Contig Sequence

Contig name: BC000006344 (Nimblegen Contig name: CONTIG43713)

Contains SNP BS00010401 at position 82 (ambiguity code highlighted in red in the sequence below).

TATTGTCCCCGTGCTCGACGGCGAGGAGTTTTCGGTGAGGGTGCTAGTGGACCATTCCATTGTTGAGAGCTTTGCAATGGG[S]GGGAGGTTGACGGCGACGTCACGGGTGTACCCAACGGAGGCCATCTATGCCAACGCTGGGGTCTACCTCTTCAACAACGCCACCAGCGCCCGGGTCAACGTCACGAGGCTCGTCGTCCATGAGATGGACTCCTCCTACAATCAGGCCTACATGGCCTCACTGTAAAAACAAAATGCAAATATGATTTTTGTTTAGCAAAATATGATAGATAGCACATTGTATGTACTGTTTTAGACCAAGGAAGGTACGAC

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 6 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
BS00020973 35
BS00010401 82 6A 25.91
BS00018594 88
BS00019913 136
BS00017382 172
BS00013448 197



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.