AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00900_mjan_reg_100.orf -o00900_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MJ0861	131	conserved hypothetical protein

Motif number 1

ACAGTATTAACAATACTGTT          	1	1	0	CAATACTGTT	    0.953011	-131
ACAGTATTGTTAATACTGTTATCCCATTTA	1	12	1	TAATACTGTT	    0.967884	-120
GTTATCCCATTTATGATTTTTATTTTTATC	1	29	1	TTATGATTTT	    0.966344	-103
TAATTATTTTAAATAAATTTACAGCCTAAC	1	65	0	AAATAAATTT	    0.829164	-67
TATAAATATTTAATTATTTTAAATAAATTT	1	75	0	TAATTATTTT	    0.948937	-57
ATTTTAATGTTTATAAATATTTAATTATTT	1	86	0	TTATAAATAT	    0.859981	-46
CTTTAATTTTTTATAATTTTAATGTTTATA	1	101	0	TTATAATTTT	    0.989453	-31
CTCTCACATCCTTTAATTTTTTATAATTTT	1	111	0	CTTTAATTTT	    0.918938	-21
          **********

Masking position 4
Map Score:   9.15348

Number of sites scoring better than the average of aligned sites = 1423
Number in coding regions = 1020
Number in noncoding regions = 403
Number of orfs with sites within 600 bp upstream = 356
Fraction of orfs with sites within 600 bp upstream = 0.0571796


Motif number 2

CATCTAAGATAAAAATAAAAATCATAAATG	1	36	0	AAAAATAAAA	     0.97308	-96
ATTTACAGCCTAACATCTAAGATAAAAATA	1	49	0	TAACATCTAA	    0.945629	-83
TAATGTTTATAAATATTTAATTATTTTAAA	1	82	0	AAATATTTAA	    0.971718	-50
AAATATTTATAAACATTAAAATTATAAAAA	1	94	1	AAACATTAAA	    0.992984	-38
TAAAATTATAAAAAATTAAAGGATGTGAGA	1	110	1	AAAAATTAAA	    0.988997	-22
          **********

Masking position 5
Map Score:   7.24233

Number of sites scoring better than the average of aligned sites = 801
Number in coding regions = 575
Number in noncoding regions = 226
Number of orfs with sites within 600 bp upstream = 205
Fraction of orfs with sites within 600 bp upstream = 0.0329264


Motif number 3

          **********

No masking
Map Score:   8.05918e-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 4

          **********

No masking
Map Score:   8.05918e-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 5

          **********

No masking
Map Score:   8.05918e-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