AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_tpal_bbur_300.orf -o039_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00138	102	AE000520

Motif number 1

CTTTTTGGTACGCGTACGTTGACCGTTTTC	1	14	0	CGCGTACGTT	    0.968846	-89
AGAGCGCGTGCACGTGCTTTTTGGTACGCG	1	30	0	CACGTGCTTT	    0.992565	-73
AGCACGTGCACGCGCTCTATCCCCTCCATC	1	42	1	CGCGCTCTAT	    0.993902	-61
CGGCAGATGCCGCTTTCGATGGAGGGGATA	1	59	0	CGCTTTCGAT	    0.994279	-44
CGCCCGTACTCACTTGCTGTTAGCGGCAGA	1	82	0	CACTTGCTGT	    0.989353	-21
          **********

Masking position 10
Map Score:   8.31746

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 5
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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 = 892
Number in coding regions = 244
Number in noncoding regions = 648
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TAGAGCGCGTGCACGTGCTTTTTGGTACGC	1	31	0	GCACGTGCTT	    0.998136	-72
GCTGTTAGCGGCAGATGCCGCTTTCGATGG	1	67	0	GCAGATGCCG	    0.989729	-36
ACGCCCGTACTCACTTGCTGTTAGCGGCAG	1	83	0	TCACTTGCTG	    0.987228	-20
CAGCAAGTGAGTACGGGCGT          	1	93	1	GTACGGGCGT	    0.985349	-10
          **********

Masking position 3
Map Score:   1.79333

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 84
Number in noncoding regions = 187
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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