AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i277_hypothetical21_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv2435c	300	hypothetical protein Rv2435c

Motif number 1

CACATGCCCCGGCACCGGCAACCGCTGCGGAGTG     	1	6	0	GACGCGCGCG	    0.963046	-295
ATAGCTCGGCCGTATCGCAATGTTCAGCGAGTCGATGGA	1	49	0	CACGGTCGCG	    0.989012	-252
TGGGTGGTCCGTAATCGAGGTGAGCCAGGATAGCTCGGC	1	78	0	GACGGGCAGG	    0.991219	-223
CTTGAGGGGTGGTAGCGATTGGTTCTGGGTGGTCCGTAA	1	103	0	GACGGTCGGG	    0.998445	-198
TCCTCGTCGCGCACGCGCTTCTTGAGGGGTGGTAGCGAT	1	123	0	GCCGTGAGGG	    0.942863	-178
CCGCGTACGGGTCCTCGTCATCGTCCTCGTCGCGCACGC	1	146	0	GCCGCTCTCG	    0.996006	-155
ACGAGGACCCGTACGCGGCGCATTCCTCGATTGGTCGCT	1	167	1	GCCGATCTCG	      0.9795	-134
TTCCTCGATTGGTCGCTGGTGGCTTTTCGGCAAACGCGA	1	189	1	GCCTGTTTCG	    0.820189	-112
TGGCTTTTCGGCAAACGCGATGATCGTGGGCTGGGCACG	1	208	1	GACGGTCTGG	    0.996208	-93
TCGTGGGCTGGGCACGTTAGTCTGCTGCGTAATCGGCGC	1	231	1	GAGTCGCGCG	    0.937824	-70
AGAGCAGCCTGCGACCGACAGCAGAGGGGAAGCCGG   	1	275	1	GACGCGAGGG	    0.991811	-26
          *  * **    * ** ***

Masking position 19
Map Score:   17.1653

Number of sites scoring better than the average of aligned sites = 19430
Number in coding regions = 18512
Number in noncoding regions = 918
Number of orfs with sites within 600 bp upstream = 629
Fraction of orfs with sites within 600 bp upstream = 0.101028


Motif number 2

 CACTCCGCAGCGGTTGCCGGTGCCGGGGCAT	1	10	1	GCGGTTGCGT	    0.961757	-291
GGTTGCCGGTGCCGGGGCATGTGTTGATCCAT	1	22	1	GCCGGGGCGT	    0.983483	-279
GCAATGTTCAGCGAGTCGATGGATCAACACAT	1	40	0	GCGAGTCGGG	     0.93403	-261
AGCCAGGATAGCTCGGCCGTATCGCAATGTTC	1	63	0	GCTCGGCCAT	    0.939254	-238
CCCTCAAGAAGCGCGTGCGCGACGAGGACGAT	1	134	1	GCGCGTGCGA	     0.98611	-167
TGCGCCGCGTACGGGTCCTCGTCATCGTCCTC	1	157	0	ACGGGTCCGT	    0.774359	-144
GAGGACCCGTACGCGGCGCATTCCTCGATTGG	1	169	1	ACGCGGCGTT	     0.93533	-132
TCGATTGGTCGCTGGTGGCTTTTCGGCAAACG	1	193	1	GCTGGTGGTT	    0.961617	-108
ATGATCGTGGGCTGGGCACGTTAGTCTGCTGC	1	227	1	GCTGGGCATT	    0.883907	-74
TGCGTAATCGGCGCGTCGTAGAGCAGCCTGCG	1	256	1	GCGCGTCGGA	    0.988738	-45
          ********  **

Masking position 2
Map Score:   8.57135

Number of sites scoring better than the average of aligned sites = 17320
Number in coding regions = 16076
Number in noncoding regions = 1244
Number of orfs with sites within 600 bp upstream = 831
Fraction of orfs with sites within 600 bp upstream = 0.133473


Motif number 3

TCGGCCGTATCGCAATGTTCAGCGAGTCGA	1	53	0	CGCAATGTTC	    0.986123	-248
GGTCCGTAATCGAGGTGAGCCAGGATAGCT	1	82	0	CGAGGTGAGC	    0.958674	-219
GGGGTGGTAGCGATTGGTTCTGGGTGGTCC	1	107	0	CGATTGGTTC	    0.887369	-194
CCGTACGCGGCGCATTCCTCGATTGGTCGC	1	175	1	CGCATTCCTC	    0.956115	-126
TTTCGGCAAACGCGATGATCGTGGGCTGGG	1	213	1	CGCGATGATC	    0.981663	-88
TGCTGTCGGTCGCAGGCTGCTCTACGACGC	1	268	0	CGCAGGCTGC	    0.975301	-33
          **********

Masking position 2
Map Score:   1.36134

Number of sites scoring better than the average of aligned sites = 6305
Number in coding regions = 5887
Number in noncoding regions = 418
Number of orfs with sites within 600 bp upstream = 365
Fraction of orfs with sites within 600 bp upstream = 0.0586251


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

          **********

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