AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_mpneu_reg_100.orf -o312_mpneu_100.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMP00155	300	Mycoplasma_pneumoniae
#2	RMP00158	67	Mycoplasma_pneumoniae
#3	RMP00161	22	Mycoplasma_pneumoniae

Motif number 1

       tagcataatactaaataaatact	1	4	1	cataatacta	    0.977455	-297
ataatactaaataaatactaataatattaa	1	15	1	ataaatacta	    0.968286	-286
ctactaatagcttaatattattagtattta	1	26	0	cttaatatta	    0.981295	-275
ataatattatcttaatattatttacctact	1	51	0	cttaatatta	    0.981295	-250
ttttctttaacataatattatcttaatatt	1	62	0	cataatatta	    0.938844	-239
gaaaaagtttctctatactatatagaagat	1	87	1	ctctatacta	    0.866581	-214
ccgtttactattaaatactaatcttctata	1	107	0	ttaaatacta	    0.942399	-194
ttccattttcctatataccactttcttttt	1	151	1	ctatatacca	    0.921743	-150
ttgggcacattttaataccacgttggtagc	1	186	1	tttaatacca	    0.944386	-115
ttggtagcatcttaataccctgatggtatt	1	208	1	cttaataccc	    0.934765	-93
taccgacgaaattaataccatcagggtatt	1	221	0	attaatacca	    0.969404	-80
ataataccggaataatactaaataaatatt	1	252	1	aataatacta	    0.933262	-49
ataatactaaataaatattagaatttaagc	1	263	1	ataaatatta	    0.915341	-38
 gatacagcgctaagtattataa       	3	4	0	ctaagtatta	    0.830226	-19
          **********

Masking position 7
Map Score:   26.1014

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 122
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

tatcttaatattatttacctactaatagct	1	44	0	ttatttacct	    0.948326	-257
gagaaactttttctttaacataatattatc	1	70	0	ttctttaaca	    0.905593	-231
gaaaacaaatttgtttgccgtttactatta	1	124	0	ttgtttgccg	     0.98511	-177
gcaaacaaatttgttttccattttcctata	1	136	1	ttgttttcca	    0.972164	-165
atataccactttctttttcgcggttgggca	1	163	1	ttctttttcg	    0.937825	-138
tattccggtattatttaccgacgaaattaa	1	236	0	ttatttaccg	     0.98647	-65
          **********

Masking position 5
Map Score:   4.61546

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 134
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

tattattagtatttatttagtattatgcta	1	11	0	atttatttag	    0.987165	-290
ccctgatggtattaatttcgtcggtaaata	1	225	1	attaatttcg	    0.973659	-76
aaattctaatatttatttagtattattccg	1	259	0	atttatttag	    0.987165	-42
          **********

Masking position 5
Map Score:   2.09894

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 1
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

ttacctactaatagcttaatattattagta	1	30	0	atagcttaat	    0.963504	-271
taacataatattatcttaatattatttacc	1	55	0	ttatcttaat	    0.962304	-246
gcggttgggcacattttaataccacgttgg	1	182	1	acattttaat	     0.94602	-119
cacgttggtagcatcttaataccctgatgg	1	204	1	gcatcttaat	      0.9832	-97
          **********

Masking position 6
Map Score:   0.564192

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 27
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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