AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_mgen_mpneu_300.orf -o198_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	RMG03275	66	Mycoplasma
#2	RMP00237	54	Mycoplasma_pneumoniae

Motif number 1

ATTACTTGAATTAATAGAAATCTTAAAACAT	1	11	1	TTAATAAAAT	    0.990499	-56
AATAGAAATCTTAAAACATATAATAATTTTA	1	23	1	TTAAAAATAT	    0.943249	-44
AAAAATATTGTTAATAAAATTATTATATGTT	1	37	0	TTAATAAATT	    0.987662	-30
        ATTAAATAGAAAAATATTGTTAA	1	54	0	TAAATAAAAA	    0.937904	-13
attatattgaccaataaatttaggaa     	2	6	0	ccaataattt	    0.953322	-49
aatttattggtcaatataatttaagtaaata	2	17	1	tcaataaatt	    0.988562	-38
caatataatttaagtaaatattagttagaag	2	28	1	taagtaatat	    0.944981	-27
          ****** ****

Masking position 6
Map Score:   9.34958

Number of sites scoring better than the average of aligned sites = 164
Number in coding regions = 127
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

AGATTTCTATTAATTCAAGTAAT       	1	4	0	TAATTCAAGT	    0.985007	-63
AATTATTATATGTTTTAAGATTTCTATTAA	1	21	0	TGTTTTAAGA	    0.896251	-46
AAACATATAATAATTTTATTAACAATATTT	1	36	1	TAATTTTATT	     0.93711	-31
attgaccaataaatttaggaa         	2	2	0	aaatttagga	    0.949674	-53
ttggtcaatataatttaagtaaatattagt	2	23	1	taatttaagt	    0.994377	-32
taatttaagtaaatattagttagaagcgtc	2	33	1	aaatattagt	    0.927144	-22
          **********

Masking position 4
Map Score:   5.33873

Number of sites scoring better than the average of aligned sites = 344
Number in coding regions = 298
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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