AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_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	dnaJ2	74	dnaJ2
#2	hrcA	171	hrcA

Motif number 1

TTTGTGGATAGCCGCTTGAGAAGCGGCATAAAGAC	1	30	1	GCCGCGAAGG	    0.998368	-45
GCGGCATAAAGACGCGGCATAGGAGAATCAAGC  	1	52	1	GACGCCAGGG	     0.99846	-23
TCGGGCTTCAGCCACTCGGTAGGGAAGATCCGCCA	2	11	0	GCCACGAGGA	     0.99503	-161
GGGGGCGTGTGCCCCGACTAACGTGTCCAGCATGA	2	51	0	GCCCCCACGG	    0.991388	-121
GCAGGCGTCTGCCGATGGTCAGGGGGCGTGTGCCC	2	72	0	GCCGAGAGGG	    0.997629	-100
ACCATCGGCAGACGCCTGCTAGATGACGGTCAGTG	2	88	1	GACGCGAGAG	    0.994242	-84
ACGGTCAGTGGCCGCCGAGAACGTAAAATGAAGCC	2	113	1	GCCGCAACGA	    0.990172	-59
AACGTAAAATGAAGCCGGTCAGGCAGCGTAAGAAG	2	132	1	GAAGCGAGGA	    0.985402	-40
          *****  *  *** *

Masking position 11
Map Score:   15.2652

Number of sites scoring better than the average of aligned sites = 3942
Number in coding regions = 3655
Number in noncoding regions = 287
Number of orfs with sites within 600 bp upstream = 259
Fraction of orfs with sites within 600 bp upstream = 0.0415997


Motif number 2

CCACAAACCCTGCAGCAGGTGCGCGT     	1	6	0	TGCAGCGGTG	     0.95102	-69
GTTTGTGGATAGCCGCTTGAGAAGCGGCATA	1	29	1	AGCCGCTGAG	    0.979625	-46
GATTCTCCTATGCCGCGTCTTTATGCCGCTT	1	50	0	TGCCGCTCTT	    0.969091	-25
CATGATCTCGTCGGGCTTCAGCCACTCGGTA	2	25	0	TCGGGCTCAG	    0.981915	-147
GACTAACGTGTCCAGCATGATCTCGTCGGGC	2	40	0	TCCAGCTGAT	     0.94073	-132
CCGATGGTCAGGGGGCGTGTGCCCCGACTAA	2	65	0	GGGGGCTGTG	    0.990358	-107
CCGTCATCTAGCAGGCGTCTGCCGATGGTCA	2	86	0	GCAGGCTCTG	      0.9693	-86
TTACGTTCTCGGCGGCCACTGACCGTCATCT	2	108	0	GGCGGCACTG	     0.98504	-64
ACGCTGCCTGACCGGCTTCATTTTACGTTCT	2	130	0	ACCGGCTCAT	     0.96423	-42
AAGCCGGTCAGGCAGCGTAAGAAGTGAGGTG	2	143	1	GGCAGCTAAG	    0.961917	-29
          ****** ****

Masking position 6
Map Score:   12.7205

Number of sites scoring better than the average of aligned sites = 14432
Number in coding regions = 13593
Number in noncoding regions = 839
Number of orfs with sites within 600 bp upstream = 576
Fraction of orfs with sites within 600 bp upstream = 0.0925153


Motif number 3

CCGCTTCTCAAGCGGCTATCCACAAACCCT	1	26	0	AGCGGCTATC	    0.946851	-49
CCGCTTGAGAAGCGGCATAAAGACGCGGCA	1	41	1	AGCGGCATAA	    0.987676	-34
GGCATAAAGACGCGGCATAGGAGAATCAAG	1	54	1	CGCGGCATAG	    0.975924	-21
TTCCCTACCGAGTGGCTGAAGCCCGACGAG	2	20	1	AGTGGCTGAA	    0.970217	-152
ACACGTTAGTCGGGGCACACGCCCCCTGAC	2	60	1	CGGGGCACAC	    0.973979	-112
CCCCCTGACCATCGGCAGACGCCTGCTAGA	2	81	1	ATCGGCAGAC	    0.983669	-91
GATGACGGTCAGTGGCCGCCGAGAACGTAA	2	109	1	AGTGGCCGCC	     0.91673	-63
          **********

Masking position 5
Map Score:   5.35667

Number of sites scoring better than the average of aligned sites = 5810
Number in coding regions = 5387
Number in noncoding regions = 423
Number of orfs with sites within 600 bp upstream = 357
Fraction of orfs with sites within 600 bp upstream = 0.0573402


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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