AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_4_1_1_21_synecho_reg_300.orf -o004_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY24958	106	Synechocystis
#2	RCY23085	96	Synechocystis
#3	RCY06919	231	Synechocystis

Motif number 1

AGGTTTGACTTTAAACTGAGGCTAACCGCT	1	61	0	TTAAACTGAG	    0.927757	-46
       AAATTAAATTGAGATGACGAAGA	1	94	0	TTAAATTGAG	    0.907174	-13
TTGTAAACTTCGCCATTGATTAGGCGGTAG	2	45	1	CGCCATTGAT	    0.934027	-52
TTAATTTTGTTTCCATTGAGCTACAGACTA	2	72	0	TTCCATTGAG	    0.971794	-25
TACCAATTCTTGCCGCCGAGGAAATCAGTG	3	111	1	TGCCGCCGAG	    0.954089	-121
AGAGGTTATGTTCCACTGATTTCCTCGGCG	3	124	0	TTCCACTGAT	    0.979161	-108
AACCTCTCCCTGCCATTGGGGGTATGCCCG	3	147	1	TGCCATTGGG	    0.982376	-85
          **********

Masking position 8
Map Score:   5.15767

Number of sites scoring better than the average of aligned sites = 969
Number in coding regions = 884
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 2

CAAGATCCCAAGGAAAGATTTTTATGTCA  	1	9	0	AGGAAGATTT	    0.977484	-98
AATAGCGTATCGGAAAATCTTCAAGATCCCA	1	30	0	CGGAAATCTT	     0.95324	-77
ACGAAGATGGAGGTTTGACTTTAAACTGAGG	1	70	0	AGGTTGACTT	    0.790602	-37
    GATGTTCGGCGAAATTTCGGACGTAAA	2	7	1	CGGGAAATTT	    0.923976	-90
TGCTATGATCAGGGATGTCTTTTATCTTCTT	3	20	0	AGGATGTCTT	    0.922579	-212
GATCATAGCAAGGTCAGACTTAATTTACCCG	3	41	1	AGGCAGACTT	    0.862843	-191
TTAATTTACCCGGACAAATCTTTGGTTGAAT	3	60	1	CGGCAAATCT	    0.855205	-172
ATTTCCTCGGCGGCAAGAATTGGTAATCGAC	3	105	0	CGGAAGAATT	    0.964684	-127
          *** *******

Masking position 11
Map Score:   4.47079

Number of sites scoring better than the average of aligned sites = 733
Number in coding regions = 620
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 3

TCAAGATCCCAAGGAAAGATTTTTATGTCA 	1	10	0	AGGAAAGATT	    0.930835	-97
TTAAATTGAGATGACGAAGATGGAGGTTTGA	1	83	0	AGACGAAGAT	    0.907177	-24
     GATGTTCGGCGAAATTTCGGACGTAA	2	6	1	TGGCGAAATT	    0.957955	-91
CGCCTAATCAATGGCGAAGTTTACAAGTTTA	2	40	0	AGGCGAAGTT	    0.991587	-57
GATTTCCTCGGCGGCAAGAATTGGTAATCGA	3	106	0	GGGCAAGAAT	    0.905805	-126
CCCCAATGGCAGGGAGAGGTTATGTTCCACT	3	137	0	AGGAGAGGTT	    0.984284	-95
          * *********

Masking position 7
Map Score:   0.87617

Number of sites scoring better than the average of aligned sites = 645
Number in coding regions = 558
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 103
Fraction of orfs with sites within 600 bp upstream = 0.0165435


Motif number 4

CTTTAAACTGAGGCTAACCGCTAATAGCGT	1	53	0	AGGCTAACCG	    0.904764	-54
CTCAGTTTAAAGTCAAACCTCCATCTTCGT	1	71	1	AGTCAAACCT	    0.981304	-36
AGAAGATAAAAGACATCCCTGATCATAGCA	3	21	1	AGACATCCCT	    0.950278	-211
GGGTAAATTAAGTCTGACCTTGCTATGATC	3	41	0	AGTCTGACCT	    0.935586	-191
TAATTTACCCGGACAAATCTTTGGTTGAAT	3	61	1	GGACAAATCT	     0.88025	-171
ATCAAGGCGCGGGCATACCCCCAATGGCAG	3	156	0	GGGCATACCC	    0.927251	-76
ATTGAATTCAGGTCATCGCTTCCCCA    	3	216	1	GGTCATCGCT	    0.913979	-16
          **********

Masking position 4
Map Score:   1.40694

Number of sites scoring better than the average of aligned sites = 1118
Number in coding regions = 985
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 5

          **********

No masking
Map Score:   -4.02005e-14

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:   -4.02005e-14

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:   -4.02005e-14

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