AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247229
 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	pheS	300	Mycoplasma pneumoniae, phenylalanyl-tRNA synthetase alpha-subunit; similar to Swiss-Prot Accession Number P17921, from B. subtilis
#3	tuf	84	Mycoplasma pneumoniae, elongation factor TU; similar to Swiss-Prot Accession Number P13927, from M. genitalium
#4	degV	158	Mycoplasma pneumoniae, homolog (degV) protein; similar to Swiss-Prot Accession Number P32436, from B. subtilis

Motif 1
TAACAATCTCCAACCGTTTTAACTCAATTAA	0	26	0
TCTTCTTTGCCTTACTGTTTTATGCCATTTG	1	20	1
CCAAGTAAATCTTGCGCTTTTCCCAGAACTT	1	94	0
TCTAATTCTGCTTCCGATTTAAAGATGTGAT	1	167	0
AAACATAACACTAAGGTTTTTTGAACGAAGG	1	208	1
GACAATTAACCAAACGCTTGTAGAACTCAAA	1	261	0
CAGACAGCTCCAAAATATTTTTGACGATTGG	2	40	1
GGAAAACTAACAAAAGCTGTTAGTTTGATGT	2	69	1
ATAAAAAAGCCAAAAGCTTTTAAAGTAACTA	2	209	1
ATAAGCCTCTCTACAGCTTTATCTCAAACTT	3	34	1
TCTAATTTTACATAAGTTTGAGATAAAGCTG	3	47	0
AAGCCAGGCACAACATCTGTATGTGCTACCG	4	53	1
TCTGTATGTGCTACCGCTTTTCATCATTGAA	4	68	1
AAACCCCGAACTAAAGGTGGTTTCAGCTTCA	4	107	0
          ****** ****
MAP Score: 8.50964

Motif 2
GACAGTAAACCAGCTAACACATAACAAATG	1	45	0
GCTTCTAATTCTGCTTCCGATTTAAAGATG	1	171	0
AAGGTATGAACTGATACCAAAGAAACTTTG	1	235	1
GAAAGGCAGACAGCTCCAAAATATTTTTGA	2	34	1
AAAAACGAGCCTGCTCCCGCTGATTTAAAT	2	129	0
GTCACTCTGCCTGCTCCCACTAAATAAATT	2	168	1
ACATCTGTATGTGCTACCGCTTTTCATCAT	4	65	1
ACTCCTGAAGCTGAAACCACCTTTAGTTCG	4	102	1
          **********
MAP Score: 7.0559

Motif 3
CCGTTTTAACTCAATTAACCATTAAGGAGTAA	0	12	0
ACAGTGACAGTAAACCAGCTAACACATAACAA	1	48	0
ATACCTTCGTTCAAAAAACCTTAGTGTTATGT	1	210	0
GATCAGAAAGACAATTAACCAAACGCTTGTAG	1	269	0
          TAAAAAAGCCATCTACCCAGAG	2	0	1
CAGGGTTTTATAAAAAAGCCAAAAGCTTTTAA	2	200	1
CAAAAGCTTTTAAAGTAACTATTTATTTGCAA	2	219	1
GTGTGCTATTTAAATTAACTATAGCACAATTA	2	267	1
          ****  ******
MAP Score: 5.94189

Motif 4
TAACAATCTCCAACCGTTTTAACTCAATTAACCAT	0	22	0
CTTCTTTGCCTTACTGTTTTATGCCATTTGTTATG	1	21	1
TGGTTTACTGTCACTGTTTGTTTTACCAGGAAAGT	1	63	1
ACCAGGCTTATCACATCTTTAAATCGGAAGCAGAA	1	158	1
TACATCAAACTAACAGCTTTTGTTAGTTTTCCAAT	2	66	0
TTTAGTAAATTCATAGTTTTGCCTCTACATCAAAC	2	91	0
ATAAGCCTCTCTACAGCTTTATCTCAAACTTATGT	3	34	1
TCTGTATGTGCTACCGCTTTTCATCATTGAATCAA	4	68	1
          * ** *****   **
MAP Score: 5.66743

Motif 5
   AATTACTCCTTAATGGTTAATTGAGTT	0	7	1
         TCCTCAGGGATCTTCTTTGCC	1	1	1
ATCTTCTTTGCCTTACTGTTTTATGCCATT	1	19	1
TAAGCCTGGTCCACAGGGTTAAAGTATTCA	1	138	0
GTTCAAAAAACCTTAGTGTTATGTTTCTTA	1	204	0
CTGCCTTTCACCTCTGGGTAGATGGCTTTT	2	13	0
CTGTTAGTAACCTCAAGGAAAGCCAGGCAC	4	34	1
ATTTAAAAACCCTCACGGACAAG       	4	145	1
          **********
MAP Score: 4.31936

Motif 6
GTTTTAACTCAATTAACCATTAAGGAGTAA	0	12	0
TGTTTCTTAAAGGCTTCTAATTCTGCTTCC	1	183	0
TCAGAAAGACAATTAACCAAACGCTTGTAG	1	269	0
AGCTTTTGTTAGTTTTCCAATCGTCAAAAA	2	57	0
CAAAACTATGAATTTACTAAATTTATTTAA	2	105	1
AAAGCTTTTAAAGTAACTATTTATTTGCAA	2	221	1
GTGCTATTTAAATTAACTATAGCACAATTA	2	269	1
TTACTAACAGAGTCAACTAAGAATGCGACT	4	14	0
GCTTTCCTTGAGGTTACTAACAGAGTCAAC	4	27	0
          **********
MAP Score: 4.01997

Motif 7
TTTAAGAAACATAACACTAAGGTTTTTTGAACGAAG	1	202	1
GTTTTATAAAAAAGCCAAAAGCTTTTAAAGTAACTA	2	204	1
AAACGCTTGTAGAACTCAAAGTTTCTTTGGTATCAG	1	245	0
ACTACTTTGTATAGCGCCAATATTTTAACAATCTCC	0	46	0
AATCGGAAGCAGAATTAGAAGCCTTTAAGAAACATA	1	179	1
CACTACTCCAAGAATTATAAGCCTCTCTACAGCTTT	3	18	1
CCCACTAAATAAATTGACAGGGTTTTATAAAAAAGC	2	183	1
AAAGGCAGACAGCTCCAAAATATTTTTGACGATTGG	2	35	1
TAATTTAAATAGCACACGAATATTTGCACTAATTTG	2	248	0
          * * *   *** ****
MAP Score: 2.36149