AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i050_Gluthatione-dependent_hydrolases_synecho_reg_300.orf -o050_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	RCY34376	300	Synechocystis

Motif number 1

AATGACCGTTGCCAAAAAGGAACGGGGTAATGATG	1	16	1	GCCAAGGAAG	    0.989231	-285
TCGGGACTGGGCAAAAGAGCAACAGATGGGGGCTT	1	56	0	GCAAAGCAAG	    0.977705	-245
CTGTTGACAGTGCACATCGGGACTGGGCAAAAGAG	1	72	0	TGCAAGGGAG	    0.986535	-229
GAATATTTCCGGGGGACAGGGAAAGGATAGTTGAC	1	115	0	GGGGAGGGAG	    0.990092	-186
CAAAAAATATGGGAGAATGGAATTGAGTAGCAAGC	1	173	1	GGGAAGGAAG	    0.995427	-128
GAATTGAGTAGCAAGCCTGGGTGCGTAGCTCAGTG	1	192	1	GCAACGGGTG	    0.975907	-109
CGTAGCTCAGTGGATAGAGCATCCGCCTTCTAAGC	1	215	1	TGGAAGCATG	    0.950707	-86
GCGGCAGGATTCGAACCTGCGACCGTCCGCTTAGA	1	243	0	TCGACGCGAG	    0.966103	-58
AACGTTGAAGGGAATAACGGGTGCGGCAGGATTCG	1	265	0	GGAAAGGGTG	    0.990867	-36
          **** *  ****  *

Masking position 9
Map Score:   11.2897

Number of sites scoring better than the average of aligned sites = 1326
Number in coding regions = 1177
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 2

CGTTCCTTTTTGGCAACGGTCATTTGGGT  	1	9	0	TGGCAACGGC	    0.994751	-292
GGGGTAATGATGTCAGCAAGCCCCCATCTGT	1	39	1	TGTCAGCAAC	    0.992382	-262
CGATGTGCACTGTCAACAGCCGTAGCTGTCA	1	88	1	TGTCAACAGC	    0.996336	-213
CAGCCGTAGCTGTCAACTATCCTTTCCCTGT	1	104	1	TGTCAACTAC	      0.9856	-197
GCATCCGCCTTCTAAGCGGACGGTCGCAGGT	1	233	1	TCTAAGCGGC	     0.96111	-68
          ********* *

Masking position 5
Map Score:   3.95274

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 159
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

TGCCAAAAAGGAACGGGGTAATGATGTCAG	1	25	1	GAACGGGGTA	    0.990138	-276
ATTTCGGTGTTAATGGAATATTTCCGGGGG	1	135	0	TAATGGAATA	    0.969954	-166
TGGGAGAATGGAATTGAGTAGCAAGCCTGG	1	182	1	GAATTGAGTA	    0.980861	-119
CCTTAACGTTGAAGGGAATAACGGGTGCGG	1	274	0	GAAGGGAATA	    0.991066	-27
          **********

Masking position 3
Map Score:   1.20485

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 116
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

AAAGGAACGGGGTAATGATGTCAGCAAGCCC	1	31	1	GGTAATGATT	    0.983232	-270
CGGGGGACAGGGAAAGGATAGTTGACAGCTA	1	110	0	GGAAAGGATG	     0.98726	-191
TATTTTTTGGGGCTAGGATTTCGGTGTTAAT	1	151	0	GGCTAGGATT	     0.98726	-150
TCCCTTCAACGTTAAGGATCTGCT       	1	287	1	GTTAAGGATT	    0.983232	-14
          ********* *

Masking position 5
Map Score:   0.477858

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 128
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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