AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i097_Phosphate_Transport_ecoli_reg_100.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	pitB	291	low-affinity phosphate transport

Motif number 1

ATTATTCTTCATAATCAGTACGGGGTTGCTA	1	20	0	ATAATCATAC	    0.984374	-272
ATTATGAAGAATAATCAGTACGGGGATTAAT	1	36	1	ATAATCATAC	    0.984374	-256
ATTAATCAAAATATTCAATATTTATATATTC	1	61	1	ATATTCATAT	    0.683029	-231
ATTCCAATATTTATTCATTTCATATGTGAAT	1	88	1	TTATTCATTC	    0.937486	-204
ACTGGTTAATATATTCACATATGAAATGAAT	1	100	0	ATATTCAATA	    0.868625	-192
ACCTTTAGAAATAATCAAAACACAGGTATTC	1	132	0	ATAATCAAAC	    0.985124	-160
CAATAAGCATTCATTCAAAACCTTTAGAAAT	1	151	0	TCATTCAAAC	    0.929358	-141
GTCCGTTCGTAAATTCAAAATGGCGTAATCT	1	266	1	AAATTCAAAT	    0.860144	-26
          ******* ***

Masking position 7
Map Score:   9.13836

Number of sites scoring better than the average of aligned sites = 573
Number in coding regions = 468
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 2

       TACATGTTGTAGCAACCCCGTACTGATTATG	1	4	1	ATTTAACCCT	    0.997314	-288
AATATTGAATATTTTGATTAATCCCCGTACTGATTATT	1	45	0	ATTTTACCCT	    0.996155	-247
AAAATATTCAATATTTATATATTCCAATATTTATTCAT	1	68	1	ATTTTACCAT	    0.991377	-224
TTAAAAAATGATATTTCACTTTGCCCATGCCGTTAAAG	1	215	1	ATTTATCCCT	    0.991255	-77
          ATATTAGATTACGCCATTTTGAATTTAC	1	274	0	ATTTAACCAT	    0.994015	-18
          ** **  *  *  *** *

Masking position 5
Map Score:   4.46018

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 15
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

ATATTTATATATTCCAATATTTATTCATTTCA	1	78	1	ATTCAATTTT	    0.974947	-214
AAACACAGGTATTCCACTGGTTAATATATTCA	1	114	0	ATTCACTGTT	    0.985846	-178
TACACAAGAAATAACACTCTTTTTATCGTTAA	1	187	1	ATACACTTTT	    0.990709	-105
GCAAAGTGAAATATCATTTTTTAACGATAAAA	1	207	0	ATACATTTTT	    0.964254	-85
   ATATTAGATTACGCCATTTTGAATTTACG	1	273	0	ATTCGCCTTT	    0.969085	-19
          *** **** ***

Masking position 2
Map Score:   1.55533

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 123
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

TTCATAATCAGTACGGGGTTGCTACAACAT	1	14	0	GTACGGGGTT	    0.998103	-278
AGAATAATCAGTACGGGGATTAATCAAAAT	1	43	1	GTACGGGGAT	    0.997621	-249
          **********

Masking position 3
Map Score:   1.35978

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 6
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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:   -4.80737e-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