AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i131_Transmembrane_Transport_5_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	ybiH	216	putative transcriptional regulator

Motif number 1

CGGGGCGGTTCGGAGTAGTT          	1	1	0	CGGAGTAGTT	     0.99592	-216
CGGTAACGGTCGGGGCGGTTCGGAGTAGTT	1	11	0	CGGGGCGGTT	    0.997049	-206
CGACCGTTACCGGTGTAGTTTTCAGGGAGA	1	29	1	CGGTGTAGTT	    0.995919	-188
TCCCTCATGACATTGTGGTTTTTGTCATTT	1	71	0	CATTGTGGTT	    0.958513	-146
GGGAGCGGAGTGTAGCAGTTTTTGTGACGC	1	97	1	TGTAGCAGTT	    0.967829	-120
TATGACTCCATAGGGGAGTTGTCCAGTATG	1	172	0	TAGGGGAGTT	    0.961957	-45
          **********

Masking position 9
Map Score:   8.16535

Number of sites scoring better than the average of aligned sites = 813
Number in coding regions = 746
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 2

GAAAAGGAAAATGACAAAAACCACAATGTC	1	63	1	ATGACAAAAA	    0.935247	-154
GTTGTCCAGTATGGCTAAGAATTTTAGCAA	1	155	0	ATGGCTAAGA	    0.988379	-62
AATCAAATGATTGATTAAGATTATGACTCC	1	193	0	TTGATTAAGA	    0.989443	-24
AATCAATCATTTGATTAAGA          	1	207	1	TTGATTAAGA	    0.989443	-10
          **********

Masking position 7
Map Score:   3.22795

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 44
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACCGGTAACGGTCGGGGCGGTTCGGAGTAG	1	13	0	GTCGGGGCGG	    0.998118	-204
ACAATGTCATGAGGGAGCGGAGTGTAGCAG	1	85	1	GAGGGAGCGG	    0.998345	-132
CAGTTTTTGTGACGCAGCGCATAAATTATC	1	112	1	GACGCAGCGC	    0.996929	-105
          **********

Masking position 4
Map Score:   2.3034

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 143
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

AACGGTCGGGGCGGTTCGGAGTAGTT    	1	7	0	GCGGTTCGGA	    0.937678	-210
AGTTTTCAGGGAGATACTGAAAAGGAAAAT	1	45	1	GAGATACTGA	    0.957795	-172
GCTCCCTCATGACATTGTGGTTTTTGTCAT	1	73	0	GACATTGTGG	    0.973401	-144
AGCAACGCCAGTCACAGGGATAATTTATGC	1	130	0	GTCACAGGGA	    0.934014	-87
AAAATTCTTAGCCATACTGGACAACTCCCC	1	160	1	GCCATACTGG	    0.993025	-57
AGATTATGACTCCATAGGGGAGTTGTCCAG	1	176	0	TCCATAGGGG	    0.955629	-41
          **********

Masking position 9
Map Score:   1.82942

Number of sites scoring better than the average of aligned sites = 1972
Number in coding regions = 1850
Number in noncoding regions = 122
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 5

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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