AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___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	HI1659	179	ribonucleoside-diphosphate reductase, alpha chain (nrdA)
#2	HI1660	141	ribonucleoside diphosphate reductase, beta chain (nrdB)

Motif number 1

AAATTTGTTGAATTTTTCACCGCACTTTGA	1	15	0	AATTTTTCAC	    0.925267	-165
AAATTCAACAAATTTTTACCGCACTTTTTC	1	30	1	AATTTTTACC	    0.899366	-150
CACTTTTTCTTATTTTTCTAAATAAAAAAT	1	51	1	TATTTTTCTA	    0.885252	-129
AAAAACCGTTTATTTTTAAATAAGTTATCT	1	99	1	TATTTTTAAA	    0.603045	-81
ACGCCCCTATTGTCTTCCCCAACTTATGGG	2	11	1	TGTCTTCCCC	    0.972703	-131
TATGTCGTGCTATCTTCCCCATAAGTTGGG	2	28	0	TATCTTCCCC	    0.993486	-114
CGAATTAGGATACTTTCCTCAGTCTTTGAT	2	59	1	TACTTTCCTC	     0.93947	-83
CAGTCTTTGATAGTTTCCCCTGATAAACAG	2	78	1	TAGTTTCCCC	     0.99054	-64
ATCATTTATTTAGCTTTCCCTGTTTATCAG	2	97	0	TAGCTTTCCC	    0.985312	-45
          **********

Masking position 5
Map Score:   9.30603

Number of sites scoring better than the average of aligned sites = 762
Number in coding regions = 650
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 95
Fraction of orfs with sites within 600 bp upstream = 0.0152586


Motif number 2

TTATTTTTCTAAATAAAAAATTTTAATTTTTAT	1	60	1	AAATAAATTT	    0.770532	-120
GGTTTTTGTGAGAATAAAAATTAAAATTTTTTA	1	73	0	AGAATAATTA	     0.81938	-107
ACTTATTTAAAAATAAACGGTTTTTGTGAGAAT	1	91	0	AAATAAGTTT	    0.965808	-89
TCTTGACAATAGATAACTTATTTAAAAATAAAC	1	106	0	AGATAAATTT	    0.579454	-74
GAATCAAATCAAAAAATTTATTACTTGCGATCT	1	137	1	AAAAAAATTA	    0.872016	-43
         AAGATAATGTGTTTGAGAAAAGAT	1	166	0	AGATAAGTTT	      0.9708	-14
AGATAGCACGACATAACGAATTAGGATACTTTC	2	43	1	ACATAAATTA	    0.962103	-99
AGGGAAAGCTAAATAAATGATAAGTTCTATTTA	2	106	1	AAATAAATAA	    0.905358	-36
          ******   ****

Masking position 6
Map Score:   6.92033

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 269
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 3

TGAATTTTTCACCGCACTTTGAAGGA    	1	7	0	ACCGCACTTT	    0.997363	-173
ACAAATTTTTACCGCACTTTTTCTTATTTT	1	37	1	ACCGCACTTT	    0.997363	-143
          **********

Masking position 6
Map Score:   2.26646

Number of sites scoring better than the average of aligned sites = 1115
Number in coding regions = 700
Number in noncoding regions = 415
Number of orfs with sites within 600 bp upstream = 285
Fraction of orfs with sites within 600 bp upstream = 0.0457758


Motif number 4

ATTTTTATTCTCACAAAAACCGTTTATTTT	1	85	1	TCACAAAAAC	    0.981217	-95
TGCGATCTTTTCTCAAACACATTATCTT  	1	162	1	TCTCAAACAC	    0.992729	-18
CAGGGGAAACTATCAAAGACTGAGGAAAGT	2	70	0	TATCAAAGAC	    0.980413	-72
          **********

Masking position 5
Map Score:   0.430291

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 13
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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