AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_SecDF_bbur_reg_300.orf -o118_borburg_300.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	RBB00112	194	3615
#2	RBB00111	23	3615
#3	RBB00109	85	3615

Motif number 1

         AAATTCTTTGTCTTTATAATTTAAAGA	1	2	1	AATTTTTTAT	    0.990582	-193
AAGATTAGTCAATATTTACATTATATAATAAAAATT	1	34	1	AATTTTATAT	    0.924143	-161
ATATAATAAAAATTTTTACTGGTTTTGTATATTTTG	1	56	1	AATTTGTTTT	    0.977435	-139
ACTGGTTTTGTATATTTTGTATTTTTTGATGCATAG	1	73	1	TATTTTTTTT	    0.935272	-122
TACTATAGCGAATGTATTAAGTTTATGTTAATCTTA	1	120	1	AATATTTTAT	    0.924151	-75
AGTTTATGTTAATCTTATATTGTTATATGTAAATTA	1	139	1	AATTAGTTAT	    0.935572	-56
GTTATATGTAAATTATTTTTATTTATAGAAAGGGGT	1	160	1	AATTTTTTAT	    0.990474	-35
       AAAAATTTTACCCCTTTCTATAAATAAAA	1	176	0	AATTATTTCT	    0.938727	-19
TTTACCTTTAAACAATACCTTTTTTTTAACT     	3	6	0	AACTATTTTT	    0.941133	-80
ATTATTAGCTAACAGTTCTAATTTTACCTTTAAACA	3	28	0	AACTTTTTTA	    0.833554	-58
ACTGTTAGCTAATAATGGTATTTTTTAAAAATTTTA	3	48	1	AATTGTTTTT	    0.956525	-38
    TATACAAATCCTTAAAATTTTTAAAAAATACC	3	64	0	AATTTTTTTT	    0.991173	-22
          ***  **    *****

Masking position 2
Map Score:   18.2246

Number of sites scoring better than the average of aligned sites = 1191
Number in coding regions = 762
Number in noncoding regions = 429
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 2

TTGACTAATCTTTAAATTATAAAGACAAAGAATTT   	1	8	0	TTAATAAAAA	    0.947263	-187
TAGTCAATATTTACATTATATAATAAAAATTTTTACTG	1	39	1	TTATAAAAAA	    0.594009	-156
AGCGTATTACTTCTATGCATCAAAAAATACAAAATATA	1	83	0	TTAATAAAAT	     0.97333	-112
TAAAAATAATTTACATATAACAATATAAGATTAACATA	1	143	0	TTAAAAAAAA	    0.904248	-52
TTTTACCCCTTTCTATAAATAAAAATAATTTACATATA	1	162	0	TTAATAAAAA	    0.830772	-33
AAGGTATTGTTTAAAGGTAAAATTAGAACTGTTAGCTA	3	21	1	TTAAAATAAA	     0.95064	-65
ATACAAATCCTTAAAATTTTTAAAAAATACCATTATTA	3	57	0	TTATTAAAAT	    0.960706	-29
          **  *   ** ** * **

Masking position 12
Map Score:   8.07635

Number of sites scoring better than the average of aligned sites = 411
Number in coding regions = 252
Number in noncoding regions = 159
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

TGACTAATCTTTAAATTATAAAGACAAAGA	1	15	0	TTAAATTATA	    0.935853	-180
TAGTCAATATTTACATTATATAATAAAAAT	1	39	1	TTACATTATA	    0.952089	-156
GCATCAAAAAATACAAAATATACAAAACCA	1	75	0	ATACAAAATA	     0.84748	-120
CAATATAAGATTAACATAAACTTAATACAT	1	131	0	TTAACATAAA	    0.882813	-64
TAAAAATAATTTACATATAACAATATAAGA	1	151	0	TTACATATAA	    0.874989	-44
ACCCCTTTCTATAAATAAAAATAATTTACA	1	166	0	ATAAATAAAA	    0.863167	-29
        AGTTAAAAAAAAGGTATTGTTT	3	3	1	TTAAAAAAAA	    0.939188	-83
AGTTCTAATTTTACCTTTAAACAATACCTT	3	21	0	TTACCTTTAA	    0.786465	-65
ATTAGAACTGTTAGCTAATAATGGTATTTT	3	42	1	TTAGCTAATA	    0.855444	-44
CTTAAAATTTTTAAAAAATACCATTATTAG	3	56	0	TTAAAAAATA	    0.939481	-30
          **********

Masking position 3
Map Score:   10.4915

Number of sites scoring better than the average of aligned sites = 1546
Number in coding regions = 898
Number in noncoding regions = 648
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 4

ACAAAATATACAAAACCAGTAAAAATTTTT	1	63	0	CAAAACCAGT	    0.981221	-132
TACCTTTAAACAATACCTTTTTTTTAACT 	3	10	0	CAATACCTTT	    0.988845	-76
AATTTTTAAAAAATACCATTATTAGCTAAC	3	51	0	AAATACCATT	    0.957262	-35
      TATACAAATCCTTAAAATTTTTAA	3	72	0	CAAATCCTTA	     0.93311	-14
          **********

Masking position 3
Map Score:   0.570298

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 168
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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