AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i233_synecho_ctra_100.orf -o233_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 RCY01914 218 Synechocystis #2 RCY22922 237 Synechocystis Motif number 1 ATTTTACCCGCCCGACCCTAGGACATCATCCC 1 11 0 CCCGCCCTGG 0.998087 -208 TCGTTACAATCCATCCCATTGGTTTTGATTTT 1 38 0 CCATCCATGG 0.98728 -181 ACATTTGCCCCCCGGCGATCGCCAAATTGGGG 1 112 1 CCCGCGATGC 0.99263 -107 TTTCGGTAAACCCCACCATAGCTTGAGCAAAC 2 18 1 CCCCCCATGC 0.994445 -220 AGGCTATGGGCCCGAGCCTGGGAAAATAATGT 2 73 1 CCCGGCCTGG 0.960742 -165 GCAACTTTACCCTGCCCCTGGGCAACCCAGAC 2 198 1 CCTGCCCTGG 0.99013 -40 CCTGGGCAACCCAGACCATTGGACTGAGGGGT 2 214 1 CCAGCCATGG 0.995833 -24 **** **** ** Masking position 9 Map Score: 16.7649 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 409 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 AGCATTTATACACATTTGCCCCCCGGCGATC 1 101 1 CACTTTGCCC 0.987563 -118 CAATTATCTAATTTTTTGCCCCAATTTGGCG 1 131 0 ATTTTTGCCC 0.990459 -88 ATAATTGCGGCGCATTTGCCCCATCCTATCC 1 155 1 CGCTTTGCCC 0.995404 -64 AGTTTAAGCCATTGTTTGCTCAAGCTATGGT 2 32 0 ATTTTTGCTC 0.910528 -206 GGCCCATAGCCTTATTTTCCACAGTTTAAGC 2 54 0 CTTTTTTCCA 0.924707 -184 GAAGTGTAACATTATTTTCCCAGGCTCGGGC 2 82 0 ATTTTTTCCC 0.953361 -156 CATCAACTAACGGTTTTGGCCAGTTGCCAGA 2 146 1 CGGTTTGGCC 0.955762 -92 GGTAAAGTTGCTCCTTTGCCAACACTGATGA 2 178 0 CTCTTTGCCA 0.986897 -60 GTCCAATGGTCTGGGTTGCCCAGGGGCAGGG 2 207 0 CTGGTTGCCC 0.983962 -31 *** ******* Masking position 6 Map Score: 13.9178 Number of sites scoring better than the average of aligned sites = 1521 Number in coding regions = 1338 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 3 TGATGTCCTAGGGTCGGGCGGGTAAAATCA 1 15 1 GGGTCGGGCG 0.979241 -204 GCGATCGCCAAATTGGGGCAAAAAATTAGA 1 126 1 AATTGGGGCA 0.976796 -93 AAAATTAGATAATTGCGGCGCATTTGCCCC 1 147 1 AATTGCGGCG 0.888046 -72 ATCGGGGATAGGATGGGGCAAATGCGCCGC 1 161 0 GGATGGGGCA 0.970267 -58 ACCCCACCATAGCTTGAGCAAACAATGGCT 2 27 1 AGCTTGAGCA 0.801225 -211 TATTTTCCCAGGCTCGGGCCCATAGCCTTA 2 71 0 GGCTCGGGCC 0.8567 -167 GGTCAATGGTAATTTGGGCGAAGTGTAACA 2 102 0 AATTTGGGCG 0.971565 -136 ATCAACTAACGGTTTTGGCCAGTTGCCAGA 2 147 1 GGTTTTGGCC 0.966356 -91 CAACACTGATGATTCTGGCAACTGGCCAAA 2 160 0 GATTCTGGCA 0.956524 -78 CAGAATCATCAGTGTTGGCAAAGGAGCAAC 2 173 1 AGTGTTGGCA 0.848095 -65 ********** Masking position 9 Map Score: 8.84083 Number of sites scoring better than the average of aligned sites = 3616 Number in coding regions = 3319 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 317 Fraction of orfs with sites within 600 bp upstream = 0.0509155 Motif number 4 GAGATTCTACAGGTTGACGTAAGCATTTAT 1 80 1 AGGTTGACGT 0.975926 -139 GATAAACTAAAGGTTGCAGTAAGCAACGAT 1 188 1 AGGTTGCAGT 0.987907 -31 TAGGTTTAAGTATCGTTGCTT 1 208 0 AGGTTTAAGT 0.979375 -11 AATGGTAATTTGGGCGAAGTGTAACATTAT 2 98 0 TGGGCGAAGT 0.965456 -140 GCCCAGGGGCAGGGTAAAGTTGCTCCTTTG 2 191 0 AGGGTAAAGT 0.980469 -47 ********** Masking position 10 Map Score: 4.32824 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 67 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TAACTGAGATTCTACAGGTTGACGTAAGCA 1 75 1 TCTACAGGTT 0.985332 -144 TCCCCGATAAACTAAAGGTTGCAGTAAGCA 1 183 1 ACTAAAGGTT 0.984183 -36 GGTAAACCCCACCATAGCTTGAGCAAACAA 2 22 1 ACCATAGCTT 0.934244 -216 AGCCTTATTTTCCACAGTTTAAGCCATTGT 2 48 0 TCCACAGTTT 0.948056 -190 ATTGTCATCAACTAACGGTTTTGGCCAGTT 2 141 1 ACTAACGGTT 0.965556 -97 ********** Masking position 4 Map Score: 1.74796 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 139 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TAATTTTTTGCCCCAATTTGGCGATCGCCGG 1 123 0 CCCCAATTTG 0.962862 -96 GGCAAATGCGCCGCAATTATCTAATTTTTTG 1 144 0 CCGCAATTAC 0.993787 -75 CCCATCCTATCCCCGATAAACTAAAGGTTGC 1 174 1 CCCCGATAAC 0.969608 -45 GTGGGGTTTACCGAAATTAAACT 2 3 0 CCGAAATTAA 0.946992 -235 TTACACTTCGCCCAAATTACCATTGACCAGC 2 104 1 CCCAAATTAC 0.99041 -134 ********* * Masking position 6 Map Score: 1.14324 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 409 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: -8.85746e-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: -8.85746e-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 9 ********** No masking Map Score: -8.85746e-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