AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i163_synecho_ctra_300.orf -o163_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	RCY43161	299	Synechocystis

Motif number 1

       AGCGGTGACCAGCCTCCGGCGTAAGG	1	4	1	GGGACAGCTC	    0.996104	-296
ACTTGGGTAAGTAGATCAGCATCAATGGAAAGT	1	37	1	GTGACAGCTC	    0.991213	-263
GGTGTGCCCCGTCGCCCATTGTCAGACTTTCCA	1	62	0	GTGCCATTTC	    0.956075	-238
AATGGGCGACGGGGCACACCGTTTTATTCTTAA	1	75	1	GGGCCACCTT	    0.992824	-225
GGGAAAGAATATCGACCACTTTTAAGAATAAAA	1	96	0	ATGACACTTT	    0.915604	-204
TGCAACAGCGGGCGAACCCCCTTTTTGCATCGG	1	143	1	GGGACCCCTT	    0.984829	-157
GTACTTCATCGGTGATTACTATCACGGTAAGGG	1	178	0	GGGATACTTC	    0.989026	-122
GCTAAGCACTGTAGATTACTATCTCAACTTTGC	1	219	1	GTGATACTTC	    0.982707	-81
          ** ** **** **

Masking position 12
Map Score:   10.0653

Number of sites scoring better than the average of aligned sites = 901
Number in coding regions = 824
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 2

        AGCGGTGACCAGCCTCCGGCGTAA	1	3	1	CGGTGCAGCC	    0.893929	-297
GACCAGCCTCCGGCGTAAGGACTTGGGTAAGT	1	17	1	CGGCGAGGAC	    0.972227	-283
GTCTGACAATGGGCGACGGGGCACACCGTTTT	1	68	1	GGGCGGGGGC	    0.990295	-232
TATCCCCATGGGGGGGAAAGAATATCGACCAC	1	110	0	GGGGGAAGAA	    0.971175	-190
TTCCCCCCCATGGGGATAATGCAACAGCGGGC	1	124	1	TGGGGAATGC	    0.949852	-176
GATGCAAAAAGGGGGTTCGCCCGCTGTTGCAT	1	142	0	GGGGGCGCCC	    0.626408	-158
ATCACGGTAAGGGTGCCGATGCAAAAAGGGGG	1	159	0	GGGTGGATGC	     0.97923	-141
TTCACCCTATGGGGGGAAGTAAAATCCATTCC	1	259	0	GGGGGAGTAA	    0.964723	-41
TCCCCCCATAGGGTGAAAATCGAGCCTTGCCT	1	274	1	GGGTGAATCG	    0.928475	-26
          *****  *****

Masking position 5
Map Score:   5.45406

Number of sites scoring better than the average of aligned sites = 3971
Number in coding regions = 3572
Number in noncoding regions = 399
Number of orfs with sites within 600 bp upstream = 356
Fraction of orfs with sites within 600 bp upstream = 0.0571796


Motif number 3

TTACCGTGATAGTAATCACCGATGAAGTAC	1	181	1	AGTAATCACC	    0.985982	-119
AAGTTGAGATAGTAATCTACAGTGCTTAGC	1	219	0	AGTAATCTAC	    0.985723	-81
TATGGGGGGAAGTAAAATCCATTCCAGTTT	1	254	0	AGTAAAATCC	      0.9751	-46
          **********

Masking position 5
Map Score:   0.381737

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 56
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TATTCTTTCCCCCCCATGGGGATAATGCAA	1	118	1	CCCCCATGGG	    0.804831	-182
GATTACTATCACGGTAAGGGTGCCGATGCA	1	168	0	ACGGTAAGGG	    0.971408	-132
CTCGATTTTCACCCTATGGGGGGAAGTAAA	1	268	0	ACCCTATGGG	     0.85562	-32
          **********

Masking position 6
Map Score:   0.0326594

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 69
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -3.59945e-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:   -3.59945e-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:   -3.59945e-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