AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ityrR_mthe_opreg_300.orf -g0.495 -x5 
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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH545	194	conserved protein
#2	MTH546	93	cationic amino acid transporter related protein

Motif number 1

ATGGAGCTGACTCCAACTTCTGCGACGA        	1	3	0	CTCATTCGAC	    0.991734	-192
TTGGAGTCAGCTCCATACTCCTTGCCACAGTTTGGA	1	23	1	CTCTCTCGCC	    0.996622	-172
GACAGAACTTCTCAGCTTTCTCGGGCTCAGATCTCA	1	57	1	CTCCTTCGGC	    0.997515	-138
GGGCTCAGATCTCACCGTTCCAGGCCTCATACCCTT	1	79	1	CTCCTTCGCC	    0.999289	-116
TCCTCTTCATCTCTTCACTCGTAACCATAATAACAC	1	129	1	CTCCCTCACC	    0.994515	-66
     ACTATCTCAAATTCCTAAGCAGTTAGAGAGT	2	6	1	CTCATCCGCA	    0.972597	-88
          ***  * ***   ***

Masking position 2
Map Score:   7.05136

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 132
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

AGCTCCATACTCCTTGCCACAGTTTGGACAG	1	31	1	TCCTGCCACA	    0.994099	-164
TTCTCAGCTTTCTCGGGCTCAGATCTCACCG	1	65	1	TCTGGGCTCA	    0.993761	-130
ATCTCACCGTTCCAGGCCTCATACCCTTTTT	1	87	1	TCCGGCCTCA	    0.998317	-108
TTGGATTTAATCTTTCCCTCAATTTAGATGT	2	53	0	TCTTCCCTCA	    0.990362	-41
          *** *******

Masking position 1
Map Score:   3.76204

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 104
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

CTGTCCAAACTGTGGCAAGGAGTATGGAGC	1	32	0	TGTGGCAAGG	    0.986626	-163
CGGTGAGATCTGAGCCCGAGAAAGCTGAGA	1	66	0	TGAGCCCGAG	    0.981527	-129
AAAAAGGGTATGAGGCCTGGAACGGTGAGA	1	88	0	TGAGGCCTGG	    0.989765	-107
GGAGACTCGCTGAGAAAAAGGGTATGAGGC	1	102	0	TGAGAAAAAG	    0.934488	-93
ACATCTAAATTGAGGGAAAGATTAAATCCA	2	53	1	TGAGGGAAAG	    0.988232	-41
          **********

Masking position 1
Map Score:   2.37741

Number of sites scoring better than the average of aligned sites = 411
Number in coding regions = 389
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

TTCACTCGTAACCATAATAACACCATAATT	1	142	1	ACCATAATAA	     0.98599	-53
CCATAATAACACCATAATTATTTTTATTGC	1	153	1	ACCATAATTA	     0.96528	-42
      GGTAACCTTATTATAACAAGCTGC	1	181	0	ACCTTATTAT	    0.964939	-14
CCAACCAACTAACTTATTAAATCC      	2	80	1	AACTTATTAA	    0.946548	-14
          **********

Masking position 5
Map Score:   1.74722

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 23
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   3.07965e-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:   3.07965e-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:   3.07965e-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