AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_mpneu_reg_100.orf -o228_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

agtatttatttagtattatgcta       	1	4	0	tagtattatg	    0.979063	-297
ttaatattattagtatttatttagtattat	1	15	0	tagtatttat	    0.970529	-286
taaatactaataatattaagctattagtag	1	26	1	taatattaag	    0.982634	-275
agtaggtaaataatattaagataatattat	1	51	1	taatattaag	    0.982634	-250
aatattaagataatattatgttaaagaaaa	1	62	1	taatattatg	    0.943044	-239
atcttctatatagtatagagaaactttttc	1	87	0	tagtatagag	    0.875086	-214
tatagaagattagtatttaatagtaaacgg	1	107	1	tagtatttaa	    0.946369	-194
aaaaagaaagtggtatataggaaaatggaa	1	151	0	tggtatatag	    0.927028	-150
gctaccaacgtggtattaaaatgtgcccaa	1	186	0	tggtattaaa	    0.948228	-115
aataccatcagggtattaagatgctaccaa	1	208	0	gggtattaag	    0.939229	-93
aataccctgatggtattaatttcgtcggta	1	221	1	tggtattaat	    0.971569	-80
aatatttatttagtattattccggtattat	1	252	0	tagtattatt	    0.937822	-49
gcttaaattctaatatttatttagtattat	1	263	0	taatatttat	    0.921021	-38
       ttataatacttagcgctgtatc 	3	4	1	taatacttag	    0.840623	-19
          **********

Masking position 5
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

 tagcataatactaaataaatactaataat	1	10	1	actaaataaa	    0.922812	-291
gctattagtaggtaaataatattaagataa	1	45	1	ggtaaataat	    0.973404	-256
ataatattatgttaaagaaaaagtttctct	1	71	1	gttaaagaaa	    0.940789	-230
aatagtaaacggcaaacaaatttgttttcc	1	125	1	ggcaaacaaa	    0.968071	-176
ataggaaaatggaaaacaaatttgtttgcc	1	135	0	ggaaaacaaa	    0.973026	-166
gcccaaccgcgaaaaagaaagtggtatata	1	162	0	gaaaaagaaa	    0.873614	-139
taatttcgtcggtaaataataccggaataa	1	237	1	ggtaaataat	    0.973404	-64
ccggaataatactaaataaatattagaatt	1	258	1	actaaataaa	    0.922812	-43
          **********

Masking position 5
Map Score:   7.62454

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 222
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

          **********

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 4

          **********

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 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