AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_pyro_reg_100.orf -o060_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	RPH00271	204	Pyrococcus_OT3
#2	RPH00072	223	Pyrococcus_OT3

Motif number 1

TAGAAAAAGGACAAAACTTAAAA         	1	2	0	AAAAACTAAA	    0.926073	-203
ACCTTCACTGACAATTTGGAAAAGCTTAGAAA	1	28	0	AAATTTGAAA	    0.896897	-177
GAATCTAATGAAGAAATATCAATTAAACAAGA	1	121	1	AGAAATTCAA	    0.920396	-84
TTAAACAAGAAAAAAATAGAAAGATTTATTAT	1	143	1	AAAAATGAAA	     0.97656	-62
CTAACTAGTGCGAAAATATAAATAAAGCTTAT	2	25	1	CAAAATTAAA	    0.932755	-199
GAGATCAAATTGAAAATTTAAAAGTGGATAAG	2	52	0	TAAAATTAAA	    0.903178	-172
ATTGAAATAAAGAATTTCTCAAAAATTGTATA	2	88	0	AAATTTTCAA	    0.928516	-136
TTTTAATAACATAAAATTGAAATAAAGAATTT	2	103	0	AAAAATGAAA	    0.976551	-121
ATGTTATTAAAAATTATCTCAAATTGTTTTAT	2	123	1	AATTATTCAA	     0.86931	-101
TTAATCCTAAAAAATATGTCAAAAAATATATA	2	170	1	AAATATTCAA	    0.981253	-54
AATATGTCAAAAAATATATAAAAATCGTGAGC	2	182	1	AAATATTAAA	    0.982442	-42
          * ***** ****

Masking position 11
Map Score:   13.1434

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 119
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 2

CTAAACCTTCACTGACAATTTGGAAAAGCT	1	34	0	ACTGACAATT	     0.86006	-171
GTTGAAATGAGTATAAAATTCAAGAATCTA	1	98	1	GTATAAAATT	    0.885184	-107
CTGAGATCAAATTGAAAATTTAAAAGTGGA	2	56	0	ATTGAAAATT	    0.956895	-168
TGATCTCAGAATATACAATTTTTGAGAAAT	2	77	1	ATATACAATT	    0.949191	-147
TAAAATTGAAATAAAGAATTTCTCAAAAAT	2	94	0	ATAAAGAATT	    0.886331	-130
ATTTTTAATAACATAAAATTGAAATAAAGA	2	107	0	ACATAAAATT	    0.941618	-117
ATTTTATGTTATTAAAAATTATCTCAAATT	2	118	1	ATTAAAAATT	    0.953628	-106
ATTTTTTAGGATTAAAAATTCCTATTAGGA	2	155	0	ATTAAAAATT	    0.953628	-69
GTCAAAAAATATATAAAAATCGTGAGCTTA	2	187	1	ATATAAAAAT	    0.838562	-37
          **********

Masking position 5
Map Score:   10.1906

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 63
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

CTTGTAGGTGATATATTGAATAAATGACAGCTAAAC	1	58	0	ATTATGAATG	    0.984515	-147
TATCACCTACAAGTATAGTTGAAATGAGTATAAAAT	1	81	1	AATAAGAATG	    0.984501	-124
AAATTCAAGAATCTAATGAAGAAATATCAATTAAAC	1	113	1	ATTATGAATA	    0.955525	-92
AAAGGAGGTTAACTCCAGGGGGAATGAACATGGGTG	1	179	1	AATCAGAATG	    0.981359	-26
CCCCGAACCTAACTAGTGCGAAAATATAAATAAAGC	2	17	1	AATATGAATA	    0.975596	-207
AAATATATAAAAATCGTGAGCTTATGAATTTAAGGG	2	193	1	AATCTGTATG	    0.960417	-31
          ** ** **    ****

Masking position 4
Map Score:   1.09023

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 22
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   5.42445e-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 5

          **********

No masking
Map Score:   5.42445e-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:   5.42445e-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