AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_mjan_reg_300.orf -o175_mjan_300.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:
RMJ04314	50	M_jannaschii_chromosome

Input sequences:
#1	RMJ13159	50	M_jannaschii_chromosome
#2	RMJ01108	145	M_jannaschii_chromosome

Motif number 1

TTTAAAAGTTAATGTTTATTTATTGTATAT	1	23	0	AATGTTTATT	    0.986767	-28
     CAATAAATTTTAAAAGTTAATGTTT	1	36	0	AATTTTAAAA	    0.901761	-15
TCTCTTTTTTAGTTTTTATTAAATAAAATA	2	15	1	AGTTTTTATT	    0.932856	-131
AAACCAAATAAATGCTTATTTTATTTAATA	2	31	0	AATGCTTATT	    0.971028	-115
TTCCTATATCAATGATAATTGTAATTATAA	2	59	1	AATGATAATT	    0.602941	-87
TGATAATCGTAATTATTATAATTACAATTA	2	74	0	AATTATTATA	    0.917357	-72
CTTACCACAAAATGATAATCGTAATTATTA	2	86	0	AATGATAATC	    0.881116	-60
TTTTTAATCTACTGTTTAAATAACTTACCA	2	109	0	ACTGTTTAAA	    0.902049	-37
CACCTATCAAAATTTTTAATCTACTGTTTA	2	121	0	AATTTTTAAT	    0.964158	-25
          **********

Masking position 6
Map Score:   12.0305

Number of sites scoring better than the average of aligned sites = 917
Number in coding regions = 674
Number in noncoding regions = 243
Number of orfs with sites within 600 bp upstream = 242
Fraction of orfs with sites within 600 bp upstream = 0.0388693


Motif number 2

ATGTTTATTTATTGTATATAGGGTGATTTT	1	12	0	ATTGTATATA	    0.982321	-39
ATAAATGCTTATTTTATTTAATAAAAACTA	2	24	0	ATTTTATTTA	     0.97249	-122
ATCAATGATAATTGTAATTATAATAATTAC	2	66	1	ATTGTAATTA	    0.992928	-80
CAAAATGATAATCGTAATTATTATAATTAC	2	79	0	ATCGTAATTA	     0.98801	-67
          **********

Masking position 5
Map Score:   5.14294

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 55
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

ACCCTATATACAATAAATAAACATTAACTT	1	18	1	CAATAAATAA	    0.926303	-33
ATTTAATAAAAACTAAAAAAGAGAAATA  	2	9	0	AACTAAAAAA	    0.976454	-137
TTTTAGTTTTTATTAAATAAAATAAGCATT	2	21	1	TATTAAATAA	    0.937191	-125
TGATATAGGAAACCAAATAAATGCTTATTT	2	40	0	AACCAAATAA	     0.98465	-106
TTAAATAACTTACCACAAAATGATAATCGT	2	94	0	TACCACAAAA	    0.952756	-52
          **********

Masking position 5
Map Score:   2.53585

Number of sites scoring better than the average of aligned sites = 438
Number in coding regions = 345
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 4

AAGTTAATGTTTATTTATTGTATATAGGGT	1	18	0	TTATTTATTG	    0.962022	-33
ATAAATTTTAAAAGTTAATGTTTATTTATT	1	29	0	AAAGTTAATG	    0.932733	-22
TTAACTTTTAAAATTTATTG          	1	41	1	AAATTTATTG	    0.975236	-10
AATAAATGCTTATTTTATTTAATAAAAACT	2	25	0	TATTTTATTT	    0.893565	-121
CATTTTGTGGTAAGTTATTTAAACAGTAGA	2	102	1	TAAGTTATTT	    0.966102	-44
TCAAAATTTTTAATCTACTGTTTAAATAAC	2	115	0	TAATCTACTG	    0.944186	-31
          **********

Masking position 6
Map Score:   4.78073

Number of sites scoring better than the average of aligned sites = 800
Number in coding regions = 689
Number in noncoding regions = 111
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 5

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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