AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_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	HI1194	300	glycine cleavage system transcriptional activator (gcvA)
#2	HI1196	35	succinyl-CoA synthetase, beta subunit (sucC)

Motif number 1

AAAAAACGCCACTCAATGAGAGCAGCGTTT	1	25	1	ACTCAATGAG	    0.993777	-276
ATATACAGGAAGTAAATGAGTAACAAATTG	1	73	1	AGTAAATGAG	    0.990805	-228
ATTCCTTACTAGTTAATGAGTTTCAGACTT	1	152	0	AGTTAATGAG	    0.994765	-149
ATACAACCATACTTAATGATTGGTAATTCC	1	177	0	ACTTAATGAT	    0.979518	-124
          **********

Masking position 5
Map Score:   5.15274

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

GCTCTCATTGAGTGGCGTTTTTTTCATCCCG	1	17	0	AGTGCGTTTT	    0.990416	-284
ACCGAACTTGAGTAACAATTTGTTACTCATT	1	87	0	AGTACAATTT	    0.936686	-214
TTGTTACTCAAGTTCGGTTTCCCGAACTATA	1	100	1	AGTTGGTTTC	    0.938695	-201
TTCAGACTTAAGTATGATGTTGTGTTTGCAT	1	130	0	AGTAGATGTT	    0.941892	-171
CTCATTAACTAGTAAGGAATTACCAATCATT	1	162	1	AGTAGGAATT	    0.945759	-139
CCAATCATTAAGTATGGTTGTATTGTAAGGA	1	184	1	AGTAGGTTGT	    0.980093	-117
GGAAAGGACAAGTGACGTTTTTTTATTTGAG	1	223	1	AGTGCGTTTT	    0.990416	-78
          **** ******

Masking position 1
Map Score:   4.71774

Number of sites scoring better than the average of aligned sites = 223
Number in coding regions = 170
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

CTCTCATTGAGTGGCGTTTTTTTCATCCCGATT	1	14	0	GTGGTTTTTT	    0.988837	-287
GTATATTATTAAACCGATTTGGTTAAACGCTGC	1	46	0	AAAGATTTGT	    0.821948	-255
CCGAACTTGAGTAACAATTTGTTACTCATTTAC	1	84	0	GTAAATTTTT	    0.899902	-217
AGACTTAAGTATGATGTTGTGTTTGCATATAGT	1	125	0	ATGGTTGTTT	    0.934045	-176
CAATCATTAAGTATGGTTGTATTGTAAGGAAAA	1	185	1	GTAGTTGTTT	    0.977876	-116
GAAAGGACAAGTGACGTTTTTTTATTTGAGGTA	1	224	1	GTGGTTTTTT	    0.988665	-77
GTCTATAATGGACAAGATTTATTTCAAATTAGT	1	265	0	GACGATTTTT	    0.900792	-36
        TTATAAAATTTTCGTCTATAATGGA	1	286	0	ATAATTTTGT	    0.745741	-15
        GTGAACTGTTTTCATAACCAAAAAG	2	3	1	GAAGTTTTAT	    0.907809	-33
          ***  ***** **

Masking position 8
Map Score:   4.14864

Number of sites scoring better than the average of aligned sites = 660
Number in coding regions = 502
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 4

          **********

No masking
Map Score:   9.48026e-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:   9.48026e-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:   9.48026e-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