AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i152_bsub_mtub_300.orf -o152_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	yurD	21	similar to 4-hydroxybenzoyl-CoA reductase
#2	yurF	228	yurF
#3	yurH	300	similar to N-carbamyl-L-amino acid amidohydrolase
#4	Rv0375c	75	hypothetical protein Rv0375c
#5	Rv0376c	48	hypothetical protein Rv0376c

Motif number 1

    AGAAAAGCTTGCGGAACTCCGCAAGC	2	7	1	GCTTGCGGAA	    0.989685	-222
TCGTTAAAAAGCTTGCGGAGTTCCGCAAGC	2	17	0	GCTTGCGGAG	    0.984748	-212
TTCGAGAGGAGGATGCGGCA          	2	219	1	GGATGCGGCA	    0.955362	-10
TCCTGTTTTTGCGGGCTGCCGGCATTTCTG	3	12	1	GCGGGCTGCC	    0.976981	-289
TCTCTTTCGCTCTTGCTGGCTCTCTTCCTT	3	108	1	TCTTGCTGGC	    0.811854	-193
GGGTGTATCTGGTTGCTGGATGGATACTGT	3	184	1	GGTTGCTGGA	    0.910249	-117
CGCCCTTTTCGCGGGCGGCCGACACTGGGG	4	11	1	GCGGGCGGCC	    0.992112	-65
CCAGGTACTTGCATGCGCCCCAGTGTCGGC	4	28	0	GCATGCGCCC	    0.934364	-48
          GCTGGTGGCACGTTCGTATT	4	66	0	GCTGGTGGCA	    0.923745	-10
ACTTTGGGAAGCGTGCGTGAAGTGCTTGCC	5	23	1	GCGTGCGTGA	     0.91512	-26
TGCGTGAAGTGCTTGCCGAGCTG       	5	36	1	GCTTGCCGAG	    0.914429	-13
          **********

Masking position 5
Map Score:   12.2895

Number of sites scoring better than the average of aligned sites = 2567
Number in coding regions = 2417
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 122
Fraction of orfs with sites within 600 bp upstream = 0.0195952


Motif number 2

GATATGATTTCGTGTTTTCTCCAATCTGAT	2	45	1	CGTGTTTTCT	    0.983531	-184
ACAAATCATGAGTCATTTTTTCTTCCATCG	2	128	1	AGTCATTTTT	    0.846686	-101
TTTCTTCCATCGTCTATTCTTTATACAAGT	2	146	1	CGTCTATTCT	    0.979958	-83
ACTAGTTCAGCGTGATTTTATAGGTAACTT	2	172	0	CGTGATTTTA	    0.870925	-57
TTGTTTCTCACGGCAATTTTCGAGAGGAGG	2	201	1	CGGCAATTTT	    0.945819	-28
TGCGGGCTGCCGGCATTTCTGTTTTCATCC	3	21	1	CGGCATTTCT	    0.977982	-280
TCTTCCTTACCGTGTTTTCTTTTGACCTTT	3	130	1	CGTGTTTTCT	    0.983531	-171
ACCAAAAAAACGTTTATTTTTTAGCCACAG	3	210	0	CGTTTATTTT	    0.855226	-91
          **********

Masking position 7
Map Score:   7.62939

Number of sites scoring better than the average of aligned sites = 916
Number in coding regions = 791
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 3

          CATGGTAAGGAGGGCGATGTC  	1	1	1	CATGGAGGAG	    0.947889	-21
CGGCAATTTTCGAGAGGAGGATGCGGCA     	2	211	1	CGAGAGGGAG	    0.930154	-18
AGGCGATGTTCGCGGAACGGATGAAAACAGAAA	3	36	0	CGCGGAGGAG	    0.998367	-265
GAACAAGCTAAGCTGGAGAGGCGATGTTCGCGG	3	54	0	AGCTGAAGGG	    0.829459	-247
AGCCAGCAAGAGCGAAAGAGAGGGTCAAAATGC	3	96	0	AGCGAAAGAG	    0.960189	-205
CAAAAGAAAACACGGTAAGGAAGAGAGCCAGCA	3	121	0	CACGGAGGAG	    0.992919	-180
TCACCATAGCGGCCAGAGGGGGGAGTAC     	3	283	1	GGCCAAGGGG	    0.943502	-18
GTCGGCCGCCCGCGAAAAGGGCG          	4	1	0	CGCGAAGGGG	     0.99721	-75
          ***** * *** *

Masking position 10
Map Score:   4.63497

Number of sites scoring better than the average of aligned sites = 526
Number in coding regions = 465
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 4

TTCGTTTGACTCTTTTTACAAATCCTCTTT	2	79	1	TCTTTTTACA	     0.94079	-150
ATGTGTTTCATTTTCTGACAAATCATGAGT	2	111	1	TTTTCTGACA	    0.950467	-118
ATGAGTCATTTTTTCTTCCATCGTCTATTC	2	135	1	TTTTCTTCCA	    0.950467	-94
CATCGTCTATTCTTTATACAAGTTACCTAT	2	153	1	TCTTTATACA	    0.924207	-76
GGCATTTCTGTTTTCATCCGTTCCGCGAAC	3	32	1	TTTTCATCCG	    0.843466	-269
TACCGTGTTTTCTTTTGACCTTTACATCAA	3	137	1	TCTTTTGACC	    0.875254	-164
AAACGTTTATTTTTTAGCCACAGTATCCAT	3	203	0	TTTTTAGCCA	    0.936451	-98
          **********

Masking position 4
Map Score:   2.81771

Number of sites scoring better than the average of aligned sites = 903
Number in coding regions = 790
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 5

          **********

No masking
Map Score:   -4.94948e-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:   -4.94948e-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:   -4.94948e-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