AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_not_clear_synecho_reg_300.orf -o325_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	RCY40191	189	Synechocystis
#2	RCY31627	81	Synechocystis

Motif number 1

ATTGTTCTTTCCCCCCGCACCCC         	1	2	0	CCCCCGACCC	    0.999121	-188
GGGAGTTTTCCCCCCCGGAGCCCCCATTGGAT	1	47	0	CCCCCGAGCC	    0.999321	-143
GAGGGAAATCCGTCCCCAAGCCTGGGAGTTTT	1	70	0	CTCCCCAGCC	    0.997038	-120
GGGGACGGATTTCCCTCTAGCCTTGGGTTTAG	1	85	1	TCCCTCAGCC	    0.997866	-105
GCGCTGACATTGCCCCCCAGTCGGCAATAATG	1	136	1	TCCCCCAGTC	    0.995341	-54
AGCTGTTTATTTCCATGGACCCTGACGGTCAA	2	17	1	TCCATGACCC	    0.974234	-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

   GGGGTGCGGGGGGAAAGAACAATTTAA	1	8	1	GGGGGGAAAG	    0.998535	-182
GGGGGCTCCGGGGGGGAAAACTCCCAGGCT	1	54	1	GGGGGGAAAA	    0.998768	-136
ACCCAAGGCTAGAGGGAAATCCGTCCCCAA	1	83	0	AGAGGGAAAT	    0.975069	-107
ATTGCCGACTGGGGGGCAATGTCAGCGCTC	1	134	0	GGGGGGCAAT	     0.99727	-56
GTCAAGCAAGGGCAGGAAAAGTATCATGGA	2	44	1	GGCAGGAAAA	    0.983041	-38
          **********

Masking position 8
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

CCGGAGCCCCCATTGGATCTGCCAAAATTAAATT	1	31	0	CATTGAGCCA	    0.967903	-159
GGAAAACTCCCAGGCTTGGGGACGGATTTCCCTC	1	68	1	CAGGCTGACG	    0.974059	-122
TCCCTCTAGCCTTGGGTTTAGCCAGCAGTTTCTC	1	96	1	CTTGGTGCCA	    0.988978	-94
CTGGCAAAGACAAGGTTAACGACAGATACATTAT	1	162	0	CAAGGTGACA	    0.992554	-28
CGTCAGGGTCCATGGAAATAAACAGCTTTCAAC 	2	10	0	CATGGAAACA	     0.97324	-72
GGAAAAGTATCATGGATGATGACGCCCTAATTCT	2	58	1	CATGGTGACG	    0.997256	-24
          ***** *   ****

Masking position 13
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

TTTAATTTTGGCAGATCCAATGGGGGCTCCGGG	1	33	1	GCATCCAAGG	    0.983531	-157
GGAAATCCGTCCCCAAGCCTGGGAGTTTTCCCC	1	66	0	CCAAGCCTGG	    0.972624	-124
GAAACTGCTGGCTAAACCCAAGGCTAGAGGGAA	1	95	0	GCAACCCAGG	    0.996945	-95
CCGACTGGGGGGCAATGTCAGCGCTCAAAAGAG	1	127	0	GGATGTCACG	    0.936912	-63
    GGGCCTGGCAAAGACAAGGTTAACGACAG	1	171	0	GGAAGACAGG	     0.99177	-19
GGACCCTGACGGTCAAGCAAGGGCAGGAAAAGT	2	33	1	GGAAGCAAGG	    0.995332	-49
          **  ****** **

Masking position 5
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