diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
index c7734b68..bcf92dc2 100644
--- a/src/commons/LocalParameters.h
+++ b/src/commons/LocalParameters.h
@@ -35,6 +35,7 @@ class LocalParameters : public Parameters {
     static const int TMSCORE_THRESHOLD_MODE_ALIGNMENT = 0;
     static const int TMSCORE_THRESHOLD_MODE_QUERY = 1;
     static const int TMSCORE_THRESHOLD_MODE_TARGET = 2;
+    static const int TMSCORE_THRESHOLD_MODE_MIN = 3;
 
     static const int PREF_MODE_KMER = 0;
     static const int PREF_MODE_UNGAPPED = 1;
diff --git a/src/commons/TMaligner.cpp b/src/commons/TMaligner.cpp
index 9e58518c..94a2295f 100644
--- a/src/commons/TMaligner.cpp
+++ b/src/commons/TMaligner.cpp
@@ -327,12 +327,14 @@ Matcher::result_t TMaligner::align(unsigned int dbKey, float *x, float *y, float
 }
 
 unsigned int TMaligner::normalization(int mode, unsigned int alignmentLen, unsigned int queryLen, unsigned int targetLen) {
-    if(mode == LocalParameters::TMSCORE_THRESHOLD_MODE_ALIGNMENT){
+    if(mode == LocalParameters::TMSCORE_THRESHOLD_MODE_ALIGNMENT) {
         return alignmentLen;
     } else if(mode == LocalParameters::TMSCORE_THRESHOLD_MODE_QUERY){
         return queryLen;
     } else if(mode == LocalParameters::TMSCORE_THRESHOLD_MODE_TARGET){
         return targetLen;
+    } else if(mode == LocalParameters::TMSCORE_THRESHOLD_MODE_MIN){
+        return std::min(queryLen, targetLen);
     }
     return 0;
 }
diff --git a/src/strucclustutils/aln2tmscore.cpp b/src/strucclustutils/aln2tmscore.cpp
index 43b6b2ca..73807c2d 100644
--- a/src/strucclustutils/aln2tmscore.cpp
+++ b/src/strucclustutils/aln2tmscore.cpp
@@ -103,7 +103,7 @@ int aln2tmscore(int argc, const char **argv, const Command& command) {
                 // Matching residue index collection
                 TMaligner::TMscoreResult tmres = tmaln.computeTMscore(tdata, &tdata[targetLen], &tdata[targetLen + targetLen], targetLen,
                                                                       res.qStartPos, res.dbStartPos, res.backtrace,
-                                                                      TMaligner::normalization(par.tmScoreThrMode, res.backtrace.size(), res.qLen, res.dbLen));
+                                                                      TMaligner::normalization(par.tmScoreThrMode, std::min(res.qEndPos - res.qStartPos, res.dbEndPos - res.dbStartPos ), res.qLen, res.dbLen));
                 //std::cout << TMalnScore << std::endl;
                 resultsStr.append(SSTR(dbKey));
                 resultsStr.push_back(' ');
@@ -152,4 +152,4 @@ int aln2tmscore(int argc, const char **argv, const Command& command) {
     }
 
     return EXIT_SUCCESS;
-}
\ No newline at end of file
+}
diff --git a/src/strucclustutils/structurealign.cpp b/src/strucclustutils/structurealign.cpp
index c059b030..2fb525cd 100644
--- a/src/strucclustutils/structurealign.cpp
+++ b/src/strucclustutils/structurealign.cpp
@@ -388,7 +388,8 @@ int structurealign(int argc, const char **argv, const Command& command) {
                                                                   res.qStartPos,
                                                                   res.dbStartPos,
                                                                   res.backtrace,
-                                                                  TMaligner::normalization(par.tmScoreThrMode, res.backtrace.size(), res.qLen, res.dbLen));
+                                                                  TMaligner::normalization(par.tmScoreThrMode, std::min(res.qEndPos - res.qStartPos, res.dbEndPos - res.dbStartPos ), res.qLen, res.dbLen));
+
                                 if (tmres.tmscore < par.tmScoreThr) {
                                     continue;
                                 }
diff --git a/src/strucclustutils/structurerescorediagonal.cpp b/src/strucclustutils/structurerescorediagonal.cpp
index 434533e6..b7aa43d8 100644
--- a/src/strucclustutils/structurerescorediagonal.cpp
+++ b/src/strucclustutils/structurerescorediagonal.cpp
@@ -344,7 +344,7 @@ int structureungappedalign(int argc, const char **argv, const Command& command)
                         float* targetCaData = tcoords.read(tcadata, res.dbLen, tCaLength);
                         TMaligner::TMscoreResult tmres = tmaligner->computeTMscore(targetCaData, &targetCaData[res.dbLen], &targetCaData[res.dbLen+res.dbLen], res.dbLen,
                                                                                    res.qStartPos, res.dbStartPos, Matcher::uncompressAlignment(res.backtrace),
-                                                                                   TMaligner::normalization(par.tmScoreThrMode, res.backtrace.size(), res.qLen, res.dbLen));
+                                                                                   TMaligner::normalization(par.tmScoreThrMode, std::min(res.qEndPos - res.qStartPos, res.dbEndPos - res.dbStartPos ), res.qLen, res.dbLen));
                         if(tmres.tmscore < par.tmScoreThr){
                             continue;
                         }