AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248653
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
         GGGTTTAGGGCTAGGGCTAGGGCG	0	1	1
TTTAGGGCTAGGGCTAGGGCGAGTTCGTCGCCT	0	13	1
CGCCTGAGAGGGGGTAGGGCTGGGGCTTGCCCG	0	41	1
CGTATATATAGCAGTAGAGGCAGCCGTAGCTGC	0	86	1
AGTAGAGGCAGCCGTAGCTGCAGCCAACTCCC 	0	98	1
          ** *******  *
MAP Score: 9.59533

Motif 2
ACTCGCCCTAGCCCTAGCCCTAAACCC         	0	1	0
CTCAGGCGACGAACTCGCCCTAGCCCTAGCCCTAAA	0	13	0
TCACGGGCAAGCCCCAGCCCTACCCCCTCTCAGGCG	0	41	0
TGCCCGTGAAGCCCATGTCGTATATATAGCAGTAGA	0	68	1
GTTGGCTGCAGCTACGGCTGCCTCTACTGCTATATA	0	90	0
        GGGAGTTGGCTGCAGCTACGGCTGCCTC	0	102	0
          *     ****** ***
MAP Score: 5.66513