AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_aquae_reg_300.orf -o061_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	RAA00520	62	Aquifex_aeolicus
#2	RAA00521	27	Aquifex_aeolicus
#3	RAA00527	30	Aquifex_aeolicus
#4	RAA01661	39	Aquifex_aeolicus
#5	RAA01635	35	Aquifex_aeolicus

Motif number 1

CCTCCGAGACCTTTAAAATAGTATCATACCGC	1	17	1	CTTTAAAATT	    0.992374	-46
CGCCCTTTGTCGTTAAAATCATGTTTA     	1	46	1	CGTTAAAATT	    0.995056	-17
 TCTGCCACCCCTTAAGAGTTTTGAGAGTAT 	3	10	0	CCTTAAGAGT	    0.991072	-21
ATAAACTCTCCTTTAAGATATTCAAGTT    	4	7	0	CTTTAAGATT	    0.996601	-33
         AGGTTAAGATGATAAACTCTCCT	4	27	0	GGTTAAGATT	    0.992296	-13
          *********  *

Masking position 6
Map Score:   7.25583

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 27
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

AAAGGGCGGTATGATACTATTTTAAAGGTC	1	24	0	ATGATACTAT	    0.985922	-39
 TAAGTTTTTATTAGAATATCCTACATT  	2	10	1	ATTAGAATAT	    0.965939	-18
CTTAAGAGTTTTGAGAGTAT          	3	1	0	TTGAGAGTAT	     0.99186	-30
AATATCTTAAAGGAGAGTTTATCATCTTAA	4	17	1	AGGAGAGTTT	     0.95987	-23
CACCTCACTGTTTATACTATATACTTTAA 	5	10	0	TTTATACTAT	    0.959948	-26
          **********

Masking position 6
Map Score:   3.51307

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 162
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

        TTTCTACCTCCGAGACCTTTAA	1	3	1	TCTACCTCCG	    0.995185	-60
AAAATAGTATCATACCGCCCTTTGTCGTTA	1	31	1	CATACCGCCC	     0.99428	-32
          TCTGCCACCCCTTAAGAGTT	3	21	0	TCTGCCACCC	    0.996884	-10
          **********

Masking position 3
Map Score:   0.69657

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 30
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 4

TTTTAACGACAAAGGGCGGTATGATACTAT	1	34	0	AAAGGGCGGT	    0.994969	-29
CAAAACTCTTAAGGGGTGGCAGA       	3	18	1	AAGGGGTGGC	    0.993159	-13
GAATATCTTAAAGGAGAGTTTATCATCTTA	4	16	1	AAGGAGAGTT	    0.975715	-24
TATAGTATAAACAGTGAGGTGAAGGAA   	5	19	1	ACAGTGAGGT	    0.983643	-17
          **********

Masking position 1
Map Score:   1.77915

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 271
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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