Contig Sequence

Contig name: BC000024518 (Nimblegen Contig name: F0Z7V0F01BPYJC)

Contains SNP BS00063902 at position 317 (ambiguity code highlighted in red in the sequence below).

AAGCAGTGGTATCAACGCAGAGTGGGGATGAAGGTGATGATGCACGGGCAGGGCAACAAACTCTTGGAGGATGCTGTTGGTGCTAGTACTAGTGCTTTGTTATTGCCCAAGTGTATATGTGACTTGGTTACATCGCTGCACGTGTATGATAACTTGTCCATCACTAGCATCCCTGGACCTCCCCAAGGATCAGGATGGCATAGACTAAGATGGTGCCGCGTGGAGAGATGCCCCAGGTTACACACAGTCTTCACTGTCCCCCATGGCACTAGCGAGGACCTTGGCGAGGACAGCTTTCGGGATCTGGAAACATTAT[S]GGCGTCCAAGCTCCTCTATGCACTATACATCTGGGACAGGCAAGTTGAAAAAGGTTATTTGAATTCCCTGGTGTTATTGCACCTGGACCACTGCCCCAGGCTCGTACATGTGCTCCCTTCGCCATACGGACAAAACACACCTTGTATTACCTTGA

Note: The ambiguity code S, highlighted in red, translates to G 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 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, the corresponding fields in the table are left blank and, if available, a putaive location for the contig, based on our extensive NGS of various wheat lines, is given below the table.

SNPs id Position Map Location AxC cM Map Location SxR cM Map Location SxO cM
BS00063897 136
BS00063904 142
BS00063898 168
BS00063905 169
BS00063899 193
BS00063900 230
BS00063901 301
BS00063902 317 6A 25.91 6A 6.56
BS00063903 335



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 


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: 








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Maintained by Mark Winfield.