AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i268_hypothetical13_mjan_reg_100.orf -o268_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	RMJ07298	86	M_jannaschii_chromosome
#2	RMJ05688	127	M_jannaschii_chromosome

Motif number 1

ACCACAACCCTTAAATTGATGTATGTAATGTTT	1	17	1	TTAAATGATA	    0.989549	-70
TATGTAATGTTTAAAGTTATAAATCATAACTCA	1	38	1	TTAAATTAAA	    0.973168	-49
TCTCTCCTCTTTAAATTTGATTAGTGAGTTATG	1	62	0	TTAAATTGTA	    0.982496	-25
TATCTTTTTATTAAAAAGAGATT          	2	1	0	TTAAAAGATT	    0.904415	-127
TCTTTTTAATAAAAAGATAAATATATTCCAATT	2	15	1	AAAAAATATA	    0.857508	-113
TTAAAAAGTATTAAATTGGAATATATTTATCTT	2	28	0	TTAAATGGTA	    0.978867	-100
ATACTTTTTAATAAACTTAATAATAACTAAGTT	2	50	1	ATAAATTAAA	    0.949976	-78
AGTTTATTATATAAACTTAGTTATTATTAAGTT	2	63	0	ATAAATTATA	    0.983634	-65
GTTATCCCTATAAAAATTAATTTAATCCATAAT	2	104	0	TAAAATTATT	    0.919562	-24
          ***** ***  **

Masking position 5
Map Score:   11.3853

Number of sites scoring better than the average of aligned sites = 928
Number in coding regions = 630
Number in noncoding regions = 298
Number of orfs with sites within 600 bp upstream = 275
Fraction of orfs with sites within 600 bp upstream = 0.0441696


Motif number 2

GATTAGTGAGTTATGATTTATAACTTTAAA	1	47	0	TTATGATTTA	     0.94848	-40
ATTTATCTTTTTATTAAAAAGAGATT    	2	7	0	TTATTAAAAA	    0.557978	-121
ATTATTAAGTTTATTAAAAAGTATTAAATT	2	44	0	TTATTAAAAA	    0.557978	-84
ATAAACTTAGTTATTATTAAGTTTATTAAA	2	56	0	TTATTATTAA	    0.567964	-72
AAGAAACAGTTTATTATATAAACTTAGTTA	2	73	0	TTATTATATA	    0.975144	-55
AATAAACTGTTTCTTAATTATGGATTAAAT	2	88	1	TTCTTAATTA	    0.790186	-40
          **********

Masking position 6
Map Score:   9.72986

Number of sites scoring better than the average of aligned sites = 676
Number in coding regions = 485
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 183
Fraction of orfs with sites within 600 bp upstream = 0.0293929


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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