AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i107_TRK_operon_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	trkG	137	trk system potassium uptake; part of Rac prophage
#2	def	129	peptide deformylase
#3	sun	45	orf, hypothetical protein
#4	trkA	21	transport of potassium

Motif number 1

ATCAAAATGAATCATATTGTAGTTAAGATT	1	11	0	ATCATATTGT	    0.888727	-127
CTCCTCTTAGATCTTACTTCACTGTTCCTT	1	52	0	ATCTTACTTC	    0.940248	-86
CAGTATAATCATAATATTGCAGCAAGGTGG	1	94	1	ATAATATTGC	    0.965951	-44
TTCAATTATAACCACCTTGCTGCAATATTA	1	105	0	ACCACCTTGC	    0.964138	-33
    ATCTAAATATTCTTTCAATTATAACC	1	122	0	ATATTCTTTC	     0.95899	-16
      CCTTATCTCCCTGCCATAAGCAGC	2	5	1	ATCTCCCTGC	     0.97834	-125
AATAGAAGAAATAATCTTTCTAACTCCTGA	2	92	1	ATAATCTTTC	    0.968182	-38
          **********

Masking position 1
Map Score:   5.06719

Number of sites scoring better than the average of aligned sites = 1480
Number in coding regions = 1337
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 2

      AATCTTAACTACAATATGATTCATTT	1	5	1	TTCTACAATA	    0.991897	-133
AGGAGTTAAATTTTATACAGTATAATCATAAT	1	77	1	TTATACAGTA	    0.913034	-61
TTATAACCACCTTGCTGCAATATTATGATTAT	1	98	0	CTCTGCAATA	    0.993054	-40
    CCTTATCTCCCTGCCATAAGCAGCCTTA	2	7	1	CTCTGCCATA	    0.984728	-123
AGAGGGGGATTTGTCTAGAATAGAAGAAATAA	2	74	1	TTCTAGAATA	    0.963962	-56
          **  ********

Masking position 6
Map Score:   0.997425

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 124
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

CTGTTCCTTATGAAACAATCATCAAAATGA	1	31	0	TGAAACAATC	    0.985376	-107
TGGTTATAATTGAAAGAATATTTAGAT   	1	121	1	TGAAAGAATA	    0.959615	-17
CCCCTCTGATTGACAGCATCACTGACCAAT	2	51	0	TGACAGCATC	    0.983687	-79
CTAGAATAGAAGAAATAATCTTTCTAACTC	2	88	1	AGAAATAATC	    0.932515	-42
TTCTAACTCCTGAACACATCTCTGGAGATT	2	109	1	TGAACACATC	    0.956726	-21
          **********

Masking position 3
Map Score:   1.67461

Number of sites scoring better than the average of aligned sites = 377
Number in coding regions = 335
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

GTTTCATAAGGAACAGTGAAGTAAGATCTA	1	45	1	GAACAGTGAA	    0.971965	-93
TAAGATCTAAGAGGAGTTAAATTTTATACA	1	66	1	GAGGAGTTAA	    0.991875	-72
GTCTAGAATAGAAGAAATAATCTTTCTAAC	2	86	1	GAAGAAATAA	    0.868182	-44
GAGATGTGTTCAGGAGTTAGAAAGATTATT	2	101	0	CAGGAGTTAG	    0.939825	-29
ACCGGGCTTAGAAGAGTGGACTA       	3	4	0	GAAGAGTGGA	     0.98214	-42
          **********

Masking position 5
Map Score:   0.680991

Number of sites scoring better than the average of aligned sites = 376
Number in coding regions = 313
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 5

          **********

No masking
Map Score:   4.42969e-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:   4.42969e-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:   4.42969e-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