AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i189_ubih_protein_synecho_reg_100.orf -o189_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	RCY33560	226	Synechocystis

Motif number 1

          GGCCATATTCAGCTCAAAAGTT	1	1	1	GGCCATTCAG	    0.993615	-226
GCCAGATAAGTCCTAGTGACAATCTTGCCCAA	1	51	1	TCCTAGACAA	    0.940116	-176
TGACAATCTTGCCCAACTTCAATTCCCCCCCT	1	67	1	GCCCATTCAA	    0.990158	-160
CCCCCCTATCTCCCACGGACAGTAGAAATAAA	1	92	1	TCCCAGACAG	    0.996681	-135
GGTGAAACACGCCCAGGGTAAGGCATTTATCC	1	164	0	GCCCAGTAAG	    0.992717	-63
ACAATTTTTATGCCGTCGTCAGTGATGGTGAA	1	190	0	TGCCGGTCAG	    0.990748	-37
          *****  *****

Masking position 11
Map Score:   5.89417

Number of sites scoring better than the average of aligned sites = 1066
Number in coding regions = 949
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 141
Fraction of orfs with sites within 600 bp upstream = 0.022647


Motif number 2

GCTCAAAAGTTGATGGGGAATTAAACACCG	1	22	1	TGATGGGGAA	    0.991415	-205
GGGGAATTGAAGTTGGGCAAGATTGTCACT	1	65	0	AGTTGGGCAA	    0.991415	-162
CGTGGGAGATAGGGGGGGAATTGAAGTTGG	1	79	0	AGGGGGGGAA	    0.993293	-148
TTTATCCCTATGGTTGACAACGATGATTGT	1	141	0	TGGTTGACAA	    0.924466	-86
CCGTCGTCAGTGATGGTGAAACACGCCCAG	1	180	0	TGATGGTGAA	    0.966741	-47
 AGGAAAAACAATGGGACAATTTTTATGCC	1	208	0	AATGGGACAA	    0.867963	-19
          **********

Masking position 9
Map Score:   5.02647

Number of sites scoring better than the average of aligned sites = 2493
Number in coding regions = 2254
Number in noncoding regions = 239
Number of orfs with sites within 600 bp upstream = 280
Fraction of orfs with sites within 600 bp upstream = 0.0449727


Motif number 3

GGCAAGATTGTCACTAGGACTTATCTGGCG	1	50	0	TCACTAGGAC	    0.981778	-177
ATTTCTACTGTCCGTGGGAGATAGGGGGGG	1	91	0	TCCGTGGGAG	    0.994516	-136
TAAATGCCTTACCCTGGGCGTGTTTCACCA	1	167	1	ACCCTGGGCG	    0.994633	-60
   AGGAAAAACAATGGGACAATTTTTATG	1	210	0	ACAATGGGAC	    0.987547	-17
          **********

Masking position 5
Map Score:   1.83258

Number of sites scoring better than the average of aligned sites = 379
Number in coding regions = 332
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

ACTTATCTGGCGGTGTTTAATTCCCCATCA	1	32	0	CGGTGTTTAA	    0.966094	-195
CTAATTGTAACGTTGTTTATTTCTACTGTC	1	109	0	CGTTGTTTAT	    0.976928	-118
TGGTTGACAACGATGATTGTATCTAATTGT	1	131	0	CGATGATTGT	    0.980818	-96
GCATTTATCCCTATGGTTGACAACGATGAT	1	144	0	CTATGGTTGA	    0.824741	-83
ATGCCGTCGTCAGTGATGGTGAAACACGCC	1	183	0	CAGTGATGGT	    0.915265	-44
AACAATGGGACAATTTTTATGCCGTCGTCA	1	201	0	CAATTTTTAT	     0.83347	-26
AAAATTGTCCCATTGTTTTTCCT       	1	214	1	CATTGTTTTT	    0.914218	-13
          **********

Masking position 4
Map Score:   2.15143

Number of sites scoring better than the average of aligned sites = 1266
Number in coding regions = 1137
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 5

          GGCCATATTCAGCTCAAAAG	1	1	1	GGCCATATTC	    0.920196	-226
GTGTTTAATTCCCCATCAACTTTTGAGCTG	1	20	0	CCCCATCAAC	    0.989612	-207
TGACAATCTTGCCCAACTTCAATTCCCCCC	1	67	1	GCCCAACTTC	    0.980478	-160
TCAATTCCCCCCCTATCTCCCACGGACAGT	1	85	1	CCCTATCTCC	    0.986168	-142
GGGCGTGTTTCACCATCACTGACGACGGCA	1	182	1	CACCATCACT	    0.926106	-45
          **********

Masking position 5
Map Score:   0.38755

Number of sites scoring better than the average of aligned sites = 2669
Number in coding regions = 2450
Number in noncoding regions = 219
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 6

          **********

No masking
Map Score:   3.36387e-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:   3.36387e-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 8

          **********

No masking
Map Score:   3.36387e-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