AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256214
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PHS026	300	96aa long hypothetical protein
#1	PH0830	125	319aa long hypothetical protein
#2	PH0840	300	117aa long hypothetical protein
#3	PH0841	47	323aa long hypothetical protein
#4	PH0846	77	456aa long hypothetical protein
#5	PH1263	258	320aa long hypothetical protein

Motif 1
ATGTAGGATGGGAGGCCCTAAAAGTTCTTCAAGA	0	56	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAAG	0	141	1
TAGGATTTGGGGAATCCCTTGGAGGCCGCTAGAA	0	200	1
CAGGGAAGCTGAGGTCTCTTGAAGATTTTAAAAT	2	52	1
TGAATGTAAAGAAGAACCTTGAAGATGTGGGGAG	2	117	1
TTGGGAAATTGAGCATCCAAAAAGCCTTAAATAC	2	271	1
TTGCAGAAGAGAGATTCCCTGAAGTTAAGTACTC	5	59	1
AAGTACTCCAGAGAGGACTGGGAGGGGACGTTGC	5	85	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAATT	5	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTTA	5	237	0
          ****  **  ****
MAP Score: 14.1434

Motif 2
TCTCCTCAACCTCTTGAAGAACTTTTAGGG	0	71	0
TTTGGGGAATCCCTTGGAGGCCGCTAGAAA	0	205	1
GATCCCAGTACTTTTGAAGGGTGCTGAGGA	1	82	0
AAGCTGAGGTCTCTTGAAGATTTTAAAATG	2	57	1
GTAAAGAAGAACCTTGAAGATGTGGGGAGT	2	122	1
GAGTCTCCGTTTCCTGAAGGTTCCACGATG	2	148	1
GATCCCAGACTCTTTGAAGGGCAC      	3	4	0
TTATACGTTATTTTTGTAGGTATATAA   	4	7	0
ACTTGAGACACTTCTGAAGAATTGCAGAAG	5	38	1
GAAGAGAGATTCCCTGAAGTTAAGTACTCC	5	64	1
CTCCCAGTCCTCTCTGGAGTACTTAACTTC	5	79	0
TATCAACGCTCCTTTGAAAAATTGAAAGTA	5	185	0
TAACTGAAGATCCTAGGAGGATTAGCTTAG	5	236	0
          **********
MAP Score: 13.5417

Motif 3
ATATTAAGTGAAAGAGTGTGGGATAGTATTCTA	0	17	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAA	0	141	1
GGAGAAAAGGAAAGAGTCAGGAAAGAGGGTTAC	0	161	1
TTACTTAGTGTAGGATTTGGGGAATCCCTTGGA	0	190	1
GAATCCCTTGGAGGCCGCTAGAAACAGTAAATG	0	211	1
CAGGGAAGCTGAGGTCTCTTGAAGATTTTAAAA	2	52	1
GAAGAACCTTGAAGATGTGGGGAGTCTCCGTTT	2	127	1
ATTAGTATTTAAGGCTTTTTGGATGCTCAATTT	2	276	0
 GTGCCCTTCAAAGAGTCTGGGATCACGAGTTA	3	9	1
AGACACTTCTGAAGAATTGCAGAAGAGAGATTC	5	43	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAAT	5	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTT	5	238	0
          *****  ** ***
MAP Score: 9.78335

Motif 4
CAAAATATTAAGTGAAAGAGTGTGGGATAGT	0	13	1
ACGTGGAGAAAAGGAAAGAGTCAGGAAAGAG	0	157	1
AGGAAAGAGTCAGGAAAGAGGGTTACTTAGT	0	168	1
          CTGGAAAGAGTACTAAAAGAT	1	0	1
ATGAAAGTTTAGTGAATGAGTCGTTCTGCCT	2	220	0
     GTGCCCTTCAAAGAGTCTGGGATCAC	3	5	1
GCATGCGTTAAGGGAAAGAATAATCATAATT	5	117	1
CCTTTGAAAAATTGAAAGTATCCTTGGATCT	5	174	0
          * *********
MAP Score: 9.52373

Motif 5
CAAAATATTAAGTGAAAGAGTGTGGGATAGTATTCTA	0	13	1
GTATTCTAAGCATGATGTAGGATGGGAGGCCCTAAAA	0	42	1
CCTAAAAGTTCTTCAAGAGGTTGAGGAGAAGAATAAA	0	72	1
AGGGTTACTTAGTGTAGGATTTGGGGAATCCCTTGGA	0	186	1
CCTCAGCACCCTTCAAAAGTACTGGGATCTATACTTG	1	83	1
TAAAGAAGAACCTTGAAGATGTGGGGAGTCTCCGTTT	2	123	1
     GTGCCCTTCAAAGAGTCTGGGATCACGAGTTA	3	5	1
AGTACTCCAGAGAGGACTGGGAGGGGACGTTGCATGC	5	86	1
TTGGATCTTCCTTAATTAGGTTTGGGAACTCATCAAT	5	145	0
          * *  *  **  *****
MAP Score: 8.92692

Motif 6
TTGAAGAACTTTTAGGGCCTCCCATCCTACA	0	57	0
GAAAAATTAATCTAAGGCCTCGTAGGAAGAA	0	126	1
TAGTGTAGGATTTGGGGAATCCCTTGGAGGC	0	195	1
GGGGAATCCCTTGGAGGCCGCTAGAAACAGT	0	208	1
TTTGAAGGGTGCTGAGGAATCCTTTCTCAGC	1	69	0
TCACAGGGAAGCTGAGGTCTCTTGAAGATTT	2	49	1
ACCTTGAAGATGTGGGGAGTCTCCGTTTCCT	2	132	1
CCCAGACTCTTTGAAGGGCAC          	3	0	0
CTTCAAAGAGTCTGGGATCACGAGTTAAGCT	3	15	1
TATTTAGCTGTTGAGGGAGACAACTTGAGAC	5	16	1
CAGAGAGGACTGGGAGGGGACGTTGCATGCG	5	93	1
CTTAATTAGGTTTGGGAACTCATCAATTATG	5	141	0
          ******* ***
MAP Score: 8.23099

Motif 7
GAACTTTTAGGGCCTCCCATCCTACATCAT	0	53	0
CTTCCTACGAGGCCTTAGATTAATTTTTCC	0	125	0
TGTTTCTAGCGGCCTCCAAGGGATTCCCCA	0	207	0
AGTTATAGATGGCGTTCAATATCTTGTTAG	1	38	1
ATTCCTCAGCACCCTTCAAAAGTACTGGGA	1	80	1
TGGGAAATTGAGCATCCAAAAAGCCTTAAA	2	272	1
GCATCCAAAAAGCCTTAAATACTAATC   	2	283	1
        GTGCCCTTCAAAGAGTCTGGGA	3	2	1
          **********
MAP Score: 1.89825

Motif 8
GATGTAGGATGGGAGGCCCTAAAAGTTCTT	0	55	1
GTAGGATTTGGGGAATCCCTTGGAGGCCGC	0	199	1
TGAAGATGTGGGGAGTCTCCGTTTCCTGAA	2	136	1
TTGCAGAAGAGAGATTCCCTGAAGTTAAGT	5	59	1
          **********
MAP Score: 0.388507