; matrix-from-patterns  -v 1 -logo -seq $RSAT/public_html/tmp/www-data/2025/08/26/retrieve-seq_2025-08-26.164227_ANYiLm.fasta.fasta -format fasta -asmb $RSAT/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW.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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm
; Input files
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW.asmb
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/retrieve-seq_2025-08-26.164227_ANYiLm.fasta.fasta
; Output files
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices_split_matrix_list.tab
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.txt
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_log.txt
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices_logo
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_gibbs_matrices.txt
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_err.txt
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices.tf
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices_links.txt
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_sites.ft
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW.asmb
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.tf
; Number of assemblies	5
; Number of assembled patterns	5
; assemblies -> significance matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW.asmb -from assembly -to tf -return counts -decimals 2 -flanks 2 -top 20 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices.tf -from tf -to tf -return counts -decimals 3 -rescale 10 -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices_rescaled.tf -to tab -split  -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_matrices_split; rm -f /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.txt
; sites -> transfac matrices
/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -v 0 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_sig_sites.ft -from feature -to transfac -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.txt


/var/www/html/rsat/perl-scripts/convert-matrix -v 1 -i /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices.tf -from transfac -to tab -return counts -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_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/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices_logo -o /var/www/html/rsat/public_html/tmp/www-data/2025/08/26/oligo-analysis_2025-08-26.164940_8isTPW_pssm_count_matrices_links.txt
; Host name	rsat
; Job started	2025-08-26.164941
; Job done	2025-08-26.164942
; Seconds	0.1
;	user	0.1
;	system	0.01
;	cuser	0.65
;	csystem	0.15