AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00740_mjan_reg_100.orf -o00740_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	MJ0057	125	Na+/H+ antiporter
#2	MJ0303	44	riboflavin synthase beta chain (ribH)
#3	MJ0304	89	ferripyochelin binding protein (fbp)

Motif number 1

   ACTTAATAATTTTTTATTACGCATATT	1	8	1	AATTTTTTAT	    0.917133	-118
CGCATATTCCTTTTTTTAATCTCCAATTAT	1	30	1	TTTTTTTAAT	    0.922228	-96
CCTCGATAAAATATTTATATGATTTTTAGA	1	63	1	ATATTTATAT	    0.928434	-63
TATTTATATGATTTTTAGATTTTAAATATT	1	74	1	ATTTTTAGAT	    0.976159	-52
CCAAAAAGATAATTTTATATTGTGATAAC 	1	107	1	AATTTTATAT	    0.965143	-19
CTTCAAAGGATTTTTGTTATTTCTATTTAG	2	19	0	TTTTTGTTAT	    0.876068	-26
     TCACATTTTTTATACTTTTTTAAAT	3	6	1	TTTTTTATAC	     0.97309	-84
TTTTTTATACTTTTTTAAATGTTATATGTA	3	16	1	TTTTTTAAAT	    0.966575	-74
TTAGATATTTATCTTTATACAAACTACATA	3	40	0	ATCTTTATAC	    0.899355	-50
TTTTTATGTTATTTTTAGATATTTATCTTT	3	54	0	ATTTTTAGAT	    0.976159	-36
CACCAAAAAGTTTTTTATGTTATTTTTAGA	3	65	0	TTTTTTATGT	    0.946656	-25
          **********

Masking position 5
Map Score:   17.0991

Number of sites scoring better than the average of aligned sites = 1719
Number in coding regions = 1271
Number in noncoding regions = 448
Number of orfs with sites within 600 bp upstream = 372
Fraction of orfs with sites within 600 bp upstream = 0.0597494


Motif number 2

         ACTTAATAATTTTTTATTACGCAT	1	2	1	CTTATTTTTT	    0.837066	-124
TTTTTTTAATCTCCAATTATTTTCCTCGATAAA	1	40	1	CTCAAATTTT	    0.979747	-86
AATTATTTTCCTCGATAAAATATTTATATGATT	1	54	1	CTCATAATAT	    0.851291	-72
GATAAAATATTTATATGATTTTTAGATTTTAAA	1	67	1	TTAATTTTTT	    0.799536	-59
TTTTTGTTATTTCTATTTAGTTTAATTT     	2	6	0	TTCATAGTTT	    0.986564	-39
   CTTTTACTTCAAAGGATTTTTGTTATTTCT	2	25	0	TTCAAATTTT	    0.974077	-20
ACATATAACATTTAAAAAAGTATAAAAAATGTG	3	12	0	TTTAAAGTAT	    0.837075	-78
TTTTTAAATGTTATATGTAGTTTGTATAAAGAT	3	27	1	TTAATAGTTT	    0.952448	-63
     TATTTCACCAAAAAGTTTTTTATGTTAT	3	72	0	CACAAAGTTT	     0.92364	-18
          *** **  *****

Masking position 5
Map Score:   5.20676

Number of sites scoring better than the average of aligned sites = 1279
Number in coding regions = 1070
Number in noncoding regions = 209
Number of orfs with sites within 600 bp upstream = 195
Fraction of orfs with sites within 600 bp upstream = 0.0313203


Motif number 3

          **********

No masking
Map Score:   -3.95472e-13

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:   -3.95472e-13

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:   -3.95472e-13

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