AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i187_tpal_bbur_100.orf -o187_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00222	193	3615

Motif number 1

ATTTAAGGAAAAATTATTTTT         	1	2	0	AAATTATTTT	    0.564981	-192
ATTTTTCCTTAAATAATTATAAGCATAAAA	1	18	1	AAATAATTAT	     0.84155	-176
ATAAGCATAAAAGCAATTTTTCCAAAATAG	1	36	1	AAGCAATTTT	     0.98023	-158
TCAATTCTGTAAACTATTTTGGAAAAATTG	1	49	0	AAACTATTTT	    0.722597	-145
ACTATTTAATAATCAATTCTGTAAACTATT	1	61	0	AATCAATTCT	      0.9847	-133
AAATAGTGTTAATCTAATTTTAGATTTAAT	1	84	1	AATCTAATTT	    0.919767	-110
TTTCTTAATCAAACAACTCTTATTAAATCT	1	105	0	AAACAACTCT	    0.973181	-89
ATTAAACAAAAATAAACTTTCTTAATCAAA	1	122	0	AATAAACTTT	    0.890373	-72
CTGTAAACATAATCTATTTTAACACAACAT	1	157	0	AATCTATTTT	    0.970634	-37
          **********

Masking position 6
Map Score:   15.9173

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 189
Number in noncoding regions = 510
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

GCTTATAATTATTTAAGGAAAAATTATTTTT  	1	9	0	ATTAAAAAAA	    0.949993	-185
CCTTAAATAATTATAAGCATAAAAGCAATTTTT	1	24	1	TATAAATAAA	    0.880871	-170
TTCTGTAAACTATTTTGGAAAAATTGCTTTTAT	1	42	0	TTTTTAAAAA	    0.807167	-152
AGATTAACACTATTTAATAATCAATTCTGTAAA	1	66	0	TTTTAAATCA	    0.681353	-128
AAACAACTCTTATTAAATCTAAAATTAGATTAA	1	92	0	TTTAACTAAA	    0.958578	-102
AAATAAACTTTCTTAATCAAACAACTCTTATTA	1	110	0	TTTAAAAACA	    0.986125	-84
CAACATTTTATATTAAACAAAAATAAACTTTCT	1	130	0	TTTAAAAAAA	    0.986299	-64
ACATAATCTATTTTAACACAACATTTTATATTA	1	148	0	TTTAACAACA	    0.940455	-46
          * ****  *****

Masking position 13
Map Score:   8.42199

Number of sites scoring better than the average of aligned sites = 218
Number in coding regions = 58
Number in noncoding regions = 160
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

 AAAAATAATTTTTCCTTAAATAATTATAAG	1	10	1	TTTCCTTAAA	    0.968661	-184
AAAATTGCTTTTATGCTTATAATTATTTAAG	1	25	0	TTTGCTTATA	    0.957417	-169
TAAAAGCAATTTTTCCAAAATAGTTTACAGA	1	43	1	TTTCCAAAAT	    0.888726	-151
TAATAATCAATTCTGTAAACTATTTTGGAAA	1	54	0	TTTGTAAACT	    0.928724	-140
GAAAGTTTATTTTTGTTTAATATAAAATGTT	1	131	1	TTTGTTTAAT	    0.979173	-63
ATATAAAATGTTGTGTTAAAATAGATTATGT	1	150	1	TTTGTTAAAA	    0.978886	-44
TTAAAATAGATTATGTTTACAGGCGAAAGGT	1	165	1	TTTGTTTACA	    0.980689	-29
          ** ********

Masking position 9
Map Score:   6.9041

Number of sites scoring better than the average of aligned sites = 420
Number in coding regions = 128
Number in noncoding regions = 292
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -4.73059e-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 5

          **********

No masking
Map Score:   -4.73059e-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 6

          **********

No masking
Map Score:   -4.73059e-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