AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i055_tpal_bbur_300.orf -o055_tpal_bbur_300.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
#3	RBB00576	27	3615

Motif number 1

AAAAATTATGCTAAAATACTAATC      	1	5	0	CTAAAATACT	    0.935155	-174
AAAAACATAAACAAAAAATTATGCTAAAAT	1	18	0	ACAAAAAATT	    0.910417	-161
AAAACTTCAAATCAAAAACATAAACAAAAA	1	31	0	ATCAAAAACA	    0.958232	-148
AATAAAAGTTCTAAAAAACTTCAAATCAAA	1	45	0	CTAAAAAACT	    0.983086	-134
TAATATAAATATAAAAAATTGAAAAAATAA	1	70	0	ATAAAAAATT	    0.981807	-109
TTTTAATAATATTAAAAATATAATATAAAT	1	90	0	ATTAAAAATA	    0.953625	-89
TTTTAATATTATTAAAAATAGTTGATGTTT	1	103	1	ATTAAAAATA	    0.953625	-76
ATAGTTTATATTAAAAAACATCAACTATTT	1	118	0	TTAAAAAACA	    0.978406	-61
TTGTCATATATTAAAATACTATAGTTTATA	1	138	0	TTAAAATACT	    0.930359	-41
CAATCAAGTTTTTAAAAACTCATTTAACTC	2	32	0	TTTAAAAACT	    0.960599	-33
TTAATTTCACATAAAAAATACTG       	3	4	0	ATAAAAAATA	    0.978455	-24
          **********

Masking position 5
Map Score:   22.1753

Number of sites scoring better than the average of aligned sites = 466
Number in coding regions = 133
Number in noncoding regions = 333
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

ATAAACAAAAAATTATGCTAAAATACTAAT	1	12	0	AATTATGCTA	    0.720811	-167
ATAATTTTTTGTTTATGTTTTTGATTTGAA	1	26	1	GTTTATGTTT	    0.982056	-153
ATGTTTTTGATTTGAAGTTTTTTAGAACTT	1	40	1	TTTGAAGTTT	    0.903999	-139
TTTTTAGAACTTTTATTTTTTCAATTTTTT	1	58	1	TTTTATTTTT	    0.806515	-121
TTTTTCAATTTTTTATATTTATATTATATT	1	74	1	TTTTATATTT	    0.931799	-105
TTTATATTTATATTATATTTTTAATATTAT	1	85	1	TATTATATTT	    0.862932	-94
ATTAAAAATAGTTGATGTTTTTTAATATAA	1	113	1	GTTGATGTTT	    0.949931	-66
AAATACTATAGTTTATATTAAAAAACATCA	1	125	0	GTTTATATTA	    0.850021	-54
         TATTTAAGCATGTTTAAGCAT	2	2	1	ATTTAAGCAT	    0.713826	-63
ATTTAAGCATGTTTAAGCATGAGTTAAATG	2	12	1	GTTTAAGCAT	    0.798247	-53
CAACCTTTACAATCAAGTTTTTAAAAACTC	2	41	0	AATCAAGTTT	    0.657815	-24
   CAGTATTTTTTATGTGAAATTAAATTT	3	8	1	TTTTATGTGA	    0.719948	-20
TTTTATGTGAAATTAAATTT          	3	18	1	AATTAAATTT	    0.766999	-10
          **********

Masking position 5
Map Score:   10.2347

Number of sites scoring better than the average of aligned sites = 1494
Number in coding regions = 427
Number in noncoding regions = 1067
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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 4

          **********

No masking
Map Score:   -1.9652e-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 5

          **********

No masking
Map Score:   -1.9652e-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