AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_profile002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247551
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	infC	89	Mycoplasma pneumoniae, translation initiation factor IF3; similar to Swiss-Prot Accession Number Q05426, from M. fermentans
#1	C09_orf223	300	Mycoplasma pneumoniae, C09_orf223 Protein
#2	fruA	300	Mycoplasma pneumoniae, fructose-permease IIBC component; similar to Swiss-Prot Accession Number P20966, from E. coli
#3	ptsG	51	Mycoplasma pneumoniae, PTS system, glucose-specific IIABC component; similar to Swiss-Prot Accession Number P20166 and P08875, from B. subtilis

Motif 1
TTAATTGAGTTAAAACGGTTGGAGATTGTTAAA	0	26	1
TGGAGATTGTTAAAATATTGGCGCTATACAAAG	0	45	1
ACAAATGGCATAAAACAGTAAGGCAAAGAAGAT	1	19	0
TCCTGGTAAAACAAACAGTGACAGTAAACCAGC	1	61	0
AAGCAGAATTAGAAGCCTTTAAGAAACATAACA	1	185	1
CCTTCGTTCAAAAAACCTTAGTGTTATGTTTCT	1	206	0
CTGATACCAAAGAAACTTTGAGTTCTACAAGCG	1	245	1
TTTGAGTTCTACAAGCGTTTGGTTAATTGTCTT	1	261	1
AACAATTTATAAAAATTTTTGCGTTTTCTTTTA	2	12	0
ATTTATATTGAGAAATTTTTATGGCGGAAGCGG	2	150	1
GGGAGCGTACTCAAGTGGTTAAGAGGACACCCT	2	227	0
TAAATTTATTATAAATATTGGATTTTCTGACTT	2	273	1
TTTTTGTTACTTAAACATTGAGGGA        	3	2	0
TTTTAAATCCTTAAATTTTTGTTACTTAAACAT	3	17	0
          * **** **** *
MAP Score: 7.84427

Motif 2
   TCCTCAGGGATCTTCTTTGCCTTACTGT	1	7	1
ATGTGTTAGCTGGTTTACTGTCACTGTTTGT	1	53	1
ATTGTCTTTCTGATCTTCTTTATT       	1	286	1
AAAAATTTTTGCGTTTTCTTTTATT      	2	4	0
CTTAATTCCGGAATTTGCTGTTGCAAACAAT	2	39	0
AGACCATCAGTGGTCTGCTTTTTTATTGCGC	2	112	0
AGACCACTGATGGTCTGCTTACAATTTATAT	2	127	1
CACCTTAGCAGGGTGTCCTCTTAACCACTTG	2	218	1
TATAAATATTGGATTTTCTGACTTTAGG   	2	282	1
          ****** ****
MAP Score: 7.53876

Motif 3
TATTGGCGCTATACAAAGTAGTCTTTACGACTCGCCCGA	0	60	1
AATCGGAAGCAGAATTAGAAGCCTTTAAGAAACATAACA	1	179	1
TTTAAGAAACATAACACTAAGGTTTTTTGAACGAAGGTA	1	202	1
GTATGAACTGATACCAAAGAAACTTTGAGTTCTACAAGC	1	238	1
GTTGCAAACAATTTATAAAAATTTTTGCGTTTTCTTTTA	2	12	0
TGTTAACAAGAAAGAAACGGAATTTTTAGAAGAGCTCGC	2	69	0
CTTACAATTTATATTGAGAAATTTTTATGGCGGAAGCGG	2	144	1
TAAATTTATTATAAATATTGGATTTTCTGACTTTAGG  	2	273	1
          * *   *  ** ****  *
MAP Score: 7.07987

Motif 4
  AATTACTCCTTAATGGTTAATTGAGTTA	0	8	1
GTTGGAGATTGTTAAAATATTGGCGCTATA	0	43	1
TCTTCTTTGCCTTACTGTTTTATGCCATTT	1	20	1
CTGGTTTACTGTCACTGTTTGTTTTACCAG	1	62	1
GGTCCACAGGGTTAAAGTATTCAATTCGTT	1	131	0
TGTTATGTTTCTTAAAGGCTTCTAATTCTG	1	188	0
GCTTGTAGAACTCAAAGTTTCTTTGGTATC	1	247	0
TGATGGTCTGCTTACAATTTATATTGAGAA	2	134	1
       TCCCTCAATGTTTAAGTAACAAA	3	3	1
TTTTTAAATCCTTAAATTTTTGTTACTTAA	3	21	0
          **********
MAP Score: 6.83292

Motif 5
   AATTACTCCTTAATGGTTAATTGAGTTAA	0	7	1
ATCTTCTTTGCCTTACTGTTTTATGCCATTTG	1	19	1
GTTCAAAAAACCTTAGTGTTATGTTTCTTAAA	1	202	0
TTTTTATTGCGCTTTTTGTTAACAAGAAAGAA	2	92	0
GTAAGCAGACCATCAGTGGTCTGCTTTTTTAT	2	117	0
        TCCCTCAATGTTTAAGTAACAAAA	3	2	1
          ***** **** *
MAP Score: 2.4538

Motif 6
CTCCAACCGTTTTAACTCAATTAACCATTAAGGAGTAATT  	0	8	0
TGTCACTGTTTGTTTTACCAGGAAAGTTCTGGGAAAAGCGCA	1	71	1
AGATGAACGAATTGAATACTTTAACCCTGTGGACCAGGCTTA	1	126	1
ATTAGAAGCCTTTAAGAAACATAACACTAAGGTTTTTTGAAC	1	192	1
CCAAAGAAACTTTGAGTTCTACAAGCGTTTGGTTAATTGTCT	1	251	1
TATTGCGCTTTTTGTTAACAAGAAAGAAACGGAATTTTTAGA	2	78	0
TATTGAGAAATTTTTATGGCGGAAGCGGTGGGATTCGAACCC	2	155	1
ATCCTTAAATTTTTGTTACTTAAACATTGAGGGA        	3	2	0
          ***   * *   **   *  **
MAP Score: 1.15444