Contig Sequence

Contig name: BC000029387 (Nimblegen Contig name: GJKKTUG01DZ45L)

Contains SNP BS00076481 at position 107 (ambiguity code highlighted in red in the sequence below).

AAACATGTACATGCTTAAACAAAAAATGGATTTTCTCAAAAATTCTGAACTTATTTTAACGAAAATTCTGAACTCCCGCAAAGAAGAGTCCGCTGTGTGGACGTCG[M]CGGTCAAGGTGAGCTCCACCATTGACGTGGACGTGCCGGCCTCGTGGTCATCGCGGCTAGACGCGGAGCTGCCCACATTCCCGTCCGCGATCGCCTCCGCCACGATCGCGTTGCAGCTGGCACTGTGTGTGGCCTCGTAGAACGCCCGCTGCTAGTCGAGGAAGTTTGGTCCTCGCGACCATGGCCGCCATGATCTCCTTGCTTGCGAACTCGCCGTAGATTTCGCCCCTNTGCCAGCCGATGATGGCGAGGAGGGCGAAGTTGTAGTGTTGGT

Note: The ambiguity code M, highlighted in red, translates to A or C).

The highlighted SNP has not been mapped. Any other SNPs on the same contig are reported in the table below.



All SNPs on contig

There are 9 putative SNPs on this contig. If mapping information obtained from varietal crosses is available, it is shown in the table. When the SNP has NOT been mapped in a particular cross, the corresponding fields in the table are left blank.

SNPs id Position Map Location AxC cM Map Location SxR cM Map Location SxO cM
BS00076488 77
BS00076489 94
BS00076481 107 6B 59.03
BS00076482 180
BS00076483 194
BS00076484 235
BS00076485 237
BS00076486 250
BS00076487 264



BLAST information

To BLAST the above sequence against our SNP database click on the 'Query' button below. You may select an e-value cut-off for this search.

e-value cutoff 


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Alternatively, if you wish to perform a BLASTN search with this sequence, please use the drop-down fields below to select the parameters (database and e-value cutoff value) you wish to use and then click the grey 'BLAST' button.   At present your search can only be performed against Brachypodium distachyon, rice ( Oryza sativa ) or rye ( Secale cereale ) libraries.   However, this site is actively being worked on and we hope to be able to add additional libraries.

BLAST input parameters Database: 


e-value cutoff: 






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

Maintained by Mark Winfield.


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