AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i155_Hydrogenase_2_mjan_reg_100.orf -o155_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	RMJ10774	114	M_jannaschii_chromosome
#2	RMJ08031	33	M_jannaschii_chromosome

Motif number 1

TCATCCCTTTAATCTCCGGCT         	1	2	0	AATCTCCGGC	    0.990502	-113
AAAGGGATGAGTTCTCTCGGGAACCCGTCA	1	22	1	GTTCTCTCGG	    0.998525	-93
TGGGGCGGTTGTTCTCTCGGTCCCTTGACG	1	47	0	GTTCTCTCGG	    0.998525	-68
TAAGTAAGGGGTTCTCCGGCATTGCAAAAC	1	77	1	GTTCTCCGGC	    0.999045	-38
          **********

Masking position 5
Map Score:   8.79578

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 3
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

GAGATTAAAGGGATGAGTTCTCTCGGGAAC	1	16	1	GGATGAGTTC	    0.986819	-99
CTCGGTCCCTTGACGGGTTCCCGAGAGAAC	1	32	0	TGACGGGTTC	    0.993068	-83
GCCCCATAAGTAAGGGGTTCTCCGGCATTG	1	71	1	TAAGGGGTTC	    0.992124	-44
          **********

Masking position 3
Map Score:   2.31423

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 3
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

TCCCGAGAGAACTCATCCCTTTAATCTCCG	1	14	0	ACTCATCCCT	    0.982496	-101
TGCAAAACTAATTTAAACTTTTTAGG    	1	99	1	ATTTAAACTT	    0.956836	-16
TTATTTTATTATTTATGCTTAAT       	2	4	0	ATTTATGCTT	    0.981366	-30
        AAATTCACCCTTATTTTATTAT	2	22	0	ATTCACCCTT	    0.992835	-12
          **********

Masking position 5
Map Score:   1.33867

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 109
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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:   -9.70439e-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