AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_synecho_reg_300.orf -o198_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	RCY19817	175	Synechocystis
#2	RCY30474	106	Synechocystis

Motif number 1

ATATCTTTGGCACAGTTCCCAATCCATTTTC	1	29	1	CCAGTTCCCA	    0.994961	-147
CAAAAAAAATTTCCGTTGCCC          	1	165	1	TCCGTTGCCC	    0.995823	-11
GCTCTGTGACCTCCGTTGGCAAAAG      	2	5	0	CCCGTTGGCA	    0.995862	-102
ACAACTTTCCCCCCGTATCCAGGGCAGAAAT	2	37	1	CCCGTATCCA	    0.981431	-70
TATAGGGGCATCCCCTTCCCCTCTCCGGTAT	2	66	0	TCCCTTCCCC	    0.974048	-41
         ACACAGTTGACAGCCATAATTA	2	95	0	CCAGTTGACA	    0.982179	-12
          * *********

Masking position 6
Map Score:   6.54718

Number of sites scoring better than the average of aligned sites = 1387
Number in coding regions = 1295
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 108
Fraction of orfs with sites within 600 bp upstream = 0.0173466


Motif number 2

  TCACTTTTGCTATCTTTGATATCTTTGGCACAGTT	1	9	1	GCTATTTCTT	    0.991729	-167
GGCACAGTTCCCAATCCATTTTCTCTTCCTTTGTTTA	1	37	1	CCAATTTCTT	    0.996079	-139
TATGTATGTTGCAATACTTTTTAGCCTGATCTTGCCT	1	79	1	GCAATTTCCT	    0.994404	-97
TTGCCTATACCCAATGAAAGTTAATTTAGGCAATTGC	1	110	1	CCAATATTTT	    0.906497	-66
GTTAATTTAGGCAATTGCTTCTGCCTTAGTTTAAGTC	1	129	1	GCAATTTCTT	    0.997947	-47
  GGGCAACGGAAATTTTTTTTGACTTAAACTAAGGC	1	151	0	GAAATTTCTT	    0.986875	-25
          *****   *  *  ***

Masking position 12
Map Score:   5.21631

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 124
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

CATTTTCTCTTCCTTTGTTTACCGGCTATG	1	53	1	TCCTTTGTTT	     0.93821	-123
TATGTATGTTGCAATACTTTTTAGCCTGAT	1	79	1	GCAATACTTT	    0.964201	-97
GTTAATTTAGGCAATTGCTTCTGCCTTAGT	1	129	1	GCAATTGCTT	    0.957807	-47
AATTGCTTCTGCCTTAGTTTAAGTCAAAAA	1	141	1	GCCTTAGTTT	    0.991269	-35
ACAGTTGACAGCCATAATTATAGGGGCATC	2	85	0	GCCATAATTA	    0.925623	-22
          **********

Masking position 5
Map Score:   0.679314

Number of sites scoring better than the average of aligned sites = 1174
Number in coding regions = 1047
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 4

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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