AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256198
 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
ATATTAAGTGAAAGAGTGTGGGATAGTATTCTAAG	0	17	1
AGGTTGAGGAGAAGAATAAAAAAAGTTAATTTTAG	0	89	1
GGCCTCGTAGGAAGAAACGTGGAGAAAAGGAAAGA	0	141	1
GGAGAAAAGGAAAGAGTCAGGAAAGAGGGTTACTT	0	161	1
      CTGGAAAGAGTACTAAAAGATTAGTAGTA	1	4	1
GAGGTCTCTTGAAGATTTTAAAATGTGAAAAGCTT	2	62	1
TGAATGTAAAGAAGAACCTTGAAGATGTGGGGAGT	2	117	1
TGAATTGATGAAAGTTTAGTGAATGAGTCGTTCTG	2	223	0
 GTGCCCTTCAAAGAGTCTGGGATCACGAGTTAAG	3	9	1
AGACACTTCTGAAGAATTGCAGAAGAGAGATTCCC	5	43	1
CCTAATTAAGGAAGATCCAAGGATACTTTCAATTT	5	162	1
   GCTAACTGAAGATCCTAGGAGGATTAGCTTAG	5	236	0
          ***** *   *** *
MAP Score: 15.3317

Motif 2
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 3
CCCTAAAAGTTCTTCAAGAGGTTGAGGAGA	0	71	1
TTTCTAGCGGCCTCCAAGGGATTCCCCAAA	0	205	0
TCCTCAGCACCCTTCAAAAGTACTGGGATC	1	82	1
CATTTTAAAATCTTCAAGAGACCTCAGCTT	2	57	0
ACTCCCCACATCTTCAAGGTTCTTCTTTAC	2	122	0
CATCGTGGAACCTTCAGGAAACGGAGACTC	2	148	0
GGAAATTGAGCATCCAAAAAGCCTTAAATA	2	274	1
      GTGCCCTTCAAAGAGTCTGGGATC	3	4	1
   TTATATACCTACAAAAATAACGTATAA	4	7	1
CTTCTGCAATTCTTCAGAAGTGTCTCAAGT	5	38	0
GGAGTACTTAACTTCAGGGAATCTCTCTTC	5	64	0
GAAGTTAAGTACTCCAGAGAGGACTGGGAG	5	79	1
CTAAGCTAATCCTCCTAGGATCTTCAGTTA	5	236	1
          **********
MAP Score: 13.1609

Motif 4
CAGCAAAATATTAAGTGAAAGAGTGTGGGATAGT	0	10	1
CTTCAAGAGGTTGAGGAGAAGAATAAAAAAAGTT	0	82	1
AAAAGTTAATTTTAGTGGAAAAATTAATCTAAGG	0	109	1
AAGAGGGTTACTTAGTGTAGGATTTGGGGAATCC	0	183	1
TTGATGAAAGTTTAGTGAATGAGTCGTTCTGCCT	2	220	0
GTTGCATGCGTTAAGGGAAAGAATAATCATAATT	5	114	1
GGAGGATTAGCTTAGTGTTTGAGTTTGACAAGTC	5	217	0
          ** **** * ** *
MAP Score: 8.16663

Motif 5
TTAAGTGAAAGAGTGTGGGATAGTATTCTA	0	20	1
GCATGATGTAGGATGGGAGGCCCTAAAAGT	0	51	1
AGTTCTTCAAGAGGTTGAGGAGAAGAATAA	0	78	1
ACTTAGTGTAGGATTTGGGGAATCCCTTGG	0	192	1
ATATCTTGTTAGAGCTGAGAAAGGATTCCT	1	56	1
ACTTTTGAAGGGTGCTGAGGAATCCTTTCT	1	73	0
ACCCTTCAAAAGTACTGGGATCTATACTTG	1	90	1
GGATCACAGGGAAGCTGAGGTCTCTTGAAG	2	46	1
AGAACCTTGAAGATGTGGGGAGTCTCCGTT	2	129	1
GAACCTTCAGGAAACGGAGACTCCCCACAT	2	141	0
GCCCTTCAAAGAGTCTGGGATCACGAGTTA	3	12	1
TACTCCAGAGAGGACTGGGAGGGGACGTTG	5	88	1
TTCCTTAATTAGGTTTGGGAACTCATCAAT	5	145	0
          **********
MAP Score: 7.07851

Motif 6
ATCCCACACTCTTTCACTTAATATTTTGCTG	0	10	0
TGTAGGATGGGAGGCCCTAAAAGTTCTTCAA	0	57	1
GCCTCCAAGGGATTCCCCAAATCCTACACTA	0	195	0
AGGAAACGGAGACTCCCCACATCTTCAAGGT	2	132	0
CAGAACGACTCATTCACTAAACTTTCATCAA	2	223	1
AACTTTCATCAATTCACCTAAACTGGTCATT	2	242	1
GTCTCAAGTTGTCTCCCTCAACAGCTAAATA	5	16	0
GCAGAAGAGAGATTCCCTGAAGTTAAGTACT	5	61	1
TATGATTATTCTTTCCCTTAACGCATGCAAC	5	114	0
CATAATTGATGAGTTCCCAAACCTAATTAAG	5	141	1
GTATCCTTGGATCTTCCTTAATTAGGTTTGG	5	157	0
          ******** **
MAP Score: 6.78399

Motif 7
AAGGGATTCCCCAAATCCTACACTAAGTAACCCT	0	186	0
CTATTTGAAATCAACGGTAAAACTTATTAACTAA	0	264	1
TCTATACTTGTCATCAACAAAGATA         	1	110	1
ATTAAGCTTTTCACATTTTAAAATCTTCAAGAGA	2	66	0
GCAGAACGACTCATTCACTAAACTTTCATCAATT	2	222	1
GAGTCTGGGATCACGAGTTAAGCTACAAGCCAGT	3	22	1
GTTTGGGAACTCATCAATTATGATTATTCTTTCC	5	129	0
GTTTGACAAGTCAATATCAACGCTCCTTTGAAAA	5	195	0
CTTGTCAAACTCAAACACTAAGCTAATCCTCCTA	5	219	1
          ***    *******
MAP Score: 3.93046