AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i335_2_7_7_40_synecho_reg_300.orf -o335_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 RCY02837 200 Synechocystis #2 RCY48630 89 Synechocystis #3 RCY29821 289 Synechocystis #4 RCY44275 57 Synechocystis #5 RCY26100 89 Synechocystis #6 RCY38329 73 Synechocystis #7 RCY10018 177 Synechocystis #8 RCY04156 216 Synechocystis Motif number 1 TAACCAATGCCGAAACCGCCCCAATGCTAGCATTAACC 1 93 1 CACCCCAAGT 0.991142 -108 CCGCAGTTTCTCCCAGGGTGAGTAAGTTA 1 182 0 CACTCCCAGT 0.966048 -19 TATGTCCAAGCTTATTGTCCCCAGTAAACCGGAAAAA 2 10 0 CACCCCAGAA 0.802973 -80 ATCCCAGTTACCAACCATCCCCTAGGCTCCTGAAAA 3 9 0 CACCCCTAGT 0.987356 -281 AGAGAGTGTTTGAAAAGCCCCCCTGGCTCCCCAAGTTT 3 157 1 TACCCCCTGT 0.942035 -133 GTGACTTTTACTTAACTTCCCCCAAACTTGGGGAGCCA 3 180 0 CACCCCCAAT 0.997087 -110 TATTTTGCCCCCTAAATCCCCCAATAATGGGTGACTTT 3 210 0 CACCCCAAAT 0.989753 -80 CTTCCTGCTTAAAGAAAACCCCACAATTCCGGGGAGG 5 10 1 TAACCCCAAT 0.906074 -80 TGGCAACTTTCCCATTATCCCCTAGGCTGTGCCTCCCC 5 41 0 CACCCCTAGT 0.987356 -49 TAAGGGTTACTTGAATAACCCCCAAAAAAACCGGTTGA 7 23 0 TACCCCCAAA 0.961149 -155 TGATCGGCTCTGCAAAATTCCCCAGAGTGGCTAGCTGG 8 83 0 TATCCCCAAT 0.944477 -134 TCCTTTTGTACTGAGATTTCCCCAAAGTAAACATGGTA 8 146 1 CATCCCCAAT 0.981392 -71 * * ****** * * Masking position 4 Map Score: 18.2316 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 594 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 CCGCAGTTTCTCCCAGGGTGAGTAAGTTA 1 182 0 CTCCCAGGGT 0.899846 -19 AAGCTTATTGTCCCCAGTAAACCGGAAAAA 2 11 0 TCCCCAGTAA 0.835642 -79 TACCAACCATCCCCTAGGCTCCTGAAAA 3 9 0 CCCCTAGGCT 0.959024 -281 TTTGAAAAGCCCCCCTGGCTCCCCAAGTTT 3 165 1 CCCCCTGGCT 0.976758 -125 TACTTAACTTCCCCCAAACTTGGGGAGCCA 3 180 0 CCCCCAAACT 0.986069 -110 CCCCCTAAATCCCCCAATAATGGGTGACTT 3 211 0 CCCCCAATAA 0.87739 -79 TTTTATTTTGCCCCCTAAATCCCCCAATAA 3 221 0 CCCCCTAAAT 0.931702 -69 AGGCTGTGCCTCCCCGGAATTGTGGGGTTT 5 26 0 TCCCCGGAAT 0.890732 -64 TTCCCATTATCCCCTAGGCTGTGCCTCCCC 5 41 0 CCCCTAGGCT 0.959024 -49 ACTTGAATAACCCCCAAAAAAACCGGTTGA 7 23 0 CCCCCAAAAA 0.951331 -155 TCTGCAAAATTCCCCAGAGTGGCTAGCTGG 8 83 0 TCCCCAGAGT 0.974152 -134 TACTGAGATTTCCCCAAAGTAAACATGGTA 8 154 1 TCCCCAAAGT 0.945592 -63 ********** Masking position 4 Map Score: 14.971 Number of sites scoring better than the average of aligned sites = 2652 Number in coding regions = 2240 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 3 TACCTAACTATGTCCAAGCTTATTGTCCCCA 2 25 0 TGTCCAACTT 0.939827 -65 AGGTAAAATTTGACCAACTTTGCAGTCTCCC 2 51 1 TGACCAATTT 0.93664 -39 TTTCAAACACTCTCTAAATTTAAGGCTGTTT 3 141 0 TCTCTAATTT 0.935898 -149 CCCCCCTGGCTCCCCAAGTTTGGGGGAAGTT 3 174 1 TCCCCAATTT 0.984763 -116 ATAGTTAACTTCTCAAAATTTTGTGAACATT 6 29 0 TCTCAAATTT 0.935898 -45 ATTCTCTACTTGCCCAATTTATTTAGATTAT 7 72 1 TGCCCAATTA 0.913235 -106 TTATTTGAACTCACTAAATTTCTATGACTGC 7 99 1 TCACTAATTT 0.886687 -79 TACTGAGATTTCCCCAAAGTAAACATGGTAA 8 154 1 TCCCCAAGTA 0.86272 -63 AAATTCTCGGTCTCAAACCTTACCATGTTTA 8 173 0 TCTCAAACTT 0.892097 -44 ******* *** Masking position 6 Map Score: 4.96493 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 398 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 GATTGCCATAGATTTTAGTCAATTAAAAACCTCG 1 133 1 GATTGCAATT 0.900068 -68 AATATGCAACGAACGTGGTCCTATTTTACGGACC 3 84 1 GACTGCCTAT 0.978016 -206 CTATTTTACGGACCATCGACATTTATATATTCTC 3 104 1 GACTGCATTT 0.986428 -186 ATTGCTCTATGATCATCGCCCTATTTTTTGTAAT 4 15 1 GACTGCCTAT 0.978016 -43 GGGATAATGGGAAAGTTGCCATTTGGAGGGAGAC 5 58 1 GAATGCATTT 0.960941 -32 AAAATTTTGTGAACATTGGTATTTAATACCCTAA 6 12 0 GACTGTATTT 0.966056 -62 AGCTCTTTATGAAAGTTGATAAATAAGCTAGGAT 8 39 0 GAATGTAAAT 0.686971 -178 AGCTGGTTTTGATTTTAGCTCTTTATGAAAGTTG 8 55 0 GATTGTCTTT 0.904089 -162 ** * * * ***** Masking position 2 Map Score: 3.80425 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 152 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ACCTTTAGTCACTATTAACTTCAACGTTTGC 1 42 1 ACATTAACTT 0.971543 -159 AATCTTAACAATCATTAACTTACTCACCCTG 1 167 1 ATATTAACTT 0.963661 -34 TTTACTGGGGACAATAAGCTTGGACATAGTT 2 20 1 ACATAAGCTT 0.776005 -70 TGGGTGACTTTTACTTAACTTCCCCCAAACT 3 190 0 TTCTTAACTT 0.753946 -100 GTATTCACTAATAGTTAACTTCTCAAAATTT 6 39 0 ATGTTAACTT 0.962953 -35 CAAGTAGAGAATAATTAGCTTACTAAGGGTT 7 53 0 ATATTAGCTT 0.928377 -125 TGTACTGACTGTTAACTTTAATGTTTTT 8 8 1 ACGTTAACTT 0.970984 -209 TCCTAGCTTATTTATCAACTTTCATAAAGAG 8 40 1 TTATCAACTT 0.825947 -177 CTACCCGACCGTCAACTCTGCTGAAATT 8 199 0 ACGTCAACTC 0.815755 -18 ** ******** Masking position 5 Map Score: 3.69962 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 158 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ATGCTAGCATTAACCTGGATTGCCATAGAT 1 116 1 TAACCTGGAT 0.981257 -85 GATTGATGATTTACCGGGAGACTGCAAAGT 2 67 0 TTACCGGGAG 0.97245 -23 GGATGGTTGGTAACTGGGATTAATGATTTA 3 27 1 TAACTGGGAT 0.961663 -263 TCGTTGCATATTACCTGGATCAGTATTAGA 3 66 0 TTACCTGGAT 0.986795 -224 TTACTAAGGGTTACTTGAATAACCCCCAAA 7 35 0 TTACTTGAAT 0.864517 -143 ********** Masking position 3 Map Score: 2.25576 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 160 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TGGGATTGATGATTTACCGGGA 2 78 0 TGGGATTAGA 0.991689 -12 GGTTGGTAACTGGGATTAATGATTTAGATATA 3 31 1 TGGGATTAGA 0.991689 -259 CCCATTATTGGGGGATTTAGGGGGCAAAATAA 3 217 1 GGGGATTAGG 0.960341 -73 TTGTGAACATTGGTATTTAATACCCTAAA 6 8 0 TGGTATTATA 0.959178 -66 TGTTCCTCCGTGGTATTCACTAATAGTTAACT 6 50 0 TGGTATTATA 0.95917 -24 ******* * ** Masking position 6 Map Score: 1.23468 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 66 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ********** No masking Map Score: 3.38462e-12 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: 3.38462e-12 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 10 TTTTCAGGAGCCTAGGGGATGGTTGGTAAC 3 11 1 CCTAGGGGAT 0.963276 -279 GGACCACGTTCGTTGCATATTACCTGGATC 3 75 0 CGTTGCATAT 0.882715 -215 GGAGGCACAGCCTAGGGGATAATGGGAAAG 5 43 1 CCTAGGGGAT 0.963276 -47 ATATCGTAGCCGTTGCCGATGCGTAGAGCA 7 127 0 CGTTGCCGAT 0.984168 -51 GCCTACGAGGCGGTGGATATCGTAGCCGTT 7 143 0 CGGTGGATAT 0.809954 -35 TCCACCGCCTCGTAGGCGATCGCCCCTTGA 7 156 1 CGTAGGCGAT 0.984168 -22 GGGAATTTTGCAGAGCCGATCATCTCTAGA 8 99 1 CAGAGCCGAT 0.844856 -118 CTAGACCTATCGTTGCGAATTTTCCTTTTG 8 124 1 CGTTGCGAAT 0.905808 -93 ********** Masking position 9 Map Score: 3.94771 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 676 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 ********** No masking Map Score: 3.38462e-12 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: 3.38462e-12 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 13 ********** No masking Map Score: 3.38462e-12 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