; matrix-from-patterns  -v 1 -seq $RSAT/public_html/tmp/www-data/2025/05/18/tmp_sequence_2025-05-18.195907_1RyIsi.fasta.purged -subst 1 -maxfl 1 -max_asmb_size 30 -pl $RSAT/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_clusters_complete_k2.tab -sc 4 -cc 2 -max_asmb_per_cluster 2 -flanks 2 -logo -cluster sig -o $RSAT/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm
; Input files
;	sequence	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/tmp_sequence_2025-05-18.195907_1RyIsi.fasta.purged
;	patterns	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_clusters_complete_k2.tab
; Output files
;	sig_sites	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_sig_sites.ft
;	gibbs_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_gibbs_matrices.txt
;	err	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_err.txt
;	assembly	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm.asmb
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm
;	sig_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_sig_matrices.tf
;	count_matrices_tf	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_count_matrices.tf
;	sig_matrices_split	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_sig_matrices_split_matrix_list.tab
;	count_matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_count_matrices.txt
;	links	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_count_matrices_links.txt
;	logo_basename	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_count_matrices_logo
;	log	/var/www/html/rsat/public_html/tmp/www-data/2025/05/18/position-analysis_2025-05-18.195907_yp2Ycu/position-analysis_pssm_log.txt