AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i313_mixed27_synecho_reg_300.orf -o313_synecho_300.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	RCY33113	109	Synechocystis
#2	RCY42122	216	Synechocystis

Motif number 1

    TTGAAAGGGTGATCAAATTTAGTTCGATGGGG	1	7	1	GGGGAAATTG	    0.997503	-103
TTAGTTCGATGGGGGGTAGGACTGCGTCCCCGTCCT	1	29	1	GGGGGGATGG	    0.992098	-81
TATTTATTTGGCTAGATTAAAAATGGCTTTAGTATC	1	69	0	GCTGAAAATG	    0.895567	-41
CCTCATCCTAGGGTGAGTAGACAGTGATTTGAGATT	2	14	0	GGGGAGAAGG	     0.99551	-203
ACTCACCCTAGGATGAGGGAAAATCGTCCCCAGTGA	2	32	1	GGAGGAAATG	    0.967041	-185
TCTTAATCGAGGGAGGCAAAAATTGGCTAATGTTAA	2	84	0	GGGGAAATTG	    0.997503	-133
AAAAAGTGGCAGGGGCCAAAATATAGTTCCTAATCT	2	117	0	AGGGAAAATG	    0.989174	-100
TGGCTGCTTCAGGCTTTGAAAATGAGGATTTACT  	2	193	1	AGGTAAATGG	    0.909096	-24
          *** *   *** ** *

Masking position 11
Map Score:   9.10167

Number of sites scoring better than the average of aligned sites = 733
Number in coding regions = 640
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 108
Fraction of orfs with sites within 600 bp upstream = 0.0173466


Motif number 2

CTAAATTTGATCACCCTTTCAA          	1	1	0	TCCCCTTCAA	     0.94034	-109
ACGCAGTCCTACCCCCCATCGAACTAAATTTG	1	24	0	ACCCCCTCGA	    0.988123	-86
GGTAGGACTGCGTCCCCGTCCTGTAGGATACT	1	43	1	CGCCCCTCCT	    0.987122	-67
GAGGGAAAATCGTCCCCAGTGACCAAACGCTG	2	46	1	CGCCCCGTGA	    0.989951	-171
GACCAAACGCTGACCCCTTTAACATTAGCCAA	2	66	1	TGCCCCTTAA	    0.987429	-151
AGCCAATTTTTGCCTCCCTCGATTAAGATTAG	2	92	1	TGCTCCTCGA	    0.988255	-125
AACTATATTTTGGCCCCTGCCACTTTTTTATG	2	125	1	TGCCCCGCCA	    0.989346	-92
          ** **** ****

Masking position 6
Map Score:   7.62367

Number of sites scoring better than the average of aligned sites = 1187
Number in coding regions = 1092
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 102
Fraction of orfs with sites within 600 bp upstream = 0.0163829


Motif number 3

GTGTGAATATTTATTTGGCTAGATTAAAAA	1	82	0	TTATTTGGCT	    0.984493	-28
ACATTAGCCAATTTTTGCCTCCCTCGATTA	2	87	1	ATTTTTGCCT	    0.947455	-130
TTAGGAACTATATTTTGGCCCCTGCCACTT	2	120	1	TATTTTGGCC	     0.97385	-97
CCTGCCACTTTTTTATGGCAATGGGAGTCC	2	140	1	TTTTATGGCA	    0.961725	-77
CGAAGCTAGATTTTTTGGCTGCTTCAGGCT	2	178	1	TTTTTTGGCT	    0.995235	-39
          **********

Masking position 6
Map Score:   5.37882

Number of sites scoring better than the average of aligned sites = 439
Number in coding regions = 368
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 4

AGGATACTAAAGCCATTTTTAATCTAGCCA	1	67	1	AGCCATTTTT	     0.98137	-43
GACAGTGATTTGAGATTTTT          	2	1	0	TGAGATTTTT	    0.962278	-216
CTTTAACATTAGCCAATTTTTGCCTCCCTC	2	82	1	AGCCAATTTT	    0.954243	-135
TTTTGGCCCCTGCCACTTTTTTATGGCAAT	2	132	1	TGCCACTTTT	     0.98788	-85
AAAATCTAGCTTCGACTTTTAGGGACTCCC	2	162	0	TTCGACTTTT	    0.964964	-55
AAAGTCGAAGCTAGATTTTTTGGCTGCTTC	2	173	1	CTAGATTTTT	    0.834895	-44
          **********

Masking position 5
Map Score:   5.12415

Number of sites scoring better than the average of aligned sites = 605
Number in coding regions = 538
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 5

          **********

No masking
Map Score:   6.91659e-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 6

          **********

No masking
Map Score:   6.91659e-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:   6.91659e-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