diff --git a/source/ReadAlign_maxMappableLength2strands.cpp b/source/ReadAlign_maxMappableLength2strands.cpp
index 9db6618c..c0ddee78 100644
--- a/source/ReadAlign_maxMappableLength2strands.cpp
+++ b/source/ReadAlign_maxMappableLength2strands.cpp
@@ -58,12 +58,7 @@ uint ReadAlign::maxMappableLength2strands(uint pieceStartIn, uint pieceLengthIn,
         maxL=0;
         Nrep = maxMappableLength(Read1, pieceStart, pieceLength, G, SA, iSA1 & P->SAiMarkNmask, iSA2, dirR, maxL, indStartEnd, P);     
     #else
-        if (Lind < P->genomeSAindexNbases && (iSA1 & P->SAiMarkNmaskC)==0 ) {//no need for SA search
-            indStartEnd[0]=iSA1;
-            indStartEnd[1]=iSA2;
-            Nrep=indStartEnd[1]-indStartEnd[0]+1;
-            maxL=Lind;
-        } else if (iSA1==iSA2) {//unique align already, just find maxL
+        if (iSA1==iSA2) {//unique align already, just find maxL
             if ((iSA1 & P->SAiMarkNmaskC)!=0) {
                 ostringstream errOut;
                 errOut  << "BUG: in ReadAlign::maxMappableLength2strands";
@@ -75,7 +70,14 @@ uint ReadAlign::maxMappableLength2strands(uint pieceStartIn, uint pieceLengthIn,
             maxL=compareSeqToGenome(Read1,pieceStart, pieceLength, Lind, G, SA, iSA1, dirR, comparRes, P);
         } else {//SA search, pieceLength>maxL
         if ( (iSA1 & P->SAiMarkNmaskC)==0 ) {//no N in the prefix
-                maxL=Lind;
+                // iSA2 can now point to a suffix with multiple "N" bases, eg. this sort order 
+                // ACTGAAAA <- iSA1
+                // ACTGNNNN <- iSA2
+                // ACTTACTG <- next prefix
+                // As a result, we can only assume the match length is as good up to 
+                // the length that iSA2 hits, and need to compare everything past that length in the binary search
+                bool cres;
+                maxL=compareSeqToGenome(Read1,pieceStart, pieceLength, 0, G, SA, iSA2, dirR, cres, P);
             } else {
                 maxL=0;
             };