AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i275_hypothetical2_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	ygcB	300	orf, hypothetical protein

Motif number 1

GATAATTCTTCCCGCGGCGTTCACGTTTAAA	1	27	0	CCCGCGGCGT	    0.941133	-274
GCCTCAAGCACCCGACGCCATTCTATACCTG	1	57	0	CCCGACGCCT	    0.988223	-244
GCGTCGGGTGCTTGAGGCTGTCTGGCGTTAA	1	70	1	CTTGAGGCTT	    0.986859	-231
CTCGCGAATGCTTAACGCCAGACAGCCTCAA	1	81	0	CTTAACGCCG	    0.944889	-220
AGAAATATCGCCTGGGGCTTTTGTCCATCTG	1	116	0	CCTGGGGCTT	    0.988091	-185
TTTCTATCAACCTGAGGCCAGCGTTCGAACC	1	142	1	CCTGAGGCCG	    0.961585	-159
ATACACATGTCTTGCCTCCCTGCAAAGAAGA	1	194	0	CTTGCCTCCT	    0.954733	-107
          ********* *

Masking position 8
Map Score:   7.79564

Number of sites scoring better than the average of aligned sites = 1263
Number in coding regions = 1167
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

CGCCGCGGGAAGAATTATCAGGTATAGAAT	1	39	1	AGAATTATCA	     0.98003	-262
TCAGGTTGATAGAAATATCGCCTGGGGCTT	1	127	0	AGAAATATCG	    0.990647	-174
GATGCTGCTCATAAATATCGAATTACAGTG	1	227	0	ATAAATATCG	    0.980144	-74
CTGTTTTTTTAGTATTATCGATGATATCAG	1	270	0	AGTATTATCG	    0.987384	-31
          **********

Masking position 6
Map Score:   5.18794

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 43
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

CGTTTAAAATCAGGAATGCTGCTC      	1	5	0	CAGGAATGCT	    0.990989	-296
ATAGAATGGCGTCGGGTGCTTGAGGCTGTC	1	62	1	GTCGGGTGCT	     0.93844	-239
TCTGGAACCTCGCGAATGCTTAACGCCAGA	1	90	0	CGCGAATGCT	    0.988328	-211
ATTGTTTGGGTTCGAACGCTGGCCTCAGGT	1	151	0	TTCGAACGCT	    0.956463	-150
ACCCAAACAATTCGAATGTTAGTCTCTTCT	1	170	1	TTCGAATGTT	    0.863597	-131
CTCTTCTTTGCAGGGAGGCAAGACATGTGT	1	193	1	CAGGGAGGCA	    0.958086	-108
ACTAAAAAAACAGGGAGGCTATTA      	1	287	1	CAGGGAGGCT	    0.990999	-14
          **********

Masking position 4
Map Score:   4.92589

Number of sites scoring better than the average of aligned sites = 777
Number in coding regions = 716
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 4

          GAGCAGCATTCCTGATTTTA	1	1	1	GAGCAGCATT	    0.995789	-300
TGAACGCCGCGGGAAGAATTATCAGGTATA	1	35	1	GGGAAGAATT	    0.968855	-266
GCTGTCTGGCGTTAAGCATTCGCGAGGTTC	1	86	1	GTTAAGCATT	    0.937422	-215
ATCAACCTGAGGCCAGCGTTCGAACCCAAA	1	147	1	GGCCAGCGTT	    0.983992	-154
CGATATTTATGAGCAGCATCGAAAAATAGC	1	237	1	GAGCAGCATC	    0.990689	-64
          **********

Masking position 5
Map Score:   3.84492

Number of sites scoring better than the average of aligned sites = 522
Number in coding regions = 485
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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