Contig Sequence

Contig name: BC000005509 (Nimblegen Contig name: CONTIG90418)

Contains SNP BS00010477 at position 955 (ambiguity code highlighted in red in the sequence below).

CGTAAGCGCCTCGAAGCAATCCCCCTGCTTTCCCATTCGATCCACCTGCTCCCGCCGCCGCCGTCGCCGGCCGTTCATCTGACCAGGGGCGAACGATTCCCCCCTCCCCTCTCTGCCTCCTCCTCGCTGTTGCAGGTGATTCCGTCGGGGGCGGGCCACATGGCGGCGGCGCTCGCGGTGACGGACGAGCTGGCCCTGCCTCTCCGCGCGGTGGGGGACCTGGCGGCGGCTGCCGGGGTCTCGCGGGAGGAGGTCTTCGTCATCACGCAGTGCGCCTCGCTCGGTGGGAAGTTGCCTTTTGATGACGCGTCCGTGGGTGCTGTTCTGTCTGTTATAAAAAATGTTGAGAGCTTTGGAGATAAGTTGGTTGCTGAAATTAGCCGAGTGCTGAAAGCTGGTGGAATTGTGCTGGTACAGAGCTTCACACCCTCCACTGACCAGAAGCCAAACAATTATATCGAGCGCCAGCTACTCATGGGTGGTTTTGTTGAAGTGCAAGCTTCTGCTACAAACTCGCAAGATAGCGTGCAATCTGTTACTATCAAGGCAAAGAAGCCTTCTTGGATTATGGGTTCTTCCTTTCCCCTGAAGAAAGCAGTAAAGGCTCTTCCAAAGATTGAAATTGACGATGATGATGAACTGATTGACGAAGACAGCCTCTTGACTGAGGAGGACTTGAAGAAGCCACAGCTTCCAGTTGTAGGAGATTGTGAGGTGGGAGCTACAAAGAAGGCATGCAAGAACTGCAGTTGTGGCAGGGCCGAGGCTGAGCAGAAGGTGGAGAAGCTGGGGCTCACTGCAGAACAGATTGATAACCCTGTCTCAGCTTGTGGCAGTTGTGGGTTGGGCGACGCTTTCCGATGCAGCACCTGCCCATACAGAGGCCTGGCGCCGTTCAAGTTGGGCGAGAAGGTTACCTTGTCTGACAACTTCCTCTCAGCCGACATATGATGA[Y]GGACAGCAGTTGCGGATATGAAATGCGCCTTGTTGGATTTGTTGGTTCGTTAGGAAGATATATCTGCGTATGGTTTTTTCNNNNNNNNNNNNNNNNNNNNNNNNNNTACAGCAAAAGAAGGGGAGTGCGTTTGGAGTAGCAGCTCGTGTTAGCATGTCGTGCGTGTCCTTGCTCTCCCACCTAGGTTGAAGCAAGAATTGGATCGTGTGTGCGCCTCTGTATTCGGCAAGAAGATTACATGCATGTAATTTGACGAAGAAACATATGATGGAAAGACTTTGGTCTGCTACATGTTCTTGTTTTGCTCCCATCTGGTTTATACTACTACTCCCTCCGACCTCGGCCGCGACCACGCTAATCACTACC

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 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 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
BS00013941 480
BS00011098 561
BS00011135 573
BS00011944 576
BS00011557 702
BS00020437 720
BS00009417 772
BS00017339 776
BS00009025 852
BS00016123 855
BS00010477 955 2A 152.04
BS00009728 981



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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