AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i337_weak_synecho_reg_300.orf -o337_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	RCY25137	127	Synechocystis
#2	RCY52910	84	Synechocystis
#3	RCY38727	285	Synechocystis

Motif number 1

ATTCGACATTCCACTGGCAAAAGATATCAT	1	32	0	CCACTGGCAA	    0.915193	-96
ATCAACATTATCCTTTGCCTCGAACGTATA	1	75	0	TCCTTTGCCT	    0.880561	-53
    TGTAGCTCCTTGACAAACCGGTCACC	2	7	1	TCCTTGACAA	    0.802317	-78
     AGCTTCTCTTGGTAACATCGAGCAA	2	70	0	CTCTTGGTAA	    0.928966	-15
GGCGACATCGCCCTTGGTCTCACGTTAGGA	3	15	0	CCCTTGGTCT	    0.990647	-271
ACCATGATTTGCCCTAGCCAAAATCGAAAA	3	167	0	GCCCTAGCCA	    0.926597	-119
ACTGGGTTTACCCCTGGTCTTCCACCATGA	3	190	0	CCCCTGGTCT	     0.99272	-96
CAAATTACAAGCCTTGGTCTGGGGCCCATT	3	230	0	GCCTTGGTCT	    0.982256	-56
TGCTCAATTTTTCCTGGTAAATTTCCCCGT	3	266	1	TTCCTGGTAA	    0.890582	-20
          **********

Masking position 5
Map Score:   7.52081

Number of sites scoring better than the average of aligned sites = 5872
Number in coding regions = 5338
Number in noncoding regions = 534
Number of orfs with sites within 600 bp upstream = 514
Fraction of orfs with sites within 600 bp upstream = 0.082557


Motif number 2

AACCGGTCACCAAAGTTGCCACAATGATTT	2	26	1	CAAAGTTGCC	    0.987516	-59
TGCCGTTGCTCGATGTTACCAAGAGAAGCT	2	65	1	CGATGTTACC	    0.982055	-20
AGACCAAGGGCGATGTCGCCGTAAGCTACC	3	25	1	CGATGTCGCC	     0.98033	-261
GCGCCATTTTCGATTTTGGCTAGGGCAAAT	3	161	1	CGATTTTGGC	    0.962666	-125
ACCAAGGCTTGTAATTTGCCAGTCTGCTCA	3	242	1	GTAATTTGCC	    0.916217	-44
CCAGTCTGCTCAATTTTTCCTGGTAAATTT	3	260	1	CAATTTTTCC	    0.942347	-26
     ACGGGGAAATTTACCAGGAAAAATT	3	271	0	GAAATTTACC	    0.903261	-15
          **********

Masking position 3
Map Score:   4.92867

Number of sites scoring better than the average of aligned sites = 1217
Number in coding regions = 1081
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 157
Fraction of orfs with sites within 600 bp upstream = 0.0252168


Motif number 3

TTTCAAGGCTTGCCGGGATGATATCTTTTGC	1	15	1	TGCCGGATGA	    0.991701	-113
TGATATCTTTTGCCAGTGGAATGTCGAATTA	1	33	1	TGCCAGGGAA	    0.784065	-95
TCACCAAAGTTGCCACAATGATTTGTTAGCT	2	32	1	TGCCACATGA	    0.992365	-53
CCAAGGGCGATGTCGCCGTAAGCTACCCTAC	3	28	1	TGTCGCGTAA	    0.913085	-258
GTCGTGTTTTTGCCGCCCTAAAAGGGATGTT	3	94	0	TGCCGCCTAA	    0.987775	-192
ACCCCTGGTCTTCCACCATGATTTGCCCTAG	3	180	0	TTCCACATGA	    0.943576	-106
GCTTGTAATTTGCCAGTCTGCTCAATTTTTC	3	248	1	TGCCAGCTGC	    0.970484	-38
          ****** ****

Masking position 1
Map Score:   4.74715

Number of sites scoring better than the average of aligned sites = 592
Number in coding regions = 539
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 4

TTCAAGGCTTGCCGGGATGATATCTTTTGCC	1	16	1	GCCGGATGAT	    0.984687	-112
CACCAAAGTTGCCACAATGATTTGTTAGCTA	2	33	1	GCCACATGAT	    0.993305	-52
GTCGCCGTAAGCTACCCTACTTTAGGGGATT	3	39	1	GCTACCTACT	    0.910022	-247
TCGTGTTTTTGCCGCCCTAAAAGGGATGTTA	3	93	0	GCCGCCTAAA	    0.941618	-193
CCCCTGGTCTTCCACCATGATTTGCCCTAGC	3	179	0	TCCACATGAT	    0.958253	-107
CTTGTAATTTGCCAGTCTGCTCAATTTTTCC	3	249	1	GCCAGCTGCT	    0.989639	-37
          ***** *****

Masking position 8
Map Score:   2.23221

Number of sites scoring better than the average of aligned sites = 767
Number in coding regions = 731
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 5

GTGGCAACTTTGGTGACCGGTTTGTCAAGGAGC	2	15	0	TGGGACCTTT	    0.991763	-70
GGCATCCCTATGGGTCGTGTTTTTGCCGCCCTA	3	105	0	TGGTCGTTTT	    0.968057	-181
GGTTAAACAATGGAGCGCCATTTTCGATTTTGG	3	147	1	TGGGCGCTTT	    0.997914	-139
AGCCTTGGTCTGGGGCCCATTTTATCGAAAAAC	3	218	0	TGGGCCCTTT	    0.997914	-68
          *** ****  ***

Masking position 11
Map Score:   1.10533

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 36
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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