AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_synecho_ctra_100.orf -o340_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	RCY10575	182	Synechocystis

Motif number 1

TTTTATAATGGCGATCGCCCTTTAATCACC	1	16	0	GCGATCGCCC	    0.996969	-167
AGGTGAGTTACCCCTCGCCCCAGGGGAAAT	1	45	1	CCCCTCGCCC	    0.999001	-138
CGAGCATAAACCCATTGCCATTTCCCCTGG	1	64	0	CCCATTGCCA	    0.993166	-119
ACTAGCTATGGCCGTCACCATGATTAAACC	1	117	0	GCCGTCACCA	    0.983201	-66
CCTTAACACCCCCATCGAACATTT      	1	169	1	CCCATCGAAC	    0.984313	-14
          **********

Masking position 5
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

TGGCGATCGCCCTTTAATCACCAAGCC   	1	8	0	CCTTTAATCA	    0.992713	-175
GGGTAACTCACCTTTTATAATGGCGATCGC	1	28	0	CCTTTTATAA	    0.948582	-155
GTTTATGCTCGCTCCAATCAATACTGCTCC	1	83	1	GCTCCAATCA	    0.976064	-100
TGCTCCCGTTGGTTTAATCATGGTGACGGC	1	107	1	GGTTTAATCA	    0.990812	-76
GTTAAGGATAGGTTTTAGCAGAAATTTGGA	1	146	0	GGTTTTAGCA	    0.977321	-37
          **********

Masking position 7
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

   GGCTTGGTGATTAAAGGGCGATCGCCA	1	8	1	TGATTAAAGG	    0.850865	-175
CCTGGGGCGAGGGGTAACTCACCTTTTATA	1	39	0	GGGGTAACTC	    0.952198	-144
CCTCGCCCCAGGGGAAATGGCAATGGGTTT	1	57	1	GGGGAAATGG	    0.936148	-126
AAATGGCAATGGGTTTATGCTCGCTCCAAT	1	71	1	GGGTTTATGC	    0.988126	-112
CTGCTCCCGTTGGTTTAATCATGGTGACGG	1	106	1	TGGTTTAATC	    0.944997	-77
TGTTAAGGATAGGTTTTAGCAGAAATTTGG	1	147	0	AGGTTTTAGC	    0.881331	-36
GTTCGATGGGGGTGTTAAGGATAGGTTTTA	1	159	0	GGTGTTAAGG	    0.963698	-24
          **********

Masking position 2
Map Score:   2.03389

Number of sites scoring better than the average of aligned sites = 4404
Number in coding regions = 3923
Number in noncoding regions = 481
Number of orfs with sites within 600 bp upstream = 463
Fraction of orfs with sites within 600 bp upstream = 0.0743656


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