AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_aquae_reg_300.orf -o133_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	RAA01642	300	Aquifex_aeolicus
#2	RAA01643	114	Aquifex_aeolicus

Motif number 1

TATCCATAACACACCTCCCTTGGAATTTTG	1	27	0	ACACCTCCCT	    0.872214	-274
GGCTATTAGAGCTCCTCCGTAAGAAACGAG	1	125	0	GCTCCTCCGT	    0.988894	-176
ATTCGGATTCCCCGCTCACTACTGGATAAG	1	184	1	CCCGCTCACT	    0.960369	-117
ATTACCGAAAGCTGTGCACTTATCCAGTAG	1	202	0	GCTGTGCACT	    0.887519	-99
GGCTTACTCCTCCACTCCGTATTTTTTATC	1	281	0	TCCACTCCGT	    0.962261	-20
AGCGGCTACTGCCATTCCGTTCCAGAAGGC	2	19	0	GCCATTCCGT	    0.950671	-96
AATGGCAGTAGCCGCTGACTGGATGAGTGC	2	33	1	GCCGCTGACT	    0.948229	-82
CTGGATGAGTGCCGCTTCCTTCATCAGTAT	2	51	1	GCCGCTTCCT	    0.977679	-64
GGCGTAGAGTGCTCCGCCATACTGATGAAG	2	69	0	GCTCCGCCAT	    0.941123	-46
GGCGGAGCACTCTACGCCCTCGGGTACGAC	2	81	1	TCTACGCCCT	    0.947165	-34
          **********

Masking position 10
Map Score:   8.88736

Number of sites scoring better than the average of aligned sites = 812
Number in coding regions = 738
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 2

AAATTCCAAGGGAGGTGTGTTATGGATAAA	1	29	1	GGAGGTGTGT	    0.958411	-272
AAGAAAAGCTGGAGGCCTACCACAAAGCCA	1	57	1	GGAGGCCTAC	    0.907571	-244
CGTTTCTTACGGAGGAGCTCTAATAGCCAA	1	127	1	GGAGGAGCTC	    0.990314	-174
GCTCACTACTGGATAAGTGCACAGCTTTCG	1	197	1	GGATAAGTGC	    0.955288	-104
AATACGGAGTGGAGGAGTAAGCC       	1	288	1	GGAGGAGTAA	    0.983446	-13
GCCGCTGACTGGATGAGTGCCGCTTCCTTC	2	43	1	GGATGAGTGC	    0.993955	-72
TCATCAGTATGGCGGAGCACTCTACGCCCT	2	71	1	GGCGGAGCAC	    0.987581	-44
          **********

Masking position 2
Map Score:   8.64406

Number of sites scoring better than the average of aligned sites = 270
Number in coding regions = 247
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

AATCACTGTTTAAAGCGGGAACTACTATATTCG	1	156	1	TAAGCGGGAT	     0.98071	-145
TTATCCAGTAGTGAGCGGGGAATCCGAATATAG	1	180	0	GGAGCGGGAT	    0.996927	-121
TTCCGTTCCAGAAGGCGGGAATTC         	2	2	0	GAGGCGGGAT	    0.997891	-113
CACTCATCCAGTCAGCGGCTACTGCCATTCCGT	2	29	0	GCAGCGGCAT	    0.989068	-86
TACTGATGAAGGAAGCGGCACTCATCCAGTCAG	2	47	0	GAAGCGGCCC	    0.971369	-68
CGTCGTACCCGAGGGCGTAGAGTGCTCCGCCAT	2	79	0	GGGGCGTAAT	    0.920841	-36
       TATGTAGGCGAGTCGTCGTACCCGAG	2	99	0	GAGGCGAGCT	    0.980107	-16
          * ******* * *

Masking position 7
Map Score:   6.00183

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 183
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

TCAGTATTTACATAACAAAATTCCAAGGGAGG	1	12	1	CATAACAAAT	    0.990489	-289
TTTCTTTATCCATAACACACCTCCCTTGGAAT	1	31	0	CATAACACAT	    0.991183	-270
ATGTAAGGGTCATAACAATTCTGCTCATAATT	1	87	1	CATAACAATT	    0.986428	-214
CTCTAATAGCCAAATCACTGTTTAAAGCGGGA	1	144	1	CAAATCACTT	    0.904182	-157
CGAAAATCTCCACAACAAAGGTAATTACCGAA	1	223	0	CACAACAAAT	    0.983894	-78
          *********  *

Masking position 7
Map Score:   2.84051

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 11
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -6.44162e-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:   -6.44162e-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:   -6.44162e-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