AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_synecho_ctra_100.orf -o138_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	RCY38377	106	Synechocystis
#2	RCT00396	300	Chlamydia_trachomatis

Motif number 1

GCGATAGCCGAGTTGTTTGGAGAGTAGTAGTT	2	12	0	AGTTTTTGGG	    0.973991	-289
GAATATTCTTAGTTTTTTAAGATTTTATCTCC	2	64	1	AGTTTTTAAA	    0.968038	-237
GGTGAGGAACAGTTTTTTAAAGAAAAAGCAAA	2	114	0	AGTTTTTAAG	    0.983471	-187
TTCCTCACCCCGTTTTCTAAAGCTTCTCTGCT	2	137	1	CGTTTCTAAG	    0.871682	-164
TTCACATATAAATTTTTTAGTAATATGGGGTT	2	172	0	AATTTTTAGA	    0.968038	-129
TTTATATGTGAATGATTTAACGCGATTTCCCT	2	192	1	AATGTTTAAG	    0.924627	-109
CAAACAATTTCATTCTTTAGGGAAATCGCGTT	2	210	0	CATTTTTAGG	    0.966761	-91
TAAAGAATGAAATTGTTTGGAAGACAAGCCAT	2	223	1	AATTTTTGGA	    0.936728	-78
GTTCGTTGTTAATATTTTAAGATAAT      	2	285	1	AATATTTAAA	    0.808279	-16
          **** ***** *

Masking position 6
Map Score:   7.80606

Number of sites scoring better than the average of aligned sites = 390
Number in coding regions = 321
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

TTATCATTGCATAATTCCTCCACCTTGTC    	1	7	0	AAATTCTCCC	    0.981212	-100
GCCAAAGGGATAAATTTCCCATCAGCTTGATCT	1	63	1	TAATTCCCAC	    0.948563	-44
TGATCTTCACTGTATTGCACATCGGTA      	1	90	1	TTATTCACAC	    0.905262	-17
        AAACTACTACTCTCCAAACAACTCG	2	3	1	ATACTCTCTC	    0.969798	-298
TCTTTAAAAAACTGTTCCTCACCCCGTTTTCTA	2	123	1	ATGTTCTCAC	    0.983582	-178
CCCGTTTTCTAAAGCTTCTCTGCTCTGAACCCC	2	145	1	AAGCTCTCTC	    0.965678	-156
GCCATTGAACAAAATTACTCAACAATAGAATAA	2	250	1	AAATTCTCAC	    0.991448	-51
          * **** **** *

Masking position 6
Map Score:   3.93682

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 234
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 3

ATTATCGTTTATTGTCCTAATGCCAAAGGG	1	42	1	ATTGTCCTAA	    0.981925	-65
AAAAGCAAAAATTGTACGAAAAAAGCTGGA	2	93	0	ATTGTACGAA	    0.965752	-208
TCTGAACCCCATATTACTAAAAAATTTATA	2	168	1	ATATTACTAA	    0.883458	-133
ATTTAACGCGATTTCCCTAAAGAATGAAAT	2	206	1	ATTTCCCTAA	    0.941484	-95
AAGACAAGCCATTGAACAAAATTACTCAAC	2	243	1	ATTGAACAAA	    0.893273	-58
          **********

Masking position 2
Map Score:   0.785428

Number of sites scoring better than the average of aligned sites = 220
Number in coding regions = 191
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

TTGCATAATTCCTCCACCTTGTC       	1	4	0	CCTCCACCTT	     0.99167	-103
GATAAATTTCCCATCAGCTTGATCTTCACT	1	71	1	CCATCAGCTT	    0.978861	-36
TAAGATTTTATCTCCAGCTTTTTTCGTACA	2	81	1	TCTCCAGCTT	    0.995176	-220
CACCCCGTTTTCTAAAGCTTCTCTGCTCTG	2	142	1	TCTAAAGCTT	    0.950095	-159
          **********

Masking position 6
Map Score:   1.69992

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 210
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 5

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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