Contig Sequence

Contig name: BC000002663 (Nimblegen Contig name: CONTIG88487)

Contains SNP BS00012133 at position 1818 (ambiguity code highlighted in red in the sequence below).

CTGAACGACAGAATCCGCAGCCTCAGTGCTCTCCAGGGAGCTCTGAGGAAGGCCGAGGAGCATCTGTCTGGTCTCCCGGCAGACACTCCATACTCAGACTTCCACCACAGGTTCCAAGAACTTGGCCTGGAGAAGGGTTGGGGTGACTGCGCCAAGCGTGCGCAGGAGACCCTTCACCTGCTCCTCGACCTTCTCGAGGCTCCAGACCCGTCCACGCTCGAGAAGTTCCTTGGCACAATCCCGATGGTGTTCAATGTTGTCATCCTCTCGCCGCACGGTTACTTTGCCCAAGCCAATGTCTTGGGGTACCCTGACACCGGAGGCCAGGTTGTCTACATTCTGGATCAAGTCCGCGCTATGGAGAATGAGATGCTGCTGAGGATCAAGCAGCAAGGCCTCGACATCACACCACGGATCCTTATTGTTACGAGGCTTCTCCCTGATGCAACTGGTACGACCTGCGGTCAGCGTCTTGAGAAGGTCCTCGGAACAGAGCACACCCACATCCTCCGTGTGCCATTCAGAACTGAAAGTGGAATTGTTCGCAAGTGGATCTCTCGTTTTGAAGTCTGGCCGTACCTGGAGACTTTCACTGAAGATGTGGCACACGAGATTTCCGGAGAGCTCCAGGCCAATCCTGACCTGATCATTGGAAACTACAGCGATGGAAACCTTGTTGCGTGCTTGCTTGCACACAAGATGGGTGTTACACATTGTACAATTGCACACGCACTTGAGAAAACTAAGTACCCCAACTCTGACCTCTACTGGAAGAAGTTTGAGGACCACTACCACTTCTCATGCCAGTTCACTACCGATCTGATTGCAATGAACCATGCTGACTTCATCATCACTAGCACCTTCCAAGAGATTGCTGGAAACAAGGACACTGTTGGTCAGTACGAGTCTCACATGGCATTCACAATGCCTGGAATGTACCGTGTTGTCCATGGTATCGATGTTTTCGACCCCAAGTTTAACATAGTCTCACCTGGTGCGGACATGTCCATCTACTTCCCGTACTCCGAGTCACAGAGGAGGCTCACCTCCCTCCACCCAGAGATCGAGGAGCTGCTCTACAGTAATGTTGACAACAACGAGCACAAGTATGTGCTCAAGGACCGGAACAAGCCAATCATCTTCTCTATGGCTCGTTTGGACCGTGTTAAGAACTTGACTGGTCTGGTTGAGCTGTATGGCAAGAACCCTCGCTTGCAGGAGCTGGTTAACCTTGTGGTTGTCTGTGGTGACCATGGCAATCCATCAAAGGACAAGGAGGAGCAGGCTGAGTTCAAGAAGATGTTTGACCTTATTGAGCAGTACAACCTGAATGGCCATGTCCGCTGGATCTCTGCCCAGATGAACCGTGTCCGTAATGCTGAGCTCTACCGTTACATCTGCGACACCAAGGGTGCCTTTGTGCAGCCTGCTTTCTATGAGGCGTTTGGGCTTACTGTCATCGAGGCCATGACCTGCGGTCTTCCTACCTTCGCAACTGCATATGGTGGTCCTGCTGAGATCATCGTGAATGGCGTGTCTGGCTACCACATTGATCCCTACCAGGGTGACAAGGCCTCTGCTCTGCTGGTTGAGTTCTTTGAGAAGTGCCAGGTTGACCCCAGCCACTGGACCAAGATCTCACAGGGTGGGCTTCAGCGTATTGAGGAGAAGTACACCTGGAAGCTTTACTCTGAGAGGCTGATGACCCTCACCGGTGTGTATGGGTTCTGGAAGTACGTCTCCAACCTCGAAAGGCGTGAGACCCGCCGCTACCTCGAGATGCTGTACGCCCTCAAGTACCGCACCATGGCAAGCAC[Y]GTTCCGCTAGCTGTTGAGGGAGACTCCGCGAGCAAGTAATCTGGCCACCTCCTGGCCGAAAGAAGGGTGGCTTGGATTCCTGCAAAGATTGAGATTTGAGAATGCTTTGGGTTTTCTTCCTAGGCGCTGCTCTTTTTAAGATTTAAGGTCGAGTCAGTGTGCTACTTTGGTTTAGTAGTGGGAGTGAGTCGAGACAGAGGAAAATGTGGTGTGTGTCAGTCGGTTGGTGCTTGTCGTATTTCTTGGATGTTACCGTTCAATAATAGGTACGGCCTTGGTGCCGTTTCTGAAATAATAATAGTATCATCCTTCCTTGTTTACC

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 20 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
BS00010767 720
BS00014196 828
BS00009278 891
BS00012625 897
BS00011057 1152
BS00015648 1185
BS00015570 1515
BS00020490 1527
BS00018851 1530
BS00010236 1533
BS00010983 1539
BS00011407 1587
BS00009613 1716
BS00004524 1749
BS00020627 1812
BS00012133 1818 7A 31.36
BS00011181 1825
BS00010006 2076 7A 31.36
BS00010726 2122 2B 83.78
BS00017039 2133



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.