## LCRep description

Program for mapping low complexity regions in nucleotide sequences.

#### Algorithm description

Search for the low complexity regions is performed with using Shannon's information measure.
Shannon's information is defiened as follows:

where:
{a_{1}, ..., a_{k}} is the alphabet of the size *k*, and P(a_{i}) is a
fractional composition of a_{i}

The search is carried out as follows.
For each position *i* of the sequence *S* calculation of the Shannon's
information *H(i, l)* is performed in the window of size *l* within
the range [*l*_{begin}, l_{end}].
If *H(i, l)* turns out below prespecified threshold
*H*_{thr}(l) then fragment [*i, i+l*] is declared
low complex. Intersection of all such fragments at the end of calculation
gives a map of low complexity regions of the sequence *S*.

#### Output examples

>c20
Masked regions:
p1: 90 p2: 115 l: 26 chain(+) [Low Complexity Region]
p1: 220 p2: 240 l: 23 chain(+) [Low Complexity Region]
....

>c20
GCCAAGAAGATATGTAGCATTAAGGTTTAGAATACAGGCTTTGAAGTCAAACAGACCAGAGTTAACAACCTCATTTTGTT
TTTATTTTCNNNNNNNNNNNNNNNNNNNNNNNNNNCTTTAAGTTCTAGGGTACATGTGCACAACGTGCAGGTTTGTTACA
TATGTATACATGTGCCATGTTGGTGTGCTGCACCCATTAACTGGACATTTACATTAGGTNNNNNNNNNNNNNNNNNNNNN
CCCTCCTCCCCTTACCCCACAACAGGCCCCGGTGTGTGATGTTCCCCTTCCTGTGTCCAAGTGTTCTCATTGTTCAGTTC
....

>c20
gccaagaagatatgtagcattaaggtttagaatacaggctttgaagtcaaacagaccagagttaacaacctcattttgtt
tttattttcTTTTTTAAAATTTTTTTAAAATTATActttaagttctagggtacatgtgcacaacgtgcaggtttgttaca
tatgtatacatgtgccatgttggtgtgctgcacccattaactggacatttacattaggtAAAAAAAAAAAAAAAAAAAAA
ccctcctccccttaccccacaacaggccccggtgtgtgatgttccccttcctgtgtccaagtgttctcattgttcagttc
....