AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_synecho_ctra_300.orf -o008_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY18164	234	Synechocystis

Motif number 1

CTGTCGTTGAACTTGGGGGAAATCCCTGCC	1	24	1	ACTTGGGGGA	    0.997621	-211
TTTCTGCCATACTTTGGGCAGGGATTTCCC	1	40	0	ACTTTGGGCA	    0.994878	-195
GGTTACCGGAAGTTGGGGCATTGGGAAGGG	1	76	0	AGTTGGGGCA	    0.998706	-159
TAATCTTGGCCGTTGGGGAACCGAAAAATG	1	176	0	CGTTGGGGAA	    0.994011	-59
          **********

Masking position 4
Map Score:   7.15921

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 116
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

          AATGCTTGCCTGTCTGTCGT	1	1	1	AATGCTTGCC	    0.995111	-234
ACTTGGGGGAAATCCCTGCCCAAAGTATGG	1	34	1	AATCCCTGCC	    0.992568	-201
GTATGGCAGAAAACCTTTCCCTTCCCAATG	1	58	1	AAACCTTTCC	    0.989227	-177
TAATTTTGTTAATCTTGGCCGTTGGGGAAC	1	185	0	AATCTTGGCC	    0.983409	-50
TATTAACTTTTAAGTTTTCCC         	1	224	1	TAAGTTTTCC	    0.894784	-11
          **********

Masking position 2
Map Score:   4.61388

Number of sites scoring better than the average of aligned sites = 688
Number in coding regions = 587
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 3

TGCCATACTTTGGGCAGGGATTTCCCCCAA	1	36	0	TGGGCAGGGA	     0.98914	-199
GTTGGGGCATTGGGAAGGGAAAGGTTTTCT	1	65	0	TGGGAAGGGA	    0.990848	-170
AGCTCAGATCGGGTTACCGGAAGTTGGGGC	1	87	0	GGGTTACCGG	    0.980182	-148
CCGCGGTGAATTGTTACCGACGGTGAGACC	1	128	1	TTGTTACCGA	    0.930797	-107
CTTGGCCGTTGGGGAACCGAAAAATGGGCT	1	172	0	GGGGAACCGA	    0.994407	-63
          **********

Masking position 6
Map Score:   3.74778

Number of sites scoring better than the average of aligned sites = 776
Number in coding regions = 707
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 4

GAGACCACGTCCTAACTTTTAGCCCATTTT	1	152	1	CCTAACTTTT	    0.983913	-83
GATTAACAAAATTAAATTTTAGATATTAAC	1	201	1	ATTAAATTTT	    0.969394	-34
AATTTTAGATATTAACTTTTAAGTTTTCCC	1	215	1	ATTAACTTTT	    0.988509	-20
          **********

Masking position 5
Map Score:   1.12465

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 79
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 5

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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