AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249587
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0496	198	227aa long hypothetical ribonuclease HII
#1	APE2437	300	193aa long hypothetical deoxyribose-phosphate aldolase

Motif 1
GATAGTGAGAGAGACTCTGCCCGGCGGGCTAGA   	0	7	0
TTGCAGGCGAGGTAGCCAGGATAGTGAGAGAGACTC	0	26	0
CGGGCTGTGGTGTAGGGCGGCTTGGGCGCGTTTTTC	0	84	0
CACTCATGTATGAAGCCGGGCTGTGGTGTAGGGCGG	0	100	0
ATATTAATAGTATAGTTTGGCAGGCGGAGAGGATAA	0	172	1
GGGGTAATCATTTACACTGGTTAGGAGGTGTATTAA	1	55	1
TATAACCCTTGGTCTGTGGGAGGGGGAATCTAATAG	1	110	1
CCCGGCATACTCTAATCTGGAGGGGGTATCCGGATT	1	150	1
GGTATCCGGATTGCCGTCGGCCAGGGATATACTGCA	1	174	1
TGCAGCAGGGTCTAGACAGGCTAGGGAGCCCTGAGG	1	206	1
TAGACTCTACGCTACTAAGCCCTAGGGCTACGGAGG	1	257	1
AAGCCCTAGGGCTACGGAGGAGGACGTTAGGAATCT	1	273	1
          * **    *** ****
MAP Score: 11.0585

Motif 2
GCGGGACGACGTTGCAGGCGAGGTAGCCAGGATAGTGA	0	35	0
GGCTGTGGTGTAGGGCGGCTTGGGCGCGTTTTTCTTTA	0	80	0
CCCGGCTTCATACATGAGTGTGGAAAGCCTAAAGATAA	0	116	1
TTAATATTAATAGTATAGTTTGGCAGGCGGAGAGGATA	0	169	1
TCTTAAGTTTGAGAATTGTGGGGTAATCATTTACACTG	1	36	1
GGTAATCATTTACACTGGTTAGGAGGTGTATTAAGATG	1	57	1
TAACCCTTGGTCTGTGGGAGGGGGAATCTAATAGTTTT	1	112	1
CGGCATACTCTAATCTGGAGGGGGTATCCGGATTGCCG	1	152	1
CAGCAGGGTCTAGACAGGCTAGGGAGCCCTGAGGACCT	1	208	1
GCGTAGAGTCTATCCTCGAGGCGAGGTCCTCAGGGCTC	1	231	0
          **    ** * **  ***
MAP Score: 8.39465

Motif 3
         TCTAGCCCGCCGGGCAGAGTC	0	1	1
GTCTCTCTCACTATCCTGGCTACCTCGCCT	0	28	1
CGCGGGACGACGTTGCAGGCGAGGTAGCCA	0	44	0
AAAAACGCGCCCAAGCCGCCCTACACCACA	0	85	1
GCCCTACACCACAGCCCGGCTTCATACATG	0	102	1
AATAGTATAGTTTGGCAGGCGGAGAGGATA	0	177	1
AATCTAATAGTTTTCCCGGCATACTCTAAT	1	136	1
GCAGTATATCCCTGGCCGACGGCAATCCGG	1	179	0
GCAGCAGGGTCTAGACAGGCTAGGGAGCCC	1	207	1
          **********
MAP Score: 8.05145

Motif 4
CGACGTTGCAGGCGAGGTAGCCAGGATAGTG	0	36	0
TCATACATGAGTGTGGAAAGCCTAAAGATAA	0	123	1
TTTGAGAATTGTGGGGTAATCATTTACACTG	1	43	1
TGGTCTGTGGGAGGGGGAATCTAATAGTTTT	1	119	1
ATTAGAGTATGCCGGGAAAACTATTAGATTC	1	135	0
CTCTAATCTGGAGGGGGTATCCGGATTGCCG	1	159	1
GGTCTAGACAGGCTAGGGAGCCCTGAGGACC	1	214	1
          * *********
MAP Score: 7.98462

Motif 5
TCATACATGAGTGTGGAAAGCCTAAAGATAAT	0	123	1
TCCTATAATTCCGGGTTAATATTAATAGTATA	0	154	1
TTTGAGAATTGTGGGGTAATCATTTACACTGG	1	43	1
TCCCACAGACCAAGGGTTATATTTGCTTTATG	1	99	0
TGGTCTGTGGGAGGGGGAATCTAATAGTTTTC	1	119	1
CTCTAATCTGGAGGGGGTATCCGGATTGCCGT	1	159	1
TATCCCTGGCCGACGGCAATCCGGATACCCCC	1	171	0
TTGCCGTCGGCCAGGGATATACTGCAGCAGGG	1	184	1
TATACTGCAGCAGGGTCTAGACAGGCTAGGGA	1	201	1
          * **** *****
MAP Score: 7.26549