Contig Sequence

Contig name: BC000005674 (Nimblegen Contig name: CONTIG89263)

Contains SNP BS00009270 at position 881 (ambiguity code highlighted in red in the sequence below).

GCTCCCATCCCGGTGCCCGCCGCCGCCCAAGTCCCTCGCCACCCGCACAAGACCTTGACCAAATCGCCGCGCAAGCTCTACCTCCCCACCCGCACAAGACCTTGCGTGAAGTTCTGTTGATCATCAAGTCAAGTTCAGACAGGGTGTTCTTTTGGTTTGGTTGGGAGACCAGCAACGACGAGGATGAACAGGCGCTTTGTCAATCTGGTGATGCATAACTGGGTCGAAGGCGTTTATTCGGTGCGCCGGATCAATCCTTACAATCATCTCTTCTACCCGTCAGCAAAGGCAGCACTTGAAGCAGCAGATGAAGCAGCAAAGTATAAGGATTATTTTCCAGTGATGCAGTCCCTGCAGCTGCCGGACCCAGGCATCAAGTTCACAGCAACTCCCTCTGGTGTCGGTCTTGATATGTTCGCGCTCTTCAACCCCCGCGGCACCAGCGAAGGCAGAATTGTTTTTAGCAATTCGATCGGTGAGGCTGTGCTGTACGACGCCGACAAGCAGCTCTTCAACACCATGGGTTGCCTCAACGAGCCTAAGGGAGCAGACCCCATGTGCCTGCCCATCGAGCACCCTGGCACCGACCAAGACAGCTTGTATGTCCTGGACAGTTGCCCCTGGAAAGCTGATAGTCGATGCTTCGAGGTCCTTGAGTTCATGCCCGAGTGCAGTGAGCTGAGCAACTTGAGGGCCACCTGGCGTTGGCGACTACTTCCACCGCCTCCTTTTGTCCGCCAACCTGGGTACAAACCTTCCTCTGTTCTCTCTTACACTACCACAGTCGACAGCTATGGCTTTTCCACCATCTACATATCATGTGAGGGCAGCATCGGCACATACAGCTTTCAGACGGCACACCATGACTCCAAGCACCGTC[K]AGGATGGAGCCACTCGGAAGAATGGAAGCACGCCGGGAAGTGGAAGCTGCCTTTTAATGGCAGAGCTCAGTACATCCCTGAGTTCAACCTGTGGTTTGGCTTCTCAGCCATCTGGCCCAACAATCTGTGTGCTGTGGACCTCTCTGCCATGGTCCATGAGCAAACACCCACTGAGCAGCAAGCTTGGCAAGACCTGAACCCACCTGAGGGAGTGGCGTGGATTCCAATACGCCGTGAGCTTCTCAACCTGGGCGATGGCAAGTTTGTCATCGCTAAGACCTTTAAAGCAGAATCAACTGGTCAGCAGTTTGCTGTGCTCACCGGCGTAGAGATGATGCATGGTGTCGGTGATGATCAGACCCTTCAGATGGTCAAGCACAAGTGTGCACGTTATGCCTTCACGACTGATGCCATCAAGTGGGTGCTCTGAAGGAATAATTTGCTGCATTTGTTATGCAGTCATCTATTTCCTTCCTAGTAGGTCTATTTGCATAACTAAAGCTTTGTGAGTTCGCCTGTCTATGAAATTGTTTCTCACCAACTCTAGTATCTTTACTCTTTGGAAAGTGAACATTGTATCATGTTGAATGATCTGGATGGCTGGTTTTTCTGTTTCTTTTGTTGGCCGGTGAGCATGCATGGTTTTTCAGATCAAGAGCTTCCTTCTGTACTATCTACAAGTTGATTGTAACTCTGCTGGGTGAGCATGCATGTTCTTGTTTAGATCAAGTGCTACCTTCTGTATTGTCT

Note: The ambiguity code K, highlighted in red, translates to G 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 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 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
BS00021202 855
BS00009270 881 1B 76.69
BS00020100 883
BS00015448 914
BS00018931 919
BS00015458 928
BS00016347 933
BS00016487 968
BS00015542 991
BS00014424 994
BS00016768 1005
BS00010612 1043
BS00014376 1052
BS00021393 1064
BS00015399 1079
BS00018716 1108



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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