AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i137_tpal_bbur_100.orf -o137_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	RTP00721	95	AE000520
#2	RTP00722	90	AE000520
#3	RTP00723	31	AE000520

Motif number 1

AATTCTGTCGTGAACGCGAAGCCGTTG     	1	6	0	TGAACCGAAC	    0.990552	-90
ACGACAGAATTAGACGCGGGGCTTGCCTTTCT	1	27	1	TAGACCGGGC	    0.951724	-69
CACCAGGAACTGCGCACGGAACATAAGAAAGG	1	52	0	TGCGCCGGAC	    0.995719	-44
CGGTTCCATGTGGGCTCGAAAAGGG       	2	4	0	TGGGCCGAAA	    0.992281	-87
CGAGCCCACATGGAACCGGACCCATATCGATT	2	18	1	TGGAACGGAC	    0.995568	-73
TTGAAATTACTGCAAGCGAATCACTAGGTGTC	2	53	1	TGCAACGAAC	    0.989761	-38
GCGAATCACTAGGTGTCGAAAACCGCGGCGGT	2	68	1	AGGTGCGAAA	    0.886215	-23
       AGGTGGTGTCGAAACTCGTGCGCCC	3	17	0	TGGTGCGAAC	    0.994765	-15
          ***** **** *

Masking position 7
Map Score:   12.1637

Number of sites scoring better than the average of aligned sites = 489
Number in coding regions = 142
Number in noncoding regions = 347
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

ACGACAGAATTAGACGCGGGGCTTGCCTTT	1	27	1	TAGACGCGGG	    0.978504	-69
CGTGCGCAGTTCCTGGTGGGCTGGGCTATA	1	66	1	TCCTGGTGGG	    0.974836	-30
CCATGTGGGCTCGAAAAGGG          	2	1	0	TCGAAAAGGG	    0.979184	-90
TGGGTCCGGTTCCATGTGGGCTCGAAAAGG	2	12	0	TCCATGTGGG	    0.824644	-79
TTCAACGTAATCGATATGGGTCCGGTTCCA	2	28	0	TCGATATGGG	    0.984153	-63
          **********

Masking position 1
Map Score:   5.46114

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 82
Number in noncoding regions = 234
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

AAGAAAGGCAAGCCCCGCGTCTAATTCTGT	1	30	0	AGCCCCGCGT	    0.985059	-66
GTATAGCCCAGCCCACCAGGAACTGCGCAC	1	67	0	GCCCACCAGG	    0.990889	-29
         TGCCGCTGCGTATAGCCCAGC	1	85	0	GCCGCTGCGT	    0.983499	-11
CCCTTTTCGAGCCCACATGGAACCGGACCC	2	11	1	GCCCACATGG	    0.976627	-80
         AACCGCCGCGGTTTTCGACAC	2	80	0	ACCGCCGCGG	    0.995531	-11
  GAACTTGGGCGCACGAGTTTCGACACCA	3	9	1	GCGCACGAGT	    0.973558	-23
          **********

Masking position 9
Map Score:   5.71133

Number of sites scoring better than the average of aligned sites = 1314
Number in coding regions = 384
Number in noncoding regions = 930
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

       CAACGGCTTCGCGTTCACGACAG	1	4	1	CGGCTTCGCG	    0.993407	-92
ATTAGACGCGGGGCTTGCCTTTCTTATGTT	1	35	1	GGGCTTGCCT	    0.985242	-61
AGTTCCTGGTGGGCTGGGCTATACGCAGCG	1	73	1	GGGCTGGGCT	    0.997462	-23
TCGACACCTAGTGATTCGCTTGCAGTAATT	2	57	0	GTGATTCGCT	    0.981798	-34
          **********

Masking position 5
Map Score:   3.60394

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 80
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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 7

          **********

No masking
Map Score:   -2.59896e-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