AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i048_Polysaccharide_Biosynthesis_2_mjan_reg_300.orf -o048_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	RMJ11202	167	M_jannaschii_chromosome
#2	RMJ06576	178	M_jannaschii_chromosome
#3	RMJ11498	66	M_jannaschii_chromosome

Motif number 1

TGTAAGATATAAAAATATTTTGTGAGGGAT	1	15	0	AAAAATATTT	    0.574723	-153
TATCTTACATAAAATTATAAATCCTTAAAC	1	36	1	AAAATTATAA	    0.929117	-132
TATAAATCCTTAAACTTTTTGTATTTTATT	1	51	1	TAAACTTTTT	    0.679683	-117
TATATACTCCAAAACTATAAGCAATAAAAT	1	73	0	AAAACTATAA	    0.940928	-95
ATATAATAGGTGAGTTATATATACTCCAAA	1	90	0	TGAGTTATAT	     0.82948	-78
TTATCCCCAAAAATTTCTATTTAGATTGAT	1	147	0	AAATTTCTAT	    0.857607	-21
ATTCATTACGAGAGTTCTAT          	2	1	0	AGAGTTCTAT	    0.877047	-178
ATATTGCCAATAAATTATTTATTCATTACG	2	21	0	TAAATTATTT	    0.831792	-158
ATATTTTTGTAAAGTTATAAATTTAATATT	2	61	1	AAAGTTATAA	    0.947638	-118
TGCAAACACAAAAGTTCTATTAGATACTAA	2	102	1	AAAGTTCTAT	    0.963021	-77
TTAGATACTAAAAACTATTTTTTGCTACTT	2	121	1	AAAACTATTT	    0.936584	-58
TTGTTCTTTAAAAATTATAAAAGTAGCAAA	2	141	0	AAAATTATAA	    0.929117	-38
AAAAACATCTAAAGCTTTATATACAAATAT	3	22	1	AAAGCTTTAT	    0.953069	-45
AATATAAGCTTAAGCTTTATATATAGATTT	3	47	1	TAAGCTTTAT	    0.886562	-20
          AAATCTATATATAAAGCTTA	3	57	0	AAATCTATAT	     0.92938	-10
          **********

Masking position 3
Map Score:   19.1625

Number of sites scoring better than the average of aligned sites = 1852
Number in coding regions = 1403
Number in noncoding regions = 449
Number of orfs with sites within 600 bp upstream = 390
Fraction of orfs with sites within 600 bp upstream = 0.0626405


Motif number 2

CAAAATATTTTTATATCTTACATAAAATTA	1	23	1	TTATATCTTA	    0.759549	-145
CTTAAACTTTTTGTATTTTATTGCTTATAG	1	59	1	TTGTATTTTA	    0.903735	-109
AATAGGTGAGTTATATATACTCCAAAACTA	1	86	0	TTATATATAC	    0.588228	-82
AACTCACCTATTATATATAAACTGCTAATA	1	104	1	TTATATATAA	     0.49976	-64
CCCCAAAAATTTCTATTTAGATTGATTATT	1	143	0	TTCTATTTAG	    0.876879	-25
AAATAGTTTTTAGTATCTAATAGAACTTTT	2	111	0	TAGTATCTAA	    0.869773	-68
AAGCTTATATTTGTATATAAAGCTTTAGAT	3	28	0	TTGTATATAA	    0.606865	-39
AGCTTAAGCTTTATATATAGATTT      	3	53	1	TTATATATAG	    0.600281	-14
          **********

Masking position 5
Map Score:   7.66515

Number of sites scoring better than the average of aligned sites = 377
Number in coding regions = 282
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 3

TTTGTATTTTATTGCTTATAGTTTTGGAGT	1	68	1	ATTGCTTATA	    0.960312	-100
TTATATATAAACTGCTAATAATAACTGTCA	1	114	1	ACTGCTAATA	    0.989536	-54
GCTAATAATAACTGTCAATAATCAATCTAA	1	127	1	ACTGTCAATA	    0.973558	-41
ATATCGACATATTGCCAATAAATTATTTAT	2	29	0	ATTGCCAATA	    0.989536	-150
          **********

Masking position 3
Map Score:   3.43967

Number of sites scoring better than the average of aligned sites = 69
Number in coding regions = 64
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

AGATATAAAAATATTTTGTGAGGGATTGTC	1	11	0	ATATTTTGTG	    0.962086	-157
ATAAATCCTTAAACTTTTTGTATTTTATTG	1	52	1	AAACTTTTTG	    0.929163	-116
TTTATTGCTTATAGTTTTGGAGTATATATA	1	75	1	ATAGTTTTGG	    0.973272	-93
ATCTAAATAGAAATTTTTGGGGATAAA   	1	151	1	AAATTTTTGG	    0.977438	-17
GTCGATATCCATATTTTTGTAAAGTTATAA	2	51	1	ATATTTTTGT	    0.928149	-128
ATACTAAAAACTATTTTTTGCTACTTTTAT	2	125	1	CTATTTTTTG	    0.962083	-54
AAAGCTTTAGATGTTTTTTGGGGAAGTCT 	3	10	0	ATGTTTTTTG	    0.962086	-57
          **********

Masking position 5
Map Score:   7.03394

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 444
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 5

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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:   -4.73059e-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