AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247309
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	vacB	273	Mycoplasma pneumoniae, virulence associated protein homolog; similar to GenBank Accession Number G64098, from H. influenzae
#1	MG098	197	Mycoplasma pneumoniae, MG098 homolog, from M. genitalium
#2	ung	24	Mycoplasma pneumoniae, uracil DNA glycosylase; similar to Swiss-Prot Accession Number P12295, from E. coli
#3	MG288	300	Mycoplasma pneumoniae, MG288 homolog, from M. genitalium
#4	rpsF	56	Mycoplasma pneumoniae, ribosomal protein S6; similar to Swiss-Prot Accession Number P02358, from E. coli
#5	fus	22	Mycoplasma pneumoniae, elongation factor G; similar to Swiss-Prot Accession Number P13551, from T. aquaticus
#6	rpsG	53	Mycoplasma pneumoniae, ribosomal protein S7; similar to Swiss-Prot Accession Number P22744, from B. stearothermophilus
#7	rpsL	28	Mycoplasma pneumoniae, ribosomal protein S12; similar to Swiss-Prot Accession Number P09901, from B. stearothermophilus
#8	rplK	55	Mycoplasma pneumoniae, ribosomal protein L11; similar to Swiss-Prot Accession Number P29395, from T. maritima
#9	oppB	275	Mycoplasma pneumoniae, oligopeptide transport system permease protein OppB; similar to Swiss-Prot Accession Number P24138 and P24691, from B. subtilis

Motif 1
AACACACATTAAAGCATGGACGCAATTCAAATAGT	0	27	1
ACCTGAAAGCGAAGCAAGTCCGCCAGTAGAACCAT	0	115	0
AAAATAAGAAAAAGCACTACTAAAATAAACATCGT	0	210	0
CGCAAAATGAAAAACTAACCCTAAAATAAGAAAAA	0	232	0
AATTAAAGACAAAACTTTACCAAAACAG       	1	3	0
AGCGGAATAAAAATCATAAGAAAAATAATGAAAAA	1	58	0
TTGCAACTCTAAAACAAGCTTGCAAAGACAGTTTA	1	159	0
TTAGAGTTGCAAAGCAAAGTCCAAA          	1	182	1
TGGTGTACTTGAAACAATTCCCCAACTGCAAAAGG	3	15	1
ATACCGGGAAAAAGCCACTGCCCAAAAAGTCAAAT	3	120	0
TGAAACTGTTCAAACAAACTAGCAACGTTGTCCGC	3	178	0
ACTTTATGGGAAAACTAAATATAAAAGTAAAGATT	4	27	0
TTTTTTACGAAAAACATTAACTCAATCAATTAACT	6	24	1
TTAGTGGTTCAAAACATTCTACAAAAAAACGATAC	9	20	0
ACTCCGAGTGGAAACCGATTATAAATCGCGTTTCC	9	85	1
          ******    * ***
MAP Score: 14.5035

Motif 2
TTAGTAGTGCTTTTTCTTATTTTAGGGTTA	0	222	1
TTAGGGTTAGTTTTTCATTTTGCGCTTTAA	0	243	1
TTGGTAAAGTTTTGTCTTTAATTCAACAAA	1	15	1
AGCTTTAGCATTTTTCATTATTTTTCTTAT	1	48	1
TTTTTCATTATTTTTCTTATGATTTTTATT	1	58	1
GCTCGCTGTGCTTTTCTGTTTGAGTACAAG	1	91	0
AGCGAGCAGTCTTTTCTTTACAATGTAAAG	1	114	1
CTTTGCAGTTCTTTACATTGTAAAGAAAAG	1	124	0
GTTTAAGCAGCTTTGCAGTTCTTTACATTG	1	134	0
    TTTGGACTTTGCTTTGCAACTCTAAA	1	181	0
TTTTATTTCCTTTTGCAGTTGGGGAATTGT	3	28	0
ACACGGGGAATTTGACTTTGTTCATTGACA	3	78	0
AGCACGCTTATTTGACTTTTTGGGCAGTGG	3	111	1
AGGCATAAATCTTTACTTTTATATTTAGTT	4	20	1
ACCAGGTTCCTTTTTCTTTTTTATTAGTAT	9	204	1
AACGTTTGGGTTTGGCAGTGTTAGCG    	9	259	1
          **********
MAP Score: 13.9224

Motif 3
TTGACCTGAAAGCGAAGCAAGTCCGCCAGTA	0	122	0
AATAAGAAAAAGCACTACTAAAATAAACATC	0	212	0
AAAAATAATGAAAAATGCTAAAGCTTTGTTT	1	42	0
CAAACAGAAAAGCACAGCGAGCAGTCTTTTC	1	99	1
TACAATGTAAAGAACTGCAAAGCTGCTTAAA	1	132	1
AGCTTGTTTTAGAGTTGCAAAGCAAAGTCCA	1	174	1
AAAGGAAATAAAAGCTGCTAATGACATTTTC	3	45	1
GTTAGCGGACAACGTTGCTAGTTTGTTTGAA	3	174	1
TCTACAAAAAAACGATACTAGTAAGTAC   	9	7	0
      CGCTAACACTGCCAAACCCAAACGT	9	260	0
          ******** **
MAP Score: 5.53409

Motif 4
TTCCGCGGTCTTTGGTTTTGCGAAAAATTTC	0	159	0
TTATTTTAGTAGTGCTTTTTCTTATTTTAGG	0	217	1
TTATTTTAGGGTTAGTTTTTCATTTTGCGCT	0	238	1
GACTGCTCGCTGTGCTTTTCTGTTTGAGTAC	1	94	0
GCAGCTTTTATTTCCTTTTGCAGTTGGGGAA	3	32	0
TTTTTGGGCAGTGGCTTTTTCCCGGTATTGA	3	127	1
GGCATAAATCTTTACTTTTATATTTAGTTTT	4	21	1
TACTTTTATATTTAGTTTTCCCATAAAGTTA	4	33	1
  TATCTTAAATTCCTTTTTTTACGAAAAAC	6	8	1
TACTTACTAGTATCGTTTTTTTGTAGAATGT	9	11	1
TGAGAACCAGGTTCCTTTTTCTTTTTTATTA	9	199	1
          ********* *
MAP Score: 4.81487

Motif 5
TTTCCAAATCTTGACCTGAAAGCGAAGCAAGTCCGC	0	127	0
GCTTTTCTGTTTGAGTACAAGCGGAATAAAAATCAT	1	76	0
      TTCATTGAGCCGCAAAGGCAGCAA      	2	4	1
TTTCCCGGTATTGAACCCGAAAGGTTTAGGGTTAGC	3	144	1
AAAATGCTGTTTGACTCCGAGTGGAAACCGATTATA	9	72	1
CATCTGCACTTTTAGTTGGACTGGTTACATCAAATC	9	127	1
CTTTTTCTTTTTTATTAGTATTCGAAAGTGTTCAAG	9	213	1
          **** * * *  ** *
MAP Score: 1.85303