AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_synecho_reg_300.orf -o301_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	RCY23791	159	Synechocystis
#2	RCY43755	46	Synechocystis

Motif number 1

TTGCTGAAAATGGTTAATTGGACTAGAAATT	1	85	0	TGGTAATTGG	    0.988222	-75
AATGGCAGAATGGCTCCATGGCCCTAGGGGA	1	117	0	TGGTCCATGG	    0.998884	-43
GGTTCCATTGTGGATTAATGGCAGAATGGCT	1	133	0	TGGTTAATGG	    0.995305	-27
     AGGATTGGTTCCATTGTGGATTAATG	1	144	0	TGGTCCATTG	     0.99558	-16
          *** *******

Masking position 5
Map Score:   5.38559

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 93
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

GGCTAAAACTGTTTTTGCCCAGTCCA    	1	7	0	GTTTTTGCCC	    0.992774	-153
GGCAAAAACAGTTTTAGCCCCAGCATTACC	1	18	1	GTTTTAGCCC	    0.992621	-142
GTGCTTATTTGTTCTTACTCTGGCGGTAAT	1	42	0	GTTCTTACTC	    0.918733	-118
TGGTTTGGTTTTTCGTGCTTATTTGTTCTT	1	56	0	TTTCGTGCTT	    0.928708	-104
ACCAAACCAATTTCTAGTCCAATTAACCAT	1	77	1	TTTCTAGTCC	    0.978901	-83
TTGGGTGAACTTTTGAGTCTTCCTTGGCTT	2	25	1	TTTTGAGTCT	    0.892293	-22
          **********

Masking position 3
Map Score:   4.35057

Number of sites scoring better than the average of aligned sites = 1972
Number in coding regions = 1698
Number in noncoding regions = 274
Number of orfs with sites within 600 bp upstream = 304
Fraction of orfs with sites within 600 bp upstream = 0.0488275


Motif number 3

GGCTCCATGGCCCTAGGGGATTTGCTGAAA	1	107	0	CCCTAGGGGA	    0.998103	-53
AGGATTGGTTCCATTGTGGATTAATGGCAG	1	140	0	CCATTGTGGA	    0.994189	-20
         CCCCTAGTAGAATGTTGGGTG	2	2	1	CCCTAGTAGA	    0.996679	-45
          **********

Masking position 10
Map Score:   3.40711

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 86
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

TAAAACTGTTTTTGCCCAGTCCA       	1	4	0	TTTGCCCAGT	    0.868981	-156
AAAAACAGTTTTAGCCCCAGCATTACCGCC	1	21	1	TTAGCCCCAG	      0.9487	-139
AGCCCCAGCATTACCGCCAGAGTAAGAACA	1	33	1	TTACCGCCAG	    0.974588	-127
AAACCAATTTCTAGTCCAATTAACCATTTT	1	80	1	CTAGTCCAAT	    0.944176	-80
AGCAAATCCCCTAGGGCCATGGAGCCATTC	1	111	1	CTAGGGCCAT	    0.730652	-49
CCATGGAGCCATTCTGCCATTAATCCACAA	1	127	1	ATTCTGCCAT	    0.863501	-33
      AGGATTGGTTCCATTGTGGATTAA	1	146	0	TTGGTTCCAT	    0.913803	-14
          **********

Masking position 2
Map Score:   1.2486

Number of sites scoring better than the average of aligned sites = 3101
Number in coding regions = 2776
Number in noncoding regions = 325
Number of orfs with sites within 600 bp upstream = 340
Fraction of orfs with sites within 600 bp upstream = 0.0546097


Motif number 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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:   3.50598e-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