AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_pyro_reg_300.orf -o129_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	RPH00900	127	Pyrococcus_OT3

Motif number 1

TGTTTTTTCTAAGCTTTTTAAAGGTATCACC	1	50	1	AAGTTTTTAA	    0.996033	-78
CGGATAAGTGAAGTTACTTAACAGAATGTTT	1	80	1	AAGTACTTAA	    0.988167	-48
TACTTAACAGAATGTTTTTAAGTTAACAATC	1	94	1	AATTTTTTAA	    0.984421	-34
ACTAATCCTCAAGATTGTTAACTTAAAAACA	1	106	0	AAGTTGTTAA	    0.995283	-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

CGAAGAGAGCTCTAGGGATAACT       	1	4	0	TCTAGGGATA	    0.815281	-124
AGAAAAAACATCACGCGAGATGGAAGCGAA	1	30	0	TCACGCGAGA	    0.516835	-98
TTTAAAGGTATCACCGGATAAGTGAAGTTA	1	66	1	TCACCGGATA	    0.690447	-62
          **********

Masking position 8
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

CCTAGAGCTCTCTTCGCTTCCATCTCGCGT	1	18	1	TCTTCGCTTC	    0.986738	-110
TGATGTTTTTTCTAAGCTTTTTAAAGGTAT	1	47	1	TCTAAGCTTT	    0.933974	-81
CTGTTAAGTAACTTCACTTATCCGGTGATA	1	74	0	ACTTCACTTA	    0.987959	-54
AAGTGAAGTTACTTAACAGAATGTTTTTAA	1	85	1	ACTTAACAGA	    0.912235	-43
TCCTCAAGATTGTTAACTTAAAAACATTCT	1	102	0	TGTTAACTTA	    0.968692	-26
          **********

Masking position 3
Map Score:   1.39429

Number of sites scoring better than the average of aligned sites = 632
Number in coding regions = 570
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


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