AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i106_Potassium_Transport_kdp_operon_mtub_reg_300.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	kdpD_kdpA	325	kdpD: kdpD, kdpA: kdpA

Motif number 1

TTCGCGGCGCTGCTGTTTCCGGAGAAGTTCTG  	1	9	0	TGCTGTCGGG	    0.980507	-317
GCGCTAATGGCGTTCCTATTCGCGGCGCTGCTGT	1	27	0	CGTTCTTCGG	    0.875577	-299
ATCGTCGGGTTGGTGATCGCGGTGGCGCTAATGG	1	51	0	TGGTGTCGGG	    0.997718	-275
ATCACCAACCCGACGATGTTGTCGACCGTAGTCA	1	68	1	CGACGTTGTG	    0.835974	-258
GCCGGCCGAATGGCGATGACTACGGTCGACAACA	1	84	0	TGGCGTCTAG	    0.944214	-242
GCCATTCGGCCGGCGCTCGCGTGAGTTCGACTGT	1	104	1	CGGCGTCGTA	     0.87209	-222
TCATTCGCCGCGACGAAATCGGGGAAACAACAGT	1	133	0	CGACGACGGG	    0.558016	-193
GCCTGCTCTACGTCCGTGGCTGTGAACGGATCAT	1	163	0	CGTCCTCTGG	     0.96205	-163
CTGACCGTGATGGCCTTTGCCGGGCTTTGCCTGC	1	191	0	TGGCCTCCGG	    0.995446	-135
GACTTGGTGTTGGTGCTGACCGTGATGGCCTTTG	1	206	0	TGGTGTCCGG	    0.995551	-120
AGGACTCACATGGCCGACTTGGTGTTGGTGCTGA	1	221	0	TGGCCATGGG	    0.959497	-105
ATGTGAGTCCTCTCGATTCTTGTGCACCGGCATC	1	244	1	TCTCGTTTGG	    0.765319	-82
ATCTGATGCGCTGCGATGCCGGTGCACAAGAATC	1	258	0	CTGCGTCGGG	      0.9859	-68
CCCAGCAGGATGGTAGTTGCCGGGCCCCCCAGGA	1	294	1	TGGTATCCGG	    0.946328	-32
        GGTCGTGTTCCTGGGGGGCCCGGCAA	1	310	0	TCGTGTTGGG	    0.961681	-16
          ***** *  *** *

Masking position 14
Map Score:   22.1231

Number of sites scoring better than the average of aligned sites = 44280
Number in coding regions = 42312
Number in noncoding regions = 1968
Number of orfs with sites within 600 bp upstream = 980
Fraction of orfs with sites within 600 bp upstream = 0.157404


Motif number 2

TCGCGGCGCTGCTGTTTCCGGAGAAGTTCTG	1	11	0	GCTGTTCCGG	    0.950068	-315
TAATGGCGTTCCTATTCGCGGCGCTGCTGTT	1	26	0	CCTATCGCGG	    0.851419	-300
TCGCGGTGGCGCTAATGGCGTTCCTATTCGC	1	38	0	GCTATGGCGT	    0.907232	-288
TCGTCGGGTTGGTGATCGCGGTGGCGCTAAT	1	53	0	GGTGTCGCGG	    0.995379	-273
CCATTCGGCCGGCGCTCGCGTGAGTTCGACT	1	105	1	GGCGTCGCGT	    0.962255	-221
GTTTCCCCGATTTCGTCGCGGCGAATGATCC	1	139	1	TTTCTCGCGG	    0.923667	-187
CCTGCTCTACGTCCGTGGCTGTGAACGGATC	1	165	0	GTCCTGGCTG	    0.948381	-161
GCCTTTGCCGGGCTTTGCCTGCTCTACGTCC	1	182	0	GGCTTGCCTG	    0.759238	-144
TGACCGTGATGGCCTTTGCCGGGCTTTGCCT	1	193	0	GGCCTTGCCG	     0.98194	-133
ACTTGGTGTTGGTGCTGACCGTGATGGCCTT	1	208	0	GGTGTGACCG	    0.937109	-118
TCGAGAGGACTCACATGGCCGACTTGGTGTT	1	229	0	TCACTGGCCG	    0.775719	-97
TCTGATGCGCTGCGATGCCGGTGCACAAGAA	1	260	0	TGCGTGCCGG	    0.959142	-66
CCAGCAGGATGGTAGTTGCCGGGCCCCCCAG	1	295	1	GGTATTGCCG	    0.954249	-31
    GGTCGTGTTCCTGGGGGGCCCGGCAAC	1	309	0	GTTCTGGGGG	    0.903933	-17
          **** ******

Masking position 6
Map Score:   13.8604

Number of sites scoring better than the average of aligned sites = 46715
Number in coding regions = 44258
Number in noncoding regions = 2457
Number of orfs with sites within 600 bp upstream = 1185
Fraction of orfs with sites within 600 bp upstream = 0.190331


Motif number 3

ACCGCGATCACCAACCCGACGATGTTGTCGA	1	62	1	CCACCCGACG	     0.96727	-264
CACGCGAGCGCCGGCCGAATGGCGATGACTA	1	96	0	CCGCCGAATG	     0.99485	-230
CCGATTTCGTCGCGGCGAATGATCCGTTCAC	1	145	1	CGGGCGAATG	    0.966411	-181
CCGGGCTTTGCCTGCTCTACGTCCGTGGCTG	1	175	0	CCGCTCTACG	    0.725392	-151
GCAGGCAAAGCCCGGCAAAGGCCATCACGGT	1	191	1	CCGGCAAAGG	    0.975019	-135
ATCAGATAGCCCAGCAGGATGGTAGTTGCCG	1	285	1	CCGCAGGATG	    0.985823	-41
GCCGGGCCCCCCAGGAACACGACC       	1	312	1	CCGGAACACG	    0.951079	-14
          ** ********

Masking position 9
Map Score:   3.30059

Number of sites scoring better than the average of aligned sites = 5561
Number in coding regions = 5178
Number in noncoding regions = 383
Number of orfs with sites within 600 bp upstream = 348
Fraction of orfs with sites within 600 bp upstream = 0.0558946


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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