Multiple sequence alignment - TraesCS6D01G131400

Loading Multiple Alignment...

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 TraesCS6D01G131400 chr6D 100.000 2460 0 0 1 2460 97866593 97869052 0.000000e+00 4543.0
1 TraesCS6D01G131400 chr6D 87.215 876 54 29 819 1651 97808252 97809112 0.000000e+00 944.0
2 TraesCS6D01G131400 chr6D 80.645 589 92 8 127 707 97784210 97784784 1.040000e-118 436.0
3 TraesCS6D01G131400 chr6D 93.860 114 6 1 2120 2233 77237160 77237048 1.170000e-38 171.0
4 TraesCS6D01G131400 chr6D 100.000 34 0 0 856 889 97867422 97867455 2.040000e-06 63.9
5 TraesCS6D01G131400 chr6D 100.000 34 0 0 830 863 97867448 97867481 2.040000e-06 63.9
6 TraesCS6D01G131400 chr1D 98.692 1605 9 3 856 2460 212426186 212424594 0.000000e+00 2837.0
7 TraesCS6D01G131400 chr1D 98.610 863 12 0 1 863 212427015 212426153 0.000000e+00 1528.0
8 TraesCS6D01G131400 chr1D 93.277 119 7 1 2115 2233 3824268 3824151 9.040000e-40 174.0
9 TraesCS6D01G131400 chr6B 91.017 2026 113 32 87 2073 182574857 182576852 0.000000e+00 2669.0
10 TraesCS6D01G131400 chr6B 93.273 773 46 5 1 769 182483615 182484385 0.000000e+00 1134.0
11 TraesCS6D01G131400 chr6B 88.764 267 14 3 823 1089 182353954 182354204 1.840000e-81 313.0
12 TraesCS6D01G131400 chr6B 89.952 209 14 4 1088 1295 182355650 182355852 1.880000e-66 263.0
13 TraesCS6D01G131400 chr6A 86.453 716 46 19 1109 1803 116859841 116860526 0.000000e+00 737.0
14 TraesCS6D01G131400 chrUn 100.000 395 0 0 1592 1986 479309630 479310024 0.000000e+00 730.0
15 TraesCS6D01G131400 chr2B 97.436 117 3 0 2117 2233 777494908 777495024 1.490000e-47 200.0
16 TraesCS6D01G131400 chr2B 95.763 118 4 1 2117 2233 534232622 534232739 3.230000e-44 189.0
17 TraesCS6D01G131400 chr5A 95.763 118 4 1 2116 2233 624724325 624724209 3.230000e-44 189.0
18 TraesCS6D01G131400 chr5A 91.736 121 6 1 2117 2233 7813740 7813860 5.440000e-37 165.0
19 TraesCS6D01G131400 chr5D 90.769 130 8 1 2108 2233 477331907 477332036 1.170000e-38 171.0
20 TraesCS6D01G131400 chr1A 94.393 107 6 0 2117 2223 462713247 462713353 5.440000e-37 165.0
21 TraesCS6D01G131400 chr3D 86.885 122 16 0 12 133 478106135 478106014 1.190000e-28 137.0
22 TraesCS6D01G131400 chr4A 96.970 33 1 0 2235 2267 618101627 618101595 3.420000e-04 56.5


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 TraesCS6D01G131400 chr6D 97866593 97869052 2459 False 1556.933333 4543 100.000 1 2460 3 chr6D.!!$F3 2459
1 TraesCS6D01G131400 chr6D 97808252 97809112 860 False 944.000000 944 87.215 819 1651 1 chr6D.!!$F2 832
2 TraesCS6D01G131400 chr6D 97784210 97784784 574 False 436.000000 436 80.645 127 707 1 chr6D.!!$F1 580
3 TraesCS6D01G131400 chr1D 212424594 212427015 2421 True 2182.500000 2837 98.651 1 2460 2 chr1D.!!$R2 2459
4 TraesCS6D01G131400 chr6B 182574857 182576852 1995 False 2669.000000 2669 91.017 87 2073 1 chr6B.!!$F2 1986
5 TraesCS6D01G131400 chr6B 182483615 182484385 770 False 1134.000000 1134 93.273 1 769 1 chr6B.!!$F1 768
6 TraesCS6D01G131400 chr6B 182353954 182355852 1898 False 288.000000 313 89.358 823 1295 2 chr6B.!!$F3 472
7 TraesCS6D01G131400 chr6A 116859841 116860526 685 False 737.000000 737 86.453 1109 1803 1 chr6A.!!$F1 694

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
872 883 0.179179 GCAAAGATGAGCTGCCGTTC 60.179 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 3673 0.317479 GGGAGTAGTTGTCAGCGTGT 59.683 55.0 0.0 0.0 0.0 4.49 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
51 52 0.880718 TGCGTTCGTGCCATGTGTTA 60.881 50.000 0.00 0.00 0.00 2.41
89 90 7.911651 ACTCATTTCTCTTCCTTCTATCAACA 58.088 34.615 0.00 0.00 0.00 3.33
612 622 4.448060 GGTCTTTCTCGACGACAGAAAAAT 59.552 41.667 11.84 0.00 38.98 1.82
860 871 1.464997 GCCGTTCTCTTTCGCAAAGAT 59.535 47.619 10.45 0.00 45.75 2.40
861 872 2.726066 GCCGTTCTCTTTCGCAAAGATG 60.726 50.000 10.45 6.71 45.75 2.90
862 873 2.736721 CCGTTCTCTTTCGCAAAGATGA 59.263 45.455 10.45 8.29 45.75 2.92
863 874 3.181526 CCGTTCTCTTTCGCAAAGATGAG 60.182 47.826 10.45 0.00 45.75 2.90
864 875 3.723250 CGTTCTCTTTCGCAAAGATGAGC 60.723 47.826 10.45 10.57 45.75 4.26
865 876 3.325293 TCTCTTTCGCAAAGATGAGCT 57.675 42.857 10.45 0.00 45.75 4.09
866 877 2.998670 TCTCTTTCGCAAAGATGAGCTG 59.001 45.455 10.45 1.52 45.75 4.24
867 878 1.466167 TCTTTCGCAAAGATGAGCTGC 59.534 47.619 0.00 0.00 42.31 5.25
868 879 0.523072 TTTCGCAAAGATGAGCTGCC 59.477 50.000 0.00 0.00 32.27 4.85
869 880 1.638388 TTCGCAAAGATGAGCTGCCG 61.638 55.000 0.00 0.00 32.27 5.69
870 881 2.393768 CGCAAAGATGAGCTGCCGT 61.394 57.895 0.00 0.00 32.27 5.68
871 882 1.878775 GCAAAGATGAGCTGCCGTT 59.121 52.632 0.00 0.00 0.00 4.44
872 883 0.179179 GCAAAGATGAGCTGCCGTTC 60.179 55.000 0.00 0.00 0.00 3.95
873 884 1.446907 CAAAGATGAGCTGCCGTTCT 58.553 50.000 0.00 0.00 0.00 3.01
874 885 1.396301 CAAAGATGAGCTGCCGTTCTC 59.604 52.381 0.00 0.00 0.00 2.87
875 886 0.901124 AAGATGAGCTGCCGTTCTCT 59.099 50.000 0.00 0.00 0.00 3.10
876 887 0.901124 AGATGAGCTGCCGTTCTCTT 59.099 50.000 0.00 0.00 0.00 2.85
877 888 1.277557 AGATGAGCTGCCGTTCTCTTT 59.722 47.619 0.00 0.00 0.00 2.52
878 889 1.663135 GATGAGCTGCCGTTCTCTTTC 59.337 52.381 0.00 0.00 0.00 2.62
879 890 0.667487 TGAGCTGCCGTTCTCTTTCG 60.667 55.000 0.00 0.00 0.00 3.46
880 891 1.960994 GAGCTGCCGTTCTCTTTCGC 61.961 60.000 0.00 0.00 0.00 4.70
881 892 2.317609 GCTGCCGTTCTCTTTCGCA 61.318 57.895 0.00 0.00 0.00 5.10
882 893 1.841663 GCTGCCGTTCTCTTTCGCAA 61.842 55.000 0.00 0.00 0.00 4.85
883 894 0.586319 CTGCCGTTCTCTTTCGCAAA 59.414 50.000 0.00 0.00 0.00 3.68
884 895 0.586319 TGCCGTTCTCTTTCGCAAAG 59.414 50.000 3.17 3.17 39.88 2.77
885 896 0.865769 GCCGTTCTCTTTCGCAAAGA 59.134 50.000 9.84 9.84 44.82 2.52
1584 3124 1.529865 GCTGTTTCAACGGTAGTGGTC 59.470 52.381 0.56 0.00 37.60 4.02
1986 3553 6.287525 CACAAACTGTGGGATTTATTGGTTT 58.712 36.000 0.00 0.00 44.27 3.27
2137 3707 4.720273 ACTACTCCCTCCGTTCCAAATTAT 59.280 41.667 0.00 0.00 0.00 1.28
2271 3841 2.027007 CCAAAGTTATACGTGGGTGGGA 60.027 50.000 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
710 720 1.076412 TGGAAACAAGGGTGCTGCA 60.076 52.632 0.00 0.00 37.44 4.41
860 871 0.667487 CGAAAGAGAACGGCAGCTCA 60.667 55.000 0.00 0.00 33.62 4.26
861 872 1.960994 GCGAAAGAGAACGGCAGCTC 61.961 60.000 0.00 0.00 0.00 4.09
862 873 2.029844 GCGAAAGAGAACGGCAGCT 61.030 57.895 0.00 0.00 0.00 4.24
863 874 1.841663 TTGCGAAAGAGAACGGCAGC 61.842 55.000 0.00 0.00 0.00 5.25
864 875 0.586319 TTTGCGAAAGAGAACGGCAG 59.414 50.000 0.00 0.00 0.00 4.85
865 876 0.586319 CTTTGCGAAAGAGAACGGCA 59.414 50.000 3.41 0.00 41.02 5.69
866 877 0.865769 TCTTTGCGAAAGAGAACGGC 59.134 50.000 7.09 0.00 42.31 5.68
874 885 8.724229 TCATGGATATATTCATCTTTGCGAAAG 58.276 33.333 3.27 0.00 39.88 2.62
875 886 8.620116 TCATGGATATATTCATCTTTGCGAAA 57.380 30.769 3.27 0.00 0.00 3.46
876 887 8.620116 TTCATGGATATATTCATCTTTGCGAA 57.380 30.769 3.27 1.49 0.00 4.70
877 888 8.620116 TTTCATGGATATATTCATCTTTGCGA 57.380 30.769 3.27 0.00 0.00 5.10
878 889 9.338291 CTTTTCATGGATATATTCATCTTTGCG 57.662 33.333 3.27 0.00 0.00 4.85
2102 3672 1.270147 GGGAGTAGTTGTCAGCGTGTT 60.270 52.381 0.00 0.00 0.00 3.32
2103 3673 0.317479 GGGAGTAGTTGTCAGCGTGT 59.683 55.000 0.00 0.00 0.00 4.49
2137 3707 5.738118 ATTTGAACTAAAACCACGACGAA 57.262 34.783 0.00 0.00 0.00 3.85
2278 3848 5.583854 GTCATCAAGCACATGTCAAGTAGAT 59.416 40.000 0.00 0.00 0.00 1.98
2343 3913 4.025401 GCACAAGCGGAACCCACG 62.025 66.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.