AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i085_ecoli_bsub_300.orf -o085_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	sgaT	291	orf, hypothetical protein

Motif number 1

TCATGATAGTTCAATTCGAATCAATATGTGATT	1	17	1	TCAATTAACA	    0.970104	-275
TCAGGATTAATCAAAACCAATCACATATTGATT	1	35	0	TCAAAAAACA	    0.995943	-257
CTTTCCATACTCAAAATCAACAACAACTTCCCT	1	113	0	TCAAAAAAAA	    0.974351	-179
AGTGGGATTCACACAACGAAACAATTATCCATT	1	186	0	ACACAAAACA	    0.980477	-106
GCGGGTCGCGTCACATTTAATCATAAATAATCT	1	239	1	TCACATAACA	    0.990906	-53
ACTCTAATTTTCAAAAGTAATCACAACAAGATT	1	267	0	TCAAAAAACA	    0.995932	-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	    0.941611	-277
TGAATTACACATTCCATTAAATCTTTCCAT	1	138	0	ATTCCATTAA	    0.970728	-154
GGAATGTGTAATTCAATTAACTAAATGAAT	1	153	1	ATTCAATTAA	    0.986598	-139
ATCCATTTAAATTCATTTAGTTAATTGAAT	1	163	0	ATTCATTTAG	    0.982285	-129
CGAAACAATTATCCATTTAAATTCATTTAG	1	173	0	ATCCATTTAA	    0.958578	-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	    0.990782	-163
TAATTGAATTACACATTCCATTAAATCTTT	1	142	0	ACACATTCCA	    0.985031	-150
TGTGAATCCCACTCTATCCATGTGGAATTA	1	206	1	ACTCTATCCA	    0.985031	-86
GCGACCCGCAAATAATTCCACATGGATAGA	1	218	0	AATAATTCCA	    0.964352	-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

TAGTGTCAGGATTAATCAAAACCAATCACAT	1	42	0	ATTATCAAAA	     0.98488	-250
TTCCCTGGCAAAAAGTCAAAAAATGGTCATT	1	88	0	AAAATCAAAA	    0.966047	-204
TAAATCTTTCCATACTCAAAATCAACAACAA	1	120	0	CATATCAAAA	    0.982125	-172
TCGCGTCACATTTAATCATAAATAATCTTGT	1	244	1	TTTATCATAA	    0.886935	-48
   TCACTCTAATTTTCAAAAGTAATCACAA	1	274	0	AATTTCAAAA	    0.966019	-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

TTTGATTAATCCTGACACTATTTTTTCAGG	1	53	1	CCTGACACTA	    0.986195	-239
TCATTGCCTTCCTGAAAAAATAGTGTCAGG	1	63	0	CCTGAAAAAA	    0.987458	-229
CAACAACTTCCCTGGCAAAAAGTCAAAAAA	1	96	0	CCTGGCAAAA	    0.990319	-196
TGTGACGCGACCCGCAAATAATTCCACATG	1	224	0	CCCGCAAATA	    0.974886	-68
          **********

Masking position 7
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