AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -inagC_aful_opreg_100.orf -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	AF0111	115	conserved hypothetical protein
#2	AF0373	300	transcription initiation factor IID

Motif number 1

GCTAGAATGTAACCGAGAAGCAGAATCAGGCCGC	2	18	0	AACGAGAAGA	    0.993983	-283
CAACGAAACCAACCAATAGCTAGAATGTAACCGA	2	36	0	AACAATAAGA	    0.853912	-265
ACAGCGCAGGAAACGAGGGGCAGAAGCCATCACA	2	68	0	AACGAGGAGA	    0.996198	-233
ATTAGGGATAAAACGTAGGCAACAGCGCAGGAAA	2	89	0	AACGTAGACA	    0.950279	-212
GGCAGATTATAATCGCGGGAGTGATGATTAGGGA	2	115	0	AACGCGGTGA	    0.972279	-186
AAGTAGGTAAAAGCGAGAACCTCAAAAATGGAGA	2	189	0	AACGAGATCA	    0.973802	-112
CCTACTTCTCAATCGTGATTAACAAAATAAATCA	2	216	1	AACGTGAACA	    0.977861	-85
TAACAAAATAAATCAAAGTTAAGAGGGATGGCAA	2	235	1	AACAAAGAGA	    0.942359	-66
          ** *****   ***

Masking position 2
Map Score:   7.12322

Number of sites scoring better than the average of aligned sites = 334
Number in coding regions = 316
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TTTTAAAAATAAATAAGAAAAAATA         	1	2	0	AAAAAAAAAT	    0.824723	-114
TATTAAAGAAAAGCTTTTAAAAATAAATAAGAAA	1	16	0	AAGTTAAAAT	    0.985974	-100
CCTGTGTCAGAAAATTATAAATATCTCTCACGAC	1	52	1	AAATTAATAT	    0.961624	-64
ACGACCATTAAAGAATATTAAAATTAAAAATTGG	1	81	1	AAGTTAAAAT	    0.985975	-35
TCAAAAATGGAGAGTTCTGAAAATCTCCGCAGTG	2	168	0	AGATTAAAAT	    0.950129	-133
GTGATTAACAAAATAAATCAAAGTTAAGAGGGAT	2	230	1	AAAATAAAGT	     0.87458	-71
GAGGGATGGCAAAGGTATTTATATGGTATATAAG	2	257	1	AAATTTATAT	    0.824717	-44
TATGGTATATAAGTCTTTAAAAATGGTGGTGTT 	2	278	1	AAGTTAAAAT	    0.985973	-23
          ***  * * *****

Masking position 11
Map Score:   5.32355

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 67
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

AAATATCTCTCACGACCATTAAAGAATATT	1	70	1	CACGACCATT	    0.994213	-46
    TTGCACCACCTCCAATTTTTAATTTT	1	100	0	CACCTCCAAT	    0.986358	-16
TCCGCAGTGTCAACACCCTTTTCGGTTAGG	2	147	0	CAACACCCTT	    0.985538	-154
        AACACCACCATTTTTAAAGACT	2	289	0	CACCACCATT	    0.997838	-12
          **********

Masking position 2
Map Score:   4.67717

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 70
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

GCGGCCTGATTCTGCTTCTCGGTTACATTC	2	18	1	TCTGCTTCTC	    0.995624	-283
TGTGATGGCTTCTGCCCCTCGTTTCCTGCG	2	68	1	TCTGCCCCTC	    0.995179	-233
GCGATTATAATCTGCCTAACCGAAAAGGGT	2	133	1	TCTGCCTAAC	    0.972263	-168
CTCGCTTTTACCTACTTCTCAATCGTGATT	2	206	1	CCTACTTCTC	    0.971088	-95
          **********

Masking position 3
Map Score:   2.13529

Number of sites scoring better than the average of aligned sites = 279
Number in coding regions = 266
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

TTTTCTTATTTATTTTTAAAAGCTTTTCTT	1	15	1	TATTTTTAAA	     0.91131	-101
TTTAAAAGCTTTTCTTTAATATTCCTGTGT	1	29	1	TTTCTTTAAT	    0.965896	-87
TCGTGAGAGATATTTATAATTTTCTGACAC	1	55	0	TATTTATAAT	    0.830457	-61
TAATTTTAATATTCTTTAATGGTCGTGAGA	1	77	0	ATTCTTTAAT	    0.955809	-39
CACCACCTCCAATTTTTAATTTTAATATTC	1	93	0	AATTTTTAAT	    0.947737	-23
CTTTGATTTATTTTGTTAATCACGATTGAG	2	223	0	TTTTGTTAAT	    0.879013	-78
ATGGTATATAAGTCTTTAAAAATGGTGGTG	2	279	1	AGTCTTTAAA	    0.848242	-22
          **********

Masking position 8
Map Score:   4.02466

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 81
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 6

          **********

No masking
Map Score:   -8.99957e-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:   -8.99957e-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 8

          **********

No masking
Map Score:   -8.99957e-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