AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_mjan_reg_100.orf -o182_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:
RMJ07423	27	M_jannaschii_chromosome

Input sequences:
#1	RMJ04822	125	M_jannaschii_chromosome
#2	RMJ08451	53	M_jannaschii_chromosome
#3	RMJ14035	95	M_jannaschii_chromosome

Motif number 1

AATATGCGTAATAAAAAATTATTAAGT   	1	8	0	ATAAAAAATT	    0.908191	-118
ATAATTGGAGATTAAAAAAAGGAATATGCG	1	30	0	ATTAAAAAAA	    0.913789	-96
TCTAAAAATCATATAAATATTTTATCGAGG	1	63	0	ATATAAATAT	    0.923123	-63
AATATTTAAAATCTAAAAATCATATAAATA	1	74	0	ATCTAAAAAT	    0.974701	-52
 GTTATCACAATATAAAATTATCTTTTTGG	1	107	0	ATATAAAATT	    0.961188	-19
CTAAATAGAAATAACAAAAATCCTTTGAAG	2	19	1	ATAACAAAAA	    0.863354	-35
ATTTAAAAAAGTATAAAAAATGTGAATGCC	3	12	0	GTATAAAAAA	     0.96999	-84
TACATATAACATTTAAAAAAGTATAAAAAA	3	22	0	ATTTAAAAAA	    0.962957	-74
TATGTAGTTTGTATAAAGATAAATATCTAA	3	46	1	GTATAAAGAT	    0.888785	-50
AAAGATAAATATCTAAAAATAACATAAAAA	3	60	1	ATCTAAAAAT	    0.974701	-36
TCTAAAAATAACATAAAAAACTTTTTGGTG	3	71	1	ACATAAAAAA	    0.940694	-25
          **********

Masking position 6
Map Score:   16.3792

Number of sites scoring better than the average of aligned sites = 1719
Number in coding regions = 1271
Number in noncoding regions = 448
Number of orfs with sites within 600 bp upstream = 372
Fraction of orfs with sites within 600 bp upstream = 0.0597494


Motif number 2

ATAAAATATTTATATGATTTTTAGATTTTA	1	68	1	TATATGATTT	    0.939355	-58
TTGTTATTTCTATTTAGTTTAATTT     	2	6	0	TATTTAGTTT	    0.952091	-48
TCAAAGGATTTTTGTTATTTCTATTTAGTT	2	17	0	TTTGTTATTT	    0.956998	-37
TTAAATGTTATATGTAGTTTGTATAAAGAT	3	36	1	TATGTAGTTT	    0.987502	-60
AAAAGTTTTTTATGTTATTTTTAGATATTT	3	66	0	TATGTTATTT	    0.986525	-30
          **********

Masking position 5
Map Score:   4.37787

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 98
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 3

        ACTTAATAATTTTTTATTACGC	1	3	1	TTAATAATTT	    0.785072	-123
TTTTTAATCTCCAATTATTTTCCTCGATAA	1	42	1	CCAATTATTT	    0.965048	-84
TAAAAATCATATAAATATTTTATCGAGGAA	1	61	0	ATAAATATTT	    0.853563	-65
ATCTTTTTGGCTGAATATTTAAAATCTAAA	1	87	0	CTGAATATTT	      0.9231	-39
AAATATTCAGCCAAAAAGATAATTTTATAT	1	97	1	CCAAAAAGAT	    0.940813	-29
TTTGTTATTTCTATTTAGTTTAATTT    	2	7	0	CTATTTAGTT	    0.831862	-47
AGATAAATATCTAAAAATAACATAAAAAAC	3	62	1	CTAAAAATAA	    0.747514	-34
   TATTTCACCAAAAAGTTTTTTATGTTA	3	79	0	CCAAAAAGTT	    0.977488	-17
          **********

Masking position 7
Map Score:   3.1043

Number of sites scoring better than the average of aligned sites = 2049
Number in coding regions = 1656
Number in noncoding regions = 393
Number of orfs with sites within 600 bp upstream = 319
Fraction of orfs with sites within 600 bp upstream = 0.0512367


Motif number 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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