AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i234_sensory_cassete_synecho_reg_300.orf -o234_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 RCY15995 213 Synechocystis #2 RCY35437 151 Synechocystis #3 RCY20503 101 Synechocystis #4 RCY53594 127 Synechocystis #5 RCY01388 237 Synechocystis #6 RCY44549 116 Synechocystis #7 RCY52128 194 Synechocystis #8 RCY37634 300 Synechocystis Motif number 1 AGGTTGAATGCCCCTTTACCTAAGGCAGCGG 1 28 1 CCCCTTTACT 0.871749 -186 TCTCATTGCCCCCATTGTTCCATTCACATCC 1 60 0 CCCATTGTCC 0.92125 -154 TTTAAAAGCCCCCCTGGCCCCCCAAATTTGG 2 97 0 CCCCTGGCCC 0.986076 -55 CTGCCCCATCCCCATTGATACCAACGATACC 4 12 1 CCCATTGAAC 0.896553 -116 GTGGCAAAAAGCCATTTCCCTAAGCATATAG 4 58 0 GCCATTTCCT 0.959988 -70 CATGGCAACAGCCAATGAATTTGAATGGGTT 5 51 0 GCCAATGATT 0.452026 -187 TGAGGAAGAAGCCATGGCAACAGCCAATGAA 5 63 0 GCCATGGCAC 0.924231 -175 ATCCTAAGGCCCCATTGCGGCTTTCAACCTG 5 163 0 CCCATTGCGC 0.941259 -75 CAGTATTAAAGCCAATTAACCGTAAACCACA 6 71 1 GCCAATTACC 0.884859 -46 GATGGCTTTTGCCTATGACCTAAACAATCTC 7 81 0 GCCTATGACT 0.610837 -114 GCTCCCGATCGCCATTTCTCTTCCCTTTCCC 7 132 1 GCCATTTCCT 0.959988 -63 CCATTTCTCTTCCCTTTCCCCTAGCCGGTTT 7 143 1 TCCCTTTCCC 0.835872 -52 AGCCGGTTTTGCCATTGCGCCCCTTTCCCCC 7 165 1 GCCATTGCCC 0.994401 -30 CGCCCCTTTCCCCCTTTATCCCC 7 182 1 CCCCTTTACC 0.948702 -13 CCAAAAACTCGCCTTGGCCCCGCTGGAACCT 8 79 0 GCCTTGGCCC 0.941854 -222 CTTTAAATCTCCCAATGCCCCGACCCGGGTA 8 139 1 CCCAATGCCC 0.985054 -162 AAAACAATCACCCCATTCTATTACGGCTTTG 8 178 1 CCCCATTCAT 0.55011 -123 TGGCTTACTCCCCCTGGCCCCCATTTGTCTG 8 220 0 CCCCTGGCCC 0.986076 -81 GGGGGAGTAAGCCATTGCTTTTCCTGAATGA 8 237 1 GCCATTGCTT 0.875109 -64 ******** ** Masking position 3 Map Score: 26.9342 Number of sites scoring better than the average of aligned sites = 3504 Number in coding regions = 3154 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 2 AATGGAACAATGGGGGCAATGAGATTTCCA 1 67 1 TGGGGGCAAT 0.907156 -147 CAACAGTAGACCGGGGACAGACCGAGTTGA 1 138 1 CCGGGGACAG 0.967531 -76 TTGGTCGATTGAGGGGGCAGAATAAAACTT 2 24 0 GAGGGGGCAG 0.983895 -128 CCCCCAAATTTGGGGGGAAACTGAGTGAAA 2 80 0 TGGGGGGAAA 0.846272 -72 CCCCAAATTTGGGGGGCCAGGGGGGCTTTT 2 95 1 GGGGGGCCAG 0.990248 -57 TATCAATGGGGATGGGGCAGA 4 2 0 GATGGGGCAG 0.885446 -126 GCTTCTTCCTCAGGGGAAATTTTTTCTGGG 5 82 1 CAGGGGAAAT 0.790176 -156 GGAAATTTTTTCTGGGCCATGTTTTTGAAA 5 96 1 TCTGGGCCAT 0.616728 -142 TGGGTTAAGCCAAGGGGAAGGTCTCAAAAC 5 135 0 CAAGGGGAAG 0.611784 -103 TACCAAGGTTTAGGGTACAGCTTCACCGGG 6 14 0 TAGGGTACAG 0.72723 -103 CAAAACCGGCTAGGGGAAAGGGAAGAGAAA 7 146 0 TAGGGGAAAG 0.953879 -49 GGGGATAAAGGGGGAAAGGGGCGCAATG 7 177 0 AGGGGGAAAG 0.852118 -18 ATAGGTTCCAGCGGGGCCAAGGCGAGTTTT 8 77 1 GCGGGGCCAA 0.905801 -224 TACAGACAAATGGGGGCCAGGGGGAGTAAG 8 218 1 TGGGGGCCAG 0.989442 -83 ********** Masking position 9 Map Score: 15.9271 Number of sites scoring better than the average of aligned sites = 2766 Number in coding regions = 2424 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 3 TGTTTTATCAGAAAAATAGGTTGAATGCCCCT 1 11 1 GAAAATGGTT 0.834434 -203 GATGTGAATGGAACAATGGGGGCAATGAGATT 1 61 1 GAACATGGGG 0.963924 -153 TGGAAAAGGAGCAAAATAGAGTACTTTATGGA 1 93 0 GCAAATGAGT 0.890607 -121 TAAAGCGACCGCAATACTGGGGAACTTTCACT 2 55 1 GCAATCGGGG 0.931979 -97 CCCTGGCCCCCCAAATTTGGGGGGAAACTGAG 2 85 0 CCAAATGGGG 0.990871 -67 TGGCAATTAGGCAAAGTTGGTTAGAGCTTGTT 2 127 0 GCAAATGGTT 0.953153 -25 AAGCATATAGCCAAATTGGGGGTTTGGTATCG 4 36 0 CCAAATGGGG 0.990951 -92 GTGACTCATGGCAAACTAGGCGATCGCATAGC 5 204 0 GCAAATGGCG 0.988461 -34 GGGCGCAATGGCAAAACCGGCTAGGGGAAAGG 7 155 0 GCAAACGGCT 0.923541 -40 GTGTGCTACAGACAAATGGGGGCCAGGGGGAG 8 212 1 GACAATGGGG 0.929154 -89 TAAGGAGTGCCCACAATGGGGGATCATTCAGG 8 259 0 CCACATGGGG 0.97247 -42 ***** * **** Masking position 9 Map Score: 12.1104 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 752 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 4 AAAATAGAGTACTTTATGGAAATCTCATTG 1 83 0 ACTTTATGGA 0.984219 -131 CATCAAAAAAACTTGATGGAATAATCTTAC 1 187 0 ACTTGATGGA 0.97673 -27 TTGATTAATTAATTGATGGAATAAATTGGA 3 42 0 AATTGATGGA 0.949056 -60 ATCTCCACCCACTTTATGGATGGCCTATTC 7 56 0 ACTTTATGGA 0.984219 -139 AGTCCGCTTAAATTTTTGGTGTCAGGAGTT 8 12 0 AATTTTTGGT 0.839725 -289 GGCCAAGGCGAGTTTTTGGTCACTCCATAA 8 91 1 AGTTTTTGGT 0.890161 -210 AGGATCTGCCAGGTTATGGAGTGACCAAAA 8 104 0 AGGTTATGGA 0.929461 -197 ********** Masking position 1 Map Score: 5.09961 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 124 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 GAGGGGGCAGAATAAAACTTTCCAAACACGTTT 2 7 0 AATAACTAAC 0.883988 -145 CTGCCCCCTCAATCGACCAACTAAAGCGACCGCAATA 2 34 1 AATCACAAAC 0.992116 -118 TCAATTAATTAATCAAACTAATTAATCTAAGCGAGGC 3 56 1 AATCACAAAC 0.992114 -46 AATTACAGGTAATTAAACGATTAAACCCATTCAAATT 5 28 1 AATTACAAAC 0.977011 -210 GTAAGCAGTTAGTCTAGCTAGCAAAACCGCCAGTATT 6 41 1 AGTCACAAAC 0.974823 -76 AACCGCCAGTATTAAAGCCAATTAACCGTAAACCACA 6 65 1 ATTAACAAAC 0.898243 -52 TAAACCACACAAGCTATCGAGAAAATCGCCCATT 6 93 1 AAGCACAAAC 0.970949 -24 GACCCGGGTAAATTGAGCAAAACAATCACCCCATTCT 8 160 1 AATTACAAAC 0.97702 -141 **** * * * ** * Masking position 6 Map Score: 6.08094 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 80 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TGGAGTGATTGGAGTTAGTTTCAGTGGGAAA 3 15 0 GGGTTAGTTT 0.9524 -87 TAATTACCTGGGTGATATTTTC 5 2 0 GGGATATTTT 0.969904 -236 TTCTTCCTCAGGGGAAATTTTTTCTGGGCCA 5 84 1 GGGAAATTTT 0.921863 -154 GTTAAGCCAAGGGGAAGGTCTCAAAACGTTG 5 131 0 GGGAAGGTCT 0.895974 -107 ACCTTGGTAAGCAGTTAGTCTAGCTAGCAAA 6 35 1 GCGTTAGTCT 0.70571 -82 AATGGGCGATTTTCTCGATAGCTTG 6 102 0 GGGATTTTCT 0.963745 -15 TAAAGTGGGTGGAGATTGTTTAGGTCATAGG 7 70 1 GGGATTGTTT 0.984452 -125 GCGGGGCCAAGGCGAGTTTTTGGTCACTCCA 8 87 1 GGGAGTTTTT 0.908394 -214 AATAGAATGGGGTGATTGTTTTGCTCAATTT 8 169 0 GGGATTGTTT 0.984452 -132 ** ******** Masking position 9 Map Score: 7.05242 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 447 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 ACCTGTAATTACCTGGGTGATATTTTC 5 8 0 ACCTGGGTGA 0.986396 -230 GCGGCTTTCAACCTGGGTTAAGCCAAGGGG 5 148 0 ACCTGGGTTA 0.979969 -90 CTACCCGGTGAAGCTGTACCCT 6 3 1 ACCCGGTGAA 0.920122 -114 TGTACCCTAAACCTTGGTAAGCAGTTAGTC 6 25 1 ACCTTGGTAA 0.959494 -92 CAATGCCCCGACCCGGGTAAATTGAGCAAA 8 151 1 ACCCGGGTAA 0.992562 -150 ********** Masking position 1 Map Score: 2.92526 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 165 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 AAATAGAGTACTTTATGGAAATCTCATTGC 1 82 0 CTTTATGGAA 0.983114 -132 ATCAAAAAAACTTGATGGAATAATCTTACA 1 186 0 CTTGATGGAA 0.989016 -28 TGATTAATTAATTGATGGAATAAATTGGAG 3 41 0 ATTGATGGAA 0.957736 -61 TCTCCACCCACTTTATGGATGGCCTATTCG 7 55 0 CTTTATGGAT 0.958395 -140 ********** Masking position 5 Map Score: 2.12034 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 34 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TTGAATGCCCCTTTACCTAAGGCAGCGGAG 1 31 1 CTTTACCTAA 0.918478 -183 CTCTAACCAACTTTGCCTAATTGCCAGCA 2 133 1 CTTTGCCTAA 0.976359 -19 AGATTAATTAGTTTGATTAATTAATTGATG 3 54 0 GTTTGATTAA 0.814702 -48 TTTAGCCTCGCTTAGATTAATTAGTTTGAT 3 67 0 CTTAGATTAA 0.846509 -35 CACAACCCTCCTTTGATTAACTTGTATAAC 4 104 0 CTTTGATTAA 0.963722 -24 AGACCTTCCCCTTGGCTTAACCCAGGTTGA 5 141 1 CTTGGCTTAA 0.928383 -97 CCGAGTAACCCTTTAATTGACTTCACTATT 7 17 0 CTTTAATTGA 0.804062 -178 TAAGCCATTGCTTTTCCTGAATGATCCCCC 8 244 1 CTTTTCCTGA 0.78346 -57 ********** Masking position 10 Map Score: 2.07876 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 298 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 10 GTTTTATTCTGCCCCCTCAATCGACCAACTA 2 26 1 GCCCCCCAAT 0.987987 -126 ACCAACTAAAGCGACCGCAATACTGGGGAAC 2 49 1 GCGACCCAAT 0.975162 -103 AGCCCCCCTGGCCCCCCAAATTTGGGGGGAA 2 91 0 GCCCCCAAAT 0.964227 -61 CAACGATACCAAACCCCCAATTTGGCTATAT 4 33 1 AAACCCCAAT 0.778277 -95 CGGTGAAGCTGTACCCTAAACCTTGGTAAGC 6 16 1 GTACCCAAAC 0.796351 -101 AGGTTATGGAGTGACCAAAAACTCGCCTTGG 8 93 0 GTGACCAAAA 0.648051 -208 TGTCTGTAGCACACCCGCAAAGCCGTAATAG 8 195 0 ACACCCCAAA 0.892546 -106 GATCTAAGGAGTGCCCACAATGGGGGATCAT 8 264 0 GTGCCCCAAT 0.979091 -37 CTTAGATCCGCCAACCTCAATCCT 8 287 1 CCAACCCAAT 0.862074 -14 ****** **** Masking position 9 Map Score: 1.89068 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 875 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 ATTTTGCTCCTTTTCCATCGGAAGACACGG 1 108 1 TTTTCCATCG 0.617076 -106 CCCGGTCTACTGTTGCCGTGTCTTCCGATG 1 123 0 TGTTGCCGTG 0.940369 -91 TGTTTTTCCCACTGAAACTAACT 3 4 1 TTTTCCCACT 0.784604 -98 GGAAATGGCTTTTTGCCACGAAACTTCACT 4 70 1 TTTTGCCACG 0.979352 -58 ATTCATTGGCTGTTGCCATGGCTTCTTCCT 5 62 1 TGTTGCCATG 0.969906 -176 GTTTTTGAAAGGTTGCAACGTTTTGAGACC 5 116 1 GGTTGCAACG 0.936812 -122 CGATCGCCTAGTTTGCCATGAGTCACCGTG 5 210 1 GTTTGCCATG 0.969938 -28 CCCTAGCCGGTTTTGCCATTGCGCCCCTTT 7 161 1 TTTTGCCATT 0.837355 -34 ACCTATTCAGGTCTGCAATGCTAGGCAATA 8 50 1 GTCTGCAATG 0.741696 -251 CTAGGCAATAGGTTCCAGCGGGGCCAAGGC 8 70 1 GGTTCCAGCG 0.837563 -231 ********** Masking position 4 Map Score: 6.03295 Number of sites scoring better than the average of aligned sites = 1150 Number in coding regions = 1016 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 12 ********** No masking Map Score: -3.95472e-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 13 ********** No masking Map Score: -3.95472e-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: -3.95472e-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