AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i264_hypothetical1_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	Rv1419	179	hypothetical protein Rv1419
#2	uvrC	63	uvrC

Motif number 1

          CGCCAGCCCCCATGCTCTTCGCGG	1	1	1	CGCCAGCCCG	    0.995497	-179
GCCGGTTCAAACCCGCCCGCGAAGAGCATGGGGG	1	17	0	ACCCGCCCGG	    0.993512	-163
GTGACTTTGACCCCGTTTGGCCGGTTCAAACCCG	1	36	0	CCCCGTTTCG	    0.957967	-144
TTTGAGTATGCCCAGGCCGCCGTGACTTTGACCC	1	57	0	CCCAGGCCCG	    0.998493	-123
CAAATGTGTCCCACGGCCCACCATCGGATCCCGA	1	87	1	CCACGGCCCT	    0.994718	-93
CGGATCCCGACGACGGCCCACTGTGAACTGCGCC	1	111	1	CGACGGCCCT	    0.990925	-69
CTGTGAACTGCGCCGCTCGTGGTGCATTACCCAG	1	131	1	CGCCGCTCGG	    0.935494	-49
TGGTGCATTACCCAGACCACGATGAGAGAATGGC	1	150	1	CCCAGACCGG	    0.985583	-30
        TTCCCCGCCATTCTCTCATCGTGGTC	1	164	0	CCCCGCCACT	    0.989749	-16
GGCGGGGGTTCGCCGGGCAGGCCGG         	2	2	0	CGCCGGGCGG	    0.981857	-62
CCCGGCGAACCCCCGCCTTTCTGGGCGCCGTCGA	2	19	1	CCCCGCCTCG	     0.99849	-45
          ********  *  *

Masking position 5
Map Score:   26.0814

Number of sites scoring better than the average of aligned sites = 16157
Number in coding regions = 15275
Number in noncoding regions = 882
Number of orfs with sites within 600 bp upstream = 619
Fraction of orfs with sites within 600 bp upstream = 0.0994218


Motif number 2

TCAAACCCGCCCGCGAAGAGCATGGGGGCT	1	15	0	CCGCGAAGAG	    0.965815	-165
TATGCCCAGGCCGCCGTGACTTTGACCCCG	1	55	0	CCGCCGTGAC	    0.989451	-125
GTCCCACGGCCCACCATCGGATCCCGACGA	1	94	1	CCACCATCGG	    0.981537	-86
TCACAGTGGGCCGTCGTCGGGATCCGATGG	1	107	0	CCGTCGTCGG	    0.649442	-73
CGACGACGGCCCACTGTGAACTGCGCCGCT	1	118	1	CCACTGTGAA	    0.943177	-62
TCTGGGTAATGCACCACGAGCGGCGCAGTT	1	136	0	GCACCACGAG	    0.976057	-44
ATTACCCAGACCACGATGAGAGAATGGCGG	1	156	1	CCACGATGAG	    0.988488	-24
   CCGGCCTGCCCGGCGAACCCCCGCCTT	2	8	1	GCCCGGCGAA	    0.896584	-56
GCCTTTCTGGGCGCCGTCGAAGCGACCACT	2	33	1	GCGCCGTCGA	    0.972436	-31
          **********

Masking position 2
Map Score:   9.50396

Number of sites scoring better than the average of aligned sites = 21688
Number in coding regions = 20213
Number in noncoding regions = 1475
Number of orfs with sites within 600 bp upstream = 848
Fraction of orfs with sites within 600 bp upstream = 0.136203


Motif number 3

GCGAAGAGCATGGGGGCTGGCG         	1	2	0	TGGGGGTGGC	    0.878884	-178
CCAGCCCCCATGCTCTTCGCGGGCGGGTTTG	1	13	1	TGCTCTCGCG	    0.896155	-167
CCAGGCCGCCGTGACTTTGACCCCGTTTGGC	1	49	0	GTGACTTGAC	    0.894676	-131
TGGGACACATTTGAGTATGCCCAGGCCGCCG	1	69	0	TTGAGTTGCC	     0.95448	-111
TCCGATGGTGGGCCGTGGGACACATTTGAGT	1	84	0	GGCCGTGGAC	    0.711087	-96
CGGCCCACTGTGAACTGCGCCGCTCGTGGTG	1	124	1	TGAACTCGCC	    0.940943	-56
CCAGAAAGGCGGGGGTTCGCCGGGCAGGCCG	2	12	0	GGGGGTCGCC	     0.98861	-52
ACCCCCGCCTTTCTGGGCGCCGTCGAAGCGA	2	27	1	TTCTGGCGCC	    0.945912	-37
TAGGCTAGTGGTCGCTTCGACGGCGCCCAGA	2	38	0	GTCGCTCGAC	    0.915159	-26
          ****** ****

Masking position 9
Map Score:   1.73994

Number of sites scoring better than the average of aligned sites = 24315
Number in coding regions = 22579
Number in noncoding regions = 1736
Number of orfs with sites within 600 bp upstream = 990
Fraction of orfs with sites within 600 bp upstream = 0.159011


Motif number 4

TGCTCTTCGCGGGCGGGTTTGAACCGGCCA	1	23	1	GGGCGGGTTT	    0.944712	-157
TGACCCCGTTTGGCCGGTTCAAACCCGCCC	1	33	0	TGGCCGGTTC	    0.989629	-147
GAGTATGCCCAGGCCGCCGTGACTTTGACC	1	58	0	AGGCCGCCGT	    0.935117	-122
    CCGGCCTGCCCGGCGAACCCCCGCCT	2	7	1	TGCCCGGCGA	    0.957238	-57
CCCGCCTTTCTGGGCGCCGTCGAAGCGACC	2	30	1	TGGGCGCCGT	    0.967298	-34
TCTAGGCTAGTGGTCGCTTCGACGGCGCCC	2	41	0	TGGTCGCTTC	    0.971665	-23
          **********

Masking position 6
Map Score:   4.4185

Number of sites scoring better than the average of aligned sites = 13027
Number in coding regions = 12314
Number in noncoding regions = 713
Number of orfs with sites within 600 bp upstream = 527
Fraction of orfs with sites within 600 bp upstream = 0.084645


Motif number 5

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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