AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_mjan_pyro_100.orf -o325_mjan_pyro_100.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	RMJ08781	131	M_jannaschii_chromosome
#2	RMJ06449	72	M_jannaschii_chromosome
#3	RPH00818	60	Pyrococcus_OT3

Motif number 1

CCTTAAAACTTAGGTATTAAAAAATTAGAAAAAT	1	11	0	TAGTTAAAAA	    0.980355	-121
AGATTGGATGAAAACCTTAAAACTTAGGTATTAA	1	25	0	AAATTAAAAT	    0.984001	-107
TTTCTTGTAAAACATTTTGAAAGAAACTTTTAGG	1	61	0	AAATTGAAAA	    0.989598	-71
TAAAATAGAAAAAAAGTTGAAATATAGTTTCTTG	1	88	0	AAATTGAAAA	    0.989598	-44
CTCACCTAATTAAACATTAAAATAGAAAAAAAGT	1	105	0	TAATTAAAAA	      0.9903	-27
ATAATCACCATACATCTTATAATAATAGTTAAAA	2	11	1	TAATTATAAA	    0.969933	-62
TAATAGTTAAAATATTTTATAAAAAGTATTTTAA	2	33	1	AAATTATAAA	    0.983999	-40
GTTATCACCAAAGACATTAAAATACTTTTTATAA	2	49	0	AAATTAAAAA	    0.994888	-24
TCCCGAGGTAAAGGTATTAAAAATAGTAACGTTA	3	30	0	AAGTTAAAAT	    0.967807	-31
          ** *  ****** *

Masking position 7
Map Score:   19.272

Number of sites scoring better than the average of aligned sites = 694
Number in coding regions = 558
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

TAGGTATTAAAAAATTAGAAAAAT      	1	5	0	AAAATTAGAA	    0.870521	-127
AAAAAAGTTGAAATATAGTTTCTTGTAAAA	1	83	0	AAATATAGTT	    0.841727	-49
AATTAAACATTAAAATAGAAAAAAAGTTGA	1	102	0	TAAAATAGAA	    0.961193	-30
TACATCTTATAATAATAGTTAAAATATTTT	2	21	1	AATAATAGTT	    0.951206	-52
ATACTTTTTATAAAATATTTTAACTATTAT	2	32	0	TAAAATATTT	    0.843106	-41
CCAAAGACATTAAAATACTTTTTATAAAAT	2	46	0	TAAAATACTT	    0.940001	-27
TAAAGGTATTAAAAATAGTAACGTTAAAGT	3	26	0	AAAAATAGTA	    0.981879	-35
          **********

Masking position 7
Map Score:   7.22572

Number of sites scoring better than the average of aligned sites = 595
Number in coding regions = 428
Number in noncoding regions = 167
Number of orfs with sites within 600 bp upstream = 156
Fraction of orfs with sites within 600 bp upstream = 0.0250562


Motif number 3

TCTAATTTTTTAATACCTAAGTTTTAAGGT	1	16	1	TAATACCTAA	    0.859877	-116
TTTCATCCAATCTTTCCTAAAAGTTTCTTT	1	46	1	TCTTTCCTAA	    0.963713	-86
CCTAAAAGTTTCTTTCAAAATGTTTTACAA	1	61	1	TCTTTCAAAA	    0.817673	-71
        AATCTCACCTAATTAAACATTA	1	120	0	TCTCACCTAA	    0.992131	-12
        ATAATCACCATACATCTTATAA	2	3	1	AATCACCATA	    0.802819	-70
        GTTATCACCAAAGACATTAAAA	2	61	0	TATCACCAAA	    0.987573	-12
        GCTCTCACCACGAAAACTTTAA	3	3	1	TCTCACCACG	    0.948645	-58
          **********

Masking position 6
Map Score:   4.88776

Number of sites scoring better than the average of aligned sites = 784
Number in coding regions = 626
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 183
Fraction of orfs with sites within 600 bp upstream = 0.0293929


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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