AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i081_PTS_cellobiose_specific_Transport_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	celC	50	PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin
#2	celB	84	PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin
#3	celA	298	PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin

Motif number 1

          TCGATGCCGGTACGGGTAATCG	1	1	1	TCATGCCGGA	    0.992931	-50
TTCCTCTCTTTTCTTACCGGCACGATTACCCG	1	23	0	TTTTACCGGA	      0.9611	-28
ATGAAATAACTCTTTGACGGGAAAATTTAAAA	2	15	0	TCTTGACGGA	    0.993353	-70
ATTTCATAAATCAATACCGCAATATTTAAATT	2	40	1	TCATACCGCA	    0.908468	-45
TAAATTGCGGTTTTTAAGGGTATTTTTCT   	2	66	1	TTTTAAGGGA	    0.786872	-19
GCGCCGGTTTTTTTTGGCCTGAGTTCTTAATT	3	54	1	TTTTGGCCTA	    0.793157	-245
CTTCGCGAATTATTTGCCCGAAATGTGAAGAG	3	88	1	TATTGCCCGA	    0.939428	-211
AAATTGTTTCTCCTTGACCTGTGGTTATGACC	3	120	0	TCTTGACCTT	    0.902173	-179
CAATAGTATTTCTTTGACCTTATAAATTGTTT	3	143	0	TCTTGACCTA	      0.9738	-156
ATTGCTCAGGTCTATACCGTATACTCCTTTCA	3	171	1	TCATACCGTT	    0.845362	-128
CAGATAATCGTCGATGAGGGCAGTTTT     	3	282	1	TCATGAGGGA	    0.954543	-17
          ** ******* *

Masking position 5
Map Score:   8.82566

Number of sites scoring better than the average of aligned sites = 3430
Number in coding regions = 3162
Number in noncoding regions = 268
Number of orfs with sites within 600 bp upstream = 277
Fraction of orfs with sites within 600 bp upstream = 0.0444908


Motif number 2

CCGCAATTTAAATATTGCGGTATTGATTTAT	2	45	0	AATATTGCGT	    0.721815	-40
CCGCAATATTTAAATTGCGGTTTTTAAGGGT	2	56	1	TAAATTGCGT	    0.895144	-29
ATTCGTCTGAAAGCTTGAGTAACAACGGAAA	3	14	1	AAGCTTGAGA	    0.908104	-285
GTAACAACGGAAACCGGCCATTGCGCCGGTT	3	32	1	AAACCGGCCT	    0.910457	-267
AGGCCAAAAAAAACCGGCGCAATGGCCGGTT	3	43	0	AAACCGGCGA	    0.972903	-256
CGGTTTTTTTTGGCCTGAGTTCTTAATTATC	3	58	1	TGGCCTGAGT	     0.92488	-241
TGTTTCTCCTTGACCTGTGGTTATGACCCTC	3	117	0	TGACCTGTGT	    0.872538	-182
TATACGGTATAGACCTGAGCAATAGTATTTC	3	163	0	AGACCTGAGA	    0.961069	-136
ATGCTCTGGGTAACTTGCGAAACCAACATGA	3	216	0	TAACTTGCGA	    0.966669	-83
AAGCAGGTTAAGGCTTGCGGAGTGTCTGGCT	3	249	1	AGGCTTGCGA	    0.970373	-50
          AAAACTGCCCTCATCGACGAT	3	288	0	AAAACTGCCT	    0.867654	-11
          ********* *

Masking position 7
Map Score:   8.56491

Number of sites scoring better than the average of aligned sites = 4335
Number in coding regions = 4029
Number in noncoding regions = 306
Number of orfs with sites within 600 bp upstream = 319
Fraction of orfs with sites within 600 bp upstream = 0.0512367


Motif number 3

CCTCTCTTTTCTTACCGGCACGATTACCCG	1	23	0	CTTACCGGCA	    0.977544	-28
GTTACTCAAGCTTTCAGACGAATTGA    	3	7	0	CTTTCAGACG	    0.975798	-292
CCCTCTTCACATTTCGGGCAAATAATTCGC	3	92	0	ATTTCGGGCA	    0.964845	-207
CCGTATACTCCTTTCAGCCACAAAAAAAGT	3	187	1	CTTTCAGCCA	    0.995921	-112
CGACGATTATCTGTCAGCCAGACACTCCGC	3	265	0	CTGTCAGCCA	     0.99099	-34
          **********

Masking position 2
Map Score:   3.55408

Number of sites scoring better than the average of aligned sites = 352
Number in coding regions = 321
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

GCCGGTTTTTTTTGGCCTGAGTTCTTAATT	3	56	1	TTTGGCCTGA	    0.927795	-243
GTATACTCCTTTCAGCCACAAAAAAAGTCA	3	189	1	TTCAGCCACA	    0.981007	-110
GGTTTCGCAAGTTACCCAGAGCATGGAAGC	3	223	1	GTTACCCAGA	    0.981961	-76
ACGATTATCTGTCAGCCAGACACTCCGCAA	3	263	0	GTCAGCCAGA	    0.995526	-36
          **********

Masking position 2
Map Score:   0.597715

Number of sites scoring better than the average of aligned sites = 457
Number in coding regions = 427
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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