AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i159_bsub_mtub_300.orf -o159_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	ysfA	118	ysfA
#2	ysfB	68	similar to hypothetical proteins
#3	ysfC	102	similar to glycolate oxidase subunit

Motif number 1

ACATCATGTTAAAAAAAGGAGCGCCACATA	1	15	0	AAAAAAAGGA	    0.992321	-104
CTTGCGATATAATAACATCATGTTAAAAAA	1	29	0	AATAACATCA	    0.887491	-90
ATTATATCGCAAGAACAGCACATAATAAAC	1	46	1	AAGAACAGCA	    0.972732	-73
ATTACATTTTAGAAAAAGGAGCGTTTTAC 	1	100	1	AGAAAAAGGA	    0.967939	-19
TATATAAGAAAAAAACCGGGCGCTGTCACC	2	23	0	AAAAACCGGG	    0.955749	-46
CTTATATAATAAAAACATGATGAGGGGGAA	2	45	1	AAAAACATGA	    0.981989	-24
GAGAAACATACAAAAAATGAAACTGAAACT	3	15	0	CAAAAAATGA	    0.908213	-88
ATTGTAAAAGAAAAAAAGCAAAGCCTTCCA	3	47	0	AAAAAAAGCA	    0.990505	-56
TCCCCCTGTCAAAAAACGCTTTCAATCTAT	3	75	0	AAAAAACGCT	    0.901362	-28
          **********

Masking position 5
Map Score:   12.7498

Number of sites scoring better than the average of aligned sites = 2798
Number in coding regions = 2243
Number in noncoding regions = 555
Number of orfs with sites within 600 bp upstream = 535
Fraction of orfs with sites within 600 bp upstream = 0.08593


Motif number 2

ACGTATATTCTAACCCTGCACCTGGTTTATTATGT	1	65	0	TACCCCCCGG	    0.998806	-54
CCGGGCGCTGTCACCCGGTTTCATGTC        	2	3	0	TACCCTTCTG	    0.995708	-66
      GGCGTTCCCCCTCATCATGTTTTTATTAT	2	50	0	TCCCCCTCTG	    0.998154	-19
         TTCACCCATCCCCCTGTCAAAAAACG	3	87	0	TACCCCCCTG	    0.999299	-16
          * ****  * ** **

Masking position 1
Map Score:   3.41491

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 5
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

ACATAATAAACCAGGTGCAGGGTTAGAATATAC	1	65	1	CCGGGCGGGT	     0.99852	-54
        GACATGAAACCGGGTGACAGCGCCC	2	3	1	CAGAACGGGT	    0.994705	-66
ATAATAAAAACATGATGAGGGGGAACGCC    	2	50	1	CAGAGAGGGG	    0.996474	-19
CGTTTTTTGACAGGGGGATGGGTGAA       	3	87	1	CAGGGAGGGT	    0.998659	-16
          ** ** ** ****

Masking position 4
Map Score:   2.82735

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 34
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

ATAATAACATCATGTTAAAAAAAGGAGCGC	1	21	0	CATGTTAAAA	       0.951	-98
GTTCTTGCGATATAATAACATCATGTTAAA	1	32	0	TATAATAACA	    0.914148	-87
AAGAACAGCACATAATAAACCAGGTGCAGG	1	56	1	CATAATAAAC	    0.945454	-63
ATACGTATTACATTTTAGAAAAAGGAGCGT	1	94	1	CATTTTAGAA	    0.894111	-25
TTTTTTCTTATATAATAAAAACATGATGAG	2	39	1	TATAATAAAA	     0.96505	-30
GCTTTCAATCTATTGTAAAAGAAAAAAAGC	3	58	0	TATTGTAAAA	    0.922338	-45
          **********

Masking position 6
Map Score:   1.88233

Number of sites scoring better than the average of aligned sites = 619
Number in coding regions = 416
Number in noncoding regions = 203
Number of orfs with sites within 600 bp upstream = 235
Fraction of orfs with sites within 600 bp upstream = 0.0377449


Motif number 5

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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:   3.08538e-14

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