AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i055_Arginine_Metabolism_synecho_reg_300.orf -o055_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	RCY34497	112	Synechocystis
#2	RCY24958	106	Synechocystis

Motif number 1

CATCACTGCCATCCCCCCAAGACCATTAACCGAGT	1	18	1	ATCCCCGCCA	    0.999103	-95
GATCGAATTAAGCCCCATTTTGCCATACTCGGTTA	1	44	0	AGCCCCTCCA	    0.996102	-69
AATTCGATCGATGTTAATTCGACCACCACATTGGA	1	70	1	ATGTTAGCCA	    0.941453	-43
   AGCCGTTATCCCCGATTGTCCAATGTGGTGGT	1	91	0	ATCCCCGCCA	    0.999106	-22
GTATCGGAAAATCTTCAAGATCCCAAGGAAAGATT	2	20	0	ATCTTCTCCA	    0.996544	-87
TCAAACCTCCATCTTCGTCATCTCAATTTAATTT 	2	83	1	ATCTTCTTCA	    0.978074	-24
          ******    * ***

Masking position 1
Map Score:   6.98163

Number of sites scoring better than the average of aligned sites = 586
Number in coding regions = 518
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

ATCACTGCCATCCCCCCAAGACCATTAACCGAGT	1	19	1	TCCCCAGCCA	    0.998549	-94
ATCGAATTAAGCCCCATTTTGCCATACTCGGTTA	1	44	0	GCCCCTTCCA	    0.995414	-69
  AGCCGTTATCCCCGATTGTCCAATGTGGTGGT	1	91	0	TCCCCTGCCA	    0.998068	-22
TATCGGAAAATCTTCAAGATCCCAAGGAAAGATT	2	20	0	TCTTCATCCA	    0.992703	-87
CAAACCTCCATCTTCGTCATCTCAATTTAATTT 	2	84	1	TCTTCATTCA	    0.963075	-23
          *****   ** ***

Masking position 14
Map Score:   4.06497

Number of sites scoring better than the average of aligned sites = 512
Number in coding regions = 451
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 3

AATTAACATCGATCGAATTAAGCCCCATTT	1	59	0	GATCGAATTA	    0.994997	-54
CCAATGTGGTGGTCGAATTAACATCGATCG	1	74	0	GGTCGAATTA	    0.996622	-39
          **********

Masking position 6
Map Score:   0.891555

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 3
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   4.28758e-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:   4.28758e-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:   4.28758e-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