AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249555
 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
GGCTTGTGAAGGAGTATGTAGACCGGGTTTA	0	17	1
GGGCAAGGTTATAGCGTCGGGCAAGCCCGAC	0	60	1
TGAACAACCCCGTAGTTCTGGAGAGCTACCT	0	98	1
AGAGCATCTTGTTGTATCTGGTAACGTCT  	1	8	0
AGGGCTACTGCCAGCATCGAGAGCATCTTGT	1	27	0
GGCGCGAAGAGTAGGGTCAGGGCTACTGCCA	1	45	0
TCTTCGCGCCGCAGGGACTGGCCGCTCTATA	1	66	1
GAATCTTTTCGGAGTATAGAGCGGCCAGTCC	1	80	0
GCCAGGCTTCCCAGGCTGAGGGGAGGCTAGG	1	113	1
CAGGCTGAGGGGAGGCTAGGGG         	1	124	1
ATACAACTCTAGAGGATCGGGGAAAAACAAA	2	50	0
GTGGGTTAATGGTGTGTAGAGATTGGAAGCT	2	84	1
TGTAGAGATTGGAAGCTGAGGCTGTAACGTC	2	98	1
ACTCATCGGAGGAGCCTATGCCCTCGTAGCG	2	147	1
          ***** *****
MAP Score: 9.71401

Motif 2
CTTGTGAAGGAGTATGTAGACCGGGTTTACGCTAT	0	19	1
AGCATGGGCAAGGTTATAGCGTCGGGCAAGCCCGA	0	55	1
GCGTCGGGCAAGCCCGACGAGGTGCTGAACAACCC	0	73	1
CAGTCCCTGCGGCGCGAAGAGTAGGGTCAGGGCTA	1	51	0
GAATCTTTTCGGAGTATAGAGCGGCCAGTCCCTGC	1	76	0
CAGGCTTCCCAGGCTGAGGGGAGGCTAGGGG    	1	115	1
ATCCTCTAGAGTTGTATAGTGTGGGTTAATGGTGT	2	64	1
GTGGGTTAATGGTGTGTAGAGATTGGAAGCTGAGG	2	84	1
TTGGAAGCTGAGGCTGTAACGTCAGCTATAGTCGA	2	106	1
          **  ***** *  **
MAP Score: 5.12572

Motif 3
GCTTGTGAAGGAGTATGTAGACCGGGTTTACG	0	18	1
AGGTTATAGCGTCGGGCAAGCCCGACGAGGTG	0	65	1
AGAGCTACCTGGGTGGGTAGCC          	0	119	1
TCGGAGTATAGAGCGGCCAGTCCCTGCGGCGC	1	71	0
TCCGAAAAGATTCAGGCCAGGCTTCCCAGGCT	1	98	1
CCAGGCTGAGGGGAGGCTAGGGG         	1	123	1
TATACAACTCTAGAGGATCGGGGAAAAACAAA	2	50	0
TGTGGGTTAATGGTGTGTAGAGATTGGAAGCT	2	83	1
TGGAAGCTGAGGCTGTAACGTCAGCTATAGTC	2	107	1
    CGCTACGAGGGCATAGGCTCCTCCGATG	2	150	0
          *** ****** *
MAP Score: 2.86204