Contig Sequence

Contig name: BC000036220 (Nimblegen Contig name: CONTIG89502)

Contains SNP BS00103478 at position 289 (ambiguity code highlighted in red in the sequence below).

GTAGGAATAATTGAACATTACGTTTGTGATGAATGCAGGTGAGCAACAGCTCAAACACCGTCATGTAGCTAAGAAAGTTGACAATACAAAAAGGGAGAAATGAAAAGAAAATATGCACTTCTTATGAACAATTTCTTTGGCATGATGGTGTCTGCATGGTTTGACTCGCTGAGCGCAGAAACCTTCCGTTGACTTCAAAAACCTCCAGACAACTTGCACTGGGAGCGAGTATCATACGTAATCCACAAGCACCTGCAGCGGCTTCTCCATTGAAAAAAGAAGAGGAAA[Y]GGCCAGGCCAATTTTGCACAACAATGATTCTAAGAAACTCCTTGGTGCTGCCGGTACCTAAAACAAGACGCCGCCAAGATGTACATAAAGGAGTCATAACTTCTTCTGATCTGCCTTCAAGCGGCACCTGGTTAAGGTCTCCTCGCGATGTTGTGCAGGCACCCCATTTAAGACCACCTCTATGTCAGCCTTGTGTTTTCTTCGCAGCGCACTGAGCTCCTCTTTCTGATTGGCTAACAAATCTGCCAACTTTTCATTAAGATCTGCTGTGAGATAACCGCCATCTGAAAGACGAGAGCTAGTGCCAGCAGAAGCTCCTCCCGAGTTCCTGTTGACCACATCCGGGTTCGACAAGTGCACTGATGATGACATTCGCTCACACATACCGTCTACATTATTGTTTTTCAATATCCCATTTGGCATATTATCATCAGTCTGTTGGTCCTCCACCGAGTGAGAGATTTCAATATCTCTTCTGGGTGAGTCTGACCAGTATTTCCGGCCAGAAGGAAGCTGCTCTTGTATAAAACCATTGTTTGTTGCATCAACCTCGTTACGAAGCTCAGAAGTCTCACCGTTGTCGGATTCTGAATTATCAGTCTCGGAATGACCTCCTTCATCCCCTTGGTTGTCAACCGATTCATCAAACGCCCATTCAGGAATATGTGCCTGTATTTCAGAATCTATCATTTCTGCAATCGCAGTAACATCTTGGTCTGTGAGATCCAGCTGTACAACCATCTCAGTAGCAACGCTAATTGAAGTGTCAGCTTCAATATCAAACGGAAAATGGATGTTTTGGGCATGACCTGTTGAATCGGCAATCCGCAGTTTCAAAAATATTGTATTTAGGTCCTTCCGCTGACTCTCAACGGTGATCCTTCGACTAGTCGCAGCATGTCGATCCCTATTGCTGTGTATATCACTTGGATGTGTTTCCCCCGTGCTACCTGTTCGTCCCCGGGAGCCAACAGACGATGCTGCTCTGTAATTCGCACTTGGGTTCGAACTGCCAGCAGCATCTGATGCATTCGTATTTGACTGTACTGGATAGAAGATTCTTTCATCATCAACATCTAGGAGAAAAGGATCCACTAATAGTTCTTCTGCTGAGAGCCTTTGGGAAGCTTGGGCTATGCATTTCTCTATAAAAAATTTAACTTCAGGATCCTCAATCTTAGCCAGTGAACCAGGCTTTTCACCATCAGAAACTTTCTTGTATATCTGTGCTGCATTGGAGCATTCACAATATGGGTACT

Note: The ambiguity code Y, highlighted in red, translates to ).

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 30 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
BS00103478 289 1A 27.45
BS00103479 350
BS00103480 362
BS00103481 364
BS00103482 392
BS00103483 419
BS00103484 458
BS00103485 482
BS00103486 585
BS00103487 605
BS00103488 611
BS00103489 742
BS00103490 746
BS00103491 748
BS00103492 749
BS00103493 813
BS00103494 828
BS00103495 867
BS00103496 869
BS00103497 893
BS00103498 900
BS00103499 926
BS00103500 989
BS00103471 1007
BS00103472 1016
BS00103473 1034
BS00103474 1040
BS00103475 1043
BS00103476 1073
BS00103477 1097



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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