AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i273_hypothetical18_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	yjgP	266	orf, hypothetical protein

Motif number 1

CCGCCGTTGTCTTTAAGATTCAGGAGCGTA	1	15	0	CTTTAAGATT	    0.990263	-252
GCCGTAATAACGTTAAGATTAACACGAAGT	1	97	0	CGTTAAGATT	    0.993684	-170
ACGGATTCACCTCTCAGATTTTGTTCTGAC	1	135	0	CTCTCAGATT	     0.98928	-132
TCGAAATCGTCGCTAAGATAATTATACTCA	1	165	0	CGCTAAGATA	    0.989723	-102
          **********

Masking position 6
Map Score:   5.54356

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 29
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

TTAAAGACAACGGCGGTGGCTACAGATAGA	1	29	1	CGGCGGTGGC	    0.998536	-238
TAACTCATGTCCGCTGTTGCGATGACTTCG	1	73	1	CCGCTGTTGC	    0.994915	-194
AACGTTATTACGGCATTGGCACGTCAGAAC	1	113	1	CGGCATTGGC	    0.996649	-154
CGTAAAAACTCGTCTTTTGCAGGATTTTAG	1	235	0	CGTCTTTTGC	    0.988419	-32
          **********

Masking position 7
Map Score:   5.39094

Number of sites scoring better than the average of aligned sites = 467
Number in coding regions = 449
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

AAAGACAACGGCGGTGGCTACAGATAGAATT	1	31	1	GCGGTGGTAC	    0.967912	-236
CGCAACAGCGGACATGAGTTACGAAAGCTTG	1	63	0	GACATGATTA	    0.937552	-204
GTCCGCTGTTGCGATGACTTCGTGTTAATCT	1	81	1	GCGATGATTC	    0.995508	-186
CAAAATCTGAGAGGTGAATCCGTTGAGTATA	1	142	1	GAGGTGATCC	    0.986963	-125
AATTATCTTAGCGACGATTTCGACGACTCAA	1	172	1	GCGACGATTC	    0.989015	-95
TGACGTTTAAGCCATGAAACAAGCTAAAATC	1	212	1	GCCATGAACA	    0.922092	-55
          ******* ***

Masking position 6
Map Score:   3.08791

Number of sites scoring better than the average of aligned sites = 1252
Number in coding regions = 1191
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 4

TAATCTTAACGTTATTACGGCATTGGCACG	1	106	1	GTTATTACGG	     0.99459	-161
CTCAGATTTTGTTCTGACGTGCCAATGCCG	1	123	0	GTTCTGACGT	     0.98823	-144
CAAAAGACGAGTTTTTACGGGCGTATTTAA	1	246	1	GTTTTTACGG	     0.99459	-21
          **********

Masking position 7
Map Score:   1.75909

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 68
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   -1.17788e-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 6

          **********

No masking
Map Score:   -1.17788e-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 7

          **********

No masking
Map Score:   -1.17788e-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