AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_mthe_reg_300.orf -o099_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	RTH01686	117	M.thermo
#2	RTH01759	83	M.thermo
#3	RTH00143	17	M.thermo
#4	RTH01466	21	M.thermo

Motif number 1

     TTATTGTGAATTAAATTCCTCTGCG	1	6	1	GTGAATTAAA	     0.98473	-112
TACCTATTTTGTGAACTAAACCCTGTGCGC	1	33	0	GTGAACTAAA	    0.994762	-85
TACTATTTTTGTGTACTTAATTACCTATTT	1	54	0	GTGTACTTAA	    0.985834	-64
CACAAAAATAGTAAATTTTAAATAGTTCTA	1	71	1	GTAAATTTTA	    0.911058	-47
TCACCTTCAAGTGAACTTTATTAACCAATA	2	44	1	GTGAACTTTA	    0.993407	-40
TAACCAATAGGTGAAATCAATAACTGAAG 	2	65	1	GTGAAATCAA	    0.971348	-19
          **********

Masking position 5
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

CTGTGCGCAGAGGAATTTAATTCACAATAA	1	11	0	AGGAATTTAA	    0.904622	-107
TTCACAAAATAGGTAATTAAGTACACAAAA	1	48	1	AGGTAATTAA	    0.976007	-70
GTAAAGGTTGAGGTGATAAA          	1	108	1	AGGTGATAAA	    0.984607	-10
AAAATGTTGTGGTTGTGAAAACCA      	2	5	0	GGTTGTGAAA	    0.889282	-79
TTGAAGGTGACGGAAAGAAAAAATGTTGTG	2	24	0	CGGAAAGAAA	     0.91807	-60
TTCACCTATTGGTTAATAAAGTTCACTTGA	2	50	0	GGTTAATAAA	    0.957843	-34
   ATAGTTGGGGGGATTAA          	3	8	1	GGGGGATTAA	    0.972064	-10
          **********

Masking position 9
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	    0.944868	-36
   TTTATCACCTCAACCTTTACCTTATCCT	1	100	0	CCCAACCTTT	    0.996191	-18
GTTTTCACAACCACAACATTTTTTCTTTCCG	2	13	1	CCCAACATTT	    0.980438	-71
TTTTTTCTTTCCGTCACCTTCAAGTGAACTT	2	31	1	CCTCACCTTC	    0.978665	-53
    TTAATCCCCCCAACTAT          	3	1	0	CCCCAACTAT	    0.992083	-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	    0.984197	-74
CTATTTAAAATTTACTATTTTTGTGTACTT	1	66	0	TTTACTATTT	    0.900365	-52
GTTATTGATTTCACCTATTGGTTAATAAAG	2	59	0	TCACCTATTG	    0.993334	-25
        CTTCAGTTATTGATTTCACCTA	2	72	0	TCAGTTATTG	    0.953227	-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