AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_bsub_mtub_300.orf -o109_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

TGTGCGGATAGAGGAACAGTGTATGAAAACA	1	61	1	GGGAACAGTG	    0.996479	-88
ATAAACGTTTGTGCGAGAGTGTTTTCATACA	1	80	0	GGCGAGAGTG	    0.977361	-69
ACATCAGACCGCGCACGGGTGGGGAGTCAGC	2	18	0	GGCACGGGTG	    0.976648	-107
AAAGGCGATCGCTGAACATTGCAGGACTCAC	2	56	0	GTGAACATTG	    0.952214	-69
TCCCGTAGCGGCGGAAAGGCGATCGCTGAAC	2	70	0	GGGAAAGGCG	     0.98448	-55
TCCGCCGCTACGGGAACGTTGTCCAAAGTCC	2	86	1	CGGAACGTTG	    0.992387	-39
ACCTTCCGGTGCGGGACTTTGGACAACGTTC	2	99	0	GGGGACTTTG	    0.975604	-26
AAGTCCCGCACCGGAAGGTCGCCA       	2	111	1	CGGAAGGTCG	    0.982522	-14
          * *********

Masking position 11
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

TGTTCCTCTATCCGCACAGCCTCTTTATTG	1	49	0	TCCGCACAGC	    0.983313	-100
CACATCAGACCGCGCACGGGTGGGGAGTCA	2	20	0	CGCGCACGGG	    0.670291	-105
GGACAACGTTCCCGTAGCGGCGGAAAGGCG	2	80	0	CCCGTAGCGG	    0.723362	-45
TGTCCAAAGTCCCGCACCGGAAGGTCGCCA	2	105	1	CCCGCACCGG	    0.671322	-20
          **********

Masking position 6
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

GTTTTCATACACTGTTCCTCTATCCGCACA	1	61	0	ACTGTTCCTC	    0.958381	-88
TGAGTCCTGCAATGTTCAGCGATCGCCTTT	2	57	1	AATGTTCAGC	    0.957259	-68
TTCAGCGATCGCCTTTCCGCCGCTACGGGA	2	71	1	GCCTTTCCGC	    0.977412	-54
GACTTTGGACAACGTTCCCGTAGCGGCGGA	2	86	0	AACGTTCCCG	    0.979945	-39
AACGTTGTCCAAAGTCCCGCACCGGAAGGT	2	100	1	AAAGTCCCGC	    0.968033	-25
      TGGCGACCTTCCGGTGCGGGACTT	2	111	0	GACCTTCCGG	    0.975909	-14
          **********

Masking position 5
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	    0.991768	-136
TCTTTATTGATAAAATAATAGCTGTCAAAGA	1	27	0	TAAAAAATAG	    0.958891	-122
TATTATTTTATCAATAAAGAGGCTGTGCGGA	1	38	1	TCAATAAGAG	    0.982678	-111
CCTTTCTGAATAAAACAAGTGTCATATAATA	1	121	0	TAAAAAAGTG	    0.981328	-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