Contig Sequence

Contig name: BC000002751 (Nimblegen Contig name: CONTIG50594)

Contains SNP BS00010888 at position 1118 (ambiguity code highlighted in red in the sequence below).

TGGGAATGCTGAATCATGCTTTGCCTAGCAAATCAGAAAGAGACGCCTGGTTTGAAGTGAACAACCAAATTTTGAACGCATTATTCACACTGATGTGCCTTTACCAACACCCAATGCGGATCTATAACTTTGTGCTTTTGTGTCGATGGGACCAAAAGGACATTTTAAGGCTTAGGAAAGAATACTGCAAAAATGGGACATATAAGCCTAATGAGTGGATGCACATGATGGTGGTTGTGGTCTTTCTTAATCTGAACTGCTTCGCCCAGTATGCCTTGTGTGGTCTCAACATAGGGTACCGCAGATCTGAAAGGCCTCCTCTTGGTGTCGCCGTGACTATTTCTTTTGCATTTGGGGCTGCGTTATTCGCCAGTGTGTATAACATTGTCAGTCCTCTTGGAAGGATTATGATGCAGAGCTGAGAGAAGGTGATCCAGAAGCACAAGCTGGGGTCACCTCAACTGAAGGCGCAAGGGCAGCAACTTCAGGGAGGTCACTTGAGAGAAGATACTCTTTCCTTCAAAGCGAAGAGCGCCGTTTCGTGGAGAGCAGGCCTGAGTGGGTCGGCGGACTATCAGATTTCTGGGACAGCATAACCATTGCATACCTGTCAATTTTCTGCAGCTGCTGTGTTTTCGGGTGGAACGTGCAGAGGCTTGGGTTCGGCAACATGTATGTCCACATTGCAACATTCCTGCTCTTTTGCCTGGCTCCGTTCTTCATCTTCAACCTGGCAGCAGTCAATATCAACAACGAAACCCTGCGAGAAGCGCTGGGGCTCACCGGCATCGCGCTGTGCTTCTTCGGTTTGCTGTACGGCGGCTTCTGGAGAATACAGATGAGGAAGAGATTCAACCTCCCTGGGAACCCCTTCTGCTGCCGTAACCCCGATGTCGACGGACTGCTTCCAGTGGCTGTGCTGCTGCTCGTGCTCTCTCGCTCAGGAGGTGAGGACCGCTGATTACTATGACATTGCAGAGGAGAGGTCGCACAGAGGGCAAGTAAATGGGGAGAGTCAGCGTGTGATGTCCCCATTGGCTCGTGAAGACGGTCTTCCGCTTTTCAAGTCAACTCCAGCCTCGCCGTACAGGAGTAGCACAGGCACGGCTGGTCAGTC[S]ATTTTCATCATGGAGAGCCCATCAGCTCCACGGAGGTCGTCCGGTGCAACCCCTCCCGGTGCTTCGCCGATCAACGGCGGCGACAGGGTGATGAAGGCGCCTGCTCCATCTGTCTTACACAGAGAAGGTGATGATGAATCGTAGCATGTGGCGGCCCAGTTTGCTTATCATGAGGTCACGAGTCTTGCTCAGTCCATG

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 16 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
BS00018562 634
BS00004659 784
BS00006572 790
BS00012456 817 1B 87.94
BS00010779 929 1B 87.94
BS00010475 990 1B 87.94
BS00010130 1001 1B 87.94
BS00011694 1006
BS00016960 1022
BS00012928 1055
BS00011345 1101
BS00010888 1118 1B 87.94
BS00006571 1155
BS00011610 1189
BS00010105 1190
BS00012099 1250



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.