AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i332_bsub_mtub_300.orf -o332_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	yunH	174	similar to allantoinase
#2	yurH	300	similar to N-carbamyl-L-amino acid amidohydrolase

Motif number 1

          AGCGCATTCTCCTTTTCTATAAAAACATTG	1	1	1	ACGTTCCTTT	    0.980581	-174
TAGGAATTCTAGCGGTTTTGCTGATGTAATACGATCATAG	1	62	1	ACGTTTCGTT	    0.997052	-113
ATGTCAGGATGACGATTTTCCATGTCAGTTTATGTAACAC	1	133	0	GCGTTTCTTT	    0.991029	-42
TTTGCGGGCTGCCGGCATTTCTGTTTTCATCCGTTCCGCG	2	19	1	GCGATTCGTT	    0.979324	-282
TTCCGCGAACATCGCCTCTCCAGCTTAGCTTGTTCATATG	2	52	1	ACGTCTCGTT	    0.990331	-249
TCTCTTCCTTACCGTGTTTTCTTTTGACCTTTACATCAAA	2	128	1	ACGTTTCTTT	    0.993945	-173
CTAAAAAATAAACGTTTTTTTGGTTAATCTGTCAATGAAC	2	216	1	ACGTTTTGTT	    0.977767	-85
          * **  *** * * *    *

Masking position 15
Map Score:   7.50044

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 199
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

TCGTCATCCTGACATGGGGGGATCAAT    	1	158	1	GCATGGGGGG	    0.993683	-17
CAGCAAGAGCGAAAGAGAGGGTCAAAATGCC	2	95	0	GAAGAGAGGG	    0.988265	-206
AAGGAAGAGAGCCAGCAAGAGCGAAAGAGAG	2	107	0	GCAGCAAGAG	    0.969115	-194
AGAAAACACGGTAAGGAAGAGAGCCAGCAAG	2	119	0	GAAGGAAGAG	    0.966052	-182
AAATAGTTGTGACATGTAGGGTGTATCTGGT	2	166	1	GCATGTAGGG	     0.97949	-135
CACCATAGCGGCCAGAGGGGGGAGTAC    	2	284	1	GCAGAGGGGG	    0.995183	-17
          * *********

Masking position 4
Map Score:   4.76424

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 169
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

ATTGAAAATTATTCACCTTAACCAATGTTT	1	33	0	ATTCACCTTA	    0.875704	-142
ATACGATCATAGTAGCAGTAAACTGTTGAA	1	90	1	AGTAGCAGTA	    0.831323	-85
GTATCCATCCAGCAACCAGATACACCCTAC	2	181	0	AGCAACCAGA	    0.968434	-120
TTTATTTTTTAGCCACAGTATCCATCCAGC	2	198	0	AGCCACAGTA	    0.958945	-103
TCATTGACAGATTAACCAAAAAAACGTTTA	2	224	0	ATTAACCAAA	    0.717587	-77
TTATAGAAGGAGCAACATGATAGTTCATTG	2	248	0	AGCAACATGA	    0.912025	-53
TCTATAATGAAGTCACCATAGCGGCCAGAG	2	271	1	AGTCACCATA	    0.973689	-30
          **********

Masking position 1
Map Score:   0.721961

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 447
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 4

AGGAATTCTAGCGGTTTTGCTGATGTAATA	1	63	1	GCGGTTTTGC	    0.959015	-112
CACAACCAGTTCTATTTTCAACAGTTTACT	1	106	0	TCTATTTTCA	    0.943877	-69
TGTCAGGATGACGATTTTCCATGTCAGTTT	1	142	0	ACGATTTTCC	    0.933396	-33
TGCCGGCATTTCTGTTTTCATCCGTTCCGC	2	28	1	TCTGTTTTCA	    0.947796	-273
ACCCTCTCTTTCGCTCTTGCTGGCTCTCTT	2	104	1	TCGCTCTTGC	    0.958816	-197
GCTCTTGCTGGCTCTCTTCCTTACCGTGTT	2	116	1	GCTCTCTTCC	    0.951673	-185
CTTACCGTGTTTTCTTTTGACCTTTACATC	2	135	1	TTTCTTTTGA	    0.747039	-166
ACATGTCACAACTATTTTGATGTAAAGGTC	2	153	0	ACTATTTTGA	    0.900136	-148
          **********

Masking position 5
Map Score:   3.4349

Number of sites scoring better than the average of aligned sites = 2168
Number in coding regions = 1956
Number in noncoding regions = 212
Number of orfs with sites within 600 bp upstream = 221
Fraction of orfs with sites within 600 bp upstream = 0.0354963


Motif number 5

          **********

No masking
Map Score:   -6.1574e-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:   -6.1574e-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:   -6.1574e-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