AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons023_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256259
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0241	284	434aa long hypothetical asparaginyl-tRNA synthetase
#1	PH0686	30	263aa long hypothetical ORFZ protein
#2	PH0783	30	200aa long hypothetical protein
#3	PH1280	300	715aa long hypothetical protein

Motif 1
ATCATCCCTCTTTTTATTTTTCGCTAAGATT	0	21	1
AGAGAATTATTTATTAATCTTAGCGAAAAAT	0	36	0
TAAATAATTCTCTATAATTTTTAACCGGCCC	0	54	1
        GGTTTTTAATCTTTCTCCTTCTT	1	2	1
ATAGACTAGATTTTTAATGTTGGATCTTTTA	3	74	0
GAGTTTCAAGTTTTGAATATTTTCTAAGCTC	3	184	0
TCTTTTTGTTGTTATAATCTTGATTATAATC	3	213	1
CTTATCTAGGTTTATAGTGTTTATGACTTGA	3	266	0
          ******** **
MAP Score: 8.20617

Motif 2
       GGGAAAAACTCATCATCCCTCTTTTTATT	0	3	1
AATTCTCTATAATTTTTAACCGGCCCGGTTCCCGCC	0	59	1
TCAGCAAAGCAAAAGCTCTTCATCCCCTGTCGGCCC	0	129	0
GCGAAGGGCGTGGTCATCATCTGCTCAGCAAAGCAA	0	153	0
      TGAAAAGTGATGACAGGGCCTTGCTGAGCG	2	10	0
ATTAAAGTTGAATATATTACAAGATC          	3	0	0
AATAACTTAAAAATCCTTAAAAGATCCAACATTAAA	3	57	1
TCAGATCTTGAAATCGTATACTGATCGATTGGCATA	3	102	0
ATACGATTTCAAGATCTGAGAGGCTCGCAGAAGACA	3	119	1
TCCTTCTGATAAGTTCTAACCTTGTCTTCTGCGAGC	3	141	0
TCAAGTTTTGAATATTTTCTAAGCTCGTGAGCTTCC	3	174	0
TCCTAATCCTAGTTGCTTATATTCTCAAGTCATAAA	3	242	1
          ** *  * * * ****
MAP Score: 6.57251

Motif 3
CGGGGGTTCCGACCGGGCCGACAGGGGATG	0	115	1
AGAGGGCGGGAACCGGGCCGGTTAAAAATT	0	69	0
GAAAAGTGATGACAGGGCCTTGCTGAGCG 	2	9	0
CGATTCCCCGGAGAGGGCGGGAACCGGGCC	0	80	0
TTCAAGATCTGAGAGGCTCGCAGAAGACAA	3	126	1
GGGAATCGTGAACCGGGGGTTCCGACCGGG	0	102	1
GAAAAATAAAAAGAGGGATGATGAGTTTTT	0	13	0
          **********
MAP Score: 6.50391

Motif 4
AAGAGCTTTTGCTTTGCTGAGCAGATGATGAC	0	145	1
ATGACCACGCCCTTCGCTGACCTGCTATTTGA	0	172	1
       AATCCATCACTGAGCCAAATTTCCA	0	269	0
TGATGACAGGGCCTTGCTGAGCG         	2	1	0
ACTTAAAAATCCTTAAAAGATCCAACATTAAA	3	61	1
TCTTCTGCGAGCCTCTCAGATCTTGAAATCGT	3	121	0
          ** ** ******
MAP Score: 5.47884

Motif 5
GTTTCAAGTTTTGAATATTTTCTAAGCTCG	3	183	0
TGATACTTTGTTCAAAATTTCTTGGAAAAA	0	207	0
AGTATACGATTTCAAGATCTGAGAGGCTCG	3	116	1
AGATCCAACATTAAAAATCTAGTCTATGCC	3	78	1
TGAATTAAAGTTGAATATATTACAAGATC 	3	9	0
GACCTGCTATTTGACAATTTTTCCAAGAAA	0	190	1
TGTTTATGACTTGAGAATATAAGCAACTAG	3	250	0
TATTCAAAACTTGAAACTCTTTTTGTTGTT	3	196	1
GTTGGATCTTTTAAGGATTTTTAAGTTATT	3	57	0
TCAACTTTAATTCAATAATTAAATAATTAA	3	25	1
AAGTTATTACTTAATTATTTAATTATTGAA	3	35	0
ACCGGGCCGGTTAAAAATTATAGAGAATTA	0	58	0
          **********
MAP Score: 5.16099

Motif 6
TTTTTATTTTTCGCTAAGATTAATAAATAA	0	31	1
TTCTCTATAATTTTTAACCGGCCCGGTTCC	0	61	1
TGAACCGGGGGTTCCGACCGGGCCGACAGG	0	110	1
AGCTTTTGCTTTGCTGAGCAGATGATGACC	0	148	1
ACCACGCCCTTCGCTGACCTGCTATTTGAC	0	175	1
        GGTTTTTAATCTTTCTCCTTCT	1	2	1
TGACAGGGCCTTGCTGAGCG          	2	0	0
CTTCTGATAAGTTCTAACCTTGTCTTCTGC	3	145	0
TTTTGAATATTTTCTAAGCTCGTGAGCTTC	3	175	0
          **********
MAP Score: 1.54958