AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_tpal_bbur_100.orf -o307_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	RTP00131	190	AE000520
#2	RTP00159	29	AE000520

Motif number 1

CGCACTCAGGGCAACGCCCAAGCCACTTAGGATG	1	29	0	GCACCAAGCC	    0.992886	-162
CTTCGAAGAGACACCCTCGTTGTCCTCCGGCGAT	1	76	1	ACACCTTGTC	    0.942065	-115
CTTTTTTACAGCACGAACATCGCCGGAGGACAAC	1	94	0	GCAGCTCGCC	    0.995709	-97
TGTAAAAAAGGCATCTTCTTCTCCTGTACAGGCG	1	118	1	GCACCTCTCC	    0.996837	-73
CGCACAGCACACAGCGGGAACGCCTGTACAGGAG	1	138	0	ACACGACGCC	    0.994374	-53
AATACGCTGCGCATCCTGCGCGCGCACAGCACAC	1	160	0	GCACGGCGCG	    0.983898	-31
         CACAACTAATACGCTGCGCATCCTG	1	176	0	ACACAACGCT	    0.946706	-15
CGAATAGTTTGCAGCAGCCTCTTT          	2	16	1	GCACCTCTTT	    0.951396	-14
          *** *  * *****

Masking position 3
Map Score:   8.34693

Number of sites scoring better than the average of aligned sites = 1449
Number in coding regions = 430
Number in noncoding regions = 1019
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

          GTGGGGTGTGGTTACGTTCA	1	1	1	GTGGGGTGTG	    0.999137	-190
TTCATCCTAAGTGGCTTGGGCGTTGCCCTG	1	27	1	GTGGCTTGGG	    0.989346	-164
TGCCCTGAGTGCGGGGAGTGGAATTCCTTC	1	50	1	GCGGGGAGTG	    0.996291	-141
CGTTCCCGCTGTGTGCTGTGCGCGCGCAGG	1	150	1	GTGTGCTGTG	    0.993722	-41
          **********

Masking position 3
Map Score:   4.78517

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 42
Number in noncoding regions = 124
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

TGTACAGGAGAAGAAGATGCCTTTTTTACA	1	118	0	AAGAAGATGC	    0.986142	-73
   CACAACTAATACGCTGCGCATCCTGCG	1	174	0	AATACGCTGC	    0.994651	-17
   TGAGACGAATAGTTTGCAGCAGCCTCT	2	8	1	AATAGTTTGC	    0.969309	-22
         AAAGAGGCTGCTGCAAACTAT	2	19	0	AAGAGGCTGC	    0.998115	-11
          **********

Masking position 4
Map Score:   4.33846

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 12
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

GAATTCCACTCCCCGCACTCAGGGCAACGC	1	46	0	CCCCGCACTC	    0.966898	-145
GGAGTGGAATTCCTTCGAAGAGACACCCTC	1	64	1	TCCTTCGAAG	    0.954321	-127
CTCGTTGTCCTCCGGCGATGTTCGTGCTGT	1	91	1	TCCGGCGATG	    0.986378	-100
CATCTTCTTCTCCTGTACAGGCGTTCCCGC	1	129	1	TCCTGTACAG	    0.954319	-62
GTACAGGCGTTCCCGCTGTGTGCTGTGCGC	1	143	1	TCCCGCTGTG	    0.950115	-48
ACGCTGCGCATCCTGCGCGCGCACAGCACA	1	161	0	TCCTGCGCGC	    0.989539	-30
  AAAGAGGCTGCTGCAAACTATTCGTCTC	2	12	0	TGCTGCAAAC	    0.937474	-18
          **********

Masking position 3
Map Score:   3.16063

Number of sites scoring better than the average of aligned sites = 1863
Number in coding regions = 590
Number in noncoding regions = 1273
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

          **********

No masking
Map Score:   3.71914e-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:   3.71914e-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:   3.71914e-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