AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i271_hypothetical16_pyro_reg_100.orf -o271_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	RPH00534	20	Pyrococcus_OT3
#2	RPH00533	119	Pyrococcus_OT3

Motif number 1

          ATTAGTAGGAGGTATTGAAA	1	1	1	ATTAGTAGGA	    0.964661	-20
GTTGTATATAGGTAGTTGGAAGTTTAACTC	2	24	0	GGTAGTTGGA	    0.998027	-96
AAAATGGAGGGGAAGTTGTATATAGGTAGT	2	38	0	GGAAGTTGTA	      0.9746	-82
CCATCTCCTGAGTTGCTGGATCCCACCTGG	2	83	0	AGTTGCTGGA	    0.988171	-37
CCAGCAACTCAGGAGATGGAAAAAGTGAAT	2	94	1	AGGAGATGGA	    0.990893	-26
          **********

Masking position 10
Map Score:   6.00928

Number of sites scoring better than the average of aligned sites = 413
Number in coding regions = 388
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

    TTTCAATACCTCCTACTAAT      	1	5	0	TACCTCCTAC	     0.97118	-16
TTAACTCTGGTAACCCCTCA          	2	1	0	TAACCCCTCA	    0.989049	-119
CTATATACAACTTCCCCTCCATTTTAGTTT	2	43	1	CTTCCCCTCC	    0.987782	-77
TCACTTTTTCCATCTCCTGAGTTGCTGGAT	2	92	0	CATCTCCTGA	    0.988392	-28
         GTATCTATTCACTTTTTCCAT	2	109	0	TATCTATTCA	    0.885889	-11
          **********

Masking position 8
Map Score:   1.39634

Number of sites scoring better than the average of aligned sites = 1654
Number in coding regions = 1511
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 152
Fraction of orfs with sites within 600 bp upstream = 0.0244137


Motif number 3

AGTTAAACTTCCAACTACCTATATACAACT	2	25	1	CCAACTACCT	    0.995155	-95
CTACCTATATACAACTTCCCCTCCATTTTA	2	39	1	ACAACTTCCC	    0.991486	-81
CAGGTGGGATCCAGCAACTCAGGAGATGGA	2	84	1	CCAGCAACTC	     0.98989	-36
          **********

Masking position 3
Map Score:   0.337967

Number of sites scoring better than the average of aligned sites = 146
Number in coding regions = 137
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


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