AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i222_Ribosomal_Operon___Transcription_aful_reg_100.orf -o222_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG50059	112	Archaeoglobus_fulgidus
#2	RAG50211	68	Archaeoglobus_fulgidus

Motif number 1

CTTTTAGCGGTAAATTTTTATCGGCCCAAC	1	24	0	TAAATTTTTA	    0.800193	-89
TGATGCGCTAAATACTTCAAGACAGGCCTT	1	51	0	AATACTTCAA	    0.975367	-62
CCCAACCTAAAAAATTTTAACCTCAACTTC	1	81	1	AAAATTTTAA	     0.95906	-32
AATTTTAACCTCAACTTCAAGCAAAATCCA	1	93	1	TCAACTTCAA	     0.96697	-20
       CTAACCACCTCAATTAATTGTTT	2	4	1	ACCACCTCAA	    0.970215	-65
TCTCTGAAGAAACACTTTAAAACATTTCTA	2	38	1	AACACTTTAA	    0.987037	-31
AACACTTTAAAACATTTCTACTACTCAGCT	2	48	1	AACATTTCTA	    0.970699	-21
          **********

Masking position 4
Map Score:   7.67874

Number of sites scoring better than the average of aligned sites = 561
Number in coding regions = 485
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

  TGATGTTGTTCTGGTTGGGCCGATAAAA	1	9	1	TTCTGGTTGG	    0.991602	-104
GTTAAAATTTTTTAGGTTGGGTGATGCGCT	1	72	0	TTTAGGTTGG	     0.99505	-41
TTGCTTGAAGTTGAGGTTAAAATTTTTTAG	1	87	0	TTGAGGTTAA	    0.972312	-26
      TGGATTTTGCTTGAAGTTGAGGTT	1	99	0	TTTTGCTTGA	    0.962468	-14
AAACAATTAATTGAGGTGGTTAG       	2	4	0	TTGAGGTGGT	     0.98088	-65
          **********

Masking position 7
Map Score:   4.6019

Number of sites scoring better than the average of aligned sites = 606
Number in coding regions = 547
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 3

TTCTGGTTGGGCCGATAAAAATTTACCGCT	1	19	1	GCCGATAAAA	    0.991394	-94
ATAAAAATTTACCGCTAAAAGGCCTGTCTT	1	33	1	ACCGCTAAAA	    0.995305	-80
GGTTGGGTGATGCGCTAAATACTTCAAGAC	1	58	0	TGCGCTAAAT	    0.946674	-55
GCATCACCCAACCTAAAAAATTTTAACCTC	1	75	1	ACCTAAAAAA	    0.931752	-38
          **********

Masking position 7
Map Score:   1.27664

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 127
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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