Contig Sequence

Contig name: BC000022387 (Nimblegen Contig name: CONTIG93016)

Contains SNP BS00055737 at position 399 (ambiguity code highlighted in red in the sequence below).

GACAACTGGNCGCAGAACAACTCAGTCCAAAATTTATTTTGTTGCATTGTCTGGCTTAGAAAAGAAAGCGCACACAGTTTAAGATTCTAGCAACATGCACGCATCTTCTTATTAAAGCTACTCTCCGGACCGGTTACAATTTGGAGCCGAGCAGCACACCCATACCATATGCATTTGCACCATGTCCAGATCAACAAGATGTTGACACTTGACTGCCCATATGTATGCNNNNNNNNNNNNNNNNNNGATGCAATCTCAAAACGCGTTGCAGCCTGACGCCATCACTTTTCCTGTCTCTCTGTGCTTCTTCCTCTCTTCTTCAATCTTCAGAAATGTCATGACATAATGTCTCTATCGTCCACATCAAGCAGAAATTAATTATCAGCTAAGTCAACATG[Y]CTTCCATTGCTATATCTGCCAAGAATATCTCGAGCAGCCCAGTGATGCCAAGAGTGAACTTCCAGAACTCGGACTAGCGATAGCGCTGGTACATCCTCCGCAGATCTCGGCAGTGTATGCACGTCCATGGGGTCAGTGGAGGATCGAGGCAGTACGAGTGTACCCACTGCGATCGGCAGACATGGCAGCTCAGTATAAGCTCTTCGGGCTCACGGCTGTGGCACATGTAGCAGGCCCCTTGGGTAGACGATGATGATCCAAGAAGGTCGCCGTGGCCTTCGTCAGCAAACATGAAGATGTTGGTTGAAGCTCCACAAGTAACGGGGGTCTGCGAGTATATCTTCTGATCTGAAGTACCGGCCTCATCCACCTTGCTGATCCAGGAGAAACTGGCTTTGCAAAGTGGGCACGTTGAGACCTTTCCCCTGGAAGACAGACAATCCGCCCATCCTTGAATGCACGAATAACAGAACCGATGTCCACATGGTAAGATGCCCCTCGAGGAAGAAAAATCAGTCCAGCAAATGACACATGAAAGCTCTGCTTGTCTTTGCAGGCTCGATGATTCTTCCATGGTGGGCTTCTCATCATCTCCCTTGTCATGATCAGCTGTGATGCCAAGGTCAC

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 24 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
BS00055737 399 1D 23.71 1D 50.07
BS00055738 404 1D 50.07
BS00055739 463
BS00055740 465
BS00055741 517
BS00055742 527
BS00055743 536
BS00055744 539
BS00055745 542
BS00055746 545
BS00055747 573
BS00055748 578
BS00055749 581
BS00055750 592
BS00055751 719
BS00055752 722
BS00055753 800
BS00055754 812
BS00055755 908
BS00055756 934
BS00055757 952
BS00055758 957
BS00055759 959
BS00055760 997



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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