AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i298_mixed13_aquae_reg_300.orf -o298_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	RAA00894	176	Aquifex_aeolicus
#2	RAA00898	53	Aquifex_aeolicus
#3	RAA01548	29	Aquifex_aeolicus

Motif number 1

TCTTCTCAAATTCTTCTACGGAAACGAATA	1	17	0	TTCTTCTACG	    0.997492	-160
GCCTTCCTTTATCTTCTTCTCAAATTCTTC	1	31	0	ATCTTCTTCT	    0.962374	-146
AAAGGAAGGCTTCTTCCTCGAGTACGCGAA	1	51	1	TTCTTCCTCG	    0.987825	-126
TTCCTCTATGTCCTTCTTCGGCGTCCCATA	1	97	0	TCCTTCTTCG	    0.987825	-80
CGTTTATGGTTTCCTCTATGTCCTTCTTCG	1	107	0	TTCCTCTATG	     0.98891	-70
GCGCGTCCTTTTTCTCTACGTTTATGGTTT	1	125	0	TTTCTCTACG	    0.977547	-52
TATTTTCCTTATCCTCTCCG          	3	1	0	ATCCTCTCCG	    0.984685	-29
       GATTTCTTCTATTTTCCTTATCC	3	17	0	TTCTTCTATT	    0.954146	-13
          **********

Masking position 5
Map Score:   16.3124

Number of sites scoring better than the average of aligned sites = 815
Number in coding regions = 767
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 2

TCTTCTACGGAAACGAATACGTAGT       	1	4	0	AAACGAACGT	    0.977415	-173
AGAAGAAGATAAAGGAAGGCTTCTTCCTCGAG	1	41	1	AAAGGAGCTT	    0.994785	-136
TAATTTCCGTAAACGTTCGCGTACTCGAGGAA	1	64	0	AAACGTGCGT	    0.971499	-113
AGAAGGACATAGAGGAAACCATAAACGTAGAG	1	110	1	AGAGGACCAT	    0.930157	-67
AACGTAGAGAAAAAGGACGCGCTCCTTATCAT	1	133	1	AAAAGAGCGC	    0.981615	-44
       TTTAAAGGCACCCTGGACGTCTATG	1	162	0	AAAGGACCTG	    0.975355	-15
ATAGCCTTTAAAAAGTAAGCTTGTAGAAATAT	2	22	1	AAAAGAGCTT	    0.989156	-32
          ***** * ****

Masking position 3
Map Score:   6.19045

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 347
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

TACTCGAGGAAGAAGCCTTCCTTTATCTTCT	1	44	0	AGAAGCCTCC	    0.759311	-133
TCTTCCTCGAGTACGCGAACGTTTACGGAAA	1	62	1	GTACGCGACG	    0.991382	-115
AATTACTATGGGACGCCGAAGAAGGACATAG	1	91	1	GGACGCCAAG	    0.986053	-86
TAGAGAAAAAGGACGCGCTCCTTATCATAGA	1	137	1	GGACGCGTCC	    0.966914	-40
AAGGCACCCTGGACGTCTATGATAAGGAGCG	1	152	0	GGACGTCATG	    0.976466	-25
          ******* ***

Masking position 3
Map Score:   2.05354

Number of sites scoring better than the average of aligned sites = 187
Number in coding regions = 174
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

AAATTCTTCTACGGAAACGAATACGTAGT 	1	10	0	ACGGAAACGA	    0.984532	-167
GCGAACGTTTACGGAAATTACTATGGGACG	1	76	1	ACGGAAATTA	    0.990248	-101
GGCACCCTGGACGTCTATGATAAGGAGCGC	1	151	0	ACGTCTATGA	    0.940443	-26
TTACTTTTTAAAGGCTATTATAAAAGTGT 	2	10	0	AAGGCTATTA	    0.971394	-44
CGGAGAGGATAAGGAAAATAGAAGAAATC 	3	11	1	AAGGAAAATA	    0.946922	-19
          **********

Masking position 7
Map Score:   3.01394

Number of sites scoring better than the average of aligned sites = 304
Number in coding regions = 288
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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