AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i108_bsub_mtub_100.orf -o108_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	Rv1219c	141	hypothetical protein Rv1219c

Motif number 1

CTGGAACGCACGGTTCAGGGCGATTTTGCGTC	1	22	0	CGGTCAGGCG	    0.999055	-120
CTGAACCGTGCGTTCCAGGGCGATTTTGCGTC	1	36	1	CGTTCAGGCG	    0.980294	-106
TGCGTCTGCTCGGCAAAGTTCGCGGCCTTCAC	1	62	1	CGGCAAGTCG	    0.994497	-80
CGTTGGGAATCCGTGAAGGCCGCGAACTTTGC	1	74	0	CCGTAAGGCG	     0.99837	-68
CGTTCATCCCCGGTCAAGGGAGGGCGCCGTTG	1	101	0	CGGTAAGGAG	    0.997756	-41
          **** **** **

Masking position 7
Map Score:   13.4941

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 53
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 2

    TTCGGCGAGCAGACGCAAAATCGCCC	1	7	1	GAGCAGACGC	    0.997228	-135
AATCGCCCTGGAACGCACGGTTCAGGGCGA	1	31	0	GAACGCACGG	     0.97844	-111
GAACTTTGCCGAGCAGACGCAAAATCGCCC	1	53	0	GAGCAGACGC	    0.997228	-89
GGGCGCCGTTGGGAATCCGTGAAGGCCGCG	1	82	0	GGGAATCCGT	    0.938473	-60
CCCCGGTCAAGGGAGGGCGCCGTTGGGAAT	1	96	0	GGGAGGGCGC	    0.988505	-46
GACCGGGGATGAACGTACGTTTAATATCCT	1	118	1	GAACGTACGT	    0.984673	-24
          **********

Masking position 8
Map Score:   8.38103

Number of sites scoring better than the average of aligned sites = 936
Number in coding regions = 822
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

CGATTTTGCGTCTGCTCGCCGAA       	1	4	0	TCTGCTCGCC	     0.99728	-138
CGAGCAGACGCAAAATCGCCCTGAACCGTG	1	16	1	CAAAATCGCC	    0.993563	-126
CGAGCAGACGCAAAATCGCCCTGGAACGCA	1	44	0	CAAAATCGCC	    0.993563	-98
CGATTTTGCGTCTGCTCGGCAAAGTTCGCG	1	56	1	TCTGCTCGGC	    0.992561	-86
          **********

Masking position 6
Map Score:   4.80137

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 352
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


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