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_300.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	    0.994356	-276
CAATTTGTTACTCATTTACTTCCTGTATAT	1	73	0	CTCATTTACT	    0.991658	-228
AAGTCTGAAACTCATTAACTAGTAAGGAAT	1	152	1	CTCATTAACT	    0.995252	-149
GGAATTACCAATCATTAAGTATGGTTGTAT	1	177	1	ATCATTAAGT	    0.981399	-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

GGGATGAAAAAAACGCCACTCAATGAGAGCA	1	18	1	AAACGCACTC	    0.992715	-283
CGATTTGGTTAAACGCTGCTCTCATTGAGTG	1	34	0	AAACGTGCTC	    0.982238	-267
ATGAGTAACAAATTGTTACTCAAGTTCGGTT	1	88	1	AATTGTACTC	    0.910959	-213
ATAGTTCGGGAAACCGAACTTGAGTAACAAT	1	99	0	AAACCAACTT	    0.971901	-202
TGCAAACACAACATCATACTTAAGTCTGAAA	1	131	1	ACATCTACTT	    0.905388	-170
CCTTACAATACAACCATACTTAATGATTGGT	1	183	0	CAACCTACTT	    0.972282	-118
TCAAATAAAAAAACGTCACTTGTCCTTTCCT	1	222	0	AAACGCACTT	    0.978943	-79
          ***** *****

Masking position 10
Map Score:   5.34739

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 155
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

AATCGGGATGAAAAAAACGCCACTCAATGAGAG	1	14	1	AAAAAACCAC	    0.989616	-287
GCAGCGTTTAACCAAATCGGTTTAATAATATAC	1	46	1	ACAAATCTTT	    0.799391	-255
GTAAATGAGTAACAAATTGTTACTCAAGTTCGG	1	84	1	AAAAATTTAC	    0.917291	-217
ACTATATGCAAACACAACATCATACTTAAGTCT	1	125	1	AAACAACCAT	    0.954689	-176
TTTTCCTTACAATACAACCATACTTAATGATTG	1	185	0	AAACAACTAC	    0.978118	-116
TACCTCAAATAAAAAAACGTCACTTGTCCTTTC	1	224	0	AAAAAACCAC	    0.989557	-77
ACTAATTTGAAATAAATCTTGTCCATTATAGAC	1	265	1	AAAAATCGTC	    0.890058	-36
TCCATTATAGACGAAAATTTTATAA        	1	286	1	ACAAAATTAT	    0.789888	-15
          ** *****  ***

Masking position 6
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

AAGTTCGGTTTCCCGAACTATATGCAAACA	1	109	1	TCCCGAACTA	    0.978298	-192
TGATTGGTAATTCCTTACTAGTTAATGAGT	1	161	0	TTCCTTACTA	    0.992088	-140
TCCTACCCTTTTCCTTACAATACAACCATA	1	196	0	TTCCTTACAA	    0.980188	-105
ACGTCACTTGTCCTTTCCTACCCTTTTCCT	1	211	0	TCCTTTCCTA	    0.966298	-90
          **********

Masking position 1
Map Score:   1.29778

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 17
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

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 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