AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_aful_reg_100.orf -o198_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	RAG50329	222	Archaeoglobus_fulgidus
#2	RAG25938	75	Archaeoglobus_fulgidus

Motif number 1

ATGTTCCTTCCGCGGAAGGCTAAAAACGATT	1	30	0	CGCGGAAGGT	    0.992466	-193
TTTAAATCTTTGCCGCATGTTAATTTTTAAT	1	59	0	TGCCGCATGT	    0.980554	-164
GTCAAAACTACGCTGAGGTGTAGTTGATATG	1	105	1	CGCTGAGGTT	    0.979248	-118
       TGGCGCCTCATTTTTTGCTGACTC	1	209	0	CGCCTCATTT	    0.969761	-14
GCGTCCCGAACGCCGCAGGATCACCAGG   	2	8	0	CGCCGCAGGT	    0.998613	-68
CAGATGGGGCCGCCGAGATTTGAACTCGGGT	2	43	0	CGCCGAGATT	    0.984122	-33
          ********* *

Masking position 11
Map Score:   5.90375

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 193
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

ATCGTTTTTAGCCTTCCGCGGAAGGAACAT	1	31	1	GCCTTCCGCG	    0.971471	-192
GTCAAAACTACGCTGAGGTGTAGTTGATAT	1	105	1	CGCTGAGGTG	    0.937978	-118
TAAGGAAGCTGGCAGAGGAGGAAGTCAAAT	1	143	1	GGCAGAGGAG	    0.968343	-80
CCTCATTTTTTGCTGACTCGCTCAGCAGTA	1	198	0	TGCTGACTCG	    0.930372	-25
  CCTGGTGATCCTGCGGCGTTCGGGACGC	2	9	1	TCCTGCGGCG	    0.975385	-67
GCGGCGTTCGGGACGCCGTGACCCGAGTTC	2	23	1	GGACGCCGTG	    0.966721	-53
AAGCAGATGGGGCCGCCGAGATTTGAACTC	2	47	0	GGCCGCCGAG	    0.986427	-29
          **********

Masking position 10
Map Score:   5.40929

Number of sites scoring better than the average of aligned sites = 1215
Number in coding regions = 1140
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

 TAGCTTCACCTCATATCGAAATCGTTTTT	1	10	1	CTCATATCGA	    0.993151	-213
CCGCGGAAGGCTAAAAACGATTTCGATATG	1	22	0	CTAAAAACGA	    0.945175	-201
TAATGTAACGGTCAAAACTACGCTGAGGTG	1	95	1	GTCAAAACTA	    0.936144	-128
CCTTATCTTGCTCATATCAACTACACCTCA	1	118	0	CTCATATCAA	     0.97326	-105
AGAGGAGGAAGTCAAATCCAAACCTCGTTA	1	156	1	GTCAAATCCA	    0.975927	-67
AACCTCGTTACTCTCATCGATGTACTGCTG	1	176	1	CTCTCATCGA	    0.967834	-47
          **********

Masking position 6
Map Score:   4.82611

Number of sites scoring better than the average of aligned sites = 278
Number in coding regions = 249
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

TTTTGCTGACTCGCTCAGCAGTACATCGAT	1	191	0	TCGCTCAGCA	    0.963383	-32
          TGGCGCCTCATTTTTTGCTG	1	213	0	TGGCGCCTCA	    0.932103	-10
CCTGCGGCGTTCGGGACGCCGTGACCCGAG	2	20	1	TCGGGACGCC	    0.992949	-56
TTAAAGCAGATGGGGCCGCCGAGATTTGAA	2	50	0	TGGGGCCGCC	    0.928986	-26
          **********

Masking position 1
Map Score:   2.03176

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 54
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

CAGCAAAAAATGAGGCGCCA          	1	213	1	TGAGGCGCCA	    0.947103	-10
CTGCGGCGTTCGGGACGCCGTGACCCGAGT	2	21	1	CGGGACGCCG	    0.867027	-55
TAAAGCAGATGGGGCCGCCGAGATTTGAAC	2	49	0	GGGGCCGCCG	    0.983823	-27
          **********

Masking position 6
Map Score:   0.937561

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 6
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 6

          **********

No masking
Map Score:   -5.3758e-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:   -5.3758e-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:   -5.3758e-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