

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_query_matrices.meme -from meme -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/Collection_1_input_motifs_processed_1.tf -from tf -to transfac -prefix_id Collection_1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/Collection_1_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/Collection_1_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/motif


 cat /var/www/html/rsat/R-scripts/matrix-clustering.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " infile = '/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 0; draw.heatmap = 1; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'Ncor_0.55_cor_0.6_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/cluster_1_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/cluster_2_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/cluster_3_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/cluster_4_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_data/cluster_4_transfac_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m12_TQGTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices_temp.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m7_VQPTAR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices_temp.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices_temp.tf -from tf -to tf  -attr name cluster_2 -attr accession cluster_2 -set_attr merged_AC 'Collection_1:::TQGTSR_ArgR' -set_attr merged_ID 'TQGTSR_ArgR' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_cat.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices_temp.tf -from tf -to tf  -attr name cluster_3 -attr accession cluster_3 -set_attr merged_AC 'Collection_1:::VQPTAR_ArgR' -set_attr merged_ID 'VQPTAR_ArgR' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_2/cluster_2_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_3/cluster_3_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093512_PJzvLw


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093512_mYAYiF


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093512_ITRbyz


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m1_NQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf -from tf -to tf  -attr name cluster_4 -attr accession cluster_4 -set_attr merged_AC 'Collection_1:::NQSKSR_ArgR' -set_attr merged_ID 'NQSKSR_ArgR' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m11_SQAKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m14_SQSKNR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m6_TQSSSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093513_bRa44V


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_nb_motifs_6.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093513_wpCfnw


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_nb_motifs_5.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093513_v69QpY


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m4_AQATSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m8_SQGTSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m11_SQAKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m14_SQSKNR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m6_TQSSSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m11_SQAKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m14_SQSKNR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m6_TQSSSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m4_AQATSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m8_SQGTSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093514_HExnTx


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_nb_motifs_8.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093514_AgCFis


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_nb_motifs_10.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093514_M4iXY9


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m2_TQATSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m11_SQAKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m14_SQSKNR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m6_TQSSSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m13_TQSTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m9_TQATSR_ArgR_18bp_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m5_TQTTSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m10_SQSKSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m3_SQPQSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m4_AQATSR_ArgR_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/Collection_1_m8_SQGTSR_ArgR_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_nb_motifs_11.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/IC_test_2026-06-18.093515_TZLacz


cat /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_pairwise_compa_logos


cp /var/www/html/rsat/public_html/templates_html/display_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_logo_tree.html


cp /var/www/html/rsat/public_html/templates_html/display_small_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_portable_logo_tree.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_html/pairwise_compa_matrix_descriptions.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/distance_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/alignment_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2026/06/18/matrix-clustering_2026-06-18.093501_rGi9Gm/matrix-clustering_portable_logo_tree.html
