Contig Sequence

Contig name: BC000024707 (Nimblegen Contig name: F0Z7V0F01CKUHD)

Contains SNP BS00064571 at position 74 (ambiguity code highlighted in red in the sequence below).

AAGCAGTGGTATCAACGCAGAGTTAAAAATAAATGCAATGCCAATTGAACTGAAGTAAAATGTCAAGACAGCA[W]TATTATTAAATTAAAGCATAACATAACATAAGGTGCAACCGTGCAAAACCAACAGGTACATGATGAGACAAGGGGGAACAGAGTTTATCTTGGATACTTGCAGGCAGGGTAGTAATTTCGACTACTTAAGCACTACTAGTCATGCCATTCAAATAATTCCTAGAAATTTTCAACAGAACACATCACACAAGAGATCAACATAGCATCTTAATTGTTGTACCATATGTAGTGTAAACAAGTGAAAATTTCTAAAGATGACAGAGAAATTGTACAGAACATCTGGTATAATAATCTGCTTATTGATGTGTATGAGTAAAGACGAGGAAATAGCAAGCAGTTGAGTTGGTAAAGGATATGCAAGCTGCCCGCGTACTCTGCGTTGATACCACTGCTT

Note: The ambiguity code W, highlighted in red, translates to A 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 12 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
BS00064571 74 4D 10.28
BS00064560 127
BS00064561 136
BS00064569 174
BS00064562 179
BS00064563 181
BS00064564 191
BS00064565 205
BS00064566 208
BS00064567 264
BS00064568 276
BS00064570 285



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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