AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i025_1_2_1_2_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	fdhD	193	affects formate dehydrogenase-N
#2	fdhF	197	selenopolypeptide subunit of formate dehydrogenase H

Motif number 1

AAGCGAATGTAAATGGGACGTGACAATGTCGAA	1	25	0	AATGGACGGA	    0.915115	-169
ATTTACATTCGCTTGCTGCGTGTGCAGGGAGTG	1	44	1	GTTGCGCGGT	    0.970801	-150
TGCTGCGTGTGCAGGGAGTGGGAGTTATTTTTC	1	57	1	GAGGGGTGGA	    0.945762	-137
       AATGTCTGCCGCGTGATGGCTGTCAC	2	4	1	GCTGCGCGGA	    0.996389	-194
TGACGAAACGAAATACCGCGTGACAGCCATCAC	2	23	0	AATACGCGGA	    0.978336	-175
CGTCAAAACTGACGACAGCCTGTTTTTCGTCAG	2	56	1	GCGACGCCGT	    0.963811	-142
AGTTTTGAATAAATAGTGCCCGTAATATCAGGG	2	89	1	AATAGGCCGT	    0.932599	-109
GCATACTGTAGTCGAGAGCGCGTATGCGTGATT	2	154	1	GCGAGGCGGT	    0.991509	-44
TGATTTGATTAACTGGAGCGAGACCG       	2	182	1	ACTGGGCGGA	    0.994299	-16
          * **** *** **

Masking position 12
Map Score:   10.0421

Number of sites scoring better than the average of aligned sites = 2956
Number in coding regions = 2708
Number in noncoding regions = 248
Number of orfs with sites within 600 bp upstream = 175
Fraction of orfs with sites within 600 bp upstream = 0.0281079


Motif number 2

CCTGCACACGCAGCAAGCGAATGTAAATGG	1	42	0	CAGCAAGCGA	    0.952444	-152
GCTGCGTGTGCAGGGAGTGGGAGTTATTTT	1	58	1	CAGGGAGTGG	    0.986608	-136
ATTTTTCTTTGCGGAAGGGGCCGCAAAGGT	1	83	1	GCGGAAGGGG	    0.980865	-111
GCGGAAGGGGCCGCAAAGGTCCAGAATTGG	1	93	1	CCGCAAAGGT	    0.900415	-101
ACCCTTCCTGGATGGAGGGAAATTGAGCCA	1	120	0	GATGGAGGGA	    0.917051	-74
TCCCTCCATCCAGGAAGGGTTTGTAACAGA	1	130	1	CAGGAAGGGT	    0.991506	-64
CCCGTAATATCAGGGAATGACCCCACATAA	2	107	1	CAGGGAATGA	    0.949029	-91
          **********

Masking position 6
Map Score:   4.66761

Number of sites scoring better than the average of aligned sites = 1559
Number in coding regions = 1392
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 189
Fraction of orfs with sites within 600 bp upstream = 0.0303566


Motif number 3

CGACATTGTCACGTCCCATTTACATTCGCTT	1	27	1	ACGTCCATTT	    0.981909	-167
GATGGCTGTCACGCGGTATTTCGTTTCGTCA	2	25	1	ACGCGTATTT	    0.933032	-173
AAACAGGCTGTCGTCAGTTTTGACGTGACGA	2	50	0	TCGTCGTTTT	     0.90428	-148
AGCCTGTTTTTCGTCAGAGTTTTGAATAAAT	2	72	1	TCGTCGAGTT	    0.935949	-126
TGCATCTTTTATGCCACATTTTATGTGGGGT	2	126	0	ATGCCCATTT	     0.98194	-72
CGACTACAGTATGCATCTTTTATGCCACATT	2	137	0	ATGCACTTTT	    0.792295	-61
GAGAGCGCGTATGCGTGATTTGATTAACTGG	2	167	1	ATGCGGATTT	    0.955822	-31
     CGGTCTCGCTCCAGTTAATCAAATCA	2	182	0	TCGCTCAGTT	    0.903933	-16
          ***** *****

Masking position 10
Map Score:   2.84304

Number of sites scoring better than the average of aligned sites = 2103
Number in coding regions = 1870
Number in noncoding regions = 233
Number of orfs with sites within 600 bp upstream = 223
Fraction of orfs with sites within 600 bp upstream = 0.0358175


Motif number 4

ATTGCTCCTTGTTTCGACATTGTCACGTCC	1	13	1	GTTTCGACAT	    0.873232	-181
GCGGTATTTCGTTTCGTCACGTCAAAACTG	2	37	1	GTTTCGTCAC	    0.904026	-161
GAAAAACAGGCTGTCGTCAGTTTTGACGTG	2	54	0	CTGTCGTCAG	    0.580983	-144
GACAGCCTGTTTTTCGTCAGAGTTTTGAAT	2	69	1	TTTTCGTCAG	    0.980627	-129
          **********

Masking position 4
Map Score:   2.42209

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 90
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -6.86222e-14

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:   -6.86222e-14

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:   -6.86222e-14

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