AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_Sulfate_trans-Cys_Synthase_mjan_reg_300.orf -o109_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	RMJ01308	122	M_jannaschii_chromosome

Motif number 1

ATTTTCATTAAAAATTTATTAAA       	1	4	0	AAAATTTATT	    0.984184	-119
TTTTTAATGAAAATATTATACTATCAAATG	1	20	1	AAATATTATA	    0.961981	-103
AAAATTGATGACATTTGATAGTATAATATT	1	31	0	ACATTTGATA	    0.973844	-92
TGTGTTAAACAAAATTGATGACATTTGATA	1	41	0	AAAATTGATG	    0.989287	-82
TGTTTAACACAAATTTTATATAATTAGGTA	1	60	1	AAATTTTATA	    0.983206	-63
TAATTACCTTAAAAATGATTAAGATTGATT	1	93	1	AAAAATGATT	    0.980767	-30
AAAAATGATTAAGATTGATTAGGGATAGGC	1	103	1	AAGATTGATT	    0.979583	-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

         TTTAATAAATTTTTAATGAAA	1	2	1	TTAATAAATT	    0.935216	-121
AATAAATTTTTAATGAAAATATTATACTAT	1	14	1	TAATGAAAAT	    0.977123	-109
TAAACAAAATTGATGACATTTGATAGTATA	1	36	0	TGATGACATT	    0.885218	-87
AAATTTGTGTTAAACAAAATTGATGACATT	1	46	0	TAAACAAAAT	     0.94562	-77
ATTACCTAATTATATAAAATTTGTGTTAAA	1	62	0	TATATAAAAT	    0.810998	-61
TTTTATATAATTAGGTAATTTAATTACCTT	1	73	1	TTAGGTAATT	    0.952531	-50
TAATCATTTTTAAGGTAATTAAATTACCTA	1	84	0	TAAGGTAATT	    0.973985	-39
          **********

Masking position 8
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

GTATAATATTTTCATTAAAAATTTATTAAA	1	11	0	TTCATTAAAA	    0.918178	-112
GTAATTAAATTACCTAATTATATAAAATTT	1	70	0	TACCTAATTA	    0.976949	-53
GTAATTTAATTACCTTAAAAATGATTAAGA	1	87	1	TACCTTAAAA	    0.987406	-36
     GCCTATCCCTAATCAATCTTAATCA	1	108	0	TCCCTAATCA	    0.982295	-15
          **********

Masking position 5
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