AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mpneu_reg_100.orf -o216_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	RMP00094	55	Mycoplasma_pneumoniae
#2	RMP00182	150	Mycoplasma_pneumoniae
#3	RMP00183	81	Mycoplasma_pneumoniae
#4	RMP00184	65	Mycoplasma_pneumoniae

Motif number 1

tttatctatacgtagaaataataaaaaaat	1	20	1	cgtagaaata	    0.963098	-36
gcgcaagatcgttagaaacagtcttttcga	2	68	0	gttagaaaca	    0.935891	-83
     agttaggtaaaactacctaacggca	3	6	1	ggtaaaacta	    0.991291	-76
agacttgattggtaaaaataagatta    	3	66	1	ggtaaaaata	    0.992769	-16
gttcaaagagggttaaaacagtgattttca	4	14	0	ggttaaaaca	    0.971694	-52
gtttaagtaaggtcaaactacctgttcaaa	4	37	0	ggtcaaacta	    0.980871	-29
          **********

Masking position 6
Map Score:   7.02046

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 95
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

agcaagtcctcatccaaaaatcctttgaat	2	39	1	catccaaaaa	    0.898493	-112
aaatcctttgaatcgaaaagactgtttcta	2	56	1	aatcgaaaag	    0.953169	-95
cggaatagcaaagcgcaagatcgttagaaa	2	80	0	aagcgcaaga	    0.976244	-71
cagcggaaaacagcgcaaagaaaaaagtcg	2	108	0	cagcgcaaag	    0.993208	-43
aagacataagcagcggaaaacagcgcaaag	2	118	0	cagcggaaaa	    0.994373	-33
ttttaaaataaagcggataattatacattg	3	34	0	aagcggataa	    0.965189	-48
          **********

Masking position 7
Map Score:   4.90451

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 153
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

aaaaataaataattaaagcacc        	1	44	1	aattaaagca	    0.952126	-12
caagatcgtctagcgaagcaagtcctcatc	2	23	1	tagcgaagca	     0.98121	-128
aaagtcggaatagcaaagcgcaagatcgtt	2	85	0	tagcaaagcg	    0.990908	-66
tctccttttaaaataaagcggataattata	3	39	0	aaataaagcg	    0.962139	-43
          aatcgaagcgtttaagtaag	4	56	0	aatcgaagcg	    0.990908	-10
          **********

Masking position 6
Map Score:   4.76775

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 87
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          agttaggtaaaactacctaa	3	1	1	agttaggtaa	    0.990846	-81
tatacattgccgttaggtagttttacctaa	3	13	0	cgttaggtag	     0.98709	-69
gaagcgtttaagtaaggtcaaactacctgt	4	42	0	agtaaggtca	    0.980986	-24
          **********

Masking position 5
Map Score:   0.169295

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 8
Number in noncoding regions = 2
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:   -6.1574e-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:   -6.1574e-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:   -6.1574e-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