AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i295_mixed10_mpneu_reg_100.orf -o295_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	RMP00361	287	Mycoplasma_pneumoniae
#2	RMP00363	27	Mycoplasma_pneumoniae
#3	RMP00366	26	Mycoplasma_pneumoniae

Motif number 1

tcctctctagaatcttataaaatcagaatagcgtaatt	1	12	0	aactaacaaa	    0.994201	-276
ggaattcccaaacctaaggcaagcgcaagatcattcat	1	69	0	aactaacgaa	    0.981398	-219
tttctatcaaaatctttaaaaaacagattcgtgataac	1	145	1	aactaacaat	    0.992461	-143
ataacccaccaatcaccgaaaaccaaattaaggcgatg	1	178	1	aacaaacaat	    0.990207	-110
aatgggtcgtaagctttctgaaacacaagtcaaggaaa	1	224	1	aactaacaaa	    0.994201	-64
ctccattaaaaaccagaagtaattaataa         	1	269	1	aacaaatata	    0.939848	-19
     aatttaaacaataacaattagttcagt      	2	6	1	aacaaatatt	    0.919295	-22
          ** **     ** ** **

Masking position 11
Map Score:   6.44385

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 77
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

attctagagaggattaagattaagatatag	1	37	1	ggattaagat	    0.923259	-251
tcttgcgcttgccttaggtttgggaattcc	1	77	1	gccttaggtt	    0.983247	-211
ggcatacatcgccttaatttggttttcggt	1	192	0	gccttaattt	    0.982288	-96
tttaatggagcgcataatttccttgacttg	1	249	0	cgcataattt	    0.893035	-39
ttgcttacacccattaagttaaattt    	3	11	1	ccattaagtt	    0.974784	-16
          **********

Masking position 5
Map Score:   0.643745

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 137
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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