Contig Sequence

Contig name: BC000032456 (Nimblegen Contig name: CONTIG31254)

Contains SNP BS00087086 at position 90 (ambiguity code highlighted in red in the sequence below).

GAGAGATTTCTGAAGAAAGAAGATGATTATGAGCACGCTCTCACTCAGATTGGCGATCTCAAGATGTCCCTAAATAGTACCAAAGAGAA[Y]TATGAGGTAATGATAGAGGAGGCACACTATGACATCACTTGTTTAAGGAATACAGTCGGAAAATTGGAGGCTGAGGTGAGCAAGTATAGAGAAGAATGCGAAGCTAAGGAGCTTGAGATTGTCAGTTTAAACAAGCAGTCGGAGGAAGAAATTGCCACTCTTAAAGCAGAAGCTGACAGGGTAGGAGCATCATTGCGAGATGCAGAGCACGAACTACAAACTGTCAATGAGGAGAAAGAGATACTTCAAGAGAAGCTATTGCACACGGAATCAGCAGTTGTTGAAGCTAACAGGGCTGTGCAGGAGGTCAAAGCTGAGAAAGAGGGTCTTCAGGAGCAGCTAATGCGCACGGAATTAGCGGTTTCTGAAGCTAACAAGGCTATTGAGGAGGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACGGAATCAGCGGTCGCTGAAGCCAGCAAGGCTTTACAGGAAGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACGGAATCAGCGGTTACTGAAGCTAACAAGGCCTTGCAGGAGGTAAAGGCTGAGAAGGAGGATCTTCAAGAGCAGCTAATGCACACAGAATCAGGGGTTGCTGAAGCTAACAATGCTGTTCAGGAGGTGAAGGCTGAGAAACAGGGCCTTCAAGAGCAGCTAACGCACATGGAATCAGCAGTTGCTGAAGCTAACAAGGCTGCACAGGAGGCAACGTCTGAGAGTTTGCAACTGAAGGATAGGTTACTTGATAAAGAGAACGCATTGCAGAGCTTAACCCAGGAGAACGACGAATTCAGGCTGCGAGAGGCTGACGCCATGAAGAAGATAGAGGAATTATCTGCTCTCCTTGCTGAAGCCATGGAAAAGAAGCATCCTGAGGAGGAAGAGAAGCTAGTTGTTGTGGATGAGGTGCACAGTTCAGCGCGTGAAGTTGCTGAGACAGCTGCAGAAACTGAAGACACAGAAGGAGAGAGTGACAAAAAACCGAGCATGGAGCTCGTCGTCGCAAATGGAAACTCCAATGGCGACATGAACCAAGAGGAAGAGAAACACGACAGCAAGGTTGAGCAGCAGGAAGCCAAAAGTGATTTCACCACGGTACACGAGAGTGACAAAGTTGTCGAGAAGCAGCTGCAGGCAGATGTGAAACAGGAAACCGAATCGTCGAAAGACGACCTGTCCTCCAAGGAGGACAGCAGCACCGAACACGCAAATGCAAACGGAACAGCAGCATCAGCAGAGGTAACCAGCAAAGTCGCAATGTCCCCAACAACAACAAAACCGCAGAAGAAGAACAAACCCCTGCTGAAGAAGTTTGGTAACCTACTGAAAAAGAAGAACAGCAAGTAGTAGCAGGTGAACAGAAGAAAAACACATGTACTATTACTGGTGTTTATTATTACCCTGATCTTTCTTTTTCTTCTTCTTGTTTGATGACAGCAAGGTAGTGTGCTTAATTTCCACGTGTAATTTTTATACTGTCGACGCCTGTACTTTTGTGGTGATTGCAGTAGCTTTGTGGGTGNNNNNNNNNNNNNNNNNNNNNNNNATAAGCTGGACCTCCTGTTCTTTGCCCTATGGCTGTGGTTATTATTATCTACACGATCTGTGGCCGTTTGTTTGTAGTCCCTCCTGATTAAATACTGTGTAGCCCCTTATGGCAAGCTGATGTCACTCATATCATGCACCTGTACTACTATAATGTAATGTGATGTGATGTTGTTACCAGTGGGTGATAAACCCTAATACTATAACTAACCATCATGCTTGTTGGCATGATCTGTTGTTGGCTATTCT

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 27 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
BS00087076 43
BS00087099 69
BS00087100 78
BS00087086 90 1D 73.73
BS00087087 114
BS00087074 120
BS00087075 126
BS00087088 144
BS00087089 147
BS00087090 152
BS00087091 275
BS00087092 339
BS00087093 349
BS00087094 406
BS00087095 453
BS00087096 454
BS00087097 462
BS00087077 495
BS00087098 501
BS00087078 516
BS00087079 622
BS00087080 684
BS00087081 759
BS00087082 789
BS00087083 810
BS00087084 825
BS00087085 852



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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