AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_mthe_reg_100.orf -o099_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	RTH01686	117	M.thermo
#2	RTH01759	83	M.thermo
#3	RTH00143	17	M.thermo
#4	RTH01466	21	M.thermo

Motif number 1

CGCAGAGGAATTTAATTCACAATAA     	1	6	0	TTTAATTCAC	     0.98488	-112
GCGCACAGGGTTTAGTTCACAAAATAGGTA	1	33	1	TTTAGTTCAC	    0.994865	-85
AAATAGGTAATTAAGTACACAAAAATAGTA	1	54	1	TTAAGTACAC	     0.98613	-64
TAGAACTATTTAAAATTTACTATTTTTGTG	1	71	0	TAAAATTTAC	    0.912734	-47
TATTGGTTAATAAAGTTCACTTGAAGGTGA	2	44	0	TAAAGTTCAC	    0.993545	-40
 CTTCAGTTATTGATTTCACCTATTGGTTA	2	65	0	TTGATTTCAC	    0.971719	-19
          **********

Masking position 6
Map Score:   10.635

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 101
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

TTATTGTGAATTAAATTCCTCTGCGCACAG	1	11	1	TTAAATTCCT	    0.894491	-107
TTTTGTGTACTTAATTACCTATTTTGTGAA	1	48	0	TTAATTACCT	    0.973234	-70
          TTTATCACCTCAACCTTTAC	1	108	0	TTTATCACCT	    0.982811	-10
      TGGTTTTCACAACCACAACATTTT	2	5	1	TTTCACAACC	    0.877742	-79
CACAACATTTTTTCTTTCCGTCACCTTCAA	2	24	1	TTTCTTTCCG	    0.909225	-60
TCAAGTGAACTTTATTAACCAATAGGTGAA	2	50	1	TTTATTAACC	    0.953072	-34
          TTAATCCCCCCAACTAT   	3	8	0	TTAATCCCCC	    0.968851	-10
          **********

Masking position 2
Map Score:   4.71251

Number of sites scoring better than the average of aligned sites = 445
Number in coding regions = 349
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 3

TTTACCTTATCCTAGAACTATTTAAAATTTA	1	82	0	CCAGAACTAT	    0.947267	-36
   TTTATCACCTCAACCTTTACCTTATCCT	1	100	0	CCCAACCTTT	    0.996366	-18
GTTTTCACAACCACAACATTTTTTCTTTCCG	2	13	1	CCCAACATTT	    0.981319	-71
TTTTTTCTTTCCGTCACCTTCAAGTGAACTT	2	31	1	CCTCACCTTC	    0.979625	-53
    TTAATCCCCCCAACTAT          	3	1	0	CCCCAACTAT	    0.992444	-17
          ** ********

Masking position 6
Map Score:   2.7181

Number of sites scoring better than the average of aligned sites = 370
Number in coding regions = 329
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

GTGTACTTAATTACCTATTTTGTGAACTAA	1	44	0	TTACCTATTT	    0.985338	-74
CTATTTAAAATTTACTATTTTTGTGTACTT	1	66	0	TTTACTATTT	    0.906988	-52
GTTATTGATTTCACCTATTGGTTAATAAAG	2	59	0	TCACCTATTG	    0.993819	-25
        CTTCAGTTATTGATTTCACCTA	2	72	0	TCAGTTATTG	    0.956506	-12
          **********

Masking position 6
Map Score:   0.826215

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 72
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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