diff -r 4d24bebd6734 src/centrimo.c
--- a/src/centrimo.c	Mon Apr 08 15:45:07 2019 -0700
+++ b/src/centrimo.c	Wed Jul 31 14:48:07 2019 -0400
@@ -152,6 +152,7 @@
   MOTIF_T* motif;
   ARRAYLST_T *windows;
   RBTREE_T* seq_ids;
+  RBTREE_T* neg_seq_ids;
   // how many tests have been done?
   int n_tests;
   // how many bins could this motif land in
@@ -209,6 +210,7 @@
   stats = (MOTIF_STATS_T*)s;
   arraylst_destroy(destroy_window, stats->windows);
   if (stats->seq_ids) rbtree_destroy(stats->seq_ids);
+  if (stats->neg_seq_ids) rbtree_destroy(stats->neg_seq_ids);
   memset(stats, 0, sizeof(MOTIF_STATS_T));
   free(stats);
 }
@@ -926,12 +928,28 @@
 }
 
 /*************************************************************************
+ * Output JSON data for input sequences.
+ *************************************************************************/
+static void json_output_sequences(JSONWR_T* json, const char* name,
+                                  SEQ_T **sequences, int seqN) {
+  jsonwr_property(json, name);
+  jsonwr_start_array_value(json);
+
+  int i;
+  for (i = 0; i < seqN; i++) {
+    jsonwr_str_value(json, get_seq_name(sequences[i]));
+  }
+
+  jsonwr_end_array_value(json);
+}
+
+/*************************************************************************
  * Setup the JSON writer and output a lot of pre-calculation data
  *************************************************************************/
 static void start_json(CENTRIMO_OPTIONS_T* options, int argc, char** argv, 
-    ARRAY_T* bg_freqs, SEQ_T** sequences, int seqN, int seq_skipped, int neg_seqN, 
-    int neg_seq_skipped, ARRAYLST_T* dbs, int motifN, int seqlen,
-    HTMLWR_T** html_out, JSONWR_T** json_out) {
+    ARRAY_T* bg_freqs, SEQ_T** sequences, SEQ_T** neg_sequences, int seqN,
+    int seq_skipped, int neg_seqN, int neg_seq_skipped, ARRAYLST_T* dbs,
+    int motifN, int seqlen, HTMLWR_T** html_out, JSONWR_T** json_out) {
   int i;
   MOTIF_DB_T* db;
   HTMLWR_T *html;
@@ -977,6 +995,7 @@
   jsonwr_bool_prop(json, "local", options->local);
   jsonwr_dbl_prop(json, "ethresh", options->evalue_thresh);
   jsonwr_bool_prop(json, "noseq", options->noseq);
+  jsonwr_bool_prop(json, "neg_sequences", options->neg_sequences);
   jsonwr_bool_prop(json, "mcc", options->mcc);
   jsonwr_end_object_value(json);
   // output description
@@ -1021,15 +1040,15 @@
     jsonwr_end_object_value(json);
   }
   jsonwr_end_array_value(json);
+
   if (!options->noseq) {
-    // output the sequences ID
-    jsonwr_property(json, "sequences");
-    jsonwr_start_array_value(json);
-      for (i = 0; i < seqN; i++) {
-        jsonwr_str_value(json, get_seq_name(sequences[i]));
-      }
-    jsonwr_end_array_value(json);
+    json_output_sequences(json, "sequences", sequences, seqN);
+
+    if (options->neg_sequences) {
+        json_output_sequences(json, "neg_sequences", neg_sequences, neg_seqN);
+    }
   }
+
   // start the motif array
   jsonwr_property(json, "motifs");
   jsonwr_start_array_value(json);
@@ -1039,6 +1058,22 @@
 }
 
 /*************************************************************************
+ * Output JSON data for a set of sequence indices, per motif.
+ *************************************************************************/
+static void json_output_seq_indices(JSONWR_T* json, RBTREE_T* seq_ids,
+                                    const char* name, bool store_sequences) {
+  jsonwr_property(json, name);
+  jsonwr_start_array_value(json);
+  if (store_sequences) {
+    RBNODE_T *seq;
+    for (seq = rbtree_first(seq_ids); seq; seq = rbtree_next(seq)) {
+      jsonwr_lng_value(json, (long)(*((int*)rbtree_key(seq))));
+    }
+  }
+  jsonwr_end_array_value(json);
+}
+
+/*************************************************************************
  * Output JSON data for a motif.
  *************************************************************************/
 static void output_motif_json(
@@ -1051,7 +1086,6 @@
   MOTIF_T *motif;
   MATRIX_T *freqs;
   int i, j, mlen, asize, end, index;
-  RBNODE_T *seq;
   motif = stats->motif;
   freqs = get_motif_freqs(motif);
   asize = alph_size_core(get_motif_alph(motif));
@@ -1096,14 +1130,13 @@
     }
     jsonwr_end_array_value(json);
   }
-  jsonwr_property(json, "seqs");
-  jsonwr_start_array_value(json);
-  if (store_sequences) {
-    for (seq = rbtree_first(stats->seq_ids); seq; seq = rbtree_next(seq)) {
-      jsonwr_lng_value(json, (long)(*((int*)rbtree_key(seq))));
-    }
+
+  json_output_seq_indices(json, stats->seq_ids, "seqs", store_sequences);
+
+  if (negative_sequences) {
+    json_output_seq_indices(json, stats->neg_seq_ids, "neg_seqs", store_sequences);
   }
-  jsonwr_end_array_value(json);
+
   jsonwr_property(json, "peaks"); // There are several possible peaks for LocoMo output
   jsonwr_start_array_value(json);
   for (index = 0; index < arraylst_size(stats->windows); index++) {
@@ -1830,20 +1863,28 @@
   motif_stats->db = db;
   motif_stats->motif = motif;
   motif_stats->windows = best_windows;
+
   if (!options->noseq) { 
     win_stats = arraylst_get(0, best_windows);
+
     motif_stats->seq_ids = all_sequences_in_window(win_stats->center,
         win_stats->spread, best_score_thresh, pve_scores);
+
+    if (options->neg_sequences) {
+        motif_stats->neg_seq_ids = all_sequences_in_window(win_stats->center,
+            win_stats->spread, best_score_thresh, neg_scores);
+    }
   }
+
   motif_stats->n_tests = n_tests;
   motif_stats->n_bins = n_bins;
   motif_stats->score_threshold = options->optimize_score ? best_score_thresh : score_thresh;
   motif_stats->sites = best_total_sites;
   motif_stats->neg_sites = best_neg_total_sites;
-  return motif_stats;
-  
+  return motif_stats;  
 } // calculate_best_windows
 
+
 /*************************************************************************
  * Allocates memory for a best sites buffer
  *************************************************************************/
@@ -2064,8 +2105,9 @@
   // open output files
   sites_file = start_centrimo_sites(&options);
   //text_out = start_centrimo_text(&options);
-  start_json(&options, argc, argv, bg_freqs, sequences, seqN, seq_skipped, neg_seqN, 
-    neg_seq_skipped, dbs, motifN, seqlen, &html, &json);
+  start_json(&options, argc, argv, bg_freqs, sequences, neg_sequences,
+             seqN, seq_skipped, neg_seqN, neg_seq_skipped, dbs, motifN,
+             seqlen, &html, &json);
 
   // initialize local variables
   create_buffers(&options, &buffers, seqlen, seqN, neg_seqN);