AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__pyro_reg_300.orf -o056_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	RPH01583	215	Pyrococcus_OT3
#2	RPH01584	238	Pyrococcus_OT3

Motif number 1

ACTAAGATTTTCGAAAAAAATTGTGAACATTAT	1	61	0	TCAAAAATTG	    0.972107	-155
CTTAGTATTATATAGAAAAATTTTCTAAAATTT	1	88	1	TAAGAAATTT	    0.970277	-128
AATTTTAAGATCTTAAAAATTTTAGAAAATTTT	1	104	0	TCTAAAATTT	    0.937598	-112
TCTTGGATTATCGAATAAAATTTTAAGATCTTA	1	122	0	TCAAAAATTT	    0.989617	-94
TATTCGATAATCCAAGATATTTCTCGAAAATTT	1	138	1	TCAAATATTC	    0.936417	-78
TGAACCTAGGTATATAAAATTTTCGAGAAATAT	1	154	0	TAATAAATTT	    0.954753	-62
TTTAAAAAACTAAATCAAACTTTCAATC     	2	6	0	TAATAAATTT	    0.954758	-233
AGATCACTCCTAGAGCAAAGTTCATGCTATATA	2	52	0	TAAGAAATTC	    0.969695	-187
CAATTACCAATCTAAGAAAGTTCAACGTCAATG	2	157	0	TCAAAAATTC	    0.989409	-82
          ** ** *** ***

Masking position 7
Map Score:   11.2311

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 75
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

AATTGTGAACATTATAAAATAGGAGTACAA	1	46	0	ATTATAAAAT	    0.697642	-170
TCACAATTTTTTTCGAAAATCTTAGTATTA	1	68	1	TTTCGAAAAT	    0.985029	-148
AGAAAATTTTTCTATATAATACTAAGATTT	1	84	0	TCTATATAAT	    0.855306	-132
TCTTAAAAATTTTAGAAAATTTTTCTATAT	1	97	0	TTTAGAAAAT	    0.975945	-119
TTAAAATTTTATTCGATAATCCAAGATATT	1	129	1	ATTCGATAAT	    0.925837	-87
CCAAGATATTTCTCGAAAATTTTATATACC	1	149	1	TCTCGAAAAT	    0.982138	-67
          **********

Masking position 6
Map Score:   5.60617

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 87
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

TCGAAAATTTTATATACCTAGGTTCAAGAT	1	161	1	TATATACCTA	    0.945196	-55
          TATTTCCTTCCTTAATATTC	1	206	0	TATTTCCTTC	    0.964795	-10
AAGTTCATGCTATATACTTCCATAGCAGAT	2	38	0	TATATACTTC	    0.970195	-201
CTTAGATTGGTAATTGCCTCTGGTTTTTAC	2	174	1	TAATTGCCTC	    0.914024	-65
TTGCCTCTGGTTTTTACTTACCCCTTATTA	2	187	1	TTTTTACTTA	    0.835258	-52
TACCCCTTATTATTTACCTCAACTTAATTC	2	205	1	TATTTACCTC	    0.989643	-34
          **********

Masking position 5
Map Score:   4.33192

Number of sites scoring better than the average of aligned sites = 210
Number in coding regions = 199
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

TTTTCTATATAATACTAAGATTTTCGAAAA	1	77	0	AATACTAAGA	    0.958641	-139
ATTTTCTAAAATTTTTAAGATCTTAAAATT	1	107	1	ATTTTTAAGA	    0.728655	-109
TATCGAATAAAATTTTAAGATCTTAAAAAT	1	117	0	AATTTTAAGA	    0.937439	-99
ACCTAGGTTCAAGATGGAGGTGTGGGTGAT	1	176	1	AAGATGGAGG	    0.790661	-40
GTGGGTGATGAATATTAAGGAAGGAAATA 	1	197	1	AATATTAAGG	    0.977947	-19
AGCCGCACTGAAGGCTAAGATCACTCCTAG	2	72	0	AAGGCTAAGA	    0.915835	-167
CCAAGGTATCAATGAGAAGGGTAAGTCCAT	2	130	1	AATGAGAAGG	    0.917749	-109
AGTTGAGGTAAATAATAAGGGGTAAGTAAA	2	199	0	AATAATAAGG	    0.959624	-40
          **********

Masking position 8
Map Score:   4.32277

Number of sites scoring better than the average of aligned sites = 527
Number in coding regions = 478
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 5

TTATGGACAAAAGTAAAGTGTA        	1	3	0	AAGTAAAGTG	    0.925971	-213
TCCTAGAGCAAAGTTCATGCTATATACTTC	2	48	0	AAGTTCATGC	    0.913204	-191
GATAACACCGAAGTTAGGGCCCATGTGAAA	2	101	0	AAGTTAGGGC	    0.976833	-138
ACTTGGAATTAAGTTGAGGTAAATAATAAG	2	210	0	AAGTTGAGGT	    0.952619	-29
ACTTAATTCCAAGTAAAGGGATA       	2	226	1	AAGTAAAGGG	     0.98492	-13
          **********

Masking position 4
Map Score:   0.057466

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 292
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 6

          **********

No masking
Map Score:   -4.16788e-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:   -4.16788e-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:   -4.16788e-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