AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i159_glycolate_Oxidase_mthe_reg_100.orf -o159_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	RTH00981	105	M.thermo
#2	RTH01957	163	M.thermo

Motif number 1

TTTAATTGTTTATCAACACATATTAAGGTTTGTGATTT	1	42	0	TTCAATTAGG	    0.984389	-64
AACAATTAAAATTCAGTTCATTCTGAAGTTTTTCATAT	1	70	1	ATCAATTAAG	    0.942013	-36
      GCACCGTCATACCTACTTGAGGCACCCTTCTA	2	5	1	CTCATATAGG	    0.971323	-159
AGGTTACAGCATTCTGGAAATGGTTAAGTAGAAGGGTG	2	33	0	ATCTATTAAG	     0.95301	-131
TAAAGGTTACACTCTCGCGAATTTTAGGAATCTTTATA	2	71	1	ATCTAATAGG	    0.988413	-93
AGACTGTGACTCTCATCTCTATATAAAGATTCCTAAAA	2	92	0	TTCATATAAG	    0.958259	-72
GTCACAGTCTAATAAGAAAAATCTGAGGTTTGCTAACC	2	120	1	ATAAAATAGG	    0.937408	-44
GAGGTTTGCTAACCAGGGATATTTCAGGGT        	2	144	1	ACCATATAGG	    0.974791	-20
          * ***    **  * ***

Masking position 16
Map Score:   5.35512

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 206
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

ATTATCAGTTAAAATCACAAACCTTAATAT	1	31	1	AAAATCACAA	    0.925756	-75
TGTAACCTTTAAGGTTACAGCATTCTGGAA	2	52	0	AAGGTTACAG	    0.992654	-112
TGTAACCTTAAAGGTTACACTCTCGCGAAT	2	63	1	AAGGTTACAC	    0.986564	-101
TATAGAGATGAGAGTCACAGTCTAATAAGA	2	107	1	AGAGTCACAG	    0.987541	-57
          **********

Masking position 5
Map Score:   1.22214

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 135
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

ACTGATAATCTTTTAAACAATACAGACAT      	1	5	0	TTTTAATCAG	    0.971076	-101
AACAATTAAAATTCAGTTCATTCTGAAGTTTTTCA	1	70	1	ATTCTATCTG	    0.972319	-36
TTCTGAAGTTTTTCATATGAGTCAGC         	1	90	1	TTTCAAGCAG	    0.988005	-16
CTACTTAACCATTTCCAGAATGCTGTAACCTTAAA	2	40	1	ATTTAATCTG	    0.979638	-124
CTATATAAAGATTCCTAAAATTCGCGAGAGTGTAA	2	77	0	ATTCAATCGC	    0.950371	-87
ACCTCAGATTTTTCTTATTAGACTGTGACTCTCAT	2	114	0	TTTCAAGCTG	    0.991599	-50
          ****  *  ** ***

Masking position 10
Map Score:   1.22091

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 85
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

GTCTGTATTGTTTAAAAGATTATCAGTTAA	1	13	1	TTTAAAAGAT	    0.899458	-93
GGTTTGTGATTTTAACTGATAATCTTTTAA	1	24	0	TTTAACTGAT	    0.966543	-82
ATGAACTGAATTTTAATTGTTTATCAACAC	1	61	0	TTTTAATTGT	    0.884625	-45
CATTCTGAAGTTTTTCATATGAGTCAGC  	1	88	1	TTTTTCATAT	    0.949162	-18
AAACCTCAGATTTTTCTTATTAGACTGTGA	2	121	0	TTTTTCTTAT	    0.963967	-43
          **********

Masking position 3
Map Score:   0.625878

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 83
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 5

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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