AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i079_aful_mthe_300.orf -o079_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	RAG17649	26	Archaeoglobus_fulgidus
#2	RAG49198	76	Archaeoglobus_fulgidus
#3	RTH00167	222	M.thermo
#4	RTH01178	39	M.thermo

Motif number 1

GGAAGCTACTCTTTTAACTTGGATTACATTTAA	3	17	1	CTTTACTGGA	     0.99028	-206
ACTTGGATTACATTTAATCTTCAGTACATGAGT	3	33	1	CATTATTTCA	    0.923816	-190
CTTTCACCGGCATATCACATTCTGAGGTTCATC	3	74	1	CATTACTTCT	    0.951124	-149
TTCTGAGGTTCATCATATGGTGTTCATATCGCT	3	93	1	CATAATGTGT	    0.733197	-130
ATATGGTGTTCATATCGCTGTGAACTCCATGTG	3	107	1	CATTGCGTGA	    0.969586	-116
GTGACATGAACATTTCACATGGAGTTCACAGCG	3	122	0	CATTACTGGA	    0.995575	-101
GTGAAATGTTCATGTCACCGTGAACTCCATGTG	3	137	1	CATTACGTGA	    0.993501	-86
TGATAGGTTTCTTCTCACATGGAGTTCACGGTG	3	152	0	CTTTACTGGA	     0.99028	-71
CCTATCAGATCATATTACCGGTAATGGGAACAG	3	178	1	CATTACGGTA	    0.964567	-45
ACCTGTTTTACTTATAATCTGGTGTAGTCATCA	4	12	0	CTTTATTGGT	    0.928658	-28
          *** * ** ****

Masking position 3
Map Score:   14.1739

Number of sites scoring better than the average of aligned sites = 146
Number in coding regions = 127
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

GAAACGTTTCAGTATGGCAGATAAAACTTTCT	2	14	1	AGTATCAGAT	    0.910739	-63
GAAGATTAAATGTAATCCAAGTTAAAAGAGTA	3	23	0	TGTAACAAGT	    0.905147	-200
TATATACTCATGTACTGAAGATTAAATGTAAT	3	39	0	TGTACAAGAT	    0.944539	-184
GATATGCCGGTGAAAGATATATATACTCATGT	3	58	0	TGAAATATAT	    0.739646	-165
CACCATATGATGAACCTCAGAATGTGATATGC	3	83	0	TGAACCAGAA	    0.960698	-140
CACAGCGATATGAACACCATATGATGAACCTC	3	97	0	TGAACCATAT	    0.988817	-126
CATATCGCTGTGAACTCCATGTGAAATGTTCA	3	117	1	TGAACCATGT	    0.989669	-106
CATGTCACCGTGAACTCCATGTGAGAAGAAAC	3	147	1	TGAACCATGT	    0.989669	-76
    ATGATGACTACACCAGATTATAAGTAAA	4	7	1	ACTACCAGAT	      0.9106	-33
CCAGATTATAAGTAAAACAGGTGGCGG     	4	23	1	AGTAACAGGT	    0.965435	-17
          *****  *****

Masking position 4
Map Score:   9.69583

Number of sites scoring better than the average of aligned sites = 490
Number in coding regions = 463
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 3

AGTTAAAAAGCTTGCCGTGAAAGAAAGTTT	2	37	0	CTTGCCGTGA	    0.942503	-40
AGAATGTGATATGCCGGTGAAAGATATATA	3	67	0	ATGCCGGTGA	    0.926902	-156
TGATGAACCTCAGAATGTGATATGCCGGTG	3	78	0	CAGAATGTGA	    0.908376	-145
GCGATATGAACACCATATGATGAACCTCAG	3	95	0	CACCATATGA	    0.885906	-128
TGGTGTTCATATCGCTGTGAACTCCATGTG	3	110	1	ATCGCTGTGA	     0.97725	-113
TCGCTGTGAACTCCATGTGAAATGTTCATG	3	121	1	CTCCATGTGA	    0.994762	-102
AAATGTTCATGTCACCGTGAACTCCATGTG	3	140	1	GTCACCGTGA	    0.940143	-83
TCACCGTGAACTCCATGTGAGAAGAAACCT	3	151	1	CTCCATGTGA	    0.994762	-72
          **********

Masking position 10
Map Score:   7.65518

Number of sites scoring better than the average of aligned sites = 343
Number in coding regions = 326
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

          CGCTTTTCCCAAGATTTACA	1	17	0	CGCTTTTCCC	    0.986274	-10
     CAACACCCATTTCCGGAGTAAGTTA	2	62	0	CCCATTTCCG	    0.997278	-15
CTCACCTGTTCCCATTACCGGTAATATGAT	3	186	0	CCCATTACCG	    0.995733	-37
          **********

Masking position 5
Map Score:   1.67074

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 30
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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