RECON and other de novo detection programs like REPuter [ 8], Vmatch [ 9], RepeatFinder [ 10], RepeatGluer [ 11], and PILER [ 12], are designed to generate a repeat library rather than to use one.
This gene is located between the wciD and wzx genes and encodes for putative glycosyl transferase (GT) protein, involved in linking sugar molecules to generate a repeat unit [ 5].
First, we generated a list of HpaII restriction sites on the sequence and used RepeatMasker [ 56] to generate a repeat-masked sequence file.
We then (iii) generated a consensus repeat for each CRISPR locus exploiting the fact that repeats within a CRISPR locus are almost completely identical with some loci that carry few mutations, preferably at the start and end (see Supplementary Figure S3, Supplementary material).
In order to further characterize the link between repeat A sequence and its silencing ability, we generated an artificial repeat A construct that tested the potential impact of sequence variations in the individual monomers, which are particularly prevalent in the T-rich linker regions.
Due to the location of the putative RevRE within the 1st intron of the CLOCK gene, we generated a three-times repeat of the RevRE to clone upstream of the firefly luciferase gene (Figure 4a).
This observed orientation preference for expansions is less well explained by the fork-reversal model, since the sequence that is expected to form a more stable pseudohairpin on the lagging-strand template is the CTG repeat that would be predicted to preferentially generate a CTG repeat pseudohairpin on the newly synthesized leading strand.
Thus a single state of order k can generate a tandem repeat with period k, allowing for mismatches between consecutive motif occurrences.
ISPsy8 always broke the REP element at exactly the same point of the sequence, generating a direct repeat of three bases [see Additional file 1].
Although there are a number of variations in deletion, insertion and rearrangement in each sequence, they consist of phage infection-related genes (e.g. NIES39_F00750) and small conserved putative genes, generating a direct repeat in some case.
