AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i131_Transmembrane_Transport_5_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ybiH	216	putative transcriptional regulator

Motif number 1

CGGGGCGGTTCGGAGTAGTT          	1	1	0	CGGAGTAGTT	     0.99559	-216
CGGTAACGGTCGGGGCGGTTCGGAGTAGTT	1	11	0	CGGGGCGGTT	    0.996811	-206
CGACCGTTACCGGTGTAGTTTTCAGGGAGA	1	29	1	CGGTGTAGTT	     0.99559	-188
TCCCTCATGACATTGTGGTTTTTGTCATTT	1	71	0	CATTGTGGTT	      0.9553	-146
GGGAGCGGAGTGTAGCAGTTTTTGTGACGC	1	97	1	TGTAGCAGTT	    0.965311	-120
TATGACTCCATAGGGGAGTTGTCCAGTATG	1	172	0	TAGGGGAGTT	       0.959	-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	    0.939486	-154
GTTGTCCAGTATGGCTAAGAATTTTAGCAA	1	155	0	ATGGCTAAGA	    0.989181	-62
AATCAAATGATTGATTAAGATTATGACTCC	1	193	0	TTGATTAAGA	    0.990171	-24
AATCAATCATTTGATTAAGA          	1	207	1	TTGATTAAGA	    0.990171	-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	    0.998109	-204
ACAATGTCATGAGGGAGCGGAGTGTAGCAG	1	85	1	GAGGGAGCGG	    0.998336	-132
CAGTTTTTGTGACGCAGCGCATAAATTATC	1	112	1	GACGCAGCGC	    0.996914	-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

    AACTACTCCGAACCGCCCCGACCGTT	1	7	1	TCCGAACCGC	    0.932297	-210
ATTTTCCTTTTCAGTATCTCCCTGAAAACT	1	45	0	TCAGTATCTC	    0.953728	-172
ATGACAAAAACCACAATGTCATGAGGGAGC	1	73	1	CCACAATGTC	    0.970791	-144
GCATAAATTATCCCTGTGACTGGCGTTGCT	1	130	1	TCCCTGTGAC	    0.927829	-87
GGGGAGTTGTCCAGTATGGCTAAGAATTTT	1	160	0	CCAGTATGGC	    0.992425	-57
CTGGACAACTCCCCTATGGAGTCATAATCT	1	176	1	CCCCTATGGA	    0.954743	-41
          **********

Masking position 2
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