AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_synecho_ctra_100.orf -o205_synecho_ctra_100.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	RCY38416	130	Synechocystis
#2	RCT00758	300	Chlamydia_trachomatis

Motif number 1

         TTACTAAAAATTTACTATATTTT	1	2	1	TAAAAAATTT	     0.96722	-129
CGGCAATCCATAGGAAAAAATATAGTAAATTT	1	18	0	TAAAAAAATA	    0.767234	-113
TAAAGGCTGCTCCACAGAATTTTCCCTTTCC 	1	110	1	TCCAGAATTT	    0.976689	-21
GCATCGCGTGTAAAAAAAATATTGTACGATGC	2	39	0	TAAAAAATAT	    0.915268	-262
AAGCACACATTCCCAAGAAAATTATAGTGCGT	2	104	0	TCAAGAAAAT	    0.944086	-197
TTCCTTTTTCTCTTAAGAATTTTGCTTCCCAA	2	152	1	TCAAGAATTT	    0.986665	-149
AGTCTTGTATTCCCCAAAAATTCAACACCGTT	2	184	1	TCCAAAAATT	    0.963828	-117
TATTGCGTGATCGAAAAAATTTTTTATTCGTA	2	267	0	TCAAAAATTT	    0.986926	-34
          **  ********

Masking position 6
Map Score:   7.81983

Number of sites scoring better than the average of aligned sites = 434
Number in coding regions = 325
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 130
Fraction of orfs with sites within 600 bp upstream = 0.0208802


Motif number 2

TTGCCGACTTAAGTGCACTAATCAATGCAC	1	44	1	AAGTGCACTA	    0.562956	-87
ATCATCAAACTAGTGCATTGATTAGTGCAC	1	56	0	TAGTGCATTG	    0.819513	-75
AGCAGCCTTTAATTGTATGAGATTTATCGA	1	91	0	AATTGTATGA	    0.909088	-40
GTAAAAAAAATATTGTACGATGCTTATATT	2	32	0	TATTGTACGA	     0.93373	-269
AAGAAAATTATAGTGCGTTACCATGGCGGA	2	92	0	TAGTGCGTTA	    0.875459	-209
CTTTATCTAGTATTGCGTGATCGAAAAAAT	2	279	0	TATTGCGTGA	    0.978068	-22
          **********

Masking position 4
Map Score:   2.14024

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 121
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACTTAAGTCGGCAATCCATAGGAAAAAATA	1	28	0	GCAATCCATA	    0.969549	-103
GAGATTTATCGAAAGCCATCATCAAACTAG	1	73	0	GAAAGCCATC	    0.980773	-58
AAGAGAAAAAGGAATCCATCAGGGAGAAAG	2	136	0	GGAATCCATC	    0.992119	-165
TTATGTATCAGAAAACCTTCGAAACGCGAG	2	221	0	GAAAACCTTC	    0.964163	-80
          **********

Masking position 4
Map Score:   2.04723

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 152
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

ATGGCGGATCCTTTATCGCCGAAGAGCGGGCA	2	68	0	CTTTTCCCGA	    0.994904	-233
ATGTGTGCTTCTTTCTCCCTGATGGATTCCTT	2	126	1	CTTTTCCTGA	    0.992139	-175
TGATGGATTCCTTTTTCTCTTAAGAATTTTGC	2	145	1	CTTTTCCTTA	    0.991519	-156
TACATAAGAGCCTGTTCCCCTACTACGAATAA	2	244	1	CCTGTCCCTA	    0.973475	-57
        AGCTTTATCTAGTATTGCGTGATC	2	287	0	CTTTTCAGTA	    0.949573	-14
          **** ** ****

Masking position 6
Map Score:   2.03944

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 71
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

TGTACGATGCTTATATTCACGAATAGTGGAT	2	18	0	TTATATTCCG	    0.972795	-283
ACAATATTTTTTTTACACGCGATGCCCGCTC	2	46	1	TTTTACACCG	    0.982242	-255
TCCCAAAGTCTTGTATTCCCCAAAAATTCAA	2	178	1	TTGTATTCCC	     0.97325	-123
TTCAACACCGTTGTACACTCGCGTTTCGAAG	2	204	1	TTGTACACCG	    0.993415	-97
          ******** **

Masking position 5
Map Score:   0.24852

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 14
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   9.48026e-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 7

          **********

No masking
Map Score:   9.48026e-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 8

          **********

No masking
Map Score:   9.48026e-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