Contig Sequence

Contig name: BC000002305 (Nimblegen Contig name: CONTIG99072)

Contains SNP BS00009722 at position 141 (ambiguity code highlighted in red in the sequence below).

GATCATCACAGAGCAAATAAACATAGCAGGCCTGCCTAGCGCACACACAGAGTAACTTACCATGGCTGCCAGTGTCCACCATCTCCTTGTGCTGCTCCTAGCCTTCACAGCCTTCAATGGCAGCTCTGCGGCATCTCGTC[M]TCTTTTGGACACGGCAGCTGCACCAGAGGCCACACCAGCTCAGCGTTCTACACCGGAAGCTCCAACAACACCGCCTCCAATGCCTTCCATTCCCGCAGTTCCGAAACTGACAATGCCGCCAATACCATTCATTCCTATCCCGAAGGTCGCCATGGCACCAACCGCCCCTGGCACAGTTCCATCTCTTCCGATTCCGGCGATCCCAACCACCATGCCGACCATTCCTACTTTGCCTGTTACCATGCCACCAATGCCCTCAGTTCCAATTACCATTCCATCCATTCCGATCACAATACCAACAACTATCCCTACCATTCCTGGGTTCCAGATGCCACCTATTCCATTCATGTCCCCACCTCCGCAAACCACCAGCCCATGAAGGCCGTCATAGCATGAGACTGCTAGTCAGGGGCTTGATTCGTACACATAGTTATTATCACTGTGTTTGTAATGTTTGTTCTGTTGGATGTTTTACTGGCTTGCATTTGGTGTTGATTGTGAATGCAGTTAAGTTTTTGTACTGTCCTGTTTGTTAATAAAGCATTGCTTGGTTTGTTT

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 32 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
BS00020589 50
BS00014353 54
BS00005243 133
BS00009722 141 2B 95.58
BS00012636 148
BS00009141 152
BS00011709 186 2B 95.58
BS00009142 190
BS00009998 212 2B 44.61
BS00011867 259
BS00005244 268
BS00014192 289
BS00009143 305
BS00009144 331
BS00014571 394
BS00005245 412
BS00009145 438
BS00009146 440
BS00009473 442
BS00004184 445
BS00012774 448
BS00009147 448
BS00009148 481
BS00009560 482
BS00009149 482
BS00003965 502
BS00009150 524
BS00015209 524
BS00003951 554
BS00005246 581
BS00009151 600
BS00011827 625



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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