AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00340_tpal_reg_100.orf -o00340_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	TP0251	153	DNA-binding protein II
#2	TP0417	26	apolipoprotein N-acyltransferase (cutE)
#3	TP0641	140	histidyl-tRNA synthetase (hisS)

Motif number 1

ACCTTTCCGGGCAGCGGTGTCAAGTCGCT 	1	10	0	GCAGCGGTGT	    0.970412	-144
ACCGCTGCCCGGAAAGGTGTTTTCGCTAGA	1	22	1	GGAAAGGTGT	    0.974075	-132
GCCAGAAGTCCCGAATGTGTAGACTGTACA	1	65	1	CCGAATGTGT	    0.860926	-89
TGTAGACTGTACAACGGTGTGTTCTCTTCA	1	82	1	ACAACGGTGT	    0.836837	-72
CTCTTCACCCGAGGTGGTGCGCGTTTGAGG	1	105	1	GAGGTGGTGC	    0.973563	-49
TTTTAAAGGTGAGGAAGCGCTC        	3	3	0	GAGGAAGCGC	    0.873321	-138
GCCCCTCTATCCTGTGGTGCCGTAAATAGT	3	40	0	CCTGTGGTGC	    0.852593	-101
GCATTGTAATGGGAAGGTGCTGCTCTGTGC	3	68	1	GGGAAGGTGC	    0.987182	-73
GCAATGCTCACAAAAAGTGCATGTCTTGAA	3	96	1	CAAAAAGTGC	    0.924331	-45
TGCATGTCTTGAAAAAGTGTACCAGAGCCA	3	113	1	GAAAAAGTGT	    0.936954	-28
          **********

Masking position 7
Map Score:   8.25279

Number of sites scoring better than the average of aligned sites = 1889
Number in coding regions = 1726
Number in noncoding regions = 163
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

AGGTGTTTTCGCTAGAAAGGCTGTGGCTCGC	1	36	1	GCTAGAAAGC	    0.990413	-118
GCTGTGGCTCGCCAGAAGTCCCGAATGTGTA	1	55	1	GCCAGAAGCC	     0.96837	-99
CGTTGTACAGTCTACACATTCGGGACTTCTG	1	67	0	TCTACACATC	    0.797496	-87
GCAAACAGCCGCCTCAAACGCGCACCACCTC	1	115	0	GCCTCAAAGC	    0.966957	-39
     GACAAGAAACACACGCGGGCAAACAG	1	138	0	GAAACACAGC	    0.954646	-16
ACTTTCCCCTGCCAGAAAAGCATTT      	2	5	0	GCCAGAAAGC	    0.993883	-22
GGCACCACAGGATAGAGGGGCATTGTAATGG	3	49	1	GATAGAGGGC	    0.910672	-92
GTACACTTTTTCAAGACATGCACTTTTTGTG	3	104	0	TCAAGACAGC	    0.970709	-37
          ******** **

Masking position 6
Map Score:   6.60824

Number of sites scoring better than the average of aligned sites = 556
Number in coding regions = 510
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

AAACACCTTTCCGGGCAGCGGTGTCAAGTC	1	14	0	CCGGGCAGCG	    0.986932	-140
AATGTGTAGACTGTACAACGGTGTGTTCTC	1	78	1	CTGTACAACG	    0.915876	-76
GCTTTTCTGGCAGGGGAAAGTT        	2	15	1	CAGGGGAAAG	    0.970338	-12
TACGGCACCACAGGATAGAGGGGCATTGTA	3	46	1	CAGGATAGAG	    0.948867	-95
GATAGAGGGGCATTGTAATGGGAAGGTGCT	3	59	1	CATTGTAATG	    0.520412	-82
AGGTGCTGCTCTGTGCAATGCTCACAAAAA	3	82	1	CTGTGCAATG	    0.698158	-59
          CAGTGTAGTGGCTCTGGTAC	3	131	0	CAGTGTAGTG	      0.9316	-10
          **********

Masking position 7
Map Score:   5.59665

Number of sites scoring better than the average of aligned sites = 591
Number in coding regions = 547
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

 AGCGACTTGACACCGCTGCCCGGAAAGGT	1	10	1	ACACCGCTGC	    0.958795	-144
TTCTGGCGAGCCACAGCCTTTCTAGCGAAA	1	42	0	CCACAGCCTT	    0.962844	-112
ACACGCGGGCAAACAGCCGCCTCAAACGCG	1	124	0	AAACAGCCGC	    0.989618	-30
TGAGCATTGCACAGAGCAGCACCTTCCCAT	3	76	0	ACAGAGCAGC	    0.987049	-65
AAAAAGTGTACCAGAGCCACTACACTG   	3	124	1	CCAGAGCCAC	    0.989335	-17
          **********

Masking position 3
Map Score:   3.34088

Number of sites scoring better than the average of aligned sites = 310
Number in coding regions = 274
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 5

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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