Multiple sequence alignment - TraesCS4D01G149000

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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 TraesCS4D01G149000 chr4D 100.000 1778 0 0 634 2411 151983895 151982118 0.000000e+00 3284
1 TraesCS4D01G149000 chr4D 100.000 218 0 0 1 218 151984528 151984311 1.040000e-108 403
2 TraesCS4D01G149000 chr4A 90.083 1815 59 39 634 2407 253446274 253444540 0.000000e+00 2242
3 TraesCS4D01G149000 chr4A 95.455 220 2 5 1 218 253446624 253446411 6.380000e-91 344
4 TraesCS4D01G149000 chr4B 93.878 1323 28 14 634 1938 221199876 221198589 0.000000e+00 1945
5 TraesCS4D01G149000 chr4B 93.953 430 17 4 1989 2411 221198323 221197896 2.020000e-180 641
6 TraesCS4D01G149000 chr4B 95.413 218 1 7 4 218 221200228 221200017 2.970000e-89 339


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 TraesCS4D01G149000 chr4D 151982118 151984528 2410 True 1843.5 3284 100.000000 1 2411 2 chr4D.!!$R1 2410
1 TraesCS4D01G149000 chr4A 253444540 253446624 2084 True 1293.0 2242 92.769000 1 2407 2 chr4A.!!$R1 2406
2 TraesCS4D01G149000 chr4B 221197896 221200228 2332 True 975.0 1945 94.414667 4 2411 3 chr4B.!!$R1 2407

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
939 961 2.53225 ATGGGTCAATTTCAGGGGAC 57.468 50.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2555 0.032815 GCTTAGATCAGGGACCGAGC 59.967 60.0 0.0 0.0 0.0 5.03 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
37 38 2.766263 TCTCTCTCCTTGTGTGTGTGTT 59.234 45.455 0.00 0.00 0.00 3.32
39 40 3.941483 CTCTCTCCTTGTGTGTGTGTTTT 59.059 43.478 0.00 0.00 0.00 2.43
793 815 3.782046 CGTGCTAGTATTGCCTTGTACT 58.218 45.455 0.00 0.00 35.47 2.73
794 816 4.735578 GCGTGCTAGTATTGCCTTGTACTA 60.736 45.833 0.00 0.00 33.48 1.82
795 817 4.976731 CGTGCTAGTATTGCCTTGTACTAG 59.023 45.833 12.80 12.80 46.75 2.57
796 818 5.450137 CGTGCTAGTATTGCCTTGTACTAGT 60.450 44.000 16.49 0.00 46.18 2.57
797 819 6.238566 CGTGCTAGTATTGCCTTGTACTAGTA 60.239 42.308 16.49 11.71 46.18 1.82
798 820 7.035840 TGCTAGTATTGCCTTGTACTAGTAC 57.964 40.000 23.58 23.58 46.18 2.73
939 961 2.532250 ATGGGTCAATTTCAGGGGAC 57.468 50.000 0.00 0.00 0.00 4.46
1119 1144 1.338973 ACGTTCCACAAGAGCTTCGTA 59.661 47.619 0.00 0.00 0.00 3.43
1545 1583 4.580868 AGGCTAGTTCTTCCTTGCTTAAC 58.419 43.478 0.00 0.00 34.29 2.01
1557 1595 0.591170 TGCTTAACTTCTTGCCGTGC 59.409 50.000 0.00 0.00 0.00 5.34
1558 1596 0.875059 GCTTAACTTCTTGCCGTGCT 59.125 50.000 0.00 0.00 0.00 4.40
1559 1597 1.266989 GCTTAACTTCTTGCCGTGCTT 59.733 47.619 0.00 0.00 0.00 3.91
1753 1797 8.519526 CCAGGTATACAGTTAATCTGAGAGATC 58.480 40.741 5.01 0.00 46.27 2.75
1770 1814 5.200483 AGAGATCTGGGAGTTCTTGAGTAG 58.800 45.833 0.00 0.00 0.00 2.57
1772 1816 6.069323 AGAGATCTGGGAGTTCTTGAGTAGTA 60.069 42.308 0.00 0.00 0.00 1.82
1774 1818 7.129425 AGATCTGGGAGTTCTTGAGTAGTATT 58.871 38.462 0.00 0.00 0.00 1.89
1776 1820 7.554959 TCTGGGAGTTCTTGAGTAGTATTTT 57.445 36.000 0.00 0.00 0.00 1.82
1777 1821 7.612677 TCTGGGAGTTCTTGAGTAGTATTTTC 58.387 38.462 0.00 0.00 0.00 2.29
1857 1901 1.762708 ATACCGTTGCCCTTGGATTG 58.237 50.000 0.00 0.00 0.00 2.67
1870 1914 1.307878 TGGATTGGGATGGACCATGT 58.692 50.000 12.99 0.00 40.91 3.21
2028 2292 4.882427 ACGACTTGCTTCTACTGCTAGATA 59.118 41.667 0.00 0.00 36.91 1.98
2285 2555 0.594602 CCTGTGTGTGTGGCATCTTG 59.405 55.000 0.00 0.00 0.00 3.02
2308 2580 2.891580 TCGGTCCCTGATCTAAGCATAC 59.108 50.000 0.00 0.00 0.00 2.39
2340 2612 1.179152 CCACTGATTTGGCATGCTGA 58.821 50.000 18.92 3.32 0.00 4.26
2342 2614 2.167693 CCACTGATTTGGCATGCTGAAT 59.832 45.455 18.92 16.94 0.00 2.57
2391 2663 4.128643 CTGTCTACGGTAACAAACCCAAA 58.871 43.478 0.00 0.00 46.62 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.412591 AGGAGAGAGAGAGAGAGAGGG 58.587 57.143 0.00 0.00 0.00 4.30
37 38 4.447762 CCCTCTTTCTTCTCCCAGGAAAAA 60.448 45.833 0.00 0.00 0.00 1.94
39 40 2.644798 CCCTCTTTCTTCTCCCAGGAAA 59.355 50.000 0.00 0.00 0.00 3.13
42 43 1.557371 GTCCCTCTTTCTTCTCCCAGG 59.443 57.143 0.00 0.00 0.00 4.45
793 815 7.502696 AGAATAAATGTGCGGGTATTGTACTA 58.497 34.615 0.00 0.00 0.00 1.82
794 816 6.354130 AGAATAAATGTGCGGGTATTGTACT 58.646 36.000 0.00 0.00 0.00 2.73
795 817 6.613755 AGAATAAATGTGCGGGTATTGTAC 57.386 37.500 0.00 0.00 0.00 2.90
796 818 7.121463 ACAAAGAATAAATGTGCGGGTATTGTA 59.879 33.333 0.00 0.00 0.00 2.41
797 819 6.071616 ACAAAGAATAAATGTGCGGGTATTGT 60.072 34.615 0.00 0.00 0.00 2.71
798 820 6.253298 CACAAAGAATAAATGTGCGGGTATTG 59.747 38.462 0.00 0.00 38.14 1.90
824 846 7.504238 ACCCATCAAGAACATCTAGTCTACTAG 59.496 40.741 10.35 10.35 45.57 2.57
825 847 7.355101 ACCCATCAAGAACATCTAGTCTACTA 58.645 38.462 0.00 0.00 0.00 1.82
826 848 6.198639 ACCCATCAAGAACATCTAGTCTACT 58.801 40.000 0.00 0.00 0.00 2.57
827 849 6.322712 AGACCCATCAAGAACATCTAGTCTAC 59.677 42.308 0.00 0.00 0.00 2.59
828 850 6.436027 AGACCCATCAAGAACATCTAGTCTA 58.564 40.000 0.00 0.00 0.00 2.59
829 851 5.276440 AGACCCATCAAGAACATCTAGTCT 58.724 41.667 0.00 0.00 0.00 3.24
830 852 5.606348 AGACCCATCAAGAACATCTAGTC 57.394 43.478 0.00 0.00 0.00 2.59
831 853 6.380079 AAAGACCCATCAAGAACATCTAGT 57.620 37.500 0.00 0.00 0.00 2.57
939 961 2.649190 TCACCAGAGCTAGCTAGAGTG 58.351 52.381 25.15 24.36 0.00 3.51
1119 1144 1.298993 CAGGATGCTCTGCACCTGT 59.701 57.895 21.56 0.00 44.58 4.00
1469 1507 6.214191 TCTCATCAGTAACTCACATCCTTC 57.786 41.667 0.00 0.00 0.00 3.46
1545 1583 1.517242 AGAAGAAGCACGGCAAGAAG 58.483 50.000 0.00 0.00 0.00 2.85
1557 1595 2.549754 TGCGGCAAAGAAGAAGAAGAAG 59.450 45.455 0.00 0.00 0.00 2.85
1558 1596 2.571212 TGCGGCAAAGAAGAAGAAGAA 58.429 42.857 0.00 0.00 0.00 2.52
1559 1597 2.254546 TGCGGCAAAGAAGAAGAAGA 57.745 45.000 0.00 0.00 0.00 2.87
1753 1797 7.616313 AGAAAATACTACTCAAGAACTCCCAG 58.384 38.462 0.00 0.00 0.00 4.45
1857 1901 1.986882 GGATCAACATGGTCCATCCC 58.013 55.000 0.00 0.00 46.88 3.85
1870 1914 5.065090 CAGTACATGCGAATTTCAGGATCAA 59.935 40.000 0.00 0.00 0.00 2.57
1946 1990 2.092699 GGGAAAGATGACAGGGGAGAAG 60.093 54.545 0.00 0.00 0.00 2.85
1954 1998 3.262915 AGGACAGAAGGGAAAGATGACAG 59.737 47.826 0.00 0.00 0.00 3.51
2189 2457 3.119884 GGCAGCCCAAAAATTATTGCAAC 60.120 43.478 0.00 0.00 0.00 4.17
2285 2555 0.032815 GCTTAGATCAGGGACCGAGC 59.967 60.000 0.00 0.00 0.00 5.03
2308 2580 4.568152 AATCAGTGGTCAAAAAGGTTCG 57.432 40.909 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.