AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_aful_reg_300.orf -o033_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG25670	202	Archaeoglobus_fulgidus
#2	RAG30894	126	Archaeoglobus_fulgidus
#3	RAG43044	36	Archaeoglobus_fulgidus
#4	RAG31360	125	Archaeoglobus_fulgidus

Motif number 1

TATTGATACATATTGGTTTGTATGGTAAAGT	1	37	0	TATTGGTTTT	     0.97785	-166
TTTATAAGCATTTTGGTTGATTTAGCTGTGA	1	71	0	TTTTGGTTGT	    0.951493	-132
ACCACCTCCTTTTTTGCTGATGAAGTTAATG	1	104	0	TTTTTGCTGT	    0.973825	-99
AATGCAAATATATTTGCTTTTCG        	3	3	0	TATTTGCTTT	    0.988198	-34
AAAGCAAATATATTTGCATTTTTTCCTTTTT	3	14	1	TATTTGCATT	    0.953825	-23
  TGATAAACTATTTGTTTTTGTTGTATTTA	4	9	1	TATTTGTTTT	    0.981567	-117
          ********* *

Masking position 4
Map Score:   5.72745

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 57
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

ATTCCCCCTCTCTTCATCTCTTGCAACCTCTATGATGC	1	136	0	TCCCTTGCAC	    0.993048	-67
          TCCGCATCCAACGCATCTCTCTGCGCTG	1	185	0	TCCCCAGCAT	    0.995288	-18
CAACGCAAAGTCTGCACTCTATGCACCC          	2	1	0	TCCTCAGCAC	    0.995288	-126
CGTTGAGAACTGCCCCACTAAGGCAGTCAAAATCTACC	2	34	1	TGCCTAGCAC	    0.992524	-93
GGTAAGCCAGTCATCGACGAAAGCAAGTGTATATACTG	2	74	1	TCCCGAGCAT	    0.991361	-53
GATGAATACATCAACTATTGAGGCATACGTATTGTTTA	4	38	0	TCCTTAGCAC	    0.994915	-88
          **  *  ** * ***  *

Masking position 15
Map Score:   5.54439

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 120
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

ATCAGGAGTTGGTTAAATAACTTTACCATA	1	18	1	GGTTAAATAA	    0.931463	-185
ATGAAGAGAGGGGGAATTACCTGTATTTCA	1	157	1	GGGGAATTAC	    0.922874	-46
ATCTCTCTGCGCTGAAATACAGGTAATTCC	1	169	0	GCTGAAATAC	    0.969651	-34
ACGAAAGCAAGTGTATATACTGTGAAATAT	2	90	1	GTGTATATAC	    0.843988	-37
GTGTATATACTGTGAAATATGTTCAAAGGT	2	100	1	TGTGAAATAT	    0.789656	-27
CATACGTATTGTTTAAATACAACAAAAACA	4	23	0	GTTTAAATAC	    0.977352	-103
          GTTTAAATATTCCGCATGAA	4	116	0	GTTTAAATAT	    0.938403	-10
          **********

Masking position 5
Map Score:   2.77538

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 238
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 4

TCCAACGCATCTCTCTGCGCTGAAATACAG	1	177	0	CTCTCTGCGC	    0.987204	-26
      TCCGCATCCAACGCATCTCTCTGC	1	189	0	CATCCAACGC	    0.972548	-14
GCAAAGTCTGCACTCTATGCACCC      	2	5	0	CACTCTATGC	    0.958165	-122
AGTGGGGCAGTTCTCAACGCAAAGTCTGCA	2	23	0	TTCTCAACGC	    0.979178	-104
CTATATATTACTCCCAACCCTTCAGATGAA	4	70	0	CTCCCAACCC	    0.986883	-56
          **********

Masking position 5
Map Score:   1.95086

Number of sites scoring better than the average of aligned sites = 360
Number in coding regions = 340
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

TGATTTAGCTGTGATAGTATTGATACATATT	1	54	0	GTGATAGATT	    0.961928	-149
TATAAGCATTTTGGTTGATTTAGCTGTGATA	1	69	0	TTGGTTGTTT	    0.961928	-134
TGCTGATGAAGTTAATGGTTTTATAAGCATT	1	90	0	GTTAATGTTT	    0.841818	-113
AAAAAAGGAGGTGGTAGCATCATAGAGGTTG	1	120	1	GTGGTAGATC	    0.966097	-83
CTGGCTTACCGTGGTAGATTTTGACTGCCTT	2	53	0	GTGGTAGTTT	    0.986136	-74
ACTATTTGTTTTTGTTGTATTTAAACAATAC	4	17	1	TTTGTTGATT	     0.94093	-109
TGCCTCAATAGTTGATGTATTCATCTGAAGG	4	51	1	GTTGATGATT	    0.962124	-75
          ******* ***

Masking position 2
Map Score:   4.12364

Number of sites scoring better than the average of aligned sites = 299
Number in coding regions = 259
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 6

          **********

No masking
Map Score:   -8.99385e-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:   -8.99385e-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:   -8.99385e-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