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Repeat analysis
Sequences generated from maize methylation filtered and high Cot genomic DNA clones were first
repeat-masked with a filtering module from the Paracel Transcript Assembler package
(Paracel Inc.) using the Maize Repeat Database
and the TIGR cereal repeat databases
as references. The repeat content was calculated as a percentage after dividing the number of nucleotides
that were repeat-masked by the total number of nucleotides generated.
By this rationale:
- 25% of the nucleotides in the methylation-filtered raw sequences were
repeat-masked (before assembly) and 53% of the AZM (Assembled Zea mays) and singleton
sequences were masked (after assembly).
- 23% of the nucleotides in the high Cot raw sequences were
repeat-masked and 34% of the AZM and singleton sequences were masked.
- In Release 4.0ALL, when the methylation-filtered and high Cot sequences were combined,
50% of the AZM and singleton sequences were masked.
Click below for detailed views of the repeat-masking statistics, repeat classifications,
listings of repeat sequences identified from raw sequences (before assembly)
or AZM/singleton sequences (after assembly) and repeat hits for individual sequences.
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