AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i326_not_clear1_bbur_reg_100.orf -o326_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00711	300	3615

Motif number 1

GTACAAATCTTTTTATTTATCCTGGCAAGAACT	1	25	1	TTTTTTATCT	    0.978542	-276
GCAAGAACTATTGTTTTAAGTTTGTTGACATGC	1	49	1	TTTTTAAGTT	    0.969652	-252
TTGACATGCTTTTTACAAATTTTCACACACCTC	1	73	1	TTTCAAATTT	      0.8973	-228
CCTCAATCTACTCTTTTGATGCTCGTTTCTTCA	1	102	1	CTTTTGATCT	    0.890717	-199
GGCAAAGATTTTGTGTTTAGTTTTTATGAAGAA	1	141	1	TTTTTTAGTT	    0.975226	-160
TTTATAACCTTTATTTATAGCTTCTTCATAAAA	1	162	0	TTTTATAGTT	    0.946877	-139
GTTATAAATTTTTTTCTTATGGTGATGCTATGT	1	187	1	TTTCTTATGT	    0.879731	-114
TATGGTGATGCTATGTTAATTCTAAATAATATA	1	204	1	CTTTTAATCT	    0.947624	-97
TTCACAACTAATATCTATATATTATTTAGAATT	1	221	0	ATTTATATTT	    0.817727	-80
TAGTTGTGAATTATTTTAATATTTAATTTATGA	1	244	1	TTTTTAATTT	    0.978201	-57
          ** * ***** **

Masking position 9
Map Score:   7.61468

Number of sites scoring better than the average of aligned sites = 1797
Number in coding regions = 1169
Number in noncoding regions = 628
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 2

GCAAAGTACAAATCTTTTTATTTATCCTGGC	1	20	1	AATCTTTTAT	    0.940123	-281
TCCTGGCAAGAACTATTGTTTTAAGTTTGTT	1	44	1	AACTATTTTT	    0.902498	-257
CTAAACACAAAATCTTTGCCTGCAAATGAAG	1	130	0	AATCTTTCCT	    0.924998	-171
AAAAATTTATAACCTTTATTTATAGCTTCTT	1	169	0	AACCTTTTTT	    0.961275	-132
AAAGGTTATAAATTTTTTTCTTATGGTGATG	1	183	1	AATTTTTTCT	    0.966989	-118
AATAATTCACAACTAATATCTATATATTATT	1	228	0	AACTAATTCT	     0.83432	-73
ATTAGTTGTGAATTATTTTAATATTTAATTT	1	242	1	AATTATTTAA	    0.693147	-59
TAATTAAATAAGCCTTTATCATAAATTAAAT	1	264	0	AGCCTTTTCA	    0.877544	-37
          ******* ***

Masking position 1
Map Score:   2.2329

Number of sites scoring better than the average of aligned sites = 915
Number in coding regions = 669
Number in noncoding regions = 246
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

      AACAGGTCAGCAAAGTACAAATCT	1	5	1	GGTCAGCAAA	    0.986944	-296
CAATAGTTCTTGCCAGGATAAATAAAAAGA	1	32	0	TGCCAGGATA	    0.953574	-269
GTAAAAAGCATGTCAACAAACTTAAAACAA	1	59	0	TGTCAACAAA	    0.968432	-242
TAGATTGAGGTGTGTGAAAATTTGTAAAAA	1	82	0	TGTGTGAAAA	    0.893057	-219
ACAAAATCTTTGCCTGCAAATGAAGAAACG	1	125	0	TGCCTGCAAA	     0.99211	-176
          **********

Masking position 8
Map Score:   1.93025

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 68
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

TCTTGCCAGGATAAATAAAAAGATTTGTAC	1	25	0	ATAAATAAAA	    0.982507	-276
TTTATAGCTTCTTCATAAAAACTAAACACA	1	152	0	CTTCATAAAA	    0.899223	-149
TGAAGAAGCTATAAATAAAGGTTATAAATT	1	167	1	ATAAATAAAG	    0.951913	-134
TATGTTAATTCTAAATAATATATAGATATT	1	215	1	CTAAATAATA	     0.92069	-86
AGCCTTTATCATAAATTAAATATTAAAATA	1	255	0	ATAAATTAAA	    0.964961	-46
TTTCCTCCTAATTAATTAAATAAGCCTTTA	1	277	0	ATTAATTAAA	    0.885683	-24
          **********

Masking position 5
Map Score:   5.86798

Number of sites scoring better than the average of aligned sites = 613
Number in coding regions = 356
Number in noncoding regions = 257
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


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


Motif number 7

          **********

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