGGACAC 59.644 50.000 10.16 9.34 41.89 3.67
675 721 2.096248 ACTCTCACACTGGCTAGCTAC 58.904 52.381 15.72 0.00 0.00 3.58
713 762 3.187227 GGGTTTGCATAGCATAGATCGTG 59.813 47.826 8.60 0.00 38.76 4.35
716 765 3.084786 GGGGGTTTGCATAGCATAGATC 58.915 50.000 8.60 0.00 38.76 2.75
758 808 5.105877 CCGGGGTATATATATGTATGCGAGG 60.106 48.000 5.44 2.43 0.00 4.63
800 850 0.544357 ACCGATCACTGGTTGAGGGA 60.544 55.000 0.00 0.00 38.96 4.20
1735 1815 9.511144 TTTATATACATGCGTGTATTCCGATAG 57.489 33.333 31.04 0.00 46.75 2.08
1750 1832 8.837788 TGATCTTGTCTGGCTTTATATACATG 57.162 34.615 0.00 0.00 0.00 3.21
1858 1951 4.540824 GAGAACTTCAGCCAACAATGTTC 58.459 43.478 0.00 0.00 34.39 3.18
1881 1974 3.382048 AGTTGGTTACTCTGGTTCGTC 57.618 47.619 0.00 0.00 28.23 4.20
1925 2018 8.418597 TGTAGTGTCTCTGTTAGGATTTAACT 57.581 34.615 0.00 0.00 0.00 2.24
1951 2049 5.515797 GAGTATATGCGTATGCTCCCATA 57.484 43.478 25.46 0.00 41.49 2.74
2013 2129 7.518161 CGACATGCACTTATCTTTACTTTGAA 58.482 34.615 0.00 0.00 0.00 2.69
2014 2130 6.402118 GCGACATGCACTTATCTTTACTTTGA 60.402 38.462 0.00 0.00 45.45 2.69
2156 2285 3.627732 AAGTGTCGTGTCAGTAGACTG 57.372 47.619 3.12 3.12 45.20 3.51
2157 2286 5.530171 TCTTAAAGTGTCGTGTCAGTAGACT 59.470 40.000 0.00 0.00 45.20 3.24
2158 2287 5.755813 TCTTAAAGTGTCGTGTCAGTAGAC 58.244 41.667 0.00 0.00 45.19 2.59
2187 2318 4.504916 CTGACCGAGGAGCCAGCG 62.505 72.222 0.00 0.00 0.00 5.18
2188 2319 4.154347 CCTGACCGAGGAGCCAGC 62.154 72.222 0.00 0.00 46.33 4.85
2244 2375 3.050275 GCCAGTTCCACTGTCCGC 61.050 66.667 3.30 0.00 44.50 5.54
2359 2501 4.216472 GGTTGATTCAAACCTCTGGTCTTC 59.784 45.833 2.87 0.00 45.25 2.87


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

AutoCloner maintained by Alex Coulton.