AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_Glycolysis_1_synecho_reg_300.orf -o014_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 RCY09935 80 Synechocystis #2 RCY34729 121 Synechocystis #3 RCY47122 38 Synechocystis #4 RCY53017 115 Synechocystis #5 RCY11182 235 Synechocystis #6 RCY06446 94 Synechocystis #7 RCY04603 188 Synechocystis #8 RCY37403 269 Synechocystis Motif number 1 TCACCGATCTCAGCCAGGGGGCGATGATAGAAT 2 30 0 CACCGGGGGG 0.949075 -92 CTCGTATTCGGAACCAACGGGAATTATACCAGT 2 82 0 GACCACGGGA 0.886378 -40 TTCCCTTTGTAAACCTGGAGGCAATCAATCC 3 18 1 AACCGGAGGA 0.991331 -21 TTCCAAGGTAAATCATGGGGGTAGTGAGACAAT 5 33 0 AACAGGGGGA 0.98432 -203 ATACCATCAAAAACATCCGGGGCAACTCCTGCC 6 23 0 AACACCGGGC 0.921269 -72 ACTAGATTGAAAGCCAGGGCGGCATTAATTCGG 7 49 1 AACCGGGCGC 0.985157 -140 CGTCACCATTAACCAACGAGGAACTAACCCCCA 7 99 0 AACACGAGGA 0.952742 -90 TAATGGTGACGACCCCGGACGACGTAAACTGGG 7 121 1 GACCGGACGC 0.962306 -68 CAGGTGCGGTGAACCGGCAGGTGATTGTAGACG 8 42 0 GACCGCAGGG 0.917036 -228 GGTTTTGTCTATGCCTGGGGGTAGAGTTTTTGC 8 93 0 ATCCGGGGGA 0.943831 -177 GGCATAGACAAAACCCAGAGGCCACGGTAAACA 8 111 1 AACCAGAGGC 0.977425 -159 AGGCCACGGTAAACAGCGACGGAGAGAAAGGGA 8 129 1 AACACGACGA 0.863225 -141 TACTGAGCTAAAACAGAGAGGGCAAGACGAAC 8 248 1 AACAAGAGGC 0.945073 -22 ** ** ***** * Masking position 4 Map Score: 15.1693 Number of sites scoring better than the average of aligned sites = 1758 Number in coding regions = 1535 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 2 TCAATTCTTCCCTTTGTAAACCTGGAGGC 3 10 1 CCCTTTGTAA 0.990448 -29 CCCATGATTTACCTTGGAAAGGAGAAAAAT 5 47 1 ACCTTGGAAA 0.981882 -189 TTATCTAATCCCCTTTGAAAAGGGTTGGGT 5 83 0 CCCTTTGAAA 0.994857 -153 GGTAAATACAACCTTTGAAAACTGCCCTTA 5 114 1 ACCTTTGAAA 0.984933 -122 GCAAAAGATGCCCTTGATAATACCATCAAA 6 45 0 CCCTTGATAA 0.93006 -50 TTCCCACCCCCCCTTTGAAATTCGGGATCT 8 168 1 CCCTTTGAAA 0.994857 -102 ********** Masking position 5 Map Score: 11.0617 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 82 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ATCTCAGCCAGGGGGCGATGATAGAATTTGC 2 26 0 GGGGGGATGA 0.974776 -96 AATACGAGTATGGGGCAGTGAAAGG 2 107 1 TGGGGAGTGA 0.974516 -15 TAACCATGCATGGTGAAATGGGATTTACCTG 4 39 0 TGGTGAATGG 0.654978 -77 GGTAAATCATGGGGGTAGTGAGACAATTTTT 5 29 0 GGGGGAGTGA 0.992917 -207 AGAGTTGATTGGGTGAGGATAGTTTTTATTG 5 159 0 GGGTGGGATA 0.85059 -77 TCTGATGTCAGGGTGAAGAGTTGATTGGGTG 5 175 0 GGGTGAGAGT 0.962223 -61 TACTCGGTCTAGGGCAGGAGTTGCCCCGGAT 6 11 1 AGGGCGGAGT 0.828109 -84 GCTCAATTACAGGTGCGGTGAACCGGCAGGT 8 53 0 AGGTGGGTGA 0.973884 -217 GTCTATGCCTGGGGGTAGAGTTTTTGCTATG 8 89 0 GGGGGAGAGT 0.983522 -181 CGAATTTCAAAGGGGGGGTGGGAATCTTTTT 8 161 0 AGGGGGGTGG 0.983278 -109 ***** ***** Masking position 3 Map Score: 10.2571 Number of sites scoring better than the average of aligned sites = 1925 Number in coding regions = 1772 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 4 CGGTGATATCGGTGGCATTATCAACACTGG 2 57 1 GGTGGCATTA 0.987692 -65 TTGTAAACCTGGAGGCAATCAATCC 3 24 1 GGAGGCAATC 0.985931 -15 ATAACTGTAGTGAGGCAATAACC 6 82 1 TGAGGCAATA 0.96615 -13 TGAAAGCCAGGGCGGCATTAATTCGGCTTC 7 56 1 GGCGGCATTA 0.979242 -133 TCAAAGGGGGGGTGGGAATCTTTTTCCCTT 8 156 0 GGTGGGAATC 0.931259 -114 ATCTAAGTGTTCAGGCAATAGGATATGATT 8 194 1 TCAGGCAATA 0.845944 -76 GGATATGATTGGTGTCATTAATAATCCTTA 8 214 1 GGTGTCATTA 0.912528 -56 ********** Masking position 7 Map Score: 5.22774 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 692 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 ACCTTTTCCTCCTAAATGTCAAATAAACTTA 1 59 0 CCTAATGTCA 0.916237 -22 CCACCGATATCACCGATCTCAGCCAGGGGGC 2 41 0 CACGATCTCA 0.948912 -81 TGAGTTTAGCCCCAAAAGTCAGACCAAC 4 8 0 CCCAAAGTCA 0.981308 -108 CCATTGTAAACACTGATGTCAGACCGGCTTG 4 79 0 CACGATGTCA 0.97263 -37 CAACTCTTCACCCTGACATCAGATTGGTCAA 5 183 1 CCCGACATCA 0.930613 -53 AGGAACTAACCCCCAAACTCAACTGCTTGAA 7 83 0 CCCAAACTCA 0.964838 -106 ATAGACAAAACCCAGAGGCCACGGTAAACAG 8 114 1 CCCGAGGCCA 0.948954 -156 ACACTTAGATCCCGAATTTCAAAGGGGGGGT 8 173 0 CCCAATTTCA 0.949419 -97 *** ******* Masking position 6 Map Score: 4.89877 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 336 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 TTTGGGGCTTTCCATTGTCGGCGGTAACA 1 9 1 TTTCCATTGC 0.985369 -72 ATTGTCGGCGGTAACATTGACTGGTTTAATT 1 24 1 GTAACATTGC 0.807169 -57 TTTCCATTAACTTGTGCAAAT 2 1 1 TTTCCATTAC 0.971654 -121 GACATCAGTGTTTACAATGGCGATCGCCAGG 4 90 1 TTTACAATGC 0.874609 -26 AAGGTTGTATTTACCGTTATCTAATCCCCTT 5 98 0 TTACCGTTAC 0.958246 -138 TCCAACTATTTTTCCAATACC 5 225 1 TTTCCAATAC 0.915485 -11 TCCGGGGTCGTCACCATTAACCAACGAGGAA 7 109 0 TCACCATTAC 0.86668 -80 CAACCCCCAGTTTACGTCGTCCGGGGTCGTC 7 128 0 TTTACGTCGC 0.828641 -61 CCGTCGCTGTTTACCGTGGCCTCTGGGTTTT 8 120 0 TTACCGTGGC 0.922935 -150 ********* * Masking position 5 Map Score: 3.26518 Number of sites scoring better than the average of aligned sites = 1376 Number in coding regions = 1208 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 7 TTCCATTAACTTGTGCAAATTCTATCATCGC 2 12 1 TTTGCAAATT 0.822025 -110 CACCATGCATGGTTACAAATTCACCAAGCCG 4 55 1 GGTACAAATT 0.926906 -61 TGTTTAAAAAGTCTAAAAATTGTCTCACTAC 5 15 1 GTTAAAAATT 0.929573 -221 ACCTTGGAAAGGAGAAAAATTCTTAAACCCA 5 57 1 GGGAAAAATT 0.953533 -179 TAGTTTTTATTGCTAAAAATTGCGTTTTAAG 5 140 0 TGTAAAAATT 0.890788 -96 GGAAAAATAGTTGGAAAAATTAGTTGTTGAC 5 209 0 TTGAAAAATT 0.929573 -27 GGTATTGGAAAAATAGTTGGAAAAA 5 221 0 TTGAAAAATA 0.702855 -15 TAAACTGGGGGTTGGCAAATTTTGTTGTGAC 7 145 1 GTGGCAAATT 0.920762 -44 ** ******** Masking position 7 Map Score: 1.97256 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 546 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 8 AGGTAAATCATGGGGGTAGTGAGACAATTT 5 31 0 TGGGGGTAGT 0.804202 -205 TCCCCTTTGAAAAGGGTTGGGTTTAAGAAT 5 75 0 AAAGGGTTGG 0.844275 -161 CCCTTTTCAAAGGGGATTAGATAACGGTAA 5 89 1 AGGGGATTAG 0.955105 -147 CAGGGTGAAGAGTTGATTGGGTGAGGATAG 5 168 0 AGTTGATTGG 0.8212 -68 CAGTTGAGTTTGGGGGTTAGTTCCTCGTTG 7 89 1 TGGGGGTTAG 0.963038 -100 CGACGTAAACTGGGGGTTGGCAAATTTTGT 7 140 1 TGGGGGTTGG 0.992499 -49 GTGAACCGGCAGGTGATTGTAGACGTTAAC 8 37 0 AGGTGATTGT 0.874567 -233 GAATTTCAAAGGGGGGGTGGGAATCTTTTT 8 161 0 GGGGGGGTGG 0.947737 -109 AGGCAATAGGATATGATTGGTGTCATTAAT 8 206 1 ATATGATTGG 0.474897 -64 ********** Masking position 5 Map Score: 1.80366 Number of sites scoring better than the average of aligned sites = 2704 Number in coding regions = 2413 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 291 Fraction of orfs with sites within 600 bp upstream = 0.0467395 Motif number 9 ********** No masking Map Score: 2.63855e-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 ********** No masking Map Score: 2.63855e-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 11 ********** No masking Map Score: 2.63855e-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