AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons075_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244327
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0593	44	conserved hypothetical protein
#1	AF0594	55	conserved hypothetical protein
#2	AF1585	276	A. fulgidus predicted coding region AF1585
#3	AF1614	50	conserved hypothetical protein

Motif 1
ACGACAAACTGTCAGAAAAGTTAAAAATGTTGCCC	0	17	0
    GATTGCGAGAGAGTATAGGAAGTGGCTGCCA	1	6	1
TCGAGGTATGGTGAGATAGGGCAAAAATTTTTATG	2	21	0
TATGGTGAAAGTGAGATTCGAGGTATGGTGAGATA	2	38	0
GATCAGCAAGGTCAGAATTTGAGAAAGATGCTGAC	2	97	1
TAGAGTCCCCTTGAGAGTGGAAGCACGAATGGCTC	2	190	1
          ****** * *  * *
MAP Score: 3.854

Motif 2
    GAGCTTTGGGCAACATTTTTAACTTT	0	6	1
CGACAAACTGTCAGAAAAGTTAAAAATGTT	0	21	0
AATAGTTAAGGCGGCAAGAGAG        	1	43	1
TGGTGAGATAGGGCAAAAATTTTTATGGTA	2	18	0
ACTCGGCGGATCAGCAAGGTCAGAATTTGA	2	89	1
GGTCAGAATTTGAGAAAGATGCTGACAGGA	2	106	1
GCTGACAGGAGCAGAAATATCTGCAGAGCT	2	126	1
AAGATTTACTGCGTCAAGCTCTGCAGATAT	2	142	0
AGTTTAAAATTCGTAAAGATTTACTGCGTC	2	157	0
AGTTTAATTGGCACCAAAAGTAATTAACCT	3	27	0
          **********
MAP Score: 2.75897

Motif 3
    GAGCTTTGGGCAACATTTTTAACTTTTCT	0	6	1
ATTGCGAGAGAGTATAGGAAGTGGCTGCCAAGA	1	11	1
ATGGTGAGATAGGGCAAAAATTTTTATGGTAAA	2	16	0
CGGATCAGCAAGGTCAGAATTTGAGAAAGATGC	2	95	1
GACTCTAAACAGTTTAAAATTCGTAAAGATTTA	2	164	0
GATGAATAGAAGGTTAGAAAATGACGTAAGTGT	2	226	1
GTTGATGGAAAGGTTAATTACTTTTGGTGCCAA	3	17	1
          *** *** ** **
MAP Score: 0.143444