AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i211_synecho_ctra_100.orf -o211_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	RCY30174	31	Synechocystis
#2	RCY42399	64	Synechocystis
#3	RCY23794	104	Synechocystis
#4	RCT00022	75	Chlamydia_trachomatis
#5	RCT00470	138	Chlamydia_trachomatis

Motif number 1

GGGTACGGGTAAATCCAAATCTCCAA    	1	7	0	AAATCCAAAT	    0.945023	-25
         CCAAGCCAAATTAGCAAGGCA	2	2	1	CAAGCCAAAT	    0.995077	-63
GCCAAATTAGCAAGGCAAATAATTATGTCC	2	15	1	CAAGGCAAAT	    0.978876	-50
          CAAGCTCAATGGGTTTGATT	3	1	1	CAAGCTCAAT	    0.971227	-104
      TTGACAACCCCAAAATCACTATCT	4	62	0	CAACCCCAAA	    0.973652	-14
        GCAAACCCTAATAAATCTATTA	5	127	0	AAACCCTAAT	    0.948866	-12
          **********

Masking position 3
Map Score:   5.69398

Number of sites scoring better than the average of aligned sites = 713
Number in coding regions = 641
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 2

TTTTCAAAAATACCCCCGCTTAATAACGGG	2	43	0	TACCCCCGCT	    0.990071	-22
TGGGTTTGATTACTGCTGCTTGCCTTAGAG	3	20	1	TACTGCTGCT	    0.953437	-85
CCTTAGAGTAACCCCCTGTTGTTAATTTTT	3	42	1	ACCCCCTGTT	    0.960483	-63
TCGGGTATGCTCTCCCTTCTGTTATGTGAG	4	18	1	TCTCCCTTCT	    0.904387	-58
TGGAATACTATACTCCAGGTCCTTTTCTTC	5	17	0	TACTCCAGGT	    0.973931	-122
TGGAGTATAGTATTCCAGGTCTTTTAATTT	5	30	1	TATTCCAGGT	    0.914914	-109
CTTTTTATAATCCCCCTGTTTTAGTACCGT	5	73	1	TCCCCCTGTT	     0.99162	-66
          **********

Masking position 10
Map Score:   5.31242

Number of sites scoring better than the average of aligned sites = 2263
Number in coding regions = 2083
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 197
Fraction of orfs with sites within 600 bp upstream = 0.0316415


Motif number 3

  AGTTTTCAAAAATACCCCCGCTTAATAACG	2	45	0	AAATACCCCG	    0.996503	-20
CTTGCCTTAGAGTAACCCCCTGTTGTTAATTT	3	38	1	ATAACCCCCG	      0.9943	-67
GACCTGGAATACTATACTCCAGGTCCTTTTCT	5	19	0	ATATACTCCG	    0.986248	-120
AATTCTTTTTATAATCCCCCTGTTTTAGTACC	5	69	1	AAATCCCCCG	    0.997736	-70
          * ******** *

Masking position 4
Map Score:   3.38491

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 158
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

AGATTTGGATTTACCCGTACCCCTCTA   	1	15	1	TTACCCGTAC	    0.921083	-17
CCCCCGCTTAATAACGGGACATAATTATTT	2	31	0	ATAACGGGAC	    0.982474	-34
GTGTCGCATGGTAACTGAACTCCTAAAAAA	3	67	0	GTAACTGAAC	    0.944045	-38
AAGGGAGAGCATACCCGAACATTTT     	4	6	0	ATACCCGAAC	    0.987107	-70
AAAATCTCACATAACAGAAGGGAGAGCATA	4	23	0	ATAACAGAAG	    0.897794	-53
CATTAGCAACAAAACGGTACTAAAACAGGG	5	86	0	AAAACGGTAC	    0.945928	-53
          **********

Masking position 3
Map Score:   2.01192

Number of sites scoring better than the average of aligned sites = 198
Number in coding regions = 179
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

ATAACGGGACATAATTATTTGCCTTGCTAA	2	21	0	ATAATTATTT	    0.928187	-44
CCCCCTGTTGTTAATTTTTTAGGAGTTCAG	3	53	1	TTAATTTTTT	    0.927825	-52
TCCAGGTCTTTTAATTTTTATTTAAAAATT	5	43	1	TTAATTTTTA	    0.948515	-96
GATTATAAAAAGAATTTTTAAATAAAAATT	5	55	0	AGAATTTTTA	    0.966085	-84
AGCGATTAATAGATTTATTAGGGTTTGC  	5	121	1	AGATTTATTA	    0.858824	-18
          **********

Masking position 5
Map Score:   1.37927

Number of sites scoring better than the average of aligned sites = 311
Number in coding regions = 243
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 6

          **********

No masking
Map Score:   8.19556e-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:   8.19556e-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:   8.19556e-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