AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i292_3_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ybgI	270	orf, hypothetical protein
#2	ybgJ	22	putative carboxylase

Motif number 1

ATATTGCATAAATAATCAGATCTGTATCAA	1	84	0	AATAATCAGA	     0.99089	-187
TGTATATTTATGCAATCAGACAGCATATTG	1	108	0	TGCAATCAGA	    0.990389	-163
TTAACGGTGTAGCTATCAGAATACGGAAGG	1	244	1	AGCTATCAGA	    0.990463	-27
        CGAATAATCAGAGGGATCGAAA	2	3	1	AATAATCAGA	     0.99089	-20
          **********

Masking position 5
Map Score:   5.27887

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 31
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TTGACGGCAACGTCACGTAATAGTTGCGCG	1	24	1	CGTCACGTAA	    0.976353	-247
AACACAAGCACGCCGCGCAACTATTACGTG	1	37	0	CGCCGCGCAA	    0.985574	-234
TTGTTTATATCATCACGCTTCAGCTAATGT	1	135	0	CATCACGCTT	    0.976323	-136
CGTCTTTTGGCGTCGGGTTTGTTTCTTAAT	1	169	1	CGTCGGGTTT	    0.975679	-102
ACACCGTTAACATAGCGTTACCTCGCCAGT	1	224	0	CATAGCGTTA	    0.923214	-47
          CTTCGCGCCTTCCGTATTCT	1	261	0	CTTCGCGCCT	    0.974135	-10
          **********

Masking position 7
Map Score:   3.1776

Number of sites scoring better than the average of aligned sites = 2736
Number in coding regions = 2620
Number in noncoding regions = 116
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 3

AATAATTCCACAATTGACGGCAACGTCACG	1	11	1	CAATTGACGG	    0.900088	-260
AATCAGACAGCATATTGCATAAATAATCAG	1	95	0	CATATTGCAT	    0.957714	-176
AATATGCTGTCTGATTGCATAAATATACAT	1	109	1	CTGATTGCAT	    0.929994	-162
ATGATATAAACAATTTGCGTCTTTTGGCGT	1	152	1	CAATTTGCGT	    0.978891	-119
CAATTTGCGTCTTTTGGCGTCGGGTTTGTT	1	162	1	CTTTTGGCGT	     0.99052	-109
GATAGCCAATCTTTTGACATATTAAGAAAC	1	189	0	CTTTTGACAT	    0.957348	-82
          **********

Masking position 5
Map Score:   3.34867

Number of sites scoring better than the average of aligned sites = 1269
Number in coding regions = 1172
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 4

GACAGCATATTGCATAAATAATCAGATCTG	1	90	0	TGCATAAATA	    0.993664	-181
GCTGTCTGATTGCATAAATATACATTAGCT	1	114	1	TGCATAAATA	    0.993664	-157
          **********

Masking position 5
Map Score:   1.28642

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:   -7.8627e-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:   -7.8627e-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 7

          **********

No masking
Map Score:   -7.8627e-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