AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i108_ecoli_mtub_100.orf -o108_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	Rv1219c	141	hypothetical protein Rv1219c

Motif number 1

GACGCAAAATCGCCCTGAACCGTGCGTTCCAG	1	22	1	CGCCTGACCG	    0.999058	-120
GACGCAAAATCGCCCTGGAACGCACGGTTCAG	1	36	0	CGCCTGAACG	    0.980421	-106
GTGAAGGCCGCGAACTTTGCCGAGCAGACGCA	1	62	0	CGACTTGCCG	    0.994492	-80
GCAAAGTTCGCGGCCTTCACGGATTCCCAACG	1	74	1	CGCCTTACGG	    0.998369	-68
CAACGGCGCCCTCCCTTGACCGGGGATGAACG	1	101	1	CTCCTTACCG	    0.997752	-41
          ** **** ****

Masking position 6
Map Score:   13.4941

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 141
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

    TTCGGCGAGCAGACGCAAAATCGCCC	1	7	1	GAGCAGACGC	    0.997203	-135
AATCGCCCTGGAACGCACGGTTCAGGGCGA	1	31	0	GAACGCACGG	    0.977466	-111
GAACTTTGCCGAGCAGACGCAAAATCGCCC	1	53	0	GAGCAGACGC	    0.997203	-89
GGGCGCCGTTGGGAATCCGTGAAGGCCGCG	1	82	0	GGGAATCCGT	    0.935814	-60
CCCCGGTCAAGGGAGGGCGCCGTTGGGAAT	1	96	0	GGGAGGGCGC	     0.98828	-46
GACCGGGGATGAACGTACGTTTAATATCCT	1	118	1	GAACGTACGT	    0.983976	-24
          **********

Masking position 8
Map Score:   8.38103

Number of sites scoring better than the average of aligned sites = 1561
Number in coding regions = 1502
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 3

CGATTTTGCGTCTGCTCGCCGAA       	1	4	0	TCTGCTCGCC	    0.997398	-138
CGAGCAGACGCAAAATCGCCCTGAACCGTG	1	16	1	CAAAATCGCC	    0.993846	-126
CGAGCAGACGCAAAATCGCCCTGGAACGCA	1	44	0	CAAAATCGCC	    0.993846	-98
CGATTTTGCGTCTGCTCGGCAAAGTTCGCG	1	56	1	TCTGCTCGGC	    0.992866	-86
          **********

Masking position 6
Map Score:   4.80137

Number of sites scoring better than the average of aligned sites = 964
Number in coding regions = 935
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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