AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i326_mgen_mpneu_300.orf -o326_mgen_mpneu_300.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	RMG03712	200	Mycoplasma
#2	RMP00543	38	Mycoplasma_pneumoniae

Motif number 1

GCCTGATATCTATATACTAAATAGTGCCAT	1	12	1	TATATACTAA	    0.946056	-189
AACTTTTAATTTTTTACAAGTAGCTATTAG	1	49	1	TTTTTACAAG	    0.955111	-152
CTGGTAGTTTTCTTTACTAATAGCTACTTG	1	65	0	TCTTTACTAA	    0.964987	-136
ACTACCAGAAATTAAACTAGGATTACACTT	1	87	1	ATTAAACTAG	    0.954194	-114
CTAGGATTACACTTAAAAAAGTTAGTTTAA	1	103	1	ACTTAAAAAA	    0.690891	-98
TTTACTAGTTTTTAAACTAACTTTTTTAAG	1	114	0	TTTAAACTAA	    0.950535	-87
TATTAACACTTTTTTACTAGTTTTTAAACT	1	126	0	TTTTTACTAG	    0.977684	-75
AAAATTCACTAATTAACTAACAAAAATTAT	1	163	0	AATTAACTAA	    0.946083	-38
ATTTTAACTGAATATACAAGTAG       	1	188	1	AATATACAAG	    0.928493	-13
gatgagcttaattttaaaaatgtaaaataa	2	16	0	attttaaaaa	    0.699683	-23
          **********

Masking position 6
Map Score:   12.157

Number of sites scoring better than the average of aligned sites = 530
Number in coding regions = 437
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

GCTACTTGTAAAAAATTAAAAGTTAGAATTA	1	42	0	AAAAATTAAA	    0.972476	-159
TTACACTTAAAAAAGTTAGTTTAAAAACTAG	1	109	1	AAAAGTTATT	    0.883635	-92
AAGTTAGTTTAAAAACTAGTAAAAAAGTGTT	1	121	1	AAAAACTATA	    0.973344	-80
AAAACTAGTAAAAAAGTGTTAATACTCCTTA	1	132	1	AAAAAGTGTA	    0.953317	-69
ATTAACTAACAAAAATTATTAAGGAGTATTA	1	151	0	AAAAATTATA	    0.987731	-50
ATATTCAGTTAAAATTCACTAATTAACTAAC	1	172	0	AAAATTCATA	    0.930527	-29
cttaattttaaaaatgtaaaataacggcc  	2	9	0	aaaatgtaaa	    0.940117	-30
          ******** **

Masking position 4
Map Score:   6.09338

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 180
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

          **********

No masking
Map Score:   4.00336e-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 4

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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