Contig Sequence

Contig name: BC000033043 (Nimblegen Contig name: CONTIG41074)

Contains SNP BS00089269 at position 83 (ambiguity code highlighted in red in the sequence below).

TCATAAATGTCTACCATCAGCGGTACGAGAGTGGGGCGCAGTTCTGGCCCAACGTGCATCTACGCATAACCGTAGCCTTGAT[Y]GCATCGCAGCTGCTTCTCCTTGGGCTCTTAAGTACAAAAGGTTTGGAGGAGGCGACGCCAGTTCTCCTCGTTCTTCCCATATTAACCTTTTGGTTCCACAAGTACTGCACGCACCGGTACAAACCCGCGTTTGTGAGGAACCCGCTGCAGGAGGCGATGAGGAAGGACACGCTGGAGCACGCGAGGGAGCCCAACTTCGACCTCAAGTCGTACCTGGCGGACTCGTACCTGCACCCGGTGTTCAAGAGCGACGACGTCGACAAGTTCTACGTCGCCGAGGACCCCGGCGCGGAGGAGGTGATCGTGGCGACCAAGCGGCAGTCGAGGAGGACCACGCCCGTGCAGAGCAAGTATGACGGCTCCGACAGGCTATCCGTGCCGGACTCCATACCCGAAAGGTAGCACCTGGCTGGCCAGCCATGGGAGGAGTGCTATTGGTTCTTTAGGCTGTTAGCGTGTACAGAGAGAGACAGAGAGGGGGGAATGGAATTCTGCTTGATGAGATGTCACACGGCTGGGGATGTTGATTGCACTTGCAAACTTGCAATGCACACGGCACACCAGTACACCTGTTTTTCCACTAGTATCTGAACCGAATACGATCCAGAGATGCGCATTGCAGTGAGGATTGGTTTGGCGTTGGCAACCG

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
BS00089268 70
BS00089269 83 1D 107.69
BS00089249 113
BS00089250 140
BS00089251 162
BS00089252 209
BS00089253 320
BS00089254 336
BS00089255 338
BS00089256 386
BS00089257 423
BS00089258 597
BS00089259 610
BS00089260 615
BS00089261 617
BS00089262 631
BS00089263 638
BS00089264 646
BS00089265 650
BS00089266 671
BS00089267 697


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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