AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247009
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ffh	55	Mycoplasma pneumoniae, signal recognition particle protein; similar to Swiss-Prot Accession Number Q01442, from M. mycoides
#1	tuf	84	Mycoplasma pneumoniae, elongation factor TU; similar to Swiss-Prot Accession Number P13927, from M. genitalium
#2	degV	158	Mycoplasma pneumoniae, homolog (degV) protein; similar to Swiss-Prot Accession Number P32436, from B. subtilis
#3	MG447	150	Mycoplasma pneumoniae, MG447 homolog, from M. genitalium
#4	rpsP	81	Mycoplasma pneumoniae, ribosomal protein S16; similar to Swiss-Prot Accession Number P21474, from B. subtilis
#5	trmD	65	Mycoplasma pneumoniae, tRNA (guanine-N1)-methyltransferase; similar to GenBank Accession Number C64054, from H. sapiens
#6	P115	184	Mycoplasma pneumoniae, P115 protein homolog; similar to GenBank Accession Number JQ0894, from M. hyorhinis
#7	rpmE	44	Mycoplasma pneumoniae, ribosomal protein L31; similar to Swiss-Prot Accession Number P02432, from E. coli
#8	MG256	229	Mycoplasma pneumoniae, MG256 homolog, from M. genitalium
#9	MG255	167	Mycoplasma pneumoniae, MG255 homolog, from M. genitalium
#10	ygl1	56	Mycoplasma pneumoniae, hypothetical protein (ygl1) homolog; similar to Swiss-Prot Accession Number P19434, from S. viridochromogenes

Motif 1
CTTACTTAAACGCTTCGATT          	5	55	1
   TTAAATCAGGTTAGATTTTGCAATAGT	6	167	0
ACAAAGCAACGGCTTAGATTATATATTTAT	7	17	0
CAGTAAATGGAGGTTCGATTCCTCTAGGGA	8	49	1
CTGTCTGTGTGGGTTCGATTCCTTCCACCC	8	196	1
GTTAAGATGCGGGTTCGATTCCCGTTATCT	9	79	0
          **********
MAP Score: 11.3305

Motif 2
TACTAACAGAGTCAACTAAGAATGCGACTC	2	13	0
   GTGGATAGCCAACAAGATCGTCTAGCG	3	7	1
CTTGTCTTTGGCAAACTAGTACTTGTAATA	6	69	0
TTTAGCGCCCCTCAACTAGTTGCACCAACC	6	100	0
TTTCCTTAAAGCCAACTAGAATAATCTAGT	6	132	1
AGACCTAGTAGTTAACTAGGTCTCTGTGAT	8	89	0
TTCCACCCCCGCCACCTAGTG         	8	218	1
AGCTTACAATGCCAACCAGGTGCTTTTAGG	9	32	1
          **********
MAP Score: 6.19001

Motif 3
AGTTTGAGATAAAGCTGTAGAGAGGCTTAT	1	34	0
TCAATGATGAAAAGCGGTAGCACATACAGA	2	68	0
ATCAACTCCTGAAGCTGAAACCACCTTTAG	2	98	1
TCGGAATAGCAAAGCGCAAGATCGTTAGAA	3	80	0
GCAGCGGAAAACAGCGCAAAGAAAAAAGTC	3	108	0
AAAGACATAAGCAGCGGAAAACAGCGCAAA	3	118	0
CTTTTAAAATAAAGCGGATAATTATACATT	4	34	0
CTATATCTGCGCAGCTCATAATTTTAGTAT	9	137	1
          **********
MAP Score: 5.2328

Motif 4
TCTTTGCGCTGTTTTCCGCTGCTTATGTCT	3	116	1
GCAATGTATAATTATCCGCTTTATTTTAAA	4	32	1
TTTGACCTTACTTAAACGCTTCGATT    	5	49	1
ATTTTTTTAACTGAACCGCTCATGATAGTT	6	25	1
ACTCAGTCGTGTTATCCATTACACCAAGGG	8	13	0
CAGAGACCTAGTTAACTACTAGGTCTTTTG	8	93	1
AATTAAAATGATTAACCGCTAAGGGGGTGT	8	136	1
TTCGATTCCCGTTATCTGCTCCATATTAAA	9	66	0
          **********
MAP Score: 4.16686

Motif 5
CCGAACTAAAGGTGGTTTCAGCTTCAGGAGTTG	2	100	0
ACCTTTAGTTCGGGGTTTGACATTGATTTAAAA	2	120	1
ATTGCCGTTAGGTAGTTTTACCTAACT      	4	4	0
TCTTTGAACAGGTAGTTTGACCTTACTTAAACG	5	34	1
ACTAGTTGAGGGGCGCTAAACCTTTCCTTAAAG	6	110	1
GCACCTGGTTGGCATTGTAAGCTAATCAGGGCT	9	22	0
GAATCGAACCCGCATCTTAACCTTGGCAAGGTT	9	88	1
          **  **** ****
MAP Score: 3.12433

Motif 6
  GAAACTAGCTTTATCTATACGTAGAAATAA	0	8	1
TTTATTTTTTTATTATTTCTACGTATAGATAA	0	20	0
CTCTCTACAGCTTTATCTCAAACTTATGTAAA	1	40	1
TGAATTACGTCTCTAATTTTACATAAGTTTGA	1	57	0
CGGGGTTTGACATTGATTTAAAAACCCTCACG	2	130	1
TAATTATCCGCTTTATTTTAAAAGGAGACTTG	4	40	1
       TAATCTTATTTTTACCAATCAAGTC	4	66	0
GTGTGAAAATCACTGTTTTAACCCTCTTTGAA	5	10	1
GGTAGTTTGACCTTACTTAAACGCTTCGATT 	5	44	1
AGCTTAATTTTTTTAACTGAACCGCTCATGAT	6	19	1
GATAGACAAACGTTATTTTAAAAGAAAA    	10	38	1
          * ****** ***
MAP Score: 2.50241

Motif 7
AGGTTACTAACAGAGTCAACTAAGAATGCGACTCTCA 	2	9	0
TTGACTCTGTTAGTAACCTCAAGGAAAGCCAGGCACAA	2	28	1
CTTTTCATCATTGAATCAACTCCTGAAGCTGAAACCAC	2	84	1
        AATCGAAGCGTTTAAGTAAGGTCAAACTAC	5	45	0
AGACAAGTGGTTGGTGCAACTAGTTGAGGGGCGCTAAA	6	92	1
TAAAGCCAACTAGAATAATCTAGTAATGCACTATTGCA	6	138	1
AAATGGAGGTTCGATTCCTCTAGGGAAGGCCAAATTAT	8	53	1
GTGGAAGGAATCGAACCCACACAGACAGTTTTGGAGAC	8	186	0
TGATTGCAATTTGTAGAATCTATTACAGATAGACAAAC	10	11	1
          * *   * **** *  **
MAP Score: 2.41859

Motif 8
AGGAAAGCCAGGCACAACATCTGTATGTGC	2	49	1
GATGAAAAGCGGTAGCACATACAGATGTTG	2	63	0
CGCTGTTTTCCGCTGCTTATGTCTTTGTGG	3	122	1
GTAGTTTAGTGGCAGAACAACAGTCTCCAA	8	164	1
ATAGTTCAATGGCAGAACATAACCTTGCCA	9	111	0
ACTATATCTGCGCAGCTCATAATTTTAGTA	9	136	1
          **********
MAP Score: 0.873248

Motif 9
GAAACTAGCTTTATCTATACGTAGAAATAATAAAAAAATAAAT	0	10	1
TATCTCAAACTTATGTAAAATTAGAGACGTAATTCAAACAC  	1	53	1
GTTAGTAACCTCAAGGAAAGCCAGGCACAACATCTGTATGTGC	2	36	1
GGTTTGACATTGATTTAAAAACCCTCACGGACAAG        	2	133	1
        AGTTAGGTAAAACTACCTAACGGCAATGTATAATT	4	2	1
TTAGCGCCCCTCAACTAGTTGCACCAACCACTTGTCTTTGGCA	6	86	0
GGCCAAATTATCACAGAGACCTAGTTAACTACTAGGTCTTTTG	8	80	1
CATTTTAATTTAATTTATATACACAAAAGACCTAGTAGTTAAC	8	103	0
GTTCTGCCACTAAACTACACCCCCTTAGCGGTTAATCATTTTA	8	139	0
       AAATTAATAAAAAGCCCTGATTAGCTTACAATGCCA	9	3	1
GTTCTGCCATTGAACTATATCTGCGCAGCTCATAATTTTAGTA	9	123	1
ATTTGTAGAATCTATTACAGATAGACAAACGTTATTTTAAAAG	10	19	1
          * *  ** *  ***  *     *
MAP Score: 0.81105