Contig Sequence

Contig name: BC000007080 (Nimblegen Contig name: CONTIG104042)

Contains SNP BS00012109 at position 110 (ambiguity code highlighted in red in the sequence below).

TGCACCCCTACTTCCAGCGCGATTCTCTTGTCAAGTTCTGCCAGAAGCATGGGATCTGCGTCACCGCGCATACCCCCTTGGGTGGCTCCACTGCCAACACCGAGTGGTT[Y]GGGTCGGTCTCGTGCCTTGACGACCCTGTCATCAAGAGCTTGGCTGAGAAGTACGGCAAGACACCAGCACAGCTTGTCCTCCGGTGGGGTCTGCAGCGGAACACGGTGGTGATCCCCAAGACCTCCAAGTTGGAGAGGCTGCAGGAGAACTTTGAGGTCTTCGATTTCGACATCTCCGGCGAGGACATGGAGAAGATGAAGGCCGTCGACAGGAAGTACCGGACTAACCAGCCTGCCAAATTCTGGGGCATCGACCTGTTTGCTTAGCTTATTTCAGCTGCATGCATCTCAGTCTCAGCCTCCCATATGTGTGGTACGGTGTGTGGACATTATTCCTGAACCATTGCTCCATCTGTTGCTCCCAGGGCCCAGATAGCATCAATAATAAGGATTCGATCCTCATCTTCCATC

Note: The ambiguity code Y, highlighted in red, translates to C 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 is only one putative SNP on this contig, the one you entered. 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
BS00012109 110 6A 49.20
SELECT predicted_chr FROM iselect_all WHERE BS_code = 'BS00012109'

There is no putative map location for the contig containing this SNP




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.