AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i154_Hydrogenase_1_mthe_reg_300.orf -o154_mthe_300.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

CCTGGTGTTAACAACACATTTAGTATGTGGGTCAAG	1	19	1	AACACATTAT	    0.979042	-203
GGGTCAAGATATATAACACTCAGTATTACTGAACAA	1	47	1	AAAACATTAT	    0.995816	-175
AGTATTACTGAACAAAAAATTAATATTATAAACTCT	1	68	1	ACAAAATTAT	    0.973364	-154
TATTATTAGTAGAAAACAGAGTTTATAATATTAATT	1	85	0	AAAACAATAT	    0.978674	-137
ATATCATTTTATAGATCACTTATTATTAGTAGAAAA	1	105	0	AAATCATTAT	    0.971422	-117
TTATAAAAAAAGTGAAAACTATTTATATCATTTTAT	1	129	0	ATAAAATTAT	    0.976684	-93
AACTTATAACATTTAAAAATAGTTATAATATTGAAG	1	171	1	ATAAAATTAT	    0.970409	-51
TTTAAAGTTCAAAAAACCTTCAATATTATAACTATT	1	188	0	AAAACCTTAT	    0.985341	-34
          * * **** *   ***

Masking position 15
Map Score:   11.5802

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 27
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

CCTTCCTGGTGTTAACAACACATTTAGTAT	1	15	1	GTTAACAACA	    0.967648	-207
CAGTATTACTGAACAAAAAATTAATATTAT	1	67	1	GAACAAAAAA	    0.916648	-155
CTTATTATTAGTAGAAAACAGAGTTTATAA	1	93	0	GTAGAAAACA	    0.937788	-129
TCTATAAAATGATATAAATAGTTTTCACTT	1	126	1	GATATAAATA	    0.847949	-96
GTTTTTCAATTATAAAAAAAGTGAAAACTA	1	144	0	TATAAAAAAA	    0.945494	-78
ACTTATAACATTTAAAAATAGTTATAATAT	1	172	1	TTTAAAAATA	    0.951032	-50
TGTTTTTAAAGTTCAAAAAACCTTCAATAT	1	198	0	GTTCAAAAAA	    0.979654	-24
TTTTTTGAACTTTAAAAACAAGAG      	1	208	1	TTTAAAAACA	    0.977761	-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

TCAGTAATACTGAGTGTTATATATCTTGACC	1	48	0	TGATGTTATA	    0.962382	-174
ACACTCAGTATTACTGAACAAAAAATTAATA	1	62	1	TTATGAACAA	    0.828757	-160
GAACAAAAAATTAATATTATAAACTCTGTTT	1	77	1	TTATATTATA	    0.810168	-145
CTACTAATAATAAGTGATCTATAAAATGATA	1	109	1	TAATGATCTA	     0.97901	-113
AGTGATCTATAAAATGATATAAATAGTTTTC	1	121	1	AAATGATATA	    0.947153	-101
ACTTTTTTTATAATTGAAAAACTTATAACAT	1	152	1	TAATGAAAAA	    0.903595	-70
TAACTATTTTTAAATGTTATAAGTTTTTCAA	1	165	0	TAATGTTATA	    0.985239	-57
TAACATTTAAAAATAGTTATAATATTGAAGG	1	177	1	AAAAGTTATA	    0.874791	-45
 CTCTTGTTTTTAAAGTTCAAAAAACCTTCA	1	202	0	TTAAGTTCAA	    0.856161	-20
          *** *******

Masking position 3
Map Score:   7.40459

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 150
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

          **********

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 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