Contig Sequence

Contig name: BC000021417 (Nimblegen Contig name: CONTIG89183)

Contains SNP BS00050936 at position 1416 (ambiguity code highlighted in red in the sequence below).

TTCGGCACGAGGCTCCGGTCAAGTCTCCTCCCCCACCCGCGCCGGTCTACTCTCCACCACCCCCGGTGAAATCTCCTCCCCCGCCTGCTCCAGTGAGCTCTCCACCACCTCCTGTGAAATCTCCTCCACCACCTGCACCAGTGAGCTCTCCACCACCTGCACCGAAGAAGTCTCCGCCAACAGAAACACCGGTGATCCCACCTAAAGAAAAGTCAATGCCACCACCAACTCCGGCGAAGTTGTCTCCCCCTCCGACCGAGAAGTATGAACCACCAGCAAAACCTGTTGAATCATCACCACCACCGGTGAAGTCATATCCGCCAAAAGAACCTACGCCTGAGAAGTCATCACCACCACCGGTGAAGTCATATCCGCCAAAAGAACCTACGCCTGAGAAGTCATCACCACCTCCGGTGAAGTCCACACCACCGCCAACACCAGTCAGCTCACCGCCACCGGTACCAGTGAAGCCCCCACCGGCTCAAGTGAGCTCACCACCACCAGCGCCAGTTAAGGTACTTCCACCACCCACACCTGAGAAGGCGCTTCCACCACCGGTGCTAGCAAAGCCTCCACCTGCTCCAGTGAGCTCACCACCACCAGCACCTGTGAAGGTACTTCCACCACCGCACCAGAGAAGGTGCTTCCACCACCGGTGCCGGTGAAGCCTCCACCGGCTCCAGTGAGCTCACCACCACCAGCACCAGTTAAGGTACTTCCACCACCCGCACCAGAAAAGGTGCTTCCACCACCGGTTTGCGTGAAGCCTCCATCGGCTCCAGTGAGCTCACCACCACCAGCGCCAGGTTAAGGTGCTTCCACCACCCGCACCAGAGAAGGTGCTTTCCACCACCTGGGGCCGGTGAAGCCTCCACCAGGTTCCAGTGAGCTCACCACCTCCCCCTGTGAAATCTCCACCACCACCGGCTCCAGTTAGCTCGCCGCCACCTCCAGTCAAGTCTCCTCCTCCACCCGCACCGGTGAGCTCACCACCTCCTCCGGTGAAATCGCCACCACCCCCCAGCCCCAGTTAGCTCACCGCCGCCTCTAGTCAAGTCTTCTCCACCACCGGCACCGGTCAACTCACCGCCACCAGCACCAGTGTTGTTGCCTCCTCCAGCAAAATCCACCCCAGCACCGGTGAAAGAAGAGCCACAGTCACCTCCAGCGGAATCACTTACACCCCCAAAGTTCGACGAGTTCATCATGCCGCCGGTCGTGTCGGCAAAATACGCGTCACCACCACCACCCCAGTTCCAAGGATATTAAGCATGGCACCATCGAAACATCGACGAGGAGCGACCAATTATGGTTTAACACAACATCACGTGCACATGCACACTTGTACCTCATTAATTTGGATCGTGCATGCATGCATGCATGCGTCGTGACTTATTATTAATTATGTGCATGTG[K]GCGTATGCATGTGCAAACTAAGTGAGACGGCAAAGTGTATGAAATGGGAAATAGATGTGATCTATGATGCCNNNNNNNNNNNNNNNNGGAAGTGGGTAATTTTATTAAAGCATCAAGCAACNNNNNNNNNNNGGAGATGTGATCCATAATGCCTTATGTTCTGCTTTTCCCTTTAGGACAAATGTATTTCTTTCTTTTATGAGCAAACAGTGTATGAGNATNAAGGAACAAATACACAGTTA

Note: The ambiguity code K, highlighted in red, translates to G 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 28 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
BS00050929 128
BS00050937 254
BS00050938 295
BS00050939 296
BS00050940 423
BS00050941 426
BS00050942 436
BS00050943 484
BS00050944 503
BS00050945 659
BS00050946 661
BS00050947 663
BS00050948 668
BS00050949 670
BS00050950 671
BS00050951 673
BS00050952 686
BS00050925 1082
BS00050926 1126
BS00050927 1142
BS00050928 1168
BS00050930 1310
BS00050931 1320
BS00050932 1342
BS00050933 1343
BS00050934 1355
BS00050935 1358
BS00050936 1416 1A 9.36



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: 








Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

Maintained by Mark Winfield.