AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i059_bsub_mtub_300.orf -o059_bsub_mtub_300.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	ytkP	148	similar to cysteine synthase
#2	subI	124	subI

Motif number 1

TGTTTTCATACACTGTTCCTCTATCCGCACA	1	61	0	CACTGTTCCC	    0.995692	-88
TGTATGAAAACACTCTCGCACAAACGTTTAT	1	80	1	CACTCTCGCC	    0.972414	-69
GCTGACTCCCCACCCGTGCGCGGTCTGATGT	2	18	1	CACCCGTGCC	    0.971549	-107
GTGAGTCCTGCAATGTTCAGCGATCGCCTTT	2	56	1	CAATGTTCAC	    0.942097	-69
GTTCAGCGATCGCCTTTCCGCCGCTACGGGA	2	70	1	CGCCTTTCCC	    0.981058	-55
GGACTTTGGACAACGTTCCCGTAGCGGCGGA	2	86	0	CAACGTTCCG	    0.990693	-39
GAACGTTGTCCAAAGTCCCGCACCGGAAGGT	2	99	1	CAAAGTCCCC	    0.970285	-26
       TGGCGACCTTCCGGTGCGGGACTT	2	111	0	CGACCTTCCG	    0.978678	-14
          ********* *

Masking position 1
Map Score:   8.78005

Number of sites scoring better than the average of aligned sites = 738
Number in coding regions = 631
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

CAATAAAGAGGCTGTGCGGATAGAGGAACA	1	49	1	GCTGTGCGGA	    0.983866	-100
TGACTCCCCACCCGTGCGCGGTCTGATGTG	2	20	1	CCCGTGCGCG	    0.663804	-105
CGCCTTTCCGCCGCTACGGGAACGTTGTCC	2	80	1	CCGCTACGGG	    0.716312	-45
TGGCGACCTTCCGGTGCGGGACTTTGGACA	2	105	0	CCGGTGCGGG	    0.664757	-20
          **********

Masking position 5
Map Score:   5.0191

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 116
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

TGTGCGGATAGAGGAACAGTGTATGAAAAC	1	61	1	GAGGAACAGT	    0.959259	-88
AAAGGCGATCGCTGAACATTGCAGGACTCA	2	57	0	GCTGAACATT	    0.958159	-68
TCCCGTAGCGGCGGAAAGGCGATCGCTGAA	2	71	0	GCGGAAAGGC	    0.977904	-54
TCCGCCGCTACGGGAACGTTGTCCAAAGTC	2	86	1	CGGGAACGTT	    0.980385	-39
ACCTTCCGGTGCGGGACTTTGGACAACGTT	2	100	0	GCGGGACTTT	    0.968725	-25
AAGTCCCGCACCGGAAGGTCGCCA      	2	111	1	CCGGAAGGTC	    0.976435	-14
          **********

Masking position 6
Map Score:   1.62351

Number of sites scoring better than the average of aligned sites = 1331
Number in coding regions = 1253
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 4

ATAATAGCTGTCAAAGAAGGGAGTGTCAGAC	1	13	0	TCAAAAAGGG	    0.992516	-136
TCTTTATTGATAAAATAATAGCTGTCAAAGA	1	27	0	TAAAAAATAG	    0.962517	-122
TATTATTTTATCAATAAAGAGGCTGTGCGGA	1	38	1	TCAATAAGAG	     0.98424	-111
CCTTTCTGAATAAAACAAGTGTCATATAATA	1	121	0	TAAAAAAGTG	     0.98301	-28
          ***** *****

Masking position 7
Map Score:   1.14033

Number of sites scoring better than the average of aligned sites = 312
Number in coding regions = 248
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 5

          **********

No masking
Map Score:   -2.81785e-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:   -2.81785e-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:   -2.81785e-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