AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i072_tpal_bbur_100.orf -o072_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00624	136	3615

Motif number 1

CCTGAATTATTTAATAAACAAGCTAAAATG	1	24	0	TTAATAAACA	    0.986184	-113
TTATTTAATAAAAATAAACTATTTAACCTG	1	50	0	AAAATAAACT	    0.990311	-87
TTATTTTTATTAAATAAACTTAGTTTTTAT	1	63	1	TAAATAAACT	    0.997035	-74
CAATAGATCATATAAAAACTAAGTTTATTT	1	74	0	TATAAAAACT	    0.968875	-63
TCCTAAAGTCTTAATAAACTTATTGAATTA	1	111	0	TTAATAAACT	     0.99576	-26
          **********

Masking position 6
Map Score:   11.0481

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 13
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

     TTTAAAATTATAACATTTTAGCTTGT	1	6	1	AATTATACAT	    0.930333	-131
ATTTAACCTGAATTATTTAATAAACAAGCTA	1	29	0	AATTATTAAT	    0.982063	-108
AATAAAAATAAACTATTTAACCTGAATTATT	1	43	0	AACTATTAAC	    0.973508	-94
AATAGTTTATTTTTATTAAATAAACTTAGTT	1	57	1	TTTTATTAAT	    0.799484	-80
TTTTTATATGATCTATTGTATTGTATAATTC	1	86	1	ATCTATTTAT	    0.954252	-51
GTCTTAATAAACTTATTGAATTATACAATAC	1	103	0	ACTTATTAAT	    0.976442	-34
          ******* ***

Masking position 6
Map Score:   5.13085

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 56
Number in noncoding regions = 144
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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:   -9.70439e-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