AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i331_not_clear6_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	b1775	26	putative transport protein
#2	b1776	300	putative oxidoreductase

Motif number 1

AGATCACAATTACGCAGAAAATGGCTGGGTC	2	166	0	TACCAGAAAA	    0.968274	-135
TGCGTTTTACAACTCAGATCACAATTACGCA	2	181	0	AACCAGATCA	    0.996542	-120
TGAGTTGTAAAACGCAGATCATTATCTGTGT	2	196	1	AACCAGATCA	    0.996562	-105
AAATCTGTAAAACACAGATAATGATCTGCGT	2	207	0	AACCAGATAA	    0.994693	-94
CCATCATACTTACCCACATGATTTTTGAGGT	2	245	0	TACCACATGA	    0.972705	-56
AGCAAAACTAAACACAGAGGATGACGCA   	2	283	1	AACCAGAGGA	    0.992368	-18
          *** *******

Masking position 6
Map Score:   11.2228

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 54
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

GGGACTTAGCCAGGTCATGGCGAGATA         	2	2	0	CAGGTTGGAT	     0.97855	-299
GGGACGGCAAGAGATCGGACTGGGACTTAGCCAGGT	2	23	0	GAGATGGGAC	    0.994894	-278
AGAAGTCATTCAGGTGTGAACGGGACGGCAAGAGAT	2	44	0	CAGGTGGGAC	    0.998583	-257
GATTACCGGCCAAATAGGTCTGAGACTTAAGTTCAG	2	81	0	CAAATGGGAC	     0.99653	-220
GCAAAAAGAGCAAATTCGAGAGGGATTACCGGCCAA	2	104	0	CAAATGGGAT	    0.989799	-197
CTGTGTTTTACAGATTTAATGTTGACCTCAAAAATC	2	221	1	CAGATATGAC	    0.961822	-80
          *****  *   * ***

Masking position 5
Map Score:   4.66757

Number of sites scoring better than the average of aligned sites = 307
Number in coding regions = 283
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

GACCTGGCTAAGTCCCAGTCCGATCTCTTG	2	22	1	AGTCCCAGTC	    0.997048	-279
GATCTCTTGCCGTCCCGTTCACACCTGAAT	2	43	1	CGTCCCGTTC	      0.9692	-258
CCTGAACTTAAGTCTCAGACCTATTTGGCC	2	80	1	AGTCTCAGAC	    0.973474	-221
TTCGAGAGGGATTACCGGCCAAATAGGTCT	2	96	0	ATTACCGGCC	     0.95393	-205
AACCTGTAACAGACCCAGCCATTTTCTGCG	2	155	1	AGACCCAGCC	     0.99374	-146
          **********

Masking position 6
Map Score:   3.23755

Number of sites scoring better than the average of aligned sites = 467
Number in coding regions = 427
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

TCCATCAACCTGTAACAGACCCAGCCATTT	2	149	1	TGTAACAGAC	    0.986254	-152
TGATCTGAGTTGTAAAACGCAGATCATTAT	2	191	1	TGTAAAACGC	    0.992483	-110
ACATTAAATCTGTAAAACACAGATAATGAT	2	213	0	TGTAAAACAC	    0.993675	-88
          **********

Masking position 5
Map Score:   1.81081

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 22
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

GATAACGTTCCTTCAGGAGAGTGG      	1	5	0	CTTCAGGAGA	    0.994763	-22
GTGAACGGGACGGCAAGAGATCGGACTGGG	2	35	0	CGGCAAGAGA	     0.99114	-266
TGAGACTTAAGTTCAGGAGAAGTCATTCAG	2	67	0	GTTCAGGAGA	     0.98612	-234
TTCCATCAACCTGTAACAGACCCAGCCATT	2	148	1	CTGTAACAGA	    0.947117	-153
          **********

Masking position 5
Map Score:   1.26734

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 253
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 6

GGTCTGTTACAGGTTGATGGAAGGCGGGGC	2	140	0	AGGTTGATGG	    0.993742	-161
CATGTGGGTAAGTATGATGGCCATCTAAGC	2	256	1	AGTATGATGG	    0.990355	-45
CTAAACACAGAGGATGACGCA         	2	290	1	AGGATGACGC	    0.992241	-11
          **********

Masking position 7
Map Score:   1.02553

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 57
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 7

          **********

No masking
Map Score:   -5.58897e-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 8

          **********

No masking
Map Score:   -5.58897e-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 9

          **********

No masking
Map Score:   -5.58897e-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