AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -igcvA_hinf_opreg_100.orf -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	HI1194	300	glycine cleavage system transcriptional activator (gcvA)

Motif number 1

AAACGCTGCTCTCATTGAGTGGCGTTTTTT	1	25	0	CTCATTGAGT	    0.994196	-276
CAATTTGTTACTCATTTACTTCCTGTATAT	1	73	0	CTCATTTACT	    0.991422	-228
AAGTCTGAAACTCATTAACTAGTAAGGAAT	1	152	1	CTCATTAACT	    0.995117	-149
GGAATTACCAATCATTAAGTATGGTTGTAT	1	177	1	ATCATTAAGT	    0.980879	-124
          **********

Masking position 5
Map Score:   5.50491

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 14
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

CGGGATGAAAAAAACGCCACTCAATGAGAGC	1	17	1	AAAACGCACT	    0.991141	-284
CCGATTTGGTTAAACGCTGCTCTCATTGAGT	1	35	0	TAAACGTGCT	     0.90167	-266
AATGAGTAACAAATTGTTACTCAAGTTCGGT	1	87	1	AAATTGTACT	    0.932987	-214
TATAGTTCGGGAAACCGAACTTGAGTAACAA	1	100	0	GAAACCAACT	    0.926581	-201
ATGCAAACACAACATCATACTTAAGTCTGAA	1	130	1	AACATCTACT	    0.919391	-171
AATGATTGGTAATTCCTTACTAGTTAATGAG	1	162	0	AATTCCTACT	    0.926443	-139
TCCTTACAATACAACCATACTTAATGATTGG	1	184	0	ACAACCTACT	     0.97754	-117
CTCAAATAAAAAAACGTCACTTGTCCTTTCC	1	223	0	AAAACGCACT	    0.991141	-78
          ****** ****

Masking position 11
Map Score:   5.37308

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 220
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

CTCTCATTGAGTGGCGTTTTTTTCATCCCGATT	1	14	0	GTGGTTTTTT	    0.989146	-287
GTATATTATTAAACCGATTTGGTTAAACGCTGC	1	46	0	AAAGATTTGT	    0.792118	-255
CCGAACTTGAGTAACAATTTGTTACTCATTTAC	1	84	0	GTAAATTTTT	    0.913923	-217
AGACTTAAGTATGATGTTGTGTTTGCATATAGT	1	125	0	ATGGTTGTTT	    0.952716	-176
CAATCATTAAGTATGGTTGTATTGTAAGGAAAA	1	185	1	GTAGTTGTTT	    0.977138	-116
GAAAGGACAAGTGACGTTTTTTTATTTGAGGTA	1	224	1	GTGGTTTTTT	    0.989089	-77
GTCTATAATGGACAAGATTTATTTCAAATTAGT	1	265	0	GACGATTTTT	    0.885616	-36
        TTATAAAATTTTCGTCTATAATGGA	1	286	0	ATAATTTTGT	    0.783133	-15
          ***  ***** **

Masking position 8
Map Score:   3.04869

Number of sites scoring better than the average of aligned sites = 619
Number in coding regions = 470
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 4

          **********

No masking
Map Score:   7.91135e-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

GAGTGGCGTTTTTTTCATCCCGATTTTA  	1	9	0	TTTTTCATCC	    0.938558	-292
TTTGTTACTCATTTACTTCCTGTATATTAT	1	70	0	ATTTACTTCC	     0.86933	-231
TCAAGTTCGGTTTCCCGAACTATATGCAAA	1	107	1	TTTCCCGAAC	    0.846634	-194
AATGATTGGTAATTCCTTACTAGTTAATGA	1	163	0	AATTCCTTAC	    0.894977	-138
TTTCCTACCCTTTTCCTTACAATACAACCA	1	198	0	TTTTCCTTAC	    0.977407	-103
GTCACTTGTCCTTTCCTACCCTTTTCCTTA	1	209	0	CTTTCCTACC	    0.942955	-92
TTCAAATTAGTTTTTCTAATACCTCAAATA	1	246	0	TTTTTCTAAT	    0.878859	-55
GGACAAGATTTATTTCAAATTAGTTTTTCT	1	259	0	TATTTCAAAT	    0.499346	-42
   TTATAAAATTTTCGTCTATAATGGACA	1	284	0	ATTTTCGTCT	    0.828393	-17
          **********

Masking position 3
Map Score:   2.41756

Number of sites scoring better than the average of aligned sites = 1314
Number in coding regions = 1097
Number in noncoding regions = 217
Number of orfs with sites within 600 bp upstream = 184
Fraction of orfs with sites within 600 bp upstream = 0.0295535


Motif number 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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