AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246998
 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	MG447	150	Mycoplasma pneumoniae, MG447 homolog, from M. genitalium
#2	rpsP	81	Mycoplasma pneumoniae, ribosomal protein S16; similar to Swiss-Prot Accession Number P21474, from B. subtilis
#3	trmD	65	Mycoplasma pneumoniae, tRNA (guanine-N1)-methyltransferase; similar to GenBank Accession Number C64054, from H. sapiens
#4	P115	184	Mycoplasma pneumoniae, P115 protein homolog; similar to GenBank Accession Number JQ0894, from M. hyorhinis
#5	rpmE	44	Mycoplasma pneumoniae, ribosomal protein L31; similar to Swiss-Prot Accession Number P02432, from E. coli
#6	MG256	229	Mycoplasma pneumoniae, MG256 homolog, from M. genitalium
#7	ygl1	56	Mycoplasma pneumoniae, hypothetical protein (ygl1) homolog; similar to Swiss-Prot Accession Number P19434, from S. viridochromogenes

Motif 1
GTTAGAAACAGTCTTTTCGATTCAAAGGATTT	1	55	0
ATACATTGCCGTTAGGTAGTTTTACCTAACT 	2	9	0
ACCCTCTTTGAACAGGTAGTTTGACCTTACTT	3	30	1
ACCTTACTTAAACGCTTCGATT          	3	53	1
AACCGCTCATGATAGTTAGATTGTAAGTAAGT	4	38	1
     TTAAATCAGGTTAGATTTTGCAATAGT	4	167	0
TTACAAAGCAACGGCTTAGATTATATATTTAT	5	17	0
ATCAGTAAATGGAGGTTCGATTCCTCTAGGGA	6	47	1
AACCGCTAAGGGGGTGTAGTTTAGTGGCAGAA	6	149	1
AACTGTCTGTGTGGGTTCGATTCCTTCCACCC	6	194	1
          *  *********
MAP Score: 6.69753

Motif 2
TATTTTTTTATTATTTCTACGTATAGATAAAGCTAGTTTC	0	10	0
TCGTCTAGCGAAGCAAGTCCTCATCCAAAAATCCTTTGAA	1	27	1
TCCTCATCCAAAAATCCTTTGAATCGAAAAGACTGTTTCT	1	44	1
CAGCGCAAAGAAAAAAGTCGGAATAGCAAAGCGCAAGATC	1	87	0
          AATTTGGTCCACAAAGACATAAGCAGCGGA	1	130	0
GTATTACAAGTACTAGTTTGCCAAAGACAAGTGGTTGGTG	4	68	1
GAGGGGCGCTAAACCTTTCCTTAAAGCCAACTAGAATAAT	4	117	1
TGGAGGTTCGATTCCTCTAGGGAAGGCCAAATTATCACAG	6	56	1
TAATCATTTTAATTTAATTTATATACACAAAAGACCTAGT	6	110	0
CTATCTGTAATAGATTCTACAAATTGCAATCAT       	7	3	0
CAATTTGTAGAATCTATTACAGATAGACAAACGTTATTTT	7	17	1
CAGATAGACAAACGTTATTTTAAAAGAAAA          	7	36	1
          **     *    ** *****
MAP Score: 5.77655

Motif 3
TTTCTACGTATAGATAAAGCTAGTTTC     	0	5	0
       AGTTAGGTAAAACTACCTAACGGCA	2	3	1
GGAGACTTGATTGGTAAAAATAAGATTA    	2	63	1
GCGTTTAAGTAAGGTCAAACTACCTGTTCAAA	3	36	0
AGACAAGTGGTTGGTGCAACTAGTTGAGGGGC	4	92	1
TAAAGCCAACTAGAATAATCTAGTAATGCACT	4	138	1
TAATGCACTATTGCAAAATCTAACCTGATTTA	4	161	1
TGATTGCAATTTGTAGAATCTATTACAGATAG	7	11	1
          *** * ******
MAP Score: 5.70822

Motif 4
   GTGGATAGCCAACAAGATCGTCTAGCG	1	7	1
CTTGTCTTTGGCAAACTAGTACTTGTAATA	4	69	0
TTTCCTTAAAGCCAACTAGAATAATCTAGT	4	132	1
AATTATCACAGAGACCTAGTTAACTACTAG	6	85	1
ATATACACAAAAGACCTAGTAGTTAACTAG	6	100	0
TTCCACCCCCGCCACCTAGTG         	6	218	1
          **********
MAP Score: 4.93182

Motif 5
CTAGACGATCTTGTTGGCTATCCAC      	1	4	0
AACGATCTTGCGCTTTGCTATTCCGACTTTT	1	84	1
GCTATTCCGACTTTTTTCTTTGCGCTGTTTT	1	100	1
TTTTCCGCTGCTTATGTCTTTGTGGACCAAA	1	127	1
TTGCACCAACCACTTGTCTTTGGCAAACTAG	4	80	0
TAGATTATTCTAGTTGGCTTTAAGGAAAGGT	4	129	0
AGATTATATATTTATTGCTTTT         	5	1	0
ACTACTAGGTCTTTTGTGTATATAAATTAAA	6	107	1
TTTAAAATAACGTTTGTCTATCTGTAATAGA	7	29	0
          * *********
MAP Score: 3.92648

Motif 6
CTACGTATAGATAAAGCTAGTTTC         	0	1	0
GTGGATAGCCAACAAGATCGTCTAGCGAAGCAA	1	10	1
CCTTTGAATCGAAAAGACTGTTTCTAACGATCT	1	59	1
AGCGCAAAGAAAAAAGTCGGAATAGCAAAGCGC	1	93	0
     GTGTGAAAATCACTGTTTTAACCCTCTT	3	5	1
AACCCTCTTTGAACAGGTAGTTTGACCTTACTT	3	29	1
GACCTTACTTAAACGCTTCGATT          	3	52	1
      TTAAATCAGGTTAGATTTTGCAATAGT	4	167	0
TGTAATGGATAACACGACTGAGTCCTAATCAGT	6	20	1
ACAGTCTCCAAAACTGTCTGTGTGGGTTCGATT	6	183	1
TTCTTTTAAAATAACGTTTGTCTATCTGTAATA	7	31	0
          **** * * ****
MAP Score: 0.737958