AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_aful_mthe_100.orf -o138_aful_mthe_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	RAG34641	45	Archaeoglobus_fulgidus
#2	RTH01072	116	M.thermo
#3	RTH02077	102	M.thermo

Motif number 1

GCAGCGTCCGTTAAATATATATTGCGAGTC	1	21	1	TTAAATATAT	    0.915467	-25
TAAAATATATAAACATTTATTAAGATAGGA	2	17	0	AAACATTTAT	    0.936278	-100
AATTTTAACATAAAATATATAAACATTTAT	2	27	0	TAAAATATAT	    0.982539	-90
TATTTTATGTTAAAATTTATTAAATTTTAT	2	40	1	TAAAATTTAT	    0.975326	-77
TAAAATTTATTAAATTTTATCGTTTATATT	2	50	1	TAAATTTTAT	    0.961359	-67
TCGTTTATATTAACAATTATTATATGGTTG	2	69	1	TAACAATTAT	    0.958121	-48
          **********

Masking position 3
Map Score:   8.3591

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 7
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

     GCTCCGTGTTGCAGCGTCCGTTAAA	1	6	1	GTGTTGCAGC	    0.988066	-40
TCGGATACCGGGAATTCAGCATTTCAA   	3	8	0	GGAATTCAGC	    0.992849	-95
TTCAGTATCTGTGATTCAGCTGATGCTGTC	3	53	0	GTGATTCAGC	    0.997204	-50
TCACGTCATAAGGATTCAGTATCTGTGATT	3	67	0	AGGATTCAGT	    0.972181	-36
          **********

Masking position 5
Map Score:   3.82324

Number of sites scoring better than the average of aligned sites = 194
Number in coding regions = 187
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

CTCCGTGTTGCAGCGTCCGTTAAATATATA	1	12	1	CAGCGTCCGT	    0.995026	-34
GCTGAATTCCCGGTATCCGAGTACAATGAG	3	18	1	CGGTATCCGA	    0.986521	-85
GAGAAGATGACAGCATCAGCTGAATCACAG	3	45	1	CAGCATCAGC	    0.990577	-58
CATAAGGATTCAGTATCTGTGATTCAGCTG	3	61	0	CAGTATCTGT	    0.987784	-42
          **********

Masking position 6
Map Score:   2.64355

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 82
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

TAAACATTTATTAAGATAGGATCTTCC   	2	8	0	TTAAGATAGG	    0.963974	-109
AAATGTTTATATATTTTATGTTAAAATTTA	2	29	1	ATATTTTATG	    0.889046	-88
ATATTAACAATTATTATATGGTTGCGTTGA	2	75	1	TTATTATATG	     0.97421	-42
AACCACCCTGTTAAGTTATGTCAACGCAAC	2	95	0	TTAAGTTATG	    0.976445	-22
TACTGAATCCTTATGACGTGAACGATCCAA	3	76	1	TTATGACGTG	    0.945272	-27
          **********

Masking position 3
Map Score:   1.49646

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 26
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

TAATAAATGTTTATATATTTTATGTTAAAA	2	25	1	TTATATATTT	    0.903936	-92
ATTTATTAAATTTTATCGTTTATATTAACA	2	54	1	TTTTATCGTT	    0.983041	-63
TTAACAATTATTATATGGTTGCGTTGACAT	2	78	1	TTATATGGTT	    0.982315	-39
   TCCTTCCTTGGATCGTTCACGTCATAA	3	86	0	TTGGATCGTT	    0.980535	-17
          **********

Masking position 5
Map Score:   0.885916

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 24
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 6

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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 8

          **********

No masking
Map Score:   -2.39152e-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