AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_not_clear_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	tldD	47	suppresses inhibitory activity of CsrA
#2	BIME161	74	BIME
#3	yhdR	67	orf, hypothetical protein
#4	mreC	65	rod shape-determining protein
#5	mreB	244	regulator of ftsI, penicillin binding protein 3, septation function

Motif number 1

CGTTAGTTACTGCAGTAGAGGATTTTTTACG	1	14	0	TGCAGAGAGG	    0.966846	-34
TGGGCCGCCATCCGGCAAAGGGTTTTTGAGT	3	19	1	TCCGGAAAGG	    0.963868	-49
TCACATTTTTAGCAGACAAGGAGTGACGG  	3	49	1	AGCAGCAAGG	    0.993477	-19
     TCGGATGCAGGCAGGGGAAGTGTCTG	4	6	1	TGCAGCAGGG	     0.99719	-60
CTCGTATCAGACCAGGCAGGGTAAACAGACA	4	31	0	ACCAGCAGGG	    0.990514	-35
CAATCTGGCGAGCAGACAAGCACACTCCCAT	5	58	0	AGCAGCAAGC	    0.990394	-187
CTTACGCGGTTGCAAACAGGCGAGGAATGCT	5	115	1	TGCAACAGGC	     0.98549	-130
TCTGCCTGAGTCCAGAAAGGCTTAATGCATC	5	149	0	TCCAGAAGGC	     0.98528	-96
GGCAGAGATTTGTAACAAAGGAAACGAACTG	5	174	1	TGTAAAAAGG	    0.775137	-71
   ACGCAGCAGCGACAAGGCGCAAAAATCA	5	227	0	AGCGAAAGGC	    0.925974	-18
          ***** *****

Masking position 10
Map Score:   17.1672

Number of sites scoring better than the average of aligned sites = 1427
Number in coding regions = 1319
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 2

TAAAAAATCCTCTACTGCAGTAACTAACGA	1	16	1	TCTACTGCAG	    0.952187	-32
TCACTCCTTGTCTGCTAAAAATGTGACTCA	3	45	0	TCTGCTAAAA	    0.843866	-23
          TCGGATGCAGGCAGGGGAAG	4	1	1	TCGGATGCAG	    0.974862	-65
CCCTGCCTGGTCTGATACGAGAATACGCAT	4	41	1	TCTGATACGA	    0.944994	-25
CATCTGCATATGTGCTGCAACAATCTGGCG	5	79	0	TGTGCTGCAA	    0.960695	-166
ATGACCTTACGCGGTTGCAAACAGGCGAGG	5	110	1	GCGGTTGCAA	    0.912985	-135
GAGGAATGCTGCTGATGCATTAAGCCTTTC	5	136	1	GCTGATGCAT	    0.966743	-109
GCAAAAATCATCTGCTACGGTGAAAATTAG	5	207	0	TCTGCTACGG	    0.982113	-38
GCGCCTTGTCGCTGCTGCGT          	5	235	1	GCTGCTGCGT	    0.983959	-10
          **********

Masking position 6
Map Score:   8.71473

Number of sites scoring better than the average of aligned sites = 4030
Number in coding regions = 3813
Number in noncoding regions = 217
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 3

TTTGCTACTCGTTAGTTACTGCAGTAGAGGAT	1	22	0	GTAGTTATGC	    0.899712	-26
AATCTCATAGGATAATCGTTGCCAAAGGCCAA	2	36	1	GAAATCGTGC	    0.963398	-39
CCGTTTTCACGTAGAATAATGCGCGCTGCGTC	5	24	1	GTGAATATGC	    0.962739	-221
TGTCTGCTCGCCAGATTGTTGCAGCACATATG	5	71	1	CCGATTGTGC	    0.938401	-174
GCAAACAGGCGAGGAATGCTGCTGATGCATTA	5	126	1	GAGAATGTGC	    0.986683	-119
CTGCTACGGTGAAAATTAGTGCAGTTCGTTTC	5	194	0	GAAATTATGC	    0.981925	-51
CACCGTAGCAGATGATTTTTGCGCCTTGTCGC	5	215	1	GAGATTTTGC	     0.97778	-30
          ** ***** ***

Masking position 10
Map Score:   3.28238

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 763
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 4

TGACGAGGGCGCGTAATTGCCCCAATCTCA	2	13	1	GCGTAATTGC	    0.963787	-62
GATAATCGTTGCCAAAGGCCAACGAGCCAG	2	46	1	GCCAAAGGCC	    0.961166	-29
AAAACCCTTTGCCGGATGGCGGCCCAGCAT	3	15	0	GCCGGATGGC	    0.934542	-53
CACTTCCCCTGCCTGCATCCGA        	4	3	0	GCCTGCATCC	    0.855059	-63
TTGTCTGCTCGCCAGATTGTTGCAGCACAT	5	70	1	GCCAGATTGT	    0.830885	-175
TCATTCATCTGCATATGTGCTGCAACAATC	5	84	0	GCATATGTGC	    0.740678	-161
GTTTGCAACCGCGTAAGGTCATTCATCTGC	5	102	0	GCGTAAGGTC	    0.863395	-143
AGCATTCCTCGCCTGTTTGCAACCGCGTAA	5	116	0	GCCTGTTTGC	    0.713226	-129
ACAAATCTCTGCCTGAGTCCAGAAAGGCTT	5	157	0	GCCTGAGTCC	    0.988741	-88
  ACGCAGCAGCGACAAGGCGCAAAAATCA	5	227	0	GCGACAAGGC	    0.789129	-18
          **********

Masking position 2
Map Score:   5.57197

Number of sites scoring better than the average of aligned sites = 4428
Number in coding regions = 4144
Number in noncoding regions = 284
Number of orfs with sites within 600 bp upstream = 254
Fraction of orfs with sites within 600 bp upstream = 0.0407967


Motif number 5

          **********

No masking
Map Score:   -3.03101e-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:   -3.03101e-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:   -3.03101e-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