AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00730_mjan_reg_300.orf -o00730_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	MJ0028	300	thiamine monphosphate kinase (thiL)
#2	MJ1026	125	thiamine biosynthesis protein (thiC)

Motif number 1

AATATCTCTTTAAAAATGCCAATATAGGGATT	1	22	1	TAAAATGCAA	    0.937145	-279
TTTATTCGATTAATAATACAAAAAATTGATTT	1	74	0	TAATATACAA	     0.95355	-227
CCCGTCTGAGTTATGATGAGTAGCAAGCCGGC	1	194	1	TTATATGATA	    0.794485	-107
TATTAGTTGATAAATAAAAAAAGGAAAAGTGG	1	231	0	TAAAAAAAAA	    0.919291	-70
ATTTATCAACTAATAAAGAAAAGTCATAAAAA	1	248	1	TAATAAGAAA	    0.975524	-53
TTAGCCCCTCTAATTAGAATAAAAGAAGTTTT	1	277	0	TAATAGAAAA	    0.851699	-24
CCAACAATTATAAACATGATAATAGGTATATG	2	11	1	TAAAATGAAA	    0.823767	-115
TTATCATTATTAATTATGATAAATTATCTATT	2	59	0	TAATATGAAA	    0.554644	-67
TCATAATTAATAATGATAATTAGCTTAACCTT	2	72	1	TAATATAATA	    0.653264	-54
CTCGATAACTTTATTAAAACAAAACTATATAA	2	104	0	TTATAAAAAA	    0.864757	-22
          **** **** **

Masking position 6
Map Score:   12.0968

Number of sites scoring better than the average of aligned sites = 778
Number in coding regions = 579
Number in noncoding regions = 199
Number of orfs with sites within 600 bp upstream = 171
Fraction of orfs with sites within 600 bp upstream = 0.0274655


Motif number 2

TATATAAGCTAATATCTCTTTAAAAATGCCA	1	12	1	AATATTCTTT	    0.922096	-289
AAAATGCCAATATAGGGATTTAGGTTTTTGG	1	34	1	TATAGGATTT	    0.899874	-267
AATAATACAAAAAATTGATTTTTAACATATC	1	64	0	AAAATGATTT	    0.905342	-237
ATCTATTTATAATATTTTATTCGATTAATAA	1	90	0	AATATTTATT	    0.858414	-211
AGAGTATGGTAATATCTATTTATAATATTTT	1	103	0	AATATTATTT	    0.974588	-198
TACATTTATTTAAATCTTTTTAGAGTATGGT	1	124	0	TAAATTTTTT	    0.806384	-177
TAACGCTAAGAGTATTTATTTGGCAGATGAT	1	153	1	AGTATTATTT	    0.936646	-148
TTAGAATAAAAGAAGTTTTTTATGACTTTTC	1	265	0	AGAAGTTTTT	    0.789604	-36
TAAACATGATAATAGGTATATGACTCACTAA	2	21	1	AATAGTATAT	    0.820708	-105
TAAGGTAATGAATAGATAATTTATCATAATT	2	49	1	AATAGTAATT	    0.899131	-77
CTTAACCTTTTATATAGTTTTGTTTTAATAA	2	95	1	TATATGTTTT	    0.867703	-31
          ***** *****

Masking position 4
Map Score:   7.47281

Number of sites scoring better than the average of aligned sites = 1635
Number in coding regions = 1247
Number in noncoding regions = 388
Number of orfs with sites within 600 bp upstream = 328
Fraction of orfs with sites within 600 bp upstream = 0.0526823


Motif number 3

      TTATATAAGCTAATATCTCTTTAA	1	5	1	ATAAGCTAAT	    0.718536	-296
TCTTTTTAGAGTATGGTAATATCTATTTAT	1	111	0	GTATGGTAAT	    0.918017	-190
TTTTTTATTTATCAACTAATAAAGAAAAGT	1	242	1	ATCAACTAAT	    0.851728	-59
AAAACTTCTTTTATTCTAATTAGAGGGGCT	1	277	1	TTATTCTAAT	    0.770349	-24
ATATGACTCACTAAGGTAATGAATAGATAA	2	38	1	CTAAGGTAAT	    0.961538	-88
ATATAAAAGGTTAAGCTAATTATCATTATT	2	80	0	TTAAGCTAAT	    0.952587	-46
TTTTGTTTTAATAAAGTTATCGAG      	2	112	1	ATAAAGTTAT	     0.73733	-14
          **********

Masking position 9
Map Score:   2.39436

Number of sites scoring better than the average of aligned sites = 221
Number in coding regions = 190
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

          **********

No masking
Map Score:   -2.10731e-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 5

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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