AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_aquae_reg_300.orf -o142_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	RAA01041	178	Aquifex_aeolicus
#2	RAA00851	170	Aquifex_aeolicus

Motif number 1

ATTAATTATATAAGGAGAACTTTTTGAACT	1	42	1	TAAGGAGAAC	    0.992651	-137
CTTTTTGAACTATGAAAAACAGTTATTATA	1	61	1	TATGAAAAAC	    0.911556	-118
TATGTAGAGATAAGCAAATCTTATAATAAC	1	82	0	TAAGCAAATC	    0.983326	-97
TTTTATACATTAAGAAGTATTAAGGAATTC	1	118	1	TAAGAAGTAT	    0.856568	-61
TAAGAAGTATTAAGGAATTCAAAATATAAA	1	128	1	TAAGGAATTC	    0.985068	-51
        GGTAAGCAGTTCACGTAGAGAA	2	3	1	TAAGCAGTTC	    0.982044	-168
ACACCCGCTATAAGGAAAACGAGGAAGCTG	2	111	0	TAAGGAAAAC	    0.991139	-60
          **********

Masking position 6
Map Score:   10.274

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 166
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

ATAAGGAGAACTTTTTGAACTATGAAAAAC	1	51	1	CTTTTTGAAC	    0.858763	-128
ACATAATGCCCTTTTATACATTAAGAAGTA	1	107	1	CTTTTATACA	    0.776976	-72
AATATGGCTTCTCTACGTGAACTGCTTACC	2	11	0	CTCTACGTGA	    0.902302	-160
TTTCTCGGAACTTTAAGAGAGTGGCTCTTT	2	40	1	CTTTAAGAGA	    0.969782	-131
GAGAGTGGCTCTTTACTACCGATCACAAAA	2	56	1	CTTTACTACC	    0.963282	-115
GTATTCCGATCTTTTTGTGATCGGTAGTAA	2	68	0	CTTTTTGTGA	    0.879866	-103
GAATACTTTACTTTACGACCAGCTTCCTCG	2	92	1	CTTTACGACC	    0.991357	-79
ACTGCTCCAGCCTTACGAGCAGACCAAATA	2	140	0	CCTTACGAGC	    0.975618	-31
          **********

Masking position 4
Map Score:   5.61916

Number of sites scoring better than the average of aligned sites = 822
Number in coding regions = 769
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

TTCGTAAATACTAACCTAATTAATTATATA	1	24	1	CTAACCTAAT	    0.984646	-155
TTATGTAGAGATAAGCAAATCTTATAATAA	1	83	0	ATAAGCAAAT	    0.935403	-96
TCTTCACCTCCTAACCAGATTTAAATCTTC	1	159	0	CTAACCAGAT	    0.989693	-20
GCCTTACGAGCAGACCAAATACACCCGCTA	2	131	0	CAGACCAAAT	     0.97439	-40
          **********

Masking position 4
Map Score:   0.501624

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 14
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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