diff --git a/documentation/CustomBarcodes.md b/documentation/CustomBarcodes.md
index 85b9c930e..463d3c877 100644
--- a/documentation/CustomBarcodes.md
+++ b/documentation/CustomBarcodes.md
@@ -49,7 +49,7 @@ flank_left_pad = 5
 flank_right_pad = 10
 front_barcode_window = 175
 rear_barcode_window = 175
-midstrand_flank_score = 0.8
+midstrand_flank_score = 0.95
 ```
 
 #### Arrangement Options
diff --git a/dorado/utils/barcode_kits.cpp b/dorado/utils/barcode_kits.cpp
index 86ee0c465..6b1438e31 100644
--- a/dorado/utils/barcode_kits.cpp
+++ b/dorado/utils/barcode_kits.cpp
@@ -120,6 +120,7 @@ const BarcodeKitScoringParams RBK114_PARAMS{
         /*front_barcode_window*/ 175,
         /*rear_barcode_window*/ 175,
         /*min_flank_score*/ 0.0f,
+        /*midstrand_flank_score*/ 0.95f,
 };
 
 const BarcodeKitScoringParams TWIST_PARAMS{
@@ -132,6 +133,7 @@ const BarcodeKitScoringParams TWIST_PARAMS{
         /*front_barcode_window*/ 175,
         /*rear_barcode_window*/ 175,
         /*min_flank_score*/ 0.5f,
+        /*midstrand_flank_score*/ 0.95f,
 };
 
 // Some arrangement names are just aliases of each other. This is because they were released
diff --git a/dorado/utils/barcode_kits.h b/dorado/utils/barcode_kits.h
index 0b3552588..c927a42ff 100644
--- a/dorado/utils/barcode_kits.h
+++ b/dorado/utils/barcode_kits.h
@@ -17,7 +17,7 @@ struct BarcodeKitScoringParams {
     int front_barcode_window = 175;
     int rear_barcode_window = 175;
     float min_flank_score = 0.5f;
-    float midstrand_flank_score = 0.8f;
+    float midstrand_flank_score = 0.95f;
 };
 
 struct KitInfo {
diff --git a/tests/data/barcode_demux/double_end_variant/EXP-PBC096_midstrand.fasta b/tests/data/barcode_demux/double_end_variant/EXP-PBC096_midstrand.fasta
index 219607509..209763c13 100644
--- a/tests/data/barcode_demux/double_end_variant/EXP-PBC096_midstrand.fasta
+++ b/tests/data/barcode_demux/double_end_variant/EXP-PBC096_midstrand.fasta
@@ -1,2 +1,2 @@
 >a6703fe8-baa2-4dbe-a2de-4b5b22acd99
-TGTACTTCGTTCCAGTTGCATTATGCTGGTGCTGTTCGGATTCTGTGGTAACTTCCTATTAATGCCTTTCTGTTGGTGCTGATGTGCGGCGTCTGCTTGGGTGTTTAACCTCCAAAAATCGCCGGAAGGGGCCCCTGCCCACTGAAACCGTGGTTTGCGATTCCTGGCCCTGTCGCTGAAGAATACAGCATCGCCTTTGGTCACTGGGCGTAACTGGAGGGCAAAGGTACGCCGGAAGGAGAGTATATACGCGCTGGATACCGGCTGCTGCTGGAATTCGGTACGTGCCTGCCTGCGCTGGGAAGATAAGCAGGCCTTTGTCAGCCGTCGAACCGGCATAAGGATTTGGAAATGAAACGGCGGCGTCTTAAACACCGACCTACGATATAGGAAGGCGGATAAGACGCGACCGGCGTCACATCCGGCGCTAGCCGTAAATTCTATACAAAATTACCGCCGCTCCAGATCTCAAAGCAATGAGCTGTGAGAGTTCTGCGCATCAGCATCGTGGAATTCGCTGAATACCGATTCCAGTCATCCGGCTCATCAATCGGAAATGGGTGTCGCCTTCCACTTCTGCGTCATTAATCAGATACAGTTTTTCTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCGCGATCACCCTTGGTGCGTACTACACGCCGCGATGGCTTCATCCACCAGCTACCGCGTTACGCGATCGTCAAATACCCGGTTGACTCTTCAGGGATAATATTTTTGCGTCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGGCCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCGTATGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCGATAAAAAAAATTGTCACAACCACTATGCGTAAAGCGTAAACCGTCGTCGACTGGTGCGAGGATGATGTTGAGGTTAAACACCCAAACGGAGCGCCGCAATATCAGCACCAGCAAGAAGGTTAATAGGGAAACACGATAGAATCCGAACAGCACCAGCAATACGTAATATTGTACTTCGTTCCAGTTGCATTATGCTGGTGCTGTTCGGATTCTGTGGTAACTTCCTATTAATGCCTTTCTGTTGGTGCTGATGTGCGGCGTCTGCTTGGGTGTTTAACCTCCAAAAATCGCCGGAAGGGGCCCCTGCCCACTGAAACCGTGGTTTGCGATTCCTGGCCCTGTCGCTGAAGAATACAGCATCGCCTTTGGTCACTGGGCGTAACTGGAGGGCAAAGGTACGCCGGAAGGAGAGTATATACGCGCTGGATACCGGCTGCTGCTGGAATTCGGTACGTGCCTGCCTGCGCTGGGAAGATAAGCAGGCCTTTGTCAGCCGTCGAACCGGCATAAGGATTTGGAAATGAAACGGCGGCGTCTTAAACACCGACCTACGATATAGGAAGGCGGATAAGACGCGACCGGCGTCACATCCGGCGCTAGCCGTAAATTCTATACAAAATTACCGCCGCTCCAGATCTCAAAGCAATGAGCTGTGAGAGTTCTGCGCATCAGCATCGTGGAATTCGCTGAATACCGATTCCAGTCATCCGGCTCATCAATCGGAAATGGGTGTCGCCTTCCACTTCTGCGTCATTAATCAGATACAGTTTTTCTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCGCGATCACCCTTGGTGCGTACTACACGCCGCGATGGCTTCATCCACCAGCTACCGCGTTACGCGATCGTCAAATACCCGGTTGACTCTTCAGGGATAATATTTTTGCGTCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGGCCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCGTATGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCGATAAAAAAAATTGTCACAACCACTATGCGTAAAGCGTAAACCGTCGTCGACTGGTGCGAGGATGATGTTGAGGTTAAACACCCAAACGGAGCGCCGCAATATCAGCACCAGCAAGAAGGTTAATAGGGAAACACGATAGAATCCGAACAGCACCAGCAATACGTAATAT
+TGTACTTCGTTCCAGTTGCATTATGCTGGTGCTGTTCGGATTCTGTGGTAACTTCCTATTAATGCCTTTCTGTTGGTGCTGATGTGCGGCGTCTGCTTGGGTGTTTAACCTCCAAAAATCGCCGGAAGGGGCCCCTGCCCACTGAAACCGTGGTTTGCGATTCCTGGCCCTGTCGCTGAAGAATACAGCATCGCCTTTGGTCACTGGGCGTAACTGGAGGGCAAAGGTACGCCGGAAGGAGAGTATATACGCGCTGGATACCGGCTGCTGCTGGAATTCGGTACGTGCCTGCCTGCGCTGGGAAGATAAGCAGGCCTTTGTCAGCCGTCGAACCGGCATAAGGATTTGGAAATGAAACGGCGGCGTCTTAAACACCGACCTACGATATAGGAAGGCGGATAAGACGCGACCGGCGTCACATCCGGCGCTAGCCGTAAATTCTATACAAAATTACCGCCGCTCCAGATCTCAAAGCAATGAGCTGTGAGAGTTCTGCGCATCAGCATCGTGGAATTCGCTGAATACCGATTCCAGTCATCCGGCTCATCAATCGGAAATGGGTGTCGCCTTCCACTTCTGCGTCATTAATCAGATACAGTTTTTCTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCGCGATCACCCTTGGTGCGTACTACACGCCGCGATGGCTTCATCCACCAGCTACCGCGTTACGCGATCGTCAAATACCCGGTTGACTCTTCAGGGATAATATTTTTGCGTCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGGCCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCGTATGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCGATAAAAAAAATTGTCACAACCACTATGCGTAAAGCGTAAACCGTCGTCGACTGGTGCGAGGATGATGTTGAGGTTAAACACCCAAACGGAGCGCCGCAATATCAGCACCAGCAAGAAGGTTAATAGGGAAACACGATAGAATCCGAACAGCACCAGCAATACGTAATATTGTACTTCGTTCCAGTTGCATTATGCTGGTGCTGTTCGGATTCTGTGGTAACTTCCTATTAACCTTTCTGTTGGTGCTGATATGCGGCGTCTGCTTGGGTGTTTAACCTCCAAAAATCGCCGGAAGGGGCCCCTGCCCACTGAAACCGTGGTTTGCGATTCCTGGCCCTGTCGCTGAAGAATACAGCATCGCCTTTGGTCACTGGGCGTAACTGGAGGGCAAAGGTACGCCGGAAGGAGAGTATATACGCGCTGGATACCGGCTGCTGCTGGAATTCGGTACGTGCCTGCCTGCGCTGGGAAGATAAGCAGGCCTTTGTCAGCCGTCGAACCGGCATAAGGATTTGGAAATGAAACGGCGGCGTCTTAAACACCGACCTACGATATAGGAAGGCGGATAAGACGCGACCGGCGTCACATCCGGCGCTAGCCGTAAATTCTATACAAAATTACCGCCGCTCCAGATCTCAAAGCAATGAGCTGTGAGAGTTCTGCGCATCAGCATCGTGGAATTCGCTGAATACCGATTCCAGTCATCCGGCTCATCAATCGGAAATGGGTGTCGCCTTCCACTTCTGCGTCATTAATCAGATACAGTTTTTCTGCGCTTTTGGCAAGAACTGTTCATAAACGCGACCGCCGCCGCGATCACCCTTGGTGCGTACTACACGCCGCGATGGCTTCATCCACCAGCTACCGCGTTACGCGATCGTCAAATACCCGGTTGACTCTTCAGGGATAATATTTTTGCGTCTGGCAACGGACGACCGATTGATTCCCAGGTATGGCGGCCCATAATCACGGGTTTATTTAAGGTGTTGCGTTTAAACCAGGCGAGATCGGCAGGCAGGTTCCACGGCGTATGGCGTTTTCCATGCCGATAACGCGATCTACCGCTAACGCCGCAATCAGACTGATCATTGAGATTTCCCGATAAAAAAAATTGTCACAACCACTATGCGTAAAGCGTAAACCGTCGTCGACTGGTGCGAGGATGATGTTGAGGTTAAACACCCAAACGGAGCGCCGCAATATCAGCACCAGCAAGAAGGTTAATAGGGAAACACGATAGAATCCGAACAGCACCAGCAATACGTAATAT