AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_tpal_bbur_100.orf -o203_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	RTP00159	29	AE000520
#2	RTP00160	86	AE000520
#3	RTP00161	89	AE000520

Motif number 1

ACGAAGCCTTTTCCTTTGCAA          	2	1	0	TTCCTTTGCA	    0.980527	-86
TCCCCGTCAAGCCCTCTTCCATCCAGTAATA	2	31	0	GCCCTCTTCA	      0.9904	-56
CTGATAATAATTCCCCGTCAAGCCCTCTTCC	2	42	0	TTCCCCGTCA	    0.993836	-45
TGGATAACAAGTTCATGTCCATGCTGACCC 	3	10	0	GTTCATGTCA	    0.906346	-80
TGTTATCCACGTACACTGCGAATTTCCCCGA	3	32	1	GTACACTGCA	    0.931988	-58
CACTGCGAATTTCCCCGACGAAATGTAGAAA	3	45	1	TTCCCCGACA	    0.980402	-45
AGAATCCAGTTCCCTTTTCTACATTTCGTCG	3	60	0	TCCCTTTTCA	    0.976394	-30
          ********* *

Masking position 11
Map Score:   5.72904

Number of sites scoring better than the average of aligned sites = 2113
Number in coding regions = 659
Number in noncoding regions = 1454
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

AGAGGCTGCTGCAAACTATTCGTCTCA    	1	7	0	GCAAACTTTC	    0.764955	-23
ATAGTTTGCAGCAGCCTCTTT          	1	19	1	GCAGCCTTTT	    0.985604	-11
CCAGTAATACGAAGCCTTTTCCTTTGCAA  	2	9	0	GAAGCCTTTC	    0.886211	-78
TTTTGGGGTTGAAACCACTGATAATAATTCC	2	59	0	GAAACCATGA	    0.943174	-28
CCAGAACGAAGAATCCAGTTCCCTTTTCTAC	3	69	0	GAATCCATTC	    0.984075	-21
          ******* ***

Masking position 3
Map Score:   2.95937

Number of sites scoring better than the average of aligned sites = 400
Number in coding regions = 129
Number in noncoding regions = 271
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

ACTGATAATAATTCCCCGTCAAGCCCTCTT	2	44	0	ATTCCCCGTC	    0.996838	-43
ATGAACTTGTTATCCACGTACACTGCGAAT	3	25	1	TATCCACGTA	    0.976936	-65
ACACTGCGAATTTCCCCGACGAAATGTAGA	3	44	1	TTTCCCCGAC	    0.996837	-46
          **********

Masking position 3
Map Score:   1.57154

Number of sites scoring better than the average of aligned sites = 266
Number in coding regions = 82
Number in noncoding regions = 184
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

    TTGCAAAGGAAAAGGCTTCGTATTAC	2	7	1	AGGAAAAGGC	    0.990967	-80
ATTACTGGATGGAAGAGGGCTTGACGGGGA	2	32	1	GGAAGAGGGC	    0.996039	-55
GACGAAATGTAGAAAAGGGAACTGGATTCT	3	61	1	AGAAAAGGGA	    0.992397	-29
          **********

Masking position 6
Map Score:   0.741859

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 33
Number in noncoding regions = 74
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:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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