Contig Sequence

Contig name: BC000023285 (Nimblegen Contig name: CONTIG96767)

Contains SNP BS00059365 at position 260 (ambiguity code highlighted in red in the sequence below).

GTTTCTTGGTCAGAAGAAGGCAAGGTCACCGGCGGGTCTGCCCACAACCCCAAGAACACCAACGCCGGCGACTACACCGTCATCAAGAACAGTGGCTCCGCTGGTGGCCTCAGCAACTTCACCAAGGGTGGCTATACCTGCAGCCTCAAGATCGTCAACAAGGGTGGCTTCTTCCACCACGTCAAGAACATCAGCAACGTCGGCTCAACCCGCTAATTCAAGACCCGCTAACTCAAGACCGCCAACAACGGCAAATCCA[Y]AGGTGACCTCAAGAACTTCAACGACGGCAAATTCGTATGCGGCCTCAAGAACTTCAACAACTGCAAATCCGTATGCAACCTCAAGAACGTCAACGAAGACAAATCTGCCCGCAACCTCAAGAACGTCAACAACGGCAAATCCATACGCGGCCTCAAGAATGTCAGCAGCATCAGCAGCGGTGGCTCCTTCTGCGACCTCAAGAATGTCAACAAGAGTCGCTCCATCCACGACCTCCAGAACGTCAACTAGAGCAACGATGGCCTCAAACCAGTCGACGACACTGCAGCCTGGTGCGCCGACCTCAAGAACGGCTAGGACGAGGGCCCCACCCTTGTCCGCAACGACAAGTCGTAGTCATGCCGCTCCCACACGTCCAACTGCTTCAAGCACACGCCGATGATCTCCATCCATGTACGTCGTCCATCTTCAATGAAGTTAAGTGCGTTGAGACCAAATTAGTTATGTTACAGTAAATTAATAAATTTGTAAACTCGATTGGTTCGAGCCTGTGAGATGTAAGC

Note: The ambiguity code Y, highlighted in red, translates to C or T).

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 11 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
BS00059364 113
BS00059365 260 7B 70.47
BS00059366 300
BS00059367 331
BS00059368 438
BS00059369 455
BS00059370 547
BS00059371 580
BS00059372 603
BS00059373 626
BS00059374 676



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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