AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249568
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0162	205	263aa long hypothetical Proliferating call nuclear antigen homolog
#1	APES016	123	63aa long hypothetical 50S ribosomal protein L44
#2	APE0441	129	233aa long hypothetical proliferating cell nuclear antigen
#3	APE0442	126	104aa long hypothetical DNA-directed RNA polymerase subunit M
#4	APE0446	24	219aa long hypothetical protein

Motif 1
CCCTCAAGGGGGACAGGCTTCCCCCACGGCTGGA	0	60	1
TATGTTTTATGCGCGTCCTCCCCCTTATAATCCG	2	21	1
CCCACACAGAGCACAGGGTAGCCCAGTACAGGGC	1	83	1
AAGAGGATCAGAACCTACTGCCCCAGGTGCAACA	1	49	1
ATGCTCGGACGGGCAGGAGACCCCTTTTATCACC	3	12	1
CGCATAAAACATACACCCCTCCCC          	2	0	0
AACTTCAATCCAGCTCCACACCCCTCCTGGTAGT	1	11	0
ATGGCGTACTCTTCATCGGGCCCCGGTGCACCCA	0	110	1
TCCCTGACAACCCCCGGGCACACCTCCAATAGCT	3	70	0
CCGATGAAGAGTACGCCATCGCCCGACGGACTCT	0	95	0
    AGCCCTCCTCTTACCAGCCCTGTACTGGGC	1	103	0
GAACATACCAGACCCTCCGGGACCCTCAAGGGGG	0	38	1
CTATATAATCAAGCTGGGTGCACCGGGGCCCGAT	0	124	0
AGCGTCGGCCAAACAACCGCCACCCTATAAAGCT	2	69	0
          *  * **** ****
MAP Score: 20.8647

Motif 2
TTTTCTGGAAGTCTGCGGAGATG          	0	0	0
CCCCTTGAGGGTCCCGGAGGGTCTGGTATGTTC	0	38	0
GGGGAAGCCTGTCCCCCTTGAGGGTCCCGGAGG	0	51	0
CGGCTGGAAAGAGTCCGTCGGGCGATGGCGTAC	0	86	1
GGGTGCACCGGGGCCCGATGAAGAGTACGCCAT	0	110	0
          GACTACCAGGAGGGGTGTGGAGC	1	0	1
CTGGATTGAAGTTCCCGAAGAGGATCAGAACCT	1	32	1
TCAGAACCTACTGCCCCAGGTGCAACACCCACA	1	56	1
CCCTGTACTGGGCTACCCTGTGCTCTGTGTGGG	1	83	0
CCCAGTACAGGGCTGGTAAGAGGAGGGCT    	1	104	1
GGATTATAAGGGGGAGGACGCGCATAAAACATA	2	21	0
AAAGCTAAAGCTTTGCGCCGCGGATTATAAGGG	2	42	0
ACTTTAGCGATGCCAGGACGTGGAGATAT    	2	110	1
       GGATGCTCGGACGGGCAGGAGACCCC	3	3	1
GCTATTGGAGGTGTGCCCGGGGGTTGTCAGGGA	3	71	1
GCCTAATGTCCACCCGGCGGCGGG         	4	1	0
          *******  * **
MAP Score: 14.0671

Motif 3
GGTCCCGGAGGGTCTGGTATGTTCGCTAATT	0	31	0
TCCAGCCGTGGGGGAAGCCTGTCCCCCTTGA	0	63	0
GCTTCCCCCACGGCTGGAAAGAGTCCGTCGG	0	76	1
TGGAAAGAGTCCGTCGGGCGATGGCGTACTC	0	90	1
TGGGTGCACCGGGGCCCGATGAAGAGTACGC	0	113	0
ATCGGGCCCCGGTGCACCCAGCTTGATTATA	0	124	1
AATTGGAATTGGGGTGCTCTATT        	0	192	1
    GACTACCAGGAGGGGTGTGGAGCTGGA	1	6	1
TGTTGCACCTGGGGCAGTAGGTTCTGATCCT	1	52	0
ACTGGGCTACCCTGTGCTCTGTGTGGGTGTT	1	79	0
GCCCAGTACAGGGCTGGTAAGAGGAGGGCT 	1	103	1
          GGGGAGGGGTGTATGTTTTAT	2	0	1
GGATTATAAGGGGGAGGACGCGCATAAAACA	2	23	0
CTTATAATCCGCGGCGCAAAGCTTTAGCTTT	2	44	1
GGTTGTTTGGCCGACGCTAGGTTCTACTTTA	2	85	1
TTCTACTTTAGCGATGCCAGGACGTGGAGAT	2	106	1
   GGATGCTCGGACGGGCAGGAGACCCCTT	3	7	1
AGCTATTGGAGGTGTGCCCGGGGGTTGTCAG	3	70	1
TAATGTCCACCCGGCGGCGGG          	4	0	0
          ******* ***
MAP Score: 12.9251