AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_synecho_ctra_300.orf -o325_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY40191	189	Synechocystis
#2	RCY31627	81	Synechocystis

Motif number 1

ATTGTTCTTTCCCCCCGCACCCC         	1	2	0	CCCCCGACCC	    0.999092	-188
GGGAGTTTTCCCCCCCGGAGCCCCCATTGGAT	1	47	0	CCCCCGAGCC	    0.999313	-143
GAGGGAAATCCGTCCCCAAGCCTGGGAGTTTT	1	70	0	CTCCCCAGCC	    0.996939	-120
GGGGACGGATTTCCCTCTAGCCTTGGGTTTAG	1	85	1	TCCCTCAGCC	    0.997794	-105
GCGCTGACATTGCCCCCCAGTCGGCAATAATG	1	136	1	TCCCCCAGTC	    0.995186	-54
AGCTGTTTATTTCCATGGACCCTGACGGTCAA	2	17	1	TCCATGACCC	    0.973392	-65
          * ***** ****

Masking position 9
Map Score:   13.0068

Number of sites scoring better than the average of aligned sites = 535
Number in coding regions = 476
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 2

TTAAATTGTTCTTTCCCCCCGCACCCC   	1	8	0	CTTTCCCCCC	    0.998583	-182
AGCCTGGGAGTTTTCCCCCCCGGAGCCCCC	1	54	0	TTTTCCCCCC	    0.998808	-136
TTGGGGACGGATTTCCCTCTAGCCTTGGGT	1	83	1	ATTTCCCTCT	    0.975863	-107
GAGCGCTGACATTGCCCCCCAGTCGGCAAT	1	134	1	ATTGCCCCCC	    0.997359	-56
TCCATGATACTTTTCCTGCCCTTGCTTGAC	2	44	0	TTTTCCTGCC	    0.983586	-38
          **********

Masking position 3
Map Score:   9.94981

Number of sites scoring better than the average of aligned sites = 594
Number in coding regions = 513
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

AATTTAATTTTGGCAGATCCAATGGGGGCTCCGG	1	31	1	TGGCTCAATG	     0.96765	-159
GAGGGAAATCCGTCCCCAAGCCTGGGAGTTTTCC	1	68	0	CGTCAGCCTG	    0.973854	-122
GAGAAACTGCTGGCTAAACCCAAGGCTAGAGGGA	1	96	0	TGGCACCAAG	    0.988889	-94
ATAATGTATCTGTCGTTAACCTTGTCTTTGCCAG	1	162	1	TGTCACCTTG	    0.992494	-28
 GTTGAAAGCTGTTTATTTCCATGGACCCTGACG	2	10	1	TGTTTCCATG	    0.973028	-72
AGAATTAGGGCGTCATCATCCATGATACTTTTCC	2	58	0	CGTCACCATG	    0.997234	-24
          ****   * *****

Masking position 2
Map Score:   2.48731

Number of sites scoring better than the average of aligned sites = 790
Number in coding regions = 734
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

CCCGGAGCCCCCATTGGATCTGCCAAAATTAAA	1	33	0	CCTTGGATGC	    0.983531	-157
GGGGAAAACTCCCAGGCTTGGGGACGGATTTCC	1	66	1	CCAGGCTTGG	    0.972624	-124
TTCCCTCTAGCCTTGGGTTTAGCCAGCAGTTTC	1	95	1	CCTGGGTTGC	    0.996945	-95
CTCTTTTGAGCGCTGACATTGCCCCCCAGTCGG	1	127	1	CGTGACATCC	    0.936912	-63
CTGTCGTTAACCTTGTCTTTGCCAGGCCC    	1	171	1	CCTGTCTTCC	     0.99177	-19
ACTTTTCCTGCCCTTGCTTGACCGTCAGGGTCC	2	33	0	CCTTGCTTCC	    0.995332	-49
          ** ******  **

Masking position 9
Map Score:   3.14339

Number of sites scoring better than the average of aligned sites = 1408
Number in coding regions = 1289
Number in noncoding regions = 119
Number of orfs with sites within 600 bp upstream = 129
Fraction of orfs with sites within 600 bp upstream = 0.0207196


Motif number 5

          **********

No masking
Map Score:   -4.38104e-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:   -4.38104e-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:   -4.38104e-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