AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_synecho_ctra_100.orf -o202_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY44546	80	Synechocystis
#2	RCY49953	300	Synechocystis

Motif number 1

TCTCCAACAAAAAAAGGGAAGACCTCTAGT	1	52	0	AAAAAGGGAA	     0.92132	-29
TAACTAATCAAAACGGGGATCACCCATTGC	2	68	1	AAACGGGGAT	    0.926066	-233
GAATCAGTGGACATAGAGCAATGGGTGATC	2	85	0	ACATAGAGCA	     0.94603	-216
TCGGGGTCAAAAACAGGGAATCTGGGCACA	2	124	1	AAACAGGGAA	    0.986961	-177
CTAAACCTACACCCACGGCTGTACCCAGGG	2	210	1	ACCCACGGCT	    0.965017	-91
CCACGGCTGTACCCAGGGCAACAGCACAAT	2	222	1	ACCCAGGGCA	    0.996438	-79
GCTGATTCTAACATAGCGCTTTTATTGTGC	2	245	0	ACATAGCGCT	    0.941842	-56
AATCAGCAATACACAGGGCACGCTGAGGTG	2	268	1	ACACAGGGCA	    0.997985	-33
          **********

Masking position 1
Map Score:   11.1334

Number of sites scoring better than the average of aligned sites = 1203
Number in coding regions = 1117
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

TTCATCCTATGGTAATGGCCCGCTGGGGGA	1	16	0	GGTAATGGCC	    0.949323	-65
GAGGACTAGAGGTCTTCCCTTTTTTTGTTG	1	48	1	GGTCTTCCCT	    0.924314	-33
  GGTCATCAGGCGATCGCCAAAATATTTC	2	9	1	GGCGATCGCC	    0.499936	-292
TAGAGCAATGGGTGATCCCCGTTTTGATTA	2	72	0	GGTGATCCCC	      0.7188	-229
GTTGAGGTGAGGAAAACCCCACAGACGCAG	2	165	1	GGAAAACCCC	    0.889268	-136
CCCCACAGACGCAGTTCGCCATTCCACCGC	2	181	1	GCAGTTCGCC	    0.950699	-120
TACACCCACGGCTGTACCCAGGGCAACAGC	2	217	1	GCTGTACCCA	    0.857808	-84
CTTTTATTGTGCTGTTGCCCTGGGTACAGC	2	227	0	GCTGTTGCCC	    0.986115	-74
GGCACGCTGAGGTGATGGATTTAGATT   	2	284	1	GGTGATGGAT	    0.766218	-17
          **********

Masking position 1
Map Score:   9.22373

Number of sites scoring better than the average of aligned sites = 8655
Number in coding regions = 7908
Number in noncoding regions = 747
Number of orfs with sites within 600 bp upstream = 495
Fraction of orfs with sites within 600 bp upstream = 0.0795053


Motif number 3

TTAGGTCCCCCAGCGGGCCATTACCATAGGAT	1	11	1	CAGGGCCATT	    0.987274	-70
AATCAGTGGACATAGAGCAATGGGTGATCCCC	2	82	0	CATGGCAATG	     0.58707	-219
CCCACAGACGCAGTTCGCCATTCCACCGCTAA	2	182	1	CAGTGCCATT	    0.947575	-119
CTGATTCTAACATAGCGCTTTTATTGTGCTGT	2	242	0	CATGGCTTTT	    0.782194	-59
TCCATCACCTCAGCGTGCCCTGTGTATTGCTG	2	271	0	CAGGGCCCTG	    0.711095	-30
          *** * ******

Masking position 2
Map Score:   2.98983

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 149
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

AGGTCCCCCAGCGGGCCATTACCATAGGAT	1	13	1	GCGGGCCATT	    0.979485	-68
AAGACCTCTAGTCCTCCCTTCATCCTATGG	1	34	0	GTCCTCCCTT	    0.988179	-47
AGGACTAGAGGTCTTCCCTTTTTTTGTTGG	1	49	1	GTCTTCCCTT	    0.981832	-32
CACAGACGCAGTTCGCCATTCCACCGCTAA	2	184	1	GTTCGCCATT	    0.968393	-117
CATCACCTCAGCGTGCCCTGTGTATTGCTG	2	271	0	GCGTGCCCTG	    0.983339	-30
          **********

Masking position 9
Map Score:   1.94421

Number of sites scoring better than the average of aligned sites = 295
Number in coding regions = 266
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 5

CCCTTCATCCTATGGTAATGGCCCGCTGGGG	1	18	0	TATGGTAATG	    0.838036	-63
TCAGAAATATTTTGGCGATCGCCTGATGACC	2	11	0	TTTGGCGATG	    0.985719	-290
TCAGTGGACATAGAGCAATGGGTGATCCCCG	2	81	0	TAGAGCAATG	    0.954611	-220
GGCACAGGATTATGGCGGTTGAGGTGAGGAA	2	148	1	TATGGCGGTG	    0.994642	-153
TGGGTGTAGGTTTAGCGGTGGAATGGCGAAC	2	194	0	TTTAGCGGTG	    0.989091	-107
TTGCCCTGGGTACAGCCGTGGGTGTAGGTTT	2	212	0	TACAGCCGTG	    0.952013	-89
AGCGCTTTTATTGTGCTGTTGCCCTGGGTAC	2	230	0	TTGTGCTGTG	    0.882176	-71
          ********* *

Masking position 9
Map Score:   3.57369

Number of sites scoring better than the average of aligned sites = 1566
Number in coding regions = 1413
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 165
Fraction of orfs with sites within 600 bp upstream = 0.0265018


Motif number 6

          **********

No masking
Map Score:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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