AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i041_Ribose_Metabolism_1_synecho_reg_300.orf -o041_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	RCY48931	211	Synechocystis

Motif number 1

  ACCTCGATTAACTATTGTTTATTTTAGCA	1	9	1	TAACATTGTT	    0.986797	-203
TCATCGCTACTAATTAATGCCAGTGCTAATT	1	49	1	TAATAATGCC	    0.979694	-163
AAACTGACCATAATAAACGTCGTTTCCATCC	1	109	1	TAATAACGTC	    0.979694	-103
TAAATTAATCTAACCATTGTCAGTCAAGCCA	1	142	1	TAACATTGTC	    0.994097	-70
TTCCACTTTATAACGAATGTTATCCTAGGGC	1	177	0	TAACAATGTT	    0.990749	-35
          **** ******

Masking position 6
Map Score:   6.22882

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 92
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TAATTAAGCAGTGATATTGCTATTATTTTG	1	75	1	GTGATATTGC	     0.97458	-137
GTTTATTATGGTCAGTTTGCGCCAAAATAA	1	97	0	GTCAGTTTGC	    0.995559	-115
TGTCAGTCAAGCCATTCTGCCCTAGGATAA	1	159	1	GCCATTCTGC	     0.97927	-53
AGTGGAATCCGTGAGGTTGCA         	1	201	1	GTGAGGTTGC	    0.994812	-11
          **********

Masking position 4
Map Score:   3.84343

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 134
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TAACTATTGTTTATTTTAGCAATCCTCTCG	1	19	1	TTATTTTAGC	     0.99333	-193
AATGCCAGTGCTAATTAAGCAGTGATATTG	1	64	1	CTAATTAAGC	    0.934338	-148
GATATTGCTATTATTTTGGCGCAAACTGAC	1	87	1	TTATTTTGGC	    0.993818	-125
GAAACGACGTTTATTATGGTCAGTTTGCGC	1	105	0	TTATTATGGT	      0.9035	-107
AATGGTTAGATTAATTTACCGGATGGAAAC	1	130	0	TTAATTTACC	     0.96723	-82
          **********

Masking position 5
Map Score:   3.61791

Number of sites scoring better than the average of aligned sites = 624
Number in coding regions = 524
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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