AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_mjan_pyro_300.orf -o223_mjan_pyro_300.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	RPH01735	233	Pyrococcus_OT3
#2	RPH01736	42	Pyrococcus_OT3

Motif number 1

CTTGTTTTTGTCAAAAATCCTTTTAAGTAA	1	29	0	TCAAAAATCC	     0.97352	-205
CGTCTCTCCTTTAAAAAACTTTGCTAGCTT	1	56	0	TTAAAAAACT	    0.966691	-178
AGGAGAGACGTCAAAGAACTAATTTGATGA	1	76	1	TCAAAGAACT	    0.996621	-158
GTTCGAAAAATCAAAGAAGTTCATTGCTTT	1	141	0	TCAAAGAAGT	    0.988204	-93
AACCAAAGATTCAAAAATCTTTCGGAACAG	1	182	0	TCAAAAATCT	    0.990152	-52
GGTTAACATTTCAAAGAAATTCCGAGGTGG	1	208	1	TCAAAGAAAT	    0.982616	-26
          **********

Masking position 5
Map Score:   11.14

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 114
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

TTTTTGACAAAAACAAGCTAGCAAAGTTTT	1	42	1	AAACAAGCTA	    0.970563	-192
GATGATTAGGGAACAAGATATCAGCTTTAA	1	101	1	GAACAAGATA	    0.986299	-133
TAACGAATTAGTAAAAGCAATGAACTTCTT	1	128	1	GTAAAAGCAA	    0.970971	-106
TAGCATGTTCGAAAAATCAAAGAAGTTCAT	1	147	0	GAAAAATCAA	    0.978638	-87
TTGATTTTTCGAACATGCTATCCAACTGTT	1	157	1	GAACATGCTA	    0.981135	-77
TAAGAAGGTGGAAAAATAAAGT        	2	3	0	GAAAAATAAA	    0.939323	-40
          **********

Masking position 5
Map Score:   6.6313

Number of sites scoring better than the average of aligned sites = 448
Number in coding regions = 407
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

CCGAAAGATTTTTGAATCTTTGGTTAACAT	1	187	1	TTTGAATCTT	    0.920417	-47
       TCCTTACCACCTCGGAATTTCTT	1	221	0	TTACCACCTC	    0.983801	-13
  ACTTTATTTTTCCACCTTCTTATTTATT	2	9	1	TTTCCACCTT	    0.994552	-34
        GATTTGCACCTATTAATAAATA	2	31	0	TTTGCACCTA	    0.990424	-12
          **********

Masking position 6
Map Score:   2.11127

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 30
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:   -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