AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_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	ytgA	279	similar to ABC transporter (membrane protein)

Motif number 1

  GAAAAAAGCATTTTGCTATTTTGAATAA	1	9	1	CATTTTGCTA	    0.962281	-271
CATCCCTTCTCGTTTGGACCGGCTGCTGAC	1	78	1	CGTTTGGACC	    0.980931	-202
AAAATTATCGCGTTTGGCCATTTTTGTCAA	1	135	0	CGTTTGGCCA	    0.996921	-145
ATGAGGGAAACTTTTTGTCCTGTGTAAATA	1	167	1	CTTTTTGTCC	    0.968058	-113
ATAAAACATGCTTTTGGCTAATTTAATGTC	1	194	1	CTTTTGGCTA	    0.990231	-86
ATTTCTCCTCCTCTTTGCCATCAATGTCCG	1	260	0	CTCTTTGCCA	    0.985867	-20
          **********

Masking position 5
Map Score:   7.98927

Number of sites scoring better than the average of aligned sites = 430
Number in coding regions = 395
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 2

AACGAACACTTTTACTGTAACAGCACAGTG	1	43	0	TTTACTGTAA	    0.922201	-237
CAGCCGGTTTTTTTATGTAAATCAGCTTGA	1	109	1	TTTTATGTAA	    0.952627	-171
GCGTTTGGCCATTTTTGTCAAGCTGATTTA	1	126	0	ATTTTTGTCA	    0.957215	-154
TTTTGGCTAATTTAATGTCACATGTCTAAG	1	205	1	TTTAATGTCA	    0.983543	-75
TGTTTTATCTTATGTTGTCAGTTCTTAGAC	1	228	0	TATGTTGTCA	    0.940931	-52
ACAATCGGACATTGATGGCAAAGAGGAGGA	1	255	1	ATTGATGGCA	    0.947729	-25
          **********

Masking position 6
Map Score:   3.32999

Number of sites scoring better than the average of aligned sites = 825
Number in coding regions = 708
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 3

CTATTTTGAATAAATGACACTGTGCTGTTACA	1	26	1	TAAATGACTG	     0.97887	-254
CTGATTTACATAAAAAAACCGGCTGGGTCAGC	1	102	0	TAAAAAACGG	    0.979736	-178
TTTTTTTATGTAAATCAGCTTGACAAAAATGG	1	116	1	TAAATCATTG	    0.959671	-164
CCTGTGTAAATAAAACATGCTTTTGGCTAATT	1	185	1	TAAAACACTT	    0.971508	-95
CAACATAAGATAAAACAATCGGACATTGATGG	1	241	1	TAAAACACGG	     0.99482	-39
          *******  ***

Masking position 7
Map Score:   2.06898

Number of sites scoring better than the average of aligned sites = 375
Number in coding regions = 319
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 4

CGGCTGGGTCAGCAGCCGGTCCAAACGAGA	1	85	0	AGCAGCCGGT	    0.758313	-195
CGGCTGCTGACCCAGCCGGTTTTTTTATGT	1	97	1	CCCAGCCGGT	    0.704882	-183
          **********

Masking position 4
Map Score:   0.00823374

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 8
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   5.70866e-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:   5.70866e-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:   5.70866e-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