AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_synecho_ctra_100.orf -o257_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	RCY34400	122	Synechocystis
#2	RCY25319	96	Synechocystis
#3	RCY52064	162	Synechocystis
#4	RCT00107	37	Chlamydia_trachomatis
#5	RCT00108	171	Chlamydia_trachomatis

Motif number 1

TTTAGCTAAATTAGCACTCGTGAGGTGGGA	1	40	1	TTAGCACTCG	    0.997204	-83
GGGAGAGGGTTTAGCACTCCCACCTCACGA	1	57	0	TTAGCACTCC	    0.993409	-66
CTGACCTGTGTTAAAACTTGCAGGATTTTT	2	32	1	TTAAAACTTG	    0.852032	-65
TTTCCCGGTCTTAGAGCTTGGCGATCGCCC	3	46	0	TTAGAGCTTG	    0.931917	-117
CTTACCTGACTTAGCACTCCACTGCCAAGA	3	82	1	TTAGCACTCC	    0.993409	-81
ATAAAGCACTTTAGCACTCTTGGCAGTGGA	3	99	0	TTAGCACTCT	    0.982213	-64
ATTTTTAAAAATAGCAGTTGATCATGCCAA	5	11	1	ATAGCAGTTG	    0.934613	-161
TGCAACTGGTTTAGCAGTTGGCATGATCAA	5	28	0	TTAGCAGTTG	    0.987618	-144
          **********

Masking position 3
Map Score:   14.2145

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 75
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

GCACTCGTGAGGTGGGAGTGCTAAACCCTCT	1	53	1	GGGGGAGTGC	    0.958537	-70
TCAGTAGTAATTTGGGAGAGGGTTTAGCACT	1	69	0	TTGGGAGAGG	    0.944619	-54
TTTAACACAGGTCAGGATCGGTAAAAATTAA	2	16	0	GTAGGATCGG	    0.992293	-81
ATTTAAATGGGGGAGTAACGGACGTTTAATG	3	12	0	GGAGTAACGG	    0.790209	-151
GTCTTAGAGCTTGGCGATCGCCCTGGATTTA	3	38	0	TTGCGATCGC	    0.861263	-125
GCTAAGTCAGGTAAGGTTCGGTTTCCCGGTC	3	66	0	GTAGGTTCGG	    0.953044	-97
TGAAGAAGATTTAAGGAGCGCATCA      	4	23	1	TTAGGAGCGC	    0.971825	-15
CGCTACCAACGTAGGGATTTGAACGATAGAA	5	96	0	GTGGGATTTG	    0.850122	-76
AAATCCCTACGTTGGTAGCGGAACAAAGCCG	5	107	1	GTGGTAGCGG	    0.987501	-65
          ** ********

Masking position 7
Map Score:   4.77005

Number of sites scoring better than the average of aligned sites = 2206
Number in coding regions = 2029
Number in noncoding regions = 177
Number of orfs with sites within 600 bp upstream = 199
Fraction of orfs with sites within 600 bp upstream = 0.0319627


Motif number 3

CACTCCCACCTCACGAGTGCTAATTTAGCT	1	43	0	TCACGAGTGC	    0.985401	-80
AAAAGTAAAACCTCGTGGGCAAATTAATGC	2	77	0	CCTCGTGGGC	    0.989244	-20
CACTCCACTGCCAAGAGTGCTAAAGTGCTT	3	96	1	CCAAGAGTGC	    0.989498	-67
CAAAGCCGGACCACGAGGCCTCATAGAATA	5	130	1	CCACGAGGCC	     0.99546	-42
          **********

Masking position 5
Map Score:   2.97111

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 45
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

ACTGGGTCAAGCAATTTAGCTAAATTAGCA	1	26	1	GCAATTTAGC	    0.903104	-97
   GTCGATTAATTTTTACCGATCCTGACC	2	8	1	AATTTTTACC	    0.868533	-89
AAACTTGCAGGATTTTTACCCATTCATCTA	2	45	1	GATTTTTACC	    0.960342	-52
AGTCCATAAAGCACTTTAGCACTCTTGGCA	3	104	0	GCACTTTAGC	    0.947798	-59
GTTATTTGTAACTTTTTAGTCT        	3	151	1	ACTTTTTAGT	    0.804845	-12
CAAAGTCCTCGCTTTTTTGCAACTGGTTTA	5	45	0	GCTTTTTTGC	    0.979586	-127
TCGTGGTCCGGCTTTGTTCCGCTACCAACG	5	116	0	GCTTTGTTCC	    0.922344	-56
          **********

Masking position 5
Map Score:   2.11826

Number of sites scoring better than the average of aligned sites = 998
Number in coding regions = 856
Number in noncoding regions = 142
Number of orfs with sites within 600 bp upstream = 164
Fraction of orfs with sites within 600 bp upstream = 0.0263412


Motif number 5

CCGGGGTGTTGCACTGGGTCAAGCAATTTA	1	14	1	GCACTGGGTC	    0.986245	-109
CTTGGCGATCGCCCTGGATTTAAATGGGGG	3	30	0	GCCCTGGATT	    0.971117	-133
AGCACTCTTGGCAGTGGAGTGCTAAGTCAG	3	87	0	GCAGTGGAGT	    0.982253	-76
AGTCCATAAAGCACTTTAGCACTCTTGGCA	3	104	0	GCACTTTAGC	    0.939041	-59
TTTAAAAATAGCAGTTGATCATGCCAACTG	5	14	1	GCAGTTGATC	     0.98087	-158
          **********

Masking position 5
Map Score:   1.76957

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 401
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 6

          **********

No masking
Map Score:   -7.08111e-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:   -7.08111e-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 8

          **********

No masking
Map Score:   -7.08111e-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