AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_bbur_reg_300.orf -o198_borburg_300.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	    0.992074	-115
TCTTTTGGAAAAATACTACACATTTAAACT	1	40	1	AAATACTACA	    0.985639	-76
AAACTTTTTAACATTATACTAAAAATATAC	1	65	1	ACATTATACT	    0.980541	-51
CATTATACTAAAAATATACATTAAAGTAAA	1	76	1	AAAATATACA	    0.985043	-40
ACATTAAAGTAAATAATACGAGGAGTACAA	1	93	1	AAATAATACG	    0.988934	-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

AGAATTATTATTGTGAGCTTTGTGTATAAT	1	13	0	TTGTGAGCTT	    0.980997	-103
ACATTTAAACTTTTTAACATTATACTAAAA	1	59	1	TTTTTAACAT	    0.975698	-57
TTAATGTATATTTTTAGTATAATGTTAAAA	1	70	0	TTTTTAGTAT	     0.91594	-46
ACTCCTCGTATTATTTACTTTAATGTATAT	1	89	0	TTATTTACTT	    0.954218	-27
         TTTTTGTACTCCTCGTATTAT	1	105	0	TTTTGTACTC	    0.962525	-11
          **********

Masking position 4
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