Contig Sequence

Contig name: BC000002044 (Nimblegen Contig name: CONTIG68514)

Contains SNP BS00009619 at position 539 (ambiguity code highlighted in red in the sequence below).

TCCAAATCCGAAGCCATGCCCAGAAGTTTTTCTCAAAGGTGGTGCGTGAACCTGGTGCTAAAATTGAGATCGAGATCCCTCCCCCCAGGCCAAAGAGGAAACCAGTACATCCATATCCTCGCAAGCGTGCGAACTCCTGCAATGGAGCAAACCTAGCAAATGGGCAATCCAAGCTTGCTCCTATGTCATCTTCTTCTGGTTCTGACCAAGAGAATGGTTCTCCTGTGTCGGTGCTATCTGCGATGCAGTCGGATGCTTTTGGATCATCGATGTCAAACCCGTCATCTCGCAGTACCTCCCCAGAGTCGTCAGATGAGGAGAACAGTGTTCTTCCAATGGTGAACGGAGGGGAAGGTCAACAAACAGGGATAGATCAACCCCACAAGGAAGCTGATCAGGAAAACAAAGATACGGGTACCTCTGAAGAGGATTCTTCTGATGAGGTACAGGTAACAAGCGTGAAGCTGTTCGGGAAGACGGTCGTCATCCCAGACCCGAGGAAAAGATGCTCCCCGGATACAGGCTCAGGGCATGAAAA[Y]GGAGAGCAAACCTCACAATCCTCTAACAAAGGAACATCACAAGCCCCACTGGCTGTAGAGATTCCAACACATACAAAGGGAGAGCAAATCTCACAATCCTCTAACAAGGCAACATCACCAGCCCCATTGGCTGTAGAGGTTCCGACGTATACAAATGGAGAGCAAATCTCAGAGTTCTCTAACAAGGCAACATCACAAGCCCCATTGGCTGTAGAGATTCAAGCATACGCTGCGCCGACAAGTGGGTGGGTTCTTCCATACAATTCATTCCCGCTCCATTTCGGGGAATCAGCGGAAGCCAGAATTGCCCGTTTGCACATGTGGTGGCCATACTATGGGTTTCCTATGGTCCATCCAAGTGGACCGAGTGCAGTGGCACACAACGGAAAAGCTACTGATGAGAGCGAAGCTGCGAAGAGCCCTCCAGTTGAATCAAGCTCGGACTTCAATGACAATACTCAGGCAACAGCCAGCAAGCAGTGGAAAGTGCTTGAGTCGCTTGGAACAGCGCAGGCCCCTCCGTCGGTTTCTAATTTTCAGCTTAAACCAAGCATGAACTCGGCCTTCGTGAGAGTGAAGCCGATCATCAGCAGCGGAGATGAGCCGGTGAGGGGGTTCGCGCCGTACAAAAGATGTAGAGTCGAATGACGAAAGCGGGGATCTTCTTCCCCGTTTCTAATTTAACTATGAACCCTAGGAGGAGCCTGTTCCACATATTCCTTTGCTCCGGTGCTATTCTTAGGTTTTACTTGCACATAGAGGTTGGCGGCGGTCTGGCCCGGGAAATGCGCGTTGTTTCCTGCTTGCGCCTTGTAATGAGCAGGGCACAGGTGGTTGCTGTAAGTGCTTGTAGGATAAAAGCAGGAGGTTTTGTAGGGATGCCAATTCTCTCTC

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 8 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
BS00003756 105 7B 67.68
BS00003609 154
BS00012019 323
BS00009619 539 7B 67.68
BS00014478 549
BS00012940 557
BS00010511 599
BS00003959 952



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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Maintained by Mark Winfield.