Output

Output is formatted in the following way:

Gen.  Adj. Rseq  Rfreq     Rseq      MI        BG-Sum    NCR-Sum    TFs       BG-Size    Fitness
772,  5.046941,  5.965784, 6.128962, 5.047216, 4.476329, 7.538286, 34.000000, 1000,      0.000000

Site      Pos. Occ.    Exp.    Target
GGGACATG, 0,   0.4857, 1.2688, 1.0000
AGCGCATC, 0,   0.4972, 1.2988, 1.0000
CGCAAAGA, 0,   0.4597, 1.2010, 1.0000
GGAATAGC, 0,   0.4898, 1.2796, 1.0000
GGAACACG, 0,   0.4983, 1.3019, 1.0000
GTAACATA, 0,   0.4570, 1.1939, 1.0000
TGTAAGTG, 0,   0.3969, 1.0369, 1.0000
TGAACATC, 0,   0.4997, 1.3056, 1.0000
AGCAAATC, 0,   0.4995, 1.3049, 1.0000
AGAACGGA, 0,   0.4777, 1.2479, 1.0000
AGTACACC, 0,   0.4988, 1.3030, 1.0000
CGTACGGG, 0,   0.4661, 1.2176, 1.0000
AGTACTTC, 0,   0.4465, 1.1663, 1.0000
AGGACATA, 0,   0.4609, 1.2041, 1.0000
GGCCCATG, 0,   0.4204, 1.0982, 1.0000
CGCATATC, 0,   0.4842, 1.2649, 1.0000

Field	Explanation
Gen.	Number of generations which have elapsed (number of iterations of genetic algorithm).
Adj. Rseq	Corrected Rsequence (corrects for small sample bias). Rsequence is a measure of the column wise information content in the motif.
Rfreq	This is the expected value of Rsequence (a measure of the minimum information content required to identify each of the binding sites.
Rseq	Rsequence value prioer to correction.
MI	Mutual information. A measure of the dependency between positions in sites.
BG-Sum	Sum of scores which the recognizer assigns to sites in the background (non-binding sites).
NCR-Sum	Sum of scores assigned to binding sites.
TFs	Quantity of transcription factor molecules in organism.
BG-Size	Number of times the background is sampled (analgous to the size of the genome).
Site	The binding site.
Pos.	The position in the promoter region at which the site is found.
Occ.	Occupancy. How much time the transcription factor spends here.
Exp.	Expression level. How "turned on" the gene associated with this binding site is.
Target	Minimum expression level required for perfect fitness.