AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i101_synecho_ctra_100.orf -o101_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	RCY33239	167	Synechocystis
#2	RCY02899	51	Synechocystis
#3	RCY35187	264	Synechocystis

Motif number 1

ATAAACAGCGATCGCCATGGACAAGGCAGGG	1	13	1	ACGCCATGGA	    0.954147	-155
TCAATAAAAGGGGGCAACCGGAATAGTTCCC	1	41	0	GGGCAACCGG	    0.935691	-127
AAAGTAAAGAACGGAGTCGGGCAATTAGGTT	1	95	1	AGGAGTCGGG	      0.9377	-73
GCATTGGAGAAAGGGCACGGATCTTTAGGTA	1	132	0	AGGGCACGGA	    0.950044	-36
TTAGCCTGGAATGGCCTTGGGTTGTCTTTGG	2	31	0	AGGCCTTGGG	    0.994535	-21
ACAAGTAAATGAGGTCATGGGG         	3	2	0	GGGTCATGGG	    0.988451	-263
TAAATGCTTGGTCGCCATGGGGATTCTTCCT	3	150	0	GCGCCATGGG	    0.992703	-115
ACTGGGGGACAGGGAAATGGGTTTTAATGCC	3	195	0	AGGAAATGGG	    0.974633	-70
GATTATTGTAGAGGACTGGGGGACAGGGAAA	3	209	0	GGGACTGGGG	    0.976459	-56
          * *********

Masking position 4
Map Score:   9.63758

Number of sites scoring better than the average of aligned sites = 2610
Number in coding regions = 2370
Number in noncoding regions = 240
Number of orfs with sites within 600 bp upstream = 241
Fraction of orfs with sites within 600 bp upstream = 0.0387086


Motif number 2

AGGGGGCAACCGGAATAGTTCCCTGCCTTGT	1	33	0	CGGAATGTTC	    0.959802	-135
TAGGGATTAACCTAATTGCCCGACTCCGTTC	1	103	0	CCTAATGCCC	    0.988886	-65
TTAATCCCTACCTAAAGATCCGTGCCCTTTC	1	124	1	CCTAAAATCC	    0.953018	-44
     TCAAACCTAACGGGTCAACTCCAAAG	2	6	1	CCTAACGGTC	     0.96225	-46
TCTTACTATTCCTAATTATTCTTAACAATTA	3	89	1	CCTAATATTC	    0.976982	-176
GGTTTTAATGCCGAATAGTCCTCTGTTAAAT	3	176	0	CCGAATGTCC	     0.99393	-89
          ****** ****

Masking position 5
Map Score:   3.61534

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 137
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

GGCAATTAGGTTAATCCCTACCTAAAGATC	1	114	1	TTAATCCCTA	    0.983057	-54
TTCTTAACAATTAATAGCCACTACAGCAAT	3	107	1	TTAATAGCCA	    0.955817	-158
GGAAAAAGGAAGAATCCCCATGGCGACCAA	3	144	1	AGAATCCCCA	    0.947032	-121
CTATTCGGCATTAAAACCCATTTCCCTGTC	3	189	1	TTAAAACCCA	      0.9347	-76
GTCCTCTACAATAATCTCTAATCTTATTAG	3	224	1	ATAATCTCTA	    0.886713	-41
GTAGTTAATCTTAATAACTATG        	3	253	1	TTAATAACTA	    0.902791	-12
          **********

Masking position 4
Map Score:   1.70606

Number of sites scoring better than the average of aligned sites = 580
Number in coding regions = 508
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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