Contig Sequence

Contig name: BC000036156 (Nimblegen Contig name: CONTIG89174)

Contains SNP BS00102828 at position 1029 (ambiguity code highlighted in red in the sequence below).

GACCACATGGCTCTTGAAGCAGCCTTCCACTACCTGCAGCTCGCCGGCGTCCATGGCACATCCACGCCGGCACTACTGCTCACCGTTCTCCTGCTACTCATCATTCGACTAGCATGGGTGAGGACCACAACGGTGTCAACAAGATTCGGCAAGCAGCAGCAGCTCCCGCCTTCACCTCCAGGCAAGCTGCCCATCATCGGCCACCTCCACCTCCTCGGCTCCCAGACACACATATCCATCCGGGACCTCGATGCCAAGCATGGCCGCAATGGCCTCTTGCTCCTCCGCATCGGTGCCGTACCCACCTTGTTCGTGTCCTCGCCGAGCGCCGCCGAGGCCGTCCTGCGCACCCACGACCAAATCTTTGCGTCGCGGCCGCCATCCATGGCCGCCGACATCATTCGCTACGGCCCGACAGACATCGCGTTTGCACCCTATGGTGAGTACTGGCGGCAGGCCAGGAAGCTGTTAACCACGCATATGCTCAGCGCCAAGGTGGTGCACTCCTTCCGCCATGGTCGTCAGGAAGAGGTGCGCCTTGTTATCAACAAGATCCGTGAGGCGGCCACCAGAGGCACGGTGGTGGACATGAGCGACCTCCTGTCCGGCTACACCAACGACGTCGTGTGCCGTGCGGTCCTCGGAGAATCCCACCGCAAGGCAGGCCGGAACAGGCTTTTCAGCGAGCTCACAGAGATCAACGTCTCCCTTCTCGGCGGGTTCAGCCTCGAGAATTACATCCCCCCAAACATGGTAATGGCGGATGTGCTCTTGAGGCTGGTTTCCGTCAAGGCTCAACGACTCAACAAGAGGTGGGACGACTTGTTCAACGAGATCATTGAGGAACACCTGCACCCCAGCAAACCATCATCCGGCGAGCAGCAAGCAGCAGATTTCATAGATCTTCTGCTCTCTCTCAAGGAAGAGTACGGTCTCACTACGGATAACATCAAGGCCATCTTGGTGGACATGTTTGAGGCTGGCATAGAAACATCCTATCTGACGTTGGAGTACGGCATGGCTGAGCT[M]ATGAACAACAGACACATTCTGAAGAAATTACAGGAGGAGGTAAGATCCCAAGGCAAAAAATTAGACATGATAACAGAGGAGGACCTTAGCAGCATGGCCTACCTAAGGGCAACCATCAAGGAGACGCTGCGCATGCACCCACCAGCGCCCTTCCTCCTCCCGCACTTCTCCACCGCTGACTGCAAGGTCGACGGATACTTGATACCCGCCAACACACGTGTCCTTGTGAATGCCTGGGCCCTAGGGAGGGATCCGTCGTCTTGGGAGAGGCCAGATGATTTCTGGCCTGAGAGGTTTCTGCAGGATCAAGCTGGCGATGTGGACACCCAGATGAGGGGTAAAGATCTTAGGTTCCTGCCATTTGGGTTCGGGCGGAGGATTTGTCCAGGGATGAATTTCGGGTTCGCCACCATGGAGGTTATGTTAGCAAATCTCATGTACCATTTTGATTGGGATGTTCCGAATATGATGGGTACCGGTGCAGGGGTTGATATGGCTGAGTCGTTCGGGTTAACGCTTCGCCGAAAGGAGAAGCTTCAACTTGTTGCTCAGATTCCCTAAATCTACTATGTACAAGTTTATTTCGACATGAGCACAAGAATAAAGGCAAGGAATAAAATGACTACTGTACTACTGTTT

Note: The ambiguity code M, highlighted in red, translates to A 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 15 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 in a particular cross, the corresponding fields in the table are left blank.

SNPs id Position Map Location AxC cM Map Location SxR cM Map Location SxO cM
BS00102835 46
BS00102831 134
BS00102833 327
BS00102834 386
BS00102836 525
BS00102837 540
BS00102838 597
BS00102839 637
BS00102840 942
BS00102841 948
BS00102842 960
BS00102828 1029 5B 17.59
BS00102829 1248
BS00102830 1305
BS00102832 1507



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 


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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.


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