AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_tpal_reg_100.orf -o061_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00963	233	AE000520

Motif number 1

AAACAGTTGTGCAAGGTACATACAC     	1	6	0	GCAAGGTACA	    0.937166	-228
TGATAGAAAAGCCTGCCGCACGCAGAAATG	1	37	0	GCCTGCCGCA	    0.979295	-197
CTTTTCTATCACGCGGTACACGCCTGTACC	1	56	1	ACGCGGTACA	    0.967068	-178
CTAGTGACACGCCTGGTACAGGCGTGTACC	1	70	0	GCCTGGTACA	    0.992584	-164
CGTGTCACTAGTGGGCTTCACGTTGGAACT	1	89	1	GTGGGCTTCA	    0.963177	-145
GCTGCCATTGGCGTGCTTCATCGCGTCGCT	1	119	1	GCGTGCTTCA	    0.996076	-115
GTGCTTCATCGCGTCGCTCATTTTTACCAT	1	131	1	GCGTCGCTCA	    0.985295	-103
TTTTGAGCATGTGCGGCTCAGTCCTTGCTA	1	196	0	GTGCGGCTCA	    0.987141	-38
          **********

Masking position 10
Map Score:   11.4246

Number of sites scoring better than the average of aligned sites = 750
Number in coding regions = 692
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

ATTTCTGCGTGCGGCAGGCTTTTCTATCACG	1	38	1	GCGGCAGGCT	    0.956676	-196
GTACAGGCGTGTACCGCGTGATAGAAAAGCC	1	54	0	GTACCGCGTA	    0.963074	-180
GTACACGCCTGTACCAGGCGTGTCACTAGTG	1	71	1	GTACCAGGCT	    0.968125	-163
GTTCCAACGTGAAGCCCACTAGTGACACGCC	1	87	0	GAAGCCCACA	    0.963957	-147
GCGACGCGATGAAGCACGCCAATGGCAGCAG	1	117	0	GAAGCACGCA	    0.992964	-117
TGGTAAAAATGAGCGACGCGATGAAGCACGC	1	129	0	GAGCGACGCA	    0.977783	-105
TTGCTAGGCAGTGTCCCGTTACCTAGATGCT	1	171	0	GTGTCCCGTA	    0.888901	-63
AGCAAGGACTGAGCCGCACATGCTCAAAAAA	1	197	1	GAGCCGCACT	    0.969284	-37
          ********* *

Masking position 1
Map Score:   3.89468

Number of sites scoring better than the average of aligned sites = 1652
Number in coding regions = 1516
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

GAAATGCAAACAGTTGTGCAAGGTACATACA	1	12	0	CAGTGTGCAA	    0.993987	-222
CTGCCGCACGCAGAAATGCAAACAGTTGTGC	1	24	0	CAGAATGCAA	    0.962349	-210
ACGCGGTACACGCCTGTACCAGGCGTGTCAC	1	66	1	CGCTGTACCA	    0.959866	-168
ACGTGAAGCCCACTAGTGACACGCCTGGTAC	1	81	0	CACAGTGACA	    0.975737	-153
ACGCCAATGGCAGCAGTTCCAACGTGAAGCC	1	102	0	CAGAGTTCCA	    0.991097	-132
GACTGAGCCGCACATGCTCAAAAAAGAGGCT	1	203	1	CACTGCTCAA	    0.964065	-31
          *** *******

Masking position 11
Map Score:   3.62738

Number of sites scoring better than the average of aligned sites = 356
Number in coding regions = 339
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

AGAAATGCAAACAGTTGTGCAAGGTACATA	1	14	0	ACAGTTGTGC	    0.868728	-220
CCTGCCGCACGCAGAAATGCAAACAGTTGT	1	26	0	GCAGAAATGC	    0.726671	-208
CACGCCAATGGCAGCAGTTCCAACGTGAAG	1	104	0	GCAGCAGTTC	    0.985829	-130
CCATTGGCGTGCTTCATCGCGTCGCTCATT	1	123	1	GCTTCATCGC	    0.922184	-111
CCGTTACCTAGATGCTGTGCCGTTTGATGG	1	157	0	GATGCTGTGC	    0.966781	-77
GGACTGAGCCGCACATGCTCAAAAAAGAGG	1	202	1	GCACATGCTC	    0.789287	-32
          GCTGCTTCTCAGCCTCTTTT	1	224	0	GCTGCTTCTC	    0.979747	-10
          **********

Masking position 10
Map Score:   2.64642

Number of sites scoring better than the average of aligned sites = 2869
Number in coding regions = 2717
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 5

CGTGATAGAAAAGCCTGCCGCACGCAGAAA	1	39	0	AAGCCTGCCG	    0.990209	-195
CACTAGTGACACGCCTGGTACAGGCGTGTA	1	72	0	ACGCCTGGTA	    0.975877	-162
TTCCAACGTGAAGCCCACTAGTGACACGCC	1	87	0	AAGCCCACTA	    0.985992	-147
CGACGCGATGAAGCACGCCAATGGCAGCAG	1	117	0	AAGCACGCCA	    0.984329	-117
          **********

Masking position 1
Map Score:   1.49812

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 101
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 6

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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 8

          **********

No masking
Map Score:   -3.30951e-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