AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i094_Ribose_Transport_ecoli_hinf_reg_300.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	yjcW	33	putative ATP-binding component of a transport system
#2	BIME216	65	BIME
#3	yjcX	58	putative LACI-type transcriptional regulator
#4	rpiR	300	transcriptional repressor of rpiB expression

Motif number 1

CTTATCCGGCCAACAAAATAACCTGAAC     	2	48	1	CAAAAAAACC	    0.993072	-18
       TCACAATCAAAAAACATTTGTGATGT	4	4	1	CAAAAAAACA	    0.992499	-297
GTTTTTAATTCATTAACATCACAAATGTTTTTT	4	19	0	CATACACACA	    0.917196	-282
GATGTTAATGAATTAAAAACACCCAAAATCGAT	4	32	1	AATAAACACC	    0.887322	-269
CAACATCTATCATCTAAAAAACCAGAAAAACAA	4	140	1	CATAAAAACC	    0.984827	-161
AAAAACCAGAAAAACAAATAACATCATGTTTTT	4	156	1	AAAAAAAACA	    0.973913	-145
TAAACTAATTAAATGAAATAAAATTTTAAGCCA	4	188	1	AAAAAAAAAA	     0.94094	-113
CCATTGTTCACAATAAAATAAACTTTATAAATT	4	225	1	CAAAAAAAAC	    0.983916	-76
GGCGACTTCACAAAAAAATAAAATTTATAAAGT	4	246	0	CAAAAAAAAA	    0.982598	-55
ATCACCACAGCAAGAACAGAAAAGATGCTGGCG	4	275	0	CAAACAAAAA	    0.960441	-26
          ***  *** ****

Masking position 6
Map Score:   16.9193

Number of sites scoring better than the average of aligned sites = 339
Number in coding regions = 246
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 2

         AAATAACCTCTCTGCACGAAA	1	23	0	AATAACCTCT	    0.983969	-11
CGGCCAACAAAATAACCTGAAC        	2	54	1	AATAACCTGA	    0.945844	-12
GCGATGGCGGAATTACCTTTTTC       	3	4	0	AATTACCTTT	    0.946859	-55
GCCATCGCGGAGTTACCTGTCCCCTTACCG	3	26	1	AGTTACCTGT	    0.907097	-33
 TCACAATCAAAAAACATTTGTGATGTTAA	4	10	1	AAAAACATTT	    0.813924	-291
TTTTTAATTCATTAACATCACAAATGTTTT	4	21	0	ATTAACATCA	    0.796903	-280
TGTTTTACAGAGTTACATCTGACAGCGCAA	4	84	1	AGTTACATCT	    0.939701	-217
CTCACCATCCAGCAACATCTATCATCTAAA	4	128	1	AGCAACATCT	    0.852526	-173
CAGAAAAACAAATAACATCATGTTTTTAAA	4	162	1	AATAACATCA	    0.965381	-139
TTTTTAAACTAATTAAATGAAATAAAATTT	4	184	1	AATTAAATGA	    0.695195	-117
AATTAAATGAAATAAAATTTTAAGCCACTC	4	194	1	AATAAAATTT	    0.915663	-107
TTCACAATAAAATAAACTTTATAAATTTTA	4	231	1	AATAAACTTT	    0.917106	-70
TTCACAAAAAAATAAAATTTATAAAGTTTA	4	243	0	AATAAAATTT	    0.915663	-58
          **********

Masking position 5
Map Score:   16.4837

Number of sites scoring better than the average of aligned sites = 669
Number in coding regions = 508
Number in noncoding regions = 161
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 3

  AACTGAATGATGCCGGATGATGATGCTAA	2	9	1	GATGCGGATG	    0.997009	-57
GTAACTCCGCGATGGCGGAATTACCTTTTTC	3	11	0	GATGCGGAAT	    0.932002	-48
GTAATTCATCGATTTTGGGTGTTTTTAATTC	4	41	0	GATTTGGGTG	    0.946312	-260
ACGCTATTGCGCTGTCAGATGTAACTCTGTA	4	89	0	GCTGCAGATG	    0.977432	-212
GATGTTGCTGGATGGTGAGTGTCTTTAACGC	4	116	0	GATGTGAGTG	    0.984051	-185
TGGTTTTTTAGATGATAGATGTTGCTGGATG	4	133	0	GATGTAGATG	    0.967634	-168
TATTGTGAACAATGGCGAGTGGCTTAAAATT	4	209	0	AATGCGAGTG	    0.946313	-92
CAGAAAAGATGCTGGCGACTTCACAAAAAAA	4	261	0	GCTGCGACTT	    0.884077	-40
          **** ******

Masking position 3
Map Score:   7.11048

Number of sites scoring better than the average of aligned sites = 2764
Number in coding regions = 2439
Number in noncoding regions = 325
Number of orfs with sites within 600 bp upstream = 167
Fraction of orfs with sites within 600 bp upstream = 0.026823


Motif number 4

GTTGGCCGGATAAGACACTTCATTAGCATC	2	32	0	TAAGACACTT	    0.980268	-34
 TCACAATCAAAAAACATTTGTGATGTTAA	4	10	1	AAAAACATTT	    0.858137	-291
TTAATGAATTAAAAACACCCAAAATCGATG	4	36	1	AAAAACACCC	     0.96976	-265
CAATAGCGTTAAAGACACTCACCATCCAGC	4	111	1	AAAGACACTC	    0.993803	-190
AATAAAATTTTAAGCCACTCGCCATTGTTC	4	204	1	TAAGCCACTC	    0.980555	-97
          **********

Masking position 7
Map Score:   3.27627

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 69
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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