AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ideoR_mthe_opreg_100.orf -g0.495 -x5 
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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH816	43	sporulation protein IVFB related protein
#2	MTH817	56	conserved protein

Motif number 1

          GCTATAAAAAATGATTTATTC	1	1	1	GCTATAAAAA	    0.997982	-43
TATATGGGGTGCTATGAATAAATCATTTTTT	1	16	0	GCTATAATAA	     0.99503	-28
        CCAGGATCAAAAAACTCGAGCGA	2	3	1	AGGATAAAAA	    0.986584	-54
AAAAACTCGAGCGATGAAAAACCGAATGGAT	2	20	1	GCGATAAAAA	    0.998721	-37
          ***** *****

Masking position 5
Map Score:   7.65418

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 19
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

      GCTATAAAAAATGATTTATTCATA	1	5	1	TAAAAAATGA	     0.95866	-39
AGCGATGAAAAACCGAATGGATATGATGTA	2	29	1	AACCGAATGG	    0.995565	-28
GGATATGATGTACAGAATGG          	2	47	1	TACAGAATGG	    0.997881	-10
          **********

Masking position 6
Map Score:   2.00368

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 42
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          **********

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 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