AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i029_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

ACATCATGTTAAAAAAAGGAGCGCCACATA	1	15	0	AAAAAAAGGA	    0.992081	-104
CTTGCGATATAATAACATCATGTTAAAAAA	1	29	0	AATAACATCA	    0.884365	-90
ATTATATCGCAAGAACAGCACATAATAAAC	1	46	1	AAGAACAGCA	    0.971899	-73
ATTACATTTTAGAAAAAGGAGCGTTTTAC 	1	100	1	AGAAAAAGGA	    0.966965	-19
TATATAAGAAAAAAACCGGGCGCTGTCACC	2	23	0	AAAAACCGGG	    0.954422	-46
CTTATATAATAAAAACATGATGAGGGGGAA	2	45	1	AAAAACATGA	    0.981434	-24
GAGAAACATACAAAAAATGAAACTGAAACT	3	15	0	CAAAAAATGA	    0.905601	-88
ATTGTAAAAGAAAAAAAGCAAAGCCTTCCA	3	47	0	AAAAAAAGCA	     0.99021	-56
TCCCCCTGTCAAAAAACGCTTTCAATCTAT	3	75	0	AAAAAACGCT	    0.898577	-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	CCGGGGGGTA	    0.998733	-54
        GACATGAAACCGGGTGACAGCGCCCGG	2	3	1	CAGAAGGGTA	    0.995449	-66
ATAATAAAAACATGATGAGGGGGAACGCC      	2	50	1	CAGAGGGGGA	    0.998042	-19
CGTTTTTTGACAGGGGGATGGGTGAA         	3	87	1	CAGGGGGGTA	    0.999257	-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	    0.998584	-54
GGGCGCTGTCACCCGGTTTCATGTC        	2	3	0	ACCCGTTCTG	    0.994936	-66
    GGCGTTCCCCCTCATCATGTTTTTATTAT	2	50	0	CCCCTCTCTG	    0.996627	-19
       TTCACCCATCCCCCTGTCAAAAAACG	3	87	0	ACCCTCCCTG	    0.998718	-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	    0.956906	-98
TTTAACATGATGTTATTATATCGCAAGAAC	1	32	1	TGTTATTATA	    0.923437	-87
CCTGCACCTGGTTTATTATGTGCTGTTCTT	1	56	0	GTTTATTATG	    0.951993	-63
ACGCTCCTTTTTCTAAAATGTAATACGTAT	1	94	0	TTCTAAAATG	    0.906201	-25
CTCATCATGTTTTTATTATATAAGAAAAAA	2	39	0	TTTTATTATA	    0.968559	-30
GCTTTTTTTCTTTTACAATAGATTGAAAGC	3	58	1	TTTTACAATA	    0.930737	-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