AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i272_aful_mthe_300.orf -o272_aful_mthe_300.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	RAG10817	83	Archaeoglobus_fulgidus
#2	RAG45610	36	Archaeoglobus_fulgidus
#3	RAG45611	139	Archaeoglobus_fulgidus

Motif number 1

CAGTTGTAAAGAAACAAATTTAGCTGACGG	1	58	0	GAAACAAATT	    0.982885	-26
        AGGAAAAATATTTAATGATTTA	2	3	1	GAAAAATATT	     0.98114	-34
GCAAAAAATAGAAATAAATCATTAAATATT	2	17	0	GAAATAAATC	    0.981192	-20
          GCAAAAAATAGAAATAAATC	2	27	0	GCAAAAAATA	    0.934101	-10
TGTGATATCCGAAATAAATCACTGTGCTGG	3	71	0	GAAATAAATC	    0.981192	-69
CGATTTTAATGAAAAATCTTAAATTTCTGA	3	105	1	GAAAAATCTT	    0.950322	-35
          **********

Masking position 6
Map Score:   7.61645

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 57
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

  GCAAAAAATAGAAATAAATCATTAAATAT	2	18	0	TAGAAATAAT	    0.864779	-19
CCTTAAAGGCCAGAGATGAAACCATAAAGGG	3	11	1	CAGAGATAAA	    0.994279	-129
GGTATAATAGCGGAGATAAAAAGCAGGTTTC	3	41	0	CGGAGATAAA	    0.993107	-99
ATACCCAGCACAGTGATTTATTTCGGATATC	3	67	1	CAGTGATTAT	    0.924901	-73
TGATTTATTTCGGATATCACACGACCGATTT	3	80	1	CGGATATACA	    0.929871	-60
ACTTTGTAGTCAGAAATTTAAGATTTTTCAT	3	113	0	CAGAAATTAA	    0.976381	-27
          ******* ***

Masking position 6
Map Score:   3.56971

Number of sites scoring better than the average of aligned sites = 238
Number in coding regions = 211
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

CCTACTTTTCCACCAATTTTGGTGGTGGCC	1	11	0	CACCAATTTT	    0.971611	-73
ATTTATATAGCCCTACTTTTCCACCAATTT	1	22	0	CCCTACTTTT	    0.981461	-62
ATAAAGGGAAACCTGCTTTTTATCTCCGCT	3	34	1	ACCTGCTTTT	    0.967742	-106
TGCTTTTTATCTCCGCTATTATACCCAGCA	3	47	1	CTCCGCTATT	    0.967687	-93
GATATCACACGACCGATTTTAATGAAAAAT	3	92	1	GACCGATTTT	    0.966404	-48
          **********

Masking position 7
Map Score:   1.81877

Number of sites scoring better than the average of aligned sites = 605
Number in coding regions = 539
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


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