AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_pyro_reg_100.orf -o129_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	RPH00900	127	Pyrococcus_OT3

Motif number 1

TGTTTTTTCTAAGCTTTTTAAAGGTATCACC	1	50	1	AAGTTTTTAA	    0.996281	-78
CGGATAAGTGAAGTTACTTAACAGAATGTTT	1	80	1	AAGTACTTAA	    0.988903	-48
TACTTAACAGAATGTTTTTAAGTTAACAATC	1	94	1	AATTTTTTAA	    0.985386	-34
ACTAATCCTCAAGATTGTTAACTTAAAAACA	1	106	0	AAGTTGTTAA	    0.995579	-22
          *** *******

Masking position 5
Map Score:   5.63339

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 50
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

       AGTTATCCCTAGAGCTCTCTTCG	1	4	1	TATCCCTAGA	    0.822266	-124
TTCGCTTCCATCTCGCGTGATGTTTTTTCT	1	30	1	TCTCGCGTGA	    0.517935	-98
TAACTTCACTTATCCGGTGATACCTTTAAA	1	66	0	TATCCGGTGA	    0.698193	-62
          **********

Masking position 10
Map Score:   1.59773

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 41
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

AAGAGAGCTCTAGGGATAACT          	1	1	0	TGGGATAACT	    0.988784	-127
TAAAGGTATCACCGGATAAGTGAAGTTACTT	1	68	1	ACGGATAAGT	    0.994191	-60
CTTAAAAACATTCTGTTAAGTAACTTCACTT	1	85	0	TCTGTTAAGT	    0.977435	-43
TTAACAATCTTGAGGATTAGTG         	1	116	1	TAGGATTAGT	    0.984401	-12
          * *********

Masking position 7
Map Score:   1.03444

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 96
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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:   1.87173e-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