diff --git a/data/md5sum.txt b/data/md5sum.txt
index dd75a6c..00f8a14 100644
--- a/data/md5sum.txt
+++ b/data/md5sum.txt
@@ -2,15 +2,15 @@ e95a8739a378bc5628c76ffbe8293682  tests/reads_1.fq
 447647120a08d3b58162414fae4f4a39  tests/reads.mstats
 5487eb32b5492ddba3a95a8461e2ff4c  tests/reads_pbat_pe_1.fq
 aff19aeae4184c38cf364b3a94527098  tests/reads_pbat_pe_2.fq
-d5edb7b66a5db666c98b9954306bbc09  tests/reads_pbat_pe.mstats
-6976cb8096a7b36dde542dff893271bc  tests/reads_pbat_pe.sam
+adcdbadcd3cc14bfb57c170802e16bf7  tests/reads_pbat_pe.mstats
+07773c36061cbe787c568d97b9ab0d5e  tests/reads_pbat_pe.sam
 514bf940e7d5f44e57291a75e1fc6629  tests/reads_pe_1.fq
 64e17fc1e424f9cb21879d38ddf745e5  tests/reads_pe_2.fq
-e36536c8320a2acbaa66efa0baec145a  tests/reads_pe.mstats
-4fbbd861d63acee0e01aae8d0d7d071c  tests/reads_pe.sam
+771991a3d074b6587f6faa8f538f7112  tests/reads_pe.mstats
+759c446ff985911feb074fe70843e248  tests/reads_pe.sam
 e94e71292fccd255bad3f3694efe7a4b  tests/reads_rpbat_pe_1.fq
 8bfa00acd0639dc66acd5aa8ac0369d5  tests/reads_rpbat_pe_2.fq
-cc99b34bdb1f878d9d49e4140aa8fb19  tests/reads_rpbat_pe.mstats
-a0644d10b10bbe96f2fa295f4c02486f  tests/reads_rpbat_pe.sam
+3a0a49feb314f6cb8fa49c4c114b52fc  tests/reads_rpbat_pe.mstats
+64566ed0651fabe719f911b86cf05dc6  tests/reads_rpbat_pe.sam
 e7a2a3690bc17de0881e7fb2623841ec  tests/reads.sam
 bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
diff --git a/src/abismal.cpp b/src/abismal.cpp
index 2a3ac3a..1beb0f3 100644
--- a/src/abismal.cpp
+++ b/src/abismal.cpp
@@ -445,13 +445,15 @@ struct pe_element {
   }
 
   bool update(const score_t scr, const se_element &s1, const se_element &s2) {
-    if (scr > aln_score) {
+    const auto rd = r1.diffs + r2.diffs;
+    const auto sd = s1.diffs + s2.diffs;
+    if (scr > aln_score || (scr == aln_score && sd < rd)) {
       r1 = s1;
       r2 = s2;
       aln_score = scr;
       return true;
     }
-    else if (scr == aln_score) {
+    else if (scr == aln_score && sd == rd) {
       r1.set_ambig();
       return false;
     }