AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i233_protein_modification____synecho_reg_300.orf -o233_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 RCY01914 218 Synechocystis #2 RCY29942 300 Synechocystis #3 RCY22922 237 Synechocystis Motif number 1 ATTTTACCCGCCCGACCCTAGGACATCATCCC 1 11 0 CCGACCCTGG 0.998283 -208 TCGTTACAATCCATCCCATTGGTTTTGATTTT 1 38 0 CCTCCCATGG 0.969405 -181 CCCAGTATTGCCGGAGCCTTAGTGAGTTAATT 2 138 1 CCGAGCCTAG 0.996321 -163 TTATTCTTGGCCAAACCCTGACGTTGGAACGT 2 197 0 CCAACCCTAC 0.904519 -104 GTAAACCCCACCATAGCTTGAGCAAACAATGG 3 23 1 CCTAGCTTAG 0.930583 -215 AGGCTCGGGCCCATAGCCTTATTTTCCACAGT 3 60 0 CCTAGCCTAT 0.928762 -178 AGGCTATGGGCCCGAGCCTGGGAAAATAATGT 3 73 1 CCGAGCCTGG 0.982233 -165 GCAACTTTACCCTGCCCCTGGGCAACCCAGAC 3 198 1 CCGCCCCTGG 0.997113 -40 CCTGGGCAACCCAGACCATTGGACTGAGGGGT 3 214 1 CCGACCATGG 0.99368 -24 ** ****** ** Masking position 9 Map Score: 17.5186 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 477 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 ATTGGTTTTGATTTTACCCGCCCGACCCTAG 1 22 0 ATTTACCCGC 0.711676 -197 CATTTATACACATTTGCCCCCCGGCGATCGC 1 103 1 CTTTGCCCCC 0.994299 -116 ATTATCTAATTTTTTGCCCCAATTTGGCGAT 1 129 0 TTTTGCCCCA 0.968001 -90 AATTGCGGCGCATTTGCCCCATCCTATCCCC 1 157 1 CTTTGCCCCA 0.989454 -62 TTAAAAGCCCCCTTGACCCCCAAATTTGGGG 2 88 1 CTTGACCCCC 0.983472 -213 GACTTTCAGTCAGTGTCCCCCCAAATTTGGG 2 106 0 CGTGTCCCCC 0.929378 -195 TATCGATTATTCTTGGCCAAACCCTGACGTT 2 204 0 TTTGGCCAAA 0.810688 -97 CCCATAGCCTTATTTTCCACAGTTTAAGCCA 3 52 0 TTTTTCCACA 0.737761 -186 AAAATAAGGCTATGGGCCCGAGCCTGGGAAA 3 67 1 TTGGGCCCGA 0.883807 -171 CCCAAATTACCATTGACCAGCAGGGAAATTG 3 114 1 CTTGACCAGC 0.94926 -124 CGGTTTTGGCCAGTTGCCAGAATCATCAGTG 3 156 1 CGTTGCCAGA 0.902827 -82 TAAAGTTGCTCCTTTGCCAACACTGATGATT 3 176 0 CTTTGCCAAC 0.94865 -62 TTACCCTGCCCCTGGGCAACCCAGACCATTG 3 204 1 CTGGGCAACC 0.728748 -34 * ********* Masking position 7 Map Score: 13.25 Number of sites scoring better than the average of aligned sites = 5060 Number in coding regions = 4635 Number in noncoding regions = 425 Number of orfs with sites within 600 bp upstream = 417 Fraction of orfs with sites within 600 bp upstream = 0.0669772 Motif number 3 ATTGGTTTTGATTTTACCCGCCCGACCCTA 1 23 0 ATTTTACCCG 0.805984 -196 TTTTTGCCCCAATTTGGCGATCGCCGGGGG 1 120 0 AATTTGGCGA 0.874095 -99 AAAATTAGATAATTGCGGCGCATTTGCCCC 1 147 1 AATTGCGGCG 0.955785 -72 ATTGCGGCGCATTTGCCCCATCCTATCCCC 1 158 1 ATTTGCCCCA 0.853713 -61 TAATGGTCTTACTTTCGGCAATAAAATTAT 2 38 0 ACTTTCGGCA 0.896771 -263 TTGACCCCCAAATTTGGGGGGACACTGACT 2 100 1 AATTTGGGGG 0.917159 -201 AAATCGTAATATTTTCGCCGTTGCT 2 286 1 ATTTTCGCCG 0.986434 -15 AGTTTAATTTCGGTAAACCCCACCA 3 6 1 AATTTCGGTA 0.847547 -232 GTGTAACATTATTTTCCCAGGCTCGGGCCC 3 80 0 ATTTTCCCAG 0.805984 -158 GGTCAATGGTAATTTGGGCGAAGTGTAACA 3 102 0 AATTTGGGCG 0.973225 -136 AGTTGATGACAATTTCCCTGCTGGTCAATG 3 124 0 AATTTCCCTG 0.896959 -114 TCAACTAACGGTTTTGGCCAGTTGCCAGAA 3 148 1 GTTTTGGCCA 0.767049 -90 ********** Masking position 4 Map Score: 8.24231 Number of sites scoring better than the average of aligned sites = 2514 Number in coding regions = 2270 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 4 CATTTGCCCCCCGGCGATCGCCAAATTGGG 1 113 1 CCGGCGATCG 0.98812 -106 CTTTAGTTTATCGGGGATAGGATGGGGCAA 1 170 0 TCGGGGATAG 0.925598 -49 GGTCTTACTTTCGGCAATAAAATTATGCTC 2 34 0 TCGGCAATAA 0.9591 -267 CACTAAGGCTCCGGCAATACTGGGGGACTT 2 132 0 CCGGCAATAC 0.988107 -169 ACAACCATTACCGGTAATCCCCAAGGAAAT 2 243 1 CCGGTAATCC 0.971348 -58 AGCAACGGCGAAAATATTACGATT 2 287 0 ACGGCGAAAA 0.829805 -14 AGTTTAATTTCGGTAAACCCCACCATAGC 3 10 1 TCGGTAAACC 0.903653 -228 ********** Masking position 7 Map Score: 2.92477 Number of sites scoring better than the average of aligned sites = 2864 Number in coding regions = 2629 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 5 GAGATTCTACAGGTTGACGTAAGCATTTAT 1 80 1 AGGTTGACGT 0.974045 -139 GATAAACTAAAGGTTGCAGTAAGCAACGAT 1 188 1 AGGTTGCAGT 0.981772 -31 TAGGTTTAAGTATCGTTGCTT 1 208 0 AGGTTTAAGT 0.968353 -11 AATGGTAATTTGGGCGAAGTGTAACATTAT 3 98 0 TGGGCGAAGT 0.947329 -140 GCCCAGGGGCAGGGTAAAGTTGCTCCTTTG 3 191 0 AGGGTAAAGT 0.970363 -47 ********** Masking position 10 Map Score: 1.73644 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 6 CAATCCATCCCATTGGTTTTGATTTTACCC 1 34 0 CATTGGTTTT 0.901569 -185 CCCGATAAACTAAAGGTTGCAGTAAGCAAC 1 185 1 TAAAGGTTGC 0.747023 -34 TACTCCATTGCAAAGGTTTTT 2 2 0 CAAAGGTTTT 0.954994 -299 AGATTCAGTTTAATGGTCTTACTTTCGGCA 2 48 0 TAATGGTCTT 0.968122 -253 GGATTACCGGTAATGGTTGTTACAAAGATA 2 233 0 TAATGGTTGT 0.968122 -68 TACGATTTGTTAATGGTAATCATTTCCTTG 2 264 0 TAATGGTAAT 0.895189 -37 CCCTGCTGGTCAATGGTAATTTGGGCGAAG 3 109 0 CAATGGTAAT 0.916639 -129 TGTCATCAACTAACGGTTTTGGCCAGTTGC 3 143 1 TAACGGTTTT 0.932826 -95 CCCCTCAGTCCAATGGTCTGGGTTGCCCAG 3 215 0 CAATGGTCTG 0.912161 -23 ********** Masking position 7 Map Score: 6.10952 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 691 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 ********** No masking Map Score: -8.99385e-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: -8.99385e-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 9 ********** No masking Map Score: -8.99385e-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