AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i022_Hydratase_mjan_reg_300.orf -o022_mjan_300.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	RMJ07934	108	M_jannaschii_chromosome
#2	RMJ04314	50	M_jannaschii_chromosome

Motif number 1

ACCAAAAAGGTCTAAATTTTTATGTAAGAG	1	17	1	TCTAAATTTT	     0.93009	-92
TATAATTAGTTTTAAAATCTCTTACATAAA	1	35	0	TTTAAAATCT	    0.984635	-74
CCATAATTTATTTATAATTAGTTTTAAAAT	1	47	0	TTTATAATTA	    0.960503	-62
TATAGCTTACTCTATAATCAAAACCATAAT	1	70	0	TCTATAATCA	    0.966069	-39
TAGAGTAAGCTATAAAATATCAGGAGGGAT	1	86	1	TATAAAATAT	    0.966569	-23
AACATTAACTTTTAAAATTTATTG      	2	5	0	TTTAAAATTT	    0.983434	-46
AATCACCCTATATACAATAAATAAACATTA	2	28	0	TATACAATAA	      0.9091	-23
          **********

Masking position 6
Map Score:   8.45417

Number of sites scoring better than the average of aligned sites = 1742
Number in coding regions = 1317
Number in noncoding regions = 425
Number of orfs with sites within 600 bp upstream = 342
Fraction of orfs with sites within 600 bp upstream = 0.0549309


Motif number 2

TTAAAATCTCTTACATAAAAATTTAGACCT	1	24	0	TTACATAAAA	    0.944487	-85
AAAACTAATTATAAATAAATTATGGTTTTG	1	52	1	ATAAATAAAT	    0.975492	-57
AGCTTACTCTATAATCAAAACCATAATTTA	1	67	0	ATAATCAAAA	    0.945454	-42
CCTATATACAATAAATAAACATTAACTTTT	2	22	0	ATAAATAAAC	     0.98418	-29
          **********

Masking position 7
Map Score:   1.49564

Number of sites scoring better than the average of aligned sites = 696
Number in coding regions = 503
Number in noncoding regions = 193
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 3

ATCTCTTACATAAAAATTTAGACCTTTTTG	1	19	0	TAAAAATTTA	    0.878125	-90
GTAAGAGATTTTAAAACTAATTATAAATAA	1	40	1	TTAAAACTAA	    0.976102	-69
TTAAAACTAATTATAAATAAATTATGGTTT	1	50	1	TTATAAATAA	    0.885515	-59
TCCTGATATTTTATAGCTTACTCTATAATC	1	81	0	TTATAGCTTA	    0.965927	-28
 CAATAAATTTTAAAAGTTAATGTTTATTT	2	10	1	TTAAAAGTTA	     0.97878	-41
          **********

Masking position 5
Map Score:   3.87358

Number of sites scoring better than the average of aligned sites = 510
Number in coding regions = 331
Number in noncoding regions = 179
Number of orfs with sites within 600 bp upstream = 181
Fraction of orfs with sites within 600 bp upstream = 0.0290716


Motif number 4

          **********

No masking
Map Score:   -6.86222e-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:   -6.86222e-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:   -6.86222e-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