AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i100_Ion_Transporter_synecho_reg_100.orf -o100_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	RCY15084	118	Synechocystis
#2	RCY05328	25	Synechocystis
#3	RCY34497	112	Synechocystis

Motif number 1

GAGTAATGCCATCGCCAGAAGCCCAAAGATCCCCT	1	12	1	ATCGCCAGCA	    0.992773	-107
AATTTTGAGAATGCCAAAGTTTACAATGCCCTGAT	1	61	1	ATGCCATTCA	    0.982924	-58
AAAGTTTACAATGCCCTGATTGGCACGGTTTCGTT	1	76	1	ATGCCCTTCA	    0.997309	-43
CATCACTGCCATCCCCCCAAGACCATTAACCGAGT	3	18	1	ATCCCCAGCA	    0.998334	-95
GATCGAATTAAGCCCCATTTTGCCATACTCGGTTA	3	44	0	AGCCCCTTCA	    0.995997	-69
   AGCCGTTATCCCCGATTGTCCAATGTGGTGGT	3	91	0	ATCCCCTGCA	    0.999101	-22
          ******   **  **

Masking position 1
Map Score:   10.3083

Number of sites scoring better than the average of aligned sites = 262
Number in coding regions = 234
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

AGTAATGCCATCGCCAGAAGCCCAAAGATCCCCT	1	13	1	TCGCCAGCCA	    0.880296	-106
ATTTTGAGAATGCCAAAGTTTACAATGCCCTGAT	1	62	1	TGCCATTACA	     0.94549	-57
AAGTTTACAATGCCCTGATTGGCACGGTTTCGTT	1	77	1	TGCCCTTGCA	    0.512828	-42
CTTGGGGGGATGGCAGTGATGTCAGAAA      	3	5	0	TGGCAATTCA	    0.750561	-108
ATCACTGCCATCCCCCCAAGACCATTAACCGAGT	3	19	1	TCCCCAGCCA	    0.985833	-94
ATCGAATTAAGCCCCATTTTGCCATACTCGGTTA	3	44	0	GCCCCTTCCA	    0.977614	-69
TCCAATGTGGTGGTCGAATTAACATCGATCGAAT	3	71	0	TGGTCTTACA	    0.884119	-42
  AGCCGTTATCCCCGATTGTCCAATGTGGTGGT	3	91	0	TCCCCTGCCA	    0.995024	-22
          *****   ** ***

Masking position 14
Map Score:   8.53552

Number of sites scoring better than the average of aligned sites = 2218
Number in coding regions = 2021
Number in noncoding regions = 197
Number of orfs with sites within 600 bp upstream = 200
Fraction of orfs with sites within 600 bp upstream = 0.0321234


Motif number 3

CCAAAGATCCCCTATGATTGGCGAAGAAATTT	1	34	1	CCTAGATTGC	    0.914646	-85
ACTTTGGCATTCTCAAAATTTCTTCGCCAATC	1	49	0	TCTCAAATTC	    0.801746	-70
TTTTGAGAATGCCAAAGTTTACAATGCCCTGA	1	63	1	GCCAAGTTAC	    0.932662	-56
AGTTTACAATGCCCTGATTGGCACGGTTTCGT	1	78	1	GCCCGATTGC	    0.995636	-41
TTTCGTTCACGGTCTGGTTATCTGC       	1	104	1	GGTCGGTTTC	    0.968979	-15
ATCGAATTAAGCCCCATTTTGCCATACTCGGT	3	46	0	GCCCATTTGC	    0.979915	-67
CCAATGTGGTGGTCGAATTAACATCGATCGAA	3	72	0	GGTCAATTAC	    0.953324	-41
  AGCCGTTATCCCCGATTGTCCAATGTGGTG	3	93	0	TCCCGATTTC	    0.982691	-20
          **** **** **

Masking position 9
Map Score:   4.13811

Number of sites scoring better than the average of aligned sites = 2565
Number in coding regions = 2328
Number in noncoding regions = 237
Number of orfs with sites within 600 bp upstream = 265
Fraction of orfs with sites within 600 bp upstream = 0.0425634


Motif number 4

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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