AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_synecho_ctra_100.orf -o326_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 RCY00022 120 Synechocystis #2 RCY52230 73 Synechocystis #3 RCY02381 135 Synechocystis #4 RCY06056 300 Synechocystis #5 RCT00628 300 Chlamydia_trachomatis #6 RCT00820 113 Chlamydia_trachomatis #7 RCT00821 94 Chlamydia_trachomatis Motif number 1 TATAATGTGGGGGCCTCTGCTTTAACCGCC 1 28 0 GGGCCTCTGC 0.949898 -93 ATCTTTTCCTGGGTTTCTGGCTTAAACTGA 1 66 1 GGGTTTCTGG 0.976627 -55 ATATGGGGTTAGGGGTCTGGATCAAATTAA 2 50 0 AGGGGTCTGG 0.976283 -24 TATCATTTTAGTCTTTTTGGCGGCGGCACT 3 60 1 GTCTTTTTGG 0.581314 -76 CGGCACTACCATGGTTTTGGTGTGAAGATT 3 83 1 ATGGTTTTGG 0.884752 -53 CCTGCAGACTGTCTCTCTGGGGCTCCGTTG 4 94 0 GTCTCTCTGG 0.8754 -207 ACGGGCCCCCAGGGCTTTACCCATGGCCGA 4 181 1 AGGGCTTTAC 0.807448 -120 CAGATTTCCTATGGCTCTGGAGGTTTGGGA 5 59 1 ATGGCTCTGG 0.974904 -242 TTAATAAAAGGGTTCTCTGCCTATTCTAGA 6 51 1 GGTTCTCTGC 0.803366 -63 CCATTCAAAAAGGGGTCTAGAATAGGCAGA 6 66 0 AGGGGTCTAG 0.838923 -48 ATGGAAAAATGGGTTTTTGGAGAACATCGA 6 92 1 GGGTTTTTGG 0.957401 -22 ATAGTAAGAGGGGGCTTTGCGGATTTATGG 7 26 1 GGGGCTTTGC 0.98403 -69 AAATACAACAAGGGCTTTGGGACCATAAAT 7 48 0 AGGGCTTTGG 0.98643 -47 ********** Masking position 6 Map Score: 14.6533 Number of sites scoring better than the average of aligned sites = 2351 Number in coding regions = 2123 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 2 CCGAAAATGTTCCCCAACGGAGCCCCAGAG 4 80 1 TCCCCAACGG 0.990655 -221 AGACGTTCTGTTCCAACCTGCAGACTGTCT 4 110 0 TTCCAACCTG 0.864605 -191 TGAGCCTGGTTCCCAGACGTTCTGTTCCAA 4 124 0 TCCCAGACGT 0.87876 -177 TAGCCCATTCTACCAAACGGGCCCCCAGGG 4 165 1 TACCAAACGG 0.960587 -136 CCATCCTCTCCCCCCAACCGCTAGACAAGC 4 239 0 CCCCCAACCG 0.970179 -62 CACATGCAACTCCCAAACCTCCAGAGCCAT 5 69 0 TCCCAAACCT 0.976046 -232 TCTGTAAGAATCCCGAACTGCTGTTTCAAT 5 116 0 TCCCGAACTG 0.979189 -185 TTATTCAACCTTCCAAACCGTTAAGAAATG 5 218 0 TTCCAAACCG 0.987788 -83 AATAAATCTTTTCCGAACCGTATCATGGAA 5 243 1 TTCCGAACCG 0.981959 -58 ********** Masking position 4 Map Score: 11.3665 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 570 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 GGCAATATGGGGTTAGGGGTC 2 63 0 GCAATATGGG 0.979225 -11 GGCCCGTTTGGTAGAATGGGCTAGCAATCT 4 158 0 GTAGAATGGG 0.869 -143 GGAGAGGATGGCAAAATGGAACAACATAAT 4 258 1 GCAAAATGGA 0.955535 -43 AGTTGCATGTGCAACATGTGATAAGTTTAT 5 88 1 GCAACATGTG 0.935352 -213 TCACAGGCTAGCAAAATTGGGGCATGATCT 5 143 0 GCAAAATTGG 0.955405 -158 ATTTTTCCATTCAAAAAGGGGTCTAGAATA 6 72 0 TCAAAAAGGG 0.901409 -42 TTTTTGAATGGAAAAATGGGTTTTTGGAGA 6 85 1 GAAAAATGGG 0.961501 -29 ATGTTTAAATACAACAAGGGCTTTGGGACC 7 54 0 ACAACAAGGG 0.860188 -41 ********** Masking position 6 Map Score: 5.70297 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 602 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 AGGTTCGTTGCGGCCATAGTCCCGACGATG 3 31 0 CGGCCATAGT 0.989999 -105 GGCGGCGGCACTACCATGGTTTTGGTGTGA 3 78 1 CTACCATGGT 0.949923 -58 CTCGATTTTTCGGCCATGGGTAAAGCCCTG 4 190 0 CGGCCATGGG 0.992784 -111 AATCGAGCAACGGCAATGGGCTTTGAGCTT 4 213 1 CGGCAATGGG 0.946936 -88 TTTTGAAACCCTTCCATGATACGGTTCGGA 5 254 0 CTTCCATGAT 0.838049 -47 TAAAGAAACTCTGCCATACTTTTCGACTAC 6 12 0 CTGCCATACT 0.916595 -102 CTGGCGTTTTCGTTCATAGTAAGAGGGGGC 7 11 1 CGTTCATAGT 0.812689 -84 ********** Masking position 6 Map Score: 3.73318 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1089 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 CTATGGCCGCAACGAACCTATCATTTTAGTC 3 42 1 AAGAACCTAT 0.950407 -94 AAGCAAAAATAAGAATTCTATTTAACAATCT 3 108 0 AAAATTCTAT 0.918317 -28 TGATGGGGTTAACAATCCTATGCCGCGTTGA 4 46 0 AAAATCCTAT 0.946747 -255 GATTTGTTACAAACAAACTATTTATTTAGCC 5 17 1 AACAAACTAT 0.868955 -284 CTGCTGTTTCAATAAACTTATCACATGTTGC 5 98 0 AAAAACTTAT 0.768697 -203 AAGAAATGTTAACAAAACTATCTAAACTTTC 5 195 0 AAAAAACTAT 0.955666 -106 TGGAAGGTTGAATAAATCTTTTCCGAACCGT 5 233 1 AAAAATCTTT 0.880866 -68 AAGAATTTTTAAAGAAACTCTGCCATACTTT 6 20 0 AAGAAACTCT 0.787727 -94 GAGTTTCTTTAAAAATTCTTTTAATAAAAGG 6 31 1 AAAATTCTTT 0.627409 -83 ** ******** Masking position 5 Map Score: 2.841 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 234 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 GTGGGGGCCTCTGCTTTAACCGCCCATTTC 1 22 0 CTGCTTTAAC 0.982238 -99 CCTGGGTTTCTGGCTTAAACTGAGGCTGAC 1 73 1 TGGCTTAAAC 0.940627 -48 ATTCTTATTTTTGCTTAAACAAT 3 123 1 TTGCTTAAAC 0.972351 -13 CATAGGAAATCTGCTTAAAGGTTTGGCTAA 5 42 0 CTGCTTAAAG 0.981942 -259 AGACGAAGTCCTGTTTTAAGGAGGCTTG 5 283 1 CTGTTTTAAG 0.879135 -18 ********** Masking position 5 Map Score: 1.55356 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 GATCGCCGGGGGAAAAAAATGATGGTCAGC 1 97 0 GGAAAAAAAT 0.936151 -24 TTAGGGGTCTGGATCAAATTAAAGGGCATT 2 42 0 GGATCAAATT 0.827181 -32 TGTTGTTCACGGAAAATCATCGTCGGGACT 3 14 1 GGAAAATCAT 0.894549 -122 GTGTGGGAAAAATTTCCAGTTCATA 4 6 1 GGAAAAATTT 0.930186 -295 GCTCCGTTGGGGAACATTTTCGGGCTTGAT 4 73 0 GGAACATTTT 0.896088 -228 ATGGCAAAATGGAACAACATAATACAGGTG 4 265 1 GGAACAACAT 0.950282 -36 GATACGGTTCGGAAAAGATTTATTCAACCT 5 237 0 GGAAAAGATT 0.895838 -64 ********** Masking position 6 Map Score: 2.54078 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 477 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 8 GCTTAAACTGAGGCTGACCATCATTTTTTT 1 85 1 AGGCTGACCA 0.949221 -36 GGGCTTGATGGGGTTAACAATCCTATGCCG 4 52 0 GGGTTAACAA 0.917028 -249 TTGGTAGAATGGGCTAGCAATCTTGACTGA 4 151 0 GGGCTAGCAA 0.981966 -150 TTGGGGGGAGAGGATGGCAAAATGGAACAA 4 252 1 AGGATGGCAA 0.961782 -49 CGGGCTTCACAGGCTAGCAAAATTGGGGCA 5 149 0 AGGCTAGCAA 0.981195 -152 ********** Masking position 5 Map Score: 1.78383 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 172 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 TTAAAGCAGAGGCCCCCACATTATAACCAA 1 33 1 GGCCCCCACA 0.989076 -88 TCGGGACTATGGCCGCAACGAACCTATCAT 3 36 1 GGCCGCAACG 0.989048 -100 ATGGTAGTGCCGCCGCCAAAAAGACTAAAA 3 65 0 CGCCGCCAAA 0.930662 -71 CTACCAAACGGGCCCCCAGGGCTTTACCCA 4 174 1 GGCCCCCAGG 0.996281 -127 AGCCTGTGAAGCCCGGCAGGTGGTTCTTCT 5 164 1 GCCCGGCAGG 0.933719 -137 GCGGATTTATGGTCCCAAAGCCCTTGTTGT 7 44 1 GGTCCCAAAG 0.900557 -51 ********** Masking position 8 Map Score: 1.54565 Number of sites scoring better than the average of aligned sites = 1483 Number in coding regions = 1416 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 10 ********** No masking Map Score: 8.55083e-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 11 ********** No masking Map Score: 8.55083e-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 12 ********** No masking Map Score: 8.55083e-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