AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_synecho_reg_300.orf -o071_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 RCY43669 195 Synechocystis #2 RCY43837 121 Synechocystis #3 RCY45080 251 Synechocystis #4 RCY05296 114 Synechocystis #5 RCY44021 99 Synechocystis #6 RCY31101 143 Synechocystis #7 RCY07805 300 Synechocystis #8 RCY01566 145 Synechocystis #9 RCY23220 69 Synechocystis #10 RCY06784 29 Synechocystis #11 RCY29543 100 Synechocystis #12 RCY03770 231 Synechocystis #13 RCY45791 300 Synechocystis #14 RCY50255 220 Synechocystis #15 RCY34011 64 Synechocystis #16 RCY02550 36 Synechocystis #17 RCY26220 201 Synechocystis #18 RCY36788 79 Synechocystis #19 RCY23507 77 Synechocystis #20 RCY44672 300 Synechocystis Motif number 1 TGGCCCTTGTCAGCGGTAAAACAGGGTTAAT 3 100 0 CAGGGTAAAA 0.915348 -152 TTACCGCTGACAAGGGCCAAAGTATAAACAG 3 112 1 CAAGGCCAAA 0.911184 -140 AAGACTTGACCAATGGTAAAAATTGAGGGCA 5 25 0 CAAGGTAAAA 0.971612 -75 GGCCATGGGACTATGGCAAAATATGTGAGGC 6 34 1 CTAGGCAAAA 0.98086 -110 GCAGGCTAGGCTAGGACAAAAAGGAAGGTGG 6 121 0 CTAGACAAAA 0.743574 -23 ATGATTTCAGCATAGGTAAAATTTTTTAGGC 7 159 1 CATGGTAAAA 0.874851 -142 AACAATGGAAAAAATACGAGAAA 7 288 0 CAAGGAAAAA 0.955227 -13 AGGAACCAGGGGCAAAAAAGCAGCAAC 8 7 1 CAGGGCAAAA 0.959821 -139 TGGCAAAATGCTAGGGAAGCAATTGTTGTAG 9 36 1 CTAGGAAGCA 0.701173 -34 AATTTAGGGTCAATGGTAACATAGAACTATT 12 102 0 CAAGGTAACA 0.953892 -130 AGTTCTGTCGCTAAGGAAAAATTCAACCATT 13 207 0 CTAGGAAAAA 0.935317 -94 AAATCTATGGCAAGGGCAAAAACAATCGTTT 14 198 0 CAAGGCAAAA 0.986948 -23 AGGGAGAATACTACGGTAACAACACCATCTC 18 56 1 CTAGGTAACA 0.933429 -24 GTAGCCCAGACAAAGGCAGAACAAGACAATC 20 48 1 CAAGGCAGAA 0.95305 -253 GCCGGAGGAGCTTGGGCAACAAAATTAACGA 20 199 1 CTTGGCAACA 0.863516 -102 *** ******* Masking position 11 Map Score: 20.3652 Number of sites scoring better than the average of aligned sites = 957 Number in coding regions = 825 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 2 AATCTCCTTGCCAAAACTCCTATGATTCTATCTC 1 11 1 CCAAACCCAG 0.594666 -185 AGATGCTCTACCCATTGTCCTGGGGAGCAGAATT 1 76 1 CCCTTGCCGG 0.984682 -120 AAGAACTGTAACATTTCACCAAATTCTGCTCCCC 1 97 0 ACATTCCCAT 0.684315 -99 AGGGAATCCTACCACTGACCTACGGTTACCATCT 1 140 0 ACCCTGCCAG 0.86768 -56 CCGGTCAAGCGGCGATCGCCAAATCTGTTTATAC 3 133 0 GGCATCCCAT 0.757444 -119 GGCGAGAGATACCATTCCCCCGGTCAAGCGGCGA 3 152 0 ACCTTCCCGT 0.912054 -100 GGCTAAACCGCCCGATCTCCCAAGTTTGGTGGCG 4 42 1 CCCATCCCAG 0.979662 -73 CCAGTTGATCCCAATTGACCAAAGCGCCACCAAA 4 66 0 CCATTGCCAG 0.930731 -49 GGTTAGGAAAAGACTTGACCAATGGTAAAAATTG 5 31 0 AGATTGCCAG 0.703309 -69 GTTTCTTTCCCCCCTTTTCCCGTGCGTAT 5 81 1 CCCTTTCCGG 0.908284 -19 TAGTCCCATGGCCAATCCCCAAAGGATTTGCTCA 6 13 0 GCCATCCCAG 0.984552 -131 CACATATTTTGCCATAGTCCCATGGCCAATCCCC 6 27 0 GCCTAGCCAG 0.893083 -117 CTATCCCCGTCCCTTTGACCGGGTAATGATTTCA 7 134 1 CCCTTGCCGT 0.928171 -167 GGTTAGGGCGGCCTTTCCCGTGGGAATGACAGAA 7 231 0 GCCTTCCGGG 0.847524 -70 AGGGCAAATTTCCTGGGGATTTTAGGT 11 84 0 GCAATTCCGG 0.733057 -17 AAAGGGGCAGACCTATGCCCCGATGTATTATATG 12 14 0 ACCATGCCGT 0.885044 -218 TTTGTTACAAAGCTATGGCCAAGGCAATAGTTGA 12 156 0 AGCATGCCAG 0.884582 -76 AGAAGGCGATCGCCGGTGGCCATTGGGG 14 5 1 GGCATCCCGG 0.949804 -216 AGTCGACAGAACAATTCTCCTATGTAACCTGGAT 15 19 0 ACATTCCCAG 0.915136 -46 GTGCATTAACGCCGTTGCCCAATGGAGTGATCTA 17 42 1 GCCTTGCCAG 0.985881 -160 CTGTTACCATGCCGATCGCCAGTGGTCTATAAAT 17 109 1 GCCATCCCGG 0.987282 -93 *** *** ** * * Masking position 9 Map Score: 22.8683 Number of sites scoring better than the average of aligned sites = 3828 Number in coding regions = 3495 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 3 TTTTAGGGAATCCTACCACTGACCTACGGTT 1 147 0 TCCTCCACTG 0.943396 -49 TTCCTGGCTCTACTTGCTTGCG 2 2 1 TCCTGCTCTA 0.799487 -120 CATGGGTCCTTCCTAGCTTTGGTGCTACCAT 3 32 0 TCCTGCTTTG 0.948556 -220 CCTTCCCTTAGCCTAACATTGACCATAATCA 3 67 0 GCCTACATTG 0.819798 -185 GGGAAAGAAACCCTACCATTTTAGGGAGGTT 5 61 0 CCCTCCATTT 0.924852 -39 CCAACAATAAGCCTTGCTCTGAGCCTCACAT 6 56 0 GCCTGCTCTG 0.946535 -88 TAAATACCTAGCCTCGCACTTTTCAAACACT 7 76 1 GCCTGCACTT 0.892644 -225 GGGTCTATCCCCGTCCCTTTGACCGGGTAAT 7 130 1 CCGTCCTTTG 0.813113 -171 ACGGGATCAGTCCTCCCACTATTGTTGCTGC 8 30 0 TCCTCCACTA 0.786287 -116 ACAATTGCTTCCCTAGCATTTTGCCACAATC 9 31 0 CCCTGCATTT 0.956126 -39 GGAACTCCAACCCTGGCATTGGTGTTGT 10 12 1 CCCTGCATTG 0.986964 -18 ATTGCCTTGGCCATAGCTTTGTAACAAAACT 12 162 1 CCATGCTTTG 0.738527 -70 GGTATGGCCATCCTCCCATTGTATGTATAGT 12 190 0 TCCTCCATTG 0.944487 -42 TCTTCAGCTTCCCTAACTCTAGTGAGGAATT 14 150 0 CCCTACTCTA 0.607197 -71 TTGGGTAATTCCGTAGCATTTCCAGAATATT 17 165 1 CCGTGCATTT 0.78347 -37 GCAAAAATATCCCTTGCATTGACCGTCAATT 20 279 1 CCCTGCATTG 0.986981 -22 **** ****** Masking position 4 Map Score: 17.7856 Number of sites scoring better than the average of aligned sites = 843 Number in coding regions = 735 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 GTTTAACTAACGGGCGAATTTGTTAAAGGCA 2 54 1 CGGGCGATTT 0.991408 -68 GGATTAACCACGGACGATTTTCCCGTCGATT 3 216 1 CGGACGATTT 0.941289 -36 CTTGGGAGATCGGGCGGTTTAGCCGACGGAA 4 35 0 CGGGCGGTTA 0.809733 -80 CGGCTTAAAAAGGGGGACTTTCGACGTTGAT 7 18 0 AGGGGGATTT 0.951872 -283 TTACGGGGTTAGGGCGGCCTTTCCCGTGGGA 7 240 0 AGGGCGGCTT 0.800746 -61 ATCCCATCAGCGGGGGATTTTCC 9 3 0 CGGGGGATTT 0.990034 -67 GGCAAATTTCCTGGGGATTTTAGGTTGAATA 11 78 0 CTGGGGATTT 0.926304 -23 AGGGCAAATTTCCTGGGGATT 11 90 0 AGGGCAATTT 0.820585 -11 TATTACGCAACTGGCGCCTTTCATTACTTTC 12 75 0 CTGGCGCTTT 0.733293 -157 TAACCCAGACCGGTGGAATTTTACCCCAATG 14 31 0 CGGTGGATTT 0.886718 -190 CCATGCCCGCCGGGCAAGCTTGCATTTTGCA 14 118 1 CGGGCAACTT 0.920618 -103 AGTGGATTCACGGGGAAATTTTTTCACTTTT 20 136 1 CGGGGAATTT 0.951872 -165 AGTGGCTGGCCGGAGGAGCTTGGGCAACAAA 20 191 1 CGGAGGACTT 0.874497 -110 ******* *** Masking position 10 Map Score: 15.9958 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 541 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TGTTTATACTTTGGCCCTTGTCAGCGGTAA 3 112 0 TTGGCCCTTG 0.966904 -140 GCCCTCAATTTTTACCATTGGTCAAGTCTT 5 26 1 TTTACCATTG 0.90729 -74 CCTTTGGGGATTGGCCATGGGACTATGGCA 6 22 1 TTGGCCATGG 0.957392 -122 CCTCACATATTTTGCCATAGTCCCATGGCC 6 34 0 TTTGCCATAG 0.946404 -110 TTCTCGTATTTTTTCCATTGTT 7 289 1 TTTTCCATTG 0.847324 -12 TTGCTGCTTTTTTGCCCCTGGTTCCT 8 7 0 TTTGCCCCTG 0.859083 -139 TTTGCGATTGTTGAGCCTAT 11 1 1 TTTGCGATTG 0.871057 -100 ATAGTTCTATGTTACCATTGACCCTAAATT 12 103 1 GTTACCATTG 0.789738 -129 TTTGGCAAATATTGCCATGGTGATATCAAC 12 131 1 ATTGCCATGG 0.793529 -101 AACTATTGCCTTGGCCATAGCTTTGTAACA 12 158 1 TTGGCCATAG 0.935594 -74 GCGATCGCCGGTGGCCATTGGGGTAAAATT 14 16 1 GTGGCCATTG 0.952509 -205 AACGATTGTTTTTGCCCTTGCCATAGATTT 14 199 1 TTTGCCCTTG 0.972612 -22 ********** Masking position 2 Map Score: 13.5298 Number of sites scoring better than the average of aligned sites = 1128 Number in coding regions = 1022 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 6 GCTTGACCGGGGGAATGGTATCTCTCGCCC 3 157 1 GGGAATGGTA 0.660402 -95 AAAGGAAGGTGGGATTGGGATCATCTCCCT 6 103 0 GGGATTGGGA 0.981151 -41 CTTTAGTGAGGAGATTTGGGGGGATAAATA 7 52 1 GAGATTTGGG 0.640837 -249 CCCCGCTGATGGGATTGTGGCAAAATGCTA 9 19 1 GGGATTGTGG 0.973748 -51 TGCTAGGGAAGCAATTGTTGTAGGGCGGGC 9 44 1 GCAATTGTTG 0.578566 -26 CTCCAACCCTGGCATTGGTGTTGT 10 16 1 GGCATTGGTG 0.918684 -14 TTTGCGATTGTTGAGCCTATTTC 11 4 1 GCGATTGTTG 0.874558 -97 ATCGCCGGTGGCCATTGGGGTAAAATTCCA 14 19 1 GCCATTGGGG 0.953298 -202 TCCGCTTCTAGGGATTGGGAGCCAGGGGA 18 10 0 GGGATTGGGA 0.981151 -70 ATTTGTAACAGCTATTGGGGAGCTAATACA 19 15 0 GCTATTGGGG 0.882126 -63 AGTCAGGAAGGGAATTGGGAAAGTTTTATG 19 54 0 GGAATTGGGA 0.911111 -24 TTACTCTGTTGGGATTTTGAGCGA 20 5 0 GGGATTTTGA 0.699946 -296 ********** Masking position 4 Map Score: 9.83053 Number of sites scoring better than the average of aligned sites = 1632 Number in coding regions = 1502 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 7 CCATTGTCCTGGGGAGCAGAATTTGGTGAA 1 87 1 GGGGAGCAGA 0.942655 -109 GGAAGGACCCATGGAGCTGATTATGGTCAA 3 50 1 ATGGAGCTGA 0.530582 -202 GTTAGGCTAAGGGAAGGAAATTAACCCTGT 3 81 1 GGGAAGGAAA 0.704949 -171 CTACCATTTTAGGGAGGTTAGGAAAAGACT 5 50 0 AGGGAGGTTA 0.819136 -50 GCACGGGAAAAGGGGGGAAAGAAACCCTAC 5 76 0 AGGGGGGAAA 0.742653 -24 TGTCCGTTCCAGGGAGATGATCCCAATCCC 6 93 1 AGGGAGATGA 0.935161 -51 TAGGACAAAAAGGAAGGTGGGATTGGGATC 6 111 0 AGGAAGGTGG 0.732895 -33 GAGGAGATTTGGGGGGATAAATACCTAGCC 7 59 1 GGGGGGATAA 0.901643 -242 TACATACAATGGGAGGATGGCCATACCTGC 12 194 1 GGGAGGATGG 0.707263 -38 TGGCGGGGGGGTAATGGAGCAGGT 12 218 0 GGGGGGGTAA 0.935975 -14 ACTAGAGTTAGGGAAGCTGAAGAGTAGTCC 14 158 1 GGGAAGCTGA 0.910664 -63 GGCACAATCTAGGGAGAATACTACGGTAAC 18 46 1 AGGGAGAATA 0.542804 -34 GGGGAGATGGTGTTGTTACC 18 70 0 GGGGAGATGG 0.933579 -10 AACAGCTATTGGGGAGCTAATACAGCGG 19 9 0 GGGGAGCTAA 0.946806 -69 ********** Masking position 6 Map Score: 9.40894 Number of sites scoring better than the average of aligned sites = 1975 Number in coding regions = 1714 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 8 AACTGTCAAAGGTTCAGTAGTGCCTTTAACAAAT 2 71 0 GGTTAGTGCC 0.900426 -51 CTTTAATAGTGGGCGAGAGATACCATTCCCCCGG 3 163 0 GGGCAGTACC 0.935212 -89 GTAGGGGCCAGCGTTGCCCTCAATTTTT 5 5 1 GGGCAGTGCC 0.962819 -95 GGGCAGGCTAGGCTAGGACAAAAA 6 130 0 GGGCGGGGCT 0.875747 -14 TTATTTTACGGGGTTAGGGCGGCCTTTCCCGTGG 7 242 0 GGGTAGGGCC 0.981005 -59 GTTTTAAACGGGATCAGTCCTCCCACTATTGTTG 8 34 0 GGATAGTCCC 0.758255 -112 AATTGTTGTAGGGCGGGCCTTGCT 9 56 1 GGGCGGTGCT 0.964115 -14 ACCAATGCCAGGGTTGGAGTTCCA 10 1 0 GGGTGGTCCA 0.86356 -29 AATACATCGGGGCATAGGTCTGCCCCTTTTTGCT 12 19 1 GGCAAGTGCC 0.783514 -213 GGGGGTAATGGAGCAGGTATGGCCATCCTCCCAT 12 202 0 GAGCGGGGCC 0.944293 -30 TCAACCATTTGAGTAAGCTATGCTACAAGATATT 13 182 0 GAGTAGTGCT 0.836182 -119 GAATCATGCCGAGTAGGCAGTCCCTTAAAGTAAC 13 254 0 GAGTGGTCCC 0.879256 -47 TCTGGGTTAGGGCCCAGTCGTGCAAAGTTAGTGA 14 53 1 GGCCAGTGCA 0.871729 -168 **** ** **** Masking position 13 Map Score: 8.29302 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 933 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 9 TTCATAAGGTATTTTAGGGAATCCTACCAC 1 159 0 ATTTTAGGGA 0.975023 -37 AGCCGACGGAACTTTAGGGAAATTATGGCA 4 16 0 ACTTTAGGGA 0.923144 -99 AAACCCTACCATTTTAGGGAGGTTAGGAAA 5 55 0 ATTTTAGGGA 0.975023 -45 ACGAGCAGATAATTTTGGGTCTATCCCCGT 7 114 1 AATTTTGGGT 0.5661 -187 TTGTGGCAAAATGCTAGGGAAGCAATTGTT 9 33 1 ATGCTAGGGA 0.852857 -37 AATGTTCTAAATTTTAGGAAAATTGTTGAA 11 31 0 ATTTTAGGAA 0.792829 -70 TTTCCTGGGGATTTTAGGTTGAATAGTGAA 11 73 0 ATTTTAGGTT 0.634078 -28 ATATTTGCCAAATTTAGGGTCAATGGTAAC 12 113 0 AATTTAGGGT 0.902646 -119 ATATTCTCCGCTTCTAGGGATTGGGAGCCA 18 16 0 CTTCTAGGGA 0.852863 -64 AATATGGCACAATCTAGGGAGAATACTACG 18 41 1 AATCTAGGGA 0.935807 -39 ********** Masking position 5 Map Score: 5.7539 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 115 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 GAAAGAGCGAACTGTCAAAGGTTCAGTAGT 2 84 0 ACTGTCAAAG 0.789646 -38 GGAGCTGATTATGGTCAATGTTAGGCTAAG 3 62 1 ATGGTCAATG 0.934256 -190 GCGGTAAAACAGGGTTAATTTCCTTCCCTT 3 89 0 AGGGTTAATT 0.628511 -163 ACCGCTGACAAGGGCCAAAGTATAAACAGA 3 114 1 AGGGCCAAAG 0.849273 -138 AAATCATTACCCGGTCAAAGGGACGGGGAT 7 136 0 CCGGTCAAAG 0.937905 -165 TAGGCTAAGTATGGACAATGACTGTTATTT 7 185 1 ATGGACAATG 0.666618 -116 CCGTAAAATAAGGGGCAATTAGTTTTCTCG 7 265 1 AGGGGCAATT 0.831008 -36 TGCCAAATTTAGGGTCAATGGTAACATAGA 12 108 0 AGGGTCAATG 0.981165 -124 ATGCTCCTTTACGGTCAAATGTGGACGGGG 16 12 0 ACGGTCAAAT 0.924412 -25 TAACTTATTTCCTGTCAATTTAGTCAGTGC 17 16 1 CCTGTCAATT 0.646833 -186 GTTTTATGGTCGGGTCAATTTGTAACAGCT 19 32 0 CGGGTCAATT 0.929488 -46 AAATTGACGGTCAATGCAAGGGATAT 20 285 0 ACGGTCAATG 0.981165 -16 ********** Masking position 7 Map Score: 8.09254 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 769 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 11 AATCTCCTTGCCAAAACTCCTATGATTC 1 6 1 CCTTGCCAAT 0.985085 -190 TATGAAATTCCATTTTCATCCCT 1 183 1 CATTTTCACT 0.526989 -13 AAAACCTTTGCCAACATTGAAAGAGCGA 2 104 0 CTTTGCCACT 0.976287 -18 ATACTTTGGCCCTTGTCAGCGGTAAAACAGGGT 3 104 0 CCTTGTCACT 0.943644 -148 TTCCTTGCCATAATTTCCCTAAAGT 4 3 1 CCTTGCCAAT 0.985085 -112 AAATTTAGAACATTTCCATCTGTTTATTCACTA 11 47 1 CATTTCCACT 0.849803 -54 CCATGGCAATATTTGCCAAATTTAGGGTCAATG 12 118 0 ATTTGCCAAT 0.758165 -114 CAACTATTGCCTTGGCCATAGCTTTGTAACAAA 12 157 1 CTTGGCCAAT 0.881961 -75 TTGTTTTTGCCCTTGCCATAGATTTTT 14 204 1 CCTTGCCAAT 0.985085 -17 ******** * * Masking position 8 Map Score: 4.03253 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 443 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 12 CTACGGTTACCATCTGGCTTTGTCAAGAACTG 1 123 0 CATCGGCTTG 0.581055 -73 CCCTGTTTTACCGCTGACAAGGGCCAAAGTAT 3 105 1 CCGCGACAGG 0.640729 -147 GTAGGGGCCAGCGTTGCCCTCAATTT 5 5 1 GGGCAGCTTG 0.822914 -95 AATCCTTTGGGGATTGGCCATGGGACTATGGC 6 19 1 GGATGGCATG 0.727705 -125 GGGCAGGCTAGGCTAGGACAAA 6 132 0 GGGCGGCAGG 0.980721 -12 AATTGTTGTAGGGCGGGCCTTGCT 9 56 1 GGGCGGCTTG 0.984794 -14 TCCAACCCTGGCATTGGTGTTGT 10 17 1 GCATGGTTTG 0.529016 -13 GGGGGTAATGGAGCAGGTATGGCCATCCTCCC 12 204 0 GAGCGGTTGG 0.878409 -28 GGGTAAAATTCCACCGGTCTGGGTTAGGGCCC 14 36 1 CCACGGTTGG 0.890276 -185 CAAGCTTGCCCGGCGGGCATGGTAGGATATAA 14 108 0 CGGCGGCTGG 0.990408 -113 AGACCACTGGCGATCGGCATGGTAACAGTAGG 17 105 0 CGATGGCTGG 0.923 -97 TCGTTCCTCGGCACTGGCTTGGGTAATTCCGT 17 147 1 GCACGGCTGG 0.98074 -55 **** *** *** Masking position 12 Map Score: 4.62216 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1520 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 13 CCAATTGTGCAAGTTCCGCAAGCAAGTAGAG 2 18 0 AAGTTCCGAA 0.872432 -104 AATTTCCCTAAAGTTCCGTCGGCTAAACCGC 4 22 1 AAGTTCCGCG 0.992414 -93 CTCCTCACTAAAGCTCCGGCTTAAAAAGGGG 7 34 0 AAGCTCCGCT 0.973439 -267 GAATAGTTCCAAGTTCCGGATTGATTTTGAC 13 13 1 AAGTTCCGAT 0.923428 -288 AGTGTTTATTAAGTTCTGTCGCTAAGGAAAA 13 218 0 AAGTTCTGCG 0.944351 -83 ACAATCGTTTAAGATCCGACGGACTACTCTT 14 177 0 AAGATCCGCG 0.975469 -44 TTTGTTGCCCAAGCTCCTCCGGCCAGCCACT 20 191 0 AAGCTCCTCG 0.933637 -110 ******** ** Masking position 2 Map Score: 3.59476 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 65 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 AGAATTTCCAATTTCCAGGTAAATAACAGT 7 205 0 ATTTCCAGGT 0.942109 -96 AACAAATTGAATTTACAGGTGTATTTGAGC 13 73 0 ATTTACAGGT 0.911891 -228 GTATAAAAGAATTTACAGAATCATGCCGAG 13 275 0 ATTTACAGAA 0.924702 -26 CACTGACTAAATTGACAGGAAATAAGTTAC 17 15 0 ATTGACAGGA 0.875944 -187 ATTCCGTAGCATTTCCAGAATATTTCCAGA 17 172 1 ATTTCCAGAA 0.950763 -30 TTTCCAGAATATTTCCAGAAAATTACCAT 17 183 1 ATTTCCAGAA 0.950763 -19 ********** Masking position 7 Map Score: 2.57012 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 54 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 TTGTTAAAGGCACTACTGAACCTTTGACAG 2 73 1 CACTACTGAA 0.827674 -49 ATCTCTCGCCCACTATTAAAGTTAAAATAG 3 176 1 CACTATTAAA 0.868932 -76 CCTAGCCTCGCACTTTTCAAACACTTTCTA 7 82 1 CACTTTTCAA 0.940078 -219 TCTGTTTATTCACTATTCAACCTAAAATCC 11 65 1 CACTATTCAA 0.977197 -36 CGGAACTTGGAACTATTCAA 13 1 0 AACTATTCAA 0.943666 -300 GACTTGAGCAAAATATTCAAGGTCTTTAAG 13 41 1 AAATATTCAA 0.651641 -260 TTTGAATATCAACTATTCCATCTTGATTAT 13 103 1 AACTATTCCA 0.816488 -198 GAAATTTTTTCACTTTTGAACAATCCATTC 20 150 1 CACTTTTGAA 0.868765 -151 ********** Masking position 2 Map Score: 1.36437 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234