AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i036_mgen_mpneu_100.orf -o036_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	RMG04524	17	Mycoplasma
#2	RMP00409	157	Mycoplasma_pneumoniae
#3	RMP00412	30	Mycoplasma_pneumoniae
#4	RMP00414	37	Mycoplasma_pneumoniae

Motif number 1

        TGTTTTATTAATTTGGT     	1	6	0	TTTTATTAAT	    0.707291	-12
tttaactgccctctttttattgatctactg	2	20	0	ctctttttat	    0.898487	-138
aaaaaaagagcagtttaactgccctctttt	2	33	0	cagtttaact	    0.899245	-125
ttaaactgctctttttttatgtcttatttg	2	45	1	ctttttttat	    0.939869	-113
gtctataaaccattattacaggtcaaataa	2	68	0	cattattaca	    0.901042	-90
cgtctttaagcactttttaaaccatttttt	2	97	1	cactttttaa	    0.949237	-61
ctttttaaaccattttttcaattagtctta	2	109	1	cattttttca	    0.968635	-49
caattagtcttatttttaaaatttaaaaat	2	127	1	tatttttaaa	    0.953757	-31
tttaagtttttatttttaaattttaaaaat	2	138	0	tatttttaaa	    0.953757	-20
atcctctaattagtttatattttactact 	3	10	0	tagtttatat	    0.808521	-21
cctgcttacttagttttactctttacttta	4	13	0	tagttttact	     0.94978	-25
          **********

Masking position 6
Map Score:   11.9337

Number of sites scoring better than the average of aligned sites = 1251
Number in coding regions = 1108
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 2

tacaggtcaaataagacataaaaaaagagc	2	52	0	ataagacata	    0.928188	-106
aaagacgtctataaaccattattacaggtc	2	74	0	ataaaccatt	    0.967952	-84
atagacgtctttaagcactttttaaaccat	2	92	1	ttaagcactt	    0.939789	-66
taagcactttttaaaccattttttcaatta	2	103	1	ttaaaccatt	     0.95867	-55
atttttaaattttaaaaataagactaattg	2	127	0	tttaaaaata	    0.717197	-31
aaatttaaaaataaaaacttaaa       	2	145	1	ataaaaactt	    0.961555	-13
 agtagtaaaatataaactaattagaggat	3	10	1	atataaacta	    0.799508	-21
          **********

Masking position 2
Map Score:   3.14919

Number of sites scoring better than the average of aligned sites = 409
Number in coding regions = 358
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

gatcaataaaaagagggcagttaaactgct	2	25	1	aagagggcag	    0.993985	-133
aagacataaaaaaagagcagtttaactgcc	2	40	0	aaaagagcag	    0.986093	-118
      attaaagtaaagagtaaaactaag	4	5	1	aagtaaagag	    0.944752	-33
gagtaaaactaagtaagcaggttttt    	4	22	1	aagtaagcag	    0.994538	-16
          **********

Masking position 2
Map Score:   2.55968

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 31
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

agagcagtttaactgccctctttttattga	2	27	0	aactgccctc	    0.989582	-131
agggcagttaaactgctctttttttatgtc	2	38	1	aactgctctt	    0.971298	-120
atggtttaaaaagtgcttaaagacgtctat	2	92	0	aagtgcttaa	    0.940626	-66
      aaaaacctgcttacttagttttac	4	24	0	acctgcttac	    0.985537	-14
          **********

Masking position 4
Map Score:   0.567664

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 35
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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