AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifur_mjan_opreg_100.orf -g0.314 -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 =  	0.314
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MJ0165	32	conserved hypothetical protein
#2	MJ0167	122	molybdenum cofactor biosynthesis protein (moaB)

Motif number 1

        ATTTTATTTTTAAAATTTTTAA	2	3	1	TTTATTTTTA	     0.96353	-120
TTTAAAATTTTTAATTTTTATTATTAATAT	2	19	1	TTAATTTTTA	    0.967741	-104
ATTTTTATTATTAATATTTTACTTCCTTCC	2	32	1	TTAATATTTT	    0.897815	-91
TTTTGTTATTTTAATTTATATTCATTAATT	2	77	1	TTAATTTATA	    0.979985	-46
TTTATATTCATTAATTTATATATTTATTTA	2	91	1	TTAATTTATA	    0.979985	-32
AATTTATATATTTATTTAAACGGTGGAAAT	2	103	1	TTTATTTAAA	     0.77806	-20
          **********

Masking position 5
Map Score:   13.9251

Number of sites scoring better than the average of aligned sites = 501
Number in coding regions = 317
Number in noncoding regions = 184
Number of orfs with sites within 600 bp upstream = 171
Fraction of orfs with sites within 600 bp upstream = 0.0274655


Motif number 2

   ATGTTTTTTCTAAAAGTTTTGGAGGGAA	1	8	1	TTCTAAAGTT	    0.950778	-25
   ATTTTATTTTTAAAATTTTTAATTTTTA	2	8	1	TTTTAAATTT	    0.979974	-115
AATTTTTAATTTTTATTATTAATATTTTACT	2	24	1	TTTTATTTTA	    0.950373	-99
AACAAAAGAATTCTAAAGTTTTGGAAGGAAG	2	53	0	TTCTAAATTT	    0.981433	-70
TTTAGAATTCTTTTGTTATTTTAATTTATAT	2	67	1	TTTTGTTTTT	    0.937743	-56
TTATTTTAATTTATATTCATTAATTTATATA	2	82	1	TTATATTATT	    0.893917	-41
ATTCATTAATTTATATATTTATTTAAACGGT	2	96	1	TTATATATTA	    0.950839	-27
          ******* ***

Masking position 4
Map Score:   5.90453

Number of sites scoring better than the average of aligned sites = 1869
Number in coding regions = 1298
Number in noncoding regions = 571
Number of orfs with sites within 600 bp upstream = 448
Fraction of orfs with sites within 600 bp upstream = 0.0719563


Motif number 3

TTTTTTCTAAAAGTTTTGGAGGGAATTGA 	1	14	1	AAGTTTTGGA	    0.991215	-19
TTTATTTTTAAAATTTTTAATTTTTATTAT	2	13	1	AAATTTTTAA	    0.977254	-110
GGAAGGAAGTAAAATATTAATAATAAAAAT	2	32	0	AAAATATTAA	     0.90092	-91
AAGAATTCTAAAGTTTTGGAAGGAAGTAAA	2	49	0	AAGTTTTGGA	    0.991215	-74
ATAAATATATAAATTAATGAATATAAATTA	2	88	0	AAATTAATGA	    0.953338	-35
          **********

Masking position 5
Map Score:   5.1419

Number of sites scoring better than the average of aligned sites = 486
Number in coding regions = 415
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

TCCAAAACTTTTAGAAAAAACAT       	1	4	0	TTAGAAAAAA	    0.948933	-29
TCTAAAAGTTTTGGAGGGAATTGA      	1	19	1	TTGGAGGGAA	    0.996682	-14
TTCTAAAGTTTTGGAAGGAAGTAAAATATT	2	44	0	TTGGAAGGAA	     0.99718	-79
          **********

Masking position 5
Map Score:   2.3203

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 113
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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