AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i054_tpal_bbur_100.orf -o054_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	RBB00743	178	3615
#2	RBB00715	64	3615

Motif number 1

       GATTAGTATTTTAGCATAATTTT	1	4	1	TAGTATTTTA	    0.952058	-175
TATTTTAGCATAATTTTTTGTTTATGTTTT	1	17	1	TAATTTTTTG	    0.864444	-162
TTTTTTGTTTATGTTTTTGATTTGAAGTTT	1	30	1	ATGTTTTTGA	    0.960323	-149
TTTTGATTTGAAGTTTTTTAGAACTTTTAT	1	44	1	AAGTTTTTTA	    0.991391	-135
TTTATTTTTTCAATTTTTTATATTTATATT	1	69	1	CAATTTTTTA	    0.970602	-110
TATTTATATTATATTTTTAATATTATTAAA	1	89	1	ATATTTTTAA	    0.946259	-90
AAAACATCAACTATTTTTAATAATATTAAA	1	104	0	CTATTTTTAA	    0.922158	-75
AAAATAGTTGATGTTTTTTAATATAAACTA	1	117	1	ATGTTTTTTA	    0.987446	-62
ATATAAACTATAGTATTTTAATATATGACA	1	137	1	TAGTATTTTA	    0.952058	-42
CTTTACAATCAAGTTTTTAAAAACTCATTT	2	37	0	AAGTTTTTAA	    0.983716	-28
          **********

Masking position 6
Map Score:   18.2755

Number of sites scoring better than the average of aligned sites = 497
Number in coding regions = 138
Number in noncoding regions = 359
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

 GATTAGTATTTTAGCATAATTTTTTGTTT	1	10	1	TTTAGCATAA	    0.983623	-169
ATATTAAAAATATAATATAAATATAAAAAA	1	82	0	TATAATATAA	    0.908272	-97
ATATTATATTTTTAATATTATTAAAAATAG	1	94	1	TTTAATATTA	    0.935479	-85
GTTGATGTTTTTTAATATAAACTATAGTAT	1	123	1	TTTAATATAA	    0.978017	-56
ACTATAGTATTTTAATATATGACAATTTTC	1	143	1	TTTAATATAT	    0.954187	-36
       TATTTAAGCATGTTTAAGCATGA	2	4	1	TTAAGCATGT	    0.916355	-61
TTAAGCATGTTTAAGCATGAGTTAAATGAG	2	14	1	TTAAGCATGA	    0.959287	-51
          **********

Masking position 4
Map Score:   8.33763

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 29
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

GCATAATTTTTTGTTTATGTTTTTGATTTG	1	24	1	TTGTTTATGT	    0.986018	-155
ATTTTTTCAATTTTTTATATTTATATTATA	1	72	1	TTTTTTATAT	    0.966657	-107
TTTTTATATTTATATTATATTTTTAATATT	1	83	1	TATATTATAT	     0.92662	-96
TTATTAAAAATAGTTGATGTTTTTTAATAT	1	111	1	TAGTTGATGT	    0.978505	-68
TAAAATACTATAGTTTATATTAAAAAACAT	1	127	0	TAGTTTATAT	     0.98943	-52
          **********

Masking position 5
Map Score:   5.68163

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 6
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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