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The removed single reads accounted for up to 20% of some libraries.
We did not attempt to match pairs, thus this analysis rests effectively on single reads.
High quality single reads, as obtained from ABI chromatograms, were used for sequence comparison with publicly available vectorNTI tools (Invitrogen).
This method can only detect the coevolving substitutions covered by single reads (35 bp in this study).
While it is likely that a proportion of these single reads represent real miRNAs we set this cut-off to filter out potential sequence errors.
Single reads can easily be artifacts.
Single reads are not available from these data sets.
Single reads run sequencing was done with Illumina HiSeq 2000.
Single reads were put into FASTQ format for analysis.
We therefore collapsed duplicate reads into single reads.
Paired and single reads were randomly separated into three sets.
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