AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_synecho_reg_300.orf -o340_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	RCY10575	182	Synechocystis

Motif number 1

GGTGATTAAAGGGCGATCGCCATTATAAAA	1	16	1	GGGCGATCGC	    0.996969	-167
ATTTCCCCTGGGGCGAGGGGTAACTCACCT	1	45	0	GGGCGAGGGG	    0.999001	-138
CCAGGGGAAATGGCAATGGGTTTATGCTCG	1	64	1	TGGCAATGGG	    0.993166	-119
GGTTTAATCATGGTGACGGCCATAGCTAGT	1	117	1	TGGTGACGGC	    0.983201	-66
      AAATGTTCGATGGGGGTGTTAAGG	1	169	0	GTTCGATGGG	    0.984313	-14
          **********

Masking position 6
Map Score:   6.67981

Number of sites scoring better than the average of aligned sites = 1881
Number in coding regions = 1733
Number in noncoding regions = 148
Number of orfs with sites within 600 bp upstream = 185
Fraction of orfs with sites within 600 bp upstream = 0.0297141


Motif number 2

   GGCTTGGTGATTAAAGGGCGATCGCCA	1	8	1	TGATTAAAGG	    0.991986	-175
GCGATCGCCATTATAAAAGGTGAGTTACCC	1	28	1	TTATAAAAGG	    0.943586	-155
GGAGCAGTATTGATTGGAGCGAGCATAAAC	1	83	0	TGATTGGAGC	    0.973664	-100
GCCGTCACCATGATTAAACCAACGGGAGCA	1	107	0	TGATTAAACC	    0.990263	-76
TCCAAATTTCTGCTAAAACCTATCCTTAAC	1	146	1	TGCTAAAACC	    0.975071	-37
          **********

Masking position 4
Map Score:   4.27382

Number of sites scoring better than the average of aligned sites = 294
Number in coding regions = 254
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

CCTGGGGCGAGGGGTAACTCACCTTTTATA	1	39	0	GGGGTAACTC	    0.963949	-144
CCTCGCCCCAGGGGAAATGGCAATGGGTTT	1	57	1	GGGGAAATGG	    0.933042	-126
AAATGGCAATGGGTTTATGCTCGCTCCAAT	1	71	1	GGGTTTATGC	    0.991544	-112
CTGCTCCCGTTGGTTTAATCATGGTGACGG	1	106	1	TGGTTTAATC	    0.922351	-77
TGTTAAGGATAGGTTTTAGCAGAAATTTGG	1	147	0	AGGTTTTAGC	    0.896769	-36
GTTCGATGGGGGTGTTAAGGATAGGTTTTA	1	159	0	GGTGTTAAGG	    0.958947	-24
          **********

Masking position 2
Map Score:   1.48203

Number of sites scoring better than the average of aligned sites = 3320
Number in coding regions = 2971
Number in noncoding regions = 349
Number of orfs with sites within 600 bp upstream = 359
Fraction of orfs with sites within 600 bp upstream = 0.0576614


Motif number 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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