AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_mixed11_pyro_reg_100.orf -o296_pyro_100.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	RPH00798	50	Pyrococcus_OT3
#2	RPH00797	116	Pyrococcus_OT3
#3	RPH01183	186	Pyrococcus_OT3

Motif number 1

CCTTCATTGGATAATTTCTCCAGTGATGAAAA      	1	29	1	ATATTCCAGG	    0.990656	-22
TCCTTACGGGATAAAATATCCATACTAGCAACTCTTAA	2	51	1	ATATTCCATG	    0.954291	-66
TATTCTATGAAACAATATTTAAGAGTTGCTAGTATGGA	2	69	0	AAAATTAAGG	     0.90776	-48
TGTTTCATAGAATAGAATCCCAGGGGTGAGAAAA    	2	93	1	AAAACCCAGG	    0.996863	-24
TAATACAACAAAGAAAAGCCCAGGAAAGCATTCTATAG	3	15	1	AAAACCCAGG	    0.996862	-172
TGAAATTATTATCAAAAATGCAGAGGAGAACTTAAGGT	3	60	0	ATAATGCAGG	    0.986208	-127
CAGTATGACCAATATATGTGAAGATAGGGCGTTTACCT	3	99	0	AAATTGAAGG	    0.933659	-88
CATACTGTTAAATAAAAATCCTTTTAAGAGGGCTTTAC	3	130	1	AAAATCCTTG	    0.922842	-57
GGGCTTTACAAACATCAACCCAGACCGGGGGGAGCATC	3	159	1	AAAACCCAGG	    0.996863	-28
          ** *  * *****    *

Masking position 4
Map Score:   11.5757

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 207
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

CATTGGATAATTTCTCCAGTGATGAAAA   	1	33	1	TTTCCCAGTG	    0.951066	-18
       TTTTCTCACCCCTGGGATTCTATT	2	103	0	TCTCCCCCTG	    0.991831	-14
CCTATAGAATGCTTTCCTGGGCTTTTCTTTG	3	23	0	GCTTCCTGGG	     0.98462	-164
TAAACCTTAAGTTCTCCTCTGCATTTTTGAT	3	57	1	GTTCCCTCTG	    0.995298	-130
AAGATAGGGCGTTTACCTTTGAAATTATTAT	3	86	0	GTTTCCTTTG	     0.94738	-101
       GATGCTCCCCCCGGTCTGGGTTGA	3	173	0	GCTCCCCCGG	    0.996654	-14
          **** ******

Masking position 3
Map Score:   6.01871

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 172
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

     CCCTTATCTTTTTAACTTCCTTCAT	1	6	1	ATCTTTTTAA	      0.9159	-45
TGGAGAAATTATCCAATGAAGGAAGTTAAA	1	21	0	ATCCAATGAA	    0.975817	-30
CCACTCCCAGTTCCAATGAATTTGTTAAGT	2	21	1	TTCCAATGAA	    0.894039	-96
CTGGGATTCTATTCTATGAAACAATATTTA	2	86	0	ATTCTATGAA	    0.945196	-31
ATAGGGCGTTTACCTTTGAAATTATTATCA	3	84	0	TACCTTTGAA	    0.927104	-103
TTAAAAGGATTTTTATTTAACAGTATGACC	3	127	0	TTTTATTTAA	    0.636825	-60
TTAAATAAAAATCCTTTTAAGAGGGCTTTA	3	137	1	ATCCTTTTAA	    0.975501	-50
          **********

Masking position 9
Map Score:   5.33251

Number of sites scoring better than the average of aligned sites = 668
Number in coding regions = 613
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

TGGATAATTTCTCCAGTGATGAAAA     	1	36	1	CTCCAGTGAT	    0.966523	-15
TGTTAAGTTCCTTACGGGATAAAATATCCA	2	43	1	CTTACGGGAT	    0.918807	-74
  TTTTCTCACCCCTGGGATTCTATTCTAT	2	99	0	CCCCTGGGAT	    0.992957	-18
ATAGAATGCTTTCCTGGGCTTTTCTTTGTT	3	21	0	TTCCTGGGCT	    0.962566	-166
GGAAAGCATTCTATAGGGATTAAACCTTAA	3	37	1	CTATAGGGAT	    0.883911	-150
   GATGCTCCCCCCGGTCTGGGTTGATGT	3	170	0	CCCCCGGTCT	    0.970982	-17
          **********

Masking position 10
Map Score:   2.09718

Number of sites scoring better than the average of aligned sites = 871
Number in coding regions = 813
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 5

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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:   -6.15168e-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