Contig Sequence

Contig name: BC000004687 (Nimblegen Contig name: CONTIG59298)

Contains SNP BS00010791 at position 517 (ambiguity code highlighted in red in the sequence below).

CCTCCAGCTTTATTTATATGAGAAGTCCAGGTCTCCTGGAAGGTTCTTTGATCTAGTTTACCATGAAAATGCTCGGGTTCTTCTCCATGACGAGAGCATATATCGATTTGAACGGCGCTCAAATCCTACGAGATTATCTGTTCAGCTCATGGAGTATGGGCATGAAAAGCCTGAAGTAACTGCAGTCTCAATTGATCCAAACTTTTCGTCATATCTTCATGACGAGTACTTGTCGAGTATTTCGGATTCAAAAGTGTCTGAAGATGTGTTCCTTGAGAGGAATAAGCGGAAACGCGGGAGCAGCAATGGTCCTCAAGCTTCCTTAGCGGTCATGGATGGTTTCAAGGTCGCGAATGGCCTTGAATGCAAGATAACCTGCAAATCCTCAAAGGTTTCATATGTCCTTGATACAGAAGACTTTTTATTCCGTATGAGGAACAGGAGGAGAATCTCATCTGGTGCAACCGCCGCACCTGGCAAGGCCGATTTTGTCAAGGCAGCTGATGTCGTGAAAGC[R]CAGCGGTTTCATAAATTTCTTCTTTCTAGGTCCTAGGGCCATGCTGGCAGATTCTGCCATGGTATCATCTAATCCAGAGACGACGCTGACGTGCTTTCAACAAATGTGGTGGGTGGGAAGCTAAAGCTGCTTTCCAACCTTTTTGTGCCGAGAGGGACCGCTGGAGCTGGTAAATACCAACCAACCAAAGCATGTAGGCAGTCTTCTTGTTAAGTTGTTACCCGATGGGATGCGATGTCGCTGCTGCTGCTGGGAATGTGTATATTATTAATGTTATGTATACCCAGAAGAGAATGTGACGTCGTGTTATCCATGAGGGAGGGAGGTTATTGTTATTAATCTTGCCGGTGGTCTGATCAACTGATCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTCGTGGTGAAGCAAACGCAGACTTGATTCAAATCTGGACATTGCTATATTTGTTGGTGATGCCAGCCATCTGTGTTAATTGGATTGCGTTCCTAGTGGTTCTGGATCGTCATATGATTAATTTTGCTGTAACTTTGATCATCAATTCATACACAATATTTACTTGC

Note: The ambiguity code R, highlighted in red, translates to A or G).

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 22 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, the corresponding fields in the table are left blank and, if available, a putaive location for the contig, based on our extensive NGS of various wheat lines, is given below the table.

SNPs id Position Map Location AxC cM Map Location SxR cM Map Location SxO cM
BS00016019 293
BS00018610 295
BS00012902 325
BS00016386 454
BS00015069 460
BS00018984 461
BS00020155 466
BS00016429 467
BS00014812 475
BS00014541 508
BS00010791 517 1B 20.71
BS00007747 517
BS00013701 520
BS00020035 541
BS00017207 588
BS00013248 593
BS00020039 603
BS00013876 604
BS00015276 615
BS00020641 662
BS00019638 673
BS00013213 861



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 


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.