AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i344_weak5_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	HI1578	300	glycosyl transferase, putative

Motif number 1

CACCACGGTGTTACTTTGCCATTTCG        	1	3	0	TTTGCCATTT	    0.975829	-298
GTGGTGGTTATGAATATGCAATCTGCAACACTGT	1	31	1	TTAGCAATCT	    0.919521	-270
ATAATAATACTACCTTGTTTATTTTCTCGAATAA	1	71	0	TTTTTTATTT	    0.949799	-230
GGTTATGATATTCTTAAGCTATATTTAAAGGAAT	1	120	1	TTAGCTATAT	    0.952779	-181
TTAAAAAAACTCAAATTTCTATTTCAAAACAATT	1	180	1	TATTCTATTT	    0.843211	-121
TAGGAGAGTTTTAATTGGTTATCTATGCATCTCC	1	218	1	TTTGTTATCT	    0.982352	-83
TCTATGCATCTCCTTTTGTTATTTAAATAACGTA	1	239	1	TTTGTTATTT	    0.988055	-62
TTTAAACTATTTTATACGTTATTTAAATAACAAA	1	253	0	TTAGTTATTT	    0.980974	-48
          *   ** *******

Masking position 11
Map Score:   5.51747

Number of sites scoring better than the average of aligned sites = 312
Number in coding regions = 229
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 95
Fraction of orfs with sites within 600 bp upstream = 0.0152586


Motif number 2

CCGTGGTGGTTATGAATATGCAATCTGCAA	1	29	1	TATGAATATG	    0.975333	-272
AGTATTATTATATGAATTTCTACAGAGGTT	1	94	1	TATGAATTTC	    0.987493	-207
AAATATAGCTTAAGAATATCATAACCTCTG	1	116	0	TAAGAATATC	    0.976914	-185
TTTAAAGGAATATGAATGGCGTTTTAATCA	1	143	1	TATGAATGGC	    0.981385	-158
ATTGGTTATCTATGCATCTCCTTTTGTTAT	1	231	1	TATGCATCTC	    0.981385	-70
          **********

Masking position 6
Map Score:   4.53445

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 63
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

GAATATGAATGGCGTTTTAATCACAGTGAT	1	150	1	GGCGTTTTAA	    0.950496	-151
TTTTAATCACAGTGATTTAAAAAAACTCAA	1	164	1	AGTGATTTAA	    0.954871	-137
GTTTTGAAATAGAAATTTGAGTTTTTTTAA	1	180	0	AGAAATTTGA	    0.781109	-121
TCCTAAATTAATTGTTTTGAAATAGAAATT	1	193	0	ATTGTTTTGA	    0.927508	-108
TTAATTTAGGAGAGTTTTAATTGGTTATCT	1	212	1	AGAGTTTTAA	    0.986888	-89
TATTTTATACGTTATTTAAATAACAAAAGG	1	250	0	GTTATTTAAA	    0.645861	-51
AACGTATAAAATAGTTTAAAGAAGAGTGTA	1	267	1	ATAGTTTAAA	    0.948288	-34
AGTTTAAAGAAGAGTGTAAAATTAGAGCTT	1	279	1	AGAGTGTAAA	    0.925715	-22
          **********

Masking position 10
Map Score:   4.079

Number of sites scoring better than the average of aligned sites = 853
Number in coding regions = 704
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 171
Fraction of orfs with sites within 600 bp upstream = 0.0274655


Motif number 4

TATTCATAACCACCACGGTGTTACTTTGCC	1	17	0	CACCACGGTG	    0.743384	-284
ATGCAATCTGCAACACTGTTACCGATTATT	1	46	1	CAACACTGTT	    0.971036	-255
TCGAGAAAATAAACAAGGTAGTATTATTAT	1	75	1	AAACAAGGTA	    0.918221	-226
AGAATATCATAACCTCTGTAGAAATTCATA	1	104	0	AACCTCTGTA	    0.960997	-197
AGTTTTTTTAAATCACTGTGATTAAAACGC	1	161	0	AATCACTGTG	    0.979799	-140
          **********

Masking position 2
Map Score:   1.87185

Number of sites scoring better than the average of aligned sites = 571
Number in coding regions = 540
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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