AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i229_sel_operon_mjan_reg_100.orf -o229_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	RMJ09342	119	M_jannaschii_chromosome
#2	RMJ09012	34	M_jannaschii_chromosome

Motif number 1

TTAAGTTTTTAATTTTTTAATTTAATAAAA	1	26	1	AATTTTTTAA	     0.97518	-94
TATTATTTAAGTTTTATTAAATTAAAAAAT	1	37	0	GTTTTATTAA	    0.940239	-83
CAAAAGTTTTTATTATTTAAGTTTTATTAA	1	47	0	TATTATTTAA	    0.970637	-73
ATACTACACATATTTTTTAACAAAAGTTTT	1	67	0	TATTTTTTAA	    0.993752	-53
TAGTGTGTTGTATTTAGAAATTTTTATACT	1	92	0	TATTTAGAAA	    0.928962	-28
TACAACACACTATTTATTGA          	1	110	1	TATTTATTGA	    0.984561	-10
ATCACCAAATTATTTATTAATTAT      	2	5	0	TATTTATTAA	    0.995162	-30
          **********

Masking position 10
Map Score:   13.0207

Number of sites scoring better than the average of aligned sites = 667
Number in coding regions = 516
Number in noncoding regions = 151
Number of orfs with sites within 600 bp upstream = 140
Fraction of orfs with sites within 600 bp upstream = 0.0224863


Motif number 2

  GAATATCCCCCATTATTAAGTTTTTAATT	1	9	1	CCATTATTAA	    0.968527	-111
TATTAAGTTTTTAATTTTTTAATTTAATAAA	1	24	1	TTATTTTTTA	    0.919623	-96
AACAAAAGTTTTTATTATTTAAGTTTTATTA	1	48	0	TTATTATTTA	    0.941641	-72
TTATACTACACATATTTTTTAACAAAAGTTT	1	68	0	CAATTTTTTA	      0.9909	-52
CTAAATACAACACACTATTTATTGA      	1	105	1	CAACTATTTA	    0.986831	-15
TAGAAATCACCAAATTATTTATTAATTAT  	2	9	0	CAATTATTTA	    0.866211	-26
          ** ********

Masking position 6
Map Score:   9.95388

Number of sites scoring better than the average of aligned sites = 280
Number in coding regions = 234
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

TTTTATTATTTAAGTTTTATTAAATTAAAA	1	40	0	TAAGTTTTAT	    0.948885	-80
TTAACAAAAGTTTTTATTATTTAAGTTTTA	1	51	0	TTTTTATTAT	    0.891761	-69
TTAAAAAATATGTGTAGTATAAAAATTTCT	1	77	1	TGTGTAGTAT	    0.991305	-43
CAATAAATAGTGTGTTGTATTTAGAAATTT	1	99	0	TGTGTTGTAT	    0.993921	-21
AATAATTTGGTGATTTCTATGGAA      	2	21	1	TGATTTCTAT	    0.964915	-14
          **********

Masking position 5
Map Score:   3.87306

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 272
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 4

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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