AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_mgen_mpneu_100.orf -o099_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	RMG05422	23	Mycoplasma
#2	RMG04313	147	Mycoplasma
#3	RMP00232	241	Mycoplasma_pneumoniae

Motif number 1

     TTGAAAATTTTTTCAAAGTGCTT    	1	7	0	AATTTTTAAA	    0.989961	-17
    ATTTGCAATTAATAAAAATGCATTTCAT	2	7	1	AATTATAAAA	     0.89025	-141
TTCACAAGCCAATTAATTTAAATGAAATGCAT	2	28	0	AATTATTAAA	    0.981022	-120
AAACAGATTAAATCTTTTCTAAAGAGAATTCG	2	94	0	AATCTTTTAA	    0.938391	-54
GAAAAGATTTAATCTGTTTAAAAAGTGCTAAA	2	107	1	AATCTTTAAA	    0.979675	-41
AAAGTTTAGAAATTTCTTTAAA          	2	136	1	AATTTTTAAA	     0.98996	-12
ttcctttgctaatttctttttacgagaggctg	3	114	0	aattttttta	    0.830859	-128
gttgtgctttaagtagttaaaaacaacgattt	3	172	0	aagtattaaa	    0.961954	-70
gcttaattaaaagttggttaaaaagtaccgaa	3	219	1	aagttgtaaa	    0.918445	-23
          ***** ** ***

Masking position 2
Map Score:   11.9504

Number of sites scoring better than the average of aligned sites = 263
Number in coding regions = 236
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

    AAGCACTTTGAAAAAATTTTCAA   	1	7	1	TTTGAAAAAA	    0.926118	-17
  ATTTGCAATTAATAAAAATGCATTTCAT	2	9	1	TTAATAAAAA	    0.917274	-139
GCCAATTAATTTAAATGAAATGCATTTTTA	2	23	0	TTAAATGAAA	    0.923129	-125
TTAATTGGCTTGTGAAAAAACTAGACTAAA	2	44	1	TGTGAAAAAA	    0.775135	-104
CGAATTCTCTTTAGAAAAGATTTAATCTGT	2	94	1	TTAGAAAAGA	     0.91516	-54
TTTAGCACTTTTTAAACAGATTAAATCTTT	2	109	0	TTTAAACAGA	     0.75633	-39
          TTTAAAGAAATTTCTAAACT	2	138	0	TTTAAAGAAA	     0.96343	-10
ggttgaatgattaaaagaaaagcagcctct	3	92	1	ttaaaagaaa	    0.979762	-150
cagcctctcgtaaaaagaaattagcaaagg	3	114	1	taaaaagaaa	    0.872485	-128
ctttaagtagttaaaaacaacgattttctg	3	168	0	ttaaaaacaa	    0.894203	-74
tgcaacttgcttaattaaaagttggttaaa	3	211	1	ttaattaaaa	    0.733205	-31
          **********

Masking position 10
Map Score:   11.3889

Number of sites scoring better than the average of aligned sites = 847
Number in coding regions = 777
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

TTAGTCTAGTTTTTTCACAAGCCAATTAAT	2	43	0	TTTTTCACAA	    0.773318	-105
GATTAAATCTTTTCTAAAGAGAATTCGAAT	2	91	0	TTTCTAAAGA	    0.889073	-57
ACTTTAGCACTTTTTAAACAGATTAAATCT	2	111	0	TTTTTAAACA	    0.826293	-37
TTTAAAGAAATTTCTAAACTTTAGCACTTT	2	128	0	TTTCTAAACT	    0.720451	-20
ggctgcttttcttttaatcattcaaccaat	3	89	0	cttttaatca	    0.950431	-153
ttgctaatttctttttacgagaggctgctt	3	111	0	ctttttacga	    0.842353	-131
aaaatcgttgtttttaactacttaaagcac	3	171	1	tttttaacta	    0.952242	-71
ttttaaccaacttttaattaagcaagttgc	3	212	0	cttttaatta	     0.86668	-30
 tttcggtactttttaaccaacttttaatt	3	223	0	tttttaacca	    0.978833	-19
          **********

Masking position 5
Map Score:   7.05278

Number of sites scoring better than the average of aligned sites = 427
Number in coding regions = 379
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

          AAGCACTTTGAAAAAATTTT	1	1	1	AAGCACTTTG	    0.990158	-23
TTCTAAACTTTAGCACTTTTTAAACAGATT	2	117	0	TAGCACTTTT	    0.968912	-31
tggttagttttagcactagt          	3	1	0	tagcactagt	    0.910934	-241
ttagcaaaggaaacaattggcaaagaataa	3	134	1	aaacaattgg	    0.902336	-108
acttttaattaagcaagttgcatttcttag	3	203	0	aagcaagttg	    0.952568	-39
          **********

Masking position 5
Map Score:   0.568575

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 118
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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:   -4.73059e-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