MACSE alignment costs:

Reliable sequences:

Frameshift cost  _{Cost of an internal frameshift (those between the first and last codon)}  

Terminal frameshift cost  _{Cost of a terminal frameshift (those in the first and last codon)}  

STOP codon cost  _{Cost of a stop codon arising between the first and the last codon}  

Less reliable sequences:

Frameshift cost  _{Cost of an internal frameshift (those between the first and last codon)}  

Terminal frameshift cost  _{Cost of a terminal frameshift (those in the first and last codon)}  

STOP codon cost  _{Cost of a stop codon arising between the first and the last codon}  

Common costs:

Gap opening  _{Cost of internal gap opening (those between the first and last codon)}  

Gap extension  _{Cost of internal gap extension (between the first and last codon)}  

Terminal gap opening  _{Cost of terminal gap op. (before the first nt and after the last one)} 

Terminal gap extension  _{Cost of terminal gap ext. (before the first nt and after the last one)}