AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icoldbox_tpal_opreg_100.orf -g0.528 -x5 
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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0768	138	membrane protein (tmpA)
#2	TP0770	44	ATP-dependent RNA helicase

Motif number 1

AGGACGCGCCGCCTAGCACGTTACGC          	1	1	0	GCCAGACGCC	    0.996512	-138
TCGCCACCGCGTCGAGAAGGACGCGCCGCCTAGCAC	1	18	0	GTCAGAGGCC	    0.999416	-121
GTACCGTTCGGCCCGGGAGGGTACACCAGAAAGCCC	1	68	0	GCCGGAGGCC	    0.999749	-71
CCTCACATGAGCCGAGGAGGTATCACGTGGGAGGTT	1	107	1	GCCAGAGGCC	    0.999871	-32
          *** ** ***   * *

Masking position 8
Map Score:   9.23679

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 3
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

TAACGTGCTAGGCGGCGCGTCCTTCTCGAC	1	14	1	GGCGGCGCGT	     0.98739	-125
TTCGCCACCGCGTCGAGAAGGACGCGCCGC	1	25	0	CGTCGAGAAG	    0.959258	-114
TTCTCGACGCGGTGGCGAAGTCTTGAATAA	1	36	1	GGTGGCGAAG	    0.994701	-103
TACCCTCCCGGGCCGAACGGTACTCTCCTC	1	81	1	GGCCGAACGG	     0.96474	-58
TCGGCTCATGTGAGGAGAGTACCGTTCGGC	1	92	0	TGAGGAGAGT	     0.97538	-47
TCTCCTCACATGAGCCGAGGAGGTATCACG	1	104	1	TGAGCCGAGG	    0.971194	-35
       CCTTGTGGAAAAGGGGAAAAAGC	2	32	0	TGTGGAAAAG	    0.964894	-13
          **********

Masking position 2
Map Score:   5.65923

Number of sites scoring better than the average of aligned sites = 1769
Number in coding regions = 1566
Number in noncoding regions = 203
Number of orfs with sites within 600 bp upstream = 145
Fraction of orfs with sites within 600 bp upstream = 0.0232894


Motif number 3

AGGCGGCGCGTCCTTCTCGACGCGGTGGCG	1	23	1	TCCTTCTCGA	    0.981054	-116
CCAGAAAGCCCCCTTATTCAAGACTTCGCC	1	49	0	CCCTTATTCA	    0.984711	-90
AGCGTATACGCTCTTGTCTATCCG      	2	5	0	CTCTTGTCTA	    0.972224	-40
ACGCTTTTTCCCCTTTTCCACAAGG     	2	30	1	CCCTTTTCCA	    0.996108	-15
          **********

Masking position 5
Map Score:   1.54025

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 109
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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 5

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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