AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i116_Peptide_Transport_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	sapA	248	homolog of Salmonella peptide transport periplasmic protein
#2	HI1638	69	peptide ABC transporter, periplasmic-binding protein (sapA)

Motif number 1

CCATCTGTTCAACATTCGTACCCGTGATTTC	1	106	0	ACATTCGTAC	    0.866124	-143
AGGTGACGTCGCCATCTGTTCAACATTCGTA	1	117	0	GCATCTGTTC	    0.990419	-132
AGATGGCGACGTCACCTGTTCAACGACCAAC	1	131	1	GCACCTGTTC	    0.985814	-118
CAACCACACGGCCCTCATTACGACCCCTGAA	1	158	1	GCCTCATTAC	    0.971511	-91
CCCTCATTACGACCCCTGAACACAAACGGTA	1	169	1	GCCCCTGAAC	    0.975656	-80
TTAGTAAGATAGCCTCTTTACATAAAATCCC	1	220	1	ACCTCTTTAC	    0.974308	-29
CAATATCCTAGCCATTTTTACTAATATGCCT	2	12	1	GCATTTTTAC	    0.969135	-58
          * *********

Masking position 3
Map Score:   5.76206

Number of sites scoring better than the average of aligned sites = 702
Number in coding regions = 645
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 2

GACACGCACTGCAGCGTGCTTTAATGGGTT	1	18	1	GCAGCGTGCT	    0.994874	-231
TTAGCGAGGAGCAGAGCGGTACGATCGTGA	1	50	0	GCAGAGCGGT	    0.992218	-199
CGTAATGAGGGCCGTGTGGTTGGTCGTTGA	1	150	0	GCCGTGTGGT	    0.994956	-99
   AACAAATGCATTGTGATAAATTATGTG	2	53	0	GCATTGTGAT	    0.975368	-17
          **********

Masking position 10
Map Score:   2.66916

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 220
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

CAGCGTGCTTTAATGGGTTTCTCACGATCG	1	29	1	TAATGGGTTT	    0.971993	-220
     AATATTAAGGGATTTTATGTAAAGA	1	234	0	TAAGGGATTT	    0.988365	-15
TGTCAAATTGTAAGGCATATTAGTAAAAAT	2	25	0	TAAGGCATAT	    0.972751	-45
TAATTTATCACAATGCATTTGTT       	2	57	1	CAATGCATTT	    0.747745	-13
          **********

Masking position 3
Map Score:   1.66196

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 47
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

ATGTCATTAAATATTAGTAAGATAGCCTCT	1	207	1	ATATTAGTAA	    0.969936	-42
ATTGTAAGGCATATTAGTAAAAATGGCTAG	2	19	0	ATATTAGTAA	    0.969936	-51
          **********

Masking position 5
Map Score:   0.713096

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 5

GGTACGAATGTTGAACAGATGGCGACGTCA	1	115	1	TTGAACAGAT	    0.986985	-134
TGGTTGGTCGTTGAACAGGTGACGTCGCCA	1	134	0	TTGAACAGGT	    0.971567	-115
ATTACGACCCCTGAACACAAACGGTAATGG	1	174	1	CTGAACACAA	    0.971906	-75
TGCCTTACAATTTGACACATAATTTATCAC	2	38	1	TTTGACACAT	     0.95669	-32
TGACACATAATTTATCACAATGCATTTGTT	2	50	1	TTTATCACAA	     0.91225	-20
          **********

Masking position 7
Map Score:   1.49686

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 171
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 6

          **********

No masking
Map Score:   -8.2833e-14

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:   -8.2833e-14

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:   -8.2833e-14

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