AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_mjan_reg_300.orf -o320_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	RMJ01269	211	M_jannaschii_chromosome
#2	RMJ02550	225	M_jannaschii_chromosome

Motif number 1

TGAAATTCTATATAAACCTTTCGGTTTTGTG	1	55	1	TATAAACTTT	    0.962719	-157
ACTGTAAATATATAAATACTTATATCTTACA	1	108	1	TATAAATCTT	    0.957039	-104
AAAGCTATCTTATAAATCTTTGTTTCATCAG	1	147	0	TATAAATTTT	    0.978516	-65
       CACTATCATCCTTAAATACGTTTT	1	198	0	TATCATCTTA	    0.845255	-14
GTTATGGCAATTTCATTTTTTATATATGAGC	2	76	1	TTTCATTTTT	     0.94121	-150
ATGAGCAATATTTAAATTTTTCGAGATAGAT	2	101	1	TTTAAATTTT	    0.959857	-125
CCAACAATATTATCATTATTTTTAATAACTT	2	136	1	TATCATTTTT	    0.968253	-90
TTACTAATACTTTAAAGCTTTTTGATACGGA	2	166	0	TTTAAAGTTT	    0.880393	-60
TTTGATATTATATAATTACTATTATTATTAC	2	193	0	TATAATTCTA	    0.850287	-33
          ******* ***

Masking position 5
Map Score:   7.86181

Number of sites scoring better than the average of aligned sites = 1158
Number in coding regions = 828
Number in noncoding regions = 330
Number of orfs with sites within 600 bp upstream = 288
Fraction of orfs with sites within 600 bp upstream = 0.0462576


Motif number 2

ATGTATATGTTAATGAAATTCTATATAAACCTT	1	42	1	TAATGAATTA	    0.717744	-170
TATTTACAGTTATTGATGTTGAATCAACTTTAC	1	85	0	TATTGTGTAA	    0.980037	-127
TCTTACAAAATTATGCTGATGAAACAAAGATTT	1	132	1	TTATGTGTAA	    0.931713	-80
ACGTTTTGTTTTTTGTAAATAAATAGCAAAGCT	1	172	0	TTTTGAATAA	    0.900922	-40
ATTGCCCTATTATTGGGGGGCTATTCTCATAGG	2	15	0	TATTGGGGTA	    0.951909	-211
TGCCATAACATTTTGAGGTGATACCATTAAAAG	2	52	0	TTTTGGGGTA	    0.951908	-174
AAAATTTAAATATTGCTCATATATAAAAAATGA	2	88	0	TATTGTCTTA	     0.91802	-138
ATAATGATAATATTGTTGGTTAAATCTATCTCG	2	122	0	TATTGTGTAA	    0.979979	-104
CTTTAAAGCTTTTTGATACGGAAGTTATTAAAA	2	155	0	TTTTGTAGAA	    0.946755	-71
ACTATCCCGCTTTTGATATTATATAATTACTAT	2	202	0	TTTTGTATTA	    0.961506	-24
          ***** ** * **

Masking position 4
Map Score:   8.29552

Number of sites scoring better than the average of aligned sites = 913
Number in coding regions = 767
Number in noncoding regions = 146
Number of orfs with sites within 600 bp upstream = 136
Fraction of orfs with sites within 600 bp upstream = 0.0218439


Motif number 3

ATATGTTAATGAAATTCTATATAAACCTTTC	1	46	1	GAATTCTATA	    0.951904	-166
ATCAATAACTGTAAATATATAAATACTTATA	1	101	1	GAAATATATA	    0.982275	-111
AGCATAATTTTGTAAGATATAAGTATTTATA	1	118	0	TTAAGATATA	    0.724248	-94
TAAATAAATAGCAAAGCTATCTTATAAATCT	1	159	0	GAAAGCTATC	    0.945714	-53
TTTGTTTTTTGTAAATAAATAGCAAAGCTAT	1	170	0	GAAATAAATA	    0.908535	-42
TTTAAATATTGCTCATATATAAAAAATGAAA	2	86	0	GTCATATATA	    0.843492	-140
ATATTGTTGGTTAAATCTATCTCGAAAAATT	2	115	0	TAAATCTATC	    0.875569	-111
AATAATAATAGTAATTATATAATATCAAAAG	2	195	1	GAATTATATA	    0.952971	-31
          * *********

Masking position 9
Map Score:   3.90238

Number of sites scoring better than the average of aligned sites = 541
Number in coding regions = 461
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 4

          **********

No masking
Map Score:   -8.6443e-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:   -8.6443e-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:   -8.6443e-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