AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_aquae_reg_100.orf -o217_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01773	43	Aquifex_aeolicus
#2	RAA00886	18	Aquifex_aeolicus
#3	RAA00888	49	Aquifex_aeolicus

Motif number 1

ATTTAAAGGAGAGAGAAGGGC         	1	2	0	GAGAGAAGGG	    0.994399	-42
TTTTATTTAGGAGGATATTGGA        	1	32	1	GAGGATATTG	    0.983461	-12
  GCTTTAAGGAGGTAGGTG          	2	9	1	GAGGTAGGTG	    0.997092	-10
ATAATTTTCTGAGCCAATTGCAAAAGAGGT	3	23	1	GAGCCAATTG	    0.990836	-27
AATTGCAAAAGAGGTAAGGGAA        	3	38	1	GAGGTAAGGG	    0.998809	-12
          **********

Masking position 2
Map Score:   8.60748

Number of sites scoring better than the average of aligned sites = 371
Number in coding regions = 342
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

CTCTCTCCTTTAAATTTTTATTTAGGAGGA	1	17	1	TAAATTTTTA	    0.768905	-27
          CAAATTTATGTTATAATTTT	3	1	1	CAAATTTATG	    0.921351	-49
ATTTATGTTATAATTTTCTGAGCCAATTGC	3	14	1	TAATTTTCTG	    0.987171	-36
          **********

Masking position 3
Map Score:   0.872747

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 42
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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:   -5.44113e-14

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