AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_aquae_reg_100.orf -o117_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA00348	137	Aquifex_aeolicus
#2	RAA00349	69	Aquifex_aeolicus
#3	RAA00355	36	Aquifex_aeolicus
#4	RAA00486	113	Aquifex_aeolicus
#5	RAA00837	118	Aquifex_aeolicus

Motif number 1

      AAGGAAGTATTTTAAAGGTGGACTAA	1	5	1	AAGTTTTAAA	     0.98707	-133
AAGGTGGACTAAGAATTTTTAAGAAATAAAAT	1	25	1	AAGTTTTTAA	    0.931884	-113
CCTCCCTTGAAAGTTTTTTACACTTTTTATTT	1	53	0	AAGTTTTACA	    0.991809	-85
CAGCCTCAACAAAGGTTTTACC          	1	126	1	AAATTTTACC	    0.986812	-12
AAAAATCAAAAAGTGTTTTAAATTAACTTGAC	4	60	0	AAGTTTTAAA	     0.98707	-54
      ACTTAAAGATTTTACCTCTAGAGATT	4	98	0	AAATTTTACC	    0.986812	-16
AAAAGGGCGTATATATTTTAAAGAC       	5	4	0	ATATTTTAAA	    0.896105	-115
       AGTAAAAATTTTACCGCTCGGAAAC	5	104	0	AAATTTTACC	    0.986812	-15
          ***  *******

Masking position 1
Map Score:   13.826

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 157
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

TGAAAGTTTTTTACACTTTTTATTTTATTTCTT	1	45	0	TTCCTTTTAT	    0.916705	-93
ATGAGTCAAGTTACTCAATCTTTCAGAAAAAGT	1	91	1	TTCCAATTTT	    0.885952	-47
 TCTGCTAGGTTGCACCCTTCTTTCTTTTTCCT	2	10	1	TTCCCCTCTT	    0.990473	-60
TTCTTTCTTTTTCCTCTTTTCTTTTAACCTTTA	2	28	1	TTCCTTTCTT	    0.995327	-42
CTCTTTTCTTTTAACCTTTATTTATATAGGATT	2	41	1	TTACTTTTTT	    0.886314	-29
TCGCCTTGATTTTGGCTTTCCTTATT       	3	21	1	TTGCTTTCTT	    0.972418	-16
ATGAATAAAATTACACTCTACTTTCGGAGGAGA	4	14	0	TTCCTCTCTT	    0.997049	-100
TAAATTAACTTGACACACTTCTTCAAAATGAAT	4	41	0	TGCCACTCTT	    0.966555	-73
TGGTGGAAATTTTCGCTCTACTTGTCACACTAT	5	63	1	TTCCTCTCTT	    0.997049	-56
          ** * **** ***

Masking position 9
Map Score:   13.5749

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 396
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

TTAGTCCACCTTTAAAATACTTCCTT     	1	6	0	TTTAAAAACT	    0.948397	-132
ATTTTATTTCTTAAAAATTCTTAGTCCACCT	1	26	0	TTAAAAATCT	    0.915515	-112
AAATAAAAAGTGTAAAAAACTTTCAAGGGAG	1	53	1	TGTAAAAACT	    0.972187	-85
TCAATCTTTCAGAAAAAGTCTCAGCCTCAAC	1	105	1	AGAAAAATCT	    0.899621	-33
          GGTAAAACCTTTGTTGAGGCT	1	127	0	GGTAAAACTT	    0.952307	-11
         GATAAAAATCCTATATAAATAA	2	58	0	ATAAAAACCT	    0.850584	-12
TTCTTCAAAATGAATAAAATTACACTCTACT	4	25	0	TGAATAAATT	    0.652641	-89
GTCAAGTTAATTTAAAACACTTTTTGATTTT	4	60	1	TTTAAAAACT	    0.948399	-54
TTTGATTTTTGTTATAAATCTCTAGAGGTAA	4	82	1	GTTATAATCT	    0.854463	-32
AATCTCTAGAGGTAAAATCTTTAAGT     	4	98	1	GGTAAAACTT	    0.952307	-16
GTTTCCGAGCGGTAAAATTTTTACT      	5	104	1	GGTAAAATTT	     0.94297	-15
          ******* ***

Masking position 6
Map Score:   11.2565

Number of sites scoring better than the average of aligned sites = 823
Number in coding regions = 752
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

AGGTGTGCCATGAGTCAAGTTACTCAATCT	1	82	1	TGAGTCAAGT	    0.994137	-56
TTTGAAGAAGTGTGTCAAGTTAATTTAAAA	4	47	1	TGTGTCAAGT	    0.996666	-67
GTATCTATAGTGTGACAAGTAGAGCGAAAA	5	72	0	TGTGACAAGT	    0.994137	-47
          **********

Masking position 7
Map Score:   4.07456

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 = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   5.92755e-14

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:   5.92755e-14

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:   5.92755e-14

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