AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i267_hypothetical12_aquae_reg_100.orf -o267_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	RAA01463	148	Aquifex_aeolicus
#2	RAA01560	69	Aquifex_aeolicus
#3	RAA01561	17	Aquifex_aeolicus

Motif number 1

GGTTCGAGTCCCGCCGGGCACACCACTTAA	1	14	0	CCGCCGGGCA	    0.999174	-135
ATCCGCCTGAGCTACGGGCACTACCACTAA	1	75	1	GCTACGGGCA	    0.996324	-74
   CTTTCCACCTCCGGTTAGTATATTCTA	2	53	0	CCTCCGGTTA	    0.994418	-17
    AAAACTCCTCCGGGCCT         	3	2	0	CCTCCGGGCC	    0.997878	-16
          **********

Masking position 5
Map Score:   7.93671

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 23
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

CGCCGGGCACACCACTTAATCT        	1	3	0	ACCACTTAAT	    0.991759	-146
TACGGGCACTACCACTAAATAAATATTATA	1	87	1	ACCACTAAAT	    0.994252	-62
         AATCCTTAAATTTTAATTCCT	1	138	0	ATCCTTAAAT	    0.973538	-11
TTACTTAATTATCCTTTAATTTATTTTTAT	2	11	1	ATCCTTTAAT	    0.962457	-59
TATATTCTAACCCACTACATAATAAAAATA	2	32	0	CCCACTACAT	    0.972313	-38
          **********

Masking position 6
Map Score:   5.10694

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 46
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

CCCGTAGCTCAGGCGGATAGAGCGCGAGAT	1	63	0	AGGCGGATAG	    0.997431	-86
CTTTTTCTGTAGGCGAAAGGATATATAATA	1	110	0	AGGCGAAAGG	    0.995282	-39
TACTAACCGGAGGTGGAAAG          	2	60	1	AGGTGGAAAG	    0.996031	-10
          **********

Masking position 7
Map Score:   3.08868

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 28
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

CCCGGCGGGACTCGAACCCGCGACCTCGAG	1	26	1	CTCGAACCCG	    0.992472	-123
GATTCCTAATCTCGAGGTCGCGGGTTCGAG	1	36	0	CTCGAGGTCG	    0.996951	-113
GATTAGGAATCTCGCGCTCTATCCGCCTGA	1	55	1	CTCGCGCTCT	    0.994377	-94
   AAAACTCCTCCGGGCCT          	3	1	0	CTCCGGGCCT	     0.99073	-17
          **********

Masking position 2
Map Score:   2.85886

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 24
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

ACTACCACTAAATAAATATTATATATCCTT	1	94	1	AATAAATATT	    0.778997	-55
CAGAAAAAGGAATTAAAATTTAAGGATT  	1	131	1	AATTAAAATT	    0.778997	-18
CCCACTACATAATAAAAATAAATTAAAGGA	2	22	0	AATAAAAATA	    0.957835	-48
          **********

Masking position 5
Map Score:   0.99145

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 32
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 6

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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 8

          **********

No masking
Map Score:   2.15595e-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