AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i136_Transmembrane_Transport_10_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	Rv1273c	146	hypothetical protein Rv1273c

Motif number 1

GCTGTGATCGGCAGTGGGAGAGGTAGCG  	1	9	0	GCAGTGGGAG	    0.951405	-138
CGGCTACAGTGCATGCTGTGATCGGCAGTG	1	23	0	GCATGCTGTG	    0.993124	-124
TGACCCGCGGGCCTGCGGCTACAGTGCATG	1	38	0	GCCTGCGGCT	    0.979529	-109
TGGTTAACTGGCGTGTCGTGGTTGACCCGC	1	60	0	GCGTGTCGTG	    0.973592	-87
AGTTAACCAGGCATTTCGGCCTAAGACTCA	1	81	1	GCATTTCGGC	    0.933153	-66
TAAGACTCATGCCTGGCGCGGGTAGGCAGC	1	102	1	GCCTGGCGCG	    0.997759	-45
CGCACACTGCGCATGCTGCCTACCCGCGCC	1	116	0	GCATGCTGCC	    0.994403	-31
GGCAGCATGCGCAGTGTGCGACAGTTACCC	1	126	1	GCAGTGTGCG	    0.989545	-21
          **********

Masking position 8
Map Score:   11.4672

Number of sites scoring better than the average of aligned sites = 12164
Number in coding regions = 11251
Number in noncoding regions = 913
Number of orfs with sites within 600 bp upstream = 652
Fraction of orfs with sites within 600 bp upstream = 0.104722


Motif number 2

TGCCGATCACAGCATGCACTGTAGCCGCAG	1	26	1	AGCATGCACT	    0.978562	-121
GCACTGTAGCCGCAGGCCCGCGGGTCAACC	1	41	1	CGCAGGCCCG	    0.987781	-106
ATGCCTGGTTAACTGGCGTGTCGTGGTTGA	1	65	0	AACTGGCGTG	     0.98225	-82
ACGCCAGTTAACCAGGCATTTCGGCCTAAG	1	76	1	ACCAGGCATT	    0.982348	-71
GCCTACCCGCGCCAGGCATGAGTCTTAGGC	1	99	0	GCCAGGCATG	    0.978654	-48
GCGGGTAGGCAGCATGCGCAGTGTGCGACA	1	119	1	AGCATGCGCA	     0.98624	-28
     TGGGTAACTGTCGCACACTGCGCAT	1	132	0	AACTGTCGCA	     0.86829	-15
          **********

Masking position 7
Map Score:   6.26958

Number of sites scoring better than the average of aligned sites = 9102
Number in coding regions = 8393
Number in noncoding regions = 709
Number of orfs with sites within 600 bp upstream = 573
Fraction of orfs with sites within 600 bp upstream = 0.0920334


Motif number 3

TGGCGTGTCGTGGTTGACCCGCGGGCCTGC	1	52	0	TGGTTGACCC	    0.884801	-95
CCGAAATGCCTGGTTAACTGGCGTGTCGTG	1	70	0	TGGTTAACTG	    0.924192	-77
CTGCGCATGCTGCCTACCCGCGCCAGGCAT	1	110	0	TGCCTACCCG	    0.981196	-37
          TGGGTAACTGTCGCACACTG	1	137	0	TGGGTAACTG	    0.950729	-10
          **********

Masking position 5
Map Score:   3.27002

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 403
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 4

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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