AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249561
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0921	131	237aa long hypothetical high-affinity branched-chain amino acid transport ATP-binding protein
#1	APE0924	136	390aa long hypothetical high-affinity branched-chain amino acid transport permease protein
#2	APE2522	168	265aa long hypothetical high-affinity branched-chain amino acid transport permease protein

Motif 1
TCCTTCACAAGCCCTATCCT          	0	0	0
CGTCGGGCTTGCCCGACGCTATAACCTTGC	0	62	0
TGCTGAACAACCCCGTAGTTCTGGAGAGCT	0	95	1
CTGGCAGTAGCCCTGACCCTACTCTTCGCG	1	44	1
GTATAGAGCGGCCAGTCCCTGCGGCGCGAA	1	68	0
GGGAAGCCTGGCCTGAATCTTTTCGGAGTA	1	95	0
CCCTAGCCTCCCCTCAGCCTGGGAAGCCTG	1	115	0
          CCCCTAGCCTCCCCTCAGCC	1	126	0
ATTTGTTTTTCCCCGATCCTCTAGAGTTGT	2	49	1
TGACGTTACAGCCTCAGCTTCCAATCTCTA	2	100	0
          **********
MAP Score: 15.9852

Motif 2
ACATACTCCTTCACAAGCCCTATCCT        	0	2	0
GTCGGGCTTGCCCGACGCTATAACCTTGCCCATG	0	57	0
GCTGAACAACCCCGTAGTTCTGGAGAGCTACCTG	0	96	1
GCTACCCACCCAGGTAGCTCTCCAGAACTACGGG	0	106	0
CCAGATACAACAAGATGCTCTCGATGCTGGCAGT	1	18	1
CTCGATGCTGGCAGTAGCCCTGACCCTACTCTTC	1	37	1
TTTGTTTTTCCCCGATCCTCTAGAGTTGTATAGT	2	50	1
GAGATTGGAAGCTGAGGCTGTAACGTCAGCTATA	2	102	1
TTACTCATCGGAGGAGCCTATGCCCTCGTAGCG 	2	145	1
          ** ** *****  *
MAP Score: 5.77291

Motif 3
GGGCAAGCCCGACGAGGTGCTGAACAACCCCG	0	78	1
 GGCTACCCACCCAGGTAGCTCTCCAGAACTA	0	110	0
TACCAGATACAACAAGATGCTCTCGATGCTGG	1	16	1
GCGCCGCAGGGACTGGCCGCTCTATACTCCGA	1	71	1
TTCCCAGGCTGAGGGGAGGCTAGGGG      	1	120	1
GGTGTGTAGAGATTGGAAGCTGAGGCTGTAAC	2	94	1
AGCTATAGTCGATGGGTTACTCATCGGAGGAG	2	129	1
GCTACGAGGGCATAGGCTCCTCCGATGAGTAA	2	145	0
          ******  ****
MAP Score: 4.87416