AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i229_sel_operon_mjan_reg_300.orf -o229_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	RMJ09342	119	M_jannaschii_chromosome
#2	RMJ09012	34	M_jannaschii_chromosome

Motif number 1

AAAAAATTAAAAACTTAATAATGGGGGATATT	1	12	0	AACTTAATAT	     0.89006	-108
AAGTTTTATTAAATTAAAAAATTAAAAACTTA	1	27	0	AATTAAAAAT	    0.980074	-93
TAAAACTTAAATAATAAAAACTTTTGTTAAAA	1	51	1	AAATAAAAAT	    0.987679	-69
ATAAAAACTTTTGTTAAAAAATATGTGTAGTA	1	64	1	TGTTAAAAAT	     0.95409	-56
AAATATGTGTAGTATAAAAATTTCTAAATACA	1	82	1	ATATAAAAAT	    0.875248	-38
          TCAATAAATAGTGTGTTGTATT	1	108	0	TAATAAATAT	    0.987534	-12
      ATAATTAATAAATAATTTGGTGATTT	2	5	1	TAATAAATAT	    0.987534	-30
          * ******** *

Masking position 7
Map Score:   9.4112

Number of sites scoring better than the average of aligned sites = 1100
Number in coding regions = 714
Number in noncoding regions = 386
Number of orfs with sites within 600 bp upstream = 348
Fraction of orfs with sites within 600 bp upstream = 0.0558946


Motif number 2

ATTAAAAAATTAAAAACTTAATAATGGGGG	1	17	0	TAAAAACTTA	    0.811155	-103
TTTTAATTTAATAAAACTTAAATAATAAAA	1	40	1	ATAAAACTTA	    0.974852	-80
TAAAACTTAAATAATAAAAACTTTTGTTAA	1	51	1	ATAATAAAAA	    0.881413	-69
AAAACTTTTGTTAAAAAATATGTGTAGTAT	1	67	1	TTAAAAAATA	    0.960716	-53
AGAAATTTTTATACTACACATATTTTTTAA	1	77	0	ATACTACACA	    0.969249	-43
AAATTTCTAAATACAACACACTATTTATTG	1	99	1	ATACAACACA	    0.980609	-21
      ATAATTAATAAATAATTTGGTGAT	2	5	1	TTAATAAATA	    0.938369	-30
      TTCCATAGAAATCACCAAATTATT	2	21	0	ATAGAAATCA	    0.915235	-14
          **********

Masking position 6
Map Score:   8.24821

Number of sites scoring better than the average of aligned sites = 1567
Number in coding regions = 1181
Number in noncoding regions = 386
Number of orfs with sites within 600 bp upstream = 325
Fraction of orfs with sites within 600 bp upstream = 0.0522004


Motif number 3

          **********

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 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