Contig Sequence

Contig name: BC000002382 (Nimblegen Contig name: CONTIG94259)

Contains SNP BS00004241 at position 840 (ambiguity code highlighted in red in the sequence below).

CAGACCCACCGCGTGATCCATTGTAGCGATATTGGGGGCGCGAGGAGGAGGAAGAGGAGTCCGCAGTCGGCACTGGGCAGGGAGGGTGAGAGAAGGGGAATCATGAGCGGAACTGGGTACACGGTGGAAGTCACTAACCTGTCAAGCAGCGCATCTGAGAATGATCTTCATGAGTTCTTCTCATTCTCTGGACCTATTGAGCATATAGACCTTATCAGATCAGGAGGATATGGTTCAACTGCTTATGTGACTTTCAAGGAACCCTATGCCTTGGAAACTGCAGTATTACTCAGTGGGGCGACCATTGTGGATCAGCCGGTGTGCATATCTCGTTGGGGACAGCCTGATGAGCCTTGTAATTTCTGGGACAGGCCAACTTGGCAGGTCGAGGAGGAAATTGAATATAGGGACTACCAATCATGCCAGTTCAACGCCACTCCACAGGAAGCATTGACAGTGGCTCAGGACGTCGTGAAGACAATGCTGTCAAGGGGATATATACTGAGCAAGGACGCATTGTCCAGGGCTAGAGCTTTCGACGAGTCCCACCAGCTATCTGGGTCTGCGGCAGCAAAGGCTGCAGAGCTGAGCAGGAGGCTCGGCCTGACCGACAGAGTCAGTGCTGGTGTTGGTGCAATCAGATCAGTGGACGAGACATACCATGTTACCGAGACGACCAAGACCGTCGCCACTGCCACCGGAAGAACAGCGGTCAAGGTTATGAACACCATCGTGACCAGCAGCTACTTCTCCGCGGGAGCTATGATGGTGTCTGAGGCTCTCACCCGCGCCGCCAAGGCCGCTGAAAATCTGGCTGCTCACGGCAGGCAGAATTAAGT[S]GAAATAAACACCCCGTTCGAACAGTTCGTTGTGTCGGTTATACAAAAGTCAGTTATTCAGACACCAGGGTTGAACTTAAAGAGTCATAAGGTATGATATTTATG

Note: The ambiguity code S, highlighted in red, translates to G 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
BS00016399 213
BS00004111 288
BS00004216 291
BS00021465 300
BS00019674 384
BS00004242 498 2B 43.36
BS00013233 633
BS00012359 651
BS00013511 662
BS00012751 684
BS00018680 688
BS00004378 711 2B 43.36
BS00004071 774
BS00021117 795
BS00004241 840 2B 43.36



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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