line 1 an integer: the number of motifs to do ranking

line 2 an integer: the type of motifs

0 means consensus motifs on {A,C,G,T} or IUPAC alphabet (see example0)

1 means a set of motif words on {A,C,G,T} (see example1)

3 means motifs on PWM (see example3)

line3 to the end description of motifs

For type 0, a typical description is

@ID m1

ACCGTCC

"m1" is the name of the motif and it can be omitted, but the token "@ID" can't be omitted.

For type 1, a typical description is

@ID m1

@SIZE 3

TTTGTCAA

ATGAGATT

TCAAATCG

"m1" is the name of the motif and it can be omitted, but the token "@ID" can't be omitted.

“3” is the number of words in a motif set and the token “@SIZE” can’t be omitted

For type3, a typical description is

@ID GCR1

A 0 2 0 0 0

T 0 4 6 0 0

G 0 0 0 0 0

C 6 0 0 6 6

"m1" is the name of the motif and it can be omitted, but the token "@ID" can't be omitted.