AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_mjan_reg_100.orf -o340_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	RMJ01952	58	M_jannaschii_chromosome
#2	RMJ14782	184	M_jannaschii_chromosome

Motif number 1

GTTATTGTTTATTTAAATATTTTATGAGGGAGAGT  	1	9	0	ATAAATTTAA	    0.878006	-50
ATTTAAATAAACAATAACACTTTATTAACCTTAGGAA	1	28	1	AATAATTTAA	    0.992073	-31
AATATCCACCACAATAATATTTTACAATATTTATATA	2	12	1	AATAATTTAA	    0.992073	-173
GATAATCTGAATAATAATAGTTAAATATATAAATATT	2	37	0	AATAATTAAA	    0.989791	-148
CTTAATATTGAGGATGAGCTTTTAAAATTGCATAACT	2	73	1	AATACTTTAA	    0.990687	-112
GTTAAGTAACATAAATATAGTTATGCAATTTTAAAAG	2	91	0	AAAAATTATA	    0.839058	-94
TAGGAAAAGGATACTTAAAGTTAAGTAACATAAATAT	2	110	0	ACTAATTAAA	    0.965305	-75
CCATTTACCTACCATTAACTTTAAAAACCTTAACTGA	2	151	0	AATACTTAAA	    0.988535	-34
          ATTATCACCATTTACCTACCATTAACT	2	168	0	AATACTTTAT	    0.943541	-17
          *  ** * * ****  *

Masking position 7
Map Score:   12.8676

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 195
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

TTTATTTAAATATTTTATGAGGGAGAGT  	1	9	0	TATTTTATGA	    0.721651	-50
TAAACAATAACACTTTATTAACCTTAGGAA	1	35	1	CACTTTATTA	    0.896239	-24
          TAATTTCCTAAGGTTAATAA	1	49	0	TAATTTCCTA	    0.947651	-10
ACCACAATAATATTTTACAATATTTATATA	2	19	1	TATTTTACAA	    0.901229	-166
AATATTTATATATTTAACTATTATTATTCA	2	37	1	TATTTAACTA	    0.921215	-148
ATATTTATGTTACTTAACTTTAAGTATCCT	2	110	1	TACTTAACTT	    0.894598	-75
CTTTAAGTATCCTTTTCCTAATAATCAGTT	2	127	1	CCTTTTCCTA	    0.963574	-58
CATTTACCTACCATTAACTTTAAAAACCTT	2	157	0	CCATTAACTT	    0.781345	-28
  ATTATCACCATTTACCTACCATTAACTT	2	167	0	CATTTACCTA	    0.977653	-18
          **********

Masking position 5
Map Score:   6.43644

Number of sites scoring better than the average of aligned sites = 937
Number in coding regions = 739
Number in noncoding regions = 198
Number of orfs with sites within 600 bp upstream = 162
Fraction of orfs with sites within 600 bp upstream = 0.0260199


Motif number 3

TTATTGTTTATTTAAATATTTTATGAGGGAG	1	14	0	TTTAAAATTT	    0.902514	-45
AATAACACTTTATTAACCTTAGGAAATTA  	1	40	1	TATTAACTTA	     0.95734	-19
TAGTTAAATATATAAATATTGTAAAATATTA	2	26	0	TATAAAATTG	    0.979528	-159
TATTTATATATTTAACTATTATTATTCAGAT	2	39	1	TTTAACATTA	    0.889973	-146
TAACTATTATTATTCAGATTATCTTAATATT	2	51	1	TATTCAATTA	    0.910592	-134
ATTCAGATTATCTTAATATTGAGGATGAGCT	2	62	1	TCTTAAATTG	     0.95569	-123
GAGGATGAGCTTTTAAAATTGCATAACTATA	2	82	1	TTTTAAATTG	    0.973532	-103
CCATTAACTTTAAAAACCTTAACTGATTATT	2	146	0	TAAAAACTTA	    0.800952	-39
          ****** ****

Masking position 9
Map Score:   5.58872

Number of sites scoring better than the average of aligned sites = 1084
Number in coding regions = 750
Number in noncoding regions = 334
Number of orfs with sites within 600 bp upstream = 309
Fraction of orfs with sites within 600 bp upstream = 0.0496306


Motif number 4

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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