AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_mthe_reg_100.orf -o061_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	RTH00475	137	M.thermo

Motif number 1

   TTACAATTCTCATTTAATGATAAAATATT	1	8	1	TTATTTAATG	     0.99547	-130
TAGATAATTATATATTTTAAGGAGAATATTTT	1	32	0	TTTTTTAAGG	    0.997341	-106
TTTTCCATGCTGTAATTTAAGGTTTCCCATTT	1	78	0	TTATTTAAGG	    0.997323	-60
TGTTTTAACATGTTTTTTAATGAACAATTTTC	1	105	0	TTTTTTAATG	    0.995887	-33
          * * ********

Masking position 6
Map Score:   7.79341

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 15
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

ATCATTAAATGAGAATTGTAA         	1	2	0	GAGAATTGTA	    0.984176	-136
ATTTTAAGGAGAATATTTTATCATTAAATG	1	21	0	GAATATTTTA	    0.946644	-117
AGACCAGGTAGATAATTATATATTTTAAGG	1	42	0	GATAATTATA	    0.844464	-96
TTACAGCATGGAAAATTGTTCATTAAAAAA	1	95	1	GAAAATTGTT	    0.947835	-43
          **********

Masking position 5
Map Score:   3.91388

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 16
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

TATAATTATCTACCTGGTCTTTCCAGAAAT	1	52	1	TACCTGGTCT	    0.983941	-86
ATTTAAGGTTTCCCATTTCTGGAAAGACCA	1	66	0	TCCCATTTCT	    0.986338	-72
TCCCCTGTTTTAACATGTTTTTTAATGAAC	1	112	0	TAACATGTTT	    0.853189	-26
    CTAACATCCCCTGTTTTAACATGTTT	1	122	0	TCCCCTGTTT	    0.992752	-16
          **********

Masking position 8
Map Score:   2.10443

Number of sites scoring better than the average of aligned sites = 185
Number in coding regions = 175
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

GGAGAATATTTTATCATTAAATGAGAATTG	1	14	0	TTATCATTAA	     0.98276	-124
TGATAAAATATTCTCCTTAAAATATATAAT	1	28	1	TTCTCCTTAA	    0.990424	-110
CATGGAAAATTGTTCATTAAAAAACATGTT	1	101	1	TGTTCATTAA	    0.986662	-37
          **********

Masking position 9
Map Score:   1.90134

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 23
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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