AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_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	Rv1234	149	hypothetical protein Rv1234

Motif number 1

 GGTGATCAACCTATCCCGGCAACGATGCTC	1	10	1	CCTTCCCGGC	    0.987611	-140
ATCCCGGCAACGATGCTCGCCGTTCGGTGGG	1	23	1	CGAGCTCGCC	    0.995848	-127
CGCGAGCGACCGAGGCCCACCGAACGGCGAG	1	38	0	CGAGCCCACC	     0.99064	-112
ACACTATCCACTCAACCCGCGAGCGACCGAG	1	55	0	CTCACCCGCG	    0.986715	-95
TCAGGTCCAGCTACTCCCGGCACACTATCCA	1	76	0	CTATCCCGGC	    0.997101	-74
TCTCATTCTCCTCCGCCCCCCTTTTTCAGCG	1	125	0	CTCGCCCCCC	     0.99776	-25
          *** *******

Masking position 6
Map Score:   8.8407

Number of sites scoring better than the average of aligned sites = 4558
Number in coding regions = 4186
Number in noncoding regions = 372
Number of orfs with sites within 600 bp upstream = 310
Fraction of orfs with sites within 600 bp upstream = 0.0497912


Motif number 2

TCATGTCCAGTCAGGTCCAGCTACTCCCGG	1	87	0	TCAGGTCCAG	    0.999083	-63
CGCCATCGTTTCATGTCCAGTCAGGTCCAG	1	97	0	TCATGTCCAG	    0.997512	-53
CCCCCCTTTTTCAGCGCCATCGTTTCATGT	1	111	0	TCAGCGCCAT	    0.994443	-39
          **********

Masking position 3
Map Score:   3.88705

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 132
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TCAACCTATCCCGGCAACGATGCTCGCCGT	1	16	1	CCGGCAACGA	    0.992595	-134
GAGCGACCGAGGCCCACCGAACGGCGAGCA	1	36	0	GGCCCACCGA	    0.967487	-114
TCCACTCAACCCGCGAGCGACCGAGGCCCA	1	50	0	CCGCGAGCGA	     0.96759	-100
CCAGCTACTCCCGGCACACTATCCACTCAA	1	71	0	CCGGCACACT	    0.978599	-79
CCCTTTTTCAGCGCCATCGTTTCATGTCCA	1	108	0	GCGCCATCGT	    0.992872	-42
TCATTCTCCTCCGCCCCCCTTTTTCAGCGC	1	124	0	CCGCCCCCCT	     0.99247	-26
          **********

Masking position 6
Map Score:   4.9849

Number of sites scoring better than the average of aligned sites = 20173
Number in coding regions = 19124
Number in noncoding regions = 1049
Number of orfs with sites within 600 bp upstream = 759
Fraction of orfs with sites within 600 bp upstream = 0.121908


Motif number 4

          **********

No masking
Map Score:   -6.86222e-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:   -6.86222e-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:   -6.86222e-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