AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jada.reg -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	137

Input sequences:
#1	alkA 70 bp alkA 282 1-849 CDS
#2	ada 73 bp ada 354 1-1065 CDS
#3	aidB 68 bp aidB 546 1-1641 CDS

Motif number 1

AATAACGTTTATGCTGAAAGCGGATGAATAA	1	41	1	ATGCTGAAGC	    0.994577	-30
TTTTTGCGTGATGGTGACCGGGCAGCCTAAA	2	27	1	ATGGTGACGG	    0.988662	-47
CACCATTAGTATGGTCACTGCCATGGATTCA	3	38	0	ATGGTCACGC	    0.997397	-31
GACCATACTAATGGTGACTGCCATTG     	3	53	1	ATGGTGACGC	    0.999027	-16
          ******** **

Masking position 5
Map Score:   8.47272

Number of sites scoring better than the average of aligned sites = 71
Number in coding regions = 65
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

GTTATTCAGACGCTGCGCTTTGCTTTCATA	1	17	0	CGCTGCGCTT	     0.99309	-54
ATAGCCTTTAGGCTGCCCGGTCACCATCAC	2	34	0	GGCTGCCCGG	     0.99722	-40
GCAGCCTAAAGGCTATCCTTAACCAGGGAG	2	48	1	GGCTATCCTT	    0.964414	-26
TTAGTATGGTCACTGCCATGGATTCATGAC	3	34	0	CACTGCCATG	    0.989419	-35
TACTAATGGTGACTGCCATTG         	3	58	1	GACTGCCATT	    0.993158	-11
          **********

Masking position 4
Map Score:   5.52882

Number of sites scoring better than the average of aligned sites = 1008
Number in coding regions = 957
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

TCAGCATAAACGTTATTCAGACGCTGCGCTTTGC	1	24	0	CTTATTCCGC	    0.998335	-47
   CGCATCTCCTTATTCATCCGCTTTCAGCATA	1	50	0	CTTATTCCGC	    0.998317	-21
ACGCAAAAACCAACAATCTTGCGCT         	2	2	0	CACAATCCGC	    0.995012	-72
CTCTTTCTGTCATGAATCCATGGCAGTGACCATA	3	26	1	CTGAATCGGC	     0.99471	-43
          * ******   ***

Masking position 7
Map Score:   2.17963

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 98
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

TCCGCTTTCAGCATAAACGTTATTCAGACG	1	35	0	GCATAAACGT	    0.988987	-36
TCACCATCACGCAAAAACCAACAATCTTGC	2	14	0	GCAAAAACCA	    0.989037	-60
GAAAGAGATTGCTAAAACATTC        	3	3	0	GCTAAAACAT	    0.983837	-66
          **********

Masking position 5
Map Score:   0.400092

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 145
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   -4.73059e-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 6

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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