AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i315_mixed29_mjan_reg_100.orf -o315_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	RMJ11660	140	M_jannaschii_chromosome
#2	RMJ00398	110	M_jannaschii_chromosome
#3	RMJ09695	103	M_jannaschii_chromosome

Motif number 1

AGAAGATTTAAATACTTTGTCTAATATATT	1	39	0	AATACTTTGT	    0.784076	-102
CAATAAACATAATGCATTTCAACAAAATCA	1	84	1	AATGCATTTC	    0.908823	-57
AACAAAATCAAAAACTTTATATAATATTGA	1	104	1	AAAACTTTAT	    0.811687	-37
TATTCTTCCCCAAACTTTTCAAGC      	2	5	0	CAAACTTTTC	    0.959345	-106
TTTGTAATCTCATCCCTTATTTCATGTTCT	2	47	0	CATCCCTTAT	    0.922247	-64
AAATATAATAAAGCCCTTTTTGTAATCTCA	2	65	0	AAGCCCTTTT	    0.951238	-46
TTAATATAGGAAGGCATTTCCGAAT     	3	6	0	AAGGCATTTC	    0.892051	-98
CGAGGTGATGCATCCATTTTGATCAACCTT	3	70	1	CATCCATTTT	    0.972043	-34
CCATTTTGATCAACCTTTTTAGAAAAGGTT	3	83	1	CAACCTTTTT	    0.982366	-21
          CAACCTTTTCTAAAAAGGTT	3	94	0	CAACCTTTTC	    0.983721	-10
          **********

Masking position 7
Map Score:   9.39776

Number of sites scoring better than the average of aligned sites = 887
Number in coding regions = 802
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 2

ACACTCTTAATATTTTTATGTCTAATATATTA	1	16	1	TATTTTATTC	    0.955318	-125
TTAGACAAAGTATTTAAATCTTCTCTTTACAA	1	45	1	TATTAAATTT	    0.957542	-96
TGAAATGCATTATGTTTATTGTCGGATATTGT	1	73	0	TATTTTATGT	    0.978557	-68
ATGTCAATATTATATAAAGTTTTTGATTTTGT	1	105	0	TATTAAAGTT	    0.853487	-36
ATTGACATTTTATTTTTATTTT          	1	129	1	TATTTTATTT	    0.987689	-12
AGGGCTTTATTATATTTCTCTTCAAGTATGTG	2	78	1	TATTTTCTTT	    0.955325	-33
TCTTCAAGTATGTGTTGATATTACT       	2	96	1	TGTTTGATTT	     0.90604	-15
AATGCCTTCCTATATTAATAGTAGCTAAGCTA	3	18	1	TATTTAATGT	    0.968258	-86
          *** ***** **

Masking position 5
Map Score:   6.25568

Number of sites scoring better than the average of aligned sites = 611
Number in coding regions = 359
Number in noncoding regions = 252
Number of orfs with sites within 600 bp upstream = 237
Fraction of orfs with sites within 600 bp upstream = 0.0380662


Motif number 3

GTCGGATATTGTAAAGAGAAGATTTAAATACT	1	53	0	GTAAGGAAGA	    0.983183	-88
 GCTTGAAAAGTTTGGGGAAGAATATTACTTC	2	10	1	GTTGGGAAGA	    0.981166	-101
ATTAATAGTAGCTAAGCTAAGAGGCATCACCG	3	31	1	GCAAGTAAGA	    0.940721	-73
ACCTCGCTACGCTCGGTGATGCCTCTTAGCTT	3	44	0	GCCGGGATGC	    0.991709	-60
ACCGAGCGTAGCGAGGTGATGCATCCATTTTG	3	59	1	GCAGGGATGC	     0.99548	-45
          ** *** *****

Masking position 9
Map Score:   1.44769

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 40
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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