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

Motif number 1

GCTGTGATCGGCAGTGGGAGAGGTAGCG  	1	9	0	GCAGTGGGAG	    0.953628	-138
CGGCTACAGTGCATGCTGTGATCGGCAGTG	1	23	0	GCATGCTGTG	    0.993452	-124
TGACCCGCGGGCCTGCGGCTACAGTGCATG	1	38	0	GCCTGCGGCT	    0.980484	-109
TGGTTAACTGGCGTGTCGTGGTTGACCCGC	1	60	0	GCGTGTCGTG	    0.974827	-87
AGTTAACCAGGCATTTCGGCCTAAGACTCA	1	81	1	GCATTTCGGC	    0.936146	-66
TAAGACTCATGCCTGGCGCGGGTAGGCAGC	1	102	1	GCCTGGCGCG	    0.997862	-45
CGCACACTGCGCATGCTGCCTACCCGCGCC	1	116	0	GCATGCTGCC	    0.994662	-31
GGCAGCATGCGCAGTGTGCGACAGTTACCC	1	126	1	GCAGTGTGCG	    0.990041	-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

CTGCGGCTACAGTGCATGCTGTGATCGGCA	1	26	0	AGTGCATGCT	    0.979787	-121
GGTTGACCCGCGGGCCTGCGGCTACAGTGC	1	41	0	CGGGCCTGCG	    0.988485	-106
TCAACCACGACACGCCAGTTAACCAGGCAT	1	65	1	CACGCCAGTT	    0.983265	-82
CTTAGGCCGAAATGCCTGGTTAACTGGCGT	1	76	0	AATGCCTGGT	    0.983361	-71
GCCTAAGACTCATGCCTGGCGCGGGTAGGC	1	99	1	CATGCCTGGC	    0.979875	-48
TGTCGCACACTGCGCATGCTGCCTACCCGC	1	119	0	TGCGCATGCT	     0.98703	-28
ATGCGCAGTGTGCGACAGTTACCCA     	1	132	1	TGCGACAGTT	    0.875017	-15
          **********

Masking position 4
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

GCAGGCCCGCGGGTCAACCACGACACGCCA	1	52	1	GGGTCAACCA	    0.892141	-95
CACGACACGCCAGTTAACCAGGCATTTCGG	1	70	1	CAGTTAACCA	    0.930038	-77
ATGCCTGGCGCGGGTAGGCAGCATGCGCAG	1	110	1	CGGGTAGGCA	    0.980509	-37
CAGTGTGCGACAGTTACCCA          	1	137	1	CAGTTACCCA	    0.954384	-10
          **********

Masking position 6
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