Contig Sequence

Contig name: BC000002820 (Nimblegen Contig name: CONTIG53089)

Contains SNP BS00012343 at position 782 (ambiguity code highlighted in red in the sequence below).

TTCTTGTCCTGGAGACCCCGGGCTTCACCGCCTCCCGCCCGGCCGGGCCTTCCAGCGTCCCAATCGGGACTCCGCCGTCGTTCGTTCCGTGCTCACTCGCCCCACAGTCCCGTGGTGCTGCTGTTCCTAATACGCCTGTTCTACCGCGCGCGTTCGACTTTGACGCTGCTGATTTGGGGATCCCTGGGCCGGCTTTCCCCGGATCTGCCGGCCCCAACGCTGAGACACGTTTCTTCACCAACCCGCGTTTGGATGTGGCAGGCCCCTCCACTTTTCGAGGACCTTCTTCCCCGATATCTTTGGATAGTGATGATGAGCTGGATGACTTTGGGTACAAAGAGCCATCGGGCAATTTGATTTTACCCTGTGAAGAGTCCATGCGGGAAGAGGAGAGAAACGACAACACAGAAGAAGGAAAGACAACGCAGGAAAAGAGGAGACTAATAAAGGAGGGGAAAGCGAAAATGGTTGAAGAAAAGAAACGACAGCGGGAGGAAAATAAGCTCATGAAAGAAGCTATTAAAGCTCAAAAGGCAGAGCAGAAGAAAGTATGCAAAAGAAAAAGACGAGTGGGAATCAGGAAAACATGCTTTAAAATCTATTGTGGCTGAGATCGACTCAACAATCATTGAAACTGGCTCAGTTGGAGGTACTCTTCTAACACGGTTTGCAGAGAAAGGCCTTAAGTATCGAGTTCAGGTTAATCCAATCAGAGGATCGATTTTGTGGAAGATGGAGGTTCCTCAAATTGGCCAGGACCCAGCTTCAGTGTCAGAAGTGC[M]ATATATTCTATTTGTGCTTCAAGCTGAGGAATTCTGTGATCTTATCAACAGTGGGTCCTTCTGGGATCATGTTCACCTTGTTCAAGATCGCTATCCAACGTTCACTGTTTGCTTTGTCACTAATAAATTGATGAACTACATAAATAAATGCGAGCGGGCTCAGTATAGGAATGCACCCAATTTTAATAGCTGGAAACGCCCACCAGTGGAAGAGGTTTTATGCAAATTAGCAACACACCATGTTAAAGTTCACTCAAGGCAATGTGCAGATGAAGCTGAAGTAGCCGATCATGTTGTTGGCTTGACATCTAGTCTTGCAAATTGCAGATTCAGGAAACCACTGTCATGGTTATCTGTGCATGCTAATGGTGCAGTGATCCCTAAAAATTTCATTGATAAAGATCTGGCTAAGAAAGATACCTGGATGAAGGCTCTAATAGCCATCCCAAAGGTCCAGCCAAGGTTTGCCCT

Note: The ambiguity code M, 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 9 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
BS00004748 443
BS00005687 664
BS00005688 678
BS00012343 782 2A 124.54
BS00005689 1047
BS00005690 1048
BS00004909 1169
BS00005691 1200
BS00005692 1203



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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