AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_aquae_reg_300.orf -o301_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	RAA00292	187	Aquifex_aeolicus

Motif number 1

CTGGTGATATGGTTGCGGGGGCGGGATTTG	1	32	1	GGTTGCGGGG	    0.998651	-156
ATAACCCGGAGGTCGCGGGTTCAAATCCCG	1	53	0	GGTCGCGGGT	    0.993802	-135
CAGCCTGGTAGCTCGCCGGGCTCATAACCC	1	76	0	GCTCGCCGGG	    0.995043	-112
GGCAACGCGGGGTGGAGCAGCCTGGTAGCT	1	93	0	GGTGGAGCAG	    0.982637	-95
GGGAAAGGGGACTTGACGAGATAAGATTTT	1	142	0	ACTTGACGAG	    0.936425	-46
TTTTAACTCAAGTGGAGGGGAAAGGGGACT	1	159	0	AGTGGAGGGG	    0.995959	-29
          **********

Masking position 3
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	    0.986115	-164
GTTGCGGGGGCGGGATTTGAACCCGCGACC	1	43	1	CGGGATTTGA	    0.991439	-145
CCGCGACCTCCGGGTTATGAGCCCGGCGAG	1	65	1	CGGGTTATGA	     0.99144	-123
GGGGACTTGACGAGATAAGATTTTTTCTAT	1	136	0	CGAGATAAGA	    0.974313	-52
CTCAAGTGGAGGGGAAAGGGGACTTGACGA	1	153	0	GGGGAAAGGG	    0.980527	-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	    0.991188	-138
CTCCGGGTTATGAGCCCGGCGAGCTACCAG	1	72	1	TGAGCCCGGC	    0.994798	-116
GCGGGGTGGAGCAGCCTGGTAGCTCGCCGG	1	87	0	GCAGCCTGGT	    0.984052	-101
TAATAATTTGGCAACGCGGGGTGGAGCAGC	1	102	0	GCAACGCGGG	    0.984127	-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

ATCTAATAAAATAAAATCCC          	1	1	0	ATAAAATCCC	    0.987247	-187
CGCCCCCGCAACCATATCACCAGTATCTAA	1	25	0	ACCATATCAC	    0.947109	-163
AGGTCGCGGGTTCAAATCCCGCCCCCGCAA	1	44	0	TTCAAATCCC	    0.962141	-144
TAATATATAGAAAAAATCTTATCTCGTCAA	1	130	1	AAAAAATCTT	    0.904411	-58
CACTTGAGTTAAAATATCTCCTC       	1	175	1	AAAATATCTC	    0.970581	-13
          **********

Masking position 6
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