AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_tpal_bbur_100.orf -o008_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	RTP00166	135	AE000520
#2	RTP00167	41	AE000520
#3	RTP00169	57	AE000520

Motif number 1

AAGTTTGAACGCAAGTCAGCT         	1	2	0	GCAAGTCAGC	    0.975817	-134
ACCGCTTTTGGCGAGGCGTTGTTTGCAATG	1	81	1	GCGAGGCGTT	     0.98535	-55
GGCGTTGTTTGCAATGCTGCTAATGAGCGC	1	95	1	GCAATGCTGC	    0.993162	-41
     GGCGAGCAATGCGTCAAAGTGTTGT	2	6	1	GCAATGCGTC	    0.998611	-36
AAGCGGTACCGTAATGCGTCCGTTAATGTC	3	22	0	GTAATGCGTC	    0.992821	-36
          **********

Masking position 4
Map Score:   7.14009

Number of sites scoring better than the average of aligned sites = 319
Number in coding regions = 92
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

  AGCTGACTTGCGTTCAAACTTTCTGGGA	1	9	1	TGCGTTCAAA	     0.97373	-127
TTTTTTAGAATGTGCTCGAGTTGAGTAGCA	1	51	1	TGTGCTCGAG	    0.985567	-85
AAGAGGGTTATGCGCTCATTAGCAGCATTG	1	106	0	TGCGCTCATT	    0.968616	-30
CATAACCCTCTTTGTCCGAGGT        	1	124	1	TTTGTCCGAG	    0.951003	-12
 GGCGAGCAATGCGTCAAAGTGTTGTTGAT	2	10	1	TGCGTCAAAG	    0.974417	-32
GGTACCGTAATGCGTCCGTTAATGTCGGTA	3	18	0	TGCGTCCGTT	    0.989205	-40
          **********

Masking position 1
Map Score:   5.14449

Number of sites scoring better than the average of aligned sites = 422
Number in coding regions = 134
Number in noncoding regions = 288
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

CTGGGAATATGCAGCGGCTTTTTTAGAATG	1	33	1	GCAGCGGCTT	    0.997093	-103
GAGTTGAGTAGCAACCGCTTTTGGCGAGGC	1	68	1	GCAACCGCTT	    0.998671	-68
GACGCATTACGGTACCGCTTGGTGGTCGTC	3	32	1	GGTACCGCTT	    0.995699	-26
          **********

Masking position 9
Map Score:   3.10382

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 6
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

        CGTACCGTACCGACATTAACGG	3	3	1	TACCGTACCG	     0.99863	-55
ACGGACGCATTACGGTACCGCTTGGTGGTC	3	29	1	TACGGTACCG	     0.99863	-29
          **********

Masking position 6
Map Score:   1.61687

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 1
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

TAAAAAAGCCGCTGCATATTCCCAGAAAGTTTG	1	25	0	GCTGCAATCC	    0.995435	-111
GCCAAAAGCGGTTGCTACTCAACTCGAGCACAT	1	60	0	GTTGCTCTAC	    0.914754	-76
TGTTTGCAATGCTGCTAATGAGCGCATAACCCT	1	100	1	GCTGCTATAC	    0.936137	-36
GCGTCAAAGTGTTGTTGATTCTCGCTGGTTT  	2	21	1	GTTGTTATCC	    0.988637	-21
          ****** ** * *

Masking position 9
Map Score:   1.28684

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 8
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

TTTTTAGAATGTGCTCGAGTTGAGTAGCAAC	1	52	1	GTGTCGAGTT	    0.981429	-84
AACCGCTTTTGGCGAGGCGTTGTTTGCAATG	1	80	1	GGCAGGCGTT	     0.98525	-56
CGAGCAATGCGTCAAAGTGTTGTTGATTCTC	2	13	1	GTCAAGTGTT	    0.989196	-29
CCGCTTGGTGGTCGTCGTGTTA         	3	46	1	GTCTCGTGTT	    0.995998	-12
          *** *******

Masking position 10
Map Score:   0.227105

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 12
Number in noncoding regions = 47
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:   3.08538e-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 8

          **********

No masking
Map Score:   3.08538e-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 9

          **********

No masking
Map Score:   3.08538e-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