AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_mpneu_reg_300.orf -o228_mpneu_300.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	    0.977996	-297
ttaatattattagtatttatttagtattat	1	15	0	tagtatttat	    0.969041	-286
taaatactaataatattaagctattagtag	1	26	1	taatattaag	    0.981746	-275
agtaggtaaataatattaagataatattat	1	51	1	taatattaag	    0.981746	-250
aatattaagataatattatgttaaagaaaa	1	62	1	taatattatg	    0.940256	-239
atcttctatatagtatagagaaactttttc	1	87	0	tagtatagag	     0.86943	-214
tatagaagattagtatttaatagtaaacgg	1	107	1	tagtatttaa	    0.943734	-194
aaaaagaaagtggtatataggaaaatggaa	1	151	0	tggtatatag	    0.923519	-150
gctaccaacgtggtattaaaatgtgcccaa	1	186	0	tggtattaaa	    0.945678	-115
aataccatcagggtattaagatgctaccaa	1	208	0	gggtattaag	    0.936266	-93
aataccctgatggtattaatttcgtcggta	1	221	1	tggtattaat	    0.970133	-80
aatatttatttagtattattccggtattat	1	252	0	tagtattatt	    0.934795	-49
gcttaaattctaatatttatttagtattat	1	263	0	taatatttat	    0.917248	-38
       ttataatacttagcgctgtatc 	3	4	1	taatacttag	    0.833703	-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

attattagtatttatttagtattatgcta 	1	10	0	tttatttagt	    0.918146	-291
ttatcttaatattatttacctactaatagc	1	45	0	attatttacc	    0.971704	-256
agagaaactttttctttaacataatattat	1	71	0	tttctttaac	    0.937136	-230
ggaaaacaaatttgtttgccgtttactatt	1	125	0	tttgtttgcc	    0.966039	-176
ggcaaacaaatttgttttccattttcctat	1	135	1	tttgttttcc	      0.9713	-166
tatataccactttctttttcgcggttgggc	1	162	1	tttctttttc	    0.866404	-139
ttattccggtattatttaccgacgaaatta	1	237	0	attatttacc	    0.971704	-64
aattctaatatttatttagtattattccgg	1	258	0	tttatttagt	    0.918146	-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