Multiple sequence alignment - TraesCS2D01G196000

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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 TraesCS2D01G196000 chr2D 100.000 2473 0 0 1 2473 142523399 142520927 0 4567
1 TraesCS2D01G196000 chr2D 95.773 1987 59 5 1 1963 588796878 588794893 0 3181
2 TraesCS2D01G196000 chr2D 95.619 1986 61 13 1 1962 476878749 476880732 0 3162
3 TraesCS2D01G196000 chr2D 95.391 1584 55 7 387 1952 130840024 130838441 0 2505
4 TraesCS2D01G196000 chr2D 96.512 516 18 0 1958 2473 155852139 155852654 0 854
5 TraesCS2D01G196000 chr5D 95.926 1988 50 8 1 1962 365120459 365118477 0 3193
6 TraesCS2D01G196000 chr5D 95.521 1987 62 7 1 1962 304884343 304882359 0 3151
7 TraesCS2D01G196000 chr5D 96.899 516 16 0 1958 2473 340772383 340772898 0 865
8 TraesCS2D01G196000 chr1D 95.850 1976 63 7 1 1961 464935392 464937363 0 3177
9 TraesCS2D01G196000 chr1D 96.512 516 18 0 1958 2473 138638460 138638975 0 854
10 TraesCS2D01G196000 chr1D 96.686 513 17 0 1961 2473 143842185 143841673 0 854
11 TraesCS2D01G196000 chr7D 95.540 1749 60 8 1 1736 203038673 203036930 0 2782
12 TraesCS2D01G196000 chr7D 96.881 513 16 0 1961 2473 609931621 609931109 0 859
13 TraesCS2D01G196000 chr3A 93.418 1884 104 10 96 1963 658727946 658726067 0 2774
14 TraesCS2D01G196000 chr3D 95.369 1749 67 7 1 1736 365508992 365507245 0 2769
15 TraesCS2D01G196000 chr3D 96.512 516 18 0 1958 2473 140970272 140970787 0 854
16 TraesCS2D01G196000 chr3D 96.512 516 18 0 1958 2473 368326551 368327066 0 854
17 TraesCS2D01G196000 chr4B 90.519 1656 132 8 1 1633 456359503 456357850 0 2165
18 TraesCS2D01G196000 chr3B 90.235 1659 125 17 1 1633 741700720 741699073 0 2132
19 TraesCS2D01G196000 chr6B 90.012 1642 135 12 15 1633 46354155 46355790 0 2097
20 TraesCS2D01G196000 chr1A 89.640 1583 114 20 56 1633 405356358 405354821 0 1969
21 TraesCS2D01G196000 chr4D 96.881 513 15 1 1961 2473 260601863 260601352 0 857
22 TraesCS2D01G196000 chr4D 96.686 513 16 1 1961 2473 75302632 75302121 0 852


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 TraesCS2D01G196000 chr2D 142520927 142523399 2472 True 4567 4567 100.000 1 2473 1 chr2D.!!$R2 2472
1 TraesCS2D01G196000 chr2D 588794893 588796878 1985 True 3181 3181 95.773 1 1963 1 chr2D.!!$R3 1962
2 TraesCS2D01G196000 chr2D 476878749 476880732 1983 False 3162 3162 95.619 1 1962 1 chr2D.!!$F2 1961
3 TraesCS2D01G196000 chr2D 130838441 130840024 1583 True 2505 2505 95.391 387 1952 1 chr2D.!!$R1 1565
4 TraesCS2D01G196000 chr2D 155852139 155852654 515 False 854 854 96.512 1958 2473 1 chr2D.!!$F1 515
5 TraesCS2D01G196000 chr5D 365118477 365120459 1982 True 3193 3193 95.926 1 1962 1 chr5D.!!$R2 1961
6 TraesCS2D01G196000 chr5D 304882359 304884343 1984 True 3151 3151 95.521 1 1962 1 chr5D.!!$R1 1961
7 TraesCS2D01G196000 chr5D 340772383 340772898 515 False 865 865 96.899 1958 2473 1 chr5D.!!$F1 515
8 TraesCS2D01G196000 chr1D 464935392 464937363 1971 False 3177 3177 95.850 1 1961 1 chr1D.!!$F2 1960
9 TraesCS2D01G196000 chr1D 138638460 138638975 515 False 854 854 96.512 1958 2473 1 chr1D.!!$F1 515
10 TraesCS2D01G196000 chr1D 143841673 143842185 512 True 854 854 96.686 1961 2473 1 chr1D.!!$R1 512
11 TraesCS2D01G196000 chr7D 203036930 203038673 1743 True 2782 2782 95.540 1 1736 1 chr7D.!!$R1 1735
12 TraesCS2D01G196000 chr7D 609931109 609931621 512 True 859 859 96.881 1961 2473 1 chr7D.!!$R2 512
13 TraesCS2D01G196000 chr3A 658726067 658727946 1879 True 2774 2774 93.418 96 1963 1 chr3A.!!$R1 1867
14 TraesCS2D01G196000 chr3D 365507245 365508992 1747 True 2769 2769 95.369 1 1736 1 chr3D.!!$R1 1735
15 TraesCS2D01G196000 chr3D 140970272 140970787 515 False 854 854 96.512 1958 2473 1 chr3D.!!$F1 515
16 TraesCS2D01G196000 chr3D 368326551 368327066 515 False 854 854 96.512 1958 2473 1 chr3D.!!$F2 515
17 TraesCS2D01G196000 chr4B 456357850 456359503 1653 True 2165 2165 90.519 1 1633 1 chr4B.!!$R1 1632
18 TraesCS2D01G196000 chr3B 741699073 741700720 1647 True 2132 2132 90.235 1 1633 1 chr3B.!!$R1 1632
19 TraesCS2D01G196000 chr6B 46354155 46355790 1635 False 2097 2097 90.012 15 1633 1 chr6B.!!$F1 1618
20 TraesCS2D01G196000 chr1A 405354821 405356358 1537 True 1969 1969 89.640 56 1633 1 chr1A.!!$R1 1577
21 TraesCS2D01G196000 chr4D 260601352 260601863 511 True 857 857 96.881 1961 2473 1 chr4D.!!$R2 512
22 TraesCS2D01G196000 chr4D 75302121 75302632 511 True 852 852 96.686 1961 2473 1 chr4D.!!$R1 512


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
365 366 0.534412 CGAGATCAAGTCCAGCACCT 59.466 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2090 1.887198 ACGAGTTGGTGAATCGTCTCT 59.113 47.619 0.0 0.0 45.92 3.1 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
63 64 1.555075 CATCTTCTCCTGTTCCCCGAA 59.445 52.381 0.00 0.00 0.00 4.30
149 150 1.846124 TGACGCCCTTCCTTCCCTT 60.846 57.895 0.00 0.00 0.00 3.95
280 281 2.665089 CCCGTCCACATGGCCACTA 61.665 63.158 8.16 0.00 34.44 2.74
365 366 0.534412 CGAGATCAAGTCCAGCACCT 59.466 55.000 0.00 0.00 0.00 4.00
428 431 1.081556 CGACATTGCCGTTCGATCCA 61.082 55.000 0.00 0.00 0.00 3.41
594 620 2.367202 GCTCCTCGGATTGACCCCA 61.367 63.158 0.00 0.00 34.64 4.96
618 644 1.303074 CATGCCCGCTCCTATGCAT 60.303 57.895 3.79 3.79 44.79 3.96
695 729 4.673298 CCACGCCCGTGCTACACA 62.673 66.667 14.83 0.00 44.16 3.72
835 869 1.526887 CCGCCTATCCCTTTGCTCA 59.473 57.895 0.00 0.00 0.00 4.26
931 967 2.815945 CCGCATCTCTGCCCTCCAT 61.816 63.158 0.00 0.00 46.07 3.41
1166 1213 1.548269 GAGTGGAAGGAGAGGTCACAG 59.452 57.143 0.00 0.00 0.00 3.66
1175 1222 2.551071 GGAGAGGTCACAGTTGGAAAGG 60.551 54.545 0.00 0.00 0.00 3.11
1475 1529 8.460428 ACGTGTCTGTTATTTGTTTCCTAAAAA 58.540 29.630 0.00 0.00 0.00 1.94
2004 2170 5.374071 TCTGAAAACCCTAAGAAACACCTC 58.626 41.667 0.00 0.00 0.00 3.85
2305 2471 7.122353 AGTCCATGGAAGAAGAAATTGATGAAG 59.878 37.037 18.20 0.00 0.00 3.02
2399 2565 2.158900 CGTGCCCACCTTCTAATGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.555533 GTTCGGGGAACAGGAGAAGAT 59.444 52.381 3.75 0.00 41.62 2.40
63 64 4.477975 GCTCTGTAGCGACGCGGT 62.478 66.667 15.18 0.00 39.39 5.68
149 150 2.692368 GAGTGAGGCCATGGGGGA 60.692 66.667 15.13 0.00 40.01 4.81
1190 1240 4.800023 TGAACTGAGATCTCCGGGTTATA 58.200 43.478 20.03 11.21 0.00 0.98
1924 2090 1.887198 ACGAGTTGGTGAATCGTCTCT 59.113 47.619 0.00 0.00 45.92 3.10
2004 2170 3.279434 GCTAAACTCACATTGGTAGGGG 58.721 50.000 0.00 0.00 0.00 4.79
2305 2471 2.034104 TCATCCAATGAGCTCACAGC 57.966 50.000 20.97 0.00 42.84 4.40



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

AutoCloner maintained by Alex Coulton.