AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_bbur_reg_100.orf -o198_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00408	115	3615

Motif number 1

          AGATTATACACAAAGCTCAC	1	1	1	AGATTATACA	     0.99231	-115
TCTTTTGGAAAAATACTACACATTTAAACT	1	40	1	AAATACTACA	    0.986084	-76
AAACTTTTTAACATTATACTAAAAATATAC	1	65	1	ACATTATACT	    0.981133	-51
CATTATACTAAAAATATACATTAAAGTAAA	1	76	1	AAAATATACA	    0.985499	-40
ACATTAAAGTAAATAATACGAGGAGTACAA	1	93	1	AAATAATACG	    0.989278	-23
          **********

Masking position 7
Map Score:   7.28804

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 64
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

ATTATACACAAAGCTCACAATAATAATTCT	1	13	1	AAGCTCACAA	    0.981649	-103
TTTTAGTATAATGTTAAAAAGTTTAAATGT	1	59	0	ATGTTAAAAA	    0.976129	-57
TTTTAACATTATACTAAAAATATACATTAA	1	70	1	ATACTAAAAA	    0.918636	-46
ATATACATTAAAGTAAATAATACGAGGAGT	1	89	1	AAGTAAATAA	    0.955745	-27
ATAATACGAGGAGTACAAAAA         	1	105	1	GAGTACAAAA	    0.963793	-11
          **********

Masking position 7
Map Score:   1.93681

Number of sites scoring better than the average of aligned sites = 1204
Number in coding regions = 841
Number in noncoding regions = 363
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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