AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i290_ecoli_mtub_300.orf -o290_ecoli_mtub_300.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	b1970	84	orf, hypothetical protein
#2	b1971	108	putative reductase

Motif number 1

ATCCTCAAAACTCATTCACATGACAAGGAT	1	59	1	CTCATTCACA	     0.98243	-26
    GTTTATATCCTTGTCATGTGAATGAG	1	69	0	ATCCTTGTCA	    0.975223	-16
AGGGAGTGTCCTCCCTAACAGTAGCAGAGA	2	33	0	CTCCCTAACA	    0.993993	-76
AGGGAGGACACTCCCTGACAGATTAACAGT	2	47	1	CTCCCTGACA	    0.997788	-62
         AAGCCATCACACTTTTTTGTC	2	98	0	AGCCATCACA	    0.970632	-11
          **********

Masking position 6
Map Score:   5.90977

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 125
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

GTAATGCTGCTGTAAGGTTACCCTGGACGCTTTT	1	20	1	TGTGTTACCT	    0.996588	-65
CCCTGGACGCTTTTTCGCTATCCTCAAAACTCAT	1	40	1	TTTGCTACCT	    0.996524	-45
GCAAGAGCCGTTTACTGTTAATCTGTCAGGGAGT	2	56	0	TTTGTTATCT	    0.992094	-53
ATCACACTTTTTTGTCGTTAGCCAGCAAGAGCCG	2	80	0	TTTGTTACCA	    0.994915	-29
          ***   **** ***

Masking position 9
Map Score:   2.34024

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 44
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

GGGTAACCTTACAGCAGCATTACAATTTTG	1	13	0	ACAGCAGCAT	    0.989248	-72
GTCCTCCCTAACAGTAGCAGAGATCTGCTT	2	26	0	ACAGTAGCAG	    0.995783	-83
TGACAGATTAACAGTAAACGGCTCTTGCTG	2	62	1	ACAGTAAACG	    0.970462	-47
TTGTCGTTAGCCAGCAAGAGCCGTTTACTG	2	73	0	CCAGCAAGAG	    0.986898	-36
          **********

Masking position 6
Map Score:   1.6479

Number of sites scoring better than the average of aligned sites = 876
Number in coding regions = 840
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

CAGCAGCATTACAATTTTGTA          	1	1	0	ACAATTTTTA	    0.959185	-84
GTTACCCTGGACGCTTTTTCGCTATCCTCAA	1	36	1	ACGCTTTTCG	    0.988717	-49
ATCTGCTTTTACATATTTATGCA        	2	3	0	ACATATTTTG	    0.973651	-106
  AAGCCATCACACTTTTTTGTCGTTAGCCA	2	90	0	ACACTTTTTG	    0.996089	-19
          ******** **

Masking position 6
Map Score:   0.932639

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 135
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 5

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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