AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i159_glycolate_Oxidase_mjan_reg_100.orf -o159_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
RMJ06212	36	M_jannaschii_chromosome

Input sequences:
#1	RMJ04644	134	M_jannaschii_chromosome
#2	RMJ10046	23	M_jannaschii_chromosome
#3	RMJ15227	18	M_jannaschii_chromosome
#4	RMJ03004	83	M_jannaschii_chromosome
#5	RMJ05116	95	M_jannaschii_chromosome
#6	RMJ02377	221	M_jannaschii_chromosome

Motif number 1

AATTATATAAAAAATAGAAAAAAG         	1	2	0	AAAATAGAAA	     0.98163	-133
CAATATTCATAAAAATTATATAAAAAATAGAAA	1	15	0	AAAAATTAAA	    0.956346	-120
AAACTACCGAAAAATATATATTAGATATTAAAA	1	74	1	AAAATATATA	    0.936901	-61
GATATGAACAAAAATTTTTAATATCTAATATAT	1	89	0	AAAATTTATA	    0.956346	-46
CATATAGCCTAAAATGGTGACAAT         	1	121	1	AAAATGGAAA	    0.942669	-14
          AATAATTCAAAAAATGTGATAGT	2	1	1	AATAATTAAA	    0.930594	-23
ATATGACCTCATTATATAAAAAAGA        	4	3	0	ATTATATAAA	    0.689524	-81
TTTGAAGTATAAAATAGCAATAACCAATATGAC	4	29	0	AAAATAGAAA	     0.98163	-55
AATATAATTTAAAATTTAAAAAAATTTCTAAGT	4	60	1	AAAATTTAAA	     0.98427	-24
AAACTTAAGCAAAATTTTCAGTTCATCCATATT	5	15	0	AAAATTTATT	    0.779563	-81
ATTCTGCAATAATATTTAAACTTAAGCAAAATT	5	32	0	AATATTTATT	    0.683983	-64
ATTATTGCAGAATATATTCAAAAACAAACTTTA	5	52	1	AATATATAAA	    0.962902	-44
ATTTCCTCCGAAAATAGAAAGAAAATTTTGT  	6	9	0	AAAATAGAAA	     0.98163	-213
TTGAAAAAGAAATAATGAGAAAAAGATATTTCC	6	36	0	AATAATGAAA	    0.944118	-186
TTACATTTAAAATATTGTAATAAAGTATAATGG	6	117	1	AATATTGAAA	    0.979697	-105
ATAAAAACATAAAAATGACAAAAATAGTCCCAA	6	170	1	AAAAATGAAA	    0.965041	-52
          *******  * **

Masking position 4
Map Score:   26.2685

Number of sites scoring better than the average of aligned sites = 1694
Number in coding regions = 1258
Number in noncoding regions = 436
Number of orfs with sites within 600 bp upstream = 318
Fraction of orfs with sites within 600 bp upstream = 0.0510761


Motif number 2

ATTCATAAAAATTATATAAAAAATAGAAAAAA	1	12	0	ATATATAAAA	    0.720048	-123
TTATATAATTTTTATGAATATTGATGTATTTT	1	25	1	TTATGAAATT	      0.3129	-110
TCGGTAGTTTATCAAAAATAATCGTTAAAAAT	1	52	0	ATAAAAAAAT	    0.920967	-83
ACAAAAATTTTTAATATCTAATATATATTTTT	1	83	0	TTATATCAAT	    0.577821	-52
GCTATATGATATGAACAAAAATTTTTAATATC	1	97	0	ATAACAAAAT	    0.647861	-38
ATATGACCTCATTATATAAAAAAGA       	4	4	0	ATATATAAAA	    0.720048	-80
TATTTGAAGTATAAAATAGCAATAACCAATAT	4	32	0	ATAAATACAA	    0.669737	-52
TATTTTATACTTCAAATATAATTTAAAATTTA	4	46	1	TTAAATAAAT	    0.966516	-38
TAATTTAAAATTTAAAAAAATTTCTAAGTG  	4	64	1	TTAAAAAATT	    0.754698	-20
TTTGCTTAAGTTTAAATATTATTGCAGAATAT	5	35	1	TTAAATATAT	    0.673982	-61
GCAGAATATATTCAAAAACAAACTTTAATTAA	5	58	1	TTAAAAAAAA	     0.93736	-38
AAAATGGGAATTGAAAAAGAAATAATGAGAAA	6	47	0	TTAAAAAAAA	    0.937351	-175
CATTGTAGTATTTAAGTAAAATAATAAAATGG	6	72	0	TTAAGTAAAT	    0.929351	-150
ATTACAATATTTTAAATGTAAAGTTCGATAAT	6	106	0	TTAAATGAAA	    0.758441	-116
AAATATTGTAATAAAGTATAATGGAAAACGAT	6	126	1	ATAAGTAAAT	     0.88925	-96
GATATATAGTTTCAAATAAAAACATAAAAATG	6	155	1	TTAAATAAAA	    0.960636	-67
          ** ***** ***

Masking position 4
Map Score:   14.9931

Number of sites scoring better than the average of aligned sites = 2418
Number in coding regions = 1773
Number in noncoding regions = 645
Number of orfs with sites within 600 bp upstream = 463
Fraction of orfs with sites within 600 bp upstream = 0.0743656


Motif number 3

ATATTCATAAAAATTATATAAAAAATAGAA	1	16	0	AAATTATATA	    0.842372	-119
AATTTTTAATATCTAATATATATTTTTCGG	1	80	0	ATCTAATATA	    0.910817	-55
ATTTTAGGCTATATGATATGAACAAAAATT	1	106	0	ATATGATATG	    0.907054	-29
        ACTAATAATATACTATTA    	3	7	0	TAATAATATA	    0.802289	-12
AAATAGCAATAACCAATATGACCTCATTAT	4	21	0	AACCAATATG	    0.895404	-63
TATACTTCAAATATAATTTAAAATTTAAAA	4	51	1	ATATAATTTA	      0.7671	-33
          ATACAATATGGATGAACTGA	5	1	1	ATACAATATG	    0.934276	-95
TATTTAAGTAAAATAATAAAATGGGAATTG	6	66	0	AAATAATAAA	    0.802289	-156
GTATAATGGAAAACGATATATAGTTTCAAA	6	141	1	AAACGATATA	    0.923214	-81
          **********

Masking position 6
Map Score:   3.98263

Number of sites scoring better than the average of aligned sites = 445
Number in coding regions = 325
Number in noncoding regions = 120
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 4

          **********

No masking
Map Score:   8.76972e-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:   8.76972e-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:   8.76972e-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