AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	b0762	128	orf, hypothetical protein
#2	modA	166	molybdate-binding periplasmic protein; permease

Motif number 1

  AACAATGTCCTGGCAAAAGTCTTATTGTG	1	9	1	CCGGCAAAAG	    0.995317	-120
AAAACGAACGCCACGCAAAGCTGACCGCACA	1	44	1	CCCGCAAAGC	    0.996117	-85
GCAAAGCTGACCGCACAAAAGGGGAGTGCTT	1	58	1	CCCACAAAAG	    0.992608	-71
TAACCGCTAAGCACAGAAAAGCACTCCCCTT	1	76	0	GCCAGAAAAG	     0.97209	-53
AAAGAAAATGCCCGACTAAGCGGGCATTCAG	2	15	0	CCGACTAAGC	    0.966136	-152
AAAAATATCGGCAGGAAAAGCAGGAAGTTGA	2	49	0	GCGGAAAAGC	    0.960725	-118
TTCTTATCTACCTCACAAAGGTTAGCAATAA	2	79	1	CCCACAAAGG	    0.993385	-88
AGCAATAACTGCTGGGAAAATTCCGAGTTAG	2	102	1	GCGGGAAAAT	      0.9137	-65
          ** ********

Masking position 8
Map Score:   12.1784

Number of sites scoring better than the average of aligned sites = 773
Number in coding regions = 707
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

GCCACGCAAAGCTGACCGCACAAAAGGGGA	1	53	1	GCTGACCGCA	    0.968594	-76
ATGAGACTATTCTAACCGCTAAGCACAGAA	1	89	0	TCTAACCGCT	    0.968138	-40
   TTCCCTGAATGCCCGCTTAGTCGGGCA	2	8	1	AATGCCCGCT	    0.995578	-159
AGAAAAAGAAAATGCCCGACTAAGCGGGCA	2	20	0	AATGCCCGAC	     0.94011	-147
CTTTTTCTCAACTTCCTGCTTTTCCTGCCG	2	42	1	ACTTCCTGCT	    0.967869	-125
AAAGGTTAGCAATAACTGCTGGGAAAATTC	2	95	1	AATAACTGCT	    0.955521	-72
          **********

Masking position 3
Map Score:   3.35418

Number of sites scoring better than the average of aligned sites = 2034
Number in coding regions = 1907
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 3

ATAAGACTTTTGCCAGGACATTGTT      	1	5	0	TCCAGGACAT	    0.968787	-124
CGGTCAGCTTTGCGTGGCGTTCGTTTTCCGT	1	40	0	TCGTGGCGTT	    0.985668	-89
CTCATGACTATATCTGGAGTTGACC      	1	114	1	TTCTGGAGTT	    0.977271	-15
CTTCCTGCTTTTCCTGCCGATATTTTTTCTT	2	53	1	TCCTGCCGAT	    0.991454	-114
CTCGGAATTTTCCCAGCAGTTATTGCTAACC	2	98	0	TCCAGCAGTT	    0.990784	-69
          * *********

Masking position 1
Map Score:   2.23351

Number of sites scoring better than the average of aligned sites = 840
Number in coding regions = 780
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 4

TTATTGTGACGGAAAACGAACGCCACGCAAAG	1	32	1	GAAACGAACG	    0.987362	-97
CGAACGCCACGCAAAGCTGACCGCACAAAAGG	1	48	1	GAAACTGACC	    0.956639	-81
AGGTAGATAAGAAAAAATATCGGCAGGAAAAG	2	60	0	GAAAATATCG	    0.979903	-107
TTATGTAGGCGACAATATAACGACTAACTCGG	2	124	0	GCAAATAACG	     0.99426	-43
TTATATTGTCGCCTACATAACGTTACATTAAG	2	136	1	GCTAATAACG	    0.981378	-31
          * *** ******

Masking position 5
Map Score:   0.865078

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 201
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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