AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248648
 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
CTTATTGGGCTGAAGGTTTAAAACACAAGGCT	0	77	1
ATGTAAACTATATGGGTTTAAACGTTTACAGC	0	126	1
ACAATCGTCTTGAAGCTGTAAACGTTTAAACC	0	140	0
TGGCACAGGATTTCGGTTTAAATAATAGTTCG	1	24	0
CATATAGACATAATGGTAGAAACCCGTGTGGA	1	127	1
          *** *** ****
MAP Score: 3.92554

Motif 3
GGGTGAGTGGAGTTTTTAAAGATAAGTAAGTTTTT	0	20	1
TATTGGGCTGAAGGTTTAAAACACAAGGCTGTATT	0	79	1
TTAAACCCATATAGTTTACATATAATTACATGTAA	0	112	0
TGAAGCTGTAAACGTTTAAACCCATATAGTTTACA	0	127	0
GGGGCGAACTATTATTTAAACCGAAATCCTGTGCC	1	20	1
ATCACGTTTGAATAGTCAAAACGCAAATCCACACT	1	78	1
GCAAATCCACACTCTATAAAGCACATCCATATAGA	1	100	1
          *   ****** * **
MAP Score: 3.90293

Motif 4
GGGTGAGTGGAGTTTTTAAAGATAAGTAAGTTTTTGTAGCTA	0	20	1
AAGATAAGTAAGTTTTTGTAGCTATCGTAAATCCCCGGTCTT	0	38	1
TATTGGGCTGAAGGTTTAAAACACAAGGCTGTATTACATGTA	0	79	1
ATTACATGTAATTATATGTAAACTATATGGGTTTAAACGTTT	0	111	1
TGAAGCTGTAAACGTTTAAACCCATATAGTTTACATATAATT	0	120	0
GGGGCGAACTATTATTTAAACCGAAATCCTGTGCCAGCATAT	1	20	1
GCAAATCCACACTCTATAAAGCACATCCATATAGACATAATG	1	100	1
          *   ****** *  *      *
MAP Score: 1.67356

Motif 5
AAGATAAGTAAGTTTTTGTAGCTATCGTAA	0	38	1
ACAAGGCTGTATTACATGTAATTATATGTA	0	101	1
ATTACATGTAATTATATGTAAACTATATGG	0	111	1
ATCCTGTGCCAGCATATGCACAGCCTCCCT	1	45	1
CACTCTATAAAGCACATCCATATAGACATA	1	109	1
GGTTTCTACCATTATGTCTATATGGATGTG	1	121	0
GAGGAGGTGTAGTTTTTGGAA         	1	157	1
          **********
MAP Score: 0.595022