AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i103_synecho_ctra_300.orf -o103_synecho_ctra_300.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 RCY32435 100 Synechocystis #2 RCY33367 108 Synechocystis #3 RCY00914 273 Synechocystis #4 RCY13728 55 Synechocystis Motif number 1 TTGTTAATCAAAGACCCAAGCTATCATGGGG 1 33 1 AAGACCCAGC 0.921385 -68 GCAGAGGGGAAAAACTCCAACCCCCATGATA 1 54 0 AAAACTCCAC 0.952348 -47 TTAAACTAAAAAAATTCCAGCAGAGGGGAAA 1 73 0 AAAATTCCGC 0.99597 -28 AGAAAACCGGAAAACTCCCCCAAGGGCGGTA 2 59 1 AAAACTCCCC 0.967342 -50 ATACACCCCAAAATTTACCGCCCTTGGGGGA 2 74 0 AAATTTACGC 0.931169 -35 CGAGTTAAAGAAAATCCCTGCTGGGAG 3 7 0 AAAATCCCGC 0.997469 -267 TAGATCGCCAAAAATCTCCGCAACTATTTGG 3 75 0 AAAATCTCGC 0.977784 -199 CAACCTATGGAAAAGTCCTGCCCAAGACAGA 3 123 0 AAAAGTCCGC 0.987021 -151 ACCATTGATTAAATTCCATGCAACCTATGGA 3 143 0 AAATTCCAGC 0.949849 -131 ATAAATATCAAAAATCACTGGAATAATTGTG 3 187 0 AAAATCACGG 0.909499 -87 ******** ** Masking position 2 Map Score: 14.3852 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 1274 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 AAAACTCCAACCCCCATGATAGCTTGGGTC 1 45 0 CCCCCATGAT 0.823644 -56 TGGAGTTTTTCCCCTCTGCTGGAATTTTTT 1 66 1 CCCCTCTGCT 0.944687 -35 CCCCCTATCTGTGCAATGTC 2 1 1 CCCCCTATCT 0.98008 -108 CCGGAAAACTCCCCCAAGGGCGGTAAATTT 2 65 1 CCCCCAAGGG 0.961371 -44 CTCCCAGCAGGGATTTTCTTTA 3 3 1 CCCAGCAGGG 0.601732 -271 GGACCTAAGCCCCGGTTTGTTAAATCATTA 3 46 0 CCCGGTTTGT 0.808074 -228 CGCCAAAAATCTCCGCAACTATTTGGGACC 3 71 0 CTCCGCAACT 0.812511 -203 CAGCAATGCTCCCAGCATCTGTCTTGGGCA 3 106 1 CCCAGCATCT 0.970836 -168 TTGGCAATGACTCACCATCTCCGCC 4 6 0 CTCACCATCT 0.877016 -50 ACTGGACTGACCCCCTTTGGCAATGACTCA 4 22 0 CCCCCTTTGG 0.950744 -34 ********** Masking position 3 Map Score: 5.27725 Number of sites scoring better than the average of aligned sites = 4523 Number in coding regions = 3992 Number in noncoding regions = 531 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 3 GGGGTGTATTACTATGGCTTAGT 2 96 1 ACTATGGCTT 0.93857 -13 CTCCCAGCAGGGATTTTCTTTAACT 3 6 1 AGCAGGGATT 0.980614 -268 CTCGGTCAACACTAATGATTTAACAAACCG 3 34 1 ACTAATGATT 0.749179 -240 GATTTAACAAACCGGGGCTTAGGTCCCAAA 3 50 1 ACCGGGGCTT 0.955408 -224 AGATGCTGGGAGCATTGCTGTAGATCGCCA 3 96 0 AGCATTGCTG 0.87302 -178 TTCCATAGGTTGCATGGAATTTAATCAATG 3 142 1 TGCATGGAAT 0.733196 -132 ATAATCACTTACCATTGATTAAATTCCATG 3 154 0 ACCATTGATT 0.977255 -120 TCACAATTATTCCAGTGATTTTTGATATTT 3 186 1 TCCAGTGATT 0.949986 -88 ********** Masking position 7 Map Score: 3.09728 Number of sites scoring better than the average of aligned sites = 2087 Number in coding regions = 1903 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 TTAGGTCCCAAATAGTTGCGGAGATTTTTG 3 68 1 AATAGTTGCG 0.992247 -206 AAATCACTGGAATAATTGTGAGTATAATCA 3 177 0 AATAATTGTG 0.968458 -97 ATGCTAACTTAATAGTTGAGAATTATTTGC 3 230 1 AATAGTTGAG 0.988556 -44 ********** Masking position 4 Map Score: 0.89238 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 17 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 CTAAAAAAATTCCAGCAGAGGGGAAAAACT 1 69 0 TCCAGCAGAG 0.974562 -32 ACAATCTATTTTCAACCCAGAAAACCGGAA 2 41 1 TTCAACCCAG 0.964263 -68 TATGGAAAAGTCCTGCCCAAGACAGATGCT 3 119 0 TCCTGCCCAA 0.976323 -155 TTGATATTTATTCTGAACAGATAATGCTAA 3 207 1 TTCTGAACAG 0.916347 -67 AGGGGGTCAGTCCAGTCCAGTCGTCCAGAT 4 36 1 TCCAGTCCAG 0.987639 -20 ********** Masking position 9 Map Score: 0.78183 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 676 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 AGAGGGGAAAAACTCCAACCCCCATGATAGC 1 52 0 AACTCCACCC 0.984254 -49 TATCTGTGCAATGTCCGATCCTCGTACAATC 2 16 1 ATGTCCATCC 0.982644 -93 CGTACAATCTATTTTCAACCCAGAAAACCGG 2 38 1 ATTTTCACCC 0.934433 -71 ACACCCCAAAATTTACCGCCCTTGGGGGAGT 2 72 0 ATTTACGCCC 0.957282 -37 ACCTATGGAAAAGTCCTGCCCAAGACAGATG 3 121 0 AAGTCCGCCC 0.996219 -153 CAAAGGGGGTCAGTCCAGTCCAGTCGTCCAG 4 33 1 CAGTCCGTCC 0.970198 -23 ****** **** Masking position 4 Map Score: 3.94611 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 471 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ********** No masking Map Score: -8.21797e-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: -8.21797e-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: -8.21797e-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