AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_tpal_bbur_100.orf -o039_tpal_bbur_100.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	    0.969306	-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 = 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

       CAGGAAAACGGTCAACGTACGCG	1	4	1	GAAAACGGTC	    0.979629	-99
GTGCTTTTTGGTACGCGTACGTTGACCGTT	1	17	0	GTACGCGTAC	    0.499725	-86
GGAGGGGATAGAGCGCGTGCACGTGCTTTT	1	39	0	GAGCGCGTGC	     0.69732	-64
CCCCTCCATCGAAAGCGGCATCTGCCGCTA	1	62	1	GAAAGCGGCA	    0.994443	-41
CTCACTTGCTGTTAGCGGCAGATGCCGCTT	1	74	0	GTTAGCGGCA	    0.976491	-29
AACAGCAAGTGAGTACGGGCGT        	1	91	1	GAGTACGGGC	    0.988156	-12
          **********

Masking position 6
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

ATAGAGCGCGTGCACGTGCTTTTTGGTACG	1	32	0	TGCACGTGCT	    0.515491	-71
 ACGCCCGTACTCACTTGCTGTTAGCGGCA	1	84	0	CTCACTTGCT	    0.904881	-19
          **********

Masking position 4
Map Score:   0.0362425

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


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