AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i048_Polysaccharide_Biosynthesis_2_mjan_reg_100.orf -o048_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

Input sequences:
#1	RMJ11202	167	M_jannaschii_chromosome
#2	RMJ06576	178	M_jannaschii_chromosome

Motif number 1

ATCCCTCACAAAATATTTTTATATCTTACA	1	15	1	AAATATTTTT	    0.704635	-153
GTTTAAGGATTTATAATTTTATGTAAGATA	1	36	0	TTATAATTTT	     0.97355	-132
ATTTTATTGCTTATAGTTTTGGAGTATATA	1	73	1	TTATAGTTTT	    0.927308	-95
TTTGGAGTATATATAACTCACCTATTATAT	1	90	1	ATATAACTCA	      0.7776	-78
AAACTGCTAATAATAACTGTCAATAATCAA	1	122	1	TAATAACTGT	    0.787931	-46
ATCAATCTAAATAGAAATTTTTGGGGATAA	1	147	1	ATAGAAATTT	    0.847027	-21
          ATAGAACTCTCGTAATGAAT	2	1	1	ATAGAACTCT	    0.926214	-178
CGTAATGAATAAATAATTTATTGGCAATAT	2	21	1	AAATAATTTA	    0.801032	-158
AATATTAAATTTATAACTTTACAAAAATAT	2	61	0	TTATAACTTT	    0.977039	-118
GCATATGACATTAGAATATTAAATTTATAA	2	75	0	TTAGAATATT	    0.742027	-104
TTAGTATCTAATAGAACTTTTGTGTTTGCA	2	102	0	ATAGAACTTT	    0.971721	-77
AAGTAGCAAAAAATAGTTTTTAGTATCTAA	2	121	0	AAATAGTTTT	    0.872174	-58
TTTGCTACTTTTATAATTTTTAAAGAACAA	2	141	1	TTATAATTTT	     0.97355	-38
          **********

Masking position 5
Map Score:   15.1241

Number of sites scoring better than the average of aligned sites = 1591
Number in coding regions = 1213
Number in noncoding regions = 378
Number of orfs with sites within 600 bp upstream = 336
Fraction of orfs with sites within 600 bp upstream = 0.0539672


Motif number 2

TAATTTTATGTAAGATATAAAAATATTTTGTGA	1	20	0	TAATTAAAAA	    0.945112	-148
CTATAAGCAATAAAATACAAAAAGTTTAAGGAT	1	56	0	TAATCAAAAA	    0.988693	-112
GTGAGTTATATATACTCCAAAACTATAAGCAAT	1	78	0	TTCTCAAAAC	    0.904299	-90
CTATTATATATAAACTGCTAATAATAACTGTCA	1	111	1	TACTCTAATA	     0.95579	-57
         TTTATCCCCAAAAATTTCTATTTA	1	154	0	TACCCAAAAA	    0.963373	-14
GTTATAAATTTAATATTCTAATGTCATATGCAA	2	74	1	TAATCTAATG	    0.816852	-105
TATTCTAATGTCATATGCAAACACAAAAGTTCT	2	87	1	TAATCAAACA	    0.964165	-92
AAAAGTTCTATTAGATACTAAAAACTATTTTTT	2	111	1	TAATCTAAAA	    0.978649	-68
ACTCTTCAATTGTTCTTTAAAAATTATAAAAGT	2	147	0	TTCTTAAAAA	    0.875063	-32
          * * ** ******

Masking position 10
Map Score:   5.96674

Number of sites scoring better than the average of aligned sites = 761
Number in coding regions = 616
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

CTTTTTGTATTTTATTGCTTATAGTTTTGG	1	65	1	TTTATTGCTT	    0.943193	-103
ATTGACAGTTATTATTAGCAGTTTATATAT	1	116	0	ATTATTAGCA	    0.818553	-52
ATTTAGATTGATTATTGACAGTTATTATTA	1	129	0	ATTATTGACA	    0.938347	-39
          TTTATCCCCAAAAATTTCTA	1	158	0	TTTATCCCCA	    0.926887	-10
CAATAAATTATTTATTCATTACGAGAGTTC	2	14	0	TTTATTCATT	    0.793883	-165
GAATAAATAATTTATTGGCAATATGTCGAT	2	27	1	TTTATTGGCA	    0.981857	-152
CTAAAAACTATTTTTTGCTACTTTTATAAT	2	128	1	TTTTTTGCTA	    0.887938	-51
          **********

Masking position 5
Map Score:   1.77956

Number of sites scoring better than the average of aligned sites = 824
Number in coding regions = 747
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 4

  GACAATCCCTCACAAAATATTTTTATAT	1	9	1	CTCACAAAAT	    0.959818	-159
GTATATATAACTCACCTATTATATATAAAC	1	96	1	CTCACCTATT	    0.973929	-72
    ATAGAACTCTCGTAATGAATAAATAA	2	7	1	CTCTCGTAAT	    0.976097	-172
TTTTTTGCTACTTTTATAATTTTTAAAGAA	2	138	1	CTTTTATAAT	    0.804825	-41
AGTTATCCTACTCTTCAATTGTTCTTTAAA	2	159	0	CTCTTCAATT	    0.943119	-20
          **********

Masking position 8
Map Score:   0.259087

Number of sites scoring better than the average of aligned sites = 551
Number in coding regions = 511
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 5

          **********

No masking
Map Score:   -2.60469e-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:   -2.60469e-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:   -2.60469e-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