diff --git a/alignability/halAlignability.cpp b/alignability/halAlignability.cpp
index ed664b76..bcd486b4 100644
--- a/alignability/halAlignability.cpp
+++ b/alignability/halAlignability.cpp
@@ -388,7 +388,7 @@ void printGenome(ostream& outStream,
       {
         hal_size_t readStart = seqStart >= start ? 0 : start - seqStart;
         hal_size_t readLen = min(seqLen - readStart, length);
-
+        readLen = min(readLen, length - runningLength);
         printSequence(outStream, sequence, targetSet, readStart, readLen, step);
         runningLength += readLen;
       }
diff --git a/phyloP/impl/halPhyloPMain.cpp b/phyloP/impl/halPhyloPMain.cpp
index b693ca7e..bffe33d0 100644
--- a/phyloP/impl/halPhyloPMain.cpp
+++ b/phyloP/impl/halPhyloPMain.cpp
@@ -248,7 +248,7 @@ void printGenome(PhyloP *phyloP,
       {
         hal_size_t readStart = seqStart >= start ? 0 : start - seqStart;
         hal_size_t readLen = min(seqLen - readStart, length);
-
+        readLen = min(readLen, length - runningLength);
         phyloP->processSequence(sequence, readStart, readLen, step);
         runningLength += readLen;
       }