AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247328
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	arcA	53	Mycoplasma pneumoniae, arginine deiminase; similar to Swiss-Prot Accession Number P41142, from P. putida
#1	argI	247	Mycoplasma pneumoniae, ornithine carbamoyl transferase; similar to Swiss-Prot Accession Number P04391, from E. coli
#2	arcA	300	Mycoplasma pneumoniae, arginine deiminase; similar to Swiss-Prot Accession Number P23793, from M. capricolum

Motif 1
CGTGTAACAATTAAAGCAGTAAGCTTAGCC	2	266	1
CCACCTTTATTTAAGGCAGTACAACAGCTG	2	167	1
AGTAACGCAATTAAAGCAATTGTTAATTAT	0	13	1
GTAGTAAAGTTTAAAGCAGAGTCAAGGCTA	1	60	0
GGCAACTAATTTACAGCTGTTGTACTGCCT	2	180	0
TTACTGCGTTTTAAATCAATGGCGAGGTCA	1	111	0
AAATAGTTAATTTGAGCAGTAGTAAAGTTT	1	78	0
          **********
MAP Score: 9.79612

Motif 2
ACTTAAAAGGTCGTAGCCTTGACTCTGCTT	1	47	1
ATTGACCTCGCCATTGATTTAAAACGCAGT	1	109	1
AAGATTCTACCCGTACCCGTTGTGCCTTTG	1	204	1
GAAGTGGCTGCCTTTGACTTGGGT      	1	233	1
GTTCTTCAGACCGTTGCTCTACCGACTGAG	2	48	0
AACTTTCTTACCTTACCTTTAAAACTAAGG	2	117	1
CAATAAAAAACCTTACCCTTAGTTTTAAAG	2	133	0
AATCAAGTTCACTTTGCCTTTTTTTCTTGG	2	223	1
AAAGCAGTAAGCTTAGCCTTATTACATGTA	2	278	1
          **********
MAP Score: 8.36983

Motif 3
AAGGTCGTAGCCTTGACTCTGCTTTAAACT	1	53	1
ATTTAATTGACCTCGCCATTGATTTAAAAC	1	104	1
AAGTGGCTGCCTTTGACTTGGGT       	1	234	1
AACTTTCTTACCTTACCTTTAAAACTAAGG	2	117	1
CAATAAAAAACCTTACCCTTAGTTTTAAAG	2	133	0
ATCAAGTTCACTTTGCCTTTTTTTCTTGGG	2	224	1
          **********
MAP Score: 4.11341

Motif 4
ATTAACTTAAAAGGTCGTAGCCTTGACTCTGCTTTAA	1	43	1
ACGCAGTAAATACCAAGTTGCACATCCAGAACCGTCC	1	132	1
CTGTTCCAAAAAGATTCTACCCGTACCCGTTGTGCCT	1	194	1
TGTGCCTTTGAAGTGGCTGCCTTTGACTTGGGT    	1	224	1
ACTGAGCTACAAGACCGTGGCGGTTCCAACGGGAATC	2	17	0
CACGGTTCTTCAGACCGTTGCTCTACCGACTGAGCTA	2	45	0
ACCACCATAAAACTTTCTTACCTTACCTTTAAAACTA	2	107	1
          ***   ** **  * **
MAP Score: 3.24612

Motif 5
CATCCAGAACCGTCCCTTAGCGGGGAAGAAC	1	154	1
CAAAAAGATTCTACCCGTACCCGTTGTGCCT	1	200	1
TTTGAAGTGGCTGCCTTTGACTTGGGT    	1	230	1
ACTGAGCTACAAGACCGTGGCGGTTCCAACG	2	23	0
CACGGTTCTTCAGACCGTTGCTCTACCGACT	2	51	0
CAGTTCGATTCTGCCCGAGACCACCATAAAA	2	88	1
ATAAAACTTTCTTACCTTACCTTTAAAACTA	2	113	1
          ********* *
MAP Score: 0.185876