Contig Sequence

Contig name: BC000007040 (Nimblegen Contig name: CONTIG88556)

Contains SNP BS00012014 at position 1910 (ambiguity code highlighted in red in the sequence below).

GCAGGNAATTCGGCACGAGGGGCTTGGCAACGGCGACGGACGGCAGTCGCTCCGCGACGCCAGTTATATTATTCCAAATTGAGGGGCACCATATATGCAATCCCTCTACGGAAGGAGAATAAATTCTTGCAAGTGTTTGTGTATTTGGGAAATAAAAAATGTATGGCGAGTCTAGCAAACATGAAAACCTTGAGTGCATACTACAAGATCAAAGTGCAAACCCAAGTGTTGTATCACTGAATTTTTTGAAAGAGATCACAAACAACTTTTCCGATGAGCGAGTACTCGGTAAAGGTGGTTCTAGTGTGGTATATAAGGGTGTGCTACAAAGTGGGGAAATAATCGCTGTGAAGAGACTTGAGCCATCAATGGCTGGTTCTCAGAGTTTATTTCAGAACGAGGTTGATCATCTTATGAGGCTTCAACACCCAAATATTGTGCGATTTCGGGGCTACTGCCATGAAACAGTGTGGTTATATACAGAATTCGAAGGGCAAAAAGTTTTTGCTGAGATCTCAGAAATGTTGCTTTGCTTTGAGTATCTCCCTAAAGGAAGCCTTGATGTGCATCTTTCAGGTGGATCCTCTGAATTTGATTGGCACACGCGCTACAAAATAATCGAGGGGATTTGCAATGGCTTACACTATCTTCACGACCAAATTGATAAGTCTATTCTTCACTTGGACCTAAAGCCCGCGAACATATTGCTTGATGAAAATTTGGCACCCAAAATTACAGATTTTGGGCTGTCAAGACAGTTTGATCAGCATCAAACTATTTCCTCTCCAAATCGTGTTGGTACATTAGGCTGCATGGCTCCGGAACGCATCGATGAAGGCATAATCACACCTAAGTCAGACATATTCAGTTTGGGTGTGATAATAATGGAGATAATAACGGGACACAGGCACTACCCAGGTGTTTCTGGAACATCTTCCGAGGACTTTATTGAGCTTGAACTTAAAAAATGGAGAAACACATTGGAGAAAGCACAGGGGTACACAAACCTAGAAATGGATTGCGAACAGATAAAAAGATGCATTCAGATAGGTCTAATCTGTGTGAATCCTGAGTGGACCGAAAGGCCTACAACAACAAAAATTATCAAGATGCTTCAAGGATTGGAAAGTTTGGATCGTAACATTAGCGATGAGGTAGAGTCATCGGCAGATCAGATCTCAAATGGACTCAAAAAGCACAGCGATTGCTTTGGGGTTACTGAAGAAGGAAAGCTGTCTCCTAAAAATACATTATGTATTGGGATATTGGAGCAAGCTGAAAGAAGGGAACCAGAACTTGGGGAAGCATCGGTTTCTCTTGCAATGGCTGGTGACTGCCTACATGGAAAGTTGTTGTACCTTGAAAACCGAGTTGCTTTGGCGATGATATTGTTCCCAGCCGAGGCAAGAGTAGCAATGGAAGTTGCTCAAGTGAATGGTACTTCGGAATTTACCCTTGGTTCTAGTGCAAATCCACTTACGGAGATACAACGGACAACCTTTGATCTAAATGAAACTCCTTTCAAAATGAAGGATGTGTACTTAGCTCGGATGAGAGTGCTCTCCAAAACAGTTGAACTTGGCAAACGCTTCTTCCCGCGTTGTTCGGATGTGCTGGAGAAGATGATGGATGATGAACCAGGGCTGGCTGCCCTCGGAAGCGATTACAACCTCTGAGATGAATAGGTTTCATGACCTGCCAGATGTGCTTCAGAAGGCGTTCACTGCAGGTAAGCGGAAGCAGCAGAGCAGCATGGCGGAGCAAGATGTGGTAGAGCAGGTCCAGGGGCAGGGCGCCGTGGCTGGTACTGACAACGGGAGTAGGAGGATTGCTTGATCGCCCGTTGCTATAGATTGGTATGGCATTAGTGCGTAAACTTACTTTCCTCCTAACGGATCAACTGTGATAC[M]GAATTTGTAAGATTTCTGTCTCGCCTCCTACCTAATCATATTCTAATCCAATTGGAGTTGTTAATTTGTATTTAAATCCATAACAGGAAGCCGTGACGATGTACTTATATTGCCCGTAAGTTGCCCGTATGTGTTCGTG

Note: The ambiguity code M, highlighted in red, translates to A 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 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, 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
BS00015763 185
BS00016484 398
BS00013954 1311
BS00021305 1537
BS00013070 1544
BS00013580 1559
BS00013127 1640
BS00016210 1660
BS00013475 1669
BS00015537 1679
BS00012014 1910 2DT 19.54
BS00017669 1991



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.