--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputs/expected_codon.txt	Sun Nov 09 10:56:06 2025 +0000
@@ -0,0 +1,60 @@
+              M   V   G   S   L   N   C   I   V   A   V   S   Q   N   M   G   I   G   K   N
+BC070280      ATG GTT GGT TCG CTA AAC TGC ATC GTC GCT GTG TCC CAG AAC ATG GGC ATC GGC AAG AAC
+              -   -   -   -   L   N   C   I   V   N   V   S   Q   K   M   G   I   I   R   N
+pseudogene    --- --- --- --- CTA AAC TGC ATT GTC AAT GAT TCC CAG AAG ATG GGC ATC ATC AGG AAT
+                              ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+              G   D   L   P   W   P   P   L   R   N   E   F   R   Y   F   Q   R   M   T   T
+BC070280      GGG GAC CTG CCC TGG CCA CCG CTC AGG AAT GAA TTC AGA TAT TTC CAG AGA ATG ACC ACA
+              G   D   L   P   *   P   Q   L   K   N   K   F   2   -   F   Q   R   M   T   T
+pseudogene    GGG GAC CTG CCC TGA CCT CAG CTC AAA AAT AAA TTC GA- --- TTC CAA AGA ATG ACC ACA
+              ###                                                     ### ### ### ### ### ###
+
+              T   S   S   V   E   G   K   Q   N   L   V   I   M   G   K   K   T   W   F   S
+BC070280      ACC TCT TCA GTA GAA GGT AAA CAG AAT CTG GTG ATT ATG GGT AAG AAG ACC TGG TTC TCC
+              P   S   S   A   E   G   K   E   N   L   V   F   L   I   R   K   N   W   F   S
+pseudogene    CCC TCT TCA GCA GAG GGT AAA GAA AAT TTA GTA TTT TTA ATT AGG AAG AAC TGG TTC TCG
+              ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
+
+              I   P   E   K   N   R   P   L   K   G   R   I   N   L   V   L   S   R   E   L
+BC070280      ATT CCT GAG AAG AAT CGA CCT TTA AAG GGT AGA ATT AAT TTA GTT CTC AGC AGA GAA CTC
+              I   T   E   K   N   Q   P   L   K   Y   I   I   N   L   V   V   S   R   E   S
+pseudogene    ATT ACT GAG AAG AAT CAA CCT TTA AAG TAT ATA ATT AAT TTA GTT GTC AGT AGA GAA TCC
+              ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###                    
+
+              K   E   P   P   Q   G   A   H   F   L   S   R   S   L   D   D   A   L   K   L
+BC070280      AAG GAA CCT CCA CAA GGA GCT CAT TTT CTT TCC AGA AGT CTA GAT GAT GCC TTA AAA CTT
+              K   E   P   P   Q   R   P   P   F   L   D   *   S   L   G   D   A   L   K   R
+pseudogene    AAG GAA CCA CCG CAA AGA CCT CCT TTT CTT GAC TAA AGT CTG GGT GAT GCC TTA AAA CGT
+                                                                          ### ### ### ### ###
+
+              T   E   Q   P   E   L   A   N   K   V   D   M   L   W   I   V   G   G   S   S
+BC070280      ACT GAA CAA CCA GAA TTA GCA AAT AAA GTA GAC ATG CTC TGG ATA GTT GGT GGC AGT TCT
+              I   E   Q   L   K   L   A   N   K   Q   D   V   F   F   T   V   G   G   S   S
+pseudogene    ATT GAG CAA CTA AAA TTA GCA AAT AAA CAA GAC GTG TTT TTT ACA GTG GGA GGC AGT TCT
+              ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###                
+
+              V   Y   K   E   A   M   N   H   P   G   H   L   K   L   F   V   T   R   I   M
+BC070280      GTT TAT AAG GAA GCC ATG AAT CAC CCA GGC CAT CTT AAA CTA TTT GTG ACA AGG ATC ATG
+              V   Y   K   E   S   M   N   *   -   D   H   F   K   L   F   V   T   W   I   M
+pseudogene    GTT TAT AAG GAA TCC ATG AAT TGA --- GAC CAT TTT AAA CTA TTT GTG ACA TGG ATC ATG
+                                                                                             
+
+              Q   D   F   E   S   D   T   F   F   -   P   -   E   I   D   L   E   K   Y   K
+BC070280      CAA GAC TTT GAA AGT GAC ACG TTT TTT --- CCA --- GAA ATT GAT TTG GAG AAA TAT AAA
+              Q   D   F   Q   S   D   T   F   F   S   4   -   E   G   D   L   E   K   Y   K
+pseudogene    CAG GAC TTT CAA AGT GAC ACG TTT TTT TCC CCT A-- GAA GGT GAT TTA GAG AAA TAT AAA
+                                                                                             
+
+              L   L   P   E   Y   P   -   G   V   L   S   D   V   Q   E   E   K   G   I   K
+BC070280      CTT CTG CCA GAA TAC CCA --- GGT GTT CTC TCT GAT GTC CAG GAG GAG AAA GGC ATT AAG
+              L   L   P   E   Y   P   Q   G   V   V   S   D   V   E   E   E   K   G   I   K
+pseudogene    CTT CTC CCA GAA TAC CCA CAA GGT GTT GTC TCT GAT GTG GAG GAG GAG AAA GGC ATT AAG
+                                                                                             
+
+              Y   K   F   E   V   Y   E   K   N   D
+BC070280      TAC AAA TTT GAA GTA TAT GAG AAG AAT GAT
+              Y   K   F   E   V   Y   E   K   N   D
+pseudogene    TAC AAA TTT GAA GTA TAT GAA AAG AAT GAT
+                                                     
+