AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i270_hypothetical15_aquae_reg_100.orf -o270_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	RAA01204	80	Aquifex_aeolicus
#2	RAA01206	40	Aquifex_aeolicus

Motif number 1

     CTTTCTCCTCCTTTATTTAAGATAA	1	6	1	TCCTCCTTTA	    0.998117	-75
    TCCGCTACCTCCTTTAAAGTTTTTAG	1	65	0	ACCTCCTTTA	    0.995257	-16
          TCTCCCTTTCTCCTTTTCCT	2	1	1	TCTCCCTTTC	    0.996795	-40
CCCTTTCTCCTTTTCCTTTCTTTTAAGATT	2	14	1	TTTTCCTTTC	    0.992562	-27
          **********

Masking position 7
Map Score:   7.91504

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 282
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

TCCTCCTTTATTTAAGATAAGTGTAACTCT	1	16	1	TTTAAGATAA	    0.980249	-65
TATATCAGTATGTAAGAGTTACACTTATCT	1	30	0	TGTAAGAGTT	    0.967943	-51
TTAAAGTTTTTAGAAGATTATATCAGTATG	1	48	0	TAGAAGATTA	    0.974298	-33
GCTACCTCCTTTAAAGTTTTTAGAAGATTA	1	58	0	TTAAAGTTTT	    0.931907	-23
TTTCCTTTCTTTTAAGATTAAATCTT    	2	25	1	TTTAAGATTA	    0.993908	-16
          **********

Masking position 5
Map Score:   4.8656

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 179
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

TCAGTATGTAAGAGTTACACTTATCTTAAA	1	26	0	AGAGTTACAC	    0.984452	-55
TCTTACATACTGATATAATCTTCTAAAAAC	1	43	1	TGATATAATC	    0.980635	-38
         AAGATTTAATCTTAAAAGAAA	2	30	0	AGATTTAATC	    0.993706	-11
          **********

Masking position 7
Map Score:   0.890733

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 29
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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