AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00580_tpal_reg_100.orf -o00580_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0255	118	ribosomal protein L31 (rpmE)
#2	TP0256	44	CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA)
#3	TP0257	96	glycerophosphoryldiester phosphodiesterase (glpQ)

Motif number 1

AGGCTCGTACACGCCGGGTGTAACCGACACACGTT	1	24	0	ACCGGTTACC	     0.98548	-95
TCCCCATTCTACAGCGCGCCGCGCCCTTAAAAAGG	1	80	0	ACCGCCGCCC	    0.999087	-39
      CTGAATCGCTCCTTTCCCCATTCTACAGC	1	100	0	ATCTCTTCCC	    0.985445	-19
GTGGTGTACCATTACGTCTTTCCCCTAGGTGAGT 	2	21	1	ATCGTTTCCC	    0.978629	-24
GCATATCTCCACTGAGCGCTGATCCTACCTTCAGT	3	12	0	ACAGCCGACC	    0.983819	-85
GCATAGTAGCACGCCGCATATCTCCACTGAGCGCT	3	27	0	ACCGCTTCCC	    0.999228	-70
GTTATAGAATGCACAGATCGTCACCGTGCATAGTA	3	54	0	GCAGACTCCC	    0.950709	-43
        AAACTTCTCTCCTCCCCTGTTATAGAA	3	80	0	ACCTCCTCCC	    0.997872	-17
          **  *** * ** **

Masking position 14
Map Score:   12.9693

Number of sites scoring better than the average of aligned sites = 445
Number in coding regions = 406
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

AGAAGGCTCGTACACGCCGGGTGTAACCGA	1	32	0	TACACGCCGG	    0.952166	-87
CCCATTCTACAGCGCGCCGCGCCCTTAAAA	1	83	0	AGCGCGCCGC	    0.998793	-36
      CTGAATCGCTCCTTTCCCCATTCT	1	105	0	ATCGCTCCTT	    0.974027	-14
AGGTAGGATCAGCGCTCAGTGGAGATATGC	3	17	1	AGCGCTCAGT	    0.974913	-80
CGTGCATAGTAGCACGCCGCATATCTCCAC	3	35	0	AGCACGCCGC	    0.997476	-62
      AAACTTCTCTCCTCCCCTGTTATA	3	83	0	TTCTCTCCTC	     0.91979	-14
          **********

Masking position 5
Map Score:   6.00608

Number of sites scoring better than the average of aligned sites = 1038
Number in coding regions = 948
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

CCGACACACGTTCCAGTCTCCTTAC      	1	5	0	TTCCAGCTCC	    0.957456	-114
CGTGTGTCGGTTACACCCGGCGTGTACGAGC	1	26	1	TTACACCGGC	    0.985072	-93
ATCCACCCTCTTCCAGAAGGCTCGTACACGC	1	45	0	TTCCAGAGGC	    0.995512	-74
CCTTTCCCCATTCTACAGCGCGCCGCGCCCT	1	88	0	TTCTACGCGC	     0.95958	-31
CATTACGTCTTTCCCCTAGGTGAGT      	2	30	1	TTCCCCAGGT	    0.920831	-15
ATATGCGGCGTGCTACTATGCACGGTGACGA	3	41	1	TGCTACATGC	    0.964742	-56
TCCTCCCCTGTTATAGAATGCACAGATCGTC	3	67	0	TTATAGATGC	    0.949132	-30
          ****** ****

Masking position 1
Map Score:   2.70851

Number of sites scoring better than the average of aligned sites = 469
Number in coding regions = 429
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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