AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_tpal_reg_100.orf -o039_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00138	102	AE000520

Motif number 1

CTTTTTGGTACGCGTACGTTGACCGTTTTC	1	14	0	CGCGTACGTT	    0.969306	-89
AGAGCGCGTGCACGTGCTTTTTGGTACGCG	1	30	0	CACGTGCTTT	    0.992551	-73
AGCACGTGCACGCGCTCTATCCCCTCCATC	1	42	1	CGCGCTCTAT	    0.993766	-61
CGGCAGATGCCGCTTTCGATGGAGGGGATA	1	59	0	CGCTTTCGAT	    0.994152	-44
CGCCCGTACTCACTTGCTGTTAGCGGCAGA	1	82	0	CACTTGCTGT	    0.989116	-21
          **********

Masking position 10
Map Score:   8.31746

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 485
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

CGCGTACGTTGACCGTTTTCCTG       	1	4	0	GACCGTTTTC	     0.97992	-99
GTGCTTTTTGGTACGCGTACGTTGACCGTT	1	17	0	GTACGCGTAC	    0.499749	-86
AAAAGCACGTGCACGCGCTCTATCCCCTCC	1	39	1	GCACGCGCTC	    0.692033	-64
TAGCGGCAGATGCCGCTTTCGATGGAGGGG	1	62	0	TGCCGCTTTC	    0.994645	-41
AAGCGGCATCTGCCGCTAACAGCAAGTGAG	1	74	1	TGCCGCTAAC	    0.977508	-29
        ACGCCCGTACTCACTTGCTGTT	1	91	0	GCCCGTACTC	    0.988671	-12
          **********

Masking position 5
Map Score:   8.06053

Number of sites scoring better than the average of aligned sites = 847
Number in coding regions = 790
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

GCGTACCAAAAAGCACGTGCACGCGCTCTA	1	31	1	AAGCACGTGC	    0.998156	-72
CCATCGAAAGCGGCATCTGCCGCTAACAGC	1	67	1	CGGCATCTGC	    0.989841	-36
CTGCCGCTAACAGCAAGTGAGTACGGGCGT	1	83	1	CAGCAAGTGA	    0.987366	-20
          ACGCCCGTACTCACTTGCTG	1	93	0	ACGCCCGTAC	    0.985508	-10
          **********

Masking position 8
Map Score:   1.79333

Number of sites scoring better than the average of aligned sites = 887
Number in coding regions = 830
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

          **********

No masking
Map Score:   -1.9652e-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 5

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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