AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -icoldbox_mpneu_opreg_100.orf -g0.400 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	deaD	157	ATP-dependent RNA helicase; similar to GenBank Accession Number F64056, from H. influenzae

Motif number 1

CAAAATAAGAAATTAGCCCAGTCAAGGGGT	1	35	1	AATTAGCCCA	    0.993563	-123
AACCCCACAAAATCAGCCCCCAAACTTATA	1	66	1	AATCAGCCCC	    0.997343	-92
AACTTATAATAAATAAACCAAAACAACCAC	1	88	1	AAATAAACCA	    0.949517	-70
AAATAAACCAAAACAACCACCTTAAGTGGG	1	98	1	AAACAACCAC	    0.978609	-60
ATTAATTAGTTAACAGCCCACTTAAGGTGG	1	114	0	TAACAGCCCA	    0.993441	-44
          **********

Masking position 5
Map Score:   6.8041

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 99
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

TAATTCAACAAGTATTAATTC         	1	2	0	AGTATTAATT	    0.866335	-156
TTTCTTATTTTGTTATAATTCAACAAGTAT	1	17	0	TGTTATAATT	    0.878227	-141
GACTGGGCTAATTTCTTATTTTGTTATAAT	1	28	0	ATTTCTTATT	    0.955769	-130
GTTTTGGTTTATTTATTATAAGTTTGGGGG	1	82	0	ATTTATTATA	    0.907586	-76
GTTATTAGTAATTAATTAGTTAACAGCCCA	1	124	0	ATTAATTAGT	    0.825858	-34
TGACTTTGATAGTTATTAGTAATTAATTAG	1	135	0	AGTTATTAGT	    0.900643	-23
          **********

Masking position 6
Map Score:   3.91221

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 126
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

GGTTCACCCCTTGACTGGGCTAATTTCTTA	1	40	0	TTGACTGGGC	    0.991988	-118
TGGGGGCTGATTTTGTGGGGTTCACCCCTT	1	58	0	TTTTGTGGGG	    0.993257	-100
TTTATTATAAGTTTGGGGGCTGATTTTGTG	1	71	0	GTTTGGGGGC	    0.992693	-87
AACAACCACCTTAAGTGGGCTGTTAACTAA	1	109	1	TTAAGTGGGC	    0.995554	-49
          **********

Masking position 2
Map Score:   3.8303

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 15
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

          **********

No masking
Map Score:   -2.10731e-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 5

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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