Contig Sequence

Contig name: BC000005858 (Nimblegen Contig name: CONTIG89064)

Contains SNP BS00012491 at position 1437 (ambiguity code highlighted in red in the sequence below).

TCTTCTCCTGTCAAGTCGTCGCCGCCGCCGTTCGCGCCGCCAGGCCCAGCTGCCCCCGTCGCCGGCCGGAATCTCTCCTCAGCCGACAGATCCGGCCGTCCAGGCTGACTCCCGCCGGATCCCGTCCTCGGCGCCGCCAGGTCGCGCGGGGTGGGAGGAGCTGCGACACCATGGCATAGAGGAGCTAGGCCCGACGCCGTTGACGCCCATCCCGAGCCAGGAGAAGCACCAGGACGACCGCTCTTCTTCCCCGTCCCGAGCAAGATAAACATATAATCTTAATGGGGCATGATCATATCACTCATATAGAGAAGCTCACGGCGGATGGTTCCGTTGCTGACAGGAAATGTTGCCAGGAACCTGGCTGCGATGAGATTGTCAGTGGAAGGGTAATGTACTGCAATAGTCACACTAGAGGGCATTCATCCCAACAGCTTGGTTACCTCCAGAGTTCACAGAAAACCTCAGATTTATACATGCCCCCTGTTAAAGGCAGACAGTGTACTGAACCCAGTGCCAGTGCAGAGCAAGACATAAATATCAAGTATGAGGGGAATGATCAAGGCAAACTCAATGATAGATCTGGGAATACTCAGGGAAACACTGGGCAACTAATCTTGGGTGGCCCTGACACGCTTTGCAAGCACGACAACTGCAAAAAGCAGGCCCAGAGTAACGCATTGTACTGCAAGCTACATAGTGGTGGTAGTAAGGGTTGCCTGGTACGGGACTGTGTGAAAGCTGCACATGGCGGCACGCCTCTATGCATCGGCCACGGAGGAGGGAAGCGTTGCGTTGTTGCTGGATGTCCAAACGCTGCATGTGGCCAGGGCCGCAGTGAGCACTGTGTGAGGCATGGTGGTGGCAAGAGATGCAAGTTTGAAGGGTGCGTGAAGGGTGCGCAAGGGAACACAGACTTCTGCATCAGGCATGGTGGGGGAAGGCGGTGCAAGTCCGAAGGATGCACAAAGAGCGCACAAGGACGCACGGATTTCTGCATCAAGCATGGCGGCGGCACCCGGTGCCAGTTCCAAGGATGCAACTCCAGCGACAAAATGGGGGACGGACCACTGCTCCGTGCATCGGAAGAGTTTGCTGGGCGAGACGCCTGAAGCCTTGCCGCTTCCTTCTGCCAAGCGTCGCGGAGCCAAGAAACCCAAAAAGGAAGTAAAGCCGCCGCCTCTGGCCTCCCAGCTGACTGTCACCACTGCTGGGAGCAGCGCACCGCAAGCAAAGGGTATTCTTCACATGCCTTCAAACCGTGAACTGTCGCACAAGATCGTGATGGCGGCCGGGCAAGCCGCCATGGCTCCTGCCCAGGTGTTACCGCTGTCCATGAAACCTCCAGCACCGTCGCCGTCGGGGGCGGAGAAGGAAGCGGCGGCGGCGAGCAGCACGACGCTGAATCTTTAGGAAACATCCATGGCGCAGGTGAC[Y]GCTTGCATTGTGTGCAGGCTGTCCATCTCTGATTACTGCTTCGGACCAAAAACATCCATGGGTTTAGGAGGCTTGTTGCTGCCATGGTGAAAGTTGTTGCTGCCGGCTTGACGTCGCCTTTTCTGTTTGGTCTCTCTTTGTCCGTCTAACATGTCAGATCTCTCTATAATCTGTAATGGCGTGTGGTTGGTGCGTCGTTGTGTGGGGAACTGCTCGTCGGACTATATGAGGTTGTGGACGATTGGCTAGAAAAAGAAATATCTGCATCCTG

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
BS00013388 533
BS00013432 594
BS00010026 839
BS00016248 848
BS00010431 935
BS00011461 953
BS00009960 1098
BS00010080 1116
BS00010769 1117
BS00012276 1131
BS00010533 1146
BS00010445 1155
BS00009523 1181
BS00016709 1323
BS00015541 1329
BS00013536 1384
BS00013969 1387
BS00012667 1414
BS00012491 1437 6B 31.63
BS00017226 1448
BS00010212 1449
BS00010985 1461 6B 31.63
BS00010420 1499 6B 31.63 6B 53.34
BS00021108 1550



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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