AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_mjan_reg_300.orf -o340_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	RMJ01952	58	M_jannaschii_chromosome
#2	RMJ14782	184	M_jannaschii_chromosome

Motif number 1

  ACTCTCCCTCATAAAATATTTAAATAAACAATAAC	1	9	1	TTAAATTTAT	    0.878006	-50
TTCCTAAGGTTAATAAAGTGTTATTGTTTATTTAAAT	1	28	0	TTAAATTATT	    0.992073	-31
TATATAAATATTGTAAAATATTATTGTGGTGGATATT	2	12	0	TTAAATTATT	    0.992073	-173
AATATTTATATATTTAACTATTATTATTCAGATTATC	2	37	1	TTTAATTATT	    0.989791	-148
AGTTATGCAATTTTAAAAGCTCATCCTCAATATTAAG	2	73	0	TTAAAGTATT	    0.990687	-112
CTTTTAAAATTGCATAACTATATTTATGTTACTTAAC	2	91	1	TATAATTTTT	    0.839058	-94
ATATTTATGTTACTTAACTTTAAGTATCCTTTTCCTA	2	110	1	TTTAATTAGT	    0.965305	-75
TCAGTTAAGGTTTTTAAAGTTAATGGTAGGTAAATGG	2	151	1	TTTAAGTATT	    0.988535	-34
AGTTAATGGTAGGTAAATGGTGATAAT          	2	168	1	ATAAAGTATT	    0.943541	-17
          *  **** * * **  *

Masking position 7
Map Score:   12.8676

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 195
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

GTTATTGTTTATTTAAATATTTTATGAGGG	1	16	0	ATTTAAATAT	    0.714213	-43
AATATCCACCACAATAATATTTTACAATAT	2	12	1	ACAATAATAT	    0.861937	-173
ATAGTTAAATATATAAATATTGTAAAATAT	2	28	0	ATATAAATAT	    0.571864	-157
GATAATCTGAATAATAATAGTTAAATATAT	2	44	0	ATAATAATAG	    0.861937	-141
TATTCAGATTATCTTAATATTGAGGATGAG	2	61	1	ATCTTAATAT	    0.557297	-124
TAGTTATGCAATTTTAAAAGCTCATCCTCA	2	81	0	ATTTTAAAAG	    0.676577	-104
AAGTTAAGTAACATAAATATAGTTATGCAA	2	100	0	ACATAAATAT	    0.881817	-85
          **********

Masking position 6
Map Score:   7.69544

Number of sites scoring better than the average of aligned sites = 583
Number in coding regions = 373
Number in noncoding regions = 210
Number of orfs with sites within 600 bp upstream = 189
Fraction of orfs with sites within 600 bp upstream = 0.0303566


Motif number 3

         ACTCTCCCTCATAAAATATTT	1	2	1	CTCTCCCTCA	    0.983641	-57
         TAATTTCCTAAGGTTAATAAA	1	48	0	AATTTCCTAA	    0.939214	-11
TATTATTCAGATTATCTTAATATTGAGGAT	2	58	1	ATTATCTTAA	    0.871767	-127
ATTTTAAAAGCTCATCCTCAATATTAAGAT	2	71	0	CTCATCCTCA	    0.989379	-114
TTTAAGTATCCTTTTCCTAATAATCAGTTA	2	128	1	CTTTTCCTAA	    0.991345	-57
          **********

Masking position 8
Map Score:   2.90985

Number of sites scoring better than the average of aligned sites = 421
Number in coding regions = 392
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 4

ATATTTAAATAAACAATAACACTTTATTAA	1	26	1	AAACAATAAC	    0.912602	-33
AACACTTTATTAACCTTAGGAAATTA    	1	43	1	TAACCTTAGG	    0.925993	-16
TAAAGTTAAGTAACATAAATATAGTTATGC	2	102	0	TAACATAAAT	    0.788731	-83
TTATGTTACTTAACTTTAAGTATCCTTTTC	2	114	1	TAACTTTAAG	     0.93714	-71
TTAACTTTAAAAACCTTAACTGATTATTAG	2	144	0	AAACCTTAAC	     0.97658	-41
ACCATTTACCTACCATTAACTTTAAAAACC	2	159	0	TACCATTAAC	    0.984411	-26
     ATTATCACCATTTACCTACCATTAA	2	170	0	CACCATTTAC	    0.855194	-15
          **********

Masking position 2
Map Score:   2.78423

Number of sites scoring better than the average of aligned sites = 682
Number in coding regions = 611
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 5

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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 7

          **********

No masking
Map Score:   -3.30951e-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