AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i067_2_1_1_13_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	metH	160	B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF
#2	HI1702	192	5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE)

Motif number 1

         TTTTATTGTTAGCTAATGCAATAGTTA	1	2	1	TTATTACTAT	    0.977265	-159
ATGAGATTTGTTCAACATTAACTCATCGGATCAGTT	1	41	0	TTAATACTAT	    0.964015	-120
TATGGTTTGTTGAATTTTTATTAAATCTGGGTTGAG	1	119	1	TGATTATAAT	    0.940251	-42
GCTGAATTGATTCATCGTTATTTGATAGATAAAAGA	2	29	1	TTATTATTAT	    0.986994	-164
AAAAGAATGCTTGATTATGAATTTATTTAATGTAAA	2	59	1	TTATTATTAT	    0.986994	-134
TCATTTATTATGCAAACTTATTATTTTCAGGATTTA	2	91	0	TGAATATATT	    0.859447	-102
TATAGAATGCTTGATCTTCATTTATTATGCAAACTT	2	108	0	TTATTATTTT	    0.979299	-85
ATAACTCCAATTTAAAGTAATTTTTTTAATCATTTA	2	166	0	TTAATATTTT	    0.967093	-27
          ** **  * * ** **

Masking position 10
Map Score:   7.3736

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 74
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 2

GCAACATGAGATTTGTTCAACATTAACTCATCG	1	49	0	ATTTTTAACT	     0.97836	-112
TGCCAGTATGGTTTGTTGAATTTTTATTAAATC	1	113	1	GTTTTTAATT	    0.888967	-48
AGTTAGCTGAATTGATTCATCGTTATTTGATAG	2	24	1	ATTGTTATCT	    0.986133	-169
TAGATAAAAGAATGCTTGATTATGAATTTATTT	2	54	1	AATGTTATTT	    0.937415	-139
TTGATTATGAATTTATTTAATGTAAATCCTGAA	2	69	1	ATTTTTAATT	    0.956325	-124
ACCAATATAGAATGCTTGATCTTCATTTATTAT	2	116	0	AATGTTATCT	    0.968687	-77
TTTAAAGTAATTTTTTTAATCATTTAGACGGCT	2	159	0	TTTTTTATCT	    0.935588	-34
          **** ** *** *

Masking position 9
Map Score:   4.11161

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 162
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 3

GCGTGGTGGTCGCTTTTACCACAGATGCGTT	1	80	1	CGCTTTTCCA	    0.992663	-81
ACCACAGATGCGTTTATGCCAGTATGGTTTG	1	97	1	CGTTTATCCA	    0.995559	-64
GCTCCCGACACGCTCAACCCAGATTTAATAA	1	136	0	CGCTCAACCA	    0.987819	-25
GACGGCTAAACGTCTATACCAATATAGAATG	2	135	0	CGTCTATCCA	    0.992452	-58
          ******* ***

Masking position 11
Map Score:   2.66152

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 127
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

CGTTTATGCCAGTATGGTTTGTTGAATTTT	1	107	1	AGTATGGTTT	    0.963504	-54
GATAGATAAAAGAATGCTTGATTATGAATT	2	52	1	AGAATGCTTG	    0.995737	-141
ATACCAATATAGAATGCTTGATCTTCATTT	2	121	0	AGAATGCTTG	    0.995737	-72
          **********

Masking position 4
Map Score:   1.95462

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

ACGCATCTGTGGTAAAAGCGACCACCACGC	1	80	0	GGTAAAAGCG	    0.987649	-81
AAACCATACTGGCATAAACGCATCTGTGGT	1	97	0	GGCATAAACG	     0.98682	-64
ATTCTATATTGGTATAGACGTTTAGCCGTC	2	136	1	GGTATAGACG	    0.985608	-57
          **********

Masking position 6
Map Score:   0.818595

Number of sites scoring better than the average of aligned sites = 56
Number in coding regions = 42
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 6

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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