AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i330_ecoli_mtub_100.orf -o330_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 
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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	cchB	106	detox protein
#2	b2462	220	orf, hypothetical protein

Motif number 1

TAAAATGAAAAAGGAGAGAGCGTGACGCCC	1	33	0	AAGGAGAGAG	    0.974214	-74
CCCTCCGCAGAAGGTAAAATGAAAAAGGAG	1	47	0	AAGGTAAAAT	    0.842269	-60
TGCGGAGGGTAGGGGGAGCTTTTACCTGAA	1	68	1	AGGGGGAGCT	    0.989551	-39
CTGAATATTCAGGGTAAGCGTGAGAGTTAA	2	17	0	AGGGTAAGCG	    0.988285	-204
CTGAATATTCAGGGTAAGCAGTTTAGCTGC	2	35	1	AGGGTAAGCA	    0.968686	-186
ATCACTAAGAATGGAGAGATATTCGCTGTG	2	179	0	ATGGAGAGAT	    0.947467	-42
GCGCGTTTAAAAGGTGAGGTAGATCACTAA	2	201	0	AAGGTGAGGT	    0.980344	-20
          **********

Masking position 7
Map Score:   6.89262

Number of sites scoring better than the average of aligned sites = 609
Number in coding regions = 470
Number in noncoding regions = 139
Number of orfs with sites within 600 bp upstream = 136
Fraction of orfs with sites within 600 bp upstream = 0.0218439


Motif number 2

GCCCGAATCGACGTCACACAGGGTGA     	1	6	0	ACGTACACAG	    0.983647	-101
AGCTCCCCCTACCCTCCGCAGAAGGTAAAAT	1	57	0	ACCCCCGCAG	    0.995227	-50
TACCTGAAATACGCCACGGAGGCGGGT    	1	90	1	ACGCACGGAG	    0.994865	-17
AAACTTTCATATGCAACGCATGAATATAAAT	2	142	0	ATGCACGCAT	    0.840048	-79
ATGAAAGTTTATGCACCACAGCGAATATCTC	2	163	1	ATGCCCACAG	    0.991129	-58
          **** ******

Masking position 10
Map Score:   4.30974

Number of sites scoring better than the average of aligned sites = 828
Number in coding regions = 791
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

TCCGTGGCGTATTTCAGGTAAAAGCTCCCC	1	80	0	ATTTCAGGTA	     0.98003	-27
TACCCTGAATATTCAGGGTAAGCGTGAGAG	2	21	0	ATTCAGGGTA	    0.992583	-200
TACCCTGAATATTCAGGGTAAGCAGTTTAG	2	31	1	ATTCAGGGTA	    0.992583	-190
TTACTAATATATTGCAGCTAAACTGCTTAC	2	48	0	ATTGCAGCTA	    0.964455	-173
          **********

Masking position 3
Map Score:   2.72929

Number of sites scoring better than the average of aligned sites = 88
Number in coding regions = 79
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

   TCACCCTGTGTGACGTCGATTCGGGCG	1	8	1	GTGTGACGTC	     0.97336	-99
AAAGGAGAGAGCGTGACGCCCGAATCGACG	1	24	0	GCGTGACGCC	    0.975332	-83
TTTACCTTCTGCGGAGGGTAGGGGGAGCTT	1	59	1	GCGGAGGGTA	    0.948634	-48
  ACCCGCCTCCGTGGCGTATTTCAGGTAA	1	89	0	CCGTGGCGTA	    0.988828	-18
TTATATTCATGCGTTGCATATGAAAGTTTA	2	144	1	GCGTTGCATA	    0.983019	-77
GATATTCGCTGTGGTGCATAAACTTTCATA	2	162	0	GTGGTGCATA	    0.941917	-59
          **********

Masking position 3
Map Score:   1.8215

Number of sites scoring better than the average of aligned sites = 3228
Number in coding regions = 2992
Number in noncoding regions = 236
Number of orfs with sites within 600 bp upstream = 221
Fraction of orfs with sites within 600 bp upstream = 0.0354963


Motif number 5

AGCGTGAGAGTTAAAAAAAA          	2	1	0	TTAAAAAAAA	    0.974318	-220
TTTGCGAATAATAAAAAAAAGCAGTCTATA	2	92	1	ATAAAAAAAA	    0.985346	-129
ACGCATGAATATAAATAAAATAATATCGAG	2	128	0	ATAAATAAAA	    0.974318	-93
          **********

Masking position 5
Map Score:   1.76641

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 10
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 6

          **********

No masking
Map Score:   -5.58897e-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:   -5.58897e-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 8

          **********

No masking
Map Score:   -5.58897e-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