AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i059_Sulfate_trans-cys_synthase_mjan_reg_100.orf -o059_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	RMJ01308	122	M_jannaschii_chromosome

Motif number 1

       TTTAATAAATTTTTAATGAAAAT	1	4	1	AATAAATTTT	    0.984058	-119
CATTTGATAGTATAATATTTTCATTAAAAA	1	20	0	TATAATATTT	    0.961524	-103
AATATTATACTATCAAATGTCATCAATTTT	1	31	1	TATCAAATGT	    0.973521	-92
TATCAAATGTCATCAATTTTGTTTAACACA	1	41	1	CATCAATTTT	    0.989153	-82
TACCTAATTATATAAAATTTGTGTTAAACA	1	60	0	TATAAAATTT	    0.982997	-63
AATCAATCTTAATCATTTTTAAGGTAATTA	1	93	0	AATCATTTTT	    0.980649	-30
GCCTATCCCTAATCAATCTTAATCATTTTT	1	103	0	AATCAATCTT	    0.979335	-20
          **********

Masking position 5
Map Score:   13.6838

Number of sites scoring better than the average of aligned sites = 643
Number in coding regions = 512
Number in noncoding regions = 131
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 2

TTCATTAAAAATTTATTAAA          	1	1	0	ATTTATTAAA	    0.854807	-122
TTAATAAATTTTTAATGAAAATATTATACT	1	12	1	TTTAATGAAA	    0.781314	-111
GTTAAACAAAATTGATGACATTTGATAGTA	1	38	0	ATTGATGACA	    0.938016	-85
ATTATATAAAATTTGTGTTAAACAAAATTG	1	54	0	ATTTGTGTTA	     0.94083	-69
AATTTTATATAATTAGGTAATTTAATTACC	1	71	1	AATTAGGTAA	    0.917031	-52
CTTAATCATTTTTAAGGTAATTAAATTACC	1	86	0	TTTAAGGTAA	    0.957893	-37
ATTAAGATTGATTAGGGATAGGC       	1	110	1	ATTAGGGATA	    0.961532	-13
          **********

Masking position 10
Map Score:   4.37705

Number of sites scoring better than the average of aligned sites = 1828
Number in coding regions = 1568
Number in noncoding regions = 260
Number of orfs with sites within 600 bp upstream = 219
Fraction of orfs with sites within 600 bp upstream = 0.0351751


Motif number 3

TTTAATAAATTTTTAATGAAAATATTATAC	1	11	1	TTTTAATGAA	    0.925169	-112
AAATTTTATATAATTAGGTAATTTAATTAC	1	70	1	TAATTAGGTA	    0.978819	-53
TCTTAATCATTTTTAAGGTAATTAAATTAC	1	87	0	TTTTAAGGTA	    0.988549	-36
TGATTAAGATTGATTAGGGATAGGC     	1	108	1	TGATTAGGGA	      0.9839	-15
          **********

Masking position 6
Map Score:   1.38403

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 270
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 4

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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 6

          **********

No masking
Map Score:   1.23224e-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