AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248654
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE1328	120	785aa long hypothetical hyuA
#1	APE2528	21	687aa long hypothetical hydantoinase

Motif 1
     GGGTTTAGGGCTAGGGCTAGGGCGAGT	0	5	1
GGGCTAGGGCTAGGGCGAGTTCGTCGCCTGAG	0	17	1
TGAGAGGGGGTAGGGCTGGGGCTTGCCCGTGA	0	45	1
CTGCTATATATACGACATGGGCTTCACGGGCA	0	68	0
TGGCTGCAGCTACGGCTGCCTCTACTGCTATA	0	92	0
          ******  ****
MAP Score: 13.2305

Motif 2
TTTAGGGCTAGGGCTAGGGCGAGTTCGTCGCCT	0	13	1
CGCCTGAGAGGGGGTAGGGCTGGGGCTTGCCCG	0	41	1
CGTATATATAGCAGTAGAGGCAGCCGTAGCTGC	0	86	1
AGTAGAGGCAGCCGTAGCTGCAGCCAACTCCC 	0	98	1
          ** **** ** **
MAP Score: 5.11286

Motif 3
     GGGTTTAGGGCTAGGGCTAGGGCGAGTTCG	0	5	1
GGCGAGTTCGTCGCCTGAGAGGGGGTAGGGCTGGG	0	30	1
TGAGAGGGGGTAGGGCTGGGGCTTGCCCGTGAAGC	0	45	1
GTCGTATATATAGCAGTAGAGGCAGCCGTAGCTGC	0	84	1
          ****  *** **  *
MAP Score: 2.83193