AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i019_Entner-Doudoroff_Pathway_synecho_reg_100.orf -o019_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	RCY41316	235	Synechocystis
#2	RCY05110	47	Synechocystis

Motif number 1

      TGAAAAGCAAATTTTAAATTCCGA	1	5	1	AAGCAAATTT	    0.970116	-231
CTTCCAAGTCAGGCAAATTCCATTCTTGGT	1	70	0	AGGCAAATTC	    0.991734	-166
GCAAGGTGAAAGGCTAGTTCGGAGGCTTCC	1	95	0	AGGCTAGTTC	    0.957332	-141
CTCGCTTGAAATGAAAATTTGCAAGGTGAA	1	115	0	ATGAAAATTT	    0.936127	-121
GCGAGATAGCAGAAAAATTTATGATGCAAC	1	140	1	AGAAAAATTT	    0.973691	-96
CAACCTTAGAAGGAAAACTTAATATTTTCG	1	166	1	AGGAAAACTT	    0.963494	-70
TGCCTGTTCAAAGCTAATTTTGTCGAAAAT	1	189	0	AAGCTAATTT	     0.94407	-47
AATAATTTAGAGAATAATTCAATAATTGA 	2	10	0	AGAATAATTC	    0.961214	-38
GTGAAAAGAGTGAATAATTTAGAGAATAAT	2	22	0	TGAATAATTT	    0.825721	-26
          **********

Masking position 6
Map Score:   12.8473

Number of sites scoring better than the average of aligned sites = 1653
Number in coding regions = 1352
Number in noncoding regions = 301
Number of orfs with sites within 600 bp upstream = 309
Fraction of orfs with sites within 600 bp upstream = 0.0496306


Motif number 2

AAAAGCAAATTTTAAATTCCGAAGACCCAAAT	1	13	1	TTTAAATCGA	    0.911554	-223
CCCAAATCATTTTGATTCCCGATATTTTAGTA	1	38	1	TTTGATCCGA	    0.971279	-198
GAAATGAAAATTTGCAAGGTGAAAGGCTAGTT	1	106	0	TTTGCAGGGA	    0.982487	-130
CAAATTTTCATTTCAAGCGAGATAGCAGAAAA	1	124	1	TTTCAACGGA	    0.991916	-112
GAACAGGCACTTTCCATGGCGAAACCAAAAAA	1	210	1	TTTCCAGGGA	    0.982627	-26
TATTCACTCTTTTCACACCAGA          	2	36	1	TTTCACCCGA	    0.985644	-12
          ****** ** **

Masking position 3
Map Score:   2.99699

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 252
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

CGGGAATCAAAATGATTTGGGTCTTCGGAA	1	29	0	AATGATTTGG	    0.955041	-207
TTTGATTCCCGATATTTTAGTAACCAAGAA	1	48	1	GATATTTTAG	    0.963914	-188
TTGCATCATAAATTTTTCTGCTATCTCGCT	1	139	0	AATTTTTCTG	    0.867487	-97
AGGAAAACTTAATATTTTCGACAAAATTAG	1	176	1	AATATTTTCG	      0.9709	-60
CCTGTTCAAAGCTAATTTTGTCGAAAATAT	1	187	0	GCTAATTTTG	    0.863111	-49
        TTAATTTTTTGGTTTCGCCATG	1	224	0	AATTTTTTGG	     0.97051	-12
GAAAAGAGTGAATAATTTAGAGAATAATTC	2	20	0	AATAATTTAG	    0.968235	-28
          **********

Masking position 6
Map Score:   5.01481

Number of sites scoring better than the average of aligned sites = 984
Number in coding regions = 831
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 163
Fraction of orfs with sites within 600 bp upstream = 0.0261805


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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:   6.63809e-14

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