AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00100_aquae_reg_100.orf -o00100_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	pgi	33	glucose-6-phosphate isomerase
#2	aq_759	152	hypothetical protein

Motif number 1

CTTCTTTCCCCTTATAATTTTTCCC      	1	19	1	CTTAAATTTT	    0.985003	-15
   CGCAATTAATAGAATTTAGCCTCTTTAG	2	8	1	AATAAATTTA	    0.940872	-145
GACTTTGTCCCATACACTATTTTGCTAAAGA	2	32	0	CATAACTATT	    0.958752	-121
ACAAAGTCTTAATACAATTTTATAAAGTTTT	2	55	1	AATAAATTTT	    0.979658	-98
TAATTCTTATCATAAAACTTTATAAAATTGT	2	68	0	CATAAACTTT	    0.989975	-85
AGAATTATTGCAAAAATTTTTAAAAGGAATA	2	92	1	CAAAATTTTT	    0.934384	-61
TTAAGGTTTACATATAATTTTATTATATTCC	2	117	0	CATAAATTTT	     0.98914	-36
          **** ******

Masking position 6
Map Score:   11.6979

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 97
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

CCATACACTATTTTGCTAAAGAGGCTAAAT	2	24	0	TTTTGCTAAA	    0.643303	-129
CTTTATAAAATTGTATTAAGACTTTGTCCC	2	52	0	TTGTATTAAG	    0.934809	-101
CTTAATACAATTTTATAAAGTTTTATGATA	2	62	1	TTTTATAAAG	    0.701012	-91
TTATAAAGTTTTATGATAAGAATTATTGCA	2	74	1	TTATGATAAG	    0.914843	-79
TTTTAAAAATTTTTGCAATAATTCTTATCA	2	87	0	TTTTGCAATA	     0.61368	-66
ATTGCAAAAATTTTTAAAAGGAATATAATA	2	98	1	TTTTTAAAAG	    0.780729	-55
TTACATATAATTTTATTATATTCCTTTTAA	2	111	0	TTTTATTATA	    0.871111	-42
          **********

Masking position 8
Map Score:   4.18469

Number of sites scoring better than the average of aligned sites = 671
Number in coding regions = 585
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

         TCTTTTCTCTTCTTTCCCCTT	1	2	1	CTTTTCTCTT	    0.985396	-32
CTTTTCTCTTCTTTCCCCTTATAATTTTTC	1	12	1	CTTTCCCCTT	    0.993844	-22
TTAATAGAATTTAGCCTCTTTAGCAAAATA	2	16	1	TTAGCCTCTT	    0.976362	-137
GTATTAAGACTTTGTCCCATACACTATTTT	2	40	0	TTTGTCCCAT	    0.976352	-113
          **********

Masking position 2
Map Score:   2.25856

Number of sites scoring better than the average of aligned sites = 390
Number in coding regions = 355
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   4.57179e-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:   4.57179e-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:   4.57179e-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