AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_mthe_reg_300.orf -o061_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	RTH00475	137	M.thermo

Motif number 1

AATATTTTATCATTAAATGAGAATTGTAA   	1	8	0	CATTAAATAA	    0.995401	-130
AAAATATTCTCCTTAAAATATATAATTATCTA	1	32	1	CCTTAAAAAA	    0.997292	-106
AAATGGGAAACCTTAAATTACAGCATGGAAAA	1	78	1	CCTTAAATAA	    0.997274	-60
GAAAATTGTTCATTAAAAAACATGTTAAAACA	1	105	1	CATTAAAAAA	    0.995811	-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

         TTACAATTCTCATTTAATGAT	1	2	1	TACAATTCTC	    0.984638	-136
CATTTAATGATAAAATATTCTCCTTAAAAT	1	21	1	TAAAATATTC	    0.945188	-117
CCTTAAAATATATAATTATCTACCTGGTCT	1	42	1	TATAATTATC	    0.853808	-96
TTTTTTAATGAACAATTTTCCATGCTGTAA	1	95	0	AACAATTTTC	    0.950783	-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	    0.984695	-86
ATTTAAGGTTTCCCATTTCTGGAAAGACCA	1	66	0	TCCCATTTCT	     0.98699	-72
TCCCCTGTTTTAACATGTTTTTTAATGAAC	1	112	0	TAACATGTTT	     0.85011	-26
    CTAACATCCCCTGTTTTAACATGTTT	1	122	0	TCCCCTGTTT	    0.993014	-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

          **********

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 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