AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_operons032_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944249889
 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
CCACAGAGGACTTTAGATGCCCCCTCAGCGGTGCTATTCA	0	11	1
TGCTATTCAACTCTTCACCGCTCTAAAGCTGAAGGGTGTG	0	42	1
CAGGTGAGAACCATAACCTCTCCCGAAGCGGAACTCCTAA	0	104	1
TCGCCCTAAGCCTTGCCACCCGCCTCTTAGGAGTTCCGCT	0	130	0
AGGCTTAGGGCGATAGCCTCCTGGTTCAAGGAACACCTAG	0	157	1
TCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAACCAC	0	182	1
GAGGCTGAACCACCGTCAAGCAGCTCTTATCTAATATAGG	0	209	1
CATGTAGCTCCGCTACCGCCCCCGCATGAGCCACAGAC  	1	32	1
GTGGTAGCGCCGTTCCCTCGCTGCACCGCTGGCACCCCTC	2	33	1
ATATTTTAAGCTGTTACAGCCACTTTTGCTAAAGGCAGGG	3	26	1
CTCTTTCAACCAATAAACACCAGCCCTGCCTTTAGCAAAA	3	49	0
GTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTTTCG	3	79	1
AGTCTGTTTTCGGCTTCCTCTCCGAGGGCTCCCGAAAGAG	3	107	1
     GTTACCACTGTCGTCAAGCCTCTCGTAAACTAGGC	3	188	0
          *  *  *  ** **   ***
MAP Score: 16.5841

Motif 2
CTCTTCACCGCTCTAAAGCTGAAGGGTGTGGAGACCAGGCTTCTA	0	52	1
CTTAGGAGTTCCGCTTCGGGAGAGGTTATGGTTCTCACCTGGAAA	0	100	0
CGAAGCGGAACTCCTAAGAGGCGGGTGGCAAGGCTTAGGGCGATA	0	127	1
GTTCAAGGAACACCTAGGCAGCCAGCAGAGAGGCTGAACCACCGT	0	180	1
  GTCTGTGGCTCATGCGGGGGCGGTAGCGGAGCTACATGTGGTG	1	27	0
TAGACATTACCATATTAGGTAGTGGTAGCGCCGTTCCCTCGCTGC	2	12	1
CTGTTACAGCCACTTTTGCTAAAGGCAGGGCTGGTGTTTATTGGT	3	36	1
GTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTTTCGGCTTC	3	79	1
TAGACGCTCTTTCGGGAGCCCTCGGAGAGGAAGCCGAAAACAGAC	3	108	0
          * *    **    **  * *  * *
MAP Score: 15.6725

Motif 3
ACTTTAGATGCCCCCTCAGCGGTGCTATTCAACT	0	20	1
CAACTCTTCACCGCTCTAAAGCTGAAGGGTGTGG	0	49	1
GAACCATAACCTCTCCCGAAGCGGAACTCCTAAG	0	111	1
GCCTTGCCACCCGCCTCTTAGGAGTTCCGCTTCG	0	127	0
GACGGTGGTTCAGCCTCTCTGCTGGCTGCCTAGG	0	192	0
CATGTAGCTCCGCTACCGCCCCCGCATGAGCCAC	1	32	1
AGTGGTAGCGCCGTTCCCTCGCTGCACCGCTGGC	2	32	1
GTTGAAAGAGCCGTATCGCCCCGGGGAGAGTCTG	3	79	1
AGTCTGTTTTCGGCTTCCTCTCCGAGGGCTCCCG	3	107	1
CTACCGTAGACGCTCTTTCGGGAGCCCTCGGAGA	3	125	0
          *******   ** *
MAP Score: 7.20509

Motif 4
GGACTTTAGATGCCCCCTCAGCGGTGCTATTCAA	0	18	1
AAGCCTGGTCTCCACACCCTTCAGCTTTAGAGCG	0	60	0
GAACCATAACCTCTCCCGAAGCGGAACTCCTAAG	0	111	1
GCCTTGCCACCCGCCTCTTAGGAGTTCCGCTTCG	0	127	0
GACGGTGGTTCAGCCTCTCTGCTGGCTGCCTAGG	0	192	0
GCTCCGCTACCGCCCCCGCATGAGCCACAGAC  	1	38	1
GGTAGCGCCGTTCCCTCGCTGCACCGCTGGCACC	2	35	1
GCCGAAAACAGACTCTCCCCGGGGCGATACGGCT	3	87	0
CTGTTTTCGGCTTCCTCTCCGAGGGCTCCCGAAA	3	110	1
CTACCGTAGACGCTCTTTCGGGAGCCCTCGGAGA	3	125	0
          * ***** * ** *
MAP Score: 6.63448

Motif 5
CATAACCTCTCCCGAAGCGGAACTCCTAAGAGGCGG	0	115	1
GTAGCGCCGTTCCCTCGCTGCACCGCTGGCACCCCT	2	36	1
GTGGTTCAGCCTCTCTGCTGGCTGCCTAGGTGTTCC	0	186	0
GAGGCTATCGCCCTAAGCCTTGCCACCCGCCTCTTA	0	141	0
ACAGACTCTCCCCGGGGCGATACGGCTCTTTCAACC	3	78	0
TTTAGATGCCCCCTCAGCGGTGCTATTCAACTCTTC	0	22	1
TCCGCTACCGCCCCCGCATGAGCCACAGAC      	1	40	1
     GGTTTTTCCGCGAAGAACACCACATGTAGCT	1	5	1
TTTCGGCTTCCTCTCCGAGGGCTCCCGAAAGAGCGT	3	114	1
ATATAGAGCTTTCCGCGACTGACGACAGCCTAGTTT	3	161	1
          ****  ** *  * **
MAP Score: 5.77661

Motif 6
GTTGAATAGCACCGCTGAGGGGGCATCTAAAGT	0	20	0
TCAACTCTTCACCGCTCTAAAGCTGAAGGGTGT	0	48	1
AGAACCATAACCTCTCCCGAAGCGGAACTCCTA	0	110	1
CCGAAGCGGAACTCCTAAGAGGCGGGTGGCAAG	0	126	1
GGTTCAAGGAACACCTAGGCAGCCAGCAGAGAG	0	179	1
ACCTAGGCAGCCAGCAGAGAGGCTGAACCACCG	0	191	1
AGGCTGAACCACCGTCAAGCAGCTCTTATCTAA	0	210	1
TCGATAATAAACCGTACAGTAGG          	0	251	1
    GGTTTTTCCGCGAAGAACACCACATGTAG	1	6	1
TCCGCTACCGCCCCCGCATGAGCCACAGAC   	1	40	1
TAGCGCCGTTCCCTCGCTGCACCGCTGGCACCC	2	37	1
AAAGAGCCGTATCGCCCCGGGGAGAGTCTGTTT	3	83	1
GTTTTCGGCTTCCTCTCCGAGGGCTCCCGAAAG	3	112	1
          ***** * * ***
MAP Score: 4.49611

Motif 7
CTTTAGATGCCCCCTCAGCGGTGCTATTCAA	0	21	1
CCATAACCTCTCCCGAAGCGGAACTCCTAAG	0	114	1
CGAAGCGGAACTCCTAAGAGGCGGGTGGCAA	0	127	1
GTTCAAGGAACACCTAGGCAGCCAGCAGAGA	0	180	1
   GGTTTTTCCGCGAAGAACACCACATGTA	1	7	1
CCGCTACCGCCCCCGCATGAGCCACAGAC  	1	41	1
GTAGCGCCGTTCCCTCGCTGCACCGCTGGCA	2	36	1
ACCGCTGGCACCCCTCGATACTTGTTAAAGA	2	57	1
AACAGACTCTCCCCGGGGCGATACGGCTCTT	3	84	0
TCTTTCGGGAGCCCTCGGAGAGGAAGCCGAA	3	115	0
CTCCGAGGGCTCCCGAAAGAGCGTCTACGGT	3	126	1
          ******** **
MAP Score: 3.65289

Motif 8
CTAAAGCTGAAGGGTGTGGAGACCAGGCTTCTAGTGTTTCC	0	64	1
GGAACTCCTAAGAGGCGGGTGGCAAGGCTTAGGGCGATAGC	0	133	1
AGGTGTTCCTTGAACCAGGAGGCTATCGCCCTAAGCCTTGC	0	154	0
GTGGCTCATGCGGGGGCGGTAGCGGAGCTACATGTGGTGTT	1	25	0
TTACCATATTAGGTAGTGGTAGCGCCGTTCCCTCGCTGCAC	2	18	1
TTTAACAAGTATCGAGGGGTGCCAGCGGTGCAGCGAGGGAA	2	45	0
CTCTTTCGGGAGCCCTCGGAGAGGAAGCCGAAAACAGACTC	3	106	0
          **     **** *   * * *
MAP Score: 0.400853