AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i269_hypothetical14_mjan_reg_300.orf -o269_mjan_300.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

  AATAAAATAAGTTGGGGGGATAAGTT  	1	9	1	AAGTTGGGGG	    0.996827	-18
TAGAAATGTAAAGTTGGGGGATTTAG    	2	19	1	AAGTTGGGGG	    0.996827	-16
AATATGAATTAATTTTAAGGTGGTAATTT 	3	10	0	AATTTTAAGG	    0.991055	-107
CTTTTTTATTATTTTTAAGGTTCCACAAAT	3	82	1	ATTTTTAAGG	    0.987234	-35
GGTTCCACAAATTTTTGAGGTGAAATG   	3	100	1	ATTTTTGAGG	    0.994296	-17
          **********

Masking position 5
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	    0.972606	-24
AATTCATATTTGTATATTTTCAAATTTACA	3	30	1	TGTATATTTT	    0.970487	-87
TATAAATAGTTTTTTATTTTGTAAATTTGA	3	49	0	TTTTTATTTT	     0.98075	-68
TAAAAAACTATTTATATGACTTTTTTATTA	3	63	1	TTTATATGAC	    0.960092	-54
TTATATGACTTTTTTATTATTTTTAAGGTT	3	74	1	TTTTTATTAT	    0.972585	-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

        AACTTATCCCCCCAACTTATTT	1	15	0	CTTATCCCCC	    0.995053	-12
CTTTACATTTCTAAACCAACA         	2	2	0	CTAAACCAAC	    0.988234	-33
          CTAAATCCCCCAACTTTACA	2	25	0	CTAAATCCCC	    0.995656	-10
          **********

Masking position 4
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