Designations. On an axes abscissas - sequence DNA mobile element in bp; on an ordinate axis - ascribed numbers of the regulatory sites (their titles are reduced in tab.1); 1 group - the sites of replication and transcription initiation and termination; 2 group - enhancers and silencers of chromosomal, viral, etc., genes; 3 group - the sites recognized by cellular protein transcription and translation factors; and 4 group - the sites recognized by protein receptors for inductive signals; the arrows mark the discovered location of regulatory sites on the left-directed (leftward arrows) and right-directed (rightward arrows) DNA strands.
(b) Schematic structure of the DNA sequence of retrotransposon Copia-white.
Designations. LTR, long terminal repeats; ORF1 and ORF2, big open reading frame; DRR1 and DRR2, direct repeats; P is the motif of amino acid sequence of protease domain; RT, of reverse transcriptase domain; RH, of RNase H domain; and I, of integrase domain.
(c) Consolidated distribution of the revealed motifs of functional sites along the Copia-white DNA sequence.
Designations. On an axes abscissas - number of segments of genome each size 1/15 length given MGE; on an ordinate axis - total number of nucleotides contained in the motifs of functional sites and falling within the scanning window by a size 75 bp. The upper direct line - 95%th level of the nonrandomness of the condensations of the motifs of functional sites; the lower direct line - average for 50 of casual sequences the same lengths and same nucleotide's of structure as DNA Copia-white distribution of motives functional saites.
Jamming of the motifs correlates with the locations of potential regulatory regions within LTR, DRR2, and in the interval between the ORF and rLTR.