AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_pyro_reg_100.orf -o223_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	RPH01735	233	Pyrococcus_OT3
#2	RPH01736	42	Pyrococcus_OT3

Motif number 1

CTTGTTTTTGTCAAAAATCCTTTTAAGTAA	1	29	0	TCAAAAATCC	    0.976134	-205
CGTCTCTCCTTTAAAAAACTTTGCTAGCTT	1	56	0	TTAAAAAACT	    0.969958	-178
AGGAGAGACGTCAAAGAACTAATTTGATGA	1	76	1	TCAAAGAACT	    0.996962	-158
GTTCGAAAAATCAAAGAAGTTCATTGCTTT	1	141	0	TCAAAGAAGT	    0.989385	-93
AACCAAAGATTCAAAAATCTTTCGGAACAG	1	182	0	TCAAAAATCT	    0.991139	-52
GGTTAACATTTCAAAGAAATTCCGAGGTGG	1	208	1	TCAAAGAAAT	    0.984347	-26
          **********

Masking position 5
Map Score:   11.14

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 135
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

AAAACTTTGCTAGCTTGTTTTTGTCAAAAA	1	42	0	TAGCTTGTTT	    0.966815	-192
TTAAAGCTGATATCTTGTTCCCTAATCATC	1	101	0	TATCTTGTTC	    0.984524	-133
AAGAAGTTCATTGCTTTTACTAATTCGTTA	1	128	0	TTGCTTTTAC	    0.967271	-106
ATGAACTTCTTTGATTTTTCGAACATGCTA	1	147	1	TTGATTTTTC	    0.975892	-87
AACAGTTGGATAGCATGTTCGAAAAATCAA	1	157	0	TAGCATGTTC	    0.978753	-77
        ACTTTATTTTTCCACCTTCTTA	2	3	1	TTTATTTTTC	    0.931872	-40
          **********

Masking position 6
Map Score:   6.6313

Number of sites scoring better than the average of aligned sites = 399
Number in coding regions = 368
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

CCGAAAGATTTTTGAATCTTTGGTTAACAT	1	187	1	TTTGAATCTT	    0.929744	-47
       TCCTTACCACCTCGGAATTTCTT	1	221	0	TTACCACCTC	    0.985813	-13
  ACTTTATTTTTCCACCTTCTTATTTATT	2	9	1	TTTCCACCTT	    0.995236	-34
        GATTTGCACCTATTAATAAATA	2	31	0	TTTGCACCTA	    0.991618	-12
          **********

Masking position 6
Map Score:   2.11127

Number of sites scoring better than the average of aligned sites = 69
Number in coding regions = 64
Number in noncoding regions = 5
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:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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