AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_profile003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247588
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mtlA	300	Mycoplasma pneumoniae, PTS system mannitol-specific component IIA (EIIA-MTL); similar to Swiss-Prot Accession Number P28008, from S. carnosus
#1	yihA	287	Mycoplasma pneumoniae, hypothetical protein (yihA) (era like) homolog; similar to Swiss-Prot Accession Number P24253, from E. coli
#2	hypothetical	27	Mycoplasma pneumoniae, hypothetical protein (HI1366) homolog; similar to GenBank Accession Number G64026, from H. influenzae
#3	H10_orf206	38	Mycoplasma pneumoniae, H10_orf206 Protein

Motif 1
ATTCAGTCTTTGGATTCATTGCTTTCATCAATGA	0	18	1
CAATAATCGGCATCGTCATTGATGAAAGCAATGA	0	33	0
CGATTATTGGCATCTTTATTGCTTGGGGACTTTT	0	58	1
GATAAAAACCTAGCTTTAATGGTGGAATAGGAAT	0	126	1
CCGACCATAATTGTTTTTTTGGTGGTAAAAAGAT	0	173	1
AAATACGTGGTGGTGTGATTGCTGTCATTATTGC	0	212	1
TTGCTGTCATTATTGCCATTGCTGTAATAGCTGC	0	230	1
GACCAACAATTTTTGTAAATGCTTCGGTTTGACC	0	265	0
CCCTGTTAGTCGGTGTCATTATTGGCTATTTTAT	1	111	1
TAATTTGGTTTTCGGTGATTGGTGGGTTATCACG	1	173	0
ATTAATTACTTCTGGTTTTTAATGGAGCGCATAA	1	261	0
  ACTGAACTAATTGTTATTGTTTAAATT     	2	5	0
          * * ** **** **
MAP Score: 10.9792

Motif 2
TCGGCATCGTCATTGATGAAAGCAATGAATCCAAAGA	0	24	0
TGACGATGCCGATTATTGGCATCTTTATTGCTTGGGG	0	49	1
CCTATTCCACCATTAAAGCTAGGTTTTTATCAGGTGT	0	120	0
TCCAATATGTGATTCCGACCATAATTGTTTTTTTGGT	0	159	1
GTGGTAAAAAGATTTATGAAATACGTGGTGGTGTGAT	0	194	1
GTGGTGGTGTGATTGCTGTCATTATTGCCATTGCTGT	0	218	1
TCATTATTGCCATTGCTGTAATAGCTGCTGGTCAAAC	0	236	1
AAACCGAAGCATTTACAAAAATTGTTGGTCAAAAATC	0	269	1
GATTTTATAAGATTCTAGAGAGGATTAAGATTAAGAT	1	25	1
CCTTAATTTGGTTTTCGGTGATTGGTGGGTTATCACG	1	173	0
CCGAAAACCAAATTAAGGCGATGTATGCCAAAATGGG	1	192	1
          **** * *  **   **
MAP Score: 9.51173

Motif 3
GCATCGTCATTGATGAAAGCAATGAATCCAAAGA	0	24	0
TTTTATCAGGTGTTCAACCAGATGGAATAAAAAA	0	99	0
GTTGAACACCTGATAAAAACCTAGCTTTAATGGT	0	115	1
GTAAAAAGATTTATGAAATACGTGGTGGTGTGAT	0	197	1
TTATTGCCATTGCTGTAATAGCTGCTGGTCAAAC	0	239	1
TAATAGCTGCTGGTCAAACCGAAGCATTTACAAA	0	254	1
CAAAAATTGTTGGTCAAAAATCAGTA        	0	284	1
CTCTCTAGAATCTTATAAAATCAGAATAGCGTAA	1	13	0
GAAAGGGGAATTCCCAAACCTAAGGCAAGCGCAA	1	78	0
TCTATCAAAATCTTTAAAAAACAGATTCGTGATA	1	146	1
GTCGTAAGCTTTCTGAAACACAAGTCAAGGAAAT	1	228	1
ATTATGCGCTCCATTAAAAACCAGAAGTAATTAA	1	260	1
TTATTTTACATTTTTAAAATTAAGCTCATCAAG 	3	9	0
          ** * *** * ***
MAP Score: 8.63112

Motif 4
CTTTTAGCTTCTTTTTTTATTCCATCTGGTTGAACACC	0	87	1
AAAAACCTAGCTTTAATGGTGGAATAGGAATCCAATAT	0	129	1
GTGATTCCGACCATAATTGTTTTTTTGGTGGTAAAAAG	0	167	1
  TAATTACGCTATTCTGATTTTATAAGATTCTAGAGA	1	8	1
TGGGAATTCCCCTTTCCCTGTTAGTCGGTGTCATTATT	1	96	1
TCATTATTGGCTATTTTATTTCTATCAAAATCTTTAAA	1	126	1
GCATACATCGCCTTAATTTGGTTTTCGGTGATTGGTGG	1	182	0
CGCATAATTTCCTTGACTTGTGTTTCAGAAAGCTTACG	1	230	0
  AATTTAAACAATAACAATTAGTTCAGT         	2	8	1
          * **  *  **   ****
MAP Score: 0.799153

Motif 5
GATGGAATAAAAAAAGAAGCTAAAAGTCCC	0	83	0
GCTGCTGGTCAAACCGAAGCATTTACAAAA	0	259	1
AAGCTTTCTGAAACACAAGTCAAGGAAATT	1	233	1
CTCCATTAAAAACCAGAAGTAATTAATAA 	1	268	1
          **********
MAP Score: 0.15059