AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_aquae_reg_300.orf -o135_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	RAA01681	297	Aquifex_aeolicus

Motif number 1

TCTCCCAGCTGAGCTACCGCCCCTACTGACAG	1	65	0	GACACCGCCC	    0.993445	-233
CCATATCGGCGCTCTCCCAGCTGAGCTACCGC	1	77	0	GCCCCCAGCT	    0.998151	-221
GAGGGGACTCGAACCCCCGACCTCCGACATGC	1	108	0	GACCCCGACC	    0.997532	-190
AGTCCCCTCCGCTCCACCAGTTGAGCTGCTAA	1	131	1	GCCACCAGTT	    0.974363	-167
TCTACCAACTGAGCTACCGGCTCTTAGCAGCT	1	154	0	GACACCGGCT	     0.99818	-144
AAAGGCCGTTGCTCTACCAACTGAGCTACCGG	1	166	0	GCCACCAACT	    0.993968	-132
GGCGGGACTCGAACCCGCGACCCACGGCTTAA	1	197	0	GACCGCGACC	    0.984415	-101
CGGGTTCGAGTCCCGCCCGGCTCACCATATAA	1	212	1	TCCCCCGGCT	    0.993538	-86
          ** * *******

Masking position 8
Map Score:   17.3955

Number of sites scoring better than the average of aligned sites = 92
Number in coding regions = 67
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

ATGTATTATAGATACTTGAAACCTTCATTTAAA	1	14	1	GAACTGAACC	    0.997483	-284
TGACAGAATAGAAATTATAATCCTTTTAAATGA	1	38	0	GAATTTAACC	    0.987204	-260
TGGAGCGGAGGGGACTCGAACCCCCGACCTCCG	1	114	0	GGACTGAACC	    0.998548	-184
GTAGAGCAACGGCCTTTTAAGCCGTGGGTCGCG	1	181	1	GGCTTTAACC	    0.981921	-117
TGAGCCGGGCGGGACTCGAACCCGCGACCCACG	1	203	0	GGACTGAACC	    0.998548	-95
          ** *** *** **

Masking position 6
Map Score:   8.45775

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 29
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

AGTAGGGGCGGTAGCTCAGCTGGGAGAGCG	1	70	1	GTAGCTCAGC	    0.896044	-228
CCGGCTCTTAGCAGCTCAACTGGTGGAGCG	1	140	0	GCAGCTCAAC	    0.794453	-158
CTAAGAGCCGGTAGCTCAGTTGGTAGAGCA	1	159	1	GTAGCTCAGT	    0.988321	-139
TTAAAAGGCCGTTGCTCTACCAACTGAGCT	1	171	0	GTTGCTCTAC	    0.623961	-127
          **********

Masking position 6
Map Score:   6.27321

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 5
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

AATAGAAATTATAATCCTTTTAAATGAAGGTTT	1	32	0	ATAACTTTAA	    0.953673	-266
TTGGTAGAGCAACGGCCTTTTAAGCCGTGGGTC	1	178	1	AACGCTTTAA	    0.922231	-120
CCGGCTCACCATATAACTATCAAATAATTTGAC	1	228	1	ATATCTTCAA	    0.990707	-70
TAGCTTTTAAATCTTGCTGTCAAATTATTTGAT	1	246	0	ATCTCTTCAA	    0.994075	-52
TACTATTAGTATATAGCTTTTAAATCTTGCTGT	1	259	0	ATATCTTTAA	    0.985473	-39
CTAATAGTAGATCTTTTTCTCAATA        	1	283	1	ATCTTTTCAA	    0.962903	-15
          ****  ** ****

Masking position 8
Map Score:   4.58059

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 54
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   3.29282e-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:   3.29282e-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:   3.29282e-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