AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_Sulfate_trans-Cys_Synthase_mjan_reg_100.orf -o109_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

ATTTTCATTAAAAATTTATTAAA       	1	4	0	AAAATTTATT	    0.983964	-119
TTTTTAATGAAAATATTATACTATCAAATG	1	20	1	AAATATTATA	    0.961185	-103
AAAATTGATGACATTTGATAGTATAATATT	1	31	0	ACATTTGATA	    0.973281	-92
TGTGTTAAACAAAATTGATGACATTTGATA	1	41	0	AAAATTGATG	    0.989053	-82
TGTTTAACACAAATTTTATATAATTAGGTA	1	60	1	AAATTTTATA	    0.982842	-63
TAATTACCTTAAAAATGATTAAGATTGATT	1	93	1	AAAAATGATT	     0.98056	-30
AAAAATGATTAAGATTGATTAGGGATAGGC	1	103	1	AAGATTGATT	     0.97915	-20
          **********

Masking position 8
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

TTTCATTAAAAATTTATTAAA         	1	2	0	AATTTATTAA	    0.931153	-121
ATAGTATAATATTTTCATTAAAAATTTATT	1	14	0	ATTTTCATTA	    0.975621	-109
TATACTATCAAATGTCATCAATTTTGTTTA	1	36	1	AATGTCATCA	    0.878425	-87
AATGTCATCAATTTTGTTTAACACAAATTT	1	46	1	ATTTTGTTTA	    0.942168	-77
TTTAACACAAATTTTATATAATTAGGTAAT	1	62	1	ATTTTATATA	    0.800819	-61
AAGGTAATTAAATTACCTAATTATATAAAA	1	73	0	AATTACCTAA	    0.949494	-50
TAGGTAATTTAATTACCTTAAAAATGATTA	1	84	1	AATTACCTTA	    0.972281	-39
          **********

Masking position 1
Map Score:   4.45661

Number of sites scoring better than the average of aligned sites = 1757
Number in coding regions = 1498
Number in noncoding regions = 259
Number of orfs with sites within 600 bp upstream = 230
Fraction of orfs with sites within 600 bp upstream = 0.0369419


Motif number 3

          TTTAATAAATTTTTAATGAA	1	1	1	TTTAATAAAT	    0.862369	-122
TTAATAAATTTTTAATGAAAATATTATACT	1	12	1	TTTAATGAAA	    0.739072	-111
ATCAATTTTGTTTAACACAAATTTTATATA	1	52	1	TTTAACACAA	    0.966889	-71
TTAACACAAATTTTATATAATTAGGTAATT	1	63	1	TTTTATATAA	    0.614474	-60
CTTAATCATTTTTAAGGTAATTAAATTACC	1	86	0	TTTAAGGTAA	      0.9779	-37
          **********

Masking position 5
Map Score:   5.02367

Number of sites scoring better than the average of aligned sites = 563
Number in coding regions = 421
Number in noncoding regions = 142
Number of orfs with sites within 600 bp upstream = 128
Fraction of orfs with sites within 600 bp upstream = 0.0205589


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