AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i249_min_operon_mjan_reg_300.orf -o249_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	RMJ02345	177	M_jannaschii_chromosome
#2	RMJ12182	111	M_jannaschii_chromosome

Motif number 1

  CATAGTCCTAAAGTTCAATAAGCAAATGTTG	1	9	1	TAATTAATAA	    0.968333	-169
ATTAATTGAATAAGGTTATCTAACAACATTTGC	1	32	0	TAATTTCTAA	    0.840697	-146
GATAACCTTATTCAATTAATTAATGATGTAATG	1	45	1	TTCTTATTAA	    0.879215	-133
TAGGACACGCTTATCTTCAAAAACATTACATCA	1	68	0	TTATTAAAAA	    0.937433	-110
ATATATACTCTTCGGTTTAATATTAGGACACGC	1	91	0	TTCTTAATAT	    0.959301	-87
AAAGTTATAGTTAAGTTAAATATATACTCTTCG	1	110	0	TTATTAATAT	    0.975118	-68
TCTAAAATCTTTATATTACCTATTTACAACACT	1	143	0	TTATTCCTAT	    0.856639	-35
GTAATATTTGTTAGTTTGAAAATAAACGGGGGA	2	15	0	TTATTAAAAT	     0.93726	-97
TAACAAATATTACTATTTAATAACTAATATATA	2	35	1	TACTTAATAA	    0.944816	-77
TTATTATCGTTAATCTTATATATTAGTTATTAA	2	51	0	TAATTTATAT	    0.883698	-61
ACGATAATAATAATACTAACTAATATTATTAGT	2	74	1	TAACTACTAA	    0.877374	-38
CTCTCACCCCTTAGACTAATAATATTAGTTAGT	2	88	0	TTACTATAAT	    0.621377	-24
          ***  ** *****

Masking position 12
Map Score:   11.5541

Number of sites scoring better than the average of aligned sites = 1622
Number in coding regions = 1071
Number in noncoding regions = 551
Number of orfs with sites within 600 bp upstream = 414
Fraction of orfs with sites within 600 bp upstream = 0.0664953


Motif number 2

AATTGAATAAGGTTATCTAACAACATTTGC	1	32	0	GGTTATCTAA	    0.851013	-146
TACATCATTAATTAATTGAATAAGGTTATC	1	45	0	ATTAATTGAA	    0.715672	-133
TACTCTTCGGTTTAATATTAGGACACGCTT	1	89	0	TTTAATATTA	    0.792133	-89
TAAAGTTATAGTTAAGTTAAATATATACTC	1	114	0	GTTAAGTTAA	    0.916756	-64
GTTGTAAATAGGTAATATAAAGATTTTAGA	1	146	1	GGTAATATAA	    0.958406	-32
AGTAATATTTGTTAGTTTGAAAATAAACGG	2	19	0	GTTAGTTTGA	    0.934289	-93
TATTATTATCGTTAATCTTATATATTAGTT	2	56	0	GTTAATCTTA	    0.978817	-56
AATAATATTAGTTAGTATTATTATTATCGT	2	74	0	GTTAGTATTA	    0.960379	-38
AACTAATATTATTAGTCTAAGGGGTGAGAG	2	91	1	ATTAGTCTAA	    0.933267	-21
          **********

Masking position 3
Map Score:   5.08659

Number of sites scoring better than the average of aligned sites = 653
Number in coding regions = 545
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

TAAATATATACTCTTCGGTTTAATATTAGG	1	97	0	CTCTTCGGTT	    0.982299	-81
       AATCTCCCCCGTTTATTTTCAAA	2	4	1	CTCCCCCGTT	    0.997576	-108
       TCTCTCACCCCTTAGACTAATAA	2	99	0	CTCACCCCTT	     0.99344	-13
          **********

Masking position 2
Map Score:   0.384691

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 7
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

GTAAATAGGTAATATAAAGATTTTAGAATGGT	1	149	1	AATATAAATT	    0.858309	-29
         TAATGTCACCATTCTAAAATCTT	1	165	0	AATGTACATT	    0.928493	-13
CAAACTAACAAATATTACTATTTAATAACTAA	2	30	1	AATATACATT	     0.58941	-82
AATATTAGTTAGTATTATTATTATCGTTAATC	2	69	0	AGTATATATT	    0.852625	-43
AATACTAACTAATATTATTAGTCTAAGGGGTG	2	85	1	AATATATAGT	    0.852625	-27
          ***** ** ***

Masking position 7
Map Score:   2.63215

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 136
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 5

          **********

No masking
Map Score:   5.70866e-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:   5.70866e-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:   5.70866e-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