AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons036_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234334
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE2212	165	295aa long hypothetical protein
#1	APE2213	168	163aa long hypothetical isoquinoline 1-oxidoreductase alpha subunit

Motif 1
TTTTGTAGCTATCGTAAATCCCCGGTCTTAT	0	51	1
TTGTGTTTTAAACCTTCAGCCCAATAAGACC	0	74	0
CTATTATTTAAACCGAAATCCTGTGCCAGCA	1	28	1
TGTGCCAGCATATGCACAGCCTCCCTCATAT	1	49	1
GAATAGTCAAAACGCAAATCCACACTCTATA	1	87	1
CACACTCTATAAAGCACATCCATATAGACAT	1	107	1
          **** ******
MAP Score: 5.59624

Motif 2
TGTAGCTATCGTAAATCCCCGGTCTTATTG	0	54	1
GCCAGCATATGCACAGCCTCCCTCATATCA	1	52	1
TAGTCAAAACGCAAATCCACACTCTATAAA	1	90	1
ACTCTATAAAGCACATCCATATAGACATAA	1	110	1
          **********
MAP Score: 3.44329

Motif 3
CAAAAACTTACTTATCTTTAAAAACTCCACTCA	0	23	0
TCTTATTGGGCTGAAGGTTTAAAACACAAGGCT	0	76	1
TATGTAAACTATATGGGTTTAAACGTTTACAGC	0	125	1
CTGGCACAGGATTTCGGTTTAAATAATAGTTCG	1	24	0
CCTCCCTCATATCACGTTTGAATAGTCAAAACG	1	68	1
CCATATAGACATAATGGTAGAAACCCGTGTGGA	1	126	1
          ** * **** ***
MAP Score: 3.41707

Motif 4
TTACTTATCTTTAAAAACTCCACTCACCCTAG	0	17	0
TTGTAGCTATCGTAAATCCCCGGTCTTATTGG	0	53	1
AGCCTTGTGTTTTAAACCTTCAGCCCAATAAG	0	77	0
GCTGTAAACGTTTAAACCCATATAGTTTACAT	0	126	0
GGTTTAAACGTTTACAGCTTCAAGACGATTGT	0	140	1
CGAACTATTATTTAAACCGAAATCCTGTGCCA	1	24	1
TGCCAGCATATGCACAGCCTCCCTCATATCAC	1	51	1
ATAGTCAAAACGCAAATCCACACTCTATAAAG	1	89	1
        TTCCAAAAACTACACCTCCTCCAC	1	154	0
          ****** ** **
MAP Score: 2.59638

Motif 5
         ATAGACTCTAGGGTGAGTGGAGT	0	1	1
CTGAAGGTTTAAAACACAAGGCTGTATTACAT	0	86	1
TAATTATATGTAAACTATATGGGTTTAAACGT	0	119	1
CACGTTTGAATAGTCAAAACGCAAATCCACAC	1	80	1
CACATCCATATAGACATAATGGTAGAAACCCG	1	121	1
          ****** ** **
MAP Score: 0.936553