AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_mixed11_bsub_reg_100.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	yqjC	201	similar to hypothetical proteins

Motif number 1

   GGCGCCTGCTTTTTTATCGTTATAGAAAC	1	8	1	GTTTTTTATG	    0.991921	-194
GTGATTTTGGGAGTTTTTATTCTTTCAACTGT	1	58	0	GGTTTTTATC	    0.987426	-144
CTGATGAAAAGCGTTTTGATCGTGATTTTGGG	1	79	0	GGTTTTGATG	    0.996663	-123
AATATAGACAGATTGTTTAAGGAGAGAAAATC	1	123	0	GTTGTTTAAG	    0.974735	-79
ATATTTTAGCGTGTTTTGAATGGGCGGACAAG	1	150	1	GGTTTTGAAG	    0.995223	-52
          * ******** *

Masking position 6
Map Score:   5.75984

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 157
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

TCGTTATAGAAACATGACGATTCCTGAGAG	1	27	1	AACATGACGA	    0.989801	-175
AAAAACTCCCAAAATCACGATCAAAACGCT	1	72	1	AAAATCACGA	    0.993992	-130
CATGTCTCAAAAACTGATGAAAAGCGTTTT	1	94	0	AAACTGATGA	    0.984311	-108
TTAAGGAGAGAAAATCATGTCTCAAAAACT	1	109	0	AAAATCATGT	    0.976917	-93
          **********

Masking position 5
Map Score:   3.49952

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 214
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

AAGAATAAAAACTCCCAAAATCACGATCAA	1	66	1	ACTCCCAAAA	    0.970143	-136
TCCCAAAATCACGATCAAAACGCTTTTCAT	1	78	1	ACGATCAAAA	    0.944693	-124
CCCATTCAAAACACGCTAAAATATAGACAG	1	144	0	ACACGCTAAA	    0.979835	-58
GAATGGGCGGACAAGCGATATCTATTAGCG	1	167	1	ACAAGCGATA	    0.974302	-35
AGCGATATCTATTAGCGAAAGCAGGGATGA	1	180	1	ATTAGCGAAA	     0.93082	-22
          **********

Masking position 8
Map Score:   0.88804

Number of sites scoring better than the average of aligned sites = 448
Number in coding regions = 395
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

TTTTTATCGTTATAGAAACATGACGATTCC	1	21	1	TATAGAAACA	     0.97462	-181
TTTCATCAGTTTTTGAGACATGATTTTCTC	1	102	1	TTTTGAGACA	    0.959278	-100
ACAGATTGTTTAAGGAGAGAAAATCATGTC	1	118	0	TAAGGAGAGA	    0.972233	-84
CACGCTAAAATATAGACAGATTGTTTAAGG	1	133	0	TATAGACAGA	    0.982625	-69
          **********

Masking position 6
Map Score:   0.0498771

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 129
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 5

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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:   6.63809e-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