AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_aquae_reg_100.orf -o301_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	RAA00292	187	Aquifex_aeolicus

Motif number 1

CAAATCCCGCCCCCGCAACCATATCACCAG	1	32	0	CCCCGCAACC	    0.998644	-156
CGGGATTTGAACCCGCGACCTCCGGGTTAT	1	53	1	ACCCGCGACC	    0.993774	-135
GGGTTATGAGCCCGGCGAGCTACCAGGCTG	1	76	1	CCCGGCGAGC	    0.995035	-112
AGCTACCAGGCTGCTCCACCCCGCGTTGCC	1	93	1	CTGCTCCACC	    0.982539	-95
AAAATCTTATCTCGTCAAGTCCCCTTTCCC	1	142	1	CTCGTCAAGT	    0.936084	-46
AGTCCCCTTTCCCCTCCACTTGAGTTAAAA	1	159	1	CCCCTCCACT	    0.995936	-29
          **********

Masking position 8
Map Score:   9.22325

Number of sites scoring better than the average of aligned sites = 256
Number in coding regions = 210
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

ATTAGATACTGGTGATATGGTTGCGGGGGC	1	24	1	GGTGATATGG	    0.986842	-164
GTTGCGGGGGCGGGATTTGAACCCGCGACC	1	43	1	CGGGATTTGA	     0.99189	-145
CCGCGACCTCCGGGTTATGAGCCCGGCGAG	1	65	1	CGGGTTATGA	    0.991891	-123
GGGGACTTGACGAGATAAGATTTTTTCTAT	1	136	0	CGAGATAAGA	    0.975642	-52
CTCAAGTGGAGGGGAAAGGGGACTTGACGA	1	153	0	GGGGAAAGGG	    0.981543	-35
          **********

Masking position 4
Map Score:   4.2632

Number of sites scoring better than the average of aligned sites = 176
Number in coding regions = 157
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

GGGCGGGATTTGAACCCGCGACCTCCGGGT	1	50	1	TGAACCCGCG	     0.99077	-138
CTCCGGGTTATGAGCCCGGCGAGCTACCAG	1	72	1	TGAGCCCGGC	    0.994669	-116
GCGGGGTGGAGCAGCCTGGTAGCTCGCCGG	1	87	0	GCAGCCTGGT	    0.983408	-101
TAATAATTTGGCAACGCGGGGTGGAGCAGC	1	102	0	GCAACGCGGG	    0.984316	-86
          **********

Masking position 3
Map Score:   1.06333

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 41
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          GGGATTTTATTTTATTAGAT	1	1	1	GGGATTTTAT	    0.987319	-187
TTAGATACTGGTGATATGGTTGCGGGGGCG	1	25	1	GTGATATGGT	    0.947391	-163
TTGCGGGGGCGGGATTTGAACCCGCGACCT	1	44	1	GGGATTTGAA	    0.962348	-144
TTGACGAGATAAGATTTTTTCTATATATTA	1	130	0	AAGATTTTTT	     0.90489	-58
       GAGGAGATATTTTAACTCAAGTG	1	175	0	GAGATATTTT	    0.970725	-13
          **********

Masking position 5
Map Score:   1.89661

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 299
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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:   3.50598e-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