AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i042_bsub_mtub_300.orf -o042_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	yneA	149	yneA
#2	ynzC	63	ynzC
#3	tkt	168	transketolase

Motif number 1

GTTTCTGTCAATTGTTTTTTCGAACCTATGTTTGTAC	1	66	0	ATTTTTCGAT	    0.995602	-84
AATTGACAGAAACGTTTGTTCGTATATACTGAAATTA	1	90	1	ATTGTTCGAT	    0.992259	-60
CTCCAACAGGAATGTTTGTTCGCATTTTTATAATTTC	1	120	0	ATTGTTCGAT	    0.992259	-30
 ATCAGTTGTAAAACTTTTTTTGATCTAGTACTATAT	2	10	1	ATTTTTTTAT	      0.9719	-54
     GTTAAACTCCTTTATTGCATTTTGTCTATATA	2	42	0	ATTTATTGAT	    0.948372	-22
GCAATATCGTATTCCTCTTTTGCATATACTATAATCA	3	26	1	ATCTTTTGAT	    0.959186	-143
ACAAAATTCAACAAGTTTCTCTCAAATTTAAGCTGAA	3	76	1	ATTTCTCTAT	    0.964571	-93
TAAATGTCTGACGACTTTTTCTCAACTGTTTCAGCTT	3	105	0	ATTTTTCTAT	    0.988825	-64
          *    ******* *  *

Masking position 14
Map Score:   9.58459

Number of sites scoring better than the average of aligned sites = 262
Number in coding regions = 208
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 2

AATCATGCTATAATCTTCTTAAAATCGACG	1	27	0	TAATCTTCTT	    0.974023	-123
TGCGAACAAACATTCCTGTTGGAGGTT   	1	133	1	CATTCCTGTT	    0.943896	-17
        GTTAAACTCCTTTATTGCATTT	2	52	0	TAAACTCCTT	    0.916502	-12
GATATTGCCGTATTCCTCTTATA       	3	4	0	TATTCCTCTT	    0.990616	-165
GGCAATATCGTATTCCTCTTTTGCATATAC	3	25	1	TATTCCTCTT	    0.990616	-144
ATACTATAATCAAAACTCTTATGTGACAAA	3	51	1	CAAAACTCTT	      0.8654	-118
        AAAAATCCCCTTCCTTATGTGT	3	157	0	AAATCCCCTT	     0.96565	-12
          **********

Masking position 2
Map Score:   7.55873

Number of sites scoring better than the average of aligned sites = 569
Number in coding regions = 426
Number in noncoding regions = 143
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 3

TTTAAGAAGATTATAGCATGATTTTCCTTA	1	34	1	TTATAGCATG	    0.940729	-116
ATGATTTTCCTTACAGTACAAACATAGGTT	1	51	1	TTACAGTACA	    0.967607	-99
ATTTTTATAATTTCAGTATATACGAACAAA	1	104	0	TTTCAGTATA	    0.977668	-46
AGAGTTTTGATTATAGTATATGCAAAAGAG	3	40	0	TTATAGTATA	    0.965041	-129
TTCTCAACTGTTTCAGCTTAAATTTGAGAG	3	94	0	TTTCAGCTTA	    0.944393	-75
TGTTGTACCCTTACATCATAAATGTCTGAC	3	130	0	TTACATCATA	    0.952073	-39
          **********

Masking position 5
Map Score:   4.93836

Number of sites scoring better than the average of aligned sites = 516
Number in coding regions = 434
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 4

ATTTTCCTTACAGTACAAACATAGGTTCGA	1	54	1	CAGTACAAAC	    0.956356	-96
AAACATAGGTTCGAAAAAACAATTGACAGA	1	70	1	TCGAAAAAAC	    0.973929	-80
TTCAGTATATACGAACAAACGTTTCTGTCA	1	93	0	ACGAACAAAC	    0.993307	-57
TTATAAAAATGCGAACAAACATTCCTGTTG	1	124	1	GCGAACAAAC	    0.995474	-26
          **********

Masking position 5
Map Score:   2.79416

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 37
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

CAGTTGTAAAACTTTTTTTGATCTAGTACT	2	13	1	ACTTTTTTTG	    0.878485	-51
   GTTAAACTCCTTTATTGCATTTTGTCT	2	47	0	TCCTTTATTG	    0.955575	-17
ATTGCCGTATTCCTCTTATA          	3	1	0	TCCTCTTATA	    0.936717	-168
AATATCGTATTCCTCTTTTGCATATACTAT	3	28	1	TCCTCTTTTG	    0.992759	-141
CTATAATCAAAACTCTTATGTGACAAAATT	3	54	1	AACTCTTATG	     0.88806	-115
AAAATCCCCTTCCTTATGTGTTGTACCCTT	3	148	0	TCCTTATGTG	    0.926554	-21
          **********

Masking position 4
Map Score:   1.93437

Number of sites scoring better than the average of aligned sites = 1154
Number in coding regions = 942
Number in noncoding regions = 212
Number of orfs with sites within 600 bp upstream = 230
Fraction of orfs with sites within 600 bp upstream = 0.0369419


Motif number 6

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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 8

          **********

No masking
Map Score:   4.92707e-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