Contig Sequence

Contig name: BC000005258 (Nimblegen Contig name: CONTIG31254)

Contains SNP BS00012936 at position 1735 (ambiguity code highlighted in red in the sequence below).

GAGAGATTTCTGAAGAAAGAAGATGATTATGAGCACGCTCTCACTCAGATTGGCGATCTCAAGATGTCCCTAAATAGTACCAAAGAGAATTATGAGGTAATGATAGAGGAGGCACACTATGACATCACTTGTTTAAGGAATACAGTCGGAAAATTGGAGGCTGAGGTGAGCAAGTATAGAGAAGAATGCGAAGCTAAGGAGCTTGAGATTGTCAGTTTAAACAAGCAGTCGGAGGAAGAAATTGCCACTCTTAAAGCAGAAGCTGACAGGGTAGGAGCATCATTGCGAGATGCAGAGCACGAACTACAAACTGTCAATGAGGAGAAAGAGATACTTCAAGAGAAGCTATTGCACACGGAATCAGCAGTTGTTGAAGCTAACAGGGCTGTGCAGGAGGTCAAAGCTGAGAAAGAGGGTCTTCAGGAGCAGCTAATGCGCACGGAATTAGCGGTTTCTGAAGCTAACAAGGCTATTGAGGAGGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACGGAATCAGCGGTCGCTGAAGCCAGCAAGGCTTTACAGGAAGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACGGAATCAGCGGTTACTGAAGCTAACAAGGCCTTGCAGGAGGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACAGAATCAGGGGTTGCTGAAGCTAACAATGCTGTTCAGGAGGTGAAGGCTGAGAAACAGGGCCTTCAAGAGCAGCTAACGCACATGGAATCAGCAGTTGCTGAAGCTAACAAGGCTGCACAGGAGGCAACGTCTGAGAGTTTGCAACTGAAGGATAGGTTACTTGATAAAGAGAACGCATTGCAGAGCTTAACCCAGGAGAACGACGAATTCAGGCTGCGAGAGGCTGACGCCATGAAGAAGATAGAGGAATTATCTGCTCTCCTTGCTGAAGCCATGGAAAAGAAGCATCCTGAGGAGGAAGAGAAGCTAGTTGTTGTGGATGAGGTGCACAGTTCAGCGCGTGAAGTTGCTGAGACAGCTGCAGAAACTGAAGACACAGAAGGAGAGAGTGACAAAAAACCGAGCATGGAGCTCGTCGTCGCAAATGGAAACTCCAATGGCGACATGAACCAAGAGGAAGAGAAACACGACAGCAAGGTTGAGCAGCAGGAAGCCAAAAGTGATTTCACCACGGTACACGAGAGTGACAAAGTTGTCGAGAAGCAGCTGCAGGCAGATGTGAAACAGGAAACCGAATCGTCGAAAGACGACCTGTCCTCCAAGGAGGACAGCAGCACCGAACACGCAAATGCAAACGGAACAGCAGCATCAGCAGAGGTAACCAGCAAAGTCGCAATGTCCCCAACAACAACAAAACCGCAGAAGAAGAACAAACCCCTGCTGAAGAAGTTTGGTAACCTACTGAAAAAGAAGAACAGCAAGTAGTAGCAGGTGAACAGAAGAAAAACACATGTACTATTACTGGTGTTTATTATTACCCTGATCTTTCTTTTTCTTCTTCTTGTTTGATGACAGCAAGGTAGTGTGCTTAATTTCCACGTGTAATTTTTATACTGTCGACGCCTGTACTTTTGTGGTGATTGCAGTAGCTTTGTGGGTGNNNNNNNNNNNNNNNNNNNNNNNNATAAGCTGGACCTCCTGTTCTTTGCCCTATGGCTGTGGTTATTATTATCTACACGATCTGTGGCCGTTTGTTTGTAG[W]CCCTCCTGATTAAATACTGTGTAGCCCCTTATGGCAAGCTGATGTCACTCATATCATGCACCTGTACTACTATAATGTAATGTGATGTGATGTTGTTACCAGTGGGTGATAAACCCTAATACTATAACTAACCATCATGCTTGTTGGCATGATCTGTTGTTGGCTATTCT

Note: The ambiguity code W, highlighted in red, translates to A 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 14 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, the corresponding fields in the table are left blank and, if available, a putaive location for the contig, based on our extensive NGS of various wheat lines, is given below the table.

SNPs id Position Map Location AxC cM Map Location SxR cM
BS00017652 369
BS00013109 390
BS00014881 439
BS00017817 440
BS00016529 1046
BS00016744 1100
BS00014861 1319
BS00008649 1548
BS00008650 1549
BS00008651 1572
BS00008652 1574
BS00008653 1576
BS00008654 1578
BS00012936 1735 1D 73.73



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 


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: 








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