AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_mpneu_reg_100.orf -o215_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	RMP00280	203	Mycoplasma_pneumoniae
#2	RMP00512	146	Mycoplasma_pneumoniae

Motif number 1

taagttagctttcaaaaaaagcatgttggta	1	17	1	ttcaaaaaag	    0.975005	-187
ttccccgtacttgaaacactgggatagctgc	1	72	1	ttgaaacctg	    0.928052	-132
catgagattgttcaaacaaagagcagctatc	1	94	0	ttcaaacaag	    0.993055	-110
agtttattaattaaaaagcagcttgacatga	1	120	0	ttaaaaacag	    0.969383	-84
atgttggttattaaaaccaggttagtaagtt	1	147	0	ttaaaacagg	    0.984391	-57
aatacgaaaattaaaaccaagcgagctcaac	1	182	1	ttaaaacaag	    0.994236	-22
cgccaaggatttaaaacaaatatgttttatg	2	103	1	ttaaaacaat	    0.957214	-44
          ******* ***

Masking position 6
Map Score:   10.2658

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 99
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 2

ggggaaacaggcaaccataaagggaccatg	1	48	0	gcaaccataa	    0.980155	-156
ggttttaataaccaacataagcaatacgaa	1	160	1	accaacataa	    0.983492	-44
atatacataaatatacataat         	2	2	0	atatacataa	    0.944584	-145
gatctgaatgatatacataaatatacataa	2	12	0	atatacataa	    0.944584	-135
tttggcaaagaaaaccataaaacatatttg	2	119	0	aaaaccataa	    0.937481	-28
ggttttctttgccaaaataacttt      	2	133	1	gccaaaataa	    0.884273	-14
          **********

Masking position 7
Map Score:   3.68319

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 56
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

    ccaaattaagttagctttcaaaaaaa	1	7	1	taagttagct	    0.908366	-197
cttgaaacactgggatagctgctctttgtt	1	81	1	tgggatagct	    0.983741	-123
cagcttgacatgagattgttcaaacaaaga	1	103	0	tgagattgtt	    0.972656	-101
gttttaattttcgtattgcttatgttggtt	1	169	0	tcgtattgct	    0.916692	-35
       ggttgagctcgcttggttttaat	1	191	0	tgagctcgct	    0.965291	-13
attcgcactttaatattgtttaattgggga	2	61	0	taatattgtt	    0.842168	-86
          **********

Masking position 6
Map Score:   0.927274

Number of sites scoring better than the average of aligned sites = 194
Number in coding regions = 174
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

cctgtttccccgtacttgaaacactgggat	1	67	1	cgtacttgaa	    0.987586	-137
gatcggaattcgtactgaaatcgtccccaa	2	38	1	cgtactgaaa	    0.982357	-109
tgaaatcgtccccaattaaacaatattaaa	2	53	1	cccaattaaa	    0.932112	-94
tgcgtttattcgcactttaatattgtttaa	2	68	0	cgcactttaa	    0.988131	-79
          **********

Masking position 6
Map Score:   0.675156

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 35
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:   2.79544e-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:   2.79544e-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:   2.79544e-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