AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i063_Glycine_Catabolism_aquae_reg_300.orf -o063_aquae_300.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	RAA00050	45	Aquifex_aeolicus
#2	RAA00054	20	Aquifex_aeolicus
#3	RAA00373	162	Aquifex_aeolicus
#4	RAA00814	27	Aquifex_aeolicus

Motif number 1

         GGCTTTTACCTCTTTGTAGAG	1	2	1	GCTTTTACCT	    0.931814	-44
ACTCCCCTTTACTATGTCCATAAACACCTG	3	33	1	ACTATGTCCA	      0.9374	-130
AAGTTCGTGAACTTTGCCTTCAGGTGTTTA	3	53	0	ACTTTGCCTT	    0.955002	-110
TACTGGAGTGGCATTGTCCAGCCTGCGAAG	3	80	0	GCATTGTCCA	      0.9628	-83
TACAGCCCTTACTTCTTCTATTATTGAGGT	3	111	0	ACTTCTTCTA	    0.965747	-52
AAACACTCCGGCTCTTCCCTTACAGCCCTT	3	131	0	GCTCTTCCCT	    0.943524	-32
GGAGTGTTTGACATCTCCCAC         	3	152	1	ACATCTCCCA	    0.969593	-11
AAGATAAAATACTTCTTCTA          	4	1	0	ACTTCTTCTA	    0.965747	-27
          **********

Masking position 8
Map Score:   7.593

Number of sites scoring better than the average of aligned sites = 1148
Number in coding regions = 1090
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 2

        GGCTTTTACCTCTTTGTAGAGT	1	3	1	CTTTTACCTC	     0.84926	-43
         CCTTCCACCTCCAAGAAGTT 	2	10	0	CTTCCACCTC	    0.985334	-11
CTACTTTATGCAAACTCCCCTTTACTATGT	3	20	1	CAAACTCCCC	     0.95817	-143
TTACTATGTCCATAAACACCTGAAGGCAAA	3	41	1	CATAAACACC	     0.82387	-122
AGGCTGGACAATGCCACTCCAGTACACCTC	3	86	1	ATGCCACTCC	    0.860788	-77
ATGCCACTCCAGTACACCTCAATAATAGAA	3	96	1	AGTACACCTC	    0.945996	-67
CGGCTCTTCCCTTACAGCCCTTACTTCTTC	3	123	0	CTTACAGCCC	    0.971322	-40
TGGGAGATGTCAAACACTCCGGCTCTTCCC	3	142	0	CAAACACTCC	    0.982699	-21
AAATTAAGATAAAATACTTCTTCTA     	4	6	0	AAAATACTTC	    0.684254	-22
          **********

Masking position 10
Map Score:   4.12976

Number of sites scoring better than the average of aligned sites = 1378
Number in coding regions = 1247
Number in noncoding regions = 131
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 3

CATAGTAAAGGGGAGTTTGCATAAAGTAGA	3	19	0	GGGAGTTTGC	    0.988479	-144
GCGAAGTTCGTGAACTTTGCCTTCAGGTGT	3	56	0	TGAACTTTGC	     0.99483	-107
GCAAAGTTCACGAACTTCGCAGGCTGGACA	3	66	1	CGAACTTCGC	    0.989608	-97
CTTCGCAGGCTGGACAATGCCACTCCAGTA	3	80	1	TGGACAATGC	    0.979336	-83
          **********

Masking position 4
Map Score:   1.76746

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 50
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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