AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i063_Glycine_Catabolism_aquae_reg_100.orf -o063_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	RAA00050	45	Aquifex_aeolicus
#2	RAA00054	20	Aquifex_aeolicus
#3	RAA00373	162	Aquifex_aeolicus
#4	RAA00814	27	Aquifex_aeolicus

Motif number 1

CTCTACAAAGAGGTAAAAGCC         	1	2	0	AGGTAAAAGC	    0.946728	-44
CAGGTGTTTATGGACATAGTAAAGGGGAGT	3	33	0	TGGACATAGT	    0.951156	-130
TAAACACCTGAAGGCAAAGTTCACGAACTT	3	53	1	AAGGCAAAGT	    0.965035	-110
CTTCGCAGGCTGGACAATGCCACTCCAGTA	3	80	1	TGGACAATGC	    0.971147	-83
ACCTCAATAATAGAAGAAGTAAGGGCTGTA	3	111	1	TAGAAGAAGT	     0.97345	-52
AAGGGCTGTAAGGGAAGAGCCGGAGTGTTT	3	131	1	AGGGAAGAGC	    0.955998	-32
         GTGGGAGATGTCAAACACTCC	3	152	0	TGGGAGATGT	    0.976452	-11
          TAGAAGAAGTATTTTATCTT	4	1	1	TAGAAGAAGT	     0.97345	-27
          **********

Masking position 3
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

ACTCTACAAAGAGGTAAAAGCC        	1	3	0	GAGGTAAAAG	    0.846848	-43
 AACTTCTTGGAGGTGGAAGG         	2	10	1	GAGGTGGAAG	    0.985061	-11
ACATAGTAAAGGGGAGTTTGCATAAAGTAG	3	20	0	GGGGAGTTTG	    0.957414	-143
TTTGCCTTCAGGTGTTTATGGACATAGTAA	3	41	0	GGTGTTTATG	    0.821137	-122
GAGGTGTACTGGAGTGGCATTGTCCAGCCT	3	86	0	GGAGTGGCAT	     0.85853	-77
TTCTATTATTGAGGTGTACTGGAGTGGCAT	3	96	0	GAGGTGTACT	    0.945032	-67
GAAGAAGTAAGGGCTGTAAGGGAAGAGCCG	3	123	1	GGGCTGTAAG	    0.970796	-40
GGGAAGAGCCGGAGTGTTTGACATCTCCCA	3	142	1	GGAGTGTTTG	    0.982378	-21
     TAGAAGAAGTATTTTATCTTAATTT	4	6	1	GAAGTATTTT	    0.680196	-22
          **********

Masking position 1
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	    0.987274	-144
GCGAAGTTCGTGAACTTTGCCTTCAGGTGT	3	56	0	TGAACTTTGC	    0.994187	-107
GCAAAGTTCACGAACTTCGCAGGCTGGACA	3	66	1	CGAACTTCGC	    0.988314	-97
CTTCGCAGGCTGGACAATGCCACTCCAGTA	3	80	1	TGGACAATGC	    0.976731	-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