AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_mixed4_aquae_reg_300.orf -o319_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	RAA01527	35	Aquifex_aeolicus
#2	RAA00385	55	Aquifex_aeolicus
#3	RAA00564	129	Aquifex_aeolicus
#4	RAA01083	37	Aquifex_aeolicus

Motif number 1

TATAAGTGGTAAGGAGTTTACG        	1	24	1	AAGGAGTTTA	    0.961873	-12
CGAGAACTTCAAGGAGGCGGAA        	2	3	0	AAGGAGGCGG	    0.985725	-53
ATCGGCAGAGCGGGTGGCTGTTAACCACCT	3	56	1	CGGGTGGCTG	    0.990742	-74
AACCCCCAACCAGGTGGTTAACAGCCACCC	3	67	0	CAGGTGGTTA	    0.995188	-63
AAGTAAAACTCAGGAGGTTAAAA       	4	25	1	CAGGAGGTTA	    0.996636	-13
          **********

Masking position 6
Map Score:   6.49079

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 110
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

        GTTAAACTTATTATATAAGTGGTAA	1	3	1	TAAATTTTTA	    0.953645	-33
TTACAGTCGTTAAAATGTTTTTACGAGAACTTC	2	23	0	TAAATGTTTA	    0.754536	-33
          TAAATTTAATTTACAGTCGTTAA	2	43	0	TAAATTATTA	    0.539958	-13
ATAGCCAAGATAAAATTATAAAACCTTAATTT 	3	10	0	TAAATTTAAA	    0.954243	-120
    AAAGTATAAATTTTAAGTAAAACTCAGGA	4	7	1	TAAATTAATA	    0.979187	-31
          **** ** ** **

Masking position 6
Map Score:   3.2975

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 33
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

CTGCCGATTGAGCTACCCCGGATAGCCAAG	3	34	0	AGCTACCCCG	    0.992218	-96
AACAGCCACCCGCTCTGCCGATTGAGCTAC	3	48	0	CGCTCTGCCG	    0.994301	-82
GGGAGGGACTCGAACCCCCAACCAGGTGGT	3	79	0	CGAACCCCCA	    0.980629	-51
GGGTTCGAGTCCCTCCCCCGGAGCCATTTC	3	92	1	CCCTCCCCCG	     0.99867	-38
          **********

Masking position 8
Map Score:   2.87113

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 84
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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