AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons032_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249878
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APES060	264	98aa long hypothetical protein
#1	APE1834	60	322aa long hypothetical ribose-phosphate pyrophosphokinase
#2	APE1836	82	280aa long hypothetical protein
#3	APE1868	213	202aa long hypothetical protein

Motif 1
AAACACTAGAAGCCTGGTCTCCACACCCTTCAGCTT	0	67	0
TTTCCAGGTGAGAACCATAACCTCTCCCGAAGCGGA	0	100	1
GGCAAGGCTTAGGGCGATAGCCTCCTGGTTCAAGGA	0	153	1
GAGCTGCTTGACGGTGGTTCAGCCTCTCTGCTGGCT	0	199	0
CACCACATGTAGCTCCGCTACCGCCCCCGCATGAGC	1	27	1
AGGTAGTGGTAGCGCCGTTCCCTCGCTGCACCGCTG	2	28	1
GTTCCCTCGCTGCACCGCTGGCACCCCTCGATACTT	2	44	1
ATTGGTTGAAAGAGCCGTATCGCCCCGGGGAGAGTC	3	75	1
GGAGAGTCTGTTTTCGGCTTCCTCTCCGAGGGCTCC	3	103	1
GCTCTATATTACTACCGTAGACGCTCTTTCGGGAGC	3	134	0
    GTTACCACTGTCGTCAAGCCTCTCGTAAACTA	3	191	0
          **  ****  ** * *
MAP Score: 16.7188

Motif 2
GGTGAAGAGTTGAATAGCACCGCTGAGGGGGCATCTAAAGTC	0	19	0
TCTTCACCGCTCTAAAGCTGAAGGGTGTGGAGACCAGGCTTC	0	53	1
AGACCAGGCTTCTAGTGTTTCCAGGTGAGAACCATAACCTCT	0	83	1
CCCGCCTCTTAGGAGTTCCGCTTCGGGAGAGGTTATGGTTCT	0	110	0
TTCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAACCACC	0	181	1
CGGGGGCGGTAGCGGAGCTACATGTGGTGTTCTTCGCGGAAA	1	14	0
         GTCTGTGGCTCATGCGGGGGCGGTAGCGGAGCT	1	37	0
GTAGCGCCGTTCCCTCGCTGCACCGCTGGCACCCCTCGATAC	2	36	1
TGTTACAGCCACTTTTGCTAAAGGCAGGGCTGGTGTTTATTG	3	37	1
ATTGGTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTTT	3	75	1
GAGTCTGTTTTCGGCTTCCTCTCCGAGGGCTCCCGAAAGAGC	3	106	1
          **    **  *  ** * *  *
MAP Score: 13.8486

Motif 3
AAGCGGAACTCCTAAGAGGCGGGTGGCAAGGCTTAGGGCGATA	0	129	1
TCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAACCACCGT	0	182	1
AGCAGAGAGGCTGAACCACCGTCAAGCAGCTCTTATCTAATAT	0	203	1
TTTTCCGCGAAGAACACCACATGTAGCTCCGCTACCGCCCCCG	1	13	1
TGTAGCTCCGCTACCGCCCCCGCATGAGCCACAGAC       	1	34	1
GTAGTGGTAGCGCCGTTCCCTCGCTGCACCGCTGGCACCCCTC	2	30	1
GCTGTTACAGCCACTTTTGCTAAAGGCAGGGCTGGTGTTTATT	3	35	1
GTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTTTCGGCT	3	79	1
GCTTCCTCTCCGAGGGCTCCCGAAAGAGCGTCTACGGTAGTAA	3	119	1
TAATATAGAGCTTTCCGCGACTGACGACAGCCTAGTTTACGAG	3	159	1
CTGACGACAGCCTAGTTTACGAGAGGCTTGACGACAGTGGTAA	3	179	1
          **      **  *  **  * **
MAP Score: 12.7785

Motif 4
AGAGTTGAATAGCACCGCTGAGGGGGCATCTAAAGTC	0	19	0
TCACCGCTCTAAAGCTGAAGGGTGTGGAGACCAGGCT	0	56	1
CCCGAAGCGGAACTCCTAAGAGGCGGGTGGCAAGGCT	0	125	1
GTGGTTCAGCCTCTCTGCTGGCTGCCTAGGTGTTCCT	0	185	0
GAGAGGCTGAACCACCGTCAAGCAGCTCTTATCTAAT	0	207	1
CACCACATGTAGCTCCGCTACCGCCCCCGCATGAGCC	1	27	1
AGGTAGTGGTAGCGCCGTTCCCTCGCTGCACCGCTGG	2	28	1
CCCTCGCTGCACCGCTGGCACCCCTCGATACTTGTTA	2	47	1
AAAACAGACTCTCCCCGGGGCGATACGGCTCTTTCAA	3	80	0
TTTCGGCTTCCTCTCCGAGGGCTCCCGAAAGAGCGTC	3	114	1
GCTCTATATTACTACCGTAGACGCTCTTTCGGGAGCC	3	133	0
       GTTACCACTGTCGTCAAGCCTCTCGTAAAC	3	193	0
          * * ***  * *  ***
MAP Score: 8.60787

Motif 5
GAGTTGAATAGCACCGCTGAGGGGGCATCTAA	0	23	0
CCTCTTAGGAGTTCCGCTTCGGGAGAGGTTAT	0	116	0
GAGGCGGGTGGCAAGGCTTAGGGCGATAGCCT	0	144	1
CGGTGGTTCAGCCTCTCTGCTGGCTGCCTAGG	0	192	0
CCACCGTCAAGCAGCTCTTATCTAATATAGGT	0	218	1
AACACCACATGTAGCTCCGCTACCGCCCCCGC	1	25	1
TTAGGTAGTGGTAGCGCCGTTCCCTCGCTGCA	2	26	1
CCGTTCCCTCGCTGCACCGCTGGCACCCCTCG	2	42	1
TTTGCTAAAGGCAGGGCTGGTGTTTATTGGTT	3	50	1
TGAAAGAGCCGTATCGCCCCGGGGAGAGTCTG	3	81	1
          *** ***** **
MAP Score: 7.14442

Motif 6
CGAAGCGGAACTCCTAAGAGGCGGGTGGCAAGGCTTAG	0	127	1
GTTCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAA	0	180	1
CCGCTACCGCCCCCGCATGAGCCACAGAC         	1	41	1
CGAGGGGTGCCAGCGGTGCAGCGAGGGAACGGCGCTAC	2	36	0
TGGTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTT	3	77	1
TCGGCTTCCTCTCCGAGGGCTCCCGAAAGAGCGTCTAC	3	116	1
GACTGACGACAGCCTAGTTTACGAGAGGCTTGACGACA	3	177	1
          * ***  *   ** * **
MAP Score: 3.54018

Motif 7
AGAGCGGTGAAGAGTTGAATAGCACCGCTGAGGGGGCATCTAAA	0	22	0
GGAACTCCTAAGAGGCGGGTGGCAAGGCTTAGGGCGATAGCCTC	0	133	1
GTTCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAACCACCG	0	180	1
AAGAACACCACATGTAGCTCCGCTACCGCCCCCGCATGAGCCAC	1	22	1
TCGAGGGGTGCCAGCGGTGCAGCGAGGGAACGGCGCTACCACTA	2	31	0
TAAGCTGTTACAGCCACTTTTGCTAAAGGCAGGGCTGGTGTTTA	3	32	1
ATTGGTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTTTCG	3	75	1
TTTTCGGCTTCCTCTCCGAGGGCTCCCGAAAGAGCGTCTACGGT	3	113	1
GCTTTCCGCGACTGACGACAGCCTAGTTTACGAGAGGCTTGACG	3	168	1
          *  *  *    **  * *  ** *
MAP Score: 3.24153

Motif 8
ACTTTAGATGCCCCCTCAGCGGTGCTATTCAACT	0	20	1
CAACTCTTCACCGCTCTAAAGCTGAAGGGTGTGG	0	49	1
AGAACCATAACCTCTCCCGAAGCGGAACTCCTAA	0	110	1
GCCTTGCCACCCGCCTCTTAGGAGTTCCGCTTCG	0	127	0
AGAGGCTGAACCACCGTCAAGCAGCTCTTATCTA	0	208	1
ACATGTAGCTCCGCTACCGCCCCCGCATGAGCCA	1	31	1
AGTGGTAGCGCCGTTCCCTCGCTGCACCGCTGGC	2	32	1
CCTCGCTGCACCGCTGGCACCCCTCGATACTTGT	2	48	1
GTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTG	3	79	1
AGTCTGTTTTCGGCTTCCTCTCCGAGGGCTCCCG	3	107	1
          ***** ** * * *
MAP Score: 3.17402

Motif 9
         TCCACAGAGGACTTTAGATGCC	0	1	1
TTAGATGCCCCCTCAGCGGTGCTATTCAACT	0	23	1
CTTCACCGCTCTAAAGCTGAAGGGTGTGGAG	0	54	1
ATAACCTCTCCCGAAGCGGAACTCCTAAGAG	0	116	1
AAGCGGAACTCCTAAGAGGCGGGTGGCAAGG	0	129	1
CATGTGGTGTTCTTCGCGGAAAAACC     	1	5	0
CATGCGGGGGCGGTAGCGGAGCTACATGTGG	1	29	0
TTACCATATTAGGTAGTGGTAGCGCCGTTCC	2	18	1
TAGCGCCGTTCCCTCGCTGCACCGCTGGCAC	2	37	1
CTGCCTTTAGCAAAAGTGGCTGTAACAGCTT	3	33	0
AGGCTGTCGTCAGTCGCGGAAAGCTCTATAT	3	161	0
AGAGGCTTGACGACAGTGGTAAC        	3	200	1
          ** ********
MAP Score: 1.13234

Motif 10
CTTTAGATGCCCCCTCAGCGGTGCTATTCAACT	0	21	1
CCATAACCTCTCCCGAAGCGGAACTCCTAAGAG	0	114	1
GAACTCCTAAGAGGCGGGTGGCAAGGCTTAGGG	0	134	1
GAACACCTAGGCAGCCAGCAGAGAGGCTGAACC	0	187	1
ATAAGAGCTGCTTGACGGTGGTTCAGCCTCTCT	0	206	0
CTGTGGCTCATGCGGGGGCGGTAGCGGAGCTAC	1	35	0
CATTACCATATTAGGTAGTGGTAGCGCCGTTCC	2	16	1
AGTATCGAGGGGTGCCAGCGGTGCAGCGAGGGA	2	46	0
AAACTAGGCTGTCGTCAGTCGCGGAAAGCTCTA	3	164	0
CGAGAGGCTTGACGACAGTGGTAAC        	3	198	1
          *  * ********
MAP Score: 0.124887