AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -igcvA_pyro_opreg_100.orf -g0.419 -x5 
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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH1317	58	138aa long hypothetical glycine cleavage system H protein
#2	PH1995	61	449aa long hypothetical glycine dehydrogenase subunit 1
#3	PH1996	150	225aa long hypothetical protein

Motif number 1

TTTACAGTAAAAAGGCTGGGGAGTTAACA       	1	4	0	AAAGGCTGGA	    0.996976	-55
TAAAGATTTTAAAGGTTGCTGCTAAATTGGAAG   	1	36	1	AAAGGTTGGA	    0.995429	-23
CAACCTTAGGAAAGGTATTTATTATAATCTTACTAA	2	15	1	AAAGGTATAA	     0.88001	-47
AAAGCGTAATAAAGGTTTCGGTGATAAA        	3	3	0	AAAGGTTTGA	    0.990605	-148
GGCCCTCAGAAAAGGCTTTAAATTGAAAGCGTAATA	3	28	0	AAAGGCTTAA	    0.974537	-123
AGCCTTTTCTGAGGGCCGGTGGCCTAGCCTGGATGG	3	47	1	GAGGGCCGGA	    0.990484	-104
CTTCGGCTCCGAAGGCCGACGCCCCATCCAGGCTAG	3	70	0	GAAGGCCGGA	    0.997302	-81
CTTCGGAGCCGAAGGTCCCGGGTTCAAATCCCGGCC	3	92	1	GAAGGTCCGA	    0.986527	-59
          ********  *    *

Masking position 2
Map Score:   11.9782

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 217
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

      TGTTAACTCCCCAGCCTTTTTACTG	1	5	1	AACTCCCCAC	    0.992695	-54
       TGCAAATCCCCGACTAAAAATTTA	2	48	0	AAATCCCCGC	    0.992695	-14
ATCCAGGCTAGGCCACCGGCCCTCAGAAAAG	3	50	0	GGCCACCGGC	    0.912668	-101
TCCGAAGGCCGACGCCCCATCCAGGCTAGGC	3	68	0	GACGCCCCAC	    0.977164	-83
GCCGGGATTTGAACCCGGGACCTTCGGCTCC	3	96	0	GAACCCGGGC	    0.925935	-55
TCCCGGGTTCAAATCCCGGCCGGCCCGCCAA	3	107	1	AAATCCCGGC	    0.990391	-44
AATCCCGGCCGGCCCGCCAACAATAACTTTA	3	118	1	GGCCCGCCAC	    0.978846	-33
          ********* *

Masking position 11
Map Score:   8.06287

Number of sites scoring better than the average of aligned sites = 229
Number in coding regions = 158
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

GTAAAAAGGCTGGGGAGTTAACA       	1	4	0	TGGGGAGTTA	    0.990791	-55
AATTTTTAGTCGGGGATTTGCA        	2	50	1	CGGGGATTTG	    0.997658	-12
CTAGCCTGGATGGGGCGTCGGCCTTCGGAG	3	70	1	TGGGGCGTCG	    0.992519	-81
GGCGGGCCGGCCGGGATTTGAACCCGGGAC	3	106	0	CCGGGATTTG	    0.993767	-45
          **********

Masking position 8
Map Score:   3.99799

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 50
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

         CTTCCAATTTAGCAGCAACCT	1	48	0	TTCCAATTTA	     0.98226	-11
AATCCCCGACTAAAAATTTAGTAAGATTAT	2	38	0	TAAAAATTTA	    0.865124	-24
TTTATTACGCTTTCAATTTAAAGCCTTTTC	3	26	1	TTTCAATTTA	    0.985023	-125
TTGTGGAAGTTTTAAAGTTATTGTTGGCGG	3	131	0	TTTAAAGTTA	    0.961442	-20
          **********

Masking position 5
Map Score:   1.39332

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 51
Number in noncoding regions = 23
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:   -1.9652e-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 6

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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