AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i029_bsub_mtub_300.orf -o029_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	    0.991751	-104
CTTGCGATATAATAACATCATGTTAAAAAA	1	29	0	AATAACATCA	    0.880084	-90
ATTATATCGCAAGAACAGCACATAATAAAC	1	46	1	AAGAACAGCA	    0.970751	-73
ATTACATTTTAGAAAAAGGAGCGTTTTAC 	1	100	1	AGAAAAAGGA	    0.965623	-19
TATATAAGAAAAAAACCGGGCGCTGTCACC	2	23	0	AAAAACCGGG	    0.952595	-46
CTTATATAATAAAAACATGATGAGGGGGAA	2	45	1	AAAAACATGA	    0.980668	-24
GAGAAACATACAAAAAATGAAACTGAAACT	3	15	0	CAAAAAATGA	    0.902018	-88
ATTGTAAAAGAAAAAAAGCAAAGCCTTCCA	3	47	0	AAAAAAAGCA	    0.989802	-56
TCCCCCTGTCAAAAAACGCTTTCAATCTAT	3	75	0	AAAAAACGCT	     0.89476	-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

ACATAATAAACCAGGTGCAGGGTTAGAATATACGT	1	65	1	CCGGCGGGTA	    0.998831	-54
        GACATGAAACCGGGTGACAGCGCCCGG	2	3	1	CAGACGGGTA	    0.997279	-66
ATAATAAAAACATGATGAGGGGGAACGCC      	2	50	1	CAGGAGGGGA	    0.998193	-19
CGTTTTTTGACAGGGGGATGGGTGAA         	3	87	1	CAGGAGGGTA	    0.998939	-16
          ** *  ** **** *

Masking position 15
Map Score:   3.41491

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 22
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

GTATATTCTAACCCTGCACCTGGTTTATTATGT	1	65	0	ACCCGCCCGG	    0.998571	-54
GGGCGCTGTCACCCGGTTTCATGTC        	2	3	0	ACCCGTTCTG	    0.994888	-66
    GGCGTTCCCCCTCATCATGTTTTTATTAT	2	50	0	CCCCTCTCTG	    0.996596	-19
       TTCACCCATCCCCCTGTCAAAAAACG	3	87	0	ACCCTCCCTG	    0.998705	-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

GCGCTCCTTTTTTTAACATGATGTTATTAT	1	21	1	TTTTAACATG	     0.95154	-98
TTTAACATGATGTTATTATATCGCAAGAAC	1	32	1	TGTTATTATA	    0.914998	-87
CCTGCACCTGGTTTATTATGTGCTGTTCTT	1	56	0	GTTTATTATG	    0.946052	-63
ACGCTCCTTTTTCTAAAATGTAATACGTAT	1	94	0	TTCTAAAATG	    0.895209	-25
CTCATCATGTTTTTATTATATAAGAAAAAA	2	39	0	TTTTATTATA	    0.965376	-30
GCTTTTTTTCTTTTACAATAGATTGAAAGC	3	58	1	TTTTACAATA	    0.923108	-45
          **********

Masking position 5
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