Contig Sequence

Contig name: BC000036356 (Nimblegen Contig name: CONTIG90303)

Contains SNP BS00104270 at position 247 (ambiguity code highlighted in red in the sequence below).

GTCAGCCATTCCCCAAATCCANNNNNNNNNNNNNNNNNNNNNNGGCTTAAACCCTAGCCGCCCCTCCTCCGACTCGCCGCCGCCGCCGGTTGCCATGGAGTTCTGGGGCCTTGAGGTTAAGCCTAACCAGTCCGTCAAGGTTTCACCTGATGATGACCACTTCCTCCATCTCTCCCAGGGTGCCCTTGGCGAAGTCAAGAAGGATGACAAGGCAACCATGTTCGTCAAGATCGGCGACCAGAAGCT[R]GCCATCGGGACCCTCTCTACCGACAAGTTCCCTCAGATCCAGTTTGACCTCGTCTTCGAGAAGGAGTTTGAGCTGTCACACAATTCCAAGACATCCAGCGTCTTCTTCTCTGGCTACAAGGTTTTCCAGCCTGCCGAGGGAGATGAGATGGATTTTGATTCTGAGGATGACTCTGAGGAGGAGGAAGAGAAGATCATTCCAGCACTCACCAAGGAAAATGGCAAACCTGAAGCCAAGGAGCAGAAGAAGCAGGTTAAGATTGACACTGCTGCGCCTTCAAAGTCAAAGGCCGCTGCCAAGGATGTGGGAAAATCTAAGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCCATGGAGGATGATTCTGATGACAGTGAGGATGGTGATGACTCCTCTGATGATAGCGAGGATAGCTCTGATGAGGAGGAAGAAGAAACACCCAAGAAGCAAGAGACTGGGAAGAAGAGGGTGGCTGGAAGCGTGTTGAAGACCCCTGTTACTGACAAGAAGGCCAAGATTGCAACACCGTCAGGCCAGAAGACAGGTGACAAGAAGGGAGCTGTCCATGTGGCGACTCCGCACCCGGCCAAGAAGGCAGGCAAGACCCCAGCAACCAGTGAGAAGTCGCCCAAGTCTGGAGGGTCGGTCGCGTGCAAGTCGTGCAGCAAGACATTCAACAGTGAGGGCGCTCTAGCTTCGCACTCCAAGGCCAAGCATGAGGCCAAGTAGATTAAAAGAGGAGGATGCTGGCTGGCTGCCTCCTATGAGATTATCGTTATGCTCCTGTCCTGTGTTAGGCTATCTACTATATCCTTATGTTGTCGTGCGTGTTCCCTACCCTACCTTTCCTTACCTAGCCTCATCCTTATCCTTTTGGAAGGGAAGGGAAGGCAAGGCAAGGCAAGTTAAGGGAGAAACCGTTGAGCTGTTAGTGATGATGAGTTGTTGCCGTGATTCGGAATTGGAATTGGTTGGTGGAATGCTATGGTTGCTCGTTTTGAACGAATGATTCCTCTGTGGTTTGGTATGCAAATGCTTTATTTTTGG

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 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
BS00104267 190
BS00104268 214
BS00104269 223
BS00104270 247 1B 178.19
BS00104271 322
BS00104272 325
BS00104273 340
BS00104274 943
BS00104266 1190



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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