AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i156_aful_mthe_300.orf -o156_aful_mthe_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

Purged sequences:
RAG48486	59	Archaeoglobus_fulgidus

Input sequences:
#1	RAG35803	59	Archaeoglobus_fulgidus
#2	RTH00077	20	M.thermo
#3	RTH01952	83	M.thermo
#4	RTH01119	67	M.thermo
#5	RTH01092	177	M.thermo
#6	RTH00291	110	M.thermo

Motif number 1

AGTTTTCGCAATATTTTTAAAAGCTTTTCT	1	25	0	ATATTTTTAA	    0.783506	-35
TAATAGAGTTATCTATATAAAAATTGTTAA	3	31	0	ATCTATATAA	    0.951912	-53
GGCCTCCTCCATATATATATGATCGTGATA	4	19	1	ATATATATAT	    0.497908	-49
ACACTTAAAGATCTATTTATCACGATCATA	4	36	0	ATCTATTTAT	    0.861604	-32
TTATAAGTACATCAATATAATCTTAGCATA	5	19	1	ATCAATATAA	    0.884324	-159
TTTCCCACAAATCTTTATATGTGACGGATC	6	32	1	ATCTTTATAT	    0.951912	-79
TATGTGACGGATCTTTATCTAAACATTAGT	6	49	1	ATCTTTATCT	    0.925055	-62
          **********

Masking position 1
Map Score:   6.84672

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 13
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

       TCATCATGAGCTTAAGAAAAGCT	1	4	1	TCATGAGCTT	    0.848865	-56
         CTCTTTAGTCTGACAAAATTT	3	73	0	TCTTTAGTCT	    0.891322	-11
       AATCCTTTGGCCTCCTCCATATA	4	4	1	CCTTTGGCCT	    0.988603	-64
TTTCTATCTACCTTGAGTTTGCATGAGTTC	5	52	0	CCTTGAGTTT	    0.934174	-126
ATAGTCCAGGGCGTTGGCTTCAGGCCAGCG	5	111	1	GCGTTGGCTT	    0.949383	-67
AGTCTGTAGACCGCTGGCCTGAAGCCAACG	5	122	0	CCGCTGGCCT	    0.976722	-56
CTCACGTATCCCGTGAGGCTGAGTTCCTTT	5	155	0	CCGTGAGGCT	    0.974835	-23
          **********

Masking position 10
Map Score:   2.10813

Number of sites scoring better than the average of aligned sites = 630
Number in coding regions = 601
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

TATATAAAAATTGTTAATTACCGGAAGGTGA	3	17	0	TTGTTAATAC	    0.957263	-67
TAATTAACAATTTTTATATAGATAACTCTAT	3	28	1	TTTTTATTAG	     0.93561	-56
CTGACAAAATTTTATAATTAGAATTAATAGA	3	54	0	TTTATAATAG	    0.974881	-30
ATATATGATCGTGATAAATAGATCTTTAAGT	4	33	1	GTGATAATAG	    0.921475	-35
   TACCTAATTTATAAGTACATCAATATAA	5	8	1	TTTATAATAC	     0.97482	-170
GCACGGTACATTTCTATCTACCTTGAGTTTG	5	61	0	TTTCTATTAC	    0.924317	-117
          ******* ***

Masking position 6
Map Score:   1.49059

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 17
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

ATAGATAACTCTATTAATTCTAATTATAAA	3	45	1	CTATTAATTC	     0.95046	-39
         GGTATTAATTCAATGGCATTG	6	2	1	GTATTAATTC	    0.735866	-109
GACTTTAATCCTATTAATTTGGAGAGGGTT	6	86	1	CTATTAATTT	    0.968366	-25
          **********

Masking position 6
Map Score:   1.30906

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

TTGCATGAGTTCTCCTATGCTAAGATTATA	5	34	0	TCTCCTATGC	     0.94487	-144
TACATTTCTATCTACCTTGAGTTTGCATGA	5	56	0	TCTACCTTGA	    0.970416	-122
TAGATAGAAATGTACCGTGCCCATCTCACA	5	72	1	TGTACCGTGC	    0.981489	-106
GACTATTCCCTCCACTGTGAGATGGGCACG	5	87	0	TCCACTGTGA	     0.96309	-91
 GTTCTCACGTATCCCGTGAGGCTGAGTTC	5	159	0	TATCCCGTGA	    0.972762	-19
          **********

Masking position 8
Map Score:   0.131903

Number of sites scoring better than the average of aligned sites = 171
Number in coding regions = 163
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 6

          **********

No masking
Map Score:   -5.94424e-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:   -5.94424e-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:   -5.94424e-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