; matrix-from-patterns  -v 1 -logo -seq $RSAT/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -format fasta -asmb $RSAT/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E.asmb -min_weight 5 -flanks 2 -max_asmb_nb 20 -cluster none -uth Pval 0.00025 -bginput -markov 0 -o $RSAT/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm
; Input files
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E.asmb
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta
; Output files
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices.tf
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_log.txt
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_gibbs_matrices.txt
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_links.txt
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_logo
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.txt
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_err.txt
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_matrix_list.tab
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E.asmb
; Number of assemblies	9
; Number of assembled patterns	61
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices.tf
; Rescaling significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_rescaled.tf


/var/www/html/rsat/perl-scripts/convert-matrix -from tf -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_rescaled.tf -to tab -split  -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split; rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.txt

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_1.tab -name assembly_1 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_1.tab -name assembly_1 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_2.tab -name assembly_2 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_2.tab -name assembly_2 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_3.tab -name assembly_3 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_3.tab -name assembly_3 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_4.tab -name assembly_4 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_4.tab -name assembly_4 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_5.tab -name assembly_5 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_5.tab -name assembly_5 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_6.tab -name assembly_6 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_6.tab -name assembly_6 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_7.tab -name assembly_7 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_7.tab -name assembly_7 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_8.tab -name assembly_8 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_8.tab -name assembly_8 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft

; significance matrices + sequences -> sites
/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_9.tab -name assembly_9 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft


/var/www/html/rsat/bin/matrix-scan-quick -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/tmp_sequence_2025-07-28.135243_7YU1Rc.fasta -m /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_matrices_split_assembly_9.tab -name assembly_9 -2str -t 5 -return sites >> /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft
; sites -> transfac matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf
; transfac-formatted -> tab-formatted matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.txt
; sites -> count matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf -from tf -to tab -return counts -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_links.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices.tf -from tf -to tab -return counts -return logo -logo_format png -logo_file /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_count_matrices_links.txt


rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/07/28/oligo-analysis_2025-07-28.135243_JFB60E_pssm_sig_sites.ft
; Host name	rsat
; Job started	2025-07-28.135250
; Job done	2025-07-28.135254
; Seconds	0.05
;	user	0.06
;	system	0.04
;	cuser	3.05
;	csystem	0.64