Contig Sequence

Contig name: BC000005792 (Nimblegen Contig name: CONTIG89370)

Contains SNP BS00012531 at position 1309 (ambiguity code highlighted in red in the sequence below).

GTCCAGTGGAGCACAGCAGCAATGGGAAGGTAAAAAGCTTTCAAGTTCATGATATGGTTCTTGAATATATTGTGTCCAAGTCAAGCGAAGAGAATTTTATTACTGTGGTTGGTGGCCACTGGCTGATACCAATGTCGACCAATAAAGTACGTCGACTCTCCGTGCAAAGCAGTGGTTCCGAACATGGAAGTTCAACAAAACACATGAACCTGTCGCAAGTGCGATCACTGACCATGTTCCGGAGCCTGGACCAACTTCATTTCCATTCTTTCAATAATGGAATTTTACAAGTGCTGGATCTTGAGGGTTGCAAGGGTTTGAAAGAGAAACATCTGAAGGACATGTGTAGAATGCTTGTGCTGAAGTATTTGAGCCTTCGGGGAACAGATATTTCCAAAATACCCTCTAAGATTGCAAAACTCGAGTACCTAGAAACTCTTGACCTAAGGGAGACGAATGTTACTGAGCTCCCAAAATCTGCAGGACAGCTCAAACGGATAATTAATATATTTGGCGGGAATAAAAGCTCAAGGAAGGGTTTAAAGTTGCCTCAAGAGATAACTAAGGAGACAATGAAAGCACTCCGTGTACTGTCAGGGATCGAGATTGATGACAAATCAACAGGTGTTGCTGGCCTCCATCAATTGACGGGGCTTAGGAAGCTTGCAATTTACAAGCTCAGATTACAGAAGGGTAGTGAAACCTTGACACAGTTAGGCTCTGCTATCGAGTATCTTGGCAGCTGTGGTCTGCAGACTCTGGTGCTCAACGACGAGGGATCTGATTTTATCAACTTGTTGGACACCATGTCCGGCGCACCTCCAAGATACCTCAGTGCCCTTGAGCTCTCTGGCAATTTGAAAGATGTTCCCCAGTGGATTACCAAACTCAGTAACCTCAACAAGTTGACCCTTTCTGTGACAGTTCTCCGGACAGATACTTTTGTGCTCCTGCGCGACCTGCCTTTGTTGTTTTCCCTCACCTTTTCGCTGAGTGCAGCGAAGCAGGATGAGGCCATAGTGGACATCATTGATGATAACAAATCACAGTCTGGTGGGGTAATCTACGTTCCAGGTGAGGGATTCAAGAGTCTTAAGCTGCTTCGCTTCTTTGCACCTCTAGTGCCAAAGCTGAGCTTCCCAGAAGATGCAATGCCAGCACTTGAAAGGATCGAGATGCGGTTCGAAGCCTTTGAGGGCCTTTTCGGTGTTGACACCCTGAAAAGTCTCAAGGAGGTGCACCTCAGAGTCAATAGCACAGCAGATGACATAACCAACTTCATAGTAGATGATTTGAAGGCCATCAAGG[M]GCCAAAGATAATCGTGGATCATGTTATCAGCAGCTGAAATATGGCATTCTCATGGAGCGCTTACTCATCATCCATCTTTACCCTCTGTTTGTCGAGATTACTGGTTTAGTTTGTGCCATTCGTACTTCAATAAAAACAGGACACTGCTGCGTGCCTGTAAGCCACAAGACTCTTATGATTTTTGCTTGTGAAATTCGAACGTTATTTCGTTTTGGGCTTGTAAGTTAATTTGACTTTAACTTGAAACTGTGAGCGTTTGTCAAAGATATTTGTATTACC

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 21 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
BS00016711 338
BS00013225 867
BS00012558 899
BS00013721 953
BS00021191 954
BS00013579 1021
BS00021458 1029
BS00013175 1034
BS00012158 1047
BS00021274 1078
BS00009435 1112
BS00016575 1157
BS00010199 1163
BS00012581 1226
BS00015426 1230
BS00010913 1257
BS00012013 1268
BS00009476 1289 3B 79.14 3B 14.48
BS00013223 1308
BS00012531 1309 3B 79.14
BS00017028 1339



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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