Multiple sequence alignment - TraesCS3D01G151600

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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 TraesCS3D01G151600 chr3D 100.000 2309 0 0 1 2309 116047241 116044933 0 4265
1 TraesCS3D01G151600 chr3B 95.468 2339 62 13 1 2309 169633435 169631111 0 3692
2 TraesCS3D01G151600 chr3A 84.926 1413 115 49 549 1902 112962358 112960985 0 1339
3 TraesCS3D01G151600 chr3A 96.860 414 12 1 1897 2309 112960324 112959911 0 691


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 TraesCS3D01G151600 chr3D 116044933 116047241 2308 True 4265 4265 100.000 1 2309 1 chr3D.!!$R1 2308
1 TraesCS3D01G151600 chr3B 169631111 169633435 2324 True 3692 3692 95.468 1 2309 1 chr3B.!!$R1 2308
2 TraesCS3D01G151600 chr3A 112959911 112962358 2447 True 1015 1339 90.893 549 2309 2 chr3A.!!$R1 1760

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
955 1007 1.400494 CATAGCCCGAAAAGGAAACCG 59.6 52.381 0.0 0.0 45.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1961 4.710865 TCCCTTGCAGCATGAAATAAATGA 59.289 37.5 9.87 0.0 39.69 2.57 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
73 75 1.468054 GGGCTCTGCTGCGTATTTTTG 60.468 52.381 0.00 0.00 0.00 2.44
75 77 2.351738 GGCTCTGCTGCGTATTTTTGTT 60.352 45.455 0.00 0.00 0.00 2.83
76 78 3.119990 GGCTCTGCTGCGTATTTTTGTTA 60.120 43.478 0.00 0.00 0.00 2.41
77 79 4.438744 GGCTCTGCTGCGTATTTTTGTTAT 60.439 41.667 0.00 0.00 0.00 1.89
78 80 5.095490 GCTCTGCTGCGTATTTTTGTTATT 58.905 37.500 0.00 0.00 0.00 1.40
79 81 5.572896 GCTCTGCTGCGTATTTTTGTTATTT 59.427 36.000 0.00 0.00 0.00 1.40
80 82 6.089417 GCTCTGCTGCGTATTTTTGTTATTTT 59.911 34.615 0.00 0.00 0.00 1.82
81 83 7.359181 GCTCTGCTGCGTATTTTTGTTATTTTT 60.359 33.333 0.00 0.00 0.00 1.94
198 201 7.787028 ACAACAATACCACAAATACAAAGGTT 58.213 30.769 0.00 0.00 33.91 3.50
306 309 6.874288 TGGCAACCATTTTATTTCTTTTGG 57.126 33.333 0.00 0.00 0.00 3.28
511 514 8.653984 TTTCGTTCATGATTACTTTCATTTCG 57.346 30.769 0.00 0.00 34.09 3.46
570 573 7.148086 TGGTGGCATACATGATCTTCTTAAAAC 60.148 37.037 0.00 0.00 0.00 2.43
644 647 7.986320 TGGGCCTTTTTCAAATACATGAATATG 59.014 33.333 4.53 0.00 38.98 1.78
739 742 8.606830 ACATCCTAGTCTATGAAACTTTTTCCT 58.393 33.333 4.49 0.00 0.00 3.36
955 1007 1.400494 CATAGCCCGAAAAGGAAACCG 59.600 52.381 0.00 0.00 45.00 4.44
962 1014 3.549423 CCCGAAAAGGAAACCGAGAAAAC 60.549 47.826 0.00 0.00 45.00 2.43
970 1022 1.792118 AACCGAGAAAACAAGCCCGC 61.792 55.000 0.00 0.00 0.00 6.13
1113 1184 9.542462 TTACATTCCTGTACTCATATGCTTTAC 57.458 33.333 0.00 0.06 37.58 2.01
1118 1189 5.290493 TGTACTCATATGCTTTACCCAGG 57.710 43.478 0.00 0.00 0.00 4.45
1546 1623 0.738975 TTCGCTATGGAGTCGTGAGG 59.261 55.000 0.00 0.00 0.00 3.86
1547 1624 1.299468 CGCTATGGAGTCGTGAGGC 60.299 63.158 0.00 0.00 0.00 4.70
1600 1677 6.042143 TCAGGAAAGCTTTCAATGTTGTTTC 58.958 36.000 33.88 16.45 38.92 2.78
1602 1679 4.209080 GGAAAGCTTTCAATGTTGTTTCGG 59.791 41.667 33.88 0.00 38.92 4.30
1645 1722 1.813513 CAGAACCGCTCATCAAACCT 58.186 50.000 0.00 0.00 0.00 3.50
1757 1834 6.248569 AGTAACATATAAACACTCTGGGGG 57.751 41.667 0.00 0.00 0.00 5.40
1758 1835 3.577805 ACATATAAACACTCTGGGGGC 57.422 47.619 0.00 0.00 0.00 5.80
1845 1925 8.773033 ATTAGGGATTCTTGATTTGCAGTTAT 57.227 30.769 0.00 0.00 0.00 1.89
1873 1953 7.094205 GGTTCTGTGAATTGATCTTACAATGGT 60.094 37.037 0.00 0.00 39.88 3.55
1881 1961 9.696917 GAATTGATCTTACAATGGTGAAAACTT 57.303 29.630 0.00 0.00 39.88 2.66
1972 2718 5.480073 TGCAGCAACTAGGGTGAATTTAAAT 59.520 36.000 0.00 0.00 38.52 1.40
1983 2729 7.547227 AGGGTGAATTTAAATTCGATGGAAAG 58.453 34.615 27.49 0.00 46.01 2.62
2070 2816 1.059913 AGGTCTTGGGACACTCTTGG 58.940 55.000 0.00 0.00 43.77 3.61
2083 2829 6.235664 GGACACTCTTGGTTTTAGTATGGAA 58.764 40.000 0.00 0.00 0.00 3.53
2142 2888 6.239402 GCATTTCAGGAGCCATGGTATTATTT 60.239 38.462 14.67 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 201 2.506644 TCAATGCCTCCAGATGATCACA 59.493 45.455 0.00 0.00 0.00 3.58
598 601 8.094548 AGGCCCATTTGTTAAAAAGAGTTATTC 58.905 33.333 0.00 0.00 0.00 1.75
859 872 6.082984 GCTTCAACAACTTCTAAATGAGCTC 58.917 40.000 6.82 6.82 0.00 4.09
955 1007 2.288152 TGATTTGCGGGCTTGTTTTCTC 60.288 45.455 0.00 0.00 0.00 2.87
962 1014 0.031178 GGCTATGATTTGCGGGCTTG 59.969 55.000 0.00 0.00 0.00 4.01
970 1022 3.181483 GCTTTGGACTGGGCTATGATTTG 60.181 47.826 0.00 0.00 0.00 2.32
1038 1109 2.007049 GCGCCGATGAAGGAGAAGAAA 61.007 52.381 0.00 0.00 32.51 2.52
1299 1370 2.726351 CCTCCGAGGTCAGGGCTTC 61.726 68.421 6.24 0.00 0.00 3.86
1376 1447 8.674607 CAAACAGAATAAGTGGTACTATTTCCC 58.325 37.037 0.00 0.00 0.00 3.97
1377 1448 9.227777 ACAAACAGAATAAGTGGTACTATTTCC 57.772 33.333 0.00 0.00 0.00 3.13
1411 1487 3.810386 TCGTCGGTTCATGTCATCAAAAA 59.190 39.130 0.00 0.00 0.00 1.94
1414 1490 2.333926 GTCGTCGGTTCATGTCATCAA 58.666 47.619 0.00 0.00 0.00 2.57
1535 1612 3.069980 ATCGCAGCCTCACGACTCC 62.070 63.158 0.00 0.00 41.76 3.85
1546 1623 7.576236 ACTAATAACATGTAAATCATCGCAGC 58.424 34.615 0.00 0.00 34.09 5.25
1547 1624 9.586150 GAACTAATAACATGTAAATCATCGCAG 57.414 33.333 0.00 0.00 34.09 5.18
1580 1657 4.318050 GCCGAAACAACATTGAAAGCTTTC 60.318 41.667 28.61 28.61 37.69 2.62
1600 1677 0.461163 TACCACATGAACATCGGCCG 60.461 55.000 22.12 22.12 0.00 6.13
1602 1679 4.104776 CAAATTACCACATGAACATCGGC 58.895 43.478 0.00 0.00 0.00 5.54
1645 1722 8.261349 TCAGGTTTTACCAGTAAACTACCTAA 57.739 34.615 19.25 8.73 41.08 2.69
1845 1925 5.875224 TGTAAGATCAATTCACAGAACCCA 58.125 37.500 0.00 0.00 0.00 4.51
1873 1953 7.656542 TGCAGCATGAAATAAATGAAGTTTTCA 59.343 29.630 0.00 0.00 41.31 2.69
1881 1961 4.710865 TCCCTTGCAGCATGAAATAAATGA 59.289 37.500 9.87 0.00 39.69 2.57
1983 2729 7.434013 GCTGTCTAGTTGCTATAAAGAAGAGTC 59.566 40.741 0.00 0.00 0.00 3.36
2142 2888 7.362662 GTCACTGAAATCACATAGAAAGCAAA 58.637 34.615 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.