At the beginning of an apr file there will be data that is unnecessary for the program to read in successfully. The line that the program does read in, needs to start with obj|IxAlignment|, followed by an optional length of the sequence (i.e. \345:). Next comes the sequence, which can have gaps represented by '-', '~', or '.', must end with a '|', and can not have spaces. The sequence is followed by an optional length of the name (i.e. |\30:). Next is the name, which can have spaces. Below are examples of acceptable formats for the lines being read in by the program:

obj|IxAlignment|\345:DKLEEEINRRMADDN-------KLFR|\30:hPTPalpha_D1 (NP_002827) PTPRA
obj|IXAlignment|DKLEEEINRRMADDN.......KLFR|\30:hPTPalpha_D1 (NP_002827) PTPRA
obj|IXALIGNMENT|\345:DKLEEEINRRMADDN~~~~~~~KLFR|hPTPalpha_D1 (NP_002827) PTPRA