Contig Sequence

Contig name: BC000024755 (Nimblegen Contig name: F0Z7V0F01CSP58)

Contains SNP BS00064740 at position 164 (ambiguity code highlighted in red in the sequence below).

AAGCAGTGGTATCAACGCAGAGGCGGGGGAGCCAAGAAGGCTACCCCAGAGCCGAAGTCATCTGGAAGGGGCAGAGGCCGCCCAAAGAAAACCGAGACCCCGGCTGAAAGCTCGGGACGAGGCGGGAAGAGAGGCCGAGGCAGACCCCGGAAGTCCTAGACCT[M]TGGCGAGCCTTTTTGCTGAAATCAGGTCAAGCGATATCTAACACCTGATGTGATGTGATCCAGCCCAGCCATTCGAGAGTTCTCTCTGACTGCCTGCTATTCGAGGATATTTTCCGTGTAGTGGTAATCTTGTGATTGTGAGCCTGTAATGTTAACATGCGCAACCGTATTATTCATTGGTGATAGTGAGTGAAATTTAATGCTCAATCGTGTGGAATCCGCTCTCCCAAGCAGTTGGTGGAACNNNNNNNNNNNNNNNNNGTACTACTGCGTTGATACCACTGCTT

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 15 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
BS00064751 67
BS00064752 77
BS00064753 83
BS00064754 94
BS00064743 107
BS00064740 164 2B 95.58 2B 43.36
BS00064741 174
BS00064744 193
BS00064745 232
BS00064746 238
BS00064747 240
BS00064748 252
BS00064749 261
BS00064750 325
BS00064742 349



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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