AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i229_mjan_pyro_300.orf -o229_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ09342	119	M_jannaschii_chromosome
#2	RMJ09012	34	M_jannaschii_chromosome

Motif number 1

TTTTATTAAATTAAAAAATTAAAAACTTAA	1	26	0	TTAAAAAATT	    0.987033	-94
AATTTTTTAATTTAATAAAACTTAAATAAT	1	36	1	TTTAATAAAA	    0.862516	-84
TTAATAAAACTTAAATAATAAAAACTTTTG	1	47	1	TTAAATAATA	    0.986908	-73
AAAACTTTTGTTAAAAAATATGTGTAGTAT	1	67	1	TTAAAAAATA	    0.994263	-53
ATATGTGTAGTATAAAAATTTCTAAATACA	1	84	1	TATAAAAATT	    0.890719	-36
          TCAATAAATAGTGTGTTGTA	1	110	0	TCAATAAATA	    0.965294	-10
      ATAATTAATAAATAATTTGGTGAT	2	5	1	TTAATAAATA	    0.986908	-30
          **********

Masking position 4
Map Score:   12.459

Number of sites scoring better than the average of aligned sites = 1486
Number in coding regions = 1152
Number in noncoding regions = 334
Number of orfs with sites within 600 bp upstream = 279
Fraction of orfs with sites within 600 bp upstream = 0.0448121


Motif number 2

CCCCCATTATTAAGTTTTTAATTTTTTAAT	1	17	1	TAAGTTTTTA	    0.967223	-103
TTTTATTATTTAAGTTTTATTAAATTAAAA	1	40	0	TAAGTTTTAT	    0.908508	-80
TTTTTTAACAAAAGTTTTTATTATTTAAGT	1	55	0	AAAGTTTTTA	    0.988287	-65
TATACTACACATATTTTTTAACAAAAGTTT	1	68	0	ATATTTTTTA	    0.960626	-52
TGTAGTATAAAAATTTCTAAATACAACACA	1	89	1	AAATTTCTAA	    0.948059	-31
AGAAATCACCAAATTATTTATTAATTAT  	2	9	0	AAATTATTTA	    0.944524	-26
          **********

Masking position 5
Map Score:   7.92959

Number of sites scoring better than the average of aligned sites = 975
Number in coding regions = 680
Number in noncoding regions = 295
Number of orfs with sites within 600 bp upstream = 285
Fraction of orfs with sites within 600 bp upstream = 0.0457758


Motif number 3

TTTTAATTTAATAAAACTTAAATAATAAAA	1	40	1	ATAAAACTTA	    0.946744	-80
TAAAACTTAAATAATAAAAACTTTTGTTAA	1	51	1	ATAATAAAAA	     0.88751	-69
AGAAATTTTTATACTACACATATTTTTTAA	1	77	0	ATACTACACA	    0.990924	-43
AAATTTCTAAATACAACACACTATTTATTG	1	99	1	ATACAACACA	    0.993653	-21
      TTCCATAGAAATCACCAAATTATT	2	21	0	ATAGAAATCA	     0.96342	-14
          **********

Masking position 6
Map Score:   3.87306

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 272
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 4

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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