AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i020_TCA_aquae_reg_100.orf -o020_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	RAA01423	295	Aquifex_aeolicus
#2	RAA01521	85	Aquifex_aeolicus

Motif number 1

TCACAGAATTAGGAAAATACTTTTTGCTAC	1	28	1	AGGAAAATAC	    0.982894	-268
TCAACTTAGGTGGTAAATTAAAAAGAGATG	1	135	1	TGGTAAATTA	    0.885211	-161
CCCACGATTAAGGAAAAAACAAGGATAAGT	1	200	0	AGGAAAAAAC	    0.922652	-96
CCTGTTTACAAGGTATATAATCGTGCCTCC	1	228	0	AGGTATATAA	      0.9466	-68
CCTTGTAAACAGGCAAATAAAGAACAGCAG	1	245	1	AGGCAAATAA	    0.994829	-51
CCTCCTTTTAAGGCAAATTATTAGTATATC	2	17	1	AGGCAAATTA	    0.988193	-69
CTAAAATTAAAGGCAATTAAAACCCCTTTT	2	53	1	AGGCAATTAA	    0.975575	-33
          **********

Masking position 5
Map Score:   9.50724

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 138
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AGGTGGTAAATTAAAAAGAGATGAGTGAAG	1	142	1	TTAAAAAGAG	     0.98821	-154
TGTAAATACAATAAAGAGAGCTTTGTCAAC	1	171	0	ATAAAGAGAG	    0.951119	-125
ATAATTTGCCTTAAAAGGAGGAAGCGA   	2	8	0	TTAAAAGGAG	    0.992346	-78
AAGCTCCTCCTGAAAAGGGGTTTTAATTGC	2	65	0	TGAAAAGGGG	    0.978074	-21
          **********

Masking position 5
Map Score:   1.93941

Number of sites scoring better than the average of aligned sites = 133
Number in coding regions = 108
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

AAAATTGGGTTTATTCGTAGCAAAAAGTAT	1	44	0	TTATTCGTAG	    0.987927	-252
AAGAAATTATTAATCCGTAGAGCATCAAAC	1	75	0	TAATCCGTAG	    0.943655	-221
GTATTTACACTTATCCTTGTTTTTTCCTTA	1	192	1	TTATCCTTGT	    0.865337	-104
TGTTTTTTCCTTAATCGTGGGAGGCACGAT	1	209	1	TTAATCGTGG	    0.973248	-87
TTAAGGCAAATTATTAGTATATCAAAATGC	2	24	1	TTATTAGTAT	    0.841227	-62
TTAATTGCCTTTAATTTTAGCATTTTGATA	2	43	0	TTAATTTTAG	    0.739365	-43
          **********

Masking position 3
Map Score:   0.907549

Number of sites scoring better than the average of aligned sites = 188
Number in coding regions = 175
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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