AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i159_glycolate_Oxidase_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ysfA	118	ysfA
#2	ysfB	68	similar to hypothetical proteins
#3	ysfC	102	similar to glycolate oxidase subunit

Motif number 1

TATGTGGCGCTCCTTTTTTTAACATGATGT	1	15	1	TCCTTTTTTT	    0.991491	-104
TTTTTTAACATGATGTTATTATATCGCAAG	1	29	1	TGATGTTATT	    0.876743	-90
GTTTATTATGTGCTGTTCTTGCGATATAAT	1	46	0	TGCTGTTCTT	     0.96985	-73
 GTAAAACGCTCCTTTTTCTAAAATGTAAT	1	100	0	TCCTTTTTCT	     0.96457	-19
GGTGACAGCGCCCGGTTTTTTTCTTATATA	2	23	1	CCCGGTTTTT	    0.951163	-46
TTCCCCCTCATCATGTTTTTATTATATAAG	2	45	0	TCATGTTTTT	    0.980066	-24
AGTTTCAGTTTCATTTTTTGTATGTTTCTC	3	15	1	TCATTTTTTG	    0.899219	-88
TGGAAGGCTTTGCTTTTTTTCTTTTACAAT	3	47	1	TGCTTTTTTT	    0.989481	-56
ATAGATTGAAAGCGTTTTTTGACAGGGGGA	3	75	1	AGCGTTTTTT	    0.891777	-28
          **********

Masking position 6
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	CCGGGGGGTA	    0.998763	-54
        GACATGAAACCGGGTGACAGCGCCCGG	2	3	1	CAGAAGGGTA	    0.995556	-66
ATAATAAAAACATGATGAGGGGGAACGCC      	2	50	1	CAGAGGGGGA	    0.998088	-19
CGTTTTTTGACAGGGGGATGGGTGAA         	3	87	1	CAGGGGGGTA	    0.999274	-16
          ** ** *  **** *

Masking position 15
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

GTATATTCTAACCCTGCACCTGGTTTATTATGT	1	65	0	ACCCGCCCGG	    0.998643	-54
GGGCGCTGTCACCCGGTTTCATGTC        	2	3	0	ACCCGTTCTG	    0.995148	-66
    GGCGTTCCCCCTCATCATGTTTTTATTAT	2	50	0	CCCCTCTCTG	    0.996768	-19
       TTCACCCATCCCCCTGTCAAAAAACG	3	87	0	ACCCTCCCTG	    0.998771	-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	    0.953657	-98
GTTCTTGCGATATAATAACATCATGTTAAA	1	32	0	TATAATAACA	    0.918329	-87
AAGAACAGCACATAATAAACCAGGTGCAGG	1	56	1	CATAATAAAC	    0.948395	-63
ATACGTATTACATTTTAGAAAAAGGAGCGT	1	94	1	CATTTTAGAA	    0.899528	-25
TTTTTTCTTATATAATAAAAACATGATGAG	2	39	1	TATAATAAAA	    0.966644	-30
GCTTTCAATCTATTGTAAAAGAAAAAAAGC	3	58	0	TATTGTAAAA	    0.926123	-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