AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i126_Biopolymer_Transport_synecho_reg_100.orf -o126_synecho_100.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	RCY28443	110	Synechocystis

Motif number 1

CTAACAAGCCTGGAAAAGTTGATTCCAGCA	1	14	0	TGGAAAAGTT	    0.989395	-97
TTGTTAGGATTGGGGAGGTTGATTGAGCCT	1	37	1	TGGGGAGGTT	    0.998874	-74
GACTCAATCCTGGGGAAGATGCCTAAAAAT	1	67	0	TGGGGAAGAT	    0.998259	-44
     GGTGATGGGAAGGAGAAAAAACCGG	1	96	0	TGGGAAGGAG	    0.997036	-15
          **********

Masking position 6
Map Score:   8.67313

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 174
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

CCAGGCTTGTTAGGATTGGGGAGGTTGATT	1	31	1	TAGGATTGGG	    0.995599	-80
GATTGGGGAGGTTGATTGAGCCTATTTTTA	1	44	1	GTTGATTGAG	     0.97876	-67
GCATCTTCCCCAGGATTGAGTCCGGTTTTT	1	75	1	CAGGATTGAG	    0.996729	-36
     GGTGATGGGAAGGAGAAAAAACCGG	1	96	0	TGGGAAGGAG	    0.986891	-15
          **********

Masking position 5
Map Score:   3.20285

Number of sites scoring better than the average of aligned sites = 422
Number in coding regions = 383
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

     TTTTGCTGGAATCAACTTTTCCAGG	1	6	1	CTGGAATCAA	    0.994876	-105
ATGCCTAAAAATAGGCTCAATCAACCTCCC	1	49	0	ATAGGCTCAA	    0.983245	-62
GGAGAAAAAACCGGACTCAATCCTGGGGAA	1	80	0	CCGGACTCAA	    0.997714	-31
          **********

Masking position 9
Map Score:   2.10338

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 56
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

GGAAAAGTTGATTCCAGCAAAA        	1	3	0	ATTCCAGCAA	    0.974285	-108
CAATCCTAACAAGCCTGGAAAAGTTGATTC	1	19	0	AAGCCTGGAA	    0.996765	-92
CCTGGGGAAGATGCCTAAAAATAGGCTCAA	1	59	0	ATGCCTAAAA	    0.966288	-52
AACCGGACTCAATCCTGGGGAAGATGCCTA	1	72	0	AATCCTGGGG	    0.985789	-39
          **********

Masking position 1
Map Score:   1.21336

Number of sites scoring better than the average of aligned sites = 810
Number in coding regions = 745
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 5

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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