AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icysB_ecoli_opreg_100.orf -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	cysB	209	positive transcriptional regulator for cysteine regulon
#2	cysK	184	cysteine synthase A, O-acetylserine sulfhydrolase A

Motif number 1

TCAGGTTTTTATAAACAAAGGGTCGCGAAAG	1	23	1	ATAAACAAGG	    0.962033	-187
ATAATATGCAATAAAAAAGGGCCGCTTTCGC	1	47	0	ATAAAAAGGG	    0.994914	-163
CTTCACACCTATACACTAAGGCTATAAATGA	1	83	1	ATACACAAGG	    0.970258	-127
CGATTTAATAATAAAAAAGGTGCTAACTATA	1	123	0	ATAAAAAGGT	    0.974698	-87
AACCGTTTGTGTGAAACAGGGGTGGCTTATG	2	32	1	GTGAAAAGGG	    0.974162	-153
AAATAATGACATGCAAGATGGAATAAGGGGC	2	65	0	ATGCAAATGG	    0.964219	-120
GCATATCTATATACAGAAGGGAAATAATGAC	2	86	0	ATACAGAGGG	    0.987261	-99
TGAAATTGGGATACAACAGGTAGCATACCCG	2	146	0	ATACAAAGGT	    0.980236	-39
CCTTAACTGTATGAAATTGGGATACAACAGG	2	157	0	ATGAAATGGG	    0.962176	-28
          ****** ****

Masking position 5
Map Score:   14.6973

Number of sites scoring better than the average of aligned sites = 211
Number in coding regions = 171
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 2

GGCCGCTTTCGCGACCCTTTGTTTATAAAA	1	29	0	GCGACCCTTT	    0.994385	-181
GGTCGCGAAAGCGGCCCTTTTTTATTGCAT	1	43	1	GCGGCCCTTT	    0.994796	-167
TCGTTTTTTCGTCACACCTGGCGGGTGACT	1	158	0	GTCACACCTG	    0.958402	-52
GGCGGCATAAGCCACCCCTGTTTCACACAA	2	38	0	GCCACCCCTG	    0.998409	-147
GGTGGCTTATGCCGCCCCTTATTCCATCTT	2	52	1	GCCGCCCCTT	    0.998408	-133
          **********

Masking position 9
Map Score:   8.87849

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 72
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

TATAAACAAAGGGTCGCGAAAGCGGCCCTT	1	32	1	GGGTCGCGAA	    0.992916	-178
TAGTGTATAGGTGTGAAGAAAAAATAATAT	1	71	0	GTGTGAAGAA	    0.974924	-139
CACACCTGGCGGGTGACTAATACGATTTAA	1	146	0	GGGTGACTAA	    0.995096	-64
CACCCGCCAGGTGTGACGAAAAAACGATGT	1	161	1	GTGTGACGAA	    0.995096	-49
TGTGAAACAGGGGTGGCTTATGCCGCCCCT	2	41	1	GGGTGGCTTA	    0.985201	-144
          **********

Masking position 4
Map Score:   7.27486

Number of sites scoring better than the average of aligned sites = 320
Number in coding regions = 294
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          CCTTTAATTCTGTCAGGTTTTTA	1	1	1	CCTTAATTTT	    0.924351	-209
TTTTTTATTGCATATTATTTTTTCTTCACACCT	1	60	1	CATTTATTTT	    0.968969	-150
TAACTATAACCACTATATCATTTATAGCCTTAG	1	98	0	CACATATCTT	    0.922471	-112
TAGACGCCATCAGAACATCGTTTTTTCGTCACA	1	172	0	CAGACATCTT	    0.921027	-38
   CAATCTACCGGTTATTTTGTAAACCGTTTG	2	8	1	CCGTTATTTT	    0.987323	-177
GCTTATGCCGCCCCTTATTCCATCTTGCATGTC	2	56	1	CCCTTATTCT	    0.934215	-129
TTCCATCTTGCATGTCATTATTTCCCTTCTGTA	2	73	1	CATTCATTTT	     0.95457	-112
ATCCTTACTTCCGCATATTCTCTGAGCGGGTAT	2	120	1	CCGATATTTT	    0.979817	-65
          *** ***** * *

Masking position 7
Map Score:   4.15866

Number of sites scoring better than the average of aligned sites = 312
Number in coding regions = 236
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 5

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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:   7.34864e-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