AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_synecho_ctra_100.orf -o004_synecho_ctra_100.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	RCY24958	106	Synechocystis
#2	RCY23085	96	Synechocystis
#3	RCY06919	231	Synechocystis

Motif number 1

AGGTTTGACTTTAAACTGAGGCTAACCGCT	1	61	0	TTAAACTGAG	    0.921208	-46
       AAATTAAATTGAGATGACGAAGA	1	94	0	TTAAATTGAG	    0.900212	-13
TTGTAAACTTCGCCATTGATTAGGCGGTAG	2	45	1	CGCCATTGAT	    0.928266	-52
TTAATTTTGTTTCCATTGAGCTACAGACTA	2	72	0	TTCCATTGAG	    0.973133	-25
TACCAATTCTTGCCGCCGAGGAAATCAGTG	3	111	1	TGCCGCCGAG	    0.949361	-121
AGAGGTTATGTTCCACTGATTTCCTCGGCG	3	124	0	TTCCACTGAT	     0.97717	-108
AACCTCTCCCTGCCATTGGGGGTATGCCCG	3	147	1	TGCCATTGGG	    0.980513	-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

  TGACATAAAAATCTTTCCTTGGGATCTTG	1	9	1	AAATCTTCCT	    0.981579	-98
TGGGATCTTGAAGATTTTCCGATACGCTATT	1	30	1	AAGATTTCCG	      0.9616	-77
CCTCAGTTTAAAGTCAAACCTCCATCTTCGT	1	70	1	AAGTCAACCT	    0.784974	-37
TTTACGTCCGAAATTTCGCCGAACATC    	2	7	0	AAATTTCCCG	    0.937244	-90
AAGAAGATAAAAGACATCCCTGATCATAGCA	3	20	1	AAGACATCCT	    0.935763	-212
CGGGTAAATTAAGTCTGACCTTGCTATGATC	3	41	0	AAGTCTGCCT	    0.844848	-191
ATTCAACCAAAGATTTGTCCGGGTAAATTAA	3	60	0	AGATTTGCCG	    0.878613	-172
GTCGATTACCAATTCTTGCCGCCGAGGAAAT	3	105	1	AATTCTTCCG	     0.97107	-127
          ******* ***

Masking position 1
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	    0.934679	-97
TTAAATTGAGATGACGAAGATGGAGGTTTGA	1	83	0	AGACGAAGAT	    0.912212	-24
     GATGTTCGGCGAAATTTCGGACGTAA	2	6	1	TGGCGAAATT	    0.960356	-91
CGCCTAATCAATGGCGAAGTTTACAAGTTTA	2	40	0	AGGCGAAGTT	    0.992084	-57
GATTTCCTCGGCGGCAAGAATTGGTAATCGA	3	106	0	GGGCAAGAAT	    0.910907	-126
CCCCAATGGCAGGGAGAGGTTATGTTCCACT	3	137	0	AGGAGAGGTT	    0.985204	-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

ACGCTATTAGCGGTTAGCCTCAGTTTAAAG	1	53	1	CGGTTAGCCT	    0.904764	-54
ACGAAGATGGAGGTTTGACTTTAAACTGAG	1	71	0	AGGTTTGACT	    0.981304	-36
TGCTATGATCAGGGATGTCTTTTATCTTCT	3	21	0	AGGGATGTCT	    0.950278	-211
GATCATAGCAAGGTCAGACTTAATTTACCC	3	41	1	AGGTCAGACT	    0.935586	-191
ATTCAACCAAAGATTTGTCCGGGTAAATTA	3	61	0	AGATTTGTCC	     0.88025	-171
CTGCCATTGGGGGTATGCCCGCGCCTTGAT	3	156	1	GGGTATGCCC	    0.927251	-76
    TGGGGAAGCGATGACCTGAATTCAAT	3	216	0	AGCGATGACC	    0.913979	-16
          **********

Masking position 7
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