AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i130_Transmembrane_Transport_4_mtub_reg_300.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	    0.996191	-88
CTTAGAACTCGGGTGTCCTAGACGTCCCAG	1	20	1	GGGTGTCCTA	    0.985034	-70
GGGAAGCCCGGGCGGGCTGGGACGTCTAGG	1	36	0	GGCGGGCTGG	    0.998884	-54
AGCCCGCCCGGGCTTCCCTGAGCCATGTCA	1	48	1	GGCTTCCCTG	    0.993012	-42
CGATTAGTATGGCTGGCCGGGTGACATGGC	1	69	0	GGCTGGCCGG	    0.999777	-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

  GCCAGCCACCTTAGAACTCGGGTGTCCTAG	1	9	1	CCTTAACTCG	    0.996399	-81
CCTAGACGTCCCAGCCCGCCCGGGCTTCCCTG	1	36	1	CCAGCGCCCG	    0.956975	-54
CTTCCCTGAGCCATGTCACCCGGCCAGCCATA	1	60	1	CCATGACCCG	    0.998743	-30
ACCCGGCCAGCCATACTAATCGA         	1	77	1	CCATAAATCG	    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

ACGTCTAGGACACCCGAGTTCTAAGGTGGC	1	15	0	CACCCGAGTT	    0.958436	-75
GTGTCCTAGACGTCCCAGCCCGCCCGGGCT	1	32	1	CGTCCCAGCC	    0.990209	-58
CGTCCCAGCCCGCCCGGGCTTCCCTGAGCC	1	42	1	CGCCCGGGCT	    0.527749	-48
CGCCCGGGCTTCCCTGAGCCATGTCACCCG	1	52	1	TCCCTGAGCC	    0.972793	-38
TGAGCCATGTCACCCGGCCAGCCATACTAA	1	66	1	CACCCGGCCA	    0.803385	-24
          **********

Masking position 4
Map Score:   6.05199

Number of sites scoring better than the average of aligned sites = 8672
Number in coding regions = 8013
Number in noncoding regions = 659
Number of orfs with sites within 600 bp upstream = 537
Fraction of orfs with sites within 600 bp upstream = 0.0862512


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