AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i269_hypothetical14_mjan_reg_100.orf -o269_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	RMJ10835	26	M_jannaschii_chromosome
#2	RMJ06373	34	M_jannaschii_chromosome
#3	RMJ08937	116	M_jannaschii_chromosome

Motif number 1

  AACTTATCCCCCCAACTTATTTTATT  	1	9	0	CCCCCAACTT	     0.99664	-18
    CTAAATCCCCCAACTTTACATTTCTA	2	19	0	CCCCCAACTT	     0.99664	-16
 AAATTACCACCTTAAAATTAATTCATATT	3	10	1	CCTTAAAATT	     0.99053	-107
ATTTGTGGAACCTTAAAAATAATAAAAAAG	3	82	0	CCTTAAAAAT	    0.986488	-35
   CATTTCACCTCAAAAATTTGTGGAACC	3	100	0	CCTCAAAAAT	    0.993959	-17
          **********

Masking position 6
Map Score:   10.242

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 141
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 2

ATCCCCCAACTTTACATTTCTAAACCAACA	2	11	0	TTTACATTTC	    0.975783	-24
AATTCATATTTGTATATTTTCAAATTTACA	3	30	1	TGTATATTTT	    0.973901	-87
TATAAATAGTTTTTTATTTTGTAAATTTGA	3	49	0	TTTTTATTTT	    0.982999	-68
TAAAAAACTATTTATATGACTTTTTTATTA	3	63	1	TTTATATGAC	    0.964388	-54
TTATATGACTTTTTTATTATTTTTAAGGTT	3	74	1	TTTTTATTAT	    0.975749	-43
          **********

Masking position 6
Map Score:   4.35985

Number of sites scoring better than the average of aligned sites = 930
Number in coding regions = 606
Number in noncoding regions = 324
Number of orfs with sites within 600 bp upstream = 278
Fraction of orfs with sites within 600 bp upstream = 0.0446515


Motif number 3

AAATAAGTTGGGGGGATAAGTT        	1	15	1	GGGGGATAAG	    0.995487	-12
         TGTTGGTTTAGAAATGTAAAG	2	2	1	GTTGGTTTAG	    0.989259	-33
TGTAAAGTTGGGGGATTTAG          	2	25	1	GGGGATTTAG	    0.996038	-10
          **********

Masking position 9
Map Score:   1.68016

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 27
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   1.72962e-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:   1.72962e-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:   1.72962e-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