AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i103_Ferrous_Iron_Transporter_mjan_reg_100.orf -o103_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ04246	104	M_jannaschii_chromosome

Motif number 1

TTAACCGTAGTTAAATAATAACATGCAGGG	1	34	0	TTAAATAATA	    0.937918	-71
AGTTAAAATTTTTAACCGTAGTTAAATAAT	1	45	0	TTTAACCGTA	    0.995888	-60
GGTTAAAAATTTTAACTATAATTAAATCAT	1	58	1	TTTAACTATA	    0.979572	-47
AATTAAATCATTTAACCATATATAAATGTT	1	77	1	TTTAACCATA	    0.996601	-28
          **********

Masking position 5
Map Score:   6.76238

Number of sites scoring better than the average of aligned sites = 130
Number in coding regions = 110
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

GCAGGGTATAAAAACCTTTCGGTGGCATC 	1	10	0	AAAACCTTTC	    0.979524	-95
AATTATAGTTAAAATTTTTAACCGTAGTTA	1	51	0	AAAATTTTTA	    0.899374	-54
AACTATAATTAAATCATTTAACCATATATA	1	71	1	AAATCATTTA	    0.984358	-34
    AATACCACAACATTTATATATGGTTA	1	89	0	ACAACATTTA	     0.98835	-16
          **********

Masking position 7
Map Score:   4.00078

Number of sites scoring better than the average of aligned sites = 353
Number in coding regions = 289
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 3

ATGTTATTATTTAACTACGGTTAAAAATTT	1	40	1	TTAACTACGG	    0.994177	-65
GTTAAATGATTTAATTATAGTTAAAATTTT	1	63	0	TTAATTATAG	    0.979159	-42
ACCACAACATTTATATATGGTTAAATGATT	1	82	0	TTATATATGG	    0.973024	-23
          **********

Masking position 7
Map Score:   1.25494

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 97
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


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