Contig Sequence

Contig name: BC000003937 (Nimblegen Contig name: CONTIG90868)

Contains SNP BS00023061 at position 1122 (ambiguity code highlighted in red in the sequence below).

GAGGGTAAGTGATTCAGGGCCTAAGTGCACATCCAATATCTTCGCTTCTTCCTGGAAGCTCTGCAATGGAGGCTAATGTTGGACCGGTGGTGCGCCGGCTCTACCTCTTTGTCTATAATTGGGCTGCGTTCTTTGGATGGGCACAGGTGTTGTGCTACGCAACATTGGCATTGTTGGAGAGGAGGCCTGAGGCTATCTACACCGCGATCGAGCGGCCGCTACTGGTCACACAGACTGCCGCTTTAATGGAGATTGTTCATTCACTTGTAGGGCTTGTGAAGTCTCCTGTCTCCGCAACAATTCTACAACTTATTGGAAGGATATTTGTTGCATGGGGTGTCTTGTGGAGCTTTCCCGAGACGCGCCCTCATATTCTTGTTACTTCCTTGATCCTAGCATGGTCCATTGCTGAGGTCATCAGATATCCTTACTATGGTATGAAGGAGACATTTGGATTTGCACATTTCTGGCTATTATGGCTTAGGTATAACATGTTCATCGTACTCTATCCTATCGGTATGCTAAGTGAAGTTGGCCTCATATACGTCACAATGCCTTACATGAAGGCCTCCAATAAATATTGCCTTCAAATGCCCAATAAATGGAATTTCTCCTTCAACTACCACTATGCATCTGTTCTTCTAATGGGTATCTATTTTCCAGGATTTCCACACTTGTACCGTTATATGCTCCTTAGGAGGAAGGTGGTCTTGTCAAAGGCAAAATCCGCATGATATTACTCACAAGCTTTCTAGAGTATATGTCTCAAGTGACTTCTGAATGTGTGAGTTGTGTGCTTCCACACATGATACTTCCCACCAGCGTATATCTACTATTTGTGTGACGTTGTTCTCATGTTTTCTATCGTTTCCCGATCAATAAAGTTGGGGTGGTGAGCGTTCCCCACCTGAGTGCAATTACTCAATCGCCAGCAAATTTTTCCATACGACGAGGATGACAACTTCAGTCTAAATCGAAAAGTTGAGTATGTTGGTTGTGCTAGGGTTCCGCACATCATTAAAGGACACGAGGAGTGATGCCAATCTTATGGATGCTGAAGTGGTAGCACAGAGGTAGATGCATCCGAGTTTCGGTGTGATCTTGGTGGCACAGGCTGAGGT[Y]ATCATTCAGGGTTTTATGCAGAAGCTTTTCCATTTAATCTTTAGTTTGTCTCACATAAGGAGCATTTAGCAATGAAAGTTGAAGTTATAGAATGAGGAATATCATTAATAAAGCTCTTCTCATG

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 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
BS00014514 109
BS00019837 338
BS00006580 360
BS00012341 645
BS00013614 787
BS00012841 805
BS00012643 822
BS00013260 1075
BS00016638 1110
BS00012897 1119
BS00020679 1122
BS00023061 1122 6B 84.93



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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