AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i015_mgen_mpneu_100.orf -o015_mgen_mpneu_100.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.36
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG01475	200	Mycoplasma
#2	RMG00395	18	Mycoplasma
#3	RMP00535	19	Mycoplasma_pneumoniae
#4	RMP00540	206	Mycoplasma_pneumoniae

Motif number 1

TCACTAATTAACTAACAAAAATTATTAAGGA	1	34	1	ACTAAAAAAA	    0.975443	-167
TAGTTTAAAAACTAGTAAAAAAGTGTTAATA	1	66	0	ACTAGAAAAA	    0.993178	-135
CTAGGATTACACTTAAAAAAGTTAGTTTAAA	1	88	0	ACTTAAAAAG	    0.903694	-113
ACAAGTAGCTATTAGTAAAGAAAACTACCAG	1	127	0	ATTAGAAAGA	     0.93803	-74
ACTAATAGCTACTTGTAAAAAATTAAAAGTT	1	142	1	ACTTGAAAAA	      0.9911	-59
attgagatttagtagcaaaaattgaagttag	4	18	0	agtagaaaaa	    0.976391	-189
ctttgggcaaatttgaaaaaatttcgattga	4	44	0	atttgaaaaa	      0.9741	-163
          ***** *****

Masking position 7
Map Score:   9.31258

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 95
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

GTTAATTAGTGAATTTTAACTGAATATACAAGTAG  	1	9	0	GTTTTAACAT	    0.976677	-192
AAATTCACTAATTAACTAACAAAAATTATTAAGGAGT	1	30	1	AAACTAACTT	    0.759215	-171
AATTATTAAGGAGTATTAACACTTTTTTACTAGTTTT	1	53	1	GTATTAACTT	    0.976686	-148
TTTTTTACTAGTTTTTAAACTAACTTTTTTAAGTGTA	1	75	1	GTTTAAACTT	    0.976687	-126
AAAACTACCAGAAATTAAACTAGGATTACACTTAAAA	1	101	0	GATTAAACTT	    0.938788	-100
ATAGTGCCATTAATTCTAACTTTTAATTTTTTACAAG	1	153	0	TTTCTAACAT	    0.896041	-48
        acggtttctaacttcaatttttgctacta	4	3	1	gttctaactt	    0.994521	-204
cgcacttttcgctttctaacgcgtcttctttgcggca	4	135	1	gttctaactt	    0.994521	-72
          *  *******     **

Masking position 9
Map Score:   5.52735

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 98
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

ATTTTAACTGAATATACAAGTAG       	1	4	0	AATATACAAG	     0.97357	-197
ACTACCAGAAATTAAACTAGGATTACACTT	1	105	0	ATTAAACTAG	    0.870579	-96
TTAGTAAAGAAAACTACCAGAAATTAAACT	1	117	0	AAACTACCAG	    0.815855	-84
AACTTTTAATTTTTTACAAGTAGCTATTAG	1	143	0	TTTTTACAAG	    0.837565	-58
   GTTGTAAATTATATAAGG         	2	2	0	ATTATATAAG	    0.897441	-17
cattcaaagcattataccagatcaatgatc	4	170	1	attataccag	    0.986655	-37
          **********

Masking position 6
Map Score:   1.10636

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 75
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

          **********

No masking
Map Score:   -2.10731e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -2.10731e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -2.10731e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0