AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i221_mgen_mpneu_100.orf -o221_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	RMG02253	110	Mycoplasma
#2	RMP00624	300	Mycoplasma_pneumoniae

Motif number 1

AAACTCGATAATAACTAAAAGCCATAAAAC	1	17	1	ATAACTAAAA	    0.869619	-94
AAACAAGCTAAAAACCACAAAACCAAGGTT	1	44	0	AAAACCACAA	     0.98426	-67
ATTATGCAGTAAAACTGCAATAATATTGTT	1	76	0	AAAACTGCAA	    0.974567	-35
TGCATAATGTAAAATTACACAGC       	1	98	1	AAAATTACAC	    0.971675	-13
actattgaataaaactaaaacaatcgttat	2	73	1	aaaactaaaa	    0.981306	-228
atctacacctaaaaccacaataacgattgt	2	92	0	aaaaccacaa	     0.98426	-209
aaaccaaacgaaatctacacctaaaaccac	2	104	0	aaatctacac	    0.922263	-197
tgtccactgaaaaaccaaacgaaatctaca	2	115	0	aaaaccaaac	    0.968501	-186
tcagtggacaaaaattgcccaccgaaaaat	2	135	1	aaaattgccc	    0.834796	-166
tgcccaccgaaaaattaacaccttgacgtt	2	150	1	aaaattaaca	     0.88098	-151
       cgaaacattaaaatgtaatacgt	2	288	0	aacattaaaa	    0.784108	-13
          **********

Masking position 1
Map Score:   16.8986

Number of sites scoring better than the average of aligned sites = 470
Number in coding regions = 425
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

TAATAACTAAAAGCCATAAAACCTTGGTTT	1	25	1	AAGCCATAAA	    0.866474	-86
AACAAGCTAAAAACCACAAAACCAAGGTTT	1	43	0	AAACCACAAA	     0.98423	-68
TTATGCAGTAAAACTGCAATAATATTGTTA	1	75	0	AAACTGCAAT	    0.927157	-36
tctacacctaaaaccacaataacgattgtt	2	91	0	aaaccacaat	    0.987843	-210
ctactgttacaaaccgaattgtgaaaccgt	2	206	1	aaaccgaatt	    0.935002	-95
ccgaattgtgaaaccgtgtttttaccacaa	2	219	1	aaaccgtgtt	    0.944621	-82
tgaacgagacaaaccacgtattacatttta	2	273	1	aaaccacgta	    0.969927	-28
          **********

Masking position 2
Map Score:   6.00525

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 69
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

         TCAATAAAACTCGATAATAAC	1	2	1	CAATAAAACT	    0.859212	-109
TAACTAAAAGCCATAAAACCTTGGTTTTGT	1	28	1	CCATAAAACC	    0.972831	-83
AAGCTAAAAACCACAAAACCAAGGTTTTAT	1	40	0	CCACAAAACC	    0.985529	-71
tctgtatccaacacaattccctaaaaatcc	2	23	1	acacaattcc	    0.929361	-278
gtagactattgaataaaactaaaacaatcg	2	69	1	gaataaaact	    0.720295	-232
acacctaaaaccacaataacgattgtttta	2	88	0	ccacaataac	    0.818699	-213
gtccactgaaaaaccaaacgaaatctacac	2	114	0	aaaccaaacg	    0.732491	-187
gaattattcttaataattcctcgaacgtca	2	173	0	taataattcc	    0.837518	-128
gaattattaagaataattcctcctactgtt	2	184	1	gaataattcc	    0.888555	-117
aaacacggtttcacaattcggtttgtaaca	2	210	0	tcacaattcg	    0.871467	-91
gtttttaccacaaccaatcgttagtaatta	2	236	1	caaccaatcg	    0.894144	-65
          **********

Masking position 6
Map Score:   6.91227

Number of sites scoring better than the average of aligned sites = 394
Number in coding regions = 359
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

AGGTTTTATGGCTTTTAGTTATTATCGAGT	1	19	0	GCTTTTAGTT	    0.880093	-92
        GCTGTGTAATTTTACATTATGC	1	99	0	TGTGTAATTT	     0.89044	-12
tttagggaattgtgttggatacagatttat	2	18	0	tgtgttggat	    0.924939	-283
caataacgattgttttagttttattcaata	2	75	0	tgttttagtt	    0.953179	-226
tgtggttttaggtgtagatttcgtttggtt	2	103	1	ggtgtagatt	    0.949193	-198
cgaacgtcaaggtgttaatttttcggtggg	2	152	0	ggtgttaatt	    0.976769	-149
          **********

Masking position 5
Map Score:   0.767728

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 190
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   -8.57325e-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:   -8.57325e-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:   -8.57325e-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