AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_mgen_mpneu_100.orf -o257_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	RMG04338	167	Mycoplasma
#2	RMP00269	187	Mycoplasma_pneumoniae

Motif number 1

         TTTGTATTTAAAAATTAACAATA	1	2	1	TTGTATAAAA	    0.877692	-166
TTAGCGCTAATATCAGATAAATTTAAGATAAC	1	57	1	TATCATAAAT	    0.915905	-111
TAACTTTTACTTTCTTTTAAATTAGTTTTTAA	1	85	1	TTTCTTAAAT	    0.916708	-83
TCTTTTAAATTAGTTTTTAATTATTAAAATAT	1	97	1	TAGTTTAATT	    0.917538	-71
tatatgtggttagtaattaaaactaa      	2	5	0	tagtataaaa	     0.93107	-183
cttaatctactagtaaataaatcaggcacgct	2	67	1	tagtataaat	    0.980619	-121
taccgaaatagtgctgctaaattagcgtgcct	2	90	0	gtgcttaaat	    0.978167	-98
tatttcggtagtgttgctaaattatttttatt	2	112	1	gtgtttaaat	    0.970908	-76
aatgcttaaagtgcaaataaaaataatttagc	2	127	0	gtgcataaaa	    0.954707	-61
tattaacaattagcagttaaatgcttaaagtg	2	146	0	tagcataaat	    0.986187	-42
taactgctaattgttaataattggtagaatat	2	159	1	ttgtttaatt	     0.92962	-29
          *****  *****

Masking position 9
Map Score:   16.3842

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 210
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

TGTATTTAAAAATTAACAATATCTCACTAA	1	13	1	AATTAACAAT	    0.862508	-155
ACTAAATATTAATTAATGTTTAGCGCTAAT	1	38	1	AATTAATGTT	    0.846492	-130
ATTTATCTGATATTAGCGCTAAACATTAAT	1	49	0	TATTAGCGCT	    0.982694	-119
CTTTCTTTTAAATTAGTTTTTAATTATTAA	1	94	1	AATTAGTTTT	    0.689214	-74
CGTTGTCATGAATTGGCGTTATGTTCATAA	1	134	0	AATTGGCGTT	    0.977389	-34
tgtggttagtaattaaaactaa        	2	3	0	aattaaaact	    0.645195	-185
ttgagtgccttattggcaataaacgcttaa	2	42	1	tattggcaat	    0.863357	-146
agtgctgctaaattagcgtgcctgatttat	2	83	0	aattagcgtg	    0.922174	-105
aacactaccgaaatagtgctgctaaattag	2	97	0	aaatagtgct	     0.75852	-91
aaattatttttatttgcactttaagcattt	2	130	1	tatttgcact	    0.824756	-58
aattattaacaattagcagttaaatgctta	2	151	0	aattagcagt	     0.96783	-37
attggtagaatattgacggt          	2	178	1	tattgacggt	    0.857053	-10
          **********

Masking position 2
Map Score:   8.63022

Number of sites scoring better than the average of aligned sites = 425
Number in coding regions = 385
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

ACATTAATTAATATTTAGTGAGATATTGTT	1	27	0	ATATTTAGTG	    0.976759	-141
ATATTAATTAATGTTTAGCGCTAATATCAG	1	43	1	ATGTTTAGCG	    0.990147	-125
cacatatacaaggttgagtgccttattggc	2	29	1	aggttgagtg	      0.9883	-159
atttactagtagattaagcgtttattgcca	2	55	0	agattaagcg	    0.981657	-133
          **********

Masking position 5
Map Score:   2.2572

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 4
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

atatacaaggttgagtgccttattggcaat	2	32	1	ttgagtgcct	    0.971235	-156
gctgctaaattagcgtgcctgatttattta	2	80	0	tagcgtgcct	    0.992093	-108
actaccgaaatagtgctgctaaattagcgt	2	94	0	tagtgctgct	    0.982797	-94
actatttcggtagtgttgctaaattatttt	2	110	1	tagtgttgct	    0.989839	-78
          **********

Masking position 1
Map Score:   1.73859

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
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:   -7.57276e-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 6

          **********

No masking
Map Score:   -7.57276e-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 7

          **********

No masking
Map Score:   -7.57276e-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