AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_aful_mthe_300.orf -o279_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	RAG48295	148	Archaeoglobus_fulgidus

Motif number 1

CACTGTTAGGTAACAGTGTTTGGGGTGGTG	1	16	0	TAACAGTGTT	    0.997601	-133
CACTGTTACCTAACAGTGTTTATATTTAAC	1	28	1	TAACAGTGTT	    0.997601	-121
GTTGGCCTAAAATCGGTTTTGAAAATGCAA	1	82	0	AATCGGTTTT	    0.976425	-67
GCCTAAATTTAAAAAGTTTTTGGTTGGCCT	1	104	0	AAAAAGTTTT	    0.891495	-45
ATCCTAAACATAACGGTGTTAAAA      	1	135	1	TAACGGTGTT	    0.997775	-14
          **********

Masking position 7
Map Score:   11.217

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 50
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

    CCCATCACCACCCCAAACACTGTTACC	1	7	1	ACCACCCAAA	    0.993612	-142
TTTTGAAAATGCAATCAAAAATGCATAATGC	1	65	0	GCAATCAAAA	    0.985475	-84
CCGATTTTAGGCCAACCAAAAACTTTTTAAA	1	96	1	GCCAACCAAA	    0.997607	-53
TTAAATTTAGGCTATCCTAAACATAACGGTG	1	122	1	GCTATCCAAA	    0.996298	-27
          ******* ***

Masking position 4
Map Score:   4.33684

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 29
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

GCTTATAATGTTAAATATAAACACTGTTAG	1	37	0	TTAAATATAA	    0.563855	-112
TTAGGATAGCCTAAATTTAAAAAGTTTTTG	1	112	0	CTAAATTTAA	    0.566181	-37
TTAGGCTATCCTAAACATAACGGTGTTAAA	1	128	1	CTAAACATAA	    0.967283	-21
          **********

Masking position 5
Map Score:   2.64239

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 5
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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