AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_ecoli_mtub_100.orf -o206_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	ptr	175	protease III
#2	recC	276	recC

Motif number 1

TATAAACATAGGCTGACTCGTGCAGCACAA	1	80	1	GGCTGACTCG	    0.985164	-96
     GTGGTGGGTGACGCGGTTGCTTTGG	2	6	1	GGGTGACGCG	    0.998885	-271
GGCGGTGTAGGTGTGAGGCGGTTGCCCAAA	2	31	0	GTGTGAGGCG	    0.993732	-246
ACTTCGAGATGGAGGAGGCGGTGTAGGTGT	2	47	0	GGAGGAGGCG	    0.987672	-230
AGTGTGTCACGTCCGAGGCGGCTCGTCATG	2	74	1	GTCCGAGGCG	    0.973117	-203
CGCGATGTCGGCATGACGAGCCGCCTCGGA	2	85	0	GCATGACGAG	     0.95827	-192
ACGCGCTGGGGCGTGCCGCGATGTCGGCAT	2	101	0	GCGTGCCGCG	    0.997038	-176
TAGTCGAGCGGCCGGCCGCCGACATGCATG	2	245	0	GCCGGCCGCC	    0.623667	-32
CGCTCGACTAGGGTGACGCCCG        	2	265	1	GGGTGACGCC	    0.995551	-12
          **********

Masking position 5
Map Score:   18.5957

Number of sites scoring better than the average of aligned sites = 1401
Number in coding regions = 1326
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

ATGATGCGCACCAGTCACGGACTGATGGTTATATAAA	1	49	1	CCAGCGCTGG	    0.992793	-127
AATTTTCTGTCCAGATTCAACACGTTAACGCAAATCA	1	127	0	CCAGCAACGA	     0.92277	-49
GTGTGTCACGTCCGAGGCGGCTCGTCATGCCGACATC	2	75	1	TCCGCGTCGA	    0.987211	-202
TTCCGGGATTTCATCAACGCGCTGGGGCGTGCCGCGA	2	110	0	TCATCGCTGG	    0.898795	-167
TTGATGAAATCCCGGAACGGTTCGATATCTGACCCAG	2	130	1	CCCGCGTCGA	    0.997456	-147
GATATCTGACCCAGTTCCAGGTCGACAAGAAGGCCCG	2	153	1	CCAGCATCGA	    0.975193	-124
GACAAGAAGGCCCGTACCGACTGGTAGCCCTTGTCGT	2	176	1	CCCGCGTGGG	    0.997406	-101
CGACTGGTAGCCCTTGTCGTTCGGTGATCTCGCGTCT	2	193	1	CCCTCGCGGA	    0.993598	-84
 CGGGCGTCACCCTAGTCGAGCGGCCGGCCGCCGACA	2	251	0	CCCTCGCGGG	    0.995021	-26
          ****   **  ***  *

Masking position 8
Map Score:   12.8711

Number of sites scoring better than the average of aligned sites = 1653
Number in coding regions = 1607
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

GTTGCCCAAAGCAACCGCGTCACCCACCAC	2	11	0	GCAACCGCGT	    0.993636	-266
GTTGCTTTGGGCAACCGCCTCACACCTACA	2	26	1	GCAACCGCCT	    0.979407	-251
GCCTCACACCTACACCGCCTCCTCCATCTC	2	42	1	TACACCGCCT	    0.867432	-235
GGCATGACGAGCCGCCTCGGACGTGACACA	2	76	0	GCCGCCTCGG	    0.937513	-201
TCGTCATGCCGACATCGCGGCACGCCCCAG	2	96	1	GACATCGCGG	    0.987151	-181
CGCGGCACGCCCCAGCGCGTTGATGAAATC	2	111	1	CCCAGCGCGT	    0.955306	-166
GCGCGTTGATGAAATCCCGGAACGGTTCGA	2	125	1	GAAATCCCGG	    0.944864	-152
AGGTCGACAAGAAGGCCCGTACCGACTGGT	2	171	1	GAAGGCCCGT	    0.927007	-106
GTCGTTCGGTGATCTCGCGTCTGTTTATGC	2	208	1	GATCTCGCGT	    0.845964	-69
          **********

Masking position 6
Map Score:   6.54189

Number of sites scoring better than the average of aligned sites = 4097
Number in coding regions = 3870
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 198
Fraction of orfs with sites within 600 bp upstream = 0.0318021


Motif number 4

CGCAAATCATCTGCCAGAATTTAATCTTGT	1	106	0	CTGCCAGAAT	    0.953271	-70
GCGGCTCGTCATGCCGACATCGCGGCACGC	2	91	1	ATGCCGACAT	    0.532204	-186
CTGTTTATGCACGCCAGCATGCATGTCGGC	2	228	1	ACGCCAGCAT	    0.753211	-49
GAGCGGCCGGCCGCCGACATGCATGCTGGC	2	240	0	CCGCCGACAT	    0.964078	-37
          **********

Masking position 9
Map Score:   2.79803

Number of sites scoring better than the average of aligned sites = 419
Number in coding regions = 409
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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:   -4.80737e-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