AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___aquae_reg_100.orf -o190_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	RAA01047	85	Aquifex_aeolicus
#2	RAA01049	20	Aquifex_aeolicus
#3	RAA00481	105	Aquifex_aeolicus

Motif number 1

CTGTCTTATGAATAATTTTCGCCCGGCTAT	1	17	1	AATAATTTTC	    0.987233	-69
ACGGACAATCAAAAATTTTCTTGAAGAGAG	1	50	1	AAAAATTTTC	    0.900446	-36
TGAAGAGAGGTAGAATTCTCAAATC     	1	71	1	TAGAATTCTC	    0.855051	-15
  TCGTGTTAAATTATATTCTC        	2	3	0	AATTATATTC	    0.948549	-18
ACCTCTTTTCATGAATTTTCTACTTCCAAA	3	22	1	ATGAATTTTC	    0.986162	-84
AGGATTTAGGATTTATTTTCGGGGCAACAC	3	62	1	ATTTATTTTC	    0.975929	-44
          **********

Masking position 5
Map Score:   8.60331

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 91
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

AAAATTTTCTTGAAGAGAGGTAGAATTCTC	1	61	1	TGAAGAGAGG	    0.998591	-25
AGAAAATTCATGAAAAGAGGTGTTATAATA	3	13	0	TGAAAAGAGG	    0.996167	-93
GTTTACCTCCTGAAGGGTGGAGTGTTGCCC	3	83	0	TGAAGGGTGG	    0.997049	-23
          **********

Masking position 4
Map Score:   5.09002

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 21
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

TTTTCTTGAAGAGAGGTAGAATTCTCAAAT	1	65	1	GAGAGGTAGA	    0.993459	-21
CACAGGAATTTGGAAGTAGAAAATTCATGA	3	30	0	TGGAAGTAGA	    0.990285	-76
TCCACCCTTCAGGAGGTAAACCAA      	3	92	1	AGGAGGTAAA	    0.990339	-14
          **********

Masking position 4
Map Score:   0.767972

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 40
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

AAATTATTCATAAGACAGCATTTT      	1	5	0	TAAGACAGCA	    0.951714	-81
TTCGCCCGGCTATGACACGGACAATCAAAA	1	34	1	TATGACACGG	    0.991167	-52
GAGAATATAATTTAACACGA          	2	11	1	TTTAACACGA	    0.971557	-10
     GTTATTATAACACCTCTTTTCATGA	3	6	1	TATAACACCT	    0.979978	-100
          **********

Masking position 5
Map Score:   0.153793

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 33
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

TGTCTTATGAATAATTTTCGCCCGGCTATG	1	18	1	ATAATTTTCG	    0.951246	-68
TCTCTTCAAGAAAATTTTTGATTGTCCGTG	1	49	0	AAAATTTTTG	    0.928775	-37
ACCTCTTTTCATGAATTTTCTACTTCCAAA	3	22	1	ATGAATTTTC	    0.912672	-84
ATCCTTCCACAGGAATTTGGAAGTAGAAAA	3	37	0	AGGAATTTGG	    0.988452	-69
TTCCTGTGGAAGGATTTAGGATTTATTTTC	3	52	1	AGGATTTAGG	    0.974649	-54
          **********

Masking position 6
Map Score:   0.837232

Number of sites scoring better than the average of aligned sites = 296
Number in coding regions = 278
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 6

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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 8

          **********

No masking
Map Score:   -7.57276e-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