AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iada_aquae_opreg_300.orf -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	petA	125	Rieske-I iron sulfur protein

Motif number 1

         CAAGTTTATTTTAACTTCCTAACC	1	2	1	ATTTATTTAA	    0.986618	-124
TAACTTCCTAACCTTTAATTAACTTTATGTATA	1	22	1	ATTTAATAAC	    0.991447	-104
AATTAACTTTATGTATATATAACGAAATTTTTA	1	38	1	ATATATTAAC	    0.991447	-88
ATATATAACGAAATTTTTATAAAAATTTTCACC	1	52	1	ATTTTTTAAA	    0.971375	-74
AAGTAAACCAAACTATATTTTACTACTCGGCGG	1	83	0	ATATATTTAC	     0.98416	-43
CCACCTCCTGAAATTTAAGTAAACCAAACTATA	1	99	0	ATTTAATAAA	    0.986617	-27
          *  ***** ****

Masking position 6
Map Score:   8.46263

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 33
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

TTAAAGGTTAGGAAGTTAAAATAAACTTG 	1	10	0	GGAAGTTAAA	    0.987159	-116
TTTACTACTCGGCGGTGAAAATTTTTATAA	1	68	0	GGCGGTGAAA	    0.997924	-58
TTAAATTTCAGGAGGTGGTATT        	1	114	1	GGAGGTGGTA	    0.996345	-12
          **********

Masking position 10
Map Score:   2.08919

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 65
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

AATTAAAGGTTAGGAAGTTAAAATAAACTT	1	12	0	TAGGAAGTTA	    0.979482	-114
ATTTTACTACTCGGCGGTGAAAATTTTTAT	1	70	0	TCGGCGGTGA	    0.991132	-56
ACTTAAATTTCAGGAGGTGGTATT      	1	112	1	CAGGAGGTGG	    0.995925	-14
          **********

Masking position 8
Map Score:   0.0807561

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 80
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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