AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -irhaS_synecho_opreg_100.orf -g0.48 -x5 
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 = 	0

Input sequences:
#1	pchR	242	regulatory protein PchR

Motif number 1

CTCTCATCGTTATTGAGATAATCCACAAGGT	1	42	1	TATTGAGAAA	    0.990447	-201
GTGCTGTGGCGATTGGGACAACCTTGTGGAT	1	62	0	GATTGGGAAA	    0.992665	-181
GCAGTATATTTGTTGGAAAAATGTGCTGTGG	1	84	0	TGTTGGAAAA	    0.978807	-159
GGGTTTAATTTATTGAGCAAAGCCCTAACGG	1	128	0	TATTGAGCAA	    0.974319	-115
CCATCAAATATTTAGGAATAATTTGCATTAG	1	157	1	TTTAGGAAAA	    0.886158	-86
AGCTGAAGTAGATTGAAAGAATTGATCAATC	1	201	0	GATTGAAAAA	    0.982059	-42
          ******** **

Masking position 3
Map Score:   5.59562

Number of sites scoring better than the average of aligned sites = 433
Number in coding regions = 357
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 2

          CAAGTAATACCATCTCCTATG	1	1	1	CAATAATACC	    0.923285	-242
AGATAATCCACAAGGTTGTCCCAATCGCCAC	1	57	1	CAAGTTGTCC	    0.955475	-186
ATCGCCACAGCACATTTTTCCAACAAATATA	1	80	1	CACTTTTTCC	    0.986358	-163
ACTCCTAATGCAAATTATTCCTAAATATTTG	1	161	0	CAATTATTCC	    0.993707	-82
ATAGATTGATCAATTCTTTCAATCTACTTCA	1	198	1	CAATCTTTCA	    0.960679	-45
CAATCTACTTCAGCTTATTCAGCTTCCCATC	1	217	1	CAGTTATTCA	    0.960677	-26
          *** *******

Masking position 2
Map Score:   3.1131

Number of sites scoring better than the average of aligned sites = 628
Number in coding regions = 553
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

CCATCTCCTATGGGACATTGAACTCTCATC	1	20	1	TGGGACATTG	    0.989853	-223
TCATCGTTATTGAGATAATCCACAAGGTTG	1	45	1	TGAGATAATC	    0.922408	-198
CTGTGGCGATTGGGACAACCTTGTGGATTA	1	60	0	TGGGACAACC	    0.987051	-183
GTATATTTGTTGGAAAAATGTGCTGTGGCG	1	82	0	TGGAAAAATG	    0.968289	-161
   GGGCAGATGGGAAGCTGAATAAGCTGA	1	226	0	TGGGAAGCTG	    0.976801	-17
          **********

Masking position 5
Map Score:   1.46476

Number of sites scoring better than the average of aligned sites = 747
Number in coding regions = 612
Number in noncoding regions = 135
Number of orfs with sites within 600 bp upstream = 157
Fraction of orfs with sites within 600 bp upstream = 0.0252168


Motif number 4

          **********

No masking
Map Score:   1.80068e-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:   1.80068e-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:   1.80068e-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