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Therefore, if either LHS or RHS overlaps with regions defined in the UCSC genome browser RepeatMasker track, an extra criterion (Maximum repeat sequence match allowed) is applied.
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Separate databases were created for perfect repeats, arrays with a maximum of one mismatch allowed per ten bp of repeat sequence, and arrays with a maximum of one mismatch per six bp.
Input into the script requires the sequence file in fasta format, the minimum and maximum repeat length to find, and a minimum repeat periodicity.
When 294 simple sequence repeat types shared between chicken and human genomes were compared, mean repeat array length and maximum repeat array length were significantly lower in the chicken than in human.
Simple sequence repeats (SSRs) were identified using SSRIT [ 46] with search parameters set for pentamers as the maximum repeat length and five as the minimum number of repeat units.
Moreover, when simple sequence repeat array types shared between chicken and human genomes were compared, mean repeat array length and maximum repeat array length were significantly lower in the chicken than in human.
Repeat sequence 2 more times.
Repeat sequence (skip burpees & plank).
We submitted the concatenated BAC sequences from each species to RepeatFinder using default parameters except for the following: Block Size = 2000, Minimum Repeat Size = 20, Maximum Repeat Size = 700.
The repeated sequences included direct repeated sequence, inverted repeat sequence and homology sequence.
The maximum repeat length for the BES-SSRs in this study even among class I AT/TA di-nucleotide loci was 72 bp suggesting that ultra-long SSRs are uncommon in BAC-end sequences from P. vulgaris.
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