AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_mjan_reg_300.orf -o002_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	RMJ06880	91	M_jannaschii_chromosome

Motif number 1

AATGAGAAGTAATATTAAAGAAAATATATA	1	20	1	AATATTAAAG	     0.97819	-72
TATTAAAGAAAATATATAAAGTTTAGAAAA	1	32	1	AATATATAAA	    0.988239	-60
AAGTTTAGAAAATATAAAAATTTAATAGAT	1	50	1	AATATAAAAA	    0.994379	-42
ATAAAAATTTAATAGATAAAGAAATTAGTG	1	63	1	AATAGATAAA	    0.990646	-29
          **********

Masking position 4
Map Score:   7.63188

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 164
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 137
Fraction of orfs with sites within 600 bp upstream = 0.0220045


Motif number 2

GAAGTAATATTAAAGAAAATATATAAAGTT	1	25	1	TAAAGAAAAT	    0.996317	-67
ATATATAAAGTTTAGAAAATATAAAAATTT	1	43	1	TTTAGAAAAT	    0.988605	-49
ATTTAATAGATAAAGAAATTAGTGGTGATT	1	69	1	TAAAGAAATT	    0.993523	-23
          **********

Masking position 6
Map Score:   4.79908

Number of sites scoring better than the average of aligned sites = 288
Number in coding regions = 249
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

      GTTTTCACCAATGAGAAGTAATAT	1	5	1	TCACCAATGA	    0.917584	-87
     TTAAATCACCACTAATTTCTTTATC	1	77	0	TCACCACTAA	    0.989378	-15
          **********

Masking position 6
Map Score:   1.3622

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 4

          **********

No masking
Map Score:   9.48026e-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:   9.48026e-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:   9.48026e-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