AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imelR_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	Rv0188	118	hypothetical protein Rv0188

Motif number 1

          CCGCTGGTCCGGCGCCCAATTTTCGTTG	1	1	1	CCTCGCCCCA	    0.999497	-118
CAAGATTACGCCCGTTTTCGGGATGCCAGCAACGAAAA	1	30	0	CCTCGAGCCA	    0.998282	-89
CTCGCTGCCACCCATCCATCTGCTCCAAGATTACGCCC	1	55	0	CCTTGCCCAA	    0.997567	-64
TGCAGCAAAACTTTTGGGCTCGCTGCCACCCATCCATC	1	73	0	CTTCGCGCCA	    0.999257	-46
  TTTGCAACCTTTCTGTTATGCAGCAAAACTTTTGGG	1	93	0	CTCTGCGCAA	    0.991687	-26
          **  *   *  ** ****

Masking position 18
Map Score:   5.89396

Number of sites scoring better than the average of aligned sites = 1248
Number in coding regions = 1155
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 2

AACGAAAATTGGGCGCCGGACCAGCGG          	1	1	0	GGGGCGCAGG	     0.99951	-118
TTTCGTTGCTGGCATCCCGAAAACGGGCGTAATCTTG	1	31	1	GGCTCGAAGG	     0.99307	-88
GGCGTAATCTTGGAGCAGATGGATGGGTGGCAGCGAG	1	56	1	TGGGCAGAGG	    0.993374	-63
ATGGATGGGTGGCAGCGAGCCCAAAAGTTTTGCTGCA	1	74	1	GGCGCGCAAG	    0.999242	-45
CCAAAAGTTTTGCTGCATAACAGAAAGGTTGCAAA  	1	94	1	TGCGCACGAG	    0.991529	-25
          *** **  * * *  **

Masking position 6
Map Score:   2.36271

Number of sites scoring better than the average of aligned sites = 3060
Number in coding regions = 2823
Number in noncoding regions = 237
Number of orfs with sites within 600 bp upstream = 223
Fraction of orfs with sites within 600 bp upstream = 0.0358175


Motif number 3

          **********

No masking
Map Score:   1.16119e-13

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 4

          **********

No masking
Map Score:   1.16119e-13

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:   1.16119e-13

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