Multiple sequence alignment - TraesCS2A01G542200

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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 TraesCS2A01G542200 chr2A 100.000 2516 0 0 1 2516 753046103 753043588 0.000000e+00 4647
1 TraesCS2A01G542200 chr2A 93.848 764 38 7 1 762 569286833 569287589 0.000000e+00 1142
2 TraesCS2A01G542200 chr2A 92.960 767 48 5 1 765 11312594 11313356 0.000000e+00 1112
3 TraesCS2A01G542200 chr2A 87.950 805 88 6 815 1618 752999534 752998738 0.000000e+00 941
4 TraesCS2A01G542200 chr2A 86.125 800 99 11 825 1618 752977390 752976597 0.000000e+00 852
5 TraesCS2A01G542200 chr2A 90.341 352 30 2 1843 2194 752997955 752997608 2.280000e-125 459
6 TraesCS2A01G542200 chr2A 89.489 352 33 2 1843 2194 753005825 753005478 2.300000e-120 442
7 TraesCS2A01G542200 chr2A 87.941 340 15 12 2200 2516 752978837 752978501 6.570000e-101 377
8 TraesCS2A01G542200 chr2A 91.241 137 11 1 1671 1806 752998191 752998055 4.270000e-43 185
9 TraesCS2A01G542200 chr2B 93.011 1760 99 9 763 2516 762065776 762064035 0.000000e+00 2547
10 TraesCS2A01G542200 chr2B 86.849 806 94 9 817 1618 762063319 762062522 0.000000e+00 891
11 TraesCS2A01G542200 chrUn 92.811 1711 98 10 763 2466 307394216 307395908 0.000000e+00 2455
12 TraesCS2A01G542200 chrUn 87.469 806 89 9 817 1618 314618585 314617788 0.000000e+00 918
13 TraesCS2A01G542200 chrUn 85.732 806 106 6 814 1618 329049461 329048664 0.000000e+00 843
14 TraesCS2A01G542200 chrUn 87.793 426 42 8 1783 2198 23362135 23362560 8.090000e-135 490
15 TraesCS2A01G542200 chrUn 87.793 426 42 8 1783 2198 329050999 329050574 8.090000e-135 490
16 TraesCS2A01G542200 chr2D 94.384 1478 60 8 1042 2516 621131901 621130444 0.000000e+00 2248
17 TraesCS2A01G542200 chr2D 86.358 799 97 9 817 1611 621129699 621128909 0.000000e+00 861
18 TraesCS2A01G542200 chr2D 86.392 801 94 8 821 1618 621265593 621264805 0.000000e+00 861
19 TraesCS2A01G542200 chr2D 85.897 546 50 17 1671 2194 621315048 621314508 7.860000e-155 556
20 TraesCS2A01G542200 chr2D 80.893 403 40 15 1610 1990 621151625 621151238 1.470000e-72 283
21 TraesCS2A01G542200 chr2D 93.671 158 10 0 2037 2194 621151250 621151093 1.160000e-58 237
22 TraesCS2A01G542200 chr2D 99.000 100 1 0 765 864 621132000 621131901 1.990000e-41 180
23 TraesCS2A01G542200 chr1A 93.971 763 40 6 1 762 469647933 469648690 0.000000e+00 1149
24 TraesCS2A01G542200 chr6A 93.742 767 44 4 1 765 91382557 91381793 0.000000e+00 1147
25 TraesCS2A01G542200 chr4A 93.099 768 49 4 1 767 629119942 629119178 0.000000e+00 1122
26 TraesCS2A01G542200 chr4A 93.054 763 48 5 1 762 497879367 497878609 0.000000e+00 1110
27 TraesCS2A01G542200 chr3A 93.185 763 47 3 1 762 518485076 518484318 0.000000e+00 1116
28 TraesCS2A01G542200 chr7A 92.866 771 50 4 1 769 514890366 514891133 0.000000e+00 1114
29 TraesCS2A01G542200 chr7A 93.054 763 42 7 1 762 706430061 706430813 0.000000e+00 1105


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 TraesCS2A01G542200 chr2A 753043588 753046103 2515 True 4647.000000 4647 100.000000 1 2516 1 chr2A.!!$R2 2515
1 TraesCS2A01G542200 chr2A 569286833 569287589 756 False 1142.000000 1142 93.848000 1 762 1 chr2A.!!$F2 761
2 TraesCS2A01G542200 chr2A 11312594 11313356 762 False 1112.000000 1112 92.960000 1 765 1 chr2A.!!$F1 764
3 TraesCS2A01G542200 chr2A 752976597 752978837 2240 True 614.500000 852 87.033000 825 2516 2 chr2A.!!$R3 1691
4 TraesCS2A01G542200 chr2A 752997608 752999534 1926 True 528.333333 941 89.844000 815 2194 3 chr2A.!!$R4 1379
5 TraesCS2A01G542200 chr2B 762062522 762065776 3254 True 1719.000000 2547 89.930000 763 2516 2 chr2B.!!$R1 1753
6 TraesCS2A01G542200 chrUn 307394216 307395908 1692 False 2455.000000 2455 92.811000 763 2466 1 chrUn.!!$F2 1703
7 TraesCS2A01G542200 chrUn 314617788 314618585 797 True 918.000000 918 87.469000 817 1618 1 chrUn.!!$R1 801
8 TraesCS2A01G542200 chrUn 329048664 329050999 2335 True 666.500000 843 86.762500 814 2198 2 chrUn.!!$R2 1384
9 TraesCS2A01G542200 chr2D 621128909 621132000 3091 True 1096.333333 2248 93.247333 765 2516 3 chr2D.!!$R3 1751
10 TraesCS2A01G542200 chr2D 621264805 621265593 788 True 861.000000 861 86.392000 821 1618 1 chr2D.!!$R1 797
11 TraesCS2A01G542200 chr2D 621314508 621315048 540 True 556.000000 556 85.897000 1671 2194 1 chr2D.!!$R2 523
12 TraesCS2A01G542200 chr2D 621151093 621151625 532 True 260.000000 283 87.282000 1610 2194 2 chr2D.!!$R4 584
13 TraesCS2A01G542200 chr1A 469647933 469648690 757 False 1149.000000 1149 93.971000 1 762 1 chr1A.!!$F1 761
14 TraesCS2A01G542200 chr6A 91381793 91382557 764 True 1147.000000 1147 93.742000 1 765 1 chr6A.!!$R1 764
15 TraesCS2A01G542200 chr4A 629119178 629119942 764 True 1122.000000 1122 93.099000 1 767 1 chr4A.!!$R2 766
16 TraesCS2A01G542200 chr4A 497878609 497879367 758 True 1110.000000 1110 93.054000 1 762 1 chr4A.!!$R1 761
17 TraesCS2A01G542200 chr3A 518484318 518485076 758 True 1116.000000 1116 93.185000 1 762 1 chr3A.!!$R1 761
18 TraesCS2A01G542200 chr7A 514890366 514891133 767 False 1114.000000 1114 92.866000 1 769 1 chr7A.!!$F1 768
19 TraesCS2A01G542200 chr7A 706430061 706430813 752 False 1105.000000 1105 93.054000 1 762 1 chr7A.!!$F2 761

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
725 735 1.181786 GGACAAAATCCGGCCAATCA 58.818 50.0 2.24 0.0 37.88 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 3186 1.099879 GCAGTCCAGGATGATGCACC 61.1 60.0 15.84 0.0 39.69 5.01 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
269 273 2.038329 CCACGGGAGGAGGTGGTA 59.962 66.667 2.11 0.00 46.79 3.25
725 735 1.181786 GGACAAAATCCGGCCAATCA 58.818 50.000 2.24 0.00 37.88 2.57
878 1611 2.224066 GGCATAGCCTGTAGTGTACTGG 60.224 54.545 0.00 5.81 46.69 4.00
935 1668 2.287547 GCAAACACAATCTCCGCTCAAA 60.288 45.455 0.00 0.00 0.00 2.69
955 1688 2.365582 AGACCAACACAACAACACCTC 58.634 47.619 0.00 0.00 0.00 3.85
956 1689 2.088423 GACCAACACAACAACACCTCA 58.912 47.619 0.00 0.00 0.00 3.86
1077 1817 2.289820 CGCATCTGCAGCAATCTACAAT 59.710 45.455 9.47 0.00 42.21 2.71
1264 2005 1.754380 CGTCACCACCCTCAACTCCA 61.754 60.000 0.00 0.00 0.00 3.86
1292 2033 2.525124 TTGTCACCCTCACCGCCAT 61.525 57.895 0.00 0.00 0.00 4.40
1332 2073 1.606313 CGGTTTCCCTGGCCATTGT 60.606 57.895 5.51 0.00 0.00 2.71
1357 2098 2.013563 GCGGCATGAAGGTCAAGATCA 61.014 52.381 0.00 0.00 0.00 2.92
1503 2244 2.037620 TTTTGCTTGCCATTGCCGGT 62.038 50.000 1.90 0.00 36.33 5.28
1536 2277 2.125952 CATCTCGGCAGTCGCACA 60.126 61.111 0.00 0.00 41.24 4.57
1675 2924 8.908903 TGATTTGTTTTACACCTTCACTTACAT 58.091 29.630 0.00 0.00 0.00 2.29
1689 2938 8.072567 CCTTCACTTACATCTTTCAAGTTTCAG 58.927 37.037 0.00 0.00 30.20 3.02
1731 2980 3.288964 TCCAACTTAAAAGGCCAACGAA 58.711 40.909 5.01 0.00 0.00 3.85
1863 3180 3.316588 TGCATGTTGAACCGTACAATTGT 59.683 39.130 16.68 16.68 0.00 2.71
1869 3186 1.461897 GAACCGTACAATTGTCCCACG 59.538 52.381 20.37 20.37 0.00 4.94
1890 3207 0.107361 TGCATCATCCTGGACTGCAG 60.107 55.000 20.32 13.48 37.88 4.41
1980 3297 2.855514 GCCTTGTCTTGGCGGCAAA 61.856 57.895 25.45 13.40 42.06 3.68
2006 3323 4.037222 TCTCCTACCATTTGGCATGACTA 58.963 43.478 0.00 0.00 39.32 2.59
2194 3569 8.092687 GGACTACTTTTGATACTAGTGTTGGAA 58.907 37.037 5.39 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
647 656 2.819595 GATGGGTCATGCGTGCGT 60.820 61.111 0.00 0.00 0.00 5.24
725 735 2.845795 ACCCCAAACGGACGTCCT 60.846 61.111 30.92 16.03 0.00 3.85
878 1611 5.392811 GCTGTGTCGGGTCCTATATATACAC 60.393 48.000 0.00 0.00 37.18 2.90
935 1668 2.290641 TGAGGTGTTGTTGTGTTGGTCT 60.291 45.455 0.00 0.00 0.00 3.85
1104 1844 1.000607 GTGTCGTAGTTGGTGCTGAGA 60.001 52.381 0.00 0.00 0.00 3.27
1264 2005 2.644299 TGAGGGTGACAACATCATTCCT 59.356 45.455 3.19 0.00 42.84 3.36
1357 2098 0.106819 GAGGAGCCTGGCATGACATT 60.107 55.000 22.65 0.00 0.00 2.71
1655 2904 8.617809 TGAAAGATGTAAGTGAAGGTGTAAAAC 58.382 33.333 0.00 0.00 0.00 2.43
1675 2924 4.955925 TTTGTCGCTGAAACTTGAAAGA 57.044 36.364 0.00 0.00 0.00 2.52
1863 3180 1.995066 AGGATGATGCACCGTGGGA 60.995 57.895 0.00 0.00 0.00 4.37
1869 3186 1.099879 GCAGTCCAGGATGATGCACC 61.100 60.000 15.84 0.00 39.69 5.01
1916 3233 9.715123 TTCAGTTTAATAATACATCGCACAATG 57.285 29.630 0.00 0.00 0.00 2.82
1964 3281 1.270550 AGATTTTGCCGCCAAGACAAG 59.729 47.619 0.00 0.00 31.52 3.16
1965 3282 1.269448 GAGATTTTGCCGCCAAGACAA 59.731 47.619 0.00 0.00 31.52 3.18
1977 3294 4.706476 TGCCAAATGGTAGGAGAGATTTTG 59.294 41.667 0.71 0.00 37.57 2.44
1980 3297 4.166725 TCATGCCAAATGGTAGGAGAGATT 59.833 41.667 0.63 0.00 35.76 2.40
2229 3604 4.584325 AGTTGAATTGCAGGCTGAAAACTA 59.416 37.500 20.86 7.21 0.00 2.24
2274 3651 6.377996 ACTGTTGCTGCCAAGATAAATATGAA 59.622 34.615 0.00 0.00 0.00 2.57
2350 3727 8.600449 TTGCCACTTCAAAATTTATTTTCGAT 57.400 26.923 0.00 0.00 37.86 3.59
2388 3765 3.247442 CATCTTTGCATGCGTGTCAATT 58.753 40.909 14.09 0.00 0.00 2.32
2390 3767 1.608109 ACATCTTTGCATGCGTGTCAA 59.392 42.857 14.09 9.45 0.00 3.18
2392 3769 3.680642 ATACATCTTTGCATGCGTGTC 57.319 42.857 14.09 0.53 0.00 3.67
2393 3770 4.439305 AAATACATCTTTGCATGCGTGT 57.561 36.364 14.09 14.05 0.00 4.49


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

AutoCloner maintained by Alex Coulton.