Contig Sequence
Contig name: BC000006402 (Nimblegen Contig name: NO NIMBLEGEN CONTIG)
Contains SNP BS00011532 at position 2074 (ambiguity code highlighted in red in the sequence below).
CCTCTACAAGACCTGGGTCCGCACGTCGGCGATGAGGAGCCCGCAGGAGCGGAACACGCGGCTGGAGAACATGTCCTGGCGGATCTGGAACCTCGCCAGGAAGAAGAAGCAGATTGAAGGCGAGGAAGCCTCCCGCTCATCGAAGAAACGTCTTGAGCGTGAGAAGGCCCGTCGAGATGCTGCTGCTGATTTGTCTGAGGACCTATCTGACGGAGAAAAAGGAGAACATATTAATGAATCATCTATTCACGCTGAGAGTACAAGGGGACACATGCCAAGGATAGGTTCAACTGATGCTATTGATGTTTGGGCAAATCAGCACAAAGATAAAAAACTGTACATAGTGCTAGTAAGCATTCATGGTCTTATACGTGGTGAGAATATGGAGCTTGGGCGTGATTCAGATACAGGTGGCCAGGTCAAATATGTTGTAGAGCTTGCTAGGGCGTTAGGTGAAACACCTGGAGTATATAGAGTGGATCTGCTGACAAGGCAGATTTCTGCACCTGATGTTGATTGGAGTTATGGGGAACCTACAGAGATGCTGAGTCCAAGAAATTCAGAGAATCTTGGGGATGACATGGGTGAAAGCAGTGGTGCTTATATTGTCAGGATACCATTTGGGCCAAGAGAAAAGTATATCCCTAAAGAGCAGCTCTGGCCCCACATCCAGGAATTTGTTGACGGTGCACTTGTCCATATCATGCAAATGTCCAAGGTTCTTGGAGAACAAGTTGGCAATGGCCAACCAGTATGGCCTGTTGTTATCCATGGACACTATGCTGATGCAGGCGATTCTGCTGCTTTATTATCTGGGGCACTCAATGTGCCAATGGTCTTCACAGGTCATTCTCTTGGCAGAGACAAGTTAGAGCAACTTCTAAAGCAAGGGCGTCAAACCAGGGATGAAGTAAATGCAACATACAAGATAATGCGACGGATTGAGGCTGAGGAACTTTGTCTTGATGCATCTGAAATTGTAATCACTAGCACTAGGCAAGAGATAGATAAACAATGGGGATTATATAATGGATTTGATGTGATTATGGAGAGGAAACTTAGAGCAAGAATAAAGCGTGGTGTTAGCTGCTATGGTCGTGAAATGCCTCGTATGGTTCCAATTCCTCCTGGTATGGAGTTCAGCCATATAGTGCCTCATGATGTTGATCTTGATAGTGAAGAAGCGAATGAAGTTGGCTCAGATTCACCAGATCCACCTGTTTGGGCCGATATAATGCGCTTCTTCTCGAACCCTCGCAAGCCCATGATTCTCGCTCTTGCTCGTCCAGATCCCAAGAAGAACATCACTACGCTGGTTAAGGCATTTGGTGAACACCATGAACTGAGAAATTTAGCAAACCTTACGTTGATCATGGGTAACCGTGATGTTATTGATGAAATGTCAAGCACAAATGGAGCTGTTTTGACATCAGTACTCAAGTTAATTGACAAGTATGATCTATATGGGCAAGTGGCATACCCCAAGCACCATAAGCAATCTGAAGTTCCAGATATTTATCGTCTAGCGGCAAGAACAAAGGGGGTGTTTATTAACTGTGCTTATATTGAACCATTTGGGCTCACCTTGATCGAGGCTGCTGCTTATGGTCTACCTATGGTTGCTACCCAAAATGGTGGGCCTGTCGATATACACCGGGTTCTTGACAATGGCATTCTTGTTGATCCCCACAATCAAAATGATATAGCTGAGGCACTTTATAGACTTGTTTCTGATAAGCAATTGTGGGCAAAATGCCGTCAGAATGGTCTGGATAATATCCATCGATTTTCTTGGCCTGAACATTGCAAAAACTATTTGTCACGGGTTGGTACGCTCAAGTCTAGACATCCACGATGGCAAAAGAGCGATGATGCTACTGAAGTTTCTGAAACAGATTCACCTGGTGACTCTTTGAGGGATATTCATGATATATCACTTAACTTGAAGATTTCCTTGGACAGTGAAAAATCAGGCAACATGTCGAAATATGGAAGGAGTTCAACCAGTGATAGGAGAAACCTTGAGGATGCTGTACAAAAATTTTCAGAAGCTGTTAGTGCTGGCACAAAGGA[Y]GAGTCTGGTGAGAAAGCTGAGGCCACCACAGGCTCCAATAAATGGCCATCTCTGCGAAGGAGAAAACACATCGTTGTTATTGCTGTAGATTCTGTGCAAGATGCCGACTTGGTTCAGATTATCAAAAACATTTTTCAGGCTTCAAACAAAGAAAAATCATCTGGTGCTCTTGGTTTTGTATTGTCAACATCTCGAGCAGCATCAGAGATACATCCTTTGTTAACATCTGGGGGCATAGAAATTACTGATTTTGATGCCTTCATATGCAGCAGTGGCAGTGATCTTTGCTATCCATCTTCAAATTCAGAAGACATGCTTAGCCCTGCCGAGCTTCCATTTATGATCGATCTTGATTATCACTCTCAGATTCAATATCGTTGGGGAGGAGAAGGTTTAAGGAAGACACTAATTCGTTGGGCAGCAGAAAAGAATAGCGAGAGTGGACAAGAAGCAGTTGTTGAAGATGACGAATGTTCATCCACTTACTGCATTTCATTTAAAGTGAAGAATACTGAGGCTGTCCCTCCTGTGAAGGATCTTAGGAAGACAATGAGAATTCAAGCATTGCGCTGTCATGTATTGTACAGCCATGATGGCAGCAAGTTGAACTTCATACCTGTTCTGGCATCACGATCCCAAGCACTAAGGTACTTGTATATAAGGTGGGGGGTAGAGCTGTCGAACATGACGGTGGTTGTTGGTGAAAGCGGCGATACAGATTATGAAGGGCTACTCGGAGGCGTGCAGAAGACCATCATACTCAAAGGCTCATTTAATTCCGCGCCAAACCAGCTTCATGCCGCCAGAAACTATTCGCTAGAGGATGTCGTATCGTTTGACAAGCCAGGAATTGCTTCCGTCGACGGTTATGCCCCAGATATCCTAAAATCAGCTCTACAACAATTTGGTGCCCTGCAGGGCTAGAATCACCAGCTTTGTCAGAGTCAGCAGAGGAATAAAGTAGGTGTGTGGAGGCACAC
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 6 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 |
| BS00011532 |
2074 |
3B |
80.30 |
|
|
|
|
| BS00013842 |
2232 |
|
|
|
|
|
|
| BS00016612 |
2233 |
|
|
|
|
|
|
| BS00019064 |
2617 |
|
|
|
|
|
|
| BS00011933 |
2743 |
|
|
|
|
|
|
| BS00010522 |
3007 |
|
|
|
|
|
|
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.
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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.
Based at the University of Bristol with support from BBSRC.
