AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i004_4_1_1_21_synecho_reg_100.orf -o004_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 RCY24958 106 Synechocystis #2 RCY23085 96 Synechocystis #3 RCY06919 231 Synechocystis Motif number 1 AGGTTTGACTTTAAACTGAGGCTAACCGCT 1 61 0 TTAAACTGAG 0.926803 -46 AAATTAAATTGAGATGACGAAGA 1 94 0 TTAAATTGAG 0.906168 -13 TTGTAAACTTCGCCATTGATTAGGCGGTAG 2 45 1 CGCCATTGAT 0.933191 -52 TTAATTTTGTTTCCATTGAGCTACAGACTA 2 72 0 TTCCATTGAG 0.972015 -25 TACCAATTCTTGCCGCCGAGGAAATCAGTG 3 111 1 TGCCGCCGAG 0.953399 -121 AGAGGTTATGTTCCACTGATTTCCTCGGCG 3 124 0 TTCCACTGAT 0.978872 -108 AACCTCTCCCTGCCATTGGGGGTATGCCCG 3 147 1 TGCCATTGGG 0.982105 -85 ********** Masking position 8 Map Score: 5.15767 Number of sites scoring better than the average of aligned sites = 969 Number in coding regions = 884 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 CAAGATCCCAAGGAAAGATTTTTATGTCA 1 9 0 AGGAAGATTT 0.979019 -98 AATAGCGTATCGGAAAATCTTCAAGATCCCA 1 30 0 CGGAAATCTT 0.956364 -77 ACGAAGATGGAGGTTTGACTTTAAACTGAGG 1 70 0 AGGTTGACTT 0.789158 -37 GATGTTCGGCGAAATTTCGGACGTAAA 2 7 1 CGGGAAATTT 0.928917 -90 TGCTATGATCAGGGATGTCTTTTATCTTCTT 3 20 0 AGGATGTCTT 0.927497 -212 GATCATAGCAAGGTCAGACTTAATTTACCCG 3 41 1 AGGCAGACTT 0.856785 -191 TTAATTTACCCGGACAAATCTTTGGTTGAAT 3 60 1 CGGCAAATCT 0.86386 -172 ATTTCCTCGGCGGCAAGAATTGGTAATCGAC 3 105 0 CGGAAGAATT 0.967074 -127 *** ******* Masking position 11 Map Score: 4.47079 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 620 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 TGACATAAAAATCTTTCCTTGGGATCTTGA 1 10 1 AATCTTTCCT 0.933313 -97 TCAAACCTCCATCTTCGTCATCTCAATTTAA 1 83 1 ATCTTCGTCT 0.910421 -24 TTACGTCCGAAATTTCGCCGAACATC 2 6 0 AATTTCGCCA 0.959504 -91 TAAACTTGTAAACTTCGCCATTGATTAGGCG 2 40 1 AACTTCGCCT 0.991908 -57 TCGATTACCAATTCTTGCCGCCGAGGAAATC 3 106 1 ATTCTTGCCC 0.909093 -126 AGTGGAACATAACCTCTCCCTGCCATTGGGG 3 137 1 AACCTCTCCT 0.984878 -95 ********* * Masking position 5 Map Score: 0.87617 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 558 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 4 CTTTAAACTGAGGCTAACCGCTAATAGCGT 1 53 0 AGGCTAACCG 0.915022 -54 CTCAGTTTAAAGTCAAACCTCCATCTTCGT 1 71 1 AGTCAAACCT 0.983218 -36 AGAAGATAAAAGACATCCCTGATCATAGCA 3 21 1 AGACATCCCT 0.952668 -211 GGGTAAATTAAGTCTGACCTTGCTATGATC 3 41 0 AGTCTGACCT 0.94317 -191 TAATTTACCCGGACAAATCTTTGGTTGAAT 3 61 1 GGACAAATCT 0.893352 -171 ATCAAGGCGCGGGCATACCCCCAATGGCAG 3 156 0 GGGCATACCC 0.926484 -76 ATTGAATTCAGGTCATCGCTTCCCCA 3 216 1 GGTCATCGCT 0.923939 -16 ********** Masking position 4 Map Score: 1.40694 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 985 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 ********** No masking Map Score: -4.02005e-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 6 ********** No masking Map Score: -4.02005e-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: -4.02005e-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