AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i049_Indolepyruvate_Oxidoreductase_pyro_reg_300.orf -o049_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00359	102	Pyrococcus_OT3
#2	RPH00357	40	Pyrococcus_OT3
#3	RPH00356	20	Pyrococcus_OT3
#4	RPH00355	200	Pyrococcus_OT3

Motif number 1

  TCCTCCCTCTTTTAAATTTTGATCATCA	1	9	1	CTTTTAAATT	     0.99388	-94
CTTTAGTGGACTGTAAAATTCATTGATGAT	1	32	0	CTGTAAAATT	    0.946483	-71
         ACTTTTTAATTCTTTTCTTCA	2	2	1	CTTTTTAATT	    0.979495	-39
TTGCTAAAAATTTTTAAATTTTGACCGGTA	4	65	1	TTTTTAAATT	    0.984097	-136
ACTTAAAAAACTTTTAAATTTATACCGGTC	4	87	0	CTTTTAAATT	     0.99388	-114
ATTTAAAAGTTTTTTAAGTTCATAATATCA	4	98	1	TTTTTAAGTT	    0.960306	-103
          **********

Masking position 4
Map Score:   11.2781

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 25
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

TCCCTCTTTTAAATTTTGATCATCAATGAAT	1	14	1	AAATTTTGAC	    0.994097	-89
AGGGGGAGAAATGTATTTATCGGTGGTTATT	4	23	0	ATGTATTTAC	    0.890357	-178
CAAAATTTAAAAATTTTTAGCAACACAATTG	4	57	0	AAATTTTTAC	     0.99288	-144
AAAAATTTTTAAATTTTGACCGGTATAAATT	4	70	1	AAATTTTGAC	    0.994097	-131
AAAAACTTTTAAATTTATACCGGTCAAAATT	4	81	0	AAATTTATAC	    0.966612	-120
TATTTTTGTGATATTATGAACTTAAAAAACT	4	105	0	ATATTATGAC	    0.938306	-96
TTAAGCCAAAAAATATTTAACTAGATAAACT	4	138	1	AAATATTTAC	    0.983783	-63
          ********* *

Masking position 9
Map Score:   11.0259

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 32
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          TCCTCCCTCTTTTAAATTTT	1	1	1	TCCTCCCTCT	    0.989778	-102
CTGATGCTTATACTCCTACCTTATAAGACT	1	69	0	TACTCCTACC	    0.984276	-34
         TTTCTTCCACCAATCTGATGC	1	92	0	TTCTTCCACC	    0.979448	-11
      ATTCTCCTCCTCCCCTACTG    	3	7	0	TCCTCCTCCC	    0.996228	-14
ATAAATACATTTCTCCCCCTCACCAATTGT	4	34	1	TTCTCCCCCT	    0.994177	-167
          **********

Masking position 4
Map Score:   6.53579

Number of sites scoring better than the average of aligned sites = 269
Number in coding regions = 236
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

CAGTCCACTAAAGCCTAAGAAGTCTTATAA	1	49	1	AAGCCTAAGA	     0.99486	-54
GTAGGAGTATAAGCATCAGATTGGTGGAAG	1	80	1	AAGCATCAGA	    0.986339	-23
ATCTGAAGAAAAGAATTAAAAAGT      	2	5	0	AAGAATTAAA	    0.879603	-36
AAAATAATTTAAGCCAAAAAATATTTAACT	4	130	1	AAGCCAAAAA	    0.963113	-71
AGATAAACTCAAGCCTTAGAATAGGGAATT	4	160	1	AAGCCTTAGA	     0.99486	-41
          **********

Masking position 8
Map Score:   5.19698

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 144
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

AATTTTACAGTCCACTAAAGCCTAAGAAGT	1	42	1	TCCACTAAAG	    0.992662	-61
      TTAATCACCTAAAGTTATCTGAAG	2	27	0	TCACCTAAAG	    0.989348	-14
ATTCTCCTCCTCCCCTACTG          	3	1	0	TCCCCTACTG	    0.988461	-20
AATAGGGAATTCCGCTGAAGGGTGTTGTAG	4	179	1	TCCGCTGAAG	    0.991569	-22
          **********

Masking position 6
Map Score:   3.0398

Number of sites scoring better than the average of aligned sites = 92
Number in coding regions = 86
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 6

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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 8

          **********

No masking
Map Score:   -2.53363e-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