AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_aquae_reg_300.orf -o111_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	RAA01171	28	Aquifex_aeolicus
#2	RAA01484	53	Aquifex_aeolicus
#3	RAA01691	70	Aquifex_aeolicus
#4	RAA01489	30	Aquifex_aeolicus
#5	RAA00533	32	Aquifex_aeolicus
#6	RAA00534	20	Aquifex_aeolicus

Motif number 1

ATTCTAAGTTAAAATTACACTT         	1	2	0	AAAATTACCT	    0.953538	-27
         GAACATTAGAATATTCTTATAT	2	2	1	AACATTAGAT	    0.970406	-52
AGTATATCACAATATAAGAATATTCTAATGT	2	13	0	AATATAAGAT	    0.974793	-41
CTTCCTCCAGAAATTTAGTATATCACAATAT	2	29	0	AAATTTAGAT	    0.982823	-25
TTATCAATTTAAAATAAGGCTT         	4	2	0	AAAATAAGCT	    0.988106	-29
      ACACAAAATTATCAATTTAAAATAA	4	16	0	AAAATTATAA	    0.903795	-15
GGATAAGGAAAATTTAAGGAAAAGAGAGGGA	5	11	0	AATTTAAGAA	    0.903382	-22
   AGGTGGTAAATTAATCCTTG        	6	8	1	AAATTAATCT	    0.939705	-13
          ******** **

Masking position 7
Map Score:   8.62806

Number of sites scoring better than the average of aligned sites = 216
Number in coding regions = 180
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

AAAAACATTCTAAGTTAAAATTACACTT  	1	9	0	TAAGTTAAAA	    0.987192	-20
TTATTTTTGTCAAGTTTCAAAATCACA   	3	8	0	CAAGTTTCAA	    0.964666	-63
CCAGAGTAAATAACTTAAAAGTTGAGTTTA	3	35	0	TAACTTAAAA	    0.976681	-36
ACAAAATTATCAATTTAAAATAAGGCTT  	4	9	0	CAATTTAAAA	    0.981749	-22
   CAAGGATTAATTTACCACCT       	6	4	0	TAATTTACCA	    0.960366	-17
          **********

Masking position 5
Map Score:   4.80222

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 58
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

     ACCTCTTCCTCCAGAAATTTAGTAT	2	39	0	TTCCTCCAGA	    0.981384	-15
TTTAAGTTATTTACTCTGGTAAACGGAGGA	3	46	1	TTACTCTGGT	    0.983371	-25
      AACTTTCCTCCGTTTACCAGAGTA	3	57	0	TTCCTCCGTT	    0.995761	-14
          TCCCTCTCTTTTCCTTAAAT	5	1	1	TCCCTCTCTT	    0.979762	-32
          **********

Masking position 5
Map Score:   1.52885

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 267
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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