AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ihipB_mjan_opreg_300.orf -g0.314 -x5 
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 =  	0.314
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MJ0271	300	M. jannaschii predicted coding region MJ0271

Motif number 1

CTCTATCATGTTAATAATACTTTACATTATGTTAAG	1	12	0	TTATCTTTAA	    0.956321	-289
GAGAAGTAATTTACCCATCTTTTTCCTCTATCATGT	1	37	0	TTATTTTTTC	    0.951129	-264
TCTCGGATTTTTAACAGAGTTTTTAATAATAGATGA	1	69	1	TTAATTTTTA	     0.91249	-232
GATTTTTTAAATATCTCTGCTTTTAATTCATCTATT	1	96	0	ATATCTTTTA	    0.958815	-205
GATTAACATAATGGATGATTTTTTAAATATCTCTGC	1	112	0	ATGATTTTTA	    0.852366	-189
ATCCATTATGTTAATCCTTTCTTTTTGGATTTATTT	1	132	1	TTATTCTTTT	    0.891582	-169
ATTCTTAATTTTATGGCTTTCTTTAATGTAAAAGTT	1	175	1	TTATTCTTTA	     0.98278	-126
AATGTAAAAGTTGCATTTTCTTTAGATATAGTTATA	1	199	1	TTGTCTTTAA	    0.935821	-102
TTCTTTAGATATAGTTATATTTTTAATGGCAACTTT	1	216	1	ATATTTTTTA	    0.973444	-85
TGTTTTGAATTTGATATTATCTTTTATCTACTGCTT	1	252	1	TTGTTCTTTA	    0.973315	-49
 AGTTTCACCTTAAGTGTATTTTAAAGCAGTAGATA	1	276	0	TTATTTTTAA	    0.971641	-25
          ***    * ***** *

Masking position 12
Map Score:   12.2808

Number of sites scoring better than the average of aligned sites = 901
Number in coding regions = 720
Number in noncoding regions = 181
Number of orfs with sites within 600 bp upstream = 176
Fraction of orfs with sites within 600 bp upstream = 0.0282686


Motif number 2

        ACTTAACATAATGTAAAGTATTAT	1	3	1	TTAACTATGT	     0.98358	-298
TAAAGTATTATTAACATGATAGAGGAAAAAGA	1	24	1	TTAACTATAG	    0.982932	-277
CTGCTTTTAATTCATCTATTATTAAAAACTCT	1	84	0	TTCATTTTAT	     0.70749	-217
AAAGAAAGGATTAACATAATGGATGATTTTTT	1	124	0	TTAACTATGG	    0.989578	-177
GTTCTGATTCTTAATTTTATGGCTTTCTTTAA	1	169	1	TTAATTATGG	    0.983598	-132
ATGGCTTTCTTTAATGTAAAAGTTGCATTTTC	1	187	1	TTAATTAAAG	    0.932618	-114
ACTTTTGTTTTGAATTTGATATTATCTTTTAT	1	247	1	TGAATTATAT	    0.863591	-54
       AGTTTCACCTTAAGTGTATTTTAAA	1	286	0	TTCACTAAGT	    0.925549	-15
          ***** * ****

Masking position 4
Map Score:   7.97357

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 191
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

TCATCTATTATTAAAAACTCTGTTAAAAAT	1	75	0	TTAAAAACTC	    0.875171	-226
GATGATTTTTTAAATATCTCTGCTTTTAAT	1	105	0	TAAATATCTC	    0.975575	-196
GAATCAGAACTAAATAAATCCAAAAAGAAA	1	149	0	TAAATAAATC	    0.981784	-152
ACTTTTACATTAAAGAAAGCCATAAAATTA	1	180	0	TAAAGAAAGC	    0.934498	-121
ATTAAAAATATAACTATATCTAAAGAAAAT	1	213	0	TAACTATATC	    0.944308	-88
          **********

Masking position 6
Map Score:   1.1681

Number of sites scoring better than the average of aligned sites = 402
Number in coding regions = 356
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 4

AGTAATTTACCCATCTTTTTCCTCTATCAT	1	39	0	CCATCTTTTT	    0.941221	-262
TGCTTTTAATTCATCTATTATTAAAAACTC	1	85	0	TCATCTATTA	    0.956761	-216
TTTAAATATCTCTGCTTTTAATTCATCTAT	1	97	0	TCTGCTTTTA	    0.928559	-204
TAAAGAAAATGCAACTTTTACATTAAAGAA	1	193	0	GCAACTTTTA	    0.985425	-108
ATTTTTAATGGCAACTTTTGTTTTGAATTT	1	234	1	GCAACTTTTG	    0.968229	-67
GAATTTGATATTATCTTTTATCTACTGCTT	1	258	1	TTATCTTTTA	    0.932824	-43
          **********

Masking position 6
Map Score:   3.64442

Number of sites scoring better than the average of aligned sites = 735
Number in coding regions = 673
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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