AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons033_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256551
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0520	154	333aa long hypothetical dehydrogenase
#1	PH0742	300	256aa long hypothetical protein
#2	PH1113	99	337aa long hypothetical protein
#3	PH1391	56	348aa long hypothetical protein

Motif 1
         GCCCCTCCCCTCTTAGTATGGAA	0	1	1
TGGTTTAGCTCCCATCACGGCGAGATCATTTA	1	26	1
CTACCTATGTCACCTCCAGGGAAGAAGAGGGG	1	78	1
GGATCGTTGCCCCATCATCGAGGGCTTCTAGG	1	160	1
TCTAGGCCAATCCCTCCAGCAGAGTTTAAGGT	1	186	1
TCTTCCATTAGCTCTCCACCCGCACCATGCTC	1	249	1
     GCTTTCACCTCAGCCGGTAGGTGGTTC	2	5	1
TGGTTCATCACCCCTCAGCCGGGAGTAGTTCA	2	31	1
          ******* ** *
MAP Score: 7.59862

Motif 2
CTTAGTATGGAAGGGCTAGAAGTTATTATAAT	0	21	1
TTCCATACCAAAGAATTAAGGGATATTTAGAA	0	59	1
   AGCTAGCGAGGGCTAGTGGTTTAGCTCCC	1	7	1
TAGGTAGACTAGCGGTTAGCGGAACGGTAAAT	1	53	0
GGGAAGAAGAGGGGTCTAACGGTATGACCATC	1	96	1
CCCCATCATCGAGGGCTTCTAGGCCAATCCCT	1	169	1
GGTGCGGGTGGAGAGCTAATGGAAGAACTCAT	1	243	0
       TTGGGGGATTATAAGTGAAGATAAA	1	285	0
          ********  **
MAP Score: 6.48179

Motif 3
CCCAGAAAAAGATTATTATACGGTCTTTCGATGAC	0	111	1
AGCGAGGGCTAGTGGTTTAGCTCCCATCACGGCGA	1	14	1
ATCACGGCGAGATCATTTACCGTTCCGCTAACCGC	1	39	1
AGGGAAGAAGAGGGGTCTAACGGTATGACCATCTA	1	95	1
TGTGAAGACAAGGTGTTTACCTTCAAAGGGGATCG	1	131	1
CTTCAAAGGGGATCGTTGCCCCATCATCGAGGGCT	1	151	1
TGTTATATTAAAGAATTTAACCTTAAACTCTGCTG	1	202	0
TCAGCCGGTAGGTGGTTCATCACCCCTCAGCCGGG	2	19	1
CTCAGCCGGGAGTAGTTCATCATTAGTCGCTAATG	2	44	1
ATCCACCCAAAATTATTTACCTATCCATTGTATTT	3	12	1
          *** *** * *  **
MAP Score: 4.11932

Motif 4
        GCCCCTCCCCTCTTAGTATGGAAGGG	0	2	1
CTAGTGGTTTAGCTCCCATCACGGCGAGATCATT	1	22	1
TTTACCGTTCCGCTAACCGCTAGTCTACCTATGT	1	54	1
TAGTCTACCTATGTCACCTCCAGGGAAGAAGAGG	1	74	1
GGGATCGTTGCCCCATCATCGAGGGCTTCTAGGC	1	159	1
TTCTAGGCCAATCCCTCCAGCAGAGTTTAAGGTT	1	185	1
TTCTTCCATTAGCTCTCCACCCGCACCATGCTCA	1	248	1
GTGATGAACCACCTACCGGCTGAGGTGAAAGC  	2	8	0
GTGGTTCATCACCCCTCAGCCGGGAGTAGTTCAT	2	30	1
          ***** ** *  **
MAP Score: 0.67685

Motif 5
CTCTTCCATACCAAAGAATTAAGGGATATTTA	0	56	1
AGGTATATATCTAAGGATTCTAAATATCCCTT	0	76	0
AGATGTTATATTAAAGAATTTAACCTTAAACT	1	208	0
TCATTAGTCGCTAATGATTTTAACCGATATTT	2	63	1
          CGATTAAATTTATGAAATATCG	2	87	0
 GCATCCACCCAAAATTATTTACCTATCCATT	3	9	1
ATTTACCTATCCATTGTATTTAAAGTGAGTGG	3	26	1
          * ** *******
MAP Score: 0.609649