AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_aquae_reg_100.orf -o216_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

Purged sequences:
RAA00640	24	Aquifex_aeolicus

Input sequences:
#1	RAA01073	81	Aquifex_aeolicus
#2	RAA00021	55	Aquifex_aeolicus
#3	RAA00585	38	Aquifex_aeolicus
#4	RAA00469	66	Aquifex_aeolicus
#5	RAA00639	40	Aquifex_aeolicus
#6	RAA01727	45	Aquifex_aeolicus

Motif number 1

       AAAGATAAATATTAAAGGTTTTT	1	4	1	GATAAATATT	    0.872341	-78
ATTTTAACACAATAAGTTTACCACAAAAAA	1	29	0	AATAAGTTTA	    0.961346	-53
TTTTCGGACGAATAATTTTAACACAATAAG	1	43	0	AATAATTTTA	    0.960618	-39
TTATTTAAGGGATAAAATTACAAATTG   	2	39	1	GATAAAATTA	    0.976663	-17
  TTAACTTTAATAAATTTTTAGAGTTAGG	3	9	1	AATAAATTTT	    0.972631	-30
ACAGATCAGAAATAAAATAAATTCTTTTGA	4	44	1	AATAAAATAA	    0.939871	-23
      AAGAAATAAAATATCACTTCTAAA	5	27	0	AATAAAATAT	    0.906916	-14
   TTTATGAGATAATTTTATATTCCATTT	6	8	1	GATAATTTTA	     0.96624	-38
          **********

Masking position 5
Map Score:   10.0125

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 101
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 2

AATAAGTTTACCACAAAAAACCTTTAATAT	1	19	0	CCACAAAAAA	    0.963926	-63
TAAAATTATTCGTCCGAAAATTTACGGAGG	1	53	1	CGTCCGAAAA	    0.974662	-29
 TTTCCCGTACCTCCGTAAATTTTCGGACG	1	63	0	CCTCCGTAAA	    0.972032	-19
TTACCTCCTAACTCTAAAAATTTATTAAAG	3	15	0	ACTCTAAAAA	    0.960758	-24
         CACTCAAAAGAATTTATTTTA	4	56	0	ACTCAAAAGA	    0.976943	-11
TAAAATATCACTTCTAAAGAGAAAGTTTTC	5	15	0	CTTCTAAAGA	    0.943589	-26
 TTCTCTCCTCCTCAGAAGAAATGGAATAT	6	27	0	CCTCAGAAGA	    0.994676	-19
          **********

Masking position 8
Map Score:   7.74126

Number of sites scoring better than the average of aligned sites = 418
Number in coding regions = 390
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

        TTTCCCGTACCTCCGTAAATTTTC	1	68	0	TCCTACCTCC	    0.997581	-14
     ACTATTATTATACCGACCGGTCGGTAT	2	6	1	TATTACCGAC	    0.985575	-50
ATCCCTTAAATAACATACCGACCGGTCGGTAT	2	20	0	TACTACCGAC	    0.996329	-36
          TCTCTTACCTCCTAACTCTAAA	3	27	0	TCCTACCTCC	    0.997624	-12
          ** * *******

Masking position 6
Map Score:   3.64306

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 43
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

ACCACAAAAAACCTTTAATATTTATCTTT 	1	10	0	ACCTTTAATA	    0.986335	-72
CAATAAGTTTACCACAAAAAACCTTTAATA	1	20	0	ACCACAAAAA	    0.843866	-62
TCGGACGAATAATTTTAACACAATAAGTTT	1	40	0	AATTTTAACA	    0.726695	-42
GTAATTTTATCCCTTAAATAACATACCGAC	2	30	0	CCCTTAAATA	    0.906198	-26
        TTAACTTTAATAAATTTTTAGA	3	3	1	AACTTTAATA	    0.972172	-36
CTTACCTCCTAACTCTAAAAATTTATTAAA	3	16	0	AACTCTAAAA	    0.966639	-23
CTGAAGAAATACCTGTAAAATCAAATT   	4	8	0	ACCTGTAAAA	    0.970165	-59
          **********

Masking position 7
Map Score:   4.8062

Number of sites scoring better than the average of aligned sites = 388
Number in coding regions = 356
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 5

          **********

No masking
Map Score:   -5.44113e-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:   -5.44113e-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:   -5.44113e-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