AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_exonuclease_sbcc_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	sbcD	189	ATP-dependent dsDNA exonuclease

Motif number 1

GGTTGCGATCATTAATGCGACGTCATTATGC	1	34	1	ATTATGCGAC	    0.990251	-156
TAAATCTGTCATAAATCTGACGCATAATGAC	1	55	0	ATAATCTGAC	    0.979468	-135
CGAGCTTTTCATAAATCTGTCATAAATCTGA	1	66	0	ATAATCTGTC	      0.9497	-124
TAACCTGAAGATATGTGCGACGAGCTTTTCA	1	86	0	ATATTGCGAC	    0.992073	-104
CCATTTGCTTTTTTCTGCGCCACGGAAATCA	1	118	0	TTTTTGCGCC	    0.946731	-72
TTATACCCAAACAGATGTGCCATTTGCTTTT	1	137	0	ACAGTGTGCC	    0.961001	-53
CTGTTTGGGTATAATCGCGCCCATGCTTTTT	1	154	1	ATAACGCGCC	    0.991226	-36
          **** ******

Masking position 9
Map Score:   6.94532

Number of sites scoring better than the average of aligned sites = 1014
Number in coding regions = 928
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 99
Fraction of orfs with sites within 600 bp upstream = 0.0159011


Motif number 2

TAATGACGTCGCATTAATGATCGCAACCTA	1	32	0	GCATTAATGA	    0.753069	-158
ATTATGCGTCAGATTTATGACAGATTTATG	1	58	1	AGATTTATGA	    0.992672	-132
GATTTATGACAGATTTATGAAAAGCTCGTC	1	69	1	AGATTTATGA	    0.992672	-121
ACATATCTTCAGGTTATTGATTTCCGTGGC	1	101	1	AGGTTATTGA	    0.974659	-89
          **********

Masking position 5
Map Score:   3.98652

Number of sites scoring better than the average of aligned sites = 129
Number in coding regions = 105
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

CTGTTGTAATAAATAGGTTGCGATCATTAA	1	19	1	AAATAGGTTG	    0.951872	-171
ACAGATTTATGAAAAGCTCGTCGCACATAT	1	77	1	GAAAAGCTCG	    0.985088	-113
GTGGCGCAGAAAAAAGCAAATGGCACATCT	1	126	1	AAAAAGCAAA	    0.950314	-64
TTCCCTGGCGAAAAAGCATGGGCGCGATTA	1	165	0	AAAAAGCATG	    0.992592	-25
          **********

Masking position 5
Map Score:   0.439633

Number of sites scoring better than the average of aligned sites = 375
Number in coding regions = 297
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 4

          **********

No masking
Map Score:   -3.24418e-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:   -3.24418e-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 6

          **********

No masking
Map Score:   -3.24418e-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