AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_aquae_reg_300.orf -o262_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	RAA01586	18	Aquifex_aeolicus
#2	RAA00631	49	Aquifex_aeolicus
#3	RAA00620	65	Aquifex_aeolicus

Motif number 1

GTGTTAAAATCCTCTTTAGGAGTAAGTTTA	2	11	1	CCTCTTTAGG	    0.990655	-39
  GTTTTGCCCCTCTTTCAGATAAACTTAC	2	32	0	CCTCTTTCAG	    0.998062	-18
AAAGAAGCACCCTTTTTCTCATAACCCCCA	3	35	0	CCTTTTTCTC	    0.995823	-31
AAAAAGGGTGCTTCTTTCTCTATTACTT  	3	48	1	CTTCTTTCTC	    0.995824	-18
          **********

Masking position 5
Map Score:   6.72456

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 101
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

          TTGTTAATATTTTTCCTT  	1	9	0	TTGTTAATAT	    0.881963	-10
          GTGTTAAAATCCTCTTTAGG	2	1	1	GTGTTAAAAT	    0.965153	-49
         AGTATTAAGATTAATACAATC	3	2	1	GTATTAAGAT	    0.885996	-64
          **********

Masking position 6
Map Score:   2.49933

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 8
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

          **********

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 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