def mask_sequence(seq, gaps):
seq = [i.upper() for i in seq]<EOL>for gap in gaps:<EOL><INDENT>for i in range(gap[<NUM_LIT:0>] - <NUM_LIT:1>, gap[<NUM_LIT:1>]):<EOL><INDENT>seq[i] = seq[i].lower()<EOL><DEDENT><DEDENT>return '<STR_LIT>'.join(seq)<EOL>
mask (make lower case) regions of sequence found in gaps between model alignments