AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_pyro_reg_100.orf -o222_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	RPH00451	213	Pyrococcus_OT3

Motif number 1

CCCGGATTATCCGCCCGCCTTCATTGAACG	1	12	1	CCGCCCGCCT	    0.994081	-202
TCATTGAACGCCATTCTCGGCAACCTCAGG	1	32	1	CCATTCTCGG	    0.975659	-182
GTCTCCGGGGCCGCCTGAGGTTGCCGAGAA	1	45	0	CCGCCTGAGG	    0.908179	-169
CGGACAGGGCCCGGTCTCCGGGGCCGCCTG	1	58	0	CCGGTCTCCG	    0.989007	-156
CGGGCCCTGTCCGCCCGACGACGTCACCTC	1	75	1	CCGCCCGACG	    0.996622	-139
TCATTGCGCGCCATTCTCGGCACGCTCCCT	1	107	1	CCATTCTCGG	    0.975659	-107
GCCCGGGGGCCCGACCGAGGGAGCGTGCCG	1	124	0	CCGACCGAGG	    0.958992	-90
GTCCGACCTGCCGCCCGGGGGCCCGACCGA	1	136	0	CCGCCCGGGG	     0.91197	-78
          **********

Masking position 2
Map Score:   20.059

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 53
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

GGCGGGCGGATAATCCGGGC          	1	1	0	TAATCCGGGC	     0.95508	-213
GGCGTTCAATGAAGGCGGGCGGATAATCCG	1	14	0	GAAGGCGGGC	    0.864277	-200
CTCCGGGGCCGCCTGAGGTTGCCGAGAATG	1	43	0	GCCTGAGGTT	    0.774812	-171
ACAGGGCCCGGTCTCCGGGGCCGCCTGAGG	1	55	0	GTCTCCGGGG	    0.988764	-159
ACGAGGTGACGTCGTCGGGCGGACAGGGCC	1	77	0	GTCGTCGGGC	    0.889828	-137
GGCGCGCAATGAACGAGGTGACGTCGTCGG	1	89	0	GAACGAGGTG	    0.878304	-125
CTCGGCACGCTCCCTCGGTCGGGCCCCCGG	1	122	1	TCCCTCGGTC	    0.572693	-92
CCTCGGTCGGGCCCCCGGGCGGCAGGTCGG	1	134	1	GCCCCCGGGC	    0.513013	-80
      GTTCGCACCCTGTGAGGTAAGGTT	1	200	0	GCACCCTGTG	    0.933909	-14
          **********

Masking position 8
Map Score:   9.6247

Number of sites scoring better than the average of aligned sites = 503
Number in coding regions = 374
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 3

TCCGCCCGCCTTCATTGAACGCCATTCTCG	1	21	1	TTCATTGAAC	     0.96259	-193
TTGAACGCCATTCTCGGCAACCTCAGGCGG	1	35	1	TTCTCGGCAA	    0.984943	-179
CGTCACCTCGTTCATTGCGCGCCATTCTCG	1	96	1	TTCATTGCGC	    0.978748	-118
TTGCGCGCCATTCTCGGCACGCTCCCTCGG	1	110	1	TTCTCGGCAC	    0.997164	-104
TTAAAAATTCTTTTTGGTACATTAATATGT	1	164	0	TTTTTGGTAC	    0.940886	-50
          **********

Masking position 2
Map Score:   3.67438

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 158
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

TTCAATGAAGGCGGGCGGATAATCCGGGC 	1	10	0	GCGGGCGGAT	    0.977861	-204
GCCGAGAATGGCGTTCAATGAAGGCGGGCG	1	23	0	GCGTTCAATG	    0.953236	-191
GGCCGCCTGAGGTTGCCGAGAATGGCGTTC	1	37	0	GGTTGCCGAG	    0.945255	-177
ACGTCGTCGGGCGGACAGGGCCCGGTCTCC	1	69	0	GCGGACAGGG	    0.982043	-145
GCCGAGAATGGCGCGCAATGAACGAGGTGA	1	98	0	GCGCGCAATG	    0.984183	-116
GACCGAGGGAGCGTGCCGAGAATGGCGCGC	1	112	0	GCGTGCCGAG	    0.997931	-102
          **********

Masking position 6
Map Score:   4.07911

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 101
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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 7

          **********

No masking
Map Score:   -1.68098e-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