AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i036_Acetate_Metabolism_mpneu_reg_100.orf -o036_mpneu_100.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMP00409	157	Mycoplasma_pneumoniae
#2	RMP00412	30	Mycoplasma_pneumoniae
#3	RMP00414	37	Mycoplasma_pneumoniae

Motif number 1

tttaactgccctctttttattgatctactgc	1	19	0	ctctttttat	    0.983842	-139
agttaaactgctctttttttatgtcttattt	1	43	1	ctctttttta	    0.990203	-115
ctttttttatgtcttatttgacctgtaataa	1	55	1	gtcttattta	    0.910656	-103
cgtctataaaccattattacaggtcaaataa	1	68	0	ccattattaa	    0.966812	-90
cgtctttaagcactttttaaaccattttttc	1	97	1	cactttttaa	    0.975611	-61
actttttaaaccattttttcaattagtctta	1	108	1	ccatttttta	    0.966812	-50
tcaattagtcttatttttaaaatttaaaaat	1	126	1	ttatttttaa	    0.957319	-32
 tttaagtttttatttttaaattttaaaaat	1	138	0	ttatttttaa	    0.957319	-20
      aatcctctaattagtttatatttta	2	16	0	ctctaattat	      0.8343	-15
          ********* *

Masking position 7
Map Score:   11.3867

Number of sites scoring better than the average of aligned sites = 331
Number in coding regions = 241
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 2

acaggtcaaataagacataaaaaaagagca	1	51	0	taagacataa	    0.956892	-107
aagacgtctataaaccattattacaggtca	1	73	0	taaaccatta	     0.98361	-85
tagacgtctttaagcactttttaaaccatt	1	93	1	taagcacttt	    0.883659	-65
aagcactttttaaaccattttttcaattag	1	104	1	taaaccattt	    0.964727	-54
tttttaaattttaaaaataagactaattga	1	126	0	ttaaaaataa	    0.840429	-32
aatttaaaaataaaaacttaaa        	1	146	1	taaaaactta	    0.924111	-12
     agtagtaaaatataaactaattaga	2	6	1	taaaatataa	    0.901407	-25
          **********

Masking position 3
Map Score:   4.89696

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 192
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 3

aaaaaaagagcagtttaactgccctctttt	1	33	0	cagtttaact	    0.972694	-125
ttttttcaattagtcttatttttaaaattt	1	121	1	tagtcttatt	    0.934945	-37
       tttaagtttttatttttaaattt	1	145	0	aagtttttat	    0.939533	-13
atcctctaattagtttatattttactact 	2	10	0	tagtttatat	    0.964787	-21
cctgcttacttagttttactctttacttta	3	13	0	tagttttact	    0.988639	-25
          **********

Masking position 6
Map Score:   2.88865

Number of sites scoring better than the average of aligned sites = 120
Number in coding regions = 92
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

tcaataaaaagagggcagttaaactgctct	1	27	1	gagggcagtt	    0.990027	-131
gacataaaaaaagagcagtttaactgccct	1	38	0	aagagcagtt	     0.97132	-120
atagacgtctttaagcactttttaaaccat	1	92	1	ttaagcactt	    0.943644	-66
gtaaaactaagtaagcaggttttt      	3	24	1	gtaagcaggt	     0.98631	-14
          **********

Masking position 7
Map Score:   0.733922

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 73
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   1.44541e-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:   1.44541e-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 7

          **********

No masking
Map Score:   1.44541e-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