AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_tpal_reg_300.orf -o174_tpal_300.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	RTP00382	170	AE000520
#2	RTP00949	206	AE000520

Motif number 1

TAATGTGCTCGACGTGGCTGCGCTCGCGCTCC	1	34	1	GACGTGCGCG	    0.997138	-137
CTGCGCTCGCGCTCCACCACCGTGATCTTAAA	1	51	1	GCTCCACCCG	    0.982924	-120
CGTTTTCTCCGCCGTGTCCCGGTGTTCTTCTT	1	89	1	GCCGTGCCGG	    0.990965	-82
CAGGTAATTTGACGTGTATCCGTTTTCAAAAT	1	125	1	GACGTGACCG	    0.969142	-46
TCAAAATACGCATCCGCCAGCGCCTGAAAGC 	1	150	1	CATCCGCGCG	    0.988461	-21
AGTGAATCAAGACGTGTCGGCGTCGACGCCCA	2	69	1	GACGTGCGCG	    0.997133	-138
GCAAACTCTAGCCCCAGCTCCGGCCGGAACAG	2	123	1	GCCCCACCCG	    0.991235	-84
GATTAAAAAGCCTGCGGCAGGGAGTTTGCTGT	2	151	0	CCTGCGCGGG	    0.976529	-56
  CTCAGTATGATCCGCTTGCGCCAAATAATT	2	187	0	GATCCGTGCG	    0.969142	-20
          ****** * ***

Masking position 12
Map Score:   14.7309

Number of sites scoring better than the average of aligned sites = 860
Number in coding regions = 799
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

TAATGTGCTCGACGTGGCTGCGCTCGCGCT	1	34	1	GACGTGGCTG	    0.987856	-137
TAAGATCACGGTGGTGGAGCGCGAGCGCAG	1	51	0	GTGGTGGAGC	    0.984247	-120
CGTTTTCTCCGCCGTGTCCCGGTGTTCTTC	1	89	1	GCCGTGTCCC	    0.980317	-82
CAGGTAATTTGACGTGTATCCGTTTTCAAA	1	125	1	GACGTGTATC	    0.928123	-46
  GCTTTCAGGCGCTGGCGGATGCGTATTT	1	153	0	GCGCTGGCGG	    0.987593	-18
CAATGCGGGTGTCGTGGAGTTTTGCGTATT	2	22	0	GTCGTGGAGT	    0.936842	-185
AGTGAATCAAGACGTGTCGGCGTCGACGCC	2	69	1	GACGTGTCGG	    0.989874	-138
TTTTTTCGTTGCGGTGGGCGTCGACGCCGA	2	85	0	GCGGTGGGCG	    0.984646	-122
GTTCCGGCCGGAGCTGGGGCTAGAGTTTGC	2	123	0	GAGCTGGGGC	    0.955303	-84
          **********

Masking position 5
Map Score:   13.0155

Number of sites scoring better than the average of aligned sites = 732
Number in coding regions = 657
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 3

         TGTATTCTTCGTTCCCTTAATG	1	2	1	GTATTCTCGT	    0.980148	-169
AAACGAAAGCGTTTTCTCCGCCGTGTCCCGG	1	80	1	GTTTTCTCGC	    0.995246	-91
CCGTGTCCCGGTGTTCTTCTTTGTTCAGGTA	1	100	1	GTGTTCTCTT	    0.933433	-71
TGGGGCTAGAGTTTGCAACGCCCTTTTTTTC	2	108	0	GTTTGCACGC	    0.987817	-99
GCGGCAGGGAGTTTGCTGTTCCGGCCGGAGC	2	139	0	GTTTGCTTTC	    0.945085	-68
      CTCAGTATGATCCGCTTGCGCCAAA	2	192	0	GTATGATCGC	    0.972636	-15
          ******* ***

Masking position 4
Map Score:   4.36624

Number of sites scoring better than the average of aligned sites = 397
Number in coding regions = 366
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

     TGTATTCTTCGTTCCCTTAATGATAA	1	6	1	TCTTGTTCCC	    0.991678	-165
AACGCTTTCGTTTAAGATCACGGTGGTGGAG	1	62	0	TTTAGATCAC	    0.816644	-109
CCGGTGTTCTTCTTTGTTCAGGTAATTTGAC	1	107	1	TCTTGTTCAG	    0.977741	-64
TGTCTCTGATACTTCAATGCGGGTGTCGTGG	2	35	0	ACTTAATGCG	    0.747168	-172
CGCCGACACGTCTTGATTCACTGTTTGTCTC	2	60	0	TCTTATTCAC	     0.96544	-147
AACGCCCTTTTTTTCGTTGCGGTGGGCGTCG	2	92	0	TTTTGTTGCG	     0.94881	-115
TGCCGCAGGCTTTTTAATCCCCAAATTATTT	2	164	1	TTTTAATCCC	    0.955463	-43
          **** ******

Masking position 8
Map Score:   2.17003

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 209
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

TCACGGTGGTGGAGCGCGAGCGCAGCCACG	1	46	0	GGAGCGCGAG	    0.993713	-125
TTTGCGTATTGAGGCTCAAGG         	2	2	0	GAGGCTCAAG	    0.990093	-205
GGCCGGAGCTGGGGCTAGAGTTTGCAACGC	2	118	0	GGGGCTAGAG	    0.990675	-89
CCCAAATTATTTGGCGCAAGCGGATCATAC	2	183	1	TTGGCGCAAG	    0.971734	-24
          **********

Masking position 9
Map Score:   1.59942

Number of sites scoring better than the average of aligned sites = 173
Number in coding regions = 153
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 6

          **********

No masking
Map Score:   8.26662e-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:   8.26662e-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:   8.26662e-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