diff --git a/source/Cleaner.cpp b/source/Cleaner.cpp
index 2c736ae2..335a614f 100644
--- a/source/Cleaner.cpp
+++ b/source/Cleaner.cpp
@@ -108,11 +108,10 @@ Alignment *Cleaner::cleanByCutValueOverpass(
     int residueIndex, numberColumnsToRecover, *keptResiduesGaps;
     int oldNumberKeptResidues = 0, newNumberKeptResidues = 0;
     Alignment *newAlig = new Alignment(*alig);
-    double gapThreshold = maxGaps / alig->originalNumberOfResidues;
+    double gapThreshold = maxGaps / alig->originalNumberOfSequences;
 
     debug.report(InfoCode::GapThreshold, new std::string[2]{std::to_string((int) maxGaps), std::to_string(gapThreshold)});
 
-
     // Select the columns with a gaps value
     // less or equal than the cut point.
     //
@@ -536,7 +535,7 @@ Alignment *Cleaner::cleanStrict(int gapCut, const int *gInCol, float simCut, con
     int i, x, pos, counter, lenBlock;
     Alignment *newAlig = new Alignment(*alig);
 
-    double gapThreshold = (double) gapCut / alig->originalNumberOfResidues;
+    double gapThreshold = (double) gapCut / alig->originalNumberOfSequences;
     debug.report(InfoCode::GapThreshold, new std::string[2]{std::to_string(gapCut), std::to_string(gapThreshold)});
 
     // Reject columns with gaps number greater than the gap threshold.