Contig Sequence

Contig name: BC000023959 (Nimblegen Contig name: CONTIG99324)

Contains SNP BS00061979 at position 533 (ambiguity code highlighted in red in the sequence below).

TGCAAGTCAGCAGATCTGAAGGAGTAAGAGCCAGAGATGGAGAGCAAAGCTATTTGAATTAGAATCATTAAACTAAGGAAGAGAATTACATGGAGGATGCAGATCTCTGTGATTGGAAGGATCGATGATCATCCATTAATCGCTTGCCGCACCCTTGGAATCTGTAAGACACCGAAACGGCGGCGTTGTTCATGGATTGTGAATTTGGGAGGAGAGGAGTCACCGAATACGGAGGAGAACGAGGGACTCGTGGATCCACTGGTGGAAACCGATTTGACTTCTTTGTAATCCATGATGAAGTTTCCAAAGACCGCCACAGCATCCGGCTTGGATCCCACTAGTTTGGCGGAGCTGGTCCGCTTGGTTGTTCGGGCCATGGAGGGACTGGCCGACGAGATCCGGTCGCTCGACCAGAGCAATCGTAAATGGGCGCCTAGGTGGACCAACATCGCCGCCACCGAGCTGGAGTTGCTCAAGACCAATATGCTCTAGATCTGGTTCATATCTGTCGTCGCCGATCCACGACATGAGG[Y]GCTGGTGCAGCAAGCAAGAGATGCCACGTACTCCATCGAAGTGATTCAAGACAAGATTGAGTACCGTAGGCTTCAGTCCAGCCTTGTTCCGCATCACAAGATTCTCAATCATCTGTTCAAGCTGCTTCTTGCTCTGAGGTGTCGATGGAACTGCTCC

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 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
BS00061970 163
BS00061971 165
BS00061972 167
BS00061973 418
BS00061974 423
BS00061975 447
BS00061976 448
BS00061977 459
BS00061978 490
BS00061979 533
BS00061980 536
BS00061981 600

This contig has been mapped provisionally to chromosome 2BS.




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: 








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