AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imarR_mtub_opreg_300.orf -g0.656 -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 =  	0.656
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv1404	168	hypothetical protein Rv1404
#2	Rv1931c	132	hypothetical protein Rv1931c

Motif number 1

TCGGTACCAGCCTCACCCGACGTCTCGCAGGA	1	17	0	CCCCCCGACG	    0.995277	-152
TAGCATCTGACCATCGTCGACATTGATTATTT	1	79	0	CCTGTCGACA	    0.956667	-90
TTTCCCGGGGCCGTCCCCGGCGTCAACTTCGT	1	141	0	CCTCCCGGCG	    0.999328	-28
      TACCCCTTTCCCGGGGCCGTCCCCGG	1	153	0	CCTCCCGGGG	    0.993634	-16
AGACCGTGCACCGGTCTTGGCAGACTGTGCCC	2	11	0	CCGCTTGGCA	     0.95583	-122
GGCGGCGCAGCCCTGCCCGAAAGACCGTGCAC	2	32	0	CCTCCCGAAA	    0.961695	-101
GGGCAGGGCTGCGCCGCCGGCGTGTCCTAATC	2	46	1	GCCGCCGGCG	    0.996409	-87
GGCGTCCACGCCACACACCGCACAGATTAGGA	2	70	0	CCCCACCGCA	    0.942784	-63
TTGGCCAGGCGCTGGCCTGGCGTCCACGCCAC	2	88	0	GCGCCTGGCG	    0.991817	-45
CCAGGCCAGCGCCTGGCCAACACTGGCATTCA	2	100	1	GCTGCCAACA	    0.850851	-33
GCCAACACTGGCATTCATGGCGCGAAGA    	2	115	1	GCTCATGGCG	    0.976935	-18
          ** * *******

Masking position 2
Map Score:   19.8597

Number of sites scoring better than the average of aligned sites = 25170
Number in coding regions = 23640
Number in noncoding regions = 1530
Number of orfs with sites within 600 bp upstream = 904
Fraction of orfs with sites within 600 bp upstream = 0.145198


Motif number 2

CTCCTGCGAGACGTCGGGTGAGGCTGGTAC	1	16	1	ACGTCGGGTG	    0.946712	-153
ACTTCGTCGTACACCGTGCGGGTAAGTCAG	1	118	0	ACACCGTGCG	    0.986076	-51
GACGAAGTTGACGCCGGGGACGGCCCCGGG	1	140	1	ACGCCGGGGA	    0.960258	-29
GCCGGGGACGGCCCCGGGAAAGGGGTA   	1	152	1	GCCCCGGGAA	    0.913581	-17
CCTGCCCGAAAGACCGTGCACCGGTCTTGG	2	23	0	AGACCGTGCA	    0.895081	-110
AGATTAGGACACGCCGGCGGCGCAGCCCTG	2	49	0	ACGCCGGCGG	    0.840584	-84
TGTGGCGTGGACGCCAGGCCAGCGCCTGGC	2	87	1	ACGCCAGGCC	    0.991298	-46
CGCCAGGCCAGCGCCTGGCCAACACTGGCA	2	98	1	GCGCCTGGCC	    0.963696	-35
     TCTTCGCGCCATGAATGCCAGTGTT	2	118	0	GCGCCATGAA	    0.942428	-15
          **********

Masking position 5
Map Score:   12.0023

Number of sites scoring better than the average of aligned sites = 12727
Number in coding regions = 11717
Number in noncoding regions = 1010
Number of orfs with sites within 600 bp upstream = 694
Fraction of orfs with sites within 600 bp upstream = 0.111468


Motif number 3

TGTGTCAGCAGACAACAGTATACGTTCTAA	1	51	1	GACAACAGTA	    0.684317	-118
TCTGACCATCGTCGACATTGATTATTTAGA	1	76	0	GTCGACATTG	    0.971616	-93
CAACTTCGTCGTACACCGTGCGGGTAAGTC	1	120	0	GTACACCGTG	    0.876602	-49
CGTCCCCGGCGTCAACTTCGTCGTACACCG	1	132	0	GTCAACTTCG	    0.918946	-37
CTTTCCCGGGGCCGTCCCCGGCGTCAACTT	1	144	0	GCCGTCCCCG	    0.960036	-25
ACCGGTCTTGGCAGACTGTGCCC       	2	4	0	GCAGACTGTG	    0.970927	-129
ATTAGGACACGCCGGCGGCGCAGCCCTGCC	2	47	0	GCCGGCGGCG	    0.973664	-86
CCAGCGCCTGGCCAACACTGGCATTCATGG	2	105	1	GCCAACACTG	    0.981464	-28
          **********

Masking position 6
Map Score:   1.75445

Number of sites scoring better than the average of aligned sites = 28723
Number in coding regions = 27263
Number in noncoding regions = 1460
Number of orfs with sites within 600 bp upstream = 899
Fraction of orfs with sites within 600 bp upstream = 0.144394


Motif number 4

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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:   -4.80737e-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