AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i277_hypothetical21_bbur_reg_100.orf -o277_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	RBB00299	90	3615
#2	RBB00014	191	3615

Motif number 1

GGGCTTTACATAAATTAATTGAATTATAGC	1	55	0	TAAATTAATT	    0.980615	-36
TCAAAATTTTTAAATCCATACATACTGACA	2	13	1	TAAATCCATA	     0.93176	-179
TGAATTTAGAAATATTAATAGTAGTCGTTT	2	42	0	AATATTAATA	    0.912648	-150
TTAATATTTCTAAATTCATAAAAAAATAAT	2	54	1	TAAATTCATA	    0.977933	-138
AAATTCATAAAAAAATAATATAATGTTTAA	2	65	1	AAAAATAATA	    0.956125	-127
TAAGTTAAGCTAAAATAATTCTTATCCAAA	2	92	1	TAAAATAATT	    0.956125	-100
CAAAGCAAATAAAATTAATTGACACTTACA	2	150	1	AAAATTAATT	    0.974917	-42
          **********

Masking position 4
Map Score:   9.54408

Number of sites scoring better than the average of aligned sites = 669
Number in coding regions = 404
Number in noncoding regions = 265
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

         TGTTTTAATTAGGGTTTTTATTG	1	2	1	GTTTATTAGG	    0.981341	-89
TTTAATTAGGGTTTTTATTGGAAGGCTTGTTT	1	14	1	GTTTTTTGGA	    0.980875	-77
TGGAAGGCTTGTTTGTTTTTTGTGCTATAATT	1	32	1	GTTTTTTTTG	    0.984228	-59
ATAATATAATGTTTAAGTTAAGCTAAAATAAT	2	79	1	GTTTATTAAG	    0.929759	-113
TTCACTCTTAGTTTCTCTTTGGATAAGAATTA	2	107	0	GTTTTTTTGG	    0.989912	-85
GTTAAATCTTGTTTCACTCTTAGTTTCTCTTT	2	119	0	GTTTATCTTA	    0.877151	-73
TATTCTCCTGGTTTGTTTTGTAAGTGTCAATT	2	166	0	GTTTTTTGTA	    0.970254	-26
          **** * *****

Masking position 8
Map Score:   7.10352

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 173
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

TAGCACAAAAAACAAACAAGCCTTCCAATA	1	29	0	AACAAACAAG	    0.986649	-62
CATACATACTGACAAACGACTACTATTAAT	2	29	1	GACAAACGAC	    0.973285	-163
CTTATCCAAAGAGAAACTAAGAGTGAAACA	2	112	1	GAGAAACTAA	      0.9386	-80
GAAACTAAGAGTGAAACAAGATTTAACAAA	2	124	1	GTGAAACAAG	    0.937436	-68
AACAAGATTTAACAAAGCAAATAAAATTAA	2	138	1	AACAAAGCAA	    0.920839	-54
ACACTTACAAAACAAACCAGGAGAATAATC	2	171	1	AACAAACCAG	    0.991328	-21
          **********

Masking position 5
Map Score:   3.27815

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 94
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

      AATCAAAATTTTTAAATCCATACA	2	5	1	AAAATTTTTA	    0.943769	-187
TAAACATTATATTATTTTTTTATGAATTTA	2	64	0	ATTATTTTTT	    0.930547	-128
AAAAAATAATATAATGTTTAAGTTAAGCTA	2	74	1	ATAATGTTTA	    0.966155	-118
TTAAGCTAAAATAATTCTTATCCAAAGAGA	2	96	1	ATAATTCTTA	    0.966231	-96
GTAAGTGTCAATTAATTTTATTTGCTTTGT	2	149	0	ATTAATTTTA	    0.930623	-43
          **********

Masking position 4
Map Score:   2.84815

Number of sites scoring better than the average of aligned sites = 956
Number in coding regions = 622
Number in noncoding regions = 334
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 5

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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:   -7.57276e-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