AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 = 	0

Input sequences:
#1	trpE	91	anthranilate synthase component I
#2	trpL	137	trp operon leader peptide
#3	pabB	73	p-aminobenzoate synthetase, component I
#4	pabA	31	p-aminobenzoate synthetase, component II
#5	yhfG	104	orf, hypothetical protein

Motif number 1

TCAGATACCCAGCCCGCCTAATGAGCGGGC	1	43	1	AGCCCGCCTA	    0.964962	-49
TTCAAAAAAAAGCCCGCTCATTAGGCGGGC	1	54	0	AGCCCGCTCA	    0.981153	-38
ACCGTTATGATGTCGGCGCAAAAAACATTA	2	30	0	TGTCGGCGCA	     0.99302	-108
CCTGCTAAATTGTTGGCGCTAATTATTTCA	3	19	1	TGTTGGCGCT	    0.902965	-55
ATTTCATGCTACCCGGCACATAGCCAGTAG	3	43	1	ACCCGGCACA	    0.966541	-31
CGGGCAAGATTGCCCGCGCGAGAAATCA  	5	9	0	TGCCCGCGCG	    0.968278	-96
CGGGCAATCTTGCCCGCGCTTCTGCTCTCC	5	23	1	TGCCCGCGCT	    0.801362	-82
GCTTCTGCTCTCCCGGCGTAACCCGGATTT	5	40	1	TCCCGGCGTA	    0.985619	-65
          **********

Masking position 6
Map Score:   13.309

Number of sites scoring better than the average of aligned sites = 1672
Number in coding regions = 1594
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 2

GCAAAAAACATTATCCAGAACGGGAGTGCGC	2	12	0	TTATCCAGAC	    0.980667	-126
TTTCAGAATATTTGCCAGAACCGTTATGATG	2	48	0	TTTGCCAGAC	    0.995062	-90
ATCGAACTAGTTAACTAGTACGCAAGTTCAC	2	99	1	TTAACTAGAC	    0.932602	-39
GCGCCAACAATTTAGCAGGAGTTAACA    	3	7	0	TTTAGCAGAG	    0.953507	-67
TACCCGGCACATAGCCAGTAGAGTCAGGACT	3	52	1	ATAGCCAGAG	    0.980283	-22
AACGTGTCCATTTGCCACAAGTATAAGCGGC	5	70	0	TTTGCCACAG	    0.978807	-35
          ******** **

Masking position 7
Map Score:   3.32841

Number of sites scoring better than the average of aligned sites = 912
Number in coding regions = 864
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

       AACGGGCAGTGTATTCACCATGC	1	4	1	GGGCAGTGTA	    0.983579	-88
CTCATTAGGCGGGCTGGGTATCTGATTGCT	1	38	0	GGGCTGGGTA	    0.981616	-54
TTATCCAGAACGGGAGTGCGCC        	2	3	0	CGGGAGTGCG	     0.97172	-135
TACTGGCTATGTGCCGGGTAGCATGAAATA	3	42	0	GTGCCGGGTA	    0.957504	-32
  TGATTTCTCGCGCGGGCAATCTTGCCCG	5	9	1	CGCGCGGGCA	    0.922543	-96
CGGGTTACGCCGGGAGAGCAGAAGCGCGGG	5	35	0	CGGGAGAGCA	    0.981618	-70
          **********

Masking position 6
Map Score:   3.05571

Number of sites scoring better than the average of aligned sites = 1079
Number in coding regions = 986
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 4

TAACGGTTCTGGCAAATATTCTGAAATGAGC	2	53	1	GGCAAATTTC	    0.977142	-85
TTAACTAGTACGCAAGTTCACGTAAAAAGGG	2	109	1	CGCAAGTCAC	    0.955953	-29
CATGCTACCCGGCACATAGCCAGTAGAGTCA	3	47	1	GGCACATGCC	    0.954066	-27
CAGAAGCGCGGGCAAGATTGCCCGCGCGAGA	5	16	0	GGCAAGATGC	    0.959937	-89
AAGTATAAGCGGCAAATCCGGGTTACGCCGG	5	52	0	GGCAAATCGG	    0.976649	-53
TTATACTTGTGGCAAATGGACACGTTCAGGG	5	75	1	GGCAAATGAC	     0.98115	-30
          ******* ***

Masking position 4
Map Score:   0.865886

Number of sites scoring better than the average of aligned sites = 808
Number in coding regions = 746
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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