AlignACE 3.0 10/20/99
AlignACE2 -i MP/MP_operons025_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944247505
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MG098	197	Mycoplasma pneumoniae, MG098 homolog, from M. genitalium
#1	ung	24	Mycoplasma pneumoniae, uracil DNA glycosylase; similar to Swiss-Prot Accession Number P12295, from E. coli
#2	MG288	300	Mycoplasma pneumoniae, MG288 homolog, from M. genitalium

Motif 1
GACAAAACTTTACCAAAACAG          	0	0	0
ATTCCGCTTGTACTCAAACAGAAAAGCACAG	0	85	1
CAATGTAAAGAACTGCAAAGCTGCTTAAACT	0	134	1
ACTGCAAAGCTGCTTAAACTGTCTTTGCAAG	0	145	1
TTTGCTTTGCAACTCTAAAACAAGCTTGCAA	0	169	0
   TTCATTGAGCCGCAAAGGCAGCAA    	1	7	1
ACAATTCCCCAACTGCAAAAGGAAATAAAAG	2	28	1
AGGAAATAAAAGCTGCTAATGACATTTTCCC	2	47	1
AAAAAGCCACTGCCCAAAAAGTCAAATAAGC	2	116	0
CCCGGTATTGAACCCGAAAGGTTTAGGGTTA	2	147	1
TATTGATGCTAGCTGAAACTGTTCAAACAAA	2	195	0
AGTGGTTTTGAAGTCAAACTGATTAAAACGC	2	232	1
TAACGTACCTTACTCTTAATGACAATGTCAT	2	263	0
TGCACTTCAAAGCTGTAACGTACCTTACTCT	2	278	0
          ***** *****
MAP Score: 9.92467

Motif 2
          CTGTTTTGGTAAAGTTTTGTCTTTAAT	0	0	1
AATGCTAAAGCTTTGTTTGTTGAATTAAAGACAAAAC	0	23	0
AAAGCTTTAGCATTTTTCATTATTTTTCTTATGATTT	0	46	1
TTTTTCTTATGATTTTTATTCCGCTTGTACTCAAACA	0	68	1
AGACTGCTCGCTGTGCTTTTCTGTTTGAGTACAAGCG	0	89	0
CTTGCAAAGACAGTTTAAGCAGCTTTGCAGTTCTTTA	0	139	0
CTTAAACTGTCTTTGCAAGCTTGTTTTAGAGTTGCAA	0	157	1
GTCATTAGCAGCTTTTATTTCCTTTTGCAGTTGGGGA	2	33	0
TTGGGCAGTGGCTTTTTCCCGGTATTGAACCCGAAAG	2	130	1
TAGCGGACAACGTTGCTAGTTTGTTTGAACAGTTTCA	2	176	1
ACAATGTCATGCGTTTTAATCAGTTTGACTTCAAAAC	2	236	0
          * *****  *    ***
MAP Score: 7.5231

Motif 3
GAATTAAAGACAAAACTTTACCAAAACAG        	0	2	0
TTTTGTCTTTAATTCAACAAACAAAGCTTTAGCATTT	0	24	1
AATCATAAGAAAAATAATGAAAAATGCTAAAGCTTTG	0	45	0
ATTCCGCTTGTACTCAAACAGAAAAGCACAGCGAGCA	0	85	1
CAGTTCTTTACATTGTAAAGAAAAGACTGCTCGCTGT	0	112	0
GCAACTCTAAAACAAGCTTGCAAAGACAGTTTAAGCA	0	155	0
        TTCATTGAGCCGCAAAGGCAGCAA     	1	2	1
TCCCCAACTGCAAAAGGAAATAAAAGCTGCTAATGAC	2	33	1
AGCCACTGCCCAAAAAGTCAAATAAGCGTGCTTCTAC	2	106	0
CTTTCGGGTTCAATACCGGGAAAAAGCCACTGCCCAA	2	130	0
GTTTTGAAGTCAAACTGATTAAAACGCATGACATTGT	2	236	1
          ****     * *** **
MAP Score: 6.32889

Motif 4
AAAATGCTAAAGCTTTGTTTGTTGAATTAAAGACAAAAC	0	23	0
ACAAAGCTTTAGCATTTTTCATTATTTTTCTTATGATTT	0	44	1
AGAAAAGCACAGCGAGCAGTCTTTTCTTTACAATGTAAA	0	104	1
AGAACTGCAAAGCTGCTTAAACTGTCTTTGCAAGCTTGT	0	142	1
AAATGTCATTAGCAGCTTTTATTTCCTTTTGCAGTTGGG	2	35	0
CCCGTGTAGAAGCACGCTTATTTGACTTTTTGGGCAGTG	2	101	1
          ***    *   **  ****
MAP Score: 4.7936

Motif 5
TCAACAAACAAAGCTTTAGCATTTTTCATTATTTTTCTTA	0	37	1
TCAAACAGAAAAGCACAGCGAGCAGTCTTTTCTTTACAAT	0	98	1
AAGAACTGCAAAGCTGCTTAAACTGTCTTTGCAAGCTTGT	0	141	1
CCCCGTGTAGAAGCACGCTTATTTGACTTTTTGGGCAGTG	2	100	1
AAACTGATTAAAACGCATGACATTGTCATTAAGAGTAAGG	2	247	1
          ****      *   *** **
MAP Score: 1.49335