AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i232_formulase_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yloD	233	similar to guanylate kinase
#2	yloI	80	similar to pantothenate metabolism flavoprotein
#3	def	26	polypeptide deformylase

Motif number 1

CCTAGTAAGACCGTCTGTAAACAATACGCA	1	17	0	CCGTCTGTAA	    0.990507	-217
CTTCTACGTTCCCCCTGTAAAATAGACGTC	1	57	0	CCCCCTGTAA	    0.985755	-177
TTTCGATTGTCAGCCCGGAGTCTGCGCCAA	1	145	1	CAGCCCGGAG	    0.963982	-89
ACGGATGATTCAGGATGCAAGAGACCGCGG	1	179	1	CAGGATGCAA	    0.897122	-55
GGTTCTTCGTCCGTATGTAGCGTCAATTAG	1	213	0	CCGTATGTAG	    0.976577	-21
CTTTACAAAACCGCACGGAAAAAAATAACA	2	42	0	CCGCACGGAA	    0.982853	-39
TGAATTCTCCCCCTCTGCACTTTACAAAAC	2	61	0	CCCTCTGCAC	    0.955375	-20
          **********

Masking position 9
Map Score:   5.07325

Number of sites scoring better than the average of aligned sites = 1511
Number in coding regions = 1396
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 2

GTCTGTAAACAATACGCACAGTCA      	1	5	0	AATACGCACA	    0.930602	-229
TCATCTCCGCCAATCGGATGATTTCGATTG	1	124	1	CAATCGGATG	    0.838898	-110
CTGCGCCAATCAAACGGATGATTCAGGATG	1	166	1	CAAACGGATG	    0.847372	-68
ATTGACGCTACATACGGACGAAGAACCC  	1	216	1	CATACGGACG	    0.849419	-18
GCACTTTACAAAACCGCACGGAAAAAAATA	2	45	0	AAACCGCACG	    0.981856	-36
          **********

Masking position 8
Map Score:   4.47055

Number of sites scoring better than the average of aligned sites = 375
Number in coding regions = 359
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

ATCTTCTACGTTCCCCCTGTAAAATAGACG	1	59	0	TTCCCCCTGT	    0.983242	-175
GCAATATCATCTCCGCCAATCGGATGATTT	1	118	1	CTCCGCCAAT	    0.996388	-116
AGCCCGGAGTCTGCGCCAATCAAACGGATG	1	156	1	CTGCGCCAAT	    0.990408	-78
    TGAATTCTCCCCCTCTGCACTTTACA	2	65	0	CTCCCCCTCT	    0.995728	-16
          **********

Masking position 2
Map Score:   3.30889

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 94
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

AAACTGATTAATATCGGATTTGGCAATATCA	1	96	1	ATTCGGATTT	    0.944484	-138
CAATCGGATGATTTCGATTGTCAGCCCGGAG	1	134	1	ATTCGATTGT	    0.967702	-100
CAAACGGATGATTCAGGATGCAAGAGACCGC	1	176	1	ATCAGGATGC	    0.980064	-58
AACCTACATGATATAGGTTGCTACTTGTGCT	2	12	0	ATTAGGTTGC	    0.993644	-69
AACCTATATCATGTAGGTTGTTATTTTTTTC	2	24	1	ATTAGGTTGT	    0.993142	-57
          ** ********

Masking position 9
Map Score:   3.0612

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 141
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

AATATCATCTCCGCCAATCGGATGATTTCG	1	120	1	CCGCCAATCG	    0.997592	-114
AGACTCCGGGCTGACAATCGAAATCATCCG	1	138	0	CTGACAATCG	    0.974507	-96
CCCGGAGTCTGCGCCAATCAAACGGATGAT	1	158	1	GCGCCAATCA	     0.99628	-76
TCCGTATGTAGCGTCAATTAGCATTCCGCG	1	204	0	GCGTCAATTA	     0.96111	-30
          **********

Masking position 6
Map Score:   2.81354

Number of sites scoring better than the average of aligned sites = 336
Number in coding regions = 322
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 6

          **********

No masking
Map Score:   4.64285e-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:   4.64285e-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:   4.64285e-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