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

Motif number 1

CCGCCGTTGTCTTTAAGATTCAGGAGCGTA	1	15	0	CTTTAAGATT	    0.990415	-252
GCCGTAATAACGTTAAGATTAACACGAAGT	1	97	0	CGTTAAGATT	    0.993782	-170
ACGGATTCACCTCTCAGATTTTGTTCTGAC	1	135	0	CTCTCAGATT	    0.989446	-132
TCGAAATCGTCGCTAAGATAATTATACTCA	1	165	0	CGCTAAGATA	    0.989883	-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

TCTATCTGTAGCCACCGCCGTTGTCTTTAA	1	29	0	GCCACCGCCG	    0.998664	-238
CGAAGTCATCGCAACAGCGGACATGAGTTA	1	73	0	GCAACAGCGG	    0.995359	-194
GTTCTGACGTGCCAATGCCGTAATAACGTT	1	113	0	GCCAATGCCG	    0.996942	-154
CTAAAATCCTGCAAAAGACGAGTTTTTACG	1	235	1	GCAAAAGACG	    0.989423	-32
          **********

Masking position 4
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	    0.972626	-236
CGCAACAGCGGACATGAGTTACGAAAGCTTG	1	63	0	GACATGATTA	     0.94649	-204
GTCCGCTGTTGCGATGACTTCGTGTTAATCT	1	81	1	GCGATGATTC	    0.996009	-186
CAAAATCTGAGAGGTGAATCCGTTGAGTATA	1	142	1	GAGGTGATCC	    0.988892	-125
AATTATCTTAGCGACGATTTCGACGACTCAA	1	172	1	GCGACGATTC	    0.990584	-95
TGACGTTTAAGCCATGAAACAAGCTAAAATC	1	212	1	GCCATGAACA	    0.933091	-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

CGTGCCAATGCCGTAATAACGTTAAGATTA	1	106	0	CCGTAATAAC	     0.99459	-161
CGGCATTGGCACGTCAGAACAAAATCTGAG	1	123	1	ACGTCAGAAC	     0.98823	-144
TTAAATACGCCCGTAAAAACTCGTCTTTTG	1	246	0	CCGTAAAAAC	     0.99459	-21
          **********

Masking position 6
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