Contig Sequence

Contig name: BC000031397 (Nimblegen Contig name: CONTIG12391)

Contains SNP BS00082597 at position 634 (ambiguity code highlighted in red in the sequence below).

CTAAAATATCCACTNNNNNNNNNNNNNNNNNNNNAAACTTCCACTGCTGTTTAAGACACAGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTCACTGCTGTTTACGACACAGCAAAACCTATCTCCAAACAAGTTAAAGGCTCCTGCAACCAACTTCCAGAGAGACTAGGGCACCATCACCAACCAGCAACCATTGCAGCGTGATACTCCACTAAACTATAACATTCCAGAGCTCTGGTCTTGCAAATGCCTGCCTCCTCAACTAAGATGATGACGACGATGCCTCCCCGATGCTGATAGACAGGCCGAGGCGAGGAGCGGCACGGATATTCCTCAAGTTGAAGTGTGACTTCAGCGCAACCCATGCTGACCCAAAAAACTTGTGCTTCACAACAGCACTAAGTATGCCTGAACTGCCCACACGTAGCTTGAAGCGGGTGCTCGGATCAGCATACTCGCAACCAACCATGACCACACTCGAGCCAGTTGCCAGGCAATGAATTGCTTGCGCGCCAACCATAGTTTGCGATGGAGTGGTCCGTGCCAGCAGATCATACAGATCCCCTCCCAGGTTGGTCCTCCTCACAGCGTCT[S]TGAATAAGGAACAGGGCTCCAGCTTGTGATTTAACAGCATCAACACCTGAGCATGGCTATTACACTGGATGCCACACGAGAAAGCTTCAGTGTTGAAGGAACAACCAAGGGAATAAAAGTTAGGCACCTCATTCCCCAAATTCATCTTCATAAGACCCCCATAGTTCAACCTCCTGGATCCAAAAAGGCCCGACAGAGACACCAATGCATCACCACGAACAGGGTGCATAGAAGCAATTGCACGAAAGCCAGCTTGCCGATAAAGAGCATCCAAATTAAACGAAGAGTCCCGGAATGGGTAACAGACTTTAAGGACAGGGTTCACATCACAGCCTAGCACTCCAGGGAAAGATACTATAGCGCTCACATGTTTTGTTGTATCAAATTTGAAATCAAGGCTCAGTTGGGGCTGCCGAAGTCTCAGCTGGCAGCCATGCACATTGTCATCCATTGGAGATCTCTTGGCAGATGAAGTAAGAACAAAACCATCACCACACTGCATTGACATCTGAAAGCTCAGGTCAGAGGCGAAATCCTTGTACATGAGGTCTCGACCCTGTCGGCAGATATCTTCATAAATCCCAGGTGTGGTGTCTGGTAAGAACTTTTCAAAGAACCTCTCCTTCAGTTGCTCATCCTTTGGATCCAGAACTCCTAGAAGCAATAAGAATCCGCCAAGAAATTCCAAGTACTGTCGAAACTGCTCATAGACCTGGCCTGCCTCGAATGGATACTTCGACATCCGCATGAATCTGTCAGCAAATGAACCAGTACTGCTAGGCGGAACTTCCCTCAAAGTGACAGAAATTTCCGTAAGCAACTGGATAATCTTTTCTGCATTCTCTGAAGATGTCTTCTCAGCACGCGCTCCCATAGACACCGCCTCTTTAACATGACCAGACATTGCTTCAAACTGCTGCAGAAGGTGCTCCATATCCTTGGAGTGAGCACCGATGCACTTCTCAATCGCAAGGGCATTCTCAGCACTGGAGACTTTTATGGAAGAGTTAATTTCTTTTAGGTACAGCTCCAGAAGATTTTTGAATTCAAGGAAATCATCCCT

Note: The ambiguity code S, highlighted in red, translates to G or C).

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 21 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 Map Location SxO cM
BS00082588 348
BS00082589 359
BS00082590 363
BS00082591 397
BS00082592 441
BS00082593 444
BS00082594 476
BS00082595 533
BS00082596 555
BS00082597 634 1D 108.23
BS00082598 647
BS00082599 687
BS00082579 1402
BS00082580 1424
BS00082581 1467
BS00082582 1483
BS00082583 1485
BS00082584 1535
BS00082585 1556
BS00082586 1596
BS00082587 1602



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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Maintained by Mark Winfield.