AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_Transmembrane_Transport_11_mthe_reg_300.orf -o138_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	RTH01072	116	M.thermo
#2	RTH02077	102	M.thermo

Motif number 1

 GGAAGATCCTATCTTAATAAATGTTTATA	1	10	1	TATCTTAATA	    0.961937	-107
TAACATAAAATATATAAACATTTATTAAGA	1	22	0	TATATAAACA	    0.939322	-95
AAATTTAATAAATTTTAACATAAAATATAT	1	37	0	AATTTTAACA	    0.978154	-80
ATAAACGATAAAATTTAATAAATTTTAACA	1	47	0	AAATTTAATA	    0.893303	-70
TTTTATCGTTTATATTAACAATTATTATAT	1	64	1	TATATTAACA	    0.987782	-53
TGCGTTGACATAACTTAACAGGGTGGTTGG	1	97	1	TAACTTAACA	    0.986276	-20
          **********

Masking position 5
Map Score:   8.19956

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 61
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

TCGGATACCGGGAATTCAGCATTTCAA   	2	8	0	GGAATTCAGC	    0.995848	-95
TTCAGTATCTGTGATTCAGCTGATGCTGTC	2	53	0	GTGATTCAGC	    0.995848	-50
TCACGTCATAAGGATTCAGTATCTGTGATT	2	67	0	AGGATTCAGT	     0.98876	-36
          **********

Masking position 4
Map Score:   2.32392

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 83
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

ATTTATTAAGATAGGATCTTCC        	1	3	0	ATAGGATCTT	     0.94409	-114
ATGTTTATATATTTTATGTTAAAATTTATT	1	31	1	ATTTTATGTT	    0.958022	-86
AATTTATTAAATTTTATCGTTTATATTAAC	1	53	1	ATTTTATCGT	      0.9868	-64
ATTAACAATTATTATATGGTTGCGTTGACA	1	77	1	ATTATATGGT	    0.966261	-40
    TCCTTCCTTGGATCGTTCACGTCATA	2	87	0	CTTGGATCGT	    0.982575	-16
          **********

Masking position 6
Map Score:   2.32145

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 38
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

TACCGGGAATTCAGCATTTCAA        	2	3	0	TCAGCATTTC	    0.985985	-100
GCTGATGCTGTCATCTTCTCATTGTACTCG	2	35	0	TCATCTTCTC	    0.979715	-68
TATCTGTGATTCAGCTGATGCTGTCATCTT	2	48	0	TCAGCTGATG	    0.976341	-55
TCATAAGGATTCAGTATCTGTGATTCAGCT	2	62	0	TCAGTATCTG	    0.979715	-41
          **********

Masking position 3
Map Score:   0.611617

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 214
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

GATCCTATCTTAATAAATGTTTATATATTT	1	15	1	TAATAAATGT	    0.988779	-102
AATGTTTATATATTTTATGTTAAAATTTAT	1	30	1	TATTTTATGT	    0.940389	-87
CGATAAAATTTAATAAATTTTAACATAAAA	1	42	0	TAATAAATTT	    0.923158	-75
CGCAACCATATAATAATTGTTAATATAAAC	1	71	0	TAATAATTGT	    0.970028	-46
ACCACCCTGTTAAGTTATGTCAACGCAACC	1	94	0	TAAGTTATGT	     0.95886	-23
          **********

Masking position 8
Map Score:   4.62624

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 18
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 6

          **********

No masking
Map Score:   4.28758e-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:   4.28758e-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 8

          **********

No masking
Map Score:   4.28758e-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