AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_hinf_reg_300.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	     0.99343	-276
ATATACAGGAAGTAAATGAGTAACAAATTG	1	73	1	AGTAAATGAG	    0.990293	-228
ATTCCTTACTAGTTAATGAGTTTCAGACTT	1	152	0	AGTTAATGAG	    0.994472	-149
ATACAACCATACTTAATGATTGGTAATTCC	1	177	0	ACTTAATGAT	    0.978392	-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

GGGATGAAAAAAACGCCACTCAATGAGAGCA	1	18	1	AAACGCACTC	    0.991402	-283
CGATTTGGTTAAACGCTGCTCTCATTGAGTG	1	34	0	AAACGTGCTC	    0.978494	-267
ATGAGTAACAAATTGTTACTCAAGTTCGGTT	1	88	1	AATTGTACTC	    0.893658	-213
ATAGTTCGGGAAACCGAACTTGAGTAACAAT	1	99	0	AAACCAACTT	    0.966008	-202
TGCAAACACAACATCATACTTAAGTCTGAAA	1	131	1	ACATCTACTT	    0.887107	-170
CCTTACAATACAACCATACTTAATGATTGGT	1	183	0	CAACCTACTT	    0.966448	-118
TCAAATAAAAAAACGTCACTTGTCCTTTCCT	1	222	0	AAACGCACTT	    0.979525	-79
          ***** *****

Masking position 10
Map Score:   4.75118

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

     TAAAATCGGGATGAAAAAAACGCCAC	1	6	1	TGGGATGAAA	    0.973201	-295
TGTTTGCATATAGTTCGGGAAACCGAACTTG	1	108	0	TGTTCGGGAA	    0.966156	-193
ACATCATACTTAAGTCTGAAACTCATTAACT	1	141	1	TAGTCTGAAA	    0.875565	-160
ACTCATTAACTAGTAAGGAATTACCAATCAT	1	161	1	TGTAAGGAAT	    0.938805	-140
TATGGTTGTATTGTAAGGAAAAGGGTAGGAA	1	196	1	TGTAAGGAAA	    0.986647	-105
TGTAAGGAAAAGGGTAGGAAAGGACAAGTGA	1	207	1	AGGTAGGAAA	    0.971883	-94
ACGTCCTTTTTGGTTATGAAAACAGTTCAC 	2	10	0	TGTTATGAAA	    0.985241	-26
          * *********

Masking position 10
Map Score:   4.38819

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 166
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

CGGGATGAAAAAAACGCCACTCAATGAGAG	1	17	1	AAAACGCCAC	    0.994654	-284
CCGATTTGGTTAAACGCTGCTCTCATTGAG	1	36	0	TAAACGCTGC	    0.966604	-265
CTCAAATAAAAAAACGTCACTTGTCCTTTC	1	224	0	AAAACGTCAC	     0.99091	-77
ATAACCAAAAAGGACGTCGCGA        	2	24	1	AGGACGTCGC	    0.981087	-12
          **********

Masking position 4
Map Score:   2.05415

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 92
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 5

TATTATTAAACCGATTTGGTTAAACGCTGCT	1	45	0	CCATTTGGTT	    0.989693	-256
CAATTTGTTACTCATTTACTTCCTGTATATT	1	72	0	CTATTTACTT	    0.877933	-229
ATTGGTAATTCCTTACTAGTTAATGAGTTTC	1	158	0	CCTACTAGTT	    0.945745	-143
TCCTTTCCTACCCTTTTCCTTACAATACAAC	1	200	0	CCTTTTCCTT	    0.964628	-101
AAGATTTATTTCAAATTAGTTTTTCTAATAC	1	254	0	TCAATTAGTT	    0.880599	-47
 TCGCGACGTCCTTTTTGGTTATGAAAACAG	2	16	0	CCTTTTGGTT	    0.989693	-20
          ** ********

Masking position 7
Map Score:   1.58466

Number of sites scoring better than the average of aligned sites = 274
Number in coding regions = 233
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


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


Motif number 7

          **********

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 8

          **********

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