AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_pyro_reg_300.orf -o150_pyro_300.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
#4	RPH01052	137	Pyrococcus_OT3

Motif number 1

  TGTTCTTTCTTTAATTTAGGAGGACAGA	2	9	1	CTTTAATTTA	    0.931011	-23
GAAGATGAGCCTTTTATTTTGTTTTTTGTT	3	24	1	CTTTTATTTT	    0.876222	-119
GATTATTGAACAATTATTTATAAACAAAAA	3	46	0	CAATTATTTA	    0.923309	-97
AATAATTGTTCAATAATCCTAGCAAAAAAT	3	58	1	CAATAATCCT	    0.885685	-85
AGATCATTGACATTCATTTAAAATATTTTT	3	82	0	CATTCATTTA	    0.949884	-61
GTAATTCTCCCTATCATCCAAAGGAGATGG	3	118	1	CTATCATCCA	    0.987096	-25
AACGTTTTGATTTTTATCCAAGATGGATGA	4	61	1	TTTTTATCCA	    0.844543	-77
CTTTTGGTATCTATCATCCATCTTGGATAA	4	74	0	CTATCATCCA	    0.987096	-64
          **********

Masking position 6
Map Score:   6.56593

Number of sites scoring better than the average of aligned sites = 571
Number in coding regions = 524
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

TCCTGTCACCTAGTAAAATGGAA          	1	1	0	TAGAAAAGAA	      0.9872	-24
TTCTTTAATTTAGGAGGACAGAAAG        	2	17	1	TAGAGGAGAA	    0.974035	-15
TCAATAATCCTAGCAAAAAATATTTTAAATGAA	3	67	1	TAGAAAATAT	    0.954917	-76
TAGGGAGAATTACAAGAACAGATCATTGACATT	3	98	0	TACAGAAGAT	     0.98794	-45
GGATGATAGATACCAAAAGTGATTTAACGAAAG	4	85	1	TACAAAAGAT	    0.986993	-53
          *** ****  ***

Masking position 8
Map Score:   0.986641

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 69
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

         TGTTCTTTCTTTAATTTAGGAGG	2	2	1	GTTCTTTTTA	     0.98449	-30
CTTTTATTTTGTTTTTTGTTTATAAATAATTG	3	34	1	GTTTTTTTTA	    0.990844	-109
GTTAAATTAAGTTTTATGTCTAACGTTTTGAT	4	40	1	GTTTTTTCTA	     0.98449	-98
TATGTCTAACGTTTTGATTTTTATCCAAGATG	4	54	1	GTTTTATTTT	    0.944289	-84
          ***** * ****

Masking position 5
Map Score:   0.303331

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 23
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   2.51122e-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:   2.51122e-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:   2.51122e-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