AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_pyro_reg_100.orf -o150_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH01063	24	Pyrococcus_OT3
#2	RPH01058	31	Pyrococcus_OT3
#3	RPH01055	142	Pyrococcus_OT3

Motif number 1

  TGTTCTTTCTTTAATTTAGGAGGACAGA	2	9	1	CTTTAATTTA	    0.953906	-23
GAAGATGAGCCTTTTATTTTGTTTTTTGTT	3	24	1	CTTTTATTTT	    0.917296	-119
GATTATTGAACAATTATTTATAAACAAAAA	3	46	0	CAATTATTTA	    0.971561	-97
AATAATTGTTCAATAATCCTAGCAAAAAAT	3	58	1	CAATAATCCT	    0.938582	-85
AGATCATTGACATTCATTTAAAATATTTTT	3	82	0	CATTCATTTA	    0.976569	-61
AAATGAATGTCAATGATCTGTTCTTGTAAT	3	93	1	CAATGATCTG	    0.941246	-50
GTAATTCTCCCTATCATCCAAAGGAGATGG	3	118	1	CTATCATCCA	    0.971323	-25
          **********

Masking position 6
Map Score:   5.01381

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 221
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

  TTCCTGTCACCTAGTAAAATGGAA    	1	7	0	ACCTAGTAAA	    0.991501	-18
   CTTTCTGTCCTCCTAAATTAAAGAAAG	2	15	0	TCCTCCTAAA	    0.989459	-17
TGTTCAATAATCCTAGCAAAAAATATTTTA	3	64	1	TCCTAGCAAA	    0.994244	-79
          **********

Masking position 8
Map Score:   1.65435

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 25
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          TTCCTGTCACCTAGTAAAATGG	1	13	0	TTCCTGTCCT	    0.991233	-12
     TGTTCTTTCTTTAATTTAGGAGGACAG	2	6	1	TTTCTTTTTT	    0.848849	-26
         CTTTCTGTCCTCCTAAATTAAAG	2	19	0	TTTCTGTTCC	    0.992721	-13
AAGGCTCATCTTCCTGAGTCTCAAAT      	3	5	0	TTCCTGACTC	    0.981308	-138
CAATGATCTGTTCTTGTAATTCTCCCTATCAT	3	103	1	TTCTTGTTTC	    0.975435	-40
CTTGTAATTCTCCCTATCATCCAAAGGAGATG	3	115	1	TCCCTATTCC	    0.965846	-28
          *******  ***

Masking position 5
Map Score:   2.2029

Number of sites scoring better than the average of aligned sites = 714
Number in coding regions = 652
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 4

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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