AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_sum_all006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248034
 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
TCAAAGGATTTTTGGATGAGGACTTGCTTCGCTAGACGATCT	3	24	0
AAAAGACTGTTTCTAACGATCTTGCGCTTTGCTATTCCGACT	3	70	1
CTATTCCGACTTTTTTCTTTGCGCTGTTTTCCGCTGCTTATG	3	101	1
TCCGCTTTATTTTAAAAGGAGACTTGATTGGTAAAAATAAGA	4	46	1
AAGTACTAGTTTGCCAAAGACAAGTGGTTGGTGCAACTAGTT	6	75	1
CAATAGTGCATTACTAGATTATTCTAGTTGGCTTTAAGGAAA	6	132	0
CATTTACTGATTAGGACTCAGTCGTGTTATCCATTACACCAA	8	16	0
GAAGGCCAAATTATCACAGAGACCTAGTTAACTACTAGGTCT	8	77	1
       AAATTAATAAAAAGCCCTGATTAGCTTACAATGCC	9	3	1
ATATTAAATTTTCCTAAAAGCACCTGGTTGGCATTGTAAGCT	9	32	0
CTTGCCAAGGTTAAGATGCGGGTTCGATTCCCGTTATCTGCT	9	76	0
          **   *    *   ** ** **
MAP Score: 9.08598

Motif 3
TTTCTACGTATAGATAAAGCTAGTTTC         	0	1	0
AAAGTCGGAATAGCAAAGCGCAAGATCGTTAGAAAC	3	78	0
GGAGACTTGATTGGTAAAAATAAGATTA        	4	63	1
TCGAAGCGTTTAAGTAAGGTCAAACTACCTGTTCAA	5	37	0
       ACTTAATTAAGCTTAATTTTTTTAACTGA	6	3	1
AAGTACTAGTTTGCCAAAGACAAGTGGTTGGTGCAA	6	75	1
TAATGCACTATTGCAAAATCTAACCTGATTTAA   	6	161	1
TCGATTCCTCTAGGGAAGGCCAAATTATCACAGAGA	8	63	1
CAGGTGCTTTTAGGAAAATTTAATATGGAGCAGATA	9	48	1
GAACATAACCTTGCCAAGGTTAAGATGCGGGTTCGA	9	91	0
CTATTACAGATAGACAAACGTTATTTTAAAAGAAAA	10	30	1
          ***  ***  ***  *
MAP Score: 8.36778

Motif 4
GAGTCGCATTCTTAGTTGACTCTGTTAGTA	2	13	1
CGCTAGACGATCTTGTTGGCTATCCAC   	3	7	0
TATTACAAGTACTAGTTTGCCAAAGACAAG	6	69	1
GGTTGGTGCAACTAGTTGAGGGGCGCTAAA	6	100	1
ACTAGATTATTCTAGTTGGCTTTAAGGAAA	6	132	0
ATCACAGAGACCTAGTTAACTACTAGGTCT	8	89	1
         CACTAGGTGGCGGGGGTGGAA	8	218	0
CCTAAAAGCACCTGGTTGGCATTGTAAGCT	9	32	0
          **********
MAP Score: 6.19001

Motif 5
TGTGCCTGGCTTTCCTTGAGGTTACTAACAG	2	34	0
        CTTGTCCGTGAGGGTTTTTAAAT	2	145	0
CCGCTGCTTATGTCTTTGTGGACCAAATT  	3	131	1
TAATTATACATTGCCGTTAGGTAGTTTTACC	4	15	0
TTATTCTAGTTGGCTTTAAGGAAAGGTTTAG	6	125	0
TAATTTGGCCTTCCCTAGAGGAATCGAACCT	8	59	0
TCTCCAAAACTGTCTGTGTGGGTTCGATTCC	8	187	1
          ** ********
MAP Score: 6.07744

Motif 6
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 7
  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 8
ATAAGCCTCTCTACAGCTTTATCTCAAACT	1	34	1
 GTGTTTGAATTACGTCTCTAATTTTACAT	1	65	0
TCTGTATGTGCTACCGCTTTTCATCATTGA	2	68	1
TTCTAACGATCTTGCGCTTTGCTATTCCGA	3	80	1
TTTCCGCTGCTTATGTCTTTGTGGACCAAA	3	128	1
TAGTAGTTAACTAGGTCTCTGTGATAATTT	8	84	0
TAGTTAACTACTAGGTCTTTTGTGTATATA	8	101	1
TGTAAGCTAATCAGGGCTTTTTATTAATTT	9	10	0
          **********
MAP Score: 2.01369

Motif 9
TCTAGGGAAGGCCAAATTATCACAGAGACCTAGTTAACTACTA	8	71	1
CACTGTTTTAACCCTCTTTGAACAGGTAGTTTGACCTTACTTA	5	20	1
ATAATTATCCGCTTTATTTTAAAAGGAGACTTGATTGGTAAAA	4	39	1
TATTACAAGTACTAGTTTGCCAAAGACAAGTGGTTGGTGCAAC	6	69	1
CAAAGCGCAAGATCGTTAGAAACAGTCTTTTCGATTCAAAGGA	3	58	0
AGGGGCGCTAAACCTTTCCTTAAAGCCAACTAGAATAATCTAG	6	118	1
TTTTTAACTGAACCGCTCATGATAGTTAGATTGTAAGTAAGTA	6	28	1
AAAATTATGAGCTGCGCAGATATAGTTCAATGGCAGAACATAA	9	119	0
GAAGGAATCGAACCCACACAGACAGTTTTGGAGACTGTTGTTC	8	178	0
          ***   *    ****     * *
MAP Score: 0.385947