AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -ideoR_mtub_opreg_100.orf -g0.656 -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 =  	0.656
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv0476	111	hypothetical protein Rv0476

Motif number 1

   TCGGGCTCCGAATCACCATCGACTCCG	1	8	1	CCGAATCACC	     0.99475	-104
ACCATCGACTCCGAGTCGCCCACGGGGCGA	1	25	1	CCGAGTCGCC	    0.999472	-87
CACGTCGACTCCGAGTCGCCCCGTGGGCGA	1	40	0	CCGAGTCGCC	    0.999472	-72
CGGTTTGCATCCAACACGTCGACTCCGAGT	1	54	0	CCAACACGTC	    0.990142	-58
TGGATGCAAACCGCATAGTCTGAATGCGTG	1	71	1	CCGCATAGTC	    0.990089	-41
AATGCGTGAGCCACCTCGTGGGTACCGTC 	1	93	1	CCACCTCGTG	    0.987243	-19
          **********

Masking position 2
Map Score:   14.8938

Number of sites scoring better than the average of aligned sites = 5389
Number in coding regions = 4938
Number in noncoding regions = 451
Number of orfs with sites within 600 bp upstream = 366
Fraction of orfs with sites within 600 bp upstream = 0.0587857


Motif number 2

GGGCGACTCGGAGTCGATGGTGATTCGGAG	1	16	0	GAGTCGATGG	    0.964699	-96
CATCGACTCCGAGTCGCCCACGGGGCGACT	1	27	1	GAGTCGCCCA	    0.951267	-85
CGTCGACTCCGAGTCGCCCCGTGGGCGACT	1	38	0	GAGTCGCCCC	    0.629053	-74
GGGCGACTCGGAGTCGACGTGTTGGATGCA	1	49	1	GAGTCGACGT	    0.701502	-63
CTGAATGCGTGAGCCACCTCGTGGGTACCG	1	90	1	GAGCCACCTC	    0.889551	-22
          **********

Masking position 2
Map Score:   10.3519

Number of sites scoring better than the average of aligned sites = 1278
Number in coding regions = 1161
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 3

GGCTCCGAATCACCATCGACTCCGAGTCGC	1	14	1	CACCATCGAC	    0.984702	-98
CTCCGAGTCGCCCCGTGGGCGACTCGGAGT	1	32	0	CCCCGTGGGC	    0.941496	-80
TTTGCATCCAACACGTCGACTCCGAGTCGC	1	51	0	ACACGTCGAC	    0.982329	-61
TGGATGCAAACCGCATAGTCTGAATGCGTG	1	71	1	CCGCATAGTC	    0.975159	-41
GCGTGAGCCACCTCGTGGGTACCGTC    	1	96	1	CCTCGTGGGT	    0.978732	-16
          **********

Masking position 6
Map Score:   4.71655

Number of sites scoring better than the average of aligned sites = 6925
Number in coding regions = 6477
Number in noncoding regions = 448
Number of orfs with sites within 600 bp upstream = 347
Fraction of orfs with sites within 600 bp upstream = 0.055734


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