AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_pyro_reg_300.orf -o034_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	RPH00434	225	Pyrococcus_OT3
#2	RPH00433	33	Pyrococcus_OT3
#3	RPH00430	30	Pyrococcus_OT3

Motif number 1

AGAAAAGAAAAGGTGATGAAGA        	1	3	0	AGGTGATGAA	    0.991741	-223
AAAGGCTAATAGGTGAAGAAAAGAAAAGGT	1	19	0	AGGTGAAGAA	    0.984372	-207
AAAAGACTTTCGGTAATAGTACAATCTAAA	1	60	1	CGGTAATAGT	    0.925828	-166
TACATATATTCGGCGATCAACGATTTTAGA	1	84	0	CGGCGATCAA	    0.942033	-142
GAATATATGTAGGTAATGATAGCATTTGAC	1	103	1	AGGTAATGAT	    0.969751	-123
ATGTAGTTTTCGGTGGAGGTACTAAGACAT	1	143	0	CGGTGGAGGT	    0.884917	-83
AAGCTTAAGGGGGCAAAAAAG         	1	215	1	GGGCAAAAAA	    0.835478	-11
CTCTCAAAAAGGGTAATAAAT         	3	2	0	GGGTAATAAA	    0.951935	-29
CCTTTTTGAGAGGTGATGGAT         	3	20	1	AGGTGATGGA	    0.990004	-11
          **********

Masking position 3
Map Score:   10.7774

Number of sites scoring better than the average of aligned sites = 658
Number in coding regions = 587
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 2

TTAGCCTTTCAACCCTTTATAAAAGACTTTC	1	40	1	AACCCTTATA	    0.990141	-186
AATGCTATCATTACCTACATATATTCGGCGA	1	98	0	TTACCTCATA	    0.950015	-128
ACCTCCACCGAAAACTACATAAATCTAACTT	1	153	1	AAAACTCATA	    0.964782	-73
ATCTAACTTAAAAACTCTAGATTGAACTCAG	1	175	1	AAAACTTAGA	    0.874696	-51
   TTTTCTTAAACCTTTTTATATGGAGGGA	2	8	1	AAACCTTTTA	    0.973086	-26
      AGGTATCCCTCCATATAAAAAGGTT	2	19	0	ATCCCTCATA	    0.981398	-15
    ATTTATTACCCTTTTTGAGAGGTGATG	3	7	1	TACCCTTTTG	    0.853969	-24
          ****** ****

Masking position 6
Map Score:   4.35028

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 404
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

TCAACGATTTTAGATTGTACTATTACCGAA	1	68	0	TAGATTGTAC	    0.993622	-158
TTAAAAACTCTAGATTGAACTCAGATTAAT	1	182	1	TAGATTGAAC	    0.993622	-44
          **********

Masking position 5
Map Score:   0.339012

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 4

          **********

No masking
Map Score:   3.08538e-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 5

          **********

No masking
Map Score:   3.08538e-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:   3.08538e-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