AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_synecho_reg_100.orf -o316_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	RCY43260	300	Synechocystis

Motif number 1

CAATTTGGATAGTGGTGGGTGATCAACAGCA	1	26	0	AGGGTGGGTG	    0.997956	-275
GTTTCCAAAAAGCAGTGGGACAATTTGGATA	1	46	0	AGAGTGGGAC	    0.995482	-255
CTATGCGTGGATGAGTGGGACTGCCTGGGAC	1	227	1	ATAGTGGGAC	    0.989877	-74
AGGCAAATAGATTGGTGAGTCCCAGGCAGTC	1	245	0	ATGGTGAGTC	    0.983739	-56
CGATTGAATCAGAGGTCGGTGGTGAAAACTC	1	276	0	AGGGTCGGTG	    0.992841	-25
          ** ********

Masking position 6
Map Score:   6.30013

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 180
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

AACAGCAGATCAAATCTTTTGT        	1	3	0	CAAATCTTTT	    0.920622	-298
GGAAACGGAACAAATTCTTTACACCTTGTA	1	71	1	CAAATTCTTT	    0.859738	-230
TAAGGTCTGTAAAAGCTTGCATTACAAGGT	1	93	0	AAAAGCTTGC	    0.846375	-208
GAGAGATAAACAAAGTTTATTAAGGTCTGT	1	113	0	CAAAGTTTAT	    0.927003	-188
TAGGCCCCAGAAAATCTTATTAGAGAGATA	1	135	0	AAAATCTTAT	    0.918741	-166
GCCCATAGCGAAAATCTTGTCCGCCTTTTT	1	194	1	AAAATCTTGT	    0.928777	-107
          **********

Masking position 4
Map Score:   3.88747

Number of sites scoring better than the average of aligned sites = 445
Number in coding regions = 357
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

AATTTGTTCCGTTTCCAAAAAGCAGTGGGA	1	57	0	GTTTCCAAAA	    0.967752	-244
TGTAATGCAAGCTTTTACAGACCTTAATAA	1	97	1	GCTTTTACAG	    0.947301	-204
TTCGCTATGGGCTTCCACAAACTACCACGT	1	176	0	GCTTCCACAA	    0.994714	-125
ATTTGCCTGAGTTTTCACCACCGACCTCTG	1	268	1	GTTTTCACCA	    0.978796	-33
          **********

Masking position 4
Map Score:   0.671408

Number of sites scoring better than the average of aligned sites = 304
Number in coding regions = 288
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

TGATCACCCACCACTATCCAAATTGTCCCAC	1	32	1	CCACATCCAA	     0.97974	-269
GGGGCCTAACCCCCAATTTACGTGGTAGTTT	1	157	1	CCCCATTTAC	    0.981864	-144
CTATGGGCTTCCACAAACTACCACGTAAATT	1	171	0	CCACAACTAC	    0.958028	-130
TTTGTGGAAGCCCATAGCGAAAATCTTGTCC	1	185	1	CCCAAGCGAA	    0.895253	-116
CAGGCAGTCCCACTCATCCACGCATAGTACA	1	223	0	CACTATCCAC	    0.883458	-78
GCCTGGGACTCACCAATCTATTTGCCTGAGT	1	249	1	CACCATCTAT	    0.912082	-52
GCCTGAGTTTTCACCACCGACCTCTGATTCA	1	272	1	TCACACCGAC	    0.855915	-29
         ACCCCGATTGAATCAGAGGTCG	1	289	0	CCCCATTGAA	    0.976313	-12
          **** ******

Masking position 6
Map Score:   1.4477

Number of sites scoring better than the average of aligned sites = 3763
Number in coding regions = 3390
Number in noncoding regions = 373
Number of orfs with sites within 600 bp upstream = 373
Fraction of orfs with sites within 600 bp upstream = 0.0599101


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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