AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_mixed4_aquae_reg_100.orf -o319_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	RAA01527	35	Aquifex_aeolicus
#2	RAA00564	129	Aquifex_aeolicus
#3	RAA01083	37	Aquifex_aeolicus

Motif number 1

TTATTATATAAGTGGTAAGGAGTTTACG  	1	18	1	AGTGGTAAGG	    0.965683	-18
TCTTGGCTATCCGGGGTAGCTCAATCGGCA	2	33	1	CCGGGGTAGC	    0.993336	-97
CAATCGGCAGAGCGGGTGGCTGTTAACCAC	2	54	1	AGCGGGTGGC	    0.991605	-76
CTGTTAACCACCTGGTTGGGGGTTCGAGTC	2	73	1	CCTGGTTGGG	    0.992059	-57
GAAATGGCTCCGGGGGAGGGACTCGAACCC	2	92	0	CGGGGGAGGG	    0.997991	-38
          **********

Masking position 5
Map Score:   5.35841

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 157
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

CACTTATATAATAAGTTTAAC         	1	2	0	ATAAGTTTAA	    0.942804	-34
ATAAGTGGTAAGGAGTTTACG         	1	25	1	AGGAGTTTAC	    0.993565	-11
ACCCCCAACCAGGTGGTTAACAGCCACCCG	2	66	0	AGGTGGTTAA	    0.993835	-64
AGTAAAACTCAGGAGGTTAAAA        	3	26	1	AGGAGGTTAA	    0.997548	-12
          **********

Masking position 7
Map Score:   5.35212

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 120
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

     GTTAAACTTATTATATAAGTGGTAAG	1	6	1	ACTTATATAT	    0.973799	-30
         AAATTAAGGTTTTATAATTTTA	2	2	1	AATTAAGTTT	    0.975507	-128
       AGGAATTATTGTATTGTGGAAATG	2	116	0	AATTATGTAT	     0.97491	-14
CCTGAGTTTTACTTAAAATTTATACTTT   	3	8	0	ACTTAAATTT	     0.97491	-30
          ****** ****

Masking position 5
Map Score:   1.34636

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 33
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

CCGGATAGCCAAGATAAAATTATAAAACCT	2	17	0	AAGATAAAAT	    0.965075	-113
         AAAGTATAAATTTTAAGTAAA	3	2	1	AAGTATAAAT	    0.976716	-36
TATAAATTTTAAGTAAAACTCAGGAGGTTA	3	15	1	AAGTAAAACT	    0.984546	-23
          **********

Masking position 7
Map Score:   0.357849

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 78
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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