AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i292_3_ecoli_reg_300.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	    0.989551	-187
TGTATATTTATGCAATCAGACAGCATATTG	1	108	0	TGCAATCAGA	    0.988976	-163
TTAACGGTGTAGCTATCAGAATACGGAAGG	1	244	1	AGCTATCAGA	     0.98904	-27
        CGAATAATCAGAGGGATCGAAA	2	3	1	AATAATCAGA	    0.989551	-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

CGCGCAACTATTACGTGACGTTGCCGTCAA	1	24	0	TTACGTGACG	    0.977852	-247
CACGTAATAGTTGCGCGGCGTGCTTGTGTT	1	37	1	TTGCGCGGCG	    0.986444	-234
ACATTAGCTGAAGCGTGATGATATAAACAA	1	135	1	AAGCGTGATG	    0.977821	-136
ATTAAGAAACAAACCCGACGCCAAAAGACG	1	169	0	AAACCCGACG	    0.977218	-102
ACTGGCGAGGTAACGCTATGTTAACGGTGT	1	224	1	TAACGCTATG	    0.927837	-47
AGAATACGGAAGGCGCGAAG          	1	261	1	AGGCGCGAAG	    0.975526	-10
          **********

Masking position 4
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

CGTGACGTTGCCGTCAATTGTGGAATTATT	1	11	0	CCGTCAATTG	    0.900088	-260
CTGATTATTTATGCAATATGCTGTCTGATT	1	95	1	ATGCAATATG	    0.957714	-176
ATGTATATTTATGCAATCAGACAGCATATT	1	109	0	ATGCAATCAG	    0.929994	-162
ACGCCAAAAGACGCAAATTGTTTATATCAT	1	152	0	ACGCAAATTG	    0.978891	-119
AACAAACCCGACGCCAAAAGACGCAAATTG	1	162	0	ACGCCAAAAG	     0.99052	-109
GTTTCTTAATATGTCAAAAGATTGGCTATC	1	189	1	ATGTCAAAAG	    0.957348	-82
          **********

Masking position 6
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

CAGATCTGATTATTTATGCAATATGCTGTC	1	90	1	TATTTATGCA	    0.993582	-181
AGCTAATGTATATTTATGCAATCAGACAGC	1	114	0	TATTTATGCA	    0.993582	-157
          **********

Masking position 5
Map Score:   1.28642

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 6
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


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