AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_ecoli_mtub_100.orf -o307_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	rph	126	RNase PH
#2	Rv1335	21	hypothetical protein Rv1335
#3	Rv1339	26	hypothetical protein Rv1339
#4	Rv1341	38	hypothetical protein Rv1341

Motif number 1

CCTATCCTGACAAGGCATCGATGGCTATAA	1	46	0	CAAGGCATCG	    0.943761	-81
GCTGGCCTTTCTCGGAACGGT         	2	2	0	CTCGGAACGG	    0.993577	-20
GGAAGAGATTCTCGTCACCGA         	3	16	1	CTCGTCACCG	     0.99832	-11
TCTGCATCGTCGCGGCGCGG          	4	1	0	CGCGGCGCGG	    0.989078	-38
CATCGCTCCGCTCTGCATCGTCGCGGCGCG	4	12	0	CTCTGCATCG	    0.934969	-27
        TCCTCCTCATCGCTCCGCTCTG	4	27	0	CTCCTCATCG	    0.987705	-12
          **********

Masking position 1
Map Score:   10.3219

Number of sites scoring better than the average of aligned sites = 1349
Number in coding regions = 1303
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 2

TGACAAGGCATCGATGGCTATAATCCTTCC	1	39	0	TCGATGGCTA	    0.985043	-88
          TCGGTGACGAGAATCTCTTC	3	17	0	TCGGTGACGA	    0.923782	-10
CCGCGCCGCGACGATGCAGAGCGGAGCGAT	4	11	1	ACGATGCAGA	    0.982398	-28
GCAGAGCGGAGCGATGAGGAGGA       	4	26	1	GCGATGAGGA	    0.993252	-13
          **********

Masking position 5
Map Score:   1.60487

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 796
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TATACGGACTTCCGGCGGTTATTCCTATCC	1	69	0	TCCGGCGGTT	     0.98795	-58
AACAAATGTGGCTGCGCATTATACGGACTT	1	88	0	GCTGCGCATT	    0.980313	-39
TTTGTTTCAAGCCGGAGATTTCAAT     	1	112	1	GCCGGAGATT	    0.993124	-15
          GCTGGCCTTTCTCGGAACGG	2	12	0	GCTGGCCTTT	    0.992658	-10
          **********

Masking position 9
Map Score:   0.838529

Number of sites scoring better than the average of aligned sites = 1274
Number in coding regions = 1183
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 4

          **********

No masking
Map Score:   2.227e-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 5

          **********

No masking
Map Score:   2.227e-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:   2.227e-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