AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i015_Glycolysis_2_mjan_reg_300.orf -o015_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

Input sequences:
#1	RMJ11403	170	M_jannaschii_chromosome

Motif number 1

TAATTTAATTACATTTATAGTTTTCATTTT	1	39	1	ACATTTATAG	     0.97843	-132
TCATTTTAAGACTTTCGCAGTATTATATAT	1	62	1	ACTTTCGCAG	    0.997586	-109
AAGATTTAGGACTTTCGTAGAAATAAATTT	1	134	0	ACTTTCGTAG	    0.998583	-37
          ACTTTCATAGTCAATATAAG	1	161	0	ACTTTCATAG	    0.997809	-10
          **********

Masking position 5
Map Score:   8.5001

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 14
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

AAATTTAGCTAAGTATAAATTATGTTTTAAT	1	12	1	AAGTATAATT	    0.946872	-159
AGTATAAATTATGTTTTAATTTAATTACATT	1	23	1	ATGTTTTATT	    0.932752	-148
ATTACATTTATAGTTTTCATTTTAAGACTTT	1	46	1	TAGTTTTATT	    0.969632	-125
ACTTTCGCAGTATTATATATTAAAAGGCATT	1	72	1	TATTATAATT	    0.949813	-99
AGATGCCCTTAAGCATAAATTTTCTTTAAAA	1	104	1	AAGCATAATT	    0.945156	-67
GAAAGTCCTAAATCTTATATTGACTATGAAA	1	148	1	AATCTTAATT	    0.867035	-23
          ******* ***

Masking position 6
Map Score:   5.95378

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 178
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 3

AAAACTATAAATGTAATTAAATTAAAACAT	1	33	0	ATGTAATTAA	    0.912153	-138
AATACTGCGAAAGTCTTAAAATGAAAACTA	1	56	0	AAGTCTTAAA	    0.978964	-115
GGGCATCTAAATGCCTTTTAATATATAATA	1	82	0	ATGCCTTTTA	    0.969089	-89
AGGCATTTAGATGCCCTTAAGCATAAATTT	1	96	1	ATGCCCTTAA	    0.993771	-75
ATTTCTACGAAAGTCCTAAATCTTATATTG	1	140	1	AAGTCCTAAA	    0.986299	-31
          **********

Masking position 7
Map Score:   4.43381

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 323
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

ATTTATACTTAGCTAAATTTG         	1	2	0	AGCTAAATTT	    0.977547	-169
ATTAAATTAAAACATAATTTATACTTAGCT	1	18	0	AACATAATTT	    0.922045	-153
GTTTTAATTTAATTACATTTATAGTTTTCA	1	35	1	AATTACATTT	    0.937154	-136
AAATTTTTTAAAGAAAATTTATGCTTAAGG	1	110	0	AAGAAAATTT	    0.973982	-61
ACTTTCGTAGAAATAAATTTTTTAAAGAAA	1	124	0	AAATAAATTT	    0.665384	-47
          **********

Masking position 7
Map Score:   4.05918

Number of sites scoring better than the average of aligned sites = 446
Number in coding regions = 303
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 133
Fraction of orfs with sites within 600 bp upstream = 0.021362


Motif number 5

          **********

No masking
Map Score:   -4.02577e-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:   -4.02577e-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:   -4.02577e-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