AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00580_synecho_reg_100.orf -o00580_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	sll1236	300	hypothetical protein. [EC:3.1.4.46]

Motif number 1

TAATTGCCAATTAACGGGGGAAAAATAGTAT	1	13	1	TTAACGGGGA	    0.993906	-288
TTTTGCTCCTTTTACTAGGGACAGGTAAAAG	1	150	1	TTTACAGGGA	    0.995523	-151
CCCTGGGAAATCTCCTGGGGAGAGTATCGCT	1	179	0	TCTCCGGGGA	    0.683753	-122
CCCCAGGAGATTTCCCAGGGAGTTGGACCAC	1	190	1	TTTCCAGGGA	    0.994767	-111
TCCGATGAATTTGACGGGGGTTGGGCGAATC	1	277	0	TTGACGGGGT	    0.988964	-24
          ***** *****

Masking position 1
Map Score:   7.68123

Number of sites scoring better than the average of aligned sites = 309
Number in coding regions = 271
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

GGTTTTTGGGATTAATGTTAATTAATGTTA	1	105	1	ATTAATGTTA	    0.993823	-196
ATTAATGTTAATTAATGTTAATGGTTATTA	1	115	1	ATTAATGTTA	    0.993823	-186
GTTAATGGTTATTAATGATTTTTGCTCCTT	1	131	1	ATTAATGATT	    0.936456	-170
TCAAGGTTAAAATAATGTTAAGGCTTGCTG	1	249	0	AATAATGTTA	    0.979928	-52
GGTTGGGCGAATCAAGGTTAAAATAATGTT	1	260	0	ATCAAGGTTA	    0.970293	-41
          **********

Masking position 5
Map Score:   7.62871

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 36
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

AATTGCCAATTAACGGGGGAAAAATAGTAT	1	14	1	TAACGGGGGA	    0.989988	-287
TTTGCTCCTTTTACTAGGGACAGGTAAAAG	1	151	1	TTACTAGGGA	    0.977213	-150
CCTGGGAAATCTCCTGGGGAGAGTATCGCT	1	179	0	CTCCTGGGGA	      0.9715	-122
CCCAGGAGATTTCCCAGGGAGTTGGACCAC	1	191	1	TTCCCAGGGA	    0.702987	-110
CCGATGAATTTGACGGGGGTTGGGCGAATC	1	277	0	TGACGGGGGT	     0.98064	-24
          **********

Masking position 4
Map Score:   4.68672

Number of sites scoring better than the average of aligned sites = 601
Number in coding regions = 539
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 4

AGATAAATACGGGATTTTGACAAGCTAATAG	1	47	0	GGGTTTTGAC	    0.989847	-254
TATCGGTGCAGGTTTTTGGGATTAATGTTAA	1	95	1	GGTTTTGGGA	    0.974334	-206
AGATTTCCCAGGGAGTTGGACCACACAGGGT	1	197	1	GGGGTTGGAC	    0.998333	-104
TGAATTTGACGGGGGTTGGGCGAATCAAGGT	1	272	0	GGGGTTGGGC	    0.998922	-29
          *** *******

Masking position 6
Map Score:   4.25077

Number of sites scoring better than the average of aligned sites = 280
Number in coding regions = 260
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

CCCGTTAATTGGCAATTATC          	1	1	0	GGCAATTATC	    0.933103	-300
CAATTAACGGGGGAAAAATAGTATCAGCTA	1	20	1	GGGAAAAATA	    0.959935	-281
GATTTTGACAAGCTAATAGCTGATACTATT	1	36	0	AGCTAATAGC	    0.944066	-265
TAGTAAAAGGAGCAAAAATCATTAATAACC	1	137	0	AGCAAAAATC	    0.977026	-164
TACTAGGGACAGGTAAAAGCGATACTCTCC	1	162	1	AGGTAAAAGC	    0.956477	-139
CCAACTCCCTGGGAAATCTCCTGGGGAGAG	1	186	0	GGGAAATCTC	    0.953767	-115
GGCGAATCAAGGTTAAAATAATGTTAAGGC	1	255	0	GGTTAAAATA	    0.822421	-46
          **********

Masking position 5
Map Score:   3.73724

Number of sites scoring better than the average of aligned sites = 2357
Number in coding regions = 2021
Number in noncoding regions = 336
Number of orfs with sites within 600 bp upstream = 355
Fraction of orfs with sites within 600 bp upstream = 0.057019


Motif number 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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