AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255918
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0162	209	690aa long hypothetical protein
#1	PH0164	300	160aa long hypothetical protein
#2	PH0173	300	317aa long hypothetical protein
#3	PH0175	200	162aa long hypothetical protein
#4	PH0350	70	239aa long hypothetical protein
#5	PH0918	55	377aa long hypothetical protein
#6	PH0919	35	237aa long hypothetical protein
#7	PH0921	300	121aa long hypothetical protein
#8	PHS033	271	83aa long hypothetical protein
#9	PH1252	69	267aa long hypothetical protein

Motif 1
GGATATCGGTGAAAAAATTTACAGTAACGGGCTTAG	1	22	1
GCCTGTTTCCGTAGAACTCAGTAGTGTGGAAAGACC	2	55	1
CTCCGTTTCCGTAGAACTTAGTAGTGTGGAAAGAGA	2	122	1
CTGGGTTTCCGTAGAACTTAGTAGTGTGGAAAGCCA	2	190	1
TGGTGTTTCCGTAGAACTAAATAGTGCCTAAATCAT	2	257	1
CGTGTTTGAGGGAGAGCTAAGCAAGGCCCAACTCTA	3	48	1
AGTTAGCCTGGTATAAATAAGGAGGGGATATAGTT 	4	45	1
GCCTTCATGGGGATACCTTGAGAGTGCC        	5	2	0
     GTGGTGAAGACCTATGGAGGAATACGCCTTA	8	5	1
GGGTAAAGAACCATAGCTTTGTAGGGCAAATGTAGA	8	78	0
TTTACCCACGGAATAGCGATGGAATAGGAAAGTGAG	8	107	1
AAGTGAGTGGGTAGATCTAGGGAAGTTCCTCCATGA	8	136	1
GGTTCATGAGGTAAAGCTAGGAAAGACC        	8	253	1
          * * * **  * ****
MAP Score: 21.1932

Motif 2
CACTTGCCTGTTTCCGTAGAACTCAGTAGTGTGGA	2	50	1
CCCAGAGGTCTTTCCACACTACTGAGTTCTACGGA	2	62	0
ACCACCTCCGTTTCCGTAGAACTTAGTAGTGTGGA	2	117	1
ACTGGTTCTCTTTCCACACTACTAAGTTCTACGGA	2	129	0
GGCAGCTGGGTTTCCGTAGAACTTAGTAGTGTGGA	2	185	1
AGAGTTTGGCTTTCCACACTACTAAGTTCTACGGA	2	197	0
CTCTTCCTTGTTTTCAAGCTCCTTCTCAATGGTGT	2	228	1
CTCAATGGTGTTTCCGTAGAACTAAATAGTGCCTA	2	252	1
AGAGTTGGGCCTTGCTTAGCTCTCCCTCAAACACG	3	48	0
AAGGCGTATTCCTCCATAGGTCTTCACCAC     	8	5	0
CATGGAGGAACTTCCCTAGATCTACCCACTCACTT	8	136	0
CTTTTCCTCGTTCTCATACCTCTGCTCATGGAGGA	8	162	0
          *****  **  ** *
MAP Score: 19.8628

Motif 3
AAGAGAAGATACTGCTAGGATTTATGAGAAGCTAGCCCTAT	0	152	1
AAAAATTTACAGTAACGGGCTTAGGGAGGAGTTCAGGGATA	1	34	1
TCATCTTAGTAGGCATGAGCTTGAGGAGAAGTTTAGGACTC	1	163	1
ATAGACGTTGAGGCCCTTGAAAGAGGGGAACCTCAGCCGAT	1	212	1
GTGTCGGAAAGGGCGTCGGCAATTGGCGAAGTCTTTCCACA	2	12	0
GTCTTTCCACACTACTGAGTTCTACGGAAACAGGCAAGTGT	2	49	0
CTCTTTCCACACTACTAAGTTCTACGGAAACGGAGGTGGTG	2	116	0
GGCTTTCCACACTACTAAGTTCTACGGAAACCCAGCTGCCA	2	184	0
ACCATTGAGAAGGAGCTTGAAAACAAGGAAGAGTTTGGCTT	2	220	0
TGATTTAGGCACTATTTAGTTCTACGGAAACACCATTGAGA	2	251	0
CCTCAAACACGCTGTTCTGTCTCCAAAAAAGGTAAGTTTTA	3	18	0
GCTTGAAATGAGGCTTAAGAGAATTGTAAAGGAAGATGATT	3	87	1
CGTCGTTGGGAGGGATAAGAGCCCCGTGGAGATGATAAT  	3	171	1
CTATTCCATCGCTATTCCGTGGGTAAAGAACCATAGCTTTG	8	93	0
CCATGAGCAGAGGTATGAGAACGAGGAAAAGGAAGTTCTGA	8	166	1
AACTACCATTAGTCGTCAGAACTTAAAAAACTTATCATCCC	9	22	0
          ***  *  *      * ****
MAP Score: 19.4565

Motif 4
TTGTTCCACGATATTGGAAAGCCGGTTCAGA	0	39	1
       AAAATACTGGAAGGATATCGGTGA	1	3	1
          AGTGTGGAAAGACTTCGCCAA	2	0	1
AGAACTCAGTAGTGTGGAAAGACCTCTGGGG	2	67	1
AGAACTTAGTAGTGTGGAAAGAGAACCAGTA	2	134	1
AGAACTTAGTAGTGTGGAAAGCCAAACTCTT	2	202	1
TCAAAGTTCTTTCCTGGGAAGATGTAAATTA	3	134	0
AAGAAAACAAATGCTGGAAATCATAATGTTA	7	56	1
ATATCTAAACATTTTGGGAAGGTCACGAACT	7	95	0
GAGTGGGTAGATCTAGGGAAGTTCCTCCATG	8	140	1
CATGAGGTAAAGCTAGGAAAGACC       	8	257	1
          ** ********
MAP Score: 16.4365

Motif 5
ACAAACCACCGAGGGATATCAAATCTTTAGCG	0	11	0
GTTTAAAAAGAAGGGAAGAGAAGATACTGCTA	0	137	1
GGGAGGAGTTCAGGGATAAGAAGGGACTTCTC	1	57	1
TGGTGTTGTTGTGGCAAGTCATACCCCAGAGG	2	89	0
ACTTAGTAGTGTGGAAAGAGAACCAGTAGCCT	2	137	1
ACTTAGTAGTGTGGAAAGCCAAACTCTTCCTT	2	205	1
AGCTTGAAATGAGGCTTAAGAGAATTGTAAAG	3	86	1
ACGTCGTTGGGAGGGATAAGAGCCCCGTGGAG	3	170	1
TATCCCCATGAAGGCTTAACAAGGGAACTTCT	5	23	1
TCGCTATTCCGTGGGTAAAGAACCATAGCTTT	8	94	0
CGGAATAGCGATGGAATAGGAAAGTGAGTGGG	8	115	1
TCCATGAGCAGAGGTATGAGAACGAGGAAAAG	8	165	1
GTATGAGAACGAGGAAAAGGAAGTTCTGATAG	8	178	1
AGAGGTTCATGAGGTAAAGCTAGGAAAGACC 	8	250	1
TTGACAATTTGTGGGATGATAAGTTTTTTAAG	9	10	1
          **** *** ***
MAP Score: 12.1607

Motif 6
TTTCCAATATCGTGGAACAAACCACCGAGGGATATCAAA	0	20	0
AGAAGATACTGCTAGGATTTATGAGAAGCTAGCCCTATT	0	155	1
GGCGTATCATCTTAGTAGGCATGAGCTTGAGGAGAAGTT	1	157	1
TGCCTGTTTCCGTAGAACTCAGTAGTGTGGAAAGACCTC	2	54	1
CCTCCGTTTCCGTAGAACTTAGTAGTGTGGAAAGAGAAC	2	121	1
GCTGGGTTTCCGTAGAACTTAGTAGTGTGGAAAGCCAAA	2	189	1
ATGGTGTTTCCGTAGAACTAAATAGTGCCTAAATCATAA	2	256	1
CCTTCACGTCGTTGGGAGGGATAAGAGCCCCGTGGAGAT	3	165	1
ATTTAGTTAGCCTGGTATAAATAAGGAGGGGATATAGTT	4	41	1
ACGGAATAGCGATGGAATAGGAAAGTGAGTGGGTAGATC	8	114	1
          * *** *   *  ** * *
MAP Score: 12.0014

Motif 7
CACACTACTGAGTTCTACGGAAACAGGCAAGTG	2	50	0
CACACTACTAAGTTCTACGGAAACCCAGCTGCC	2	185	0
GGCACTATTTAGTTCTACGGAAACACCATTGAG	2	252	0
CACACTACTAAGTTCTACGGAAACGGAGGTGGT	2	117	0
GTGAGTGGGTAGATCTAGGGAAGTTCCTCCATG	8	138	1
AATATAATAGACGTTTTCAGAAGGTTATATTAG	7	181	1
TAATATCTAAACATTTTGGGAAGGTCACGAACT	7	95	0
CTTCTTTTTAAACTCTTCAGCAAGTTCAAGGAG	0	117	0
ATAAAAATAGACTTCATCAGAAGAGGAGACGTC	8	215	1
ATCGGTGAAAAAATTTACAGTAACGGGCTTAGG	1	26	1
          *  *** ******
MAP Score: 10.9651

Motif 8
TTCCCTTCTTTTTAAACTCTTCAGCAAGTT	0	124	0
ATCGGCTGAGGTTCCCCTCTTTCAAGGGCC	1	223	0
TGGCGAAGTCTTTCCACACT          	2	0	0
CCCAGAGGTCTTTCCACACTACTGAGTTCT	2	67	0
ACTGGTTCTCTTTCCACACTACTAAGTTCT	2	134	0
AGAGTTTGGCTTTCCACACTACTAAGTTCT	2	202	0
GCTATGGTTCTTTACCCACGGAATAGCGAT	8	97	1
CTTCCCTAGATCTACCCACTCACTTTCCTA	8	131	0
          **********
MAP Score: 9.39632

Motif 9
TCTGAACCGGCTTTCCAATATCGTGGAACAAAC	0	37	0
AGTATCTTCTCTTCCCTTCTTTTTAAACTCTTC	0	132	0
TCACCGATATCCTTCCAGTATTTT         	1	1	0
CTTTCCGACACTTGCCTGTTTCCGTAGAACTCA	2	42	1
AAAGCCAAACTCTTCCTTGTTTTCAAGCTCCTT	2	219	1
CTACTTAAAACTTACCTTTTTTGGAGACAGAAC	3	13	1
AGAGTTGGGCCTTGCTTAGCTCTCCCTCAAACA	3	50	0
GGTGATCTTCTTTGCCTTTATTTTTAAAAGTTC	6	10	1
AAGGCGTATTCCTCCATAGGTCTTCACCAC   	8	7	0
CATGGAGGAACTTCCCTAGATCTACCCACTCAC	8	138	0
CAGAACTTCCTTTTCCTCGTTCTCATACCTCTG	8	173	0
       GGTCTTTCCTAGCTTTACCTCATGAA	8	255	0
          *** *** * ***
MAP Score: 7.2525

Motif 10
GGAAAGCCGGTTCAGAGGGCTAGTCTGTATAA	0	54	1
TCTAAGTACCATCACAAGGATAGG        	0	195	1
GAGTTCAGGGATAAGAAGGGACTTCTCTATAA	1	62	1
GGAAACACCATTGAGAAGGAGCTTGAAAACAA	2	235	0
CTTCACGTCGTTGGGAGGGATAAGAGCCCCGT	3	166	1
CCTGGTATAAATAAGGAGGGGATATAGTT   	4	51	1
TTGTTAAGCCTTCATGGGGATACCTTGAGAGT	5	13	0
CCATGAAGGCTTAACAAGGGAACTTCTAGCAT	5	28	1
TCTAAACATTTTGGGAAGGTCACGAACTTCAT	7	91	0
AATAGACGTTTTCAGAAGGTTATATTAGAAGT	7	186	1
TAAAAATTGTTTGATAAGGACATAGTAAATGT	7	236	0
AATAGACTTCATCAGAAGAGGAGACGTCATAG	8	220	1
GTCATAGAGGTTCATGAGGTAAAGCTAGGAAA	8	245	1
          *********  *
MAP Score: 6.97697

Motif 11
GAGGAGTTCAGGGATAAGAAGGGACTTCTCTA	1	59	1
TTGAAAACAAGGAAGAGTTTGGCTTTCCACAC	2	213	0
GCGTGTTTGAGGGAGAGCTAAGCAAGGCCCAA	3	47	1
TTCTTTCCTGGGAAGATGTAAATTAGAACTGA	3	127	0
AGCTTTGTAGGGCAAATGTAGAGGTAGCTAAC	8	68	0
GAATAGCGATGGAATAGGAAAGTGAGTGGGTA	8	117	1
AAAGTGAGTGGGTAGATCTAGGGAAGTTCCTC	8	135	1
ATGAGAACGAGGAAAAGGAAGTTCTGATAGGC	8	180	1
AGGTTCATGAGGTAAAGCTAGGAAAGACC   	8	252	1
          ** * *******
MAP Score: 3.32291

Motif 12
TAGGATTTATGAGAAGCTAGCCCTATTTTC	0	167	1
TAAGAGAATTGTAAAGGAAGATGATTCAGT	3	102	1
        GCCTAATGCTAGAAGTTCCCTT	5	43	0
TAGGGCAAATGTAGAGGTAGCTAACTTCAA	8	63	0
TGAGAACGAGGAAAAGGAAGTTCTGATAGG	8	181	1
GGTTCATGAGGTAAAGCTAGGAAAGACC  	8	253	1
GTTCTGACGACTAATGGTAGTTGATAAGTT	9	41	1
          **********
MAP Score: 1.62804