AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i271_mjan_pyro_100.orf -o271_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	RPH00534	20	Pyrococcus_OT3
#2	RPH00533	119	Pyrococcus_OT3

Motif number 1

TTTCAATACCTCCTACTAAT          	1	1	0	TCCTACTAAT	    0.964661	-20
GAGTTAAACTTCCAACTACCTATATACAAC	2	24	1	TCCAACTACC	    0.998027	-96
ACTACCTATATACAACTTCCCCTCCATTTT	2	38	1	TACAACTTCC	      0.9746	-82
CCAGGTGGGATCCAGCAACTCAGGAGATGG	2	83	1	TCCAGCAACT	    0.988171	-37
ATTCACTTTTTCCATCTCCTGAGTTGCTGG	2	94	0	TCCATCTCCT	    0.990893	-26
          **********

Masking position 1
Map Score:   6.00928

Number of sites scoring better than the average of aligned sites = 440
Number in coding regions = 423
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

    TTTCAATACCTCCTACTAAT      	1	5	0	TACCTCCTAC	    0.969824	-16
TTAACTCTGGTAACCCCTCA          	2	1	0	TAACCCCTCA	    0.988524	-119
CTATATACAACTTCCCCTCCATTTTAGTTT	2	43	1	CTTCCCCTCC	    0.987197	-77
TCACTTTTTCCATCTCCTGAGTTGCTGGAT	2	92	0	CATCTCCTGA	    0.987835	-28
         GTATCTATTCACTTTTTCCAT	2	109	0	TATCTATTCA	    0.881014	-11
          **********

Masking position 8
Map Score:   1.39634

Number of sites scoring better than the average of aligned sites = 992
Number in coding regions = 885
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

AGTTAAACTTCCAACTACCTATATACAACT	2	25	1	CCAACTACCT	     0.99528	-95
CTACCTATATACAACTTCCCCTCCATTTTA	2	39	1	ACAACTTCCC	    0.991704	-81
CAGGTGGGATCCAGCAACTCAGGAGATGGA	2	84	1	CCAGCAACTC	    0.990149	-36
          **********

Masking position 3
Map Score:   0.337967

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 59
Number in noncoding regions = 15
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:   2.37484e-14

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:   2.37484e-14

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:   2.37484e-14

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