AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_aful_reg_100.orf -o033_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	RAG30894	126	Archaeoglobus_fulgidus
#2	RAG43044	36	Archaeoglobus_fulgidus
#3	RAG31360	125	Archaeoglobus_fulgidus

Motif number 1

CTTTGCGTTGAGAACTGCCCCACTAAGGCAGTCAA	1	29	1	AAACTCCCTA	     0.98355	-98
AAGGCAGTCAAAATCTACCACGGTAAGCCAGTCAT	1	53	1	AATCTCCCTA	    0.991303	-74
AAACCTTTGAACATATTTCACAGTATATACACTTG	1	97	0	AATATTCCTA	    0.963016	-30
GGAAAAAGGAAAAAATGCAAATATATTTGCTTTTC	2	12	0	AAAATCAATA	    0.797162	-25
TACGTATTGTTTAAATACAACAAAAACAAATAGTT	3	16	0	TAAATCACAA	    0.797543	-110
TTTAAACAATACGTATGCCTCAATAGTTGATGTAT	3	36	1	AGTATCCCTA	    0.991303	-90
TCAATAGTTGATGTATTCATCTGAAGGGTTGGGAG	3	55	1	AGTATCACAA	    0.958824	-71
AATCTTTCCTATATATTACTCCCAACCCTTCAGAT	3	73	0	AATATACCAA	    0.941967	-53
      GTTTAAATATTCCGCATGAAATTTTATAA	3	107	0	AATATCCCGA	    0.988407	-19
          * **** ** *  **

Masking position 6
Map Score:   7.64541

Number of sites scoring better than the average of aligned sites = 309
Number in coding regions = 271
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

GGCAGTTCTCAACGCAAAGTCTGCACTCTA	1	18	0	AACGCAAAGT	    0.935635	-109
GTCATCGACGAAAGCAAGTGTATATACTGT	1	83	1	AAAGCAAGTG	    0.952285	-44
       CGAAAAGCAAATATATTTGCATT	2	4	1	AAAGCAAATA	    0.991814	-33
      GGAAAAAGGAAAAAATGCAAATAT	2	23	0	AAAGGAAAAA	    0.961633	-14
AAATACAACAAAAACAAATAGTTTATCA  	3	9	0	AAAACAAATA	    0.949353	-117
GGAGTAATATATAGGAAAGATTTATAAAAT	3	86	1	ATAGGAAAGA	    0.944027	-40
          **********

Masking position 6
Map Score:   3.33519

Number of sites scoring better than the average of aligned sites = 281
Number in coding regions = 236
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

CTGCCCCACTAAGGCAGTCAAAATCTACCA	1	43	1	AAGGCAGTCA	    0.994081	-84
CTACCACGGTAAGCCAGTCATCGACGAAAG	1	67	1	AAGCCAGTCA	    0.996769	-60
TCATCGACGAAAGCAAGTGTATATACTGTG	1	84	1	AAGCAAGTGT	    0.972096	-43
          **********

Masking position 6
Map Score:   1.11315

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 17
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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:   -5.44113e-14

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