RULES for creating USER's set of REs:
1. USER's set must include only sequences of real REs and/or their consensuses.
2. Every real RE/consensus is described in 3 lines:
LINE 1: Name/description of RE/consensus
LINE 2: Sequence of of RE/consensus
LINE 3: <par1> <par2> <par3> <par4>
3. Sequence (LINE2) may include both standard nucleotides (A/a, T/t, G/g,C/c)
and their any combinations in according to IUPAC abbreviations:R - A or G,
Y - T or C, K - G or T, M - A or C, S - G or C, W - A or T, B - G or T or C,
D - A or G or T, H - A or C or T, V - A or G or C, N - A or G or C or T.
In the case of composite REs, 2 boxes are seperated by "-".
Length of RE/consensus sequence must not exceed 80 symbols, including "-" in the case of composite elements.
Capital letters indicate Conservative nucleotides (positions) in which mismatch is not allowd.
4. In LINE 3:
<par1> - a maximal number of mismatches for the 1st box
<par2> - a maximal number of mismatches for the 2nd box (for composite REs)
If RE contains a single box, then <par2> = 0;
If any mismatch is not allowed, then <par1> = <par2> = 0 )
<par3> - minimal distance between boxes of composite RE
<par4> - maximal distance between boxes of composite RE (for a single-box REs <par3> = <par4> = 0 )
All <par1>, <par2>, <par3> and <par3> are given as INTEGER in 4i5 format.
Example of USER's set of 3 REs:
2 0 0 0
1 1 8 10
0 0 0 0