AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ityrR_mthe_opreg_100.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	    0.992286	-192
TTGGAGTCAGCTCCATACTCCTTGCCACAGTTTGGA	1	23	1	CTCTCTCGCC	    0.996849	-172
GACAGAACTTCTCAGCTTTCTCGGGCTCAGATCTCA	1	57	1	CTCCTTCGGC	    0.997682	-138
GGGCTCAGATCTCACCGTTCCAGGCCTCATACCCTT	1	79	1	CTCCTTCGCC	    0.999337	-116
TCCTCTTCATCTCTTCACTCGTAACCATAATAACAC	1	129	1	CTCCCTCACC	    0.994883	-66
     ACTATCTCAAATTCCTAAGCAGTTAGAGAGT	2	6	1	CTCATCCGCA	    0.974399	-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

CTGTCCAAACTGTGGCAAGGAGTATGGAGCT	1	31	0	TGTGGCAGGA	    0.994715	-164
CGGTGAGATCTGAGCCCGAGAAAGCTGAGAA	1	65	0	TGAGCCCAGA	    0.994416	-130
AAAAAGGGTATGAGGCCTGGAACGGTGAGAT	1	87	0	TGAGGCCGGA	    0.998455	-108
ACATCTAAATTGAGGGAAAGATTAAATCCAA	2	53	1	TGAGGGAAGA	    0.991367	-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

CAGCTCCATACTCCTTGCCACAGTTTGGAC	1	30	1	CTCCTTGCCA	    0.990616	-165
CAGAACTTCTCAGCTTTCTCGGGCTCAGAT	1	59	1	CAGCTTTCTC	    0.953102	-136
GCTCAGATCTCACCGTTCCAGGCCTCATAC	1	81	1	CACCGTTCCA	    0.978973	-114
CTCAGCGAGTCTCCTCTTCATCTCTTCACT	1	118	1	CTCCTCTTCA	     0.97273	-77
ATTTTTATTGCAGCTTGTTATAATAAGGTT	1	172	1	CAGCTTGTTA	    0.939544	-23
TGATTATTATCTACTCTCTAACTGCTTAGG	2	24	0	CTACTCTCTA	    0.944124	-70
          **********

Masking position 4
Map Score:   2.16218

Number of sites scoring better than the average of aligned sites = 454
Number in coding regions = 426
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

AATTATGGTGTTATTATGGTTACGAGTGAA	1	142	0	TTATTATGGT	     0.98599	-53
GCAATAAAAATAATTATGGTGTTATTATGG	1	153	0	TAATTATGGT	     0.96528	-42
GCAGCTTGTTATAATAAGGTTACC      	1	181	1	ATAATAAGGT	    0.964939	-14
      GGATTTAATAAGTTAGTTGGTTGG	2	80	0	TTAATAAGTT	    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