Contig Sequence

Contig name: BC000005120 (Nimblegen Contig name: CONTIG62839)

Contains SNP BS00022829 at position 338 (ambiguity code highlighted in red in the sequence below).

TCGGTTAAGATGCCGTTCCTTGGCCGGGTCATGCGTGTGCTCATCAACTCGGGCGTCTTCGCCGCCGACAACGACTGCGAGTCCGGCGTGGAGCTCTACCGCCTCACCCCGCTGTCCCGCGTTCTGGTGCATGGCGTCGTGGCGGACGAGCACCATAGCCAAAAGTATTTCGTGCTTGGTGTCACCTCGCCGCACTACACGGAGGTGGCGCTGGGGCTGGCCAACTGGTTCAAGAAAGACATCGAGCCACCGGTGCCGTCACCTTTCGAGGAGAAGTTCGGTGTGCCACTCTTTGATGAGAAAACTGCCCTCCTCGACGAAGAGCTTGACTCGGTTT[S]CAACCAAGGTTTGGCTGCCCACGACAACCTTGGGATCGCCACCATACTACGTGAGTGCGGTGACATCTTCAAGGGGCTCGAGTCCCTGACTGACTGCTGTGGTGGTGATGGTACGACGGCGAGGGCCCTCGTCAAGGCTTACCCTCACATTAAGTGCACGTTTTAACCTTCCGAAGTGAT

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 12 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
BS00008438 36
BS00008439 48
BS00008440 82
BS00008441 117
BS00008442 120
BS00013912 222
BS00016978 223
BS00019418 242
BS00019100 282
BS00016373 294
BS00016805 315
BS00022829 338 4A 242.90
SELECT predicted_chr FROM iselect_all WHERE BS_code = 'BS00022829'

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: 








Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

Maintained by Mark Winfield.