A rather bizarre but flexible format as generated by the print_horizontal/pattern option in multalign!!
#Pattern !start of pattern description
Nelm, Nchar !Number of elements in pattern/number of characters/element(10,9)
E1 !Pattern element 1 (eg. AAAGGGCCC) (80a1)
F1 !Flexible Gap range 1 (eg. 0,3)
"
"
etc
EN !Nth pattern element - this ends pattern description
#Details !Details of the first recorded pattern match
ID !Protein Identifier 10 chars
Title !Protein title - 80 chars
Len !Protein Length - 80 chars max
An,Pn !Sequence No, Pattern alignement Number
Score !Real number - max 80 chars
#Sequence !Start of sequence identifier
one letter code sequence 80a1 format
#Match !Description of the match follows
1,Pos !N,Pos - N is the pattern element, Pos is the sequence element
2,Pos !which it is aligned. If the pattern overhangs, then N is 0.
N,Pos
#Details !Start of next pattern alignment, or end of file
This format file is output by MULTALIGN in response to the
print_horizontal/pattern=fname command
Note: The An,Pn refer to the An(th) sequence aligned to the pattern,
and the Pn(th) alignment of the pattern to this sequence - thus
1,1 refers to the top scoring pattern match with sequence 1,
1,2 the second best pattern match to seq 1 etc.