AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_synecho_reg_300.orf -o047_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 RCY28537 38 Synechocystis #2 RCY25783 171 Synechocystis #3 RCY43089 119 Synechocystis #4 RCY42092 106 Synechocystis #5 RCY13382 161 Synechocystis #6 RCY40018 39 Synechocystis #7 RCY30329 44 Synechocystis #8 RCY35247 34 Synechocystis #9 RCY43999 50 Synechocystis #10 RCY08473 151 Synechocystis #11 RCY16635 290 Synechocystis #12 RCY06400 56 Synechocystis #13 RCY28245 63 Synechocystis #14 RCY37471 66 Synechocystis #15 RCY24448 85 Synechocystis #16 RCY05831 277 Synechocystis #17 RCY50309 68 Synechocystis #18 RCY54010 66 Synechocystis #19 RCY22900 17 Synechocystis #20 RCY19565 32 Synechocystis Motif number 1 GTTGAACAATGGCGATCGCCAAAGTAAGCT 2 110 1 GGCGATCGCC 0.499996 -62 AGGCGATCGCCTAGGAATTTG 3 2 1 GGCGATCGCC 0.499996 -118 TCCTCTAGAGGGCGATCGCCAAATGAAAAC 4 11 1 GGCGATCGCC 0.499996 -96 CCTCAGCGGTGGAGTTCTCCACTTTAAAGT 10 62 0 GGAGTTCTCC 0.626365 -90 ACACCAAGCCGTTGATCGCCATACAATGCC 11 41 1 GTTGATCGCC 0.814729 -250 TACTAGAATGATCGTTCGCCTCCCCACTAC 11 108 1 ATCGTTCGCC 0.87105 -183 ATCGAGTTTCGGAGACCGCTGTACCCATTA 16 152 0 GGAGACCGCT 0.760091 -126 TAGAATATGGGTAGTCCGCCGTTGCGTTTC 17 42 1 GTAGTCCGCC 0.958803 -27 ********** Masking position 4 Map Score: 13.5633 Number of sites scoring better than the average of aligned sites = 6249 Number in coding regions = 5674 Number in noncoding regions = 575 Number of orfs with sites within 600 bp upstream = 369 Fraction of orfs with sites within 600 bp upstream = 0.0592676 Motif number 2 GTTTTTTCCTGATTAAGAATTGAACAATTATTTTTTTGG 5 80 1 GATAAGAATT 0.954034 -82 CTTTAAAGGTGTATGGCAATGGCGACATT 7 1 0 GTTGAGGATT 0.983689 -44 ATAATTGTTGGTAAATTTACCGGACGATTAAGTATT 9 25 1 GTAAAGAATT 0.927244 -26 CGAGGGATTAGTGTAGTAAACGCGGAATTTAGACATAAA 10 15 0 GTTAAGGATT 0.986507 -137 CCACTTTAAAGTTTGGTGATCGAGGGATTAGTGTAGTAA 10 35 0 GTTGAGGATT 0.983689 -117 CAACGGCTTGGTGTAGTAAATGCGGGATTTAGCAATAAA 11 16 0 GTTAAGGATT 0.986507 -275 ATCGAAACAGGTGTAGTGAATGGGTCATTTCCAAAACGA 11 174 1 GTTAAGGATT 0.986507 -117 ATTACGTCATGTTTTAGAATGGCATGATTTACATCAACC 11 215 1 GTTTAGAATT 0.904927 -76 TTAACGATGAGAGAATTTAATGTAAAATTATGGAGTGTA 14 20 1 GAAAAGAATT 0.852307 -47 GATGCAAACTGATTGACTAAAGAAAAATTGAGCACCATA 18 26 1 GATGAGAATT 0.944823 -41 ** ** * * * *** Masking position 9 Map Score: 11.1625 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 38 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 CTTGAGGTCAATTTTTGCTACGCCCAAAGGCC 1 16 0 ATTTTTGCTG 0.895533 -23 AAACCATTTGTTTGTTGCCATGG 2 2 0 TTTGTTGCCG 0.920112 -170 AAAATAGGATTATCTTGCCCTGACCCTCAATG 2 147 1 TATCTTGCCG 0.979671 -25 AACAATTATTTTTTTGGCTTTGTCTGGTAAGC 5 102 1 TTTTTGGCTG 0.929874 -60 AAGCTTACGCTATCTGGTTAGGGCGTTTTAAA 5 130 1 TATCTGGTTG 0.72452 -32 CATAGTAGTCATTTTTGCTGGGTTTTTGTT 6 9 0 ATTTTTGCTG 0.895533 -31 ATATTCACCGTATCTTGCATGGTAGTGGGGAG 11 127 0 TATCTTGCAG 0.902291 -164 TGCTACTGCATATTTTGTTCCGCAAAATTCAG 15 43 0 TATTTTGTTG 0.863482 -43 AAGACTAACATATTTTGCCTAGACTTTTGTCA 16 25 0 TATTTTGCCG 0.978013 -253 ACCCATATTCTATTTTGCCCCGCCATTGTTGC 17 22 0 TATTTTGCCG 0.978013 -47 AACTTTTCTTGCTATGGTGCTCAATT 18 51 0 TTTCTTGCTG 0.97398 -16 ********* * Masking position 5 Map Score: 10.3972 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 304 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CCATGGGCCTTTGGGCGTAGCAA 1 3 1 ATGGGCTTTG 0.957954 -36 AAATGGTTTTATGAGCTATTGAAGGATTTTA 2 25 1 ATGAGCATTG 0.759935 -147 TTTCATTGTAATGGGCAAATTCCTAGGCGAT 3 16 0 ATGGGCAATT 0.694943 -104 TTACTAAATCCAGAGTTTTTTCCTGATTAAG 5 66 1 CAGAGTTTTT 0.489633 -96 GCTATCTGGTTAGGGCGTTTTAAAAACTTTA 5 138 1 TAGGGCTTTT 0.788779 -24 GTCATTTTTGCTGGGTTTTTGTT 6 3 0 CTGGGTTTTG 0.939106 -37 ACGACTAATAATGGGCATTGTATGGCGATCA 11 53 0 ATGGGCTTGT 0.916634 -238 GGTGTAGTGAATGGGTCATTTCCAAAACGAG 11 183 1 ATGGGTATTT 0.924746 -108 CTCCACATATCAGGGTTATTTATTTCAGAGG 12 16 0 CAGGGTATTT 0.873497 -41 TTAAAGGGCTTTTTTTCTCTTTAT 13 4 1 AAGGGCTTTT 0.910721 -60 CTCACCCGCTTTGGGTAATGGGTACAGCGGT 16 137 1 TTGGGTATGG 0.744459 -141 TTTCCCTGGGTAATGGAAAGGGTAGG 20 6 1 CTGGGTATGG 0.896068 -27 ****** **** Masking position 5 Map Score: 4.98368 Number of sites scoring better than the average of aligned sites = 2011 Number in coding regions = 1814 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 5 GTTTATGTCTAAATTCCGCGTTTACTACAC 10 14 1 AAATTCCGCG 0.928906 -138 TTTACTACACTAATCCCTCGATCACCAAAC 10 34 1 TAATCCCTCG 0.980821 -118 TTTTATTGCTAAATCCCGCATTTACTACAC 11 15 1 AAATCCCGCA 0.916353 -276 TTAGCAGTGGTACTGCCGCG 15 76 1 TACTGCCGCG 0.967107 -10 ACCACTAAACTACACCCGCGTGTTGTCCTA 16 65 0 TACACCCGCG 0.958301 -213 CCGTCATCCATGCTCCCTCGATAATTCCTC 16 239 1 TGCTCCCTCG 0.930137 -39 GCTCCCTCGATAATTCCTCGGTTCTGCACG 16 250 1 TAATTCCTCG 0.933115 -28 CTAATAATCTCGCAACAATGGCGG 17 5 1 TAATCTCGCA 0.769674 -64 ********** Masking position 7 Map Score: 4.04731 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 139 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GTGGTTAGATTTTCTGGCTGACCCCATCCAA 3 69 1 TTTCTGCTGA 0.873213 -51 AAGCTGCACCATTATGGCTACCGTTTTAGAC 4 68 1 ATTATGCTAC 0.816598 -39 TTTTTTGTGGTCTATGGCTAATTCCTAAAAG 5 13 1 TCTATGCTAA 0.933731 -149 TTAGTTTATGTCTAAATTCCGCGTT 10 5 1 TTTATGCTAA 0.966471 -147 TCGTTTTTATTGCTAAATCCCGCATT 11 6 1 TTTATTCTAA 0.738622 -285 TGGAGTTCAAATTAAGACTGATTTT 12 42 1 ATTAAGCTGA 0.783268 -15 TCCTAGCGTTTTTAAGACTAACATATTTTGC 16 39 0 TTTAAGCTAA 0.95901 -239 CGCCGTTGCGTTTCAGTCTAA 17 58 1 TTTCAGCTAA 0.919591 -11 TCTAAGCCTACCCTTTCCATT 20 22 0 TCTAAGCTAC 0.848259 -11 ****** **** Masking position 3 Map Score: 3.34351 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 98 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 GGCGTAGCAAAAATTGACCTCAAGT 1 24 1 AAATACCTCA 0.785565 -15 TCAACTGTTCAACCTGAGCAACTTGTGCCACG 2 83 0 AACTAGCAAC 0.934348 -89 GGCGATCGCCAAAGTAAGCTACCCATTAAAAT 2 120 1 AAATAGCTAC 0.944234 -52 TCAGCCAGAAAATCTAACCACATCAAAAATGG 3 58 0 AATTACCACA 0.675063 -62 AACAAAAACCCAGCAAAAATGACTACT 6 6 1 AAACAGCAAA 0.864351 -34 GCAGGTAAAGAAAATAAGCAACTCCT 8 19 1 AAATAGCAAC 0.981679 -16 ATCGTCCGGTAAATTTACCAACAATTATAAAA 9 21 0 AAATACCAAC 0.965051 -30 TTGTTCCGCAAAATTCAGCAAATATAGTAGTT 15 29 0 AAATAGCAAA 0.96463 -57 GACTAAAGAAAAATTGAGCACCATAGCAAGAA 18 40 1 AAATAGCACC 0.977874 -27 *** * ****** Masking position 7 Map Score: 4.28168 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 280 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 GGGTAGCTTACTTTGGCGATCGCCATTGTT 2 114 0 CTTTGGCGAT 0.913287 -58 ATTGGTTTTCATTTGGCGATCGCCCTCTAG 4 15 0 ATTTGGCGAT 0.926091 -92 AGTGAATTAATTTTAACAATTGGTTTTCAT 4 33 0 TTTTAACAAT 0.674151 -74 AACTGACAACTTTTAGGAATTAGCCATAGA 5 23 0 TTTTAGGAAT 0.933795 -139 TAAATGCGGGATTTAGCAATAAAAACGA 11 9 0 ATTTAGCAAT 0.889526 -282 ATTAGTCGTTTTTTAGGAATCACAATCTGC 11 75 1 TTTTAGGAAT 0.933795 -216 GTAATGCTCGTTTTGGAAATGACCCATTCA 11 190 0 TTTTGGAAAT 0.849106 -101 GGGATAATTTTTGGGGATGCAAACTGAT 18 9 1 TTTTGGGGAT 0.956389 -58 ********** Masking position 9 Map Score: 2.76171 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 771 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 9 CAACTGTATTTAAAATCCTTCAATAGCTCA 2 36 0 TAAAATCCTT 0.802787 -136 CGCAGAAAACTGACAACTTTTAGGAATTAG 5 30 0 TGACAACTTT 0.918707 -132 TAGGGCGTTTTAAAAACTTTATTT 5 148 1 TAAAAACTTT 0.932918 -14 CCAACAATTATAAAAACTTTTTTGA 9 6 0 TAAAAACTTT 0.932918 -45 AGTGACCTTTTAGCATCTTTTCTTCATAGC 10 95 0 TAGCATCTTT 0.898183 -57 AATAGCCAATTGGCAACTTTGTCGCCAACA 11 260 1 TGGCAACTTT 0.931728 -31 ACACTTCTGATAGAAACCTTACAACAA 13 47 1 TAGAAACCTT 0.918706 -17 ********** Masking position 5 Map Score: 2.40979 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 114 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 GCCAAAGTAAGCTACCCATTAAAATAGGAT 2 127 1 GCTACCCATT 0.941668 -45 CACCATTATGGCTACCGTTTTAGACCTTCA 4 74 1 GCTACCGTTT 0.973307 -33 ACATATTTTGCCTAGACTTTTGTCAGGAGA 16 20 0 CCTAGACTTT 0.910536 -258 CGCGTGTTGTCCTAGCGTTTTTAAGACTAA 16 49 0 CCTAGCGTTT 0.973307 -229 TCTAAGCCTACCCTTTCCATTACCCA 20 17 0 CCTACCCTTT 0.987239 -16 ********** Masking position 4 Map Score: 0.695493 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 69 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ATCGCCATTGTTCAACTGTTCAACCTGAGCAAC 2 93 0 TTCAACTTAA 0.777182 -79 ATCCAGAGTTTTTTCCTGATTAAGAATTGAACA 5 73 1 TTTTCCTTAA 0.953383 -89 GCTTATTTTCTTTACCTGCTCAACATT 8 5 0 TTTACCTTAA 0.87749 -30 AGCGGTGGAGTTCTCCACTTTAAAGTTTGGTGA 10 55 0 TTCTCCATAA 0.908185 -97 AGCAGTTTATTTTCCCCGTTAAGTAAATTAAG 10 130 0 TTTTCCCTAA 0.961253 -22 TTCTACCTCTGAAATAAATAACC 12 1 1 TTCTACCTAA 0.938983 -56 CGGGAAAGTTCTCCTGACAAAAGTCTAGGCA 16 9 1 TTCTCCTCAA 0.89609 -269 AAGGCTAAGGTTTTACCACTAAACTACACCCGC 16 76 0 TTTTACCTAA 0.906585 -202 ******* * ** Masking position 12 Map Score: 0.881233 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 131 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 12 GGTCACTTAGTTCTTAATTTACTTAACGGG 10 118 1 TTCTTAATTT 0.746411 -34 AATTCTCTCATCGTTAATTGAAATGA 14 7 0 TCGTTAATTG 0.882459 -60 TTTTGTACACTCCATAATTTTACATTAAAT 14 34 0 TCCATAATTT 0.942038 -33 TCTCCGAAACTCGATAATTTTGATTGATAA 16 167 1 TCGATAATTT 0.968843 -111 ATAATTTTGATTGATAATTTCTGATCGTCC 16 180 1 TTGATAATTT 0.913097 -98 CCATGCTCCCTCGATAATTCCTCGGTTCTG 16 246 1 TCGATAATTC 0.933368 -32 ********** Masking position 5 Map Score: 0.555174 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 125 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 13 ********** No masking Map Score: 9.82981e-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 14 ********** No masking Map Score: 9.82981e-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 15 ********** No masking Map Score: 9.82981e-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