AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons022_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256230
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0555	300	164aa long hypothetical protein
#1	PH0648	113	475aa long hypothetical protein
#2	PH0653	300	358aa long hypothetical protein
#3	PH1309	48	193aa long hypothetical protein
#4	PH1310	165	228aa long hypothetical protein

Motif 1
TATCTAATCCCCGGCGAGAGCTATAGTATAAC	0	152	1
TATAACTATCCCCGGGGGAGATACGAGCGGGA	0	178	1
GGGGGAGATACGAGCGGGAGCTTAAATCACCT	0	191	1
ATATTAATAAGCTGGGAAGGATAATCAAACTT	1	65	1
CAAGTACGATCCAGCGAAGGATGAAATCGTTA	2	25	1
       GTCCCTGCGGAGTCTCTTACCGAAA	4	3	1
CCTGGTTAGAGCGGCGGACTCTTAATCCGCAG	4	90	1
AGGCTGGCGGGCCGGGGGGGATTTGAACCCCC	4	125	0
          ** ***** ***
MAP Score: 12.4196

Motif 2
GTTATACTATAGCTCTCGCCGGGGATTAGATA	0	152	0
GCTATAGTATAACTATCCCCGGGGGAGATACG	0	171	1
AGGTGATTTAAGCTCCCGCTCGTATCTCCCCC	0	191	0
AGCTTAAATCACCTAACCCTCGCTTTCAATAA	0	209	1
ATACGTTGTTGACTCAACCTCGATTCA     	0	283	1
TAACGATTTCATCCTTCGCTGGATCGTACTTG	2	25	0
GAAAAGAGAAAACTCGTCCTGGATTGGATGAT	2	137	1
        TTAATGCACCCTGGAGATAACTTA	3	34	0
ATGGGCCGGTAGCTTAGCCTGGTTAGAGCGGC	4	73	1
TCGGGGGTTCAAATCCCCCCCGGCCCGCCAGC	4	123	1
          * *** ******
MAP Score: 8.57035

Motif 3
          ACACTTCGATATTGGTAACGTTT	0	0	1
GATATTGGTAACGTTTCGATATCTTACGTTAAT	0	17	1
TTAATTCGACTCACGTTGATGTCGCGTTCACCT	0	45	1
CCTATGTGTCTTCCGTCGATGTCACCTATCTAA	0	126	1
TCAAACTTTCATACTTTACTTTCCGGATAGCTG	1	89	1
ACGAGTTTTCTCTTTTCTATTTCATAATAGAGC	2	121	0
TCCTTCTTATTCCCTTCTCTATCATCCAATCCA	2	156	0
TCAATTGTAGTTGCTTCCCTTTCGAGTTTTTTA	2	244	0
     GGTAAACGCTTTAATATCTCAAGATAAG	3	5	1
          ** **** ** **
MAP Score: 6.83266

Motif 4
AGGACGAGTTTTCTCTTTTCTATTTCATAA	2	127	0
TTATAAGCAATTCTCATTTCATCAGACATC	4	38	1
AGCTCATCCATTCCCATACCAGTATGATAG	2	94	0
TGATGTCGCGTTCACCTATCTAGGTCAAAC	0	61	1
TCCCTGCGGAGTCTCTTACCGAAAAGCTTA	4	11	1
TTCCGTCGATGTCACCTATCTAATCCCCGG	0	136	1
TCATCTATCCTTCTTATTCCCTTCTCTATC	2	166	0
TTAACCCTCTTGCTCATTTCAATTGTAGTT	2	265	0
GAAAGTTTGATTATCCTTCCCAGCTTATTA	1	69	0
TTGTAGTTGCTTCCCTTTCGAGTTTTTTAA	2	243	0
GGGCTCCAACTTCATCTATCCTTCTTATTC	2	177	0
CAATATAGAATTCCCTAATCTGGGCTCCAA	2	198	0
ACTTTCATACTTTACTTTCCGGATAGCTGG	1	93	1
TTTTAAAGAATTCCTCTTCGTCAATATAGA	2	219	0
ACTAATAAGATTTATTTTCCAAACTTTTTA	1	32	0
          **********
MAP Score: 6.41382

Motif 5
TGGTAACGTTTCGATATCTTACGTTAATTCG	0	22	1
CACGTTGATGTCGCGTTCACCTATCTAGGTC	0	56	1
GTGTCTTCCGTCGATGTCACCTATCTAATCC	0	131	1
AACGGTTGCGTGGCGATCATAGCTTACCATT	0	239	1
TTCAGTTCTAACGATTTCATCCTTCGCTGGA	2	34	0
TCAATATTTTAAGCTATCATACTGGTATGGG	2	81	1
TATTTCATAATAGAGCTCATCCATTCCCATA	2	106	0
TTTTCTCTTTTCTATTTCATAATAGAGCTCA	2	118	0
CTTATTCCCTTCTCTATCATCCAATCCAGGA	2	153	0
AAGAGGGTTAAGGAGTTCATCTAAAG     	2	284	1
     GGTAAACGCTTTAATATCTCAAGATA	3	5	1
          ***** *****
MAP Score: 6.21652

Motif 6
AACGTTTCGATATCTTACGTTAATTCGACTCAC	0	26	1
GGTACCTATGTGTCTTCCGTCGATGTCACCTAT	0	122	1
GTTGCGTGGCGATCATAGCTTACCATTACAATG	0	243	1
ATGAAAGTTTGATTATCCTTCCCAGCTTATTAA	1	68	0
ATAATCAAACTTTCATACTTTACTTTCCGGATA	1	85	1
       ACTTAACTTCCTTTACAAGTACGATC	2	3	1
GTTCTAACGATTTCATCCTTCGCTGGATCGTAC	2	28	0
TCATAATAGAGCTCATCCATTCCCATACCAGTA	2	100	0
TTCCCTTCTCTATCATCCAATCCAGGACGAGTT	2	147	0
TCAATTGTAGTTGCTTCCCTTTCGAGTTTTTTA	2	244	0
          * ****** ** *
MAP Score: 6.0611

Motif 7
TCGATATTGGTAACGTTTCGATATCTTACGTTAATTCGA	0	15	1
TTAATTCGACTCACGTTGATGTCGCGTTCACCTATCTAG	0	45	1
CCCCCGGGGATAGTTATACTATAGCTCTCGCCGGGGATT	0	157	0
TGATTTAAGCTCCCGCTCGTATCTCCCCCGGGGATAGTT	0	181	0
GGAGCTTAAATCACCTAACCCTCGCTTTCAATAACGGTT	0	207	1
TCGCTTTCAATAACGGTTGCGTGGCGATCATAGCTTACC	0	228	1
TAGCTTACCATTACAATGGAACCGCATACGTTGTTGACT	0	258	1
CATCTATCCTTCTTATTCCCTTCTCTATCATCCAATCCA	2	156	0
         GTCCCTGCGGAGTCTCTTACCGAAAAGCTT	4	1	1
TATAAGCAATTCTCATTTCATCAGACATCGGGTTATGGG	4	39	1
GGGGTTCAAATCCCCCCCGGCCCGCCAGCCTCCTTCTAA	4	126	1
          ** *  * *  ****   *
MAP Score: 4.21383

Motif 8
CTATAGCTCTCGCCGGGGATTAGATAGGTG	0	148	0
CTCGTATCTCCCCCGGGGATAGTTATACTA	0	175	0
GGGGGAGATACGAGCGGGAGCTTAAATCAC	0	191	1
CGTTATTGAAAGCGAGGGTTAGGTGATTTA	0	213	0
AATATTAATAAGCTGGGAAGGATAATCAAA	1	64	1
GTAAGAGACTCCGCAGGGAC          	4	0	0
GCCTGGTTAGAGCGGCGGACTCTTAATCCG	4	89	1
TGAACCCCCGACCTGCGGATTAAGAGTCCG	4	104	0
GCTGGCGGGCCGGGGGGGATTTGAACCCCC	4	125	0
          **********
MAP Score: 0.894571