AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i104_Cobalt_Transport_ecoli_hinf_reg_300.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	yrbF	209	putative ATP-binding component of a transport system
#2	HI1087	300	ABC transporter, ATP-binding protein

Motif number 1

GATGCTTAATTTTGACTTTATGCGGCTAAAA	1	72	1	TTTACTTTAT	    0.910067	-138
CTGGCATTTGTTTTACTTTTTAGCCGCATAA	1	89	0	TTTACTTTTT	    0.921436	-121
          TTATTATTTATAAGCATTTAT	2	1	1	TTATATTTAT	    0.933626	-300
TAAGCATTTATCAATGTTTATTTTCCATAAA	2	21	1	TCATGTTTAT	    0.916505	-280
TTTTAATAATACTTTGTTTATGGAAAATAAA	2	37	0	ACTTGTTTAT	    0.722531	-264
TTACATTTCTTCATTATTTATTGAATTTTAA	2	62	0	TCATATTTAT	    0.951064	-239
TGTAATAGTAACATTCTTTTTGACCTCACTA	2	101	0	ACATCTTTTT	    0.860552	-200
TTTTTATAGATTAAAATTTTTGTAATAGTAA	2	121	0	TTAAATTTTT	    0.882702	-180
ATAAATTTTATTTCTATTTTTTATAGATTAA	2	138	0	TTTTATTTTT	    0.949696	-163
ATAAAATTTATCACTATTTTTATGACCACAT	2	158	1	TCATATTTTT	    0.957474	-143
AAGATGAAGTTTTTTCTTTTATCGCAACACA	2	208	0	TTTTCTTTTA	    0.729445	-93
ATTAAACAAATCTAACTTTTTCAGGTCATAT	2	242	1	TCTACTTTTT	    0.941872	-59
CTGATTGAACTTTTTATTTATAAACGAGATA	2	277	1	TTTTATTTAT	    0.942184	-24
          *** *******

Masking position 7
Map Score:   14.8947

Number of sites scoring better than the average of aligned sites = 663
Number in coding regions = 428
Number in noncoding regions = 235
Number of orfs with sites within 600 bp upstream = 258
Fraction of orfs with sites within 600 bp upstream = 0.0414391


Motif number 2

CCGCATAAAGTCAAAATTAAGCATCCGTTAC	1	66	0	TAAAATTAAG	    0.902372	-144
TTTATGCGGCTAAAAAGTAAAACAAATGCCA	1	88	1	TAAAAGTAAA	    0.902606	-122
TATGTTGGGTTCAAGGTTAAATTGAGCGCCA	1	154	1	TAAGGTTAAA	     0.96124	-56
CAAAGTATTATTAAAATTCAATAAATAATGA	2	52	1	TAAAATTCAA	    0.947048	-249
TTCTATTTTTTATAGATTAAAATTTTTGTAA	2	127	0	TTAGATTAAA	    0.858873	-174
TATGACCACATCAAAGTTAAACCAAAGAGAT	2	178	1	TAAAGTTAAA	    0.973791	-123
AAACTTCATCTTTAAATTAAACAAATCTAAC	2	227	1	TTAAATTAAA	    0.657358	-74
ATATGACCTGAAAAAGTTAGATTTGTTTAAT	2	242	0	AAAAGTTAGA	    0.790423	-59
GTTTATAAATAAAAAGTTCAATCAGTTTTAT	2	271	0	AAAAGTTCAA	    0.887534	-30
          * *********

Masking position 4
Map Score:   6.9947

Number of sites scoring better than the average of aligned sites = 257
Number in coding regions = 171
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 3

TTTAGCCGCATAAAGTCAAAATTAAGCATC	1	72	0	TAAAGTCAAA	    0.915307	-138
GCTTCTTTAGTGAGGTCAAAAAGAATGTTA	2	94	1	TGAGGTCAAA	    0.991413	-207
TTAACTTTGATGTGGTCATAAAAATAGTGA	2	168	0	TGTGGTCATA	    0.971715	-133
TCTAACTTTTTCAGGTCATATAAAACTGAT	2	252	1	TCAGGTCATA	    0.984011	-49
          **********

Masking position 6
Map Score:   1.8844

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 57
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

AATTTAACCTTGAACCCAACATATTTACAGA	1	146	0	TAACCCAACA	    0.991889	-64
GCTTAGAAAATCAACGCAAGACGAAGGGTGA	1	186	1	TAACGCAAGA	    0.991889	-24
ACATCAAAGTTAAACCAAAGAGATGTGTTGC	2	185	1	TAACCAAAGA	    0.968713	-116
GTTTTTTCTTTTATCGCAACACATCTCTTTG	2	200	0	TATCGCAACA	    0.979818	-101
          * *********

Masking position 8
Map Score:   1.04312

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 35
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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