AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_tpal_bbur_100.orf -o033_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	RTP00331	75	AE000520
#2	RTP00330	224	AE000520

Motif number 1

AAGCACTGGATGGGCTAGGGGGTTTCATCGCCT	1	24	1	TGGGTGGGGT	     0.99559	-52
AGAGTTTGATTGGGTTTGGTAGGCGATGAAACC	1	44	0	TGGGTGGAGG	    0.996437	-32
TAGTGGCGAGCGAAATTGGAGGAGCCTAAACCT	2	66	1	CGAATGGGGA	    0.923781	-159
TGTGTCTAACAGGGGTTGTAGGGCCGCGCGGGC	2	98	1	AGGGTGTGGG	    0.982917	-127
CGCGCGGGCTTGCGTTCGGTGGGTGAAATAATC	2	122	1	TGCGTGGGGG	     0.99869	-103
AAAACCTTTCTGCTATAGGCCGGATTATTTCAC	2	144	0	TGCTTGGCGG	    0.987062	-81
TCCCCGTATGCGGAATGGGGCGGACCTGCTGG 	2	203	1	CGGATGGCGG	    0.995339	-22
          **** * ** ***

Masking position 6
Map Score:   8.62306

Number of sites scoring better than the average of aligned sites = 926
Number in coding regions = 287
Number in noncoding regions = 639
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

GGATGGGCTAGGGGGTTTCATCGCCTACCA	1	31	1	GGGGGTTTCA	    0.976272	-45
          CCGGCATTCAGAGTTTGATT	1	66	0	CCGGCATTCA	    0.951312	-10
AAGAAATCAAGAGAGATTCCGAAAGTAGTG	2	41	1	GAGAGATTCC	    0.842019	-184
GCAAGCCCGCGCGGCCCTACAACCCCTGTT	2	105	0	GCGGCCCTAC	     0.96521	-120
GTAGGGCCGCGCGGGCTTGCGTTCGGTGGG	2	115	1	GCGGGCTTGC	     0.98542	-110
CCCTCTCTGTCAGGCTTTCCCAAAACCTTT	2	168	0	CAGGCTTTCC	     0.96032	-57
TTCCGCATACGGGGATTTCACCCTCTCTGT	2	188	0	GGGGATTTCA	    0.948264	-37
GCGGAATGGGGCGGACCTGCTGG       	2	212	1	GCGGACCTGC	    0.933755	-13
          **********

Masking position 8
Map Score:   5.14549

Number of sites scoring better than the average of aligned sites = 2473
Number in coding regions = 730
Number in noncoding regions = 1743
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 3

         ACTGTCGGAGGTAAAGCACTG	1	2	1	CTGTCGGAGG	    0.993378	-74
      CCGGCATTCAGAGTTTGATTGGGT	1	62	0	CATTCAGAGT	    0.955792	-14
CTCGCCACTACTTTCGGAATCTCTCTTGAT	2	46	0	CTTTCGGAAT	    0.914187	-179
AAACCTGTGTCTAACAGGGGTTGTAGGGCC	2	93	1	CTAACAGGGG	    0.946203	-132
CGCGGGCTTGCGTTCGGTGGGTGAAATAAT	2	124	1	CGTTCGGTGG	    0.962321	-101
TTGGGAAAGCCTGACAGAGAGGGTGAAATC	2	175	1	CTGACAGAGA	    0.962524	-50
CCCCATTCCGCATACGGGGATTTCACCCTC	2	193	0	CATACGGGGA	     0.96602	-32
          **********

Masking position 5
Map Score:   4.555

Number of sites scoring better than the average of aligned sites = 1135
Number in coding regions = 319
Number in noncoding regions = 816
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

AGGGGGTTTCATCGCCTACCAAACCCAATC	1	40	1	ATCGCCTACC	    0.980276	-36
CTCCTCCAATTTCGCTCGCCACTACTTTCG	2	60	0	TTCGCTCGCC	    0.990595	-165
GCCGGATTATTTCACCCACCGAACGCAAGC	2	129	0	TTCACCCACC	    0.996909	-96
ATACGGGGATTTCACCCTCTCTGTCAGGCT	2	182	0	TTCACCCTCT	    0.978743	-43
          **********

Masking position 2
Map Score:   2.37516

Number of sites scoring better than the average of aligned sites = 384
Number in coding regions = 113
Number in noncoding regions = 271
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

CCTCCAATTTCGCTCGCCACTACTTTCGGA	2	58	0	CGCTCGCCAC	     0.99514	-167
AACGCAAGCCCGCGCGGCCCTACAACCCCT	2	108	0	CGCGCGGCCC	    0.872342	-117
    CCAGCAGGTCCGCCCCATTCCGCATA	2	209	0	GGTCCGCCCC	     0.62027	-16
          **********

Masking position 5
Map Score:   0.305521

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 12
Number in noncoding regions = 31
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:   -3.38628e-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:   -3.38628e-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 8

          **********

No masking
Map Score:   -3.38628e-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