AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247348
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	araD	300	Mycoplasma pneumoniae, L-ribulose-5-phosphate 4-epimerase; similar to Swiss-Prot Accession Number P08203, from E. coli
#1	yjfS	300	Mycoplasma pneumoniae, hypothetical protein (yjfS) homolog; similar to Swiss-Prot Accession Number P39301, from E. coli
#2	yjfU	291	Mycoplasma pneumoniae, hypothetical phosphotransferase protein (yjfU) homolog; similar to Swiss-Prot Accession Number P39303, from E. coli

Motif 1
TCAGGGTGCTCTTTGGCTTCCGGACCCCAAT	0	79	1
ACTTAGTGGACTTGGGCTTTGTTAAACACAT	1	19	1
AACACATTACCCTGGCCTTAGATGCGGGGCG	1	43	1
GGAAGGAGTGCTTTGGGTTTGCATATCTGTT	1	108	1
TCGCTGAAATCCTGGCCTTTGATGCACCGCG	1	213	1
GATGCACAGCCTTGGGATTAAACTGCCGCGG	1	239	0
CCCCAACAATCTTGGCCTTAGCATTCGGGTT	2	213	0
          ********* *
MAP Score: 10.9381

Motif 2
CCACCATGGTGGACAAATTACAAACACTCTTTAATAGCAG	0	16	1
GGTGCTCTTTGGCTTCCGGACCCCAATTCTTAATTAAATG	0	83	1
GATCGTGACAGTCACAAATACCTAAATCCTTAGGGTCAAT	0	122	1
AAATCCTTAGGGTCAATGTCCCCTAAAACTGTTCTTACAA	0	145	1
GATGCGGGGCGGGTACTGTACCAAAACACTATGGTTTAGA	1	63	1
GATGCACCGCGGCAGTTTAATCCCAAGGCTGTGCATCCAC	1	233	1
TTGTGGTAACGGCATGGGTACGAGCATGCTAATCAAGATT	2	44	1
CTTCCACTTTGGCGGTGTAGCCCAACTCCTTCATAATCTT	2	93	0
CACTTAACGAGTGAGTTTAACCCGAATGCTAAGGCCAAGA	2	195	1
CATCCATCAGGTTTAACACCCCAACAATCTTGGCCTTAGC	2	222	0
          **       **** **  **
MAP Score: 10.5532

Motif 3
     CTCCGACCACCATGGTGGACAAATTA	0	5	1
ATAACATCACAAAATCAGGGTGCTCTTTGGC	0	65	1
GGTATTTGTGACTGTCACGATCATTTAATTA	0	113	0
CCCCGCATCTAAGGCCAGGGTAATGTGTTTA	1	41	0
ACTGTACCAAAACACTATGGTTTAGAAAAAG	1	77	1
GGCCATTAACACCATCTTGGTCGAAAATCTC	1	184	1
CGGTGCATCAAAGGCCAGGATTTCAGCGAGA	1	211	0
TTGGGATTAAACTGCCGCGGTGCATCAAAGG	1	228	0
CCGTGGATGCACAGCCTTGGGATTAAACTGC	1	244	0
GCTTGTGGTAACGGCATGGGTACGAGCATGC	2	42	1
CATGCTAATCAAGATTAAGGTTGAAAAGATT	2	68	1
GTTGGGCTACACCGCCAAAGTGGAAGCTTTG	2	107	1
CCCGAATGCTAAGGCCAAGATTGTTGGGGTG	2	215	1
          ******* ***
MAP Score: 9.22138

Motif 4
     CTCCGACCACCATGGTGGACAAATTAC	0	5	1
GCCAAAGAGCACCCTGATTTTGTGATGTTATC	0	64	0
TGGCTTCCGGACCCCAATTCTTAATTAAATGA	0	92	1
GGGGACATTGACCCTAAGGATTTAGGTATTTG	0	136	0
TATTGAAATAACCCTAATAATGTGTAAGCTAC	0	224	1
CTTTTTCTAAACCATAGTGTTTTGGTACAGTA	1	76	0
GAGATTTTCGACCAAGATGGTGTTAATGGCCG	1	183	0
CGGCAGTTTAATCCCAAGGCTGTGCATCCACG	1	242	1
AATCTTTTCAACCTTAATCTTGATTAGCATGC	2	67	0
AATGGGACAAACCAAGGGGATGGAGCACAGCG	2	140	1
AGTGAGTTTAACCCGAATGCTAAGGCCAAGAT	2	204	1
GGGGTGTTAAACCTGATGGATGAAAACGAAAT	2	240	1
          **** **** **
MAP Score: 8.71828

Motif 5
TCGAATGAAGCTGCTATTAAAGAGTGTTTG	0	36	0
ACTGGATAATTTGCCATTAACAGTTGTAAA	0	254	1
CTTAGTGGACTTGGGCTTTGTTAAACACAT	1	20	1
ACACATTACCCTGGCCTTAGATGCGGGGCG	1	44	1
GTTTCCGATGCGGCCATTAACACCATCTTG	1	173	1
CGCTGAAATCCTGGCCTTTGATGCACCGCG	1	214	1
ATGCACAGCCTTGGGATTAAACTGCCGCGG	1	239	0
TGTGCATCCACGGGTATTAGCACTTAAAAA	1	262	1
CCCAACAATCTTGGCCTTAGCATTCGGGTT	2	213	0
          **********
MAP Score: 7.3729

Motif 6
TTAAGAATTGGGGTCCGGAAGCCAAAGAGCACCCTG	0	80	0
ACAGTTTTAGGGGACATTGACCCTAAGGATTTAGGT	0	141	0
GATGCGGGGCGGGTACTGTACCAAAACACTATGGTT	1	63	1
GATGCACCGCGGCAGTTTAATCCCAAGGCTGTGCAT	1	233	1
GCTTCCACTTTGGCGGTGTAGCCCAACTCCTTCATA	2	98	0
CACTTAACGAGTGAGTTTAACCCGAATGCTAAGGCC	2	195	1
CAAGATTGTTGGGGTGTTAAACCTGATGGATGAAAA	2	230	1
          ***   ** * ** **
MAP Score: 6.96022