AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i332_not_clear7_mthe_reg_300.orf -o332_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	RTH01043	246	M.thermo

Motif number 1

TTCTCCTGGTGGGAGCTGGAGCTCAGGAGC	1	51	1	GGGAGCTGGA	    0.992474	-196
ACCTGAATCAGGCTCCTGAGCTCCAGCTCC	1	62	0	GGCTCCTGAG	    0.981698	-185
CGCGGCTTCAGGGACCTGAATCAGGCTCCT	1	75	0	GGGACCTGAA	    0.999056	-172
GCCAGTCATGGGGCCCTGAAGAGGTGATTA	1	115	0	GGGCCCTGAA	    0.998394	-132
ATCAGTAAATCCGACCTGAAAATCAGCCAG	1	140	0	CCGACCTGAA	    0.988393	-107
          **********

Masking position 7
Map Score:   7.93027

Number of sites scoring better than the average of aligned sites = 357
Number in coding regions = 339
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

GCTCCAGCTCCCACCAGGAGAAAACCCAAAG	1	42	0	CCACCAGGAA	     0.95968	-205
AAGCCGCGATCCATCAGTTAATCACCTCTTC	1	97	1	CCATCAGTTA	    0.990315	-150
TCAGTAAATCCGACCTGAAAATCAGCCAGTC	1	138	0	CGACCTGAAA	    0.964982	-109
TCCCGGCCAGCCATCAGTAAATCCGACCTGA	1	151	0	CCATCAGTAA	    0.993387	-96
      AAAACCTCCAGATTAAAGTGGATTT	1	232	0	CCTCCAGATA	    0.982813	-15
          ********* *

Masking position 11
Map Score:   4.69244

Number of sites scoring better than the average of aligned sites = 259
Number in coding regions = 234
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

GTGATTAACTGATGGATCGCGGCTTCAGGG	1	92	0	GATGGATCGC	    0.993028	-155
TTCAGGGCCCCATGACTGGCTGATTTTCAG	1	125	1	CATGACTGGC	    0.996036	-122
CGGATTTACTGATGGCTGGCCGGGACTCAT	1	157	1	GATGGCTGGC	      0.9974	-90
AAAAGATTTACATGAGTCCCGGCCAGCCAT	1	168	0	CATGAGTCCC	    0.980744	-79
          **********

Masking position 7
Map Score:   3.33898

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 52
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

GCTCCAGCTCCCACCAGGAGAAAACCCAAA	1	43	0	CCACCAGGAG	    0.992567	-204
AAGCCGCGATCCATCAGTTAATCACCTCTT	1	97	1	CCATCAGTTA	    0.992957	-150
TCCCGGCCAGCCATCAGTAAATCCGACCTG	1	152	0	CCATCAGTAA	    0.995981	-95
          **********

Masking position 6
Map Score:   1.87968

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 26
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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:   2.79544e-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