AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons022_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256245
 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
#5	PH1311	118	160aa long hypothetical protein

Motif 1
GGGGATTAGATAGGTGACATCGACGGAAGACACATAG	0	127	0
ATAGTTATACTATAGCTCTCGCCGGGGATTAGATAGG	0	150	0
AGAGCTATAGTATAACTATCCCCGGGGGAGATACGAG	0	168	1
       ACTTAATCACCTACAAAGGATTTAAAAAGT	1	3	1
AGTCGAATATTAATAAGCTGGGAAGGATAATCAAACT	1	59	1
CCTTTACAAGTACGATCCAGCGAAGGATGAAATCGTT	2	19	1
TATTTTAAGCTATCATACTGGTATGGGAATGGATGAG	2	85	1
TTCCCTTCTCTATCATCCAATCCAGGACGAGTTTTCT	2	143	0
AGGAATTCTTTAAAAAACTCGAAAGGGAAGCAACTAC	2	234	1
AGCTTTTCGGTAAGAGACTCCGCAGGGAC        	4	2	0
GGCGGACTCTTAATCCGCAGGTCGGGGGTTCAAATCC	4	102	1
CCCGGCCCGCCAGCCTCCTTCTAAGGGGGTTGAA   	4	141	1
          **     ** * *****
MAP Score: 14.9766

Motif 2
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: 11.4836

Motif 3
CATCAATTTTACCCTCAAGGGTTTGACCTAG	0	80	0
TCACCTATCTAATCCCCGGCGAGAGCTATAG	0	147	1
ATAGTATAACTATCCCCGGGGGAGATACGAG	0	174	1
TAGGTGATTTAAGCTCCCGCTCGTATCTCCC	0	193	0
AATATTGAGGAACCTGCTCGGAACTTCAGTT	2	58	0
CAAGATAAGTTATCTCCAGGGTGCATTAA  	3	29	1
TCGGTAAGAGACTCCGCAGGGAC        	4	2	0
GCGGATTAAGAGTCCGCCGCTCTAACCAGGC	4	89	0
GCGGACTCTTAATCCGCAGGTCGGGGGTTCA	4	103	1
CGGGGGTTCAAATCCCCCCCGGCCCGCCAGC	4	124	1
CATCTACTGCAATCTCAAGGTTTTCTAGTGC	5	51	1
          AATCTCAAAGGAAAAAATTGA	5	107	0
          ******* ***
MAP Score: 9.61154

Motif 4
CACGTTGATGTCGCGTTCACCTATCTAGGTCAAACC	0	56	1
GTGTCTTCCGTCGATGTCACCTATCTAATCCCCGGC	0	131	1
AATCCAGGACGAGTTTTCTCTTTTCTATTTCATAAT	2	126	0
CATCTATCCTTCTTATTCCCTTCTCTATCATCCAAT	2	159	0
TTCGTCAATATAGAATTCCCTAATCTGGGCTCCAAC	2	197	0
CTCATTTCAATTGTAGTTGCTTCCCTTTCGAGTTTT	2	247	0
TAATGCACCCTGGAGATAACTTATCTTGAGATATTA	3	21	0
    GTCCCTGCGGAGTCTCTTACCGAAAAGCTTAT	4	6	1
CGCGACTATGTAGAGGTGGCTTCTCTCATCTACTGC	5	25	1
          * *   ** *** ***
MAP Score: 8.85123

Motif 5
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
CGGGGGTTCAAATCCCCCCCGGCCCGCCAGCC	4	124	1
          * *** ******
MAP Score: 8.17851

Motif 6
AGCACATCAATTTTACCCTCAAGGGTTTGA	0	85	0
ATGTCACCTATCTAATCCCCGGCGAGAGCT	0	144	1
GCTTAAATCACCTAACCCTCGCTTTCAATA	0	210	1
         ACTTAATCACCTACAAAGGAT	1	1	1
AGATGAACTCCTTAACCCTCTTGCTCATTT	2	276	0
GCGGCGGACTCTTAATCCGCAGGTCGGGGG	4	100	1
CGGGGGGGATTTGAACCCCCGACCTGCGGA	4	115	0
          TTCAACCCCCTTAGAAGGAG	4	155	0
          **********
MAP Score: 7.65589

Motif 7
TACTATAGCTCTCGCCGGGGATTAGATAGGTGA	0	147	0
GGGGGAGATACGAGCGGGAGCTTAAATCACCTA	0	191	1
CTCGCTTTCAATAACGGTTGCGTGGCGATCATA	0	227	1
       TGAATCGAGGTTGAGTCAACAACGTA	0	284	0
CTATCATCCAATCCAGGACGAGTTTTCTCTTTT	2	138	0
GATAAGTTATCTCCAGGGTGCATTAA       	3	32	1
          GTCCCTGCGGAGTCTCTTACCGA	4	0	1
ATCGGGTTATGGGCCGGTAGCTTAGCCTGGTTA	4	65	1
TAGCCTGGTTAGAGCGGCGGACTCTTAATCCGC	4	87	1
TTTGAACCCCCGACCTGCGGATTAAGAGTCCGC	4	103	0
AATCCCCCCCGGCCCGCCAGCCTCCTTCTAAGG	4	134	1
CCTCTACATAGTCGCGAAAGACTTTTTAACG  	5	8	0
TCGCGACTATGTAGAGGTGGCTTCTCTCATCTA	5	24	1
          *******  ** *
MAP Score: 7.44596

Motif 8
GGTTTGACCTAGATAGGTGAACGCGACATC	0	62	0
GCCGGGGATTAGATAGGTGACATCGACGGA	0	137	0
TTTACTTTCCGGATAGCTGG          	1	103	1
GGAATAAGAAGGATAGATGAAGTTGGAGCC	2	176	1
CATACCAGTATGATAGCTTAAAATATTGAG	2	80	0
TGAAAGCGAGGGTTAGGTGATTTAAGCTCC	0	207	0
GGTTATGGGCCGGTAGCTTAGCCTGGTTAG	4	69	1
GGTAACGTTTCGATATCTTACGTTAATTCG	0	23	1
TGCACCCTGGAGATAACTTATCTTGAGATA	3	24	0
GAGATACGAGCGGGAGCTTAAATCACCTAA	0	195	1
          **********
MAP Score: 5.17676