AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons038_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944234369
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
    GGGTTTAGGGCTAGGGCTAGGGCGAGTTCGTC	0	6	1
GGCTAGGGCTAGGGCGAGTTCGTCGCCTGAGAGGGG	0	18	1
GAGAGGGGGTAGGGCTGGGGCTTGCCCGTGAAGCCC	0	46	1
TGCTATATATACGACATGGGCTTCACGGGCAAGCCC	0	63	0
GGCTGCAGCTACGGCTGCCTCTACTGCTATATATAC	0	87	0
     GGGAGTTGGCTGCAGCTACGGCTGCCTCTAC	0	99	0
          * ***  * *** * *
MAP Score: 13.8338

Motif 2
TTAGGGCTAGGGCTAGGGCGAGTTCGTCGC	0	14	1
GAGGGGGTAGGGCTGGGGCTTGCCCGTGAA	0	48	1
CTGCAGCTACGGCTGCCTCTACTGCTATAT	0	91	0
   GGGAGTTGGCTGCAGCTACGGCTGCCT	0	103	0
          **********
MAP Score: 9.45112

Motif 3
          GGGTTTAGGGCTAGGGCTAGGGCGAGTTC	0	0	1
TTTAGGGCTAGGGCTAGGGCGAGTTCGTCGCCTGAGAGG	0	13	1
AGCCCTACCCCCTCTCAGGCGACGAACTCGCCCTAGCCC	0	23	0
GCCTGAGAGGGGGTAGGGCTGGGGCTTGCCCGTGAAGCC	0	42	1
GGTAGGGCTGGGGCTTGCCCGTGAAGCCCATGTCGTATA	0	53	1
GCTATATATACGACATGGGCTTCACGGGCAAGCCCCAGC	0	59	0
GTATATATAGCAGTAGAGGCAGCCGTAGCTGCAGCCAAC	0	87	1
GAGTTGGCTGCAGCTACGGCTGCCTCTACTGCTATATAT	0	89	0
          ***** ****        *
MAP Score: 2.86185