AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i254_soj_tpal_reg_100.orf -o254_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	RTP00369	300	AE000520
#2	RTP00372	39	AE000520
#3	RTP00841	132	AE000520
#4	RTP00712	151	AE000520

Motif number 1

GTGAAGCGTGCAATACACCGGCGTAGTCT     	1	6	0	CACACGGCGT	    0.838398	-295
AATCGTCACAGAAATCCCCACTGCCACACCAAAA	1	67	1	GACCCACTGC	    0.907275	-234
CCGCCACTGAGTACGAAGGAGCGCGCGATAGTTT	1	99	0	GTAAGAGCGC	    0.905381	-202
CGTACTCAGTGGCGGTAGCTCCGCGCCAGGAATA	1	118	1	GGTACTCCGC	    0.879812	-183
CTCCGCGCCAGGAATAATCAGCGCCCACCATGTC	1	136	1	GGAACAGCGC	    0.996328	-165
GTGCATTCCCGATAGTAACGCTGCTCTCTTTTAT	1	218	0	GATACGCTGC	    0.915134	-83
TTTTGAAGCGCTGTCCATCGGTGCATTCCCGATA	1	238	0	CTCACGGTGC	    0.907998	-63
CTTCTCATAGGGGGCAAGCAGAGCACAA      	2	22	1	GGAACAGAGC	    0.976611	-18
CACGTTATGAGGTTACCTCGGCGCGTAGTTCCTT	3	20	1	GGCCCGGCGC	    0.996295	-113
TACCACGCACAACATAATCAGCGCTAAAGGAAAT	3	66	1	AAAACAGCGC	    0.935521	-67
CCCGGCCACTGATCGAAACGGCGCGCAATACCGA	4	27	0	GAAACGGCGC	    0.997347	-125
ATCAGTGGCCGGGAAAAACGCAGCTCGTCATTCC	4	48	1	GGAACGCAGC	    0.969659	-104
CGGGCACTCTGACGCACTCAGCGCAGTGGACACC	4	88	1	GAACCAGCGC	    0.989367	-64
ACTCAGCGCAGTGGACACCGGCGCCATTTCTGAC	4	103	1	GTCACGGCGC	     0.99564	-49
          **   ** ******

Masking position 13
Map Score:   19.9237

Number of sites scoring better than the average of aligned sites = 1284
Number in coding regions = 1199
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

TGACGTATCGTGCAGTGAAGCGTGCAATACACCG	1	20	0	TGCGAAGCGG	    0.961917	-281
CAGTGGGGATTTCTGTGACGATTGGATTAATTGA	1	56	0	TTCGACGATG	    0.957653	-245
CCACTGAGTACGAAGGAGCGCGCGATAGTTTTTG	1	96	0	CGAGGCGCGG	    0.886539	-205
CTCCTTCGTACTCAGTGGCGGTAGCTCCGCGCCA	1	112	1	CTCGGCGGTG	    0.969395	-189
TCGACAAAGCCTCCGACATGGTGGGCGCTGATTA	1	150	0	CTCGATGGTG	     0.97616	-151
ATACGTCTTATTCAGCAATGGTCGACAAAGCCTC	1	171	0	TTCGATGGTG	    0.980371	-130
          TTGTGCTCTGCTTGCCCCCTATGA	2	26	0	TTGGCTGCTG	    0.876638	-14
TTAGCGCTGATTATGTTGTGCGTGGTAGCATCAT	3	59	0	TTAGGTGCGG	    0.949327	-74
CTAAAGGAAATGCCGCAATGATGGCTAAACTTTT	3	89	1	TGCGATGATG	    0.957654	-44
CGGCGCGCAATACCGACGTGCTCGGGGGAGAG  	4	9	0	TACGGTGCTG	    0.970722	-143
CGCCGGTGTCCACTGCGCTGAGTGCGTCAGAGTG	4	92	0	CACGCTGAGG	    0.844102	-60
CCGGCGCCATTTCTGACAAGCGGGTGGTGGAGCG	4	120	1	TTCGAAGCGG	     0.97258	-32
          *** *  ***** *

Masking position 5
Map Score:   9.78221

Number of sites scoring better than the average of aligned sites = 1073
Number in coding regions = 991
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 3

ACACCAAAAACTATCGCGCGCTCCTTCGTAC	1	92	1	CATCGCGCGC	    0.976331	-209
CCAGGAATAATCAGCGCCCACCATGTCGGAG	1	143	1	TAGCGCCCAC	    0.944798	-158
         GCAACAGGGCACGTTATGAGGT	3	2	1	CACAGGGCAC	    0.956765	-131
AAAAATGATGCTACCACGCACAACATAATCA	3	55	1	CACCACGCAC	    0.990833	-78
    AGTCCACACTCATGCACCTGAAAAGTT	3	116	0	CCTCATGCAC	    0.859144	-17
      CTCTCCCCCGAGCACGTCGGTATTG	4	5	1	CCCCGAGCAC	    0.984249	-147
AGCTGCGTTTTTCCCGGCCACTGATCGAAAC	4	42	0	TCCCGGCCAC	    0.984196	-110
GTCATTCCCCTTTCCGGGCACTCTGACGCAC	4	74	1	TTCCGGGCAC	    0.946323	-78
CGCAGCCGCTCCACCACCCGCTTGTCAGAAA	4	129	0	CACCACCCGC	    0.981166	-23
          CACGCAGCCGCTCCACCACCC	4	141	0	CCGCAGCCGC	    0.959562	-11
          * *********

Masking position 9
Map Score:   11.4583

Number of sites scoring better than the average of aligned sites = 1328
Number in coding regions = 1217
Number in noncoding regions = 111
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

          **********

No masking
Map Score:   1.58694e-12

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:   1.58694e-12

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:   1.58694e-12

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