AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_mgen_mpneu_100.orf -o218_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	RMG02025	188	Mycoplasma
#2	RMP00219	21	Mycoplasma_pneumoniae
#3	RMP00220	157	Mycoplasma_pneumoniae

Motif number 1

TAATTCAACGTGTTTATTAATTA         	1	2	0	TGTTATTATT	    0.787115	-187
TAAGTAGGAGAATTTATTACTTCTAACCTTGG	1	60	0	AATTATTATT	    0.728919	-129
TTCTCCTACTTACTTATTACTTATAATAAATA	1	80	1	TACTATTATT	    0.874528	-109
TAATAAATATAGTTTTTATTTTTATTAATAAA	1	103	1	AGTTTTATTT	    0.738511	-86
TTTTTATTTTTATTAATAAATTCTCTCGATAT	1	115	1	TATTATAATT	    0.568939	-74
TAAATGGCTTTGTTAATTTGTTTAGATGTATA	1	163	0	TGTTATTTTT	    0.966553	-26
  cgaaacaatgttaataaacta         	2	9	1	tgttataact	     0.67573	-13
aatattaagttgttcataattaag        	3	3	0	tgttataata	    0.865309	-155
aacaacttaatattgttttattctttaatcgg	3	21	1	tatttttttt	    0.904169	-137
ggggtttgaatattatttatttggttttgttg	3	83	1	tatttttatt	    0.957712	-75
ttcacccgacaattgattaattaatgattatt	3	121	1	aattattatt	     0.64357	-37
aattaatgattattgatagtttcagtaga   	3	139	1	tattatagtt	    0.918732	-19
          **** **** **

Masking position 7
Map Score:   15.4907

Number of sites scoring better than the average of aligned sites = 483
Number in coding regions = 420
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 2

TTTATTAATAAATTCTCTCGATATTTTCGAT	1	123	1	AATCTCTCGA	    0.968517	-66
ccaagtggggaactgacccgattaaagaata	3	39	0	aatgacccga	    0.991395	-119
acccccgactaaaacaccccaagtggggaac	3	57	0	aaacacccca	    0.987715	-101
aaataatattcaaacccccgactaaaacacc	3	70	0	caacccccga	    0.986808	-88
ttgttggtggaattcacccgacaattgatta	3	109	1	aatcacccga	    0.997541	-49
          ** ********

Masking position 2
Map Score:   4.35553

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 1
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 3

GTTGAATTATAACAAAATTAGAAAACGGCT	1	25	1	AACAAAATTA	    0.981077	-164
TAAACAAATTAACAAAGCCATTTAACTT  	1	171	1	AACAAAGCCA	    0.984899	-18
       cgaaacaatgttaataaacta  	2	4	1	aacaatgtta	    0.975035	-18
taaagaataaaacaatattaagttgttcat	3	18	0	aacaatatta	    0.973103	-140
gaattccaccaacaaaaccaaataaataat	3	94	0	aacaaaacca	    0.983718	-64
          **********

Masking position 5
Map Score:   6.94868

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 127
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

ttttattctttaatcgggtcagttccccac	3	36	1	taatcgggtc	    0.959408	-122
tggggtgttttagtcgggggtttgaatatt	3	67	1	tagtcggggg	     0.99744	-91
ttatttggttttgttggtggaattcacccg	3	99	1	ttgttggtgg	    0.961089	-59
aattaatcaattgtcgggtgaattccacca	3	113	0	ttgtcgggtg	    0.996047	-45
          **********

Masking position 4
Map Score:   2.59187

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
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 5

          **********

No masking
Map Score:   3.43493e-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:   3.43493e-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:   3.43493e-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