AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i130_Transmembrane_Transport_4_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv3779	89	hypothetical protein Rv3779

Motif number 1

CCGAGTTCTAAGGTGGCTGGC         	1	2	0	AGGTGGCTGG	    0.996381	-88
CTTAGAACTCGGGTGTCCTAGACGTCCCAG	1	20	1	GGGTGTCCTA	    0.985773	-70
GGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	GGCGGGCTGG	     0.99894	-54
AGCCCGCCCGGGCTTCCCTGAGCCATGTCA	1	48	1	GGCTTCCCTG	     0.99336	-42
CGATTAGTATGGCTGGCCGGGTGACATGGC	1	69	0	GGCTGGCCGG	    0.999788	-21
          **********

Masking position 7
Map Score:   10.7613

Number of sites scoring better than the average of aligned sites = 6544
Number in coding regions = 6109
Number in noncoding regions = 435
Number of orfs with sites within 600 bp upstream = 367
Fraction of orfs with sites within 600 bp upstream = 0.0589464


Motif number 2

CTAGGACACCCGAGTTCTAAGGTGGCTGGC  	1	9	0	CGAGTTAAGG	    0.996363	-81
CAGGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	CGGGCGCTGG	    0.957415	-54
TATGGCTGGCCGGGTGACATGGCTCAGGGAAG	1	60	0	CGGGTCATGG	    0.998734	-30
         TCGATTAGTATGGCTGGCCGGGT	1	77	0	CGATTTATGG	    0.989935	-13
          *****  *****

Masking position 2
Map Score:   3.6567

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 265
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

ACCCGAGTTCTAAGGTGGCTGGC       	1	4	0	TAAGGTGGCT	    0.994856	-86
ACCTTAGAACTCGGGTGTCCTAGACGTCCC	1	18	1	TCGGGTGTCC	    0.986552	-72
CCGGGCGGGCTGGGACGTCTAGGACACCCG	1	29	0	TGGGACGTCT	    0.991062	-61
GCTGGCCGGGTGACATGGCTCAGGGAAGCC	1	58	0	TGACATGGCT	    0.966035	-32
     TCGATTAGTATGGCTGGCCGGGTGA	1	75	0	TAGTATGGCT	    0.990278	-15
          **********

Masking position 1
Map Score:   6.17498

Number of sites scoring better than the average of aligned sites = 1229
Number in coding regions = 1105
Number in noncoding regions = 124
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


Motif number 4

          **********

No masking
Map Score:   -4.67335e-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 5

          **********

No masking
Map Score:   -4.67335e-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:   -4.67335e-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