diff --git a/earlGrey b/earlGrey
index 48913dd..d40b8fe 100644
--- a/earlGrey
+++ b/earlGrey
@@ -205,14 +205,14 @@ calcDivRL()
 mergeRep()
 {
 	mkdir ${OUTDIR}/${species}_mergedRepeats/looseMerge
-	${SCRIPT_DIR}/rcMergeRepeatsLoose -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/looseMerge -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict}
+	${SCRIPT_DIR}/rcMergeRepeatsLoose -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/looseMerge -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict} -m $margin
 	if [ -f "${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.bed" ]; then
 		awk '{OFS="\t"}{print $1, $2, $3, $4, $5, $6, $7, $8, toupper($9)}' ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff > ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff.1 && mv ${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.gff{.1,}
 	fi
 	if [ ! -f "${OUTDIR}/${species}_mergedRepeats/looseMerge/${species}.filteredRepeats.bed" ]; then
 		echo "ERROR: loose merge defragmentation failed, trying strict merge..."
 		cd ${OUTDIR}/${species}_mergedRepeats/
-		${SCRIPT_DIR}/rcMergeRepeats -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/ -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict}
+		${SCRIPT_DIR}/rcMergeRepeats -f $genome -s $species -d ${OUTDIR}/${species}_mergedRepeats/ -u ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out -q ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).tbl -t $ProcNum -b ${dict} -m $margin
 		if [ ! -f "${OUTDIR}/${species}_mergedRepeats/${species}.filteredRepeats.bed" ]; then
 			echo "ERROR: strict merge also failed, check ${OUTDIR}/${species}_RepeatMasker_Against_Custom_Library/$(basename $genome).out looks as expected"
 			exit 2
diff --git a/scripts/rcMergeRepeats b/scripts/rcMergeRepeats
index 6e9c7ec..051aa6e 100644
--- a/scripts/rcMergeRepeats
+++ b/scripts/rcMergeRepeats
@@ -2,11 +2,11 @@
 
 usage()
 {
-    echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary  | -h"
+    echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary -m yes|no | -h"
 }
 
 
-while getopts f:s:d:u:q:t:b:h option
+while getopts f:s:d:u:q:t:b:m:h option
     do
         case "${option}"
         in
@@ -17,6 +17,7 @@ while getopts f:s:d:u:q:t:b:h option
         q) table=${OPTARG};;
         t) threads=${OPTARG};;
         b) dict=${OPTARG};;
+        m) cutoff=${OPTARG};;
         h) usage; exit;; 
         esac
             done
@@ -57,7 +58,7 @@ mergeRepeats()
     sort -s -k1,1 ${dir}/${spe}.rmerge.gff > ${dir}/${spe}.rmerge.gff.sorted
     #filter-gff overlap -v --progress -s 1 -d -t -c length -a length ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
     Rscript ${SCRIPT_DIR}/filteringOverlappingRepeats.R ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
-    Rscript ${SCRIPT_DIR}/mergeRepeats.R  ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $margin
+    Rscript ${SCRIPT_DIR}/mergeRepeats.R  ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $cutoff
 }             
 
 
diff --git a/scripts/rcMergeRepeatsLoose b/scripts/rcMergeRepeatsLoose
index 67f77c2..680f402 100644
--- a/scripts/rcMergeRepeatsLoose
+++ b/scripts/rcMergeRepeatsLoose
@@ -2,11 +2,11 @@
 
 usage()
 {
-    echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary  | -h"
+    echo "Usage: rcMergeRepeats -f genome.fasta -s species -d output_directory -u RepeatMasker.out -q RepeatMasker.tbl -c repeatcraft.cfg -t ThreadNum -b dictionary -m yes|no | -h"
 }
 
 
-while getopts f:s:d:u:q:t:b:h option
+while getopts f:s:d:u:q:t:b:m:h option
     do
         case "${option}"
         in
@@ -17,6 +17,7 @@ while getopts f:s:d:u:q:t:b:h option
         q) table=${OPTARG};;
         t) threads=${OPTARG};;
         b) dict=${OPTARG};;
+        m) cutoff=${OPTARG};;
         h) usage; exit;; 
         esac
             done
@@ -56,7 +57,7 @@ mergeRepeats()
 {
     sort -s -k1,1 ${dir}/${spe}.rmerge.gff > ${dir}/${spe}.rmerge.gff.sorted
     Rscript ${SCRIPT_DIR}/filteringOverlappingRepeats.R ${dir}/${spe}.rmerge.gff.sorted ${dir}/${spe}.rmerge.gff.filtered
-    Rscript ${SCRIPT_DIR}/mergeRepeats.R  ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $margin
+    Rscript ${SCRIPT_DIR}/mergeRepeats.R  ${dir}/${spe}.rmerge.gff.filtered ${dir}/${spe}.mergedRepeats.bed $genSize ${dir}/${spe}.mergedRepeats.revisedTable ${dir}/${spe}.filteredRepeats.bed ${dir}/${spe}.filteredRepeats.summary $cutoff
 }