AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_aquae_reg_300.orf -o182_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	RAA00853	79	Aquifex_aeolicus
#2	RAA01214	215	Aquifex_aeolicus
#3	RAA00663	44	Aquifex_aeolicus

Motif number 1

TTCAAGAATAAGGAGTGGAAG         	1	2	0	AGGAGTGGAA	    0.981919	-78
CTAAACATGTATGAAAAGAAATTACATTCA	1	28	0	ATGAAAAGAA	    0.909668	-52
GGAAATTTACGGAAAGGGAGTTGAGAATAA	2	44	0	GGAAAGGGAG	    0.937068	-172
AGGAAAAGAAGGGAAGGGTGGCTCCCTGTG	2	73	0	GGGAAGGGTG	    0.964563	-143
CGACCTTAAGAGGAAAAGAAGGGAAGGGTG	2	83	0	AGGAAAAGAA	    0.980821	-133
GAAACCCGGAAGGAAGAGCGACCTTAAGAG	2	101	0	AGGAAGAGCG	     0.98464	-115
GGAATGGAAAATGAGGAGAGTAAAGGTTAA	2	143	0	ATGAGGAGAG	    0.975125	-73
TGATCTACGGAGGAATGGAAAATGAGGAGA	2	154	0	AGGAATGGAA	    0.985039	-62
AAGTTCTAAAAGGAGGAGAAATCC      	3	31	1	AGGAGGAGAA	    0.993575	-14
          **********

Masking position 4
Map Score:   14.5123

Number of sites scoring better than the average of aligned sites = 1586
Number in coding regions = 1456
Number in noncoding regions = 130
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 2

TCTTGAATGTAATTTCTTTTCATACATGTT	1	25	1	AATTTCTTTT	    0.802847	-55
ACTAGGATAAAATAACATTAC         	1	69	1	AATAACATTA	    0.899637	-11
     GAAGCAAAATCTTTAACGTTAATCC	2	6	1	AAAATCTTTA	     0.91747	-210
TTTCCTTGGTAAAAGCTTAACCTTTACTCT	2	127	1	AAAAGCTTAA	    0.873034	-89
CCGTAGATCAGAAAACTTTATTATACATAA	2	174	1	GAAAACTTTA	    0.928699	-42
AAATTTAAAGAAAAACTTATGTATAATAAA	2	190	0	AAAAACTTAT	    0.907139	-26
       AGGAATAAATTTAAAGAAAAACT	2	203	0	AATAAATTTA	    0.847441	-13
CTTATTTTAAAATATCTTTT          	3	1	0	AATATCTTTT	    0.909731	-44
          **********

Masking position 2
Map Score:   5.92316

Number of sites scoring better than the average of aligned sites = 633
Number in coding regions = 559
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 3

 CTTCCACTCCTTATTCTTGAATGTAATTTC	1	10	1	CTTATTCTGA	     0.98397	-70
TCCAGGCGTGCTTATTCTCAACTCCCTTTCC	2	33	1	CTTATTCTAA	    0.982716	-183
CTTTACTCTCCTCATTTTCCATTCCTCCGTA	2	148	1	CTCATTTTCA	    0.970892	-68
TAAAGAAAAACTTATGTATAATAAAGTTTTC	2	184	0	CTTATGTAAA	    0.860864	-32
TTTAGAACTTCTTATTTTAAAATATCTTTT 	3	10	0	CTTATTTTAA	    0.985609	-35
 GGATTTCTCCTCCTTTTAGAACTTCTTATT	3	25	0	CTCCTTTTGA	    0.957347	-20
          ******** **

Masking position 5
Map Score:   3.94902

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 40
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

          **********

No masking
Map Score:   -4.94948e-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:   -4.94948e-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:   -4.94948e-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