AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_ecoli_bsub_100.orf -o296_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	yqjC	201	similar to hypothetical proteins

Motif number 1

   GGCGCCTGCTTTTTTATCGTTATAGAAAC	1	8	1	GTTTTTTATG	    0.992005	-194
GTGATTTTGGGAGTTTTTATTCTTTCAACTGT	1	58	0	GGTTTTTATC	    0.987557	-144
CTGATGAAAAGCGTTTTGATCGTGATTTTGGG	1	79	0	GGTTTTGATG	    0.996698	-123
AATATAGACAGATTGTTTAAGGAGAGAAAATC	1	123	0	GTTGTTTAAG	    0.974994	-79
ATATTTTAGCGTGTTTTGAATGGGCGGACAAG	1	150	1	GGTTTTGAAG	    0.995273	-52
          * ******** *

Masking position 6
Map Score:   5.75984

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 145
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

CTCTCAGGAATCGTCATGTTTCTATAACGA	1	27	0	TCGTCATGTT	    0.989801	-175
AGCGTTTTGATCGTGATTTTGGGAGTTTTT	1	72	0	TCGTGATTTT	    0.993992	-130
AAAACGCTTTTCATCAGTTTTTGAGACATG	1	94	1	TCATCAGTTT	    0.984311	-108
AGTTTTTGAGACATGATTTTCTCTCCTTAA	1	109	1	ACATGATTTT	    0.976917	-93
          **********

Masking position 6
Map Score:   3.49952

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 131
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

TTGATCGTGATTTTGGGAGTTTTTATTCTT	1	66	0	TTTTGGGAGT	     0.96999	-136
ATGAAAAGCGTTTTGATCGTGATTTTGGGA	1	78	0	TTTTGATCGT	    0.944417	-124
CTGTCTATATTTTAGCGTGTTTTGAATGGG	1	144	1	TTTAGCGTGT	    0.979734	-58
CGCTAATAGATATCGCTTGTCCGCCCATTC	1	167	0	TATCGCTTGT	     0.97417	-35
TCATCCCTGCTTTCGCTAATAGATATCGCT	1	180	0	TTTCGCTAAT	    0.930767	-22
          **********

Masking position 3
Map Score:   0.88804

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 664
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 4

TTTTTATCGTTATAGAAACATGACGATTCC	1	21	1	TATAGAAACA	    0.973789	-181
TTTCATCAGTTTTTGAGACATGATTTTCTC	1	102	1	TTTTGAGACA	    0.957962	-100
ACAGATTGTTTAAGGAGAGAAAATCATGTC	1	118	0	TAAGGAGAGA	    0.971318	-84
CACGCTAAAATATAGACAGATTGTTTAAGG	1	133	0	TATAGACAGA	    0.982059	-69
          **********

Masking position 6
Map Score:   0.0498771

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 42
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


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