AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0070	143	DNA repair protein (recN)
#2	HI0072	63	conserved hypothetical protein

Motif number 1

TAGGTTGGTTAAAATCATTTTGATTATGGT	1	20	1	AAAATCATTT	     0.98727	-124
TAGATTTGACAAAATACTGTAAAAAATCCT	1	68	1	AAAATACTGT	    0.926768	-76
AATACTGTAAAAAATCCTTTACTGTAAATT	1	80	1	AAAATCCTTT	    0.989603	-64
       AGCAAAATCCTTTAACTGTATAT	1	131	0	AAAATCCTTT	    0.989603	-13
TCGTTCCTTTAAAACCATTGCTCTTGTAGG	2	16	1	AAAACCATTG	    0.978874	-48
 TTGTAAGTTAATATCATTGCGAGGCTTAC	2	45	0	AATATCATTG	    0.969095	-19
          **********

Masking position 4
Map Score:   11.9959

Number of sites scoring better than the average of aligned sites = 173
Number in coding regions = 141
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

AATCGAAAATTTTTACCATAATCAAAATGA	1	34	0	TTTTACCATA	    0.976094	-110
GTAAAGGATTTTTTACAGTATTTTGTCAAA	1	72	0	TTTTACAGTA	    0.975914	-72
AACTGACTTAATTTACAGTAAAGGATTTTT	1	89	0	ATTTACAGTA	    0.946778	-55
ATTAAGTCAGTTATATCATATTAAATATAC	1	107	1	TTATATCATA	     0.96251	-37
ATCATATTAAATATACAGTTAAAGGATTTT	1	121	1	ATATACAGTT	    0.947013	-23
          TTATATCGTTCCTTTAAAAC	2	1	1	TTATATCGTT	    0.976229	-63
  TTGTAAGTTAATATCATTGCGAGGCTTA	2	46	0	TAATATCATT	    0.802327	-18
          **********

Masking position 5
Map Score:   7.76132

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 268
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

GTAGCAAATTAGGTTGGTTAAAATCATTTT	1	11	1	AGGTTGGTTA	    0.974925	-133
ACTGTAAATTAAGTCAGTTATATCATATTA	1	100	1	AAGTCAGTTA	    0.961721	-44
ACCATTGCTCTTGTAGGTAAGCCTCGCAAT	2	29	1	TTGTAGGTAA	    0.969932	-35
          TTGTAAGTTAATATCATTGC	2	54	0	TTGTAAGTTA	    0.981381	-10
          **********

Masking position 4
Map Score:   0.0661635

Number of sites scoring better than the average of aligned sites = 71
Number in coding regions = 61
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   8.05918e-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 5

          **********

No masking
Map Score:   8.05918e-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 6

          **********

No masking
Map Score:   8.05918e-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