Contig Sequence

Contig name: BC000006142 (Nimblegen Contig name: CONTIG51627)

Contains SNP BS00011078 at position 728 (ambiguity code highlighted in red in the sequence below).

TACCCCCTCGGCGGCGAGGTAGGCGACCGCCCACACCGACCGTCGTGGAGCACAGCGAGCTTGATCGCCTCGAGATGGTGGACACAGTGAGCCTGGTGGGCATGATCCTAACGATGGTGCAACTGATCGCAAGCGCCGCGAAGATGGCACAGCAGAACAAGAAGAAGTGCTGGGAGCTCGCCGAGCGCACGTACACTCTAGCCAACGTACTGCCCTACTACAAATACCCGGCGGCGAACGACCAGGAGACGGAGACAGTGATGAGGAGGCTCAAGGAGACCCTCGACGAAGCGTTGACGCTCATCCAGTCCTGCCAGACTGTAACTGTATTCTCCCGTAGCCGGAAGGCCGCCGAATTAGATGGGGTTAACAGAAAGATCAACGACTGCATCACGGACCTCAATTTCATCAGACAAGTTCGCACAAATCACGTAGCAGCACCTAGCGCAGTCCCAGTCCCTGCTCAAACTTATGACCACGGCTCCTACTATCAGCATCAGGCACAAGGAGGAGGAGGTGCCTCCAGCAGCGCCTGTGTTGGATACCCCCCGCCTCAGCACGCTCCCGTCAATGTTCACTGGACTCCGGCTCTGTCTCCCTACCATGCTTCTCCAGCCCCCTCGGCCTCGGGTTACAATCTATCTTCTTTTTACACCCTTCCAACCGTCAACAAGATCTTTGACAATGTGTGTAATGGATTCCGCTAGTGCTCGTTCATTGCATCTGG[Y]GTAATATTATCTTTCTTGATGACAAATCTGTATCCATTTGTGCACTTAATTTGTGCAGAGACTATGAATGATACATCATTTATTCGCTGCAAGTACATATGGTTATGTGCAACGAAACGATTAAT

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 21 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
BS00015604 335
BS00015501 350
BS00016617 407
BS00010729 469 2A 148.60
BS00009984 501
BS00017657 502
BS00014381 503
BS00014825 535
BS00016287 539
BS00016502 548
BS00011384 550 2B 139.75
BS00014222 593
BS00014171 643
BS00020985 643
BS00013990 650
BS00019673 652
BS00010798 668
BS00013833 684
BS00011078 728 2B 140.29
BS00017818 761
BS00020092 776



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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