AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i085_PTS_mannitol_specific_Transport_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	sgaT	291	orf, hypothetical protein

Motif number 1

TCATGATAGTTCAATTCGAATCAATATGTGATT	1	17	1	TCAATTAACA	    0.976401	-275
TCAGGATTAATCAAAACCAATCACATATTGATT	1	35	0	TCAAAAAACA	    0.996816	-257
CTTTCCATACTCAAAATCAACAACAACTTCCCT	1	113	0	TCAAAAAAAA	    0.979779	-179
AGTGGGATTCACACAACGAAACAATTATCCATT	1	186	0	ACACAAAACA	    0.984629	-106
GCGGGTCGCGTCACATTTAATCATAAATAATCT	1	239	1	TCACATAACA	    0.992851	-53
ACTCTAATTTTCAAAAGTAATCACAACAAGATT	1	267	0	TCAAAAAACA	    0.996802	-25
          ******  ** **

Masking position 9
Map Score:   9.00826

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 26
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

CTTCATGATAGTTCAATTCGAATCAATATG	1	15	1	GTTCAATTCG	    0.940815	-277
TGAATTACACATTCCATTAAATCTTTCCAT	1	138	0	ATTCCATTAA	    0.970316	-154
GGAATGTGTAATTCAATTAACTAAATGAAT	1	153	1	ATTCAATTAA	    0.986406	-139
ATCCATTTAAATTCATTTAGTTAATTGAAT	1	163	0	ATTCATTTAG	    0.982033	-129
CGAAACAATTATCCATTTAAATTCATTTAG	1	173	0	ATCCATTTAA	    0.958002	-119
          **********

Masking position 7
Map Score:   3.69817

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 24
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

CATTCCATTAAATCTTTCCATACTCAAAAT	1	129	0	AATCTTTCCA	    0.991523	-163
TAATTGAATTACACATTCCATTAAATCTTT	1	142	0	ACACATTCCA	    0.986227	-150
TGTGAATCCCACTCTATCCATGTGGAATTA	1	206	1	ACTCTATCCA	    0.986227	-86
GCGACCCGCAAATAATTCCACATGGATAGA	1	218	0	AATAATTCCA	    0.967145	-74
          **********

Masking position 7
Map Score:   3.22819

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 72
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

ATGTGATTGGTTTTGATTAATCCTGACACTA	1	42	1	TTTTGATAAT	    0.984281	-250
AATGACCATTTTTTGACTTTTTGCCAGGGAA	1	88	1	TTTTGATTTT	    0.964723	-204
TTGTTGTTGATTTTGAGTATGGAAAGATTTA	1	120	1	TTTTGATATG	    0.981415	-172
ACAAGATTATTTATGATTAAATGTGACGCGA	1	244	0	TTATGATAAA	    0.882911	-48
TTGTGATTACTTTTGAAAATTAGAGTGA   	1	274	1	TTTTGAAATT	    0.964695	-18
          ****** ****

Masking position 6
Map Score:   2.3167

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 53
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 5

CCTGAAAAAATAGTGTCAGGATTAATCAAA	1	53	0	TAGTGTCAGG	    0.984825	-239
CCTGACACTATTTTTTCAGGAAGGCAATGA	1	63	1	TTTTTTCAGG	    0.986212	-229
TTTTTTGACTTTTTGCCAGGGAAGTTGTTG	1	96	1	TTTTGCCAGG	    0.989355	-196
CATGTGGAATTATTTGCGGGTCGCGTCACA	1	224	1	TATTTGCGGG	    0.972425	-68
          **********

Masking position 4
Map Score:   1.67238

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 164
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 6

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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 8

          **********

No masking
Map Score:   -4.80737e-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