AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_mthe_reg_100.orf -o034_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	RTH00913	86	M.thermo

Motif number 1

ACTAAAATTAATGGGGGTAACGAA      	1	5	0	ATGGGGGTAA	     0.99897	-82
ATATATATACATGTTGGTCAACTAAAATTA	1	25	0	ATGTTGGTCA	    0.995074	-62
ACAATGAGAAATGGAGGTAAACT       	1	74	1	ATGGAGGTAA	    0.998475	-13
          **********

Masking position 1
Map Score:   5.62175

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 40
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

CTAAAATTAATGGGGGTAACGAA       	1	4	0	TGGGGGTAAC	    0.998143	-83
TATATATACATGTTGGTCAACTAAAATTAA	1	24	0	TGTTGGTCAA	    0.991827	-63
CAATGAGAAATGGAGGTAAACT        	1	75	1	TGGAGGTAAA	    0.995072	-12
          **********

Masking position 9
Map Score:   3.61332

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 88
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

TTACCCCCATTAATTTTAGTTGACCAACAT	1	15	1	TAATTTTAGT	    0.971987	-72
TAATATATATACATGTTGGTCAACTAAAAT	1	27	0	ACATGTTGGT	    0.970185	-60
AATCATTATAAATTTTTAATATATATACAT	1	43	0	AATTTTTAAT	    0.975319	-44
CTCCATTTCTCATTGTTAATCATTATAAAT	1	60	0	CATTGTTAAT	    0.980925	-27
          **********

Masking position 6
Map Score:   0.821506

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 29
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

          **********

No masking
Map Score:   -1.88842e-14

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:   -1.88842e-14

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:   -1.88842e-14

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