AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i133_Transmembrane_Transport_7_aquae_reg_100.orf -o133_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	RAA01643	114	Aquifex_aeolicus

Motif number 1

    GAATTCCCGCCTTCTGGAACGGAATGG	1	7	1	CCGCCTCTGG	    0.999236	-108
TCAGCGGCTACTGCCATTCCGTTCCAGAAGG	1	20	0	CTGCCTTCCG	    0.981314	-95
ATGGCAGTAGCCGCTGACTGGATGAGTGCCG	1	34	1	CCGCTACTGG	    0.984334	-81
GTAGAGTGCTCCGCCATACTGATGAAGGAAG	1	65	0	CCGCCTACTG	    0.991662	-50
GGAGCACTCTACGCCCTCGGGTACGACGACT	1	84	1	ACGCCTCGGG	    0.997895	-31
GCCCTCGGGTACGACGACTCGCCTACATA  	1	96	1	ACGACACTCG	    0.978823	-19
          ***** *****

Masking position 3
Map Score:   9.38476

Number of sites scoring better than the average of aligned sites = 300
Number in coding regions = 277
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

TTCCCGCCTTCTGGAACGGAATGGCAGTAGCCGC	1	14	1	CTGACGATGG	    0.998239	-101
TAGCCGCTGACTGGATGAGTGCCGCTTCCTTCAT	1	41	1	CTGAGGGCCG	    0.996994	-74
GTGCCGCTTCCTTCATCAGTATGGCGGAGCACTC	1	59	1	CTTACGATGG	    0.993135	-56
         TATGTAGGCGAGTCGTCGTACCCGA	1	100	0	ATGAGGGTCG	    0.995612	-15
          *** * * * ****

Masking position 5
Map Score:   0.828241

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 27
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

GCTGACTGGATGAGTGCCGCTTCCTTCATC	1	46	1	TGAGTGCCGC	    0.997227	-69
CCGAGGGCGTAGAGTGCTCCGCCATACTGA	1	74	0	AGAGTGCTCC	    0.914959	-41
          **********

Masking position 5
Map Score:   0.164721

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 10
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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 5

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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