Contig Sequence

Contig name: BC000024614 (Nimblegen Contig name: F0Z7V0F01C5CHZ)

Contains SNP BS00064231 at position 78 (ambiguity code highlighted in red in the sequence below).

AAGCAGTGGTATCAACGCAGAGACCGGGGCGTGGGAGTGGATGGCAAGGGAGCGCGCAGCCGTCGACCCCGTGCACT[R]TCTCCCTCTCTCCTCAACGACTCGCGGCGAAGAAGCCGCTGGAGGAGGAGCTCGACCCGGACGACGGTGGCCGGAGGACGTCACCATGGGGATTTGCTGCAAAGGGCCACCGGAGGAGGAGCCCAACTACAGGAGAATGCGGTGTAGCAAGAGCCTCGCCAGCATCGTCGGCATCGAGCAGTCCTCTAAAGCTCGTCCTCACCACCACGGACGCCGAAACGGCTCCAATGGAAAGGTTAGATGCTCACATGGAAGAAGTGATCTGATTTTGCTCTCTCATCTCTCTTTGTAGATTTTTGTTCATGCTGGGATGTGTTCATGTGTGGAAGCTGGGCTGTGTCTATATGTACATTTTTGTTCATGCAAG

Note: The ambiguity code R, highlighted in red, translates to A or G).

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 17 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
BS00064231 78 1B 58.81
BS00064232 109
BS00064233 133
BS00064234 177
BS00064228 201
BS00064235 203
BS00064229 214
BS00064227 243
BS00064236 262
BS00064237 270
BS00064230 288
BS00064238 304
BS00064239 342
BS00064240 354
BS00064241 360
BS00064242 375
BS00064243 414



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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