AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i077_mgen_mpneu_100.orf -o077_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	RMG02346	48	Mycoplasma
#2	RMP00559	44	Mycoplasma_pneumoniae

Motif number 1

AAAATTAAGATAAATAATTTTCCAATTTTG	1	23	1	TAAATAATTT	    0.951774	-26
       TGAAAACAAAATTGGAAAATTAT	1	36	0	AAACAAAATT	    0.977151	-13
        attaacgaattttaattctatt	2	3	1	taacgaattt	     0.99009	-42
aattttttaataatagaattaaaattcgtt	2	14	0	taatagaatt	    0.962407	-31
attctattattaaaaaatttaaacagaagc	2	25	1	taaaaaattt	    0.990779	-20
          **********

Masking position 7
Map Score:   7.36223

Number of sites scoring better than the average of aligned sites = 195
Number in coding regions = 172
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

TATCTTAATTTTAAGCAATAAGTA      	1	5	0	TTAAGCAATA	     0.96143	-44
TTGCTTAAAATTAAGATAAATAATTTTCCA	1	17	1	TTAAGATAAA	    0.887182	-32
         TGAAAACAAAATTGGAAAATT	1	38	0	GAAAACAAAA	     0.94836	-11
tttaattctattattaaaaaatttaaacag	2	21	1	ttattaaaaa	    0.875264	-24
attaaaaaatttaaacagaagc        	2	33	1	ttaaacagaa	    0.979067	-12
          **********

Masking position 3
Map Score:   2.66368

Number of sites scoring better than the average of aligned sites = 739
Number in coding regions = 663
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   5.21701e-14

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:   5.21701e-14

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:   5.21701e-14

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