AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_synecho_reg_100.orf -o257_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	RCY34400	122	Synechocystis
#2	RCY25319	96	Synechocystis
#3	RCY52064	162	Synechocystis

Motif number 1

TCACCGGGGTGTTGCACTGGGTCAAGCAAT	1	11	1	GTTGCACTGG	    0.967964	-112
TTTAGCTAAATTAGCACTCGTGAGGTGGGA	1	40	1	TTAGCACTCG	    0.998132	-83
GGGAGAGGGTTTAGCACTCCCACCTCACGA	1	57	0	TTAGCACTCC	    0.996423	-66
CCTGCAAGTTTTAACACAGGTCAGGATCGG	2	26	0	TTAACACAGG	     0.92723	-71
ATTGCATTAATTTGCCCACGAGGTTTTACT	2	74	1	TTTGCCCACG	    0.968907	-23
CTTACCTGACTTAGCACTCCACTGCCAAGA	3	82	1	TTAGCACTCC	    0.996423	-81
ATAAAGCACTTTAGCACTCTTGGCAGTGGA	3	99	0	TTAGCACTCT	     0.99034	-64
          **********

Masking position 2
Map Score:   14.0153

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 34
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

TGTTGCACTGGGTCAAGCAATTTAGCTAAATTA	1	20	1	GGTCGAATTT	    0.968246	-103
TCCAGATGATAGTCTTGCAAGGTCAGTAGTAAT	1	89	0	AGTCGAAGGT	    0.997635	-34
TTTTAACACAGGTCAGGATCGGTAAAAATTAAT	2	15	0	GGTCGTCGGT	    0.975405	-82
AATGGGTAAAAATCCTGCAAGTTTTAACACAGG	2	36	0	AATCGAAGTT	    0.978408	-61
TAAATGGGGGAGTAACGGACGTTTAATGC    	3	7	0	AGTAGACGTT	    0.968246	-156
TGGAGTGCTAAGTCAGGTAAGGTTCGGTTTCCC	3	70	0	AGTCGAAGGT	    0.997635	-93
          AGACTAAAAAGTTACAAATAACG	3	150	0	AGACAAAGTT	    0.903915	-13
          ****  * *****

Masking position 13
Map Score:   5.54953

Number of sites scoring better than the average of aligned sites = 247
Number in coding regions = 212
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

ACTCCCACCTCACGAGTGCTAATTTAGCTA	1	42	0	CACGAGTGCT	    0.990621	-81
ACTCGTGAGGTGGGAGTGCTAAACCCTCTC	1	55	1	TGGGAGTGCT	    0.963042	-68
TAGTAATTTGGGAGAGGGTTTAGCACTCCC	1	66	0	GGAGAGGGTT	     0.93057	-57
CTATCATCTGGAGGATGACTTCT       	1	110	1	GAGGATGACT	    0.842172	-13
TTAAAACTTGCAGGATTTTTACCCATTCAT	2	42	1	CAGGATTTTT	    0.831328	-55
TTAATTTGCCCACGAGGTTTTACTTTT   	2	80	1	CACGAGGTTT	     0.91694	-17
ACTCTTGGCAGTGGAGTGCTAAGTCAGGTA	3	84	0	GTGGAGTGCT	     0.97433	-79
ACTCCACTGCCAAGAGTGCTAAAGTGCTTT	3	97	1	CAAGAGTGCT	    0.985566	-66
          **********

Masking position 5
Map Score:   5.05803

Number of sites scoring better than the average of aligned sites = 732
Number in coding regions = 609
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


Motif number 4

CCAGTGCAACACCCCGGTGA          	1	1	0	ACCCCGGTGA	    0.900015	-122
AAATTGCTTGACCCAGTGCAACACCCCGGT	1	13	0	ACCCAGTGCA	    0.974452	-110
GCAAGTTTTAACACAGGTCAGGATCGGTAA	2	23	0	ACACAGGTCA	    0.984625	-74
CCCCATTTAAATCCAGGGCGATCGCCAAGC	3	31	1	ATCCAGGGCG	    0.952791	-132
CCAAGCTCTAAGACCGGGAAACCGAACCTT	3	55	1	AGACCGGGAA	    0.888865	-108
TGGAGTGCTAAGTCAGGTAAGGTTCGGTTT	3	73	0	AGTCAGGTAA	    0.923507	-90
          **********

Masking position 1
Map Score:   1.86642

Number of sites scoring better than the average of aligned sites = 1551
Number in coding regions = 1422
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 147
Fraction of orfs with sites within 600 bp upstream = 0.0236107


Motif number 5

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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:   4.92707e-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