AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i154_Hydrogenase_1_mthe_reg_100.orf -o154_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH01924	221	M.thermo

Motif number 1

CTTGACCCACATACTAAATGTGTTGTTAACACCAGG	1	19	0	ATATATGTGT	    0.983589	-203
TTGTTCAGTAATACTGAGTGTTATATATCTTGACCC	1	47	0	ATATATGTTT	    0.996124	-175
AGAGTTTATAATATTAATTTTTTGTTCAGTAATACT	1	68	0	ATATATTTTT	    0.990401	-154
AATTAATATTATAAACTCTGTTTTCTACTAATAATA	1	85	1	ATAATTGTTT	     0.95411	-137
TTTTCTACTAATAATAAGTGATCTATAAAATGATAT	1	105	1	ATATATGATT	    0.976168	-117
ATAAAATGATATAAATAGTTTTCACTTTTTTTATAA	1	129	1	ATAAATTTTT	     0.97799	-93
CTTCAATATTATAACTATTTTTAAATGTTATAAGTT	1	171	0	ATACATTTTT	    0.971167	-51
AATAGTTATAATATTGAAGGTTTTTTGAACTTTAAA	1	188	1	ATATAGGTTT	    0.985974	-34
          *** * * ****   *

Masking position 3
Map Score:   11.5802

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 20
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

CCTTCCTGGTGTTAACAACACATTTAGTAT	1	15	1	GTTAACAACA	    0.960009	-207
CAGTATTACTGAACAAAAAATTAATATTAT	1	67	1	GAACAAAAAA	    0.898233	-155
CTTATTATTAGTAGAAAACAGAGTTTATAA	1	93	0	GTAGAAAACA	    0.923654	-129
TCTATAAAATGATATAAATAGTTTTCACTT	1	126	1	GATATAAATA	    0.817438	-96
GTTTTTCAATTATAAAAAAAGTGAAAACTA	1	144	0	TATAAAAAAA	    0.933115	-78
ACTTATAACATTTAAAAATAGTTATAATAT	1	172	1	TTTAAAAATA	     0.93983	-50
TGTTTTTAAAGTTCAAAAAACCTTCAATAT	1	198	0	GTTCAAAAAA	    0.974784	-24
TTTTTTGAACTTTAAAAACAAGAG      	1	208	1	TTTAAAAACA	    0.972453	-14
          **********

Masking position 7
Map Score:   7.47037

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 186
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

GTCAAGATATATAACACTCAGTATTACTGA	1	49	1	ATAACACTCA	    0.920163	-173
AGAGTTTATAATATTAATTTTTTGTTCAGT	1	74	0	ATATTAATTT	    0.824561	-148
ATCATTTTATAGATCACTTATTATTAGTAG	1	109	0	AGATCACTTA	    0.948664	-113
AAAACTATTTATATCATTTTATAGATCACT	1	121	0	ATATCATTTT	    0.968434	-101
ATATAAATAGTTTTCACTTTTTTTATAATT	1	137	1	TTTTCACTTT	    0.903227	-85
TGTTATAAGTTTTTCAATTATAAAAAAAGT	1	152	0	TTTTCAATTA	    0.855816	-70
TGAAAAACTTATAACATTTAAAAATAGTTA	1	166	1	ATAACATTTA	    0.950603	-56
CTTCAATATTATAACTATTTTTAAATGTTA	1	177	0	ATAACTATTT	    0.831815	-45
          **********

Masking position 8
Map Score:   4.26987

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 246
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

GTGGGTCAAGATATATAACACTCAGTATTAC	1	45	1	ATAATAACAC	    0.945306	-177
ACACTCAGTATTACTGAACAAAAAATTAATA	1	62	1	TTATGAACAA	    0.945045	-160
TTATATCATTTTATAGATCACTTATTATTAG	1	112	0	TTAAGATCAC	     0.98751	-110
AATGATATAAATAGTTTTCACTTTTTTTATA	1	133	1	ATATTTTCAC	    0.923462	-89
 CTCTTGTTTTTAAAGTTCAAAAAACCTTCA	1	202	0	TTAAGTTCAA	     0.95819	-20
          *** *******

Masking position 3
Map Score:   0.562592

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 64
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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 7

          **********

No masking
Map Score:   -3.31523e-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