AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i298_mixed13_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yloB	115	similar to calcium-transporting ATPase
#2	yloC	82	similar to hypothetical proteins
#3	yloD	233	similar to guanylate kinase
#4	yloI	80	similar to pantothenate metabolism flavoprotein

Motif number 1

        TACACCCTCTCATTCTTCCTGCATTCGAT	1	3	1	CCTCTATCCC	    0.981945	-113
TATAAGCATGCTTATTCTGACTCGTCCCATTTCATGC	1	47	0	CATCTATCCC	    0.955074	-69
    TCCGCTCGTCCACTCCCCTGCTCTCTTATAGAG	1	93	0	CCACTCCTTC	    0.982733	-23
TTTAAAACACCCAATTCTTCCCTGTTCTCATAATAAA	2	56	0	CATCTCCTTC	    0.992009	-27
GTTTAATCGTCATCTTCTACGTTCCCCCTGTAAAATA	3	63	0	CCTCTCTTCC	    0.993374	-171
GATTTGGCAATATCATCTCCGCCAATCGGATGATTTC	3	112	1	TCTCTCCCTC	    0.982533	-122
ATTGTCAGCCCGGAGTCTGCGCCAATCAAACGGATGA	3	150	1	CATCTCCCTC	    0.994947	-84
  TGAATTCTCCCCCTCTGCACTTTACAAAACCGCAC	4	56	0	CCTCTCCTAC	    0.989747	-25
          *  * *** * **  **

Masking position 8
Map Score:   9.07116

Number of sites scoring better than the average of aligned sites = 474
Number in coding regions = 413
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TTATAGCATGAAATGGGACGAGTCAGAATA	1	42	1	AAATGGGACG	    0.953046	-74
GACGAGTCAGAATAAGCATGCTTATAGAGT	1	58	1	AATAAGCATG	    0.813599	-58
ATAAAAGGGCAATAGACACGCTATTACCCC	2	31	0	AATAGACACG	    0.877364	-52
GTCTGTAAACAATACGCACAGTCA      	3	5	0	AATACGCACA	    0.894076	-229
TTCCCCCTGTAAAATAGACGTCTCTAGTTT	3	49	0	AAAATAGACG	    0.800108	-185
TCATCTCCGCCAATCGGATGATTTCGATTG	3	124	1	CAATCGGATG	    0.918769	-110
CTGCGCCAATCAAACGGATGATTCAGGATG	3	166	1	CAAACGGATG	    0.962326	-68
ATTGACGCTACATACGGACGAAGAACCC  	3	216	1	CATACGGACG	    0.978295	-18
GCACTTTACAAAACCGCACGGAAAAAAATA	4	45	0	AAACCGCACG	    0.970238	-36
          **********

Masking position 8
Map Score:   5.65251

Number of sites scoring better than the average of aligned sites = 1449
Number in coding regions = 1327
Number in noncoding regions = 122
Number of orfs with sites within 600 bp upstream = 105
Fraction of orfs with sites within 600 bp upstream = 0.0168648


Motif number 3

CATGCTATAATTATCGAATGCAGGAAGAAT	1	22	0	TTATCGAATG	    0.943959	-94
CATTCGATAATTATAGCATGAAATGGGACG	1	32	1	TTATAGCATG	    0.909778	-84
ATAAGCATGCTTATAGAGTGATATCTCTAT	1	69	1	TTATAGAGTG	    0.885637	-47
AAACTGATTAATATCGGATTTGGCAATATC	3	96	1	ATATCGGATT	     0.86145	-138
CAATCGGATGATTTCGATTGTCAGCCCGGA	3	134	1	ATTTCGATTG	    0.900088	-100
CAAACGGATGATTCAGGATGCAAGAGACCG	3	176	1	ATTCAGGATG	    0.868095	-58
AACCTACATGATATAGGTTGCTACTTGTGC	4	13	0	ATATAGGTTG	    0.977649	-68
AACCTATATCATGTAGGTTGTTATTTTTTT	4	24	1	ATGTAGGTTG	    0.941157	-57
          **********

Masking position 2
Map Score:   3.28388

Number of sites scoring better than the average of aligned sites = 527
Number in coding regions = 438
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

TCGTCCACTCCCCTGCTCTCTTATAGAGAT	1	91	0	CCCTGCTCTC	    0.997256	-25
CCCAATTCTTCCCTGTTCTCATAATAAAAG	2	54	0	CCCTGTTCTC	    0.995943	-29
AATTAGCATTCCGCGGTCTCTTGCATCCTG	3	189	0	CCGCGGTCTC	    0.994015	-45
          **********

Masking position 7
Map Score:   1.53599

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 20
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

GCTATAATTATCGAATGCAGGAAGAATGAGA	1	18	0	TCGAATGAGG	    0.939083	-98
TCGAAATCATCCGATTGGCGGAGATGATATT	3	120	0	CCGATTGCGG	     0.99397	-114
TCGGATGATTTCGATTGTCAGCCCGGAGTCT	3	137	1	TCGATTGCAG	    0.979531	-97
AATCATCCGTTTGATTGGCGCAGACTCCGGG	3	158	0	TTGATTGCGC	    0.987751	-76
CCGCGGAATGCTAATTGACGCTACATACGGA	3	203	1	CTAATTGCGC	    0.943452	-31
          ******* ***

Masking position 6
Map Score:   1.22497

Number of sites scoring better than the average of aligned sites = 558
Number in coding regions = 534
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 6

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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 8

          **********

No masking
Map Score:   1.3033e-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