AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iilvY_bsub_opreg_300.orf -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	gltC	146	transcriptional regulator (LysR family)

Motif number 1

GGTCATAAAATCTAACAACTCTATAATCATTGT	1	45	1	TCTAACTCTA	    0.990952	-102
TTGTAGGTTTTCAAAACGATATAAACAATATAT	1	74	1	TCAAAATATA	    0.993536	-73
ATTCTTTTGATCTAAATTATATATTGTTTATAT	1	92	0	TCTAAATATA	    0.989978	-55
ATAATTTAGATCAAAAGAATCTCAAAATGAGAT	1	105	1	TCAAAATCTC	    0.993759	-42
   GTTTGTCTCACATCCATCTATCTCATTTTG	1	127	0	TCACAATCTA	    0.993759	-20
          *****   *****

Masking position 5
Map Score:   5.55769

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 95
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

AAATCTAACAACTCTATAATCATTGTAGGT	1	52	1	ACTCTATAAT	     0.95439	-95
TCGTTTTGAAAACCTACAATGATTATAGAG	1	63	0	AACCTACAAT	    0.970365	-84
GGTTTTCAAAACGATATAAACAATATATAA	1	79	1	ACGATATAAA	    0.955157	-68
CGATATAAACAATATATAATTTAGATCAAA	1	90	1	AATATATAAT	    0.755613	-57
          **********

Masking position 5
Map Score:   1.24046

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 62
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

          **********

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 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