AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i250_mgen_mpneu_100.orf -o250_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	RMG00426	270	Mycoplasma
#2	RMP00523	300	Mycoplasma_pneumoniae

Motif number 1

CCTATTGAGCTATGATGACAGTTGATCAAT	1	66	0	TATGATGACA	    0.860125	-205
accactgcggtattatgaaagattggatgg	2	46	1	tattatgaaa	    0.925974	-255
tgccacctactttggtggaaactgaatgaa	2	116	1	tttggtggaa	    0.961883	-185
caccaaatgttctggtgaaaaacccaaatg	2	148	0	tctggtgaaa	    0.982054	-153
caccagaacatttggtgaaaccacggaaaa	2	161	1	tttggtgaaa	    0.991433	-140
agaatcttatttttttgaaaaaaccgattt	2	236	0	ttttttgaaa	    0.852448	-65
cactgtgaaattttgtgaaatatagaatct	2	259	0	ttttgtgaaa	    0.980686	-42
tacggtgaaacactgtgaaattttgtgaaa	2	269	0	cactgtgaaa	    0.865253	-32
aatggtgaaatacggtgaaacactgtgaaa	2	279	0	tacggtgaaa	    0.984707	-22
        aaaatggtgaaatacggtgaaa	2	289	0	aatggtgaaa	    0.959367	-12
          **********

Masking position 6
Map Score:   14.6793

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 112
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

AAACTTTGGCACTTTTAGATTTAGATGTGATT	1	30	0	ACTTTTATTT	    0.875921	-241
TAAGTTGTAGTCATTTCATTTTGGACAAAAAG	1	227	1	TCATTTCTTT	    0.981268	-44
CTTAGCATAAAAATTTCTTTTTGTCCAAAATG	1	243	0	AAATTTCTTT	     0.83909	-28
ctcggttgcctcgtttattttttggatggtcc	2	84	0	tcgtttattt	    0.973385	-217
ctgaatgaaaacatttgggtttttcaccagaa	2	137	1	acatttgttt	    0.965065	-164
cgaaaccttgtcgtttcattttccgtggtttc	2	177	0	tcgtttcttt	     0.98801	-124
ttcttgacggtcgtttggatttttttcgcgaa	2	205	0	tcgtttgttt	     0.98263	-96
          *******  ***

Masking position 6
Map Score:   5.84233

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 48
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TAGGCAAATAAAGTTAATGGCGTCACCAACA	1	140	0	AAGTTATGGC	    0.936125	-131
CCAGTTATTTAACTGATAGGCAAATAAAGTT	1	156	0	AACTGAAGGC	    0.967209	-115
TCAGTTAAATAACTGGTAGGCTTTTTTATTG	1	171	1	AACTGGAGGC	    0.990819	-100
GGGTTAATTTAAGTTGTAGTCATTTCATTTT	1	218	1	AAGTTGAGTC	    0.971308	-53
ttagcttggacattgggagtcgaggcgttc 	2	10	0	cattggagtc	    0.928184	-291
cataataccgcagtggttgtccttagcttgg	2	32	0	cagtggtgtc	     0.98106	-269
gtttccaccaaagtaggtggcactcggttgc	2	107	0	aagtagtggc	     0.96822	-194
          ****** ****

Masking position 2
Map Score:   5.33907

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 19
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TTGCGGAGCTGAGGGTTACAGGTTCGATTC	1	109	1	GAGGGTTACA	     0.96193	-162
TTCGATTCCTGTTGGTGACGCCATTAACTT	1	131	1	GTTGGTGACG	    0.973641	-140
tgaaagattggatggtcacaatgggaccat	2	61	1	gatggtcaca	    0.991559	-240
ttattttttggatggtcccattgtgaccat	2	72	0	gatggtccca	    0.985697	-229
ttccaccaaagtaggtggcactcggttgcc	2	106	0	gtaggtggca	    0.950089	-195
          **********

Masking position 6
Map Score:   1.77535

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
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:   9.90086e-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:   9.90086e-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:   9.90086e-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