AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_synecho_reg_300.orf -o057_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 RCY32311 191 Synechocystis #2 RCY35515 195 Synechocystis #3 RCY47549 98 Synechocystis #4 RCY30106 164 Synechocystis #5 RCY08201 100 Synechocystis #6 RCY53401 171 Synechocystis #7 RCY46834 124 Synechocystis #8 RCY13164 111 Synechocystis #9 RCY00205 96 Synechocystis #10 RCY15170 266 Synechocystis #11 RCY16212 29 Synechocystis #12 RCY27781 300 Synechocystis #13 RCY37253 206 Synechocystis #14 RCY40141 87 Synechocystis #15 RCY11977 246 Synechocystis #16 RCY00456 110 Synechocystis #17 RCY08095 101 Synechocystis #18 RCY42619 279 Synechocystis #19 RCY23173 277 Synechocystis #20 RCY12795 137 Synechocystis #21 RCY26284 300 Synechocystis #22 RCY23327 241 Synechocystis #23 RCY31626 279 Synechocystis Motif number 1 GCGTTGCCGAACCCTAGGGGGCAAATTGGC 1 117 1 ACCCTAGGGG 0.817886 -75 TGGTGGGGTCAGCCATGGGAAAAATGCAAA 3 14 0 AGCCATGGGA 0.947464 -85 AGGCAGAGTCAGCCCAGGGGACAAAAACTT 5 65 0 AGCCCAGGGG 0.994633 -36 GATAATCCTCAGCCCTGGGGGGAAACTGTC 7 104 1 AGCCCTGGGG 0.994379 -21 AAGCCAGAGTACCCTAGGGGAGAGCGAGTA 10 110 0 ACCCTAGGGG 0.817886 -157 GCCATTGGCTAGCCATGGGAAGCTAAAATA 10 171 0 AGCCATGGGA 0.947464 -96 ATTTATTTTTAGCCCATGGGAACAGCCTAA 12 99 0 AGCCCATGGG 0.909222 -202 CCCCGGCGATCGCCAAGGGGCATTTTTATT 15 181 1 CGCCAAGGGG 0.838002 -66 GCTATCCCAACCCCAAGGAGGTGAAACCCG 15 226 1 CCCCAAGGAG 0.702539 -21 CTTCGCCAGTACCCAAGGAGTTACCAAATC 16 66 1 ACCCAAGGAG 0.934587 -45 AACTCAGTGGAGCCAAGGGGTCGGTAAATT 18 13 1 AGCCAAGGGG 0.98848 -267 GGCTGAGGTTAGCCCTGGAGTCTGCACTCT 19 90 0 AGCCCTGGAG 0.982165 -188 GTGGTCAACGCGCCCTGGAGGACTTGAACC 19 179 0 CGCCCTGGAG 0.975412 -99 GAATTCGGTCAGCCCTGGGGAAAAGCCTGG 21 75 1 AGCCCTGGGG 0.994379 -226 TACCATTATTCCCCATGGAAATTAGTTCTG 22 29 0 CCCCATGGAA 0.615971 -213 TGTACAATGCCGCCCTGTGGGAGATGATCA 23 55 1 CGCCCTGTGG 0.882072 -225 ********** Masking position 4 Map Score: 34.4278 Number of sites scoring better than the average of aligned sites = 1190 Number in coding regions = 1070 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 CAGTCCGAAGCCAATTTGCCCCCTAGGGTTCGG 1 123 0 CAATTCCCCC 0.977734 -69 TGAATCTGGAATGATTTGCCCCCCAACGTCTTT 4 19 1 AGATTCCCCC 0.877059 -146 AGATTGCAACGAAATTTATCGCCCAATACTTTA 4 116 1 GAATTTCGCC 0.885701 -49 TTATTTAGTGCCAAGTTTTGGCCGGGAAACTAA 6 48 1 CAATTTGGCC 0.951227 -124 CTGGGGGAGCCGGACTTTCTGCAATCCAATGCC 6 112 0 CGATTCTGCA 0.374141 -60 TGTTGTTATTGGGAATTTTCCCCTTTTCT 6 153 1 GGATTTCCCC 0.875531 -19 GGACAGTTTCCCCCCAGGGCTGAGG 7 110 0 AAGTTCCCCC 0.617685 -15 GTAGTTTAGCCTGAGTTGCCCCATACTGCCCCA 8 61 0 CGATTCCCCA 0.76254 -51 GGAACAAATTTTAGCCCTTTCCGTTCC 9 5 1 CAATTAGCCC 0.65748 -92 CCGATTCTCTCGGATTTTCGGCCTGCAATTTAC 10 80 1 CGATTCGGCC 0.966254 -187 CCAAATTTGTCTAATTGATTGCCTTCATTCTAT 10 236 0 CAATGTTGCC 0.587082 -31 CAGAGATCCACCGATTTTGGGCCAATCCCAACG 12 51 0 CGATTGGGCC 0.720927 -250 GAAATGACTCGGAAATTGTCGTCGC 15 3 0 GAATTTCGTC 0.384265 -244 GGCGAAGTAGGGAACTTCTCCCCGAAATAAATG 16 40 0 GAATTTCCCC 0.885701 -71 CAAGGGGTCGGTAAATTACTGCCCAATAAGCTT 18 26 1 GAATTCTGCC 0.699918 -254 CCATCATACCCTAATTTGCTGCCAATTCCCATC 19 53 0 CAATTCTGCC 0.891005 -225 CTGTTGCGCCCGGACTGTTGGCCGCTAGAATGC 20 40 0 CGATGTGGCC 0.832777 -98 CTCATCATAACTGATTTACCCTCTTTTGCAAAA 20 97 0 CGATTCCCTC 0.76254 -41 AATTGACTAGTTTTTGCCCCCAAGAACTG 21 7 1 CAGTTTGCCC 0.800423 -294 GGTTAAGGTGCCAAATTCCGGCAATGGTTTGAA 21 39 1 CAATTCGGCA 0.717484 -262 GTTGGGTTGCCAGGCTTTTCCCCAGGGCTGACC 21 81 0 CGGTTTCCCC 0.835288 -220 AAGCGAGGAACAAAATTATGGCCGCTGGTGTAG 21 229 0 CAATTTGGCC 0.951227 -72 TTGAAATTAACAAACTGTCGCCCTTCCACTGAC 22 109 1 CAATGCGCCC 0.89866 -133 CTGCCCCCCGCCAAATTTTCCTCGGTTAGTCAA 22 167 0 CAATTTCCTC 0.686252 -75 TTCCCTGCCCCTAATTTGTCCCCTCC 22 226 1 CAATTTCCCC 0.964487 -16 GGAGATGATCACAAATTCCCGCCGTTGGCCGCA 23 74 1 AAATTCCGCC 0.887091 -206 TTTCGTCCAGAGGATTTGCGGCCAACGGCGGGA 23 90 0 AGATTCGGCC 0.836682 -190 ATTTAAATTAACAATTGCTCCCC 23 267 1 AAATGTCCCC 0.577431 -13 * ** ** ***** Masking position 6 Map Score: 28.3196 Number of sites scoring better than the average of aligned sites = 2964 Number in coding regions = 2649 Number in noncoding regions = 315 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 3 TTTAAGCTAGGGAACGCCGATGCGTTGCCG 1 96 1 GGAACGCCGA 0.617503 -96 GAACGCCGATGCGTTGCCGAACCCTAGGGG 1 107 1 GCGTTGCCGA 0.85857 -85 GGATGTCAGTCCGAAGCCAATTTGCCCCCT 1 132 0 CCGAAGCCAA 0.633185 -60 GCAAAGCCAGGCAGAGTCAGCCCAGGGGAC 5 73 0 GCAGAGTCAG 0.741623 -28 AGATTTAAGCAAAGCCAGGCAGAGTCAG 5 83 0 GCAAAGCCAG 0.95586 -18 TTTCTGCAATCCAATGCCGATGATAACGCG 6 100 0 CCAATGCCGA 0.809966 -72 AATTAAGCTGGGGGAGCCGGACTTTCTGCA 6 122 0 GGGGAGCCGG 0.885341 -50 AACGAAGAAGGCATAGTCGGCCACAGAAAC 7 48 0 GCATAGTCGG 0.90166 -77 CGGTAAAATGGCAAAGTCAGCATTTTCGCT 10 53 0 GCAAAGTCAG 0.801246 -214 TTACCCTTTCCCAAAGCCAGAGTACCCTAG 10 123 0 CCAAAGCCAG 0.91664 -144 GCGGTCTTTGGCATAGCCAGTTAAATAAAT 15 44 0 GCATAGCCAG 0.960964 -203 TGCCCCTTGGCGATCGCCGGGGCTGAAGCA 15 173 0 CGATCGCCGG 0.790653 -74 ACTTGAGCCTGGATTGCCGGCAATCCCCCC 18 234 1 GGATTGCCGG 0.938335 -46 ATCACCGAACGCAAAGTCGAATAATTGCGT 19 232 0 GCAAAGTCGA 0.665561 -46 CTGCTTCAAACCATTGCCGGAATTTGGCAC 21 46 0 CCATTGCCGG 0.951539 -255 GGTCTGGGTTGGGTTGCCAGGCTTTTCCCC 21 91 0 GGGTTGCCAG 0.828731 -210 AAAAGCGGTGCCGGCAAGCAGAAC 22 5 1 GCGGTGCCGG 0.93852 -237 CGCCTAGCAACCATTGCCAGACCAGAGGCC 22 71 0 CCATTGCCAG 0.907538 -171 ********** Masking position 6 Map Score: 16.5294 Number of sites scoring better than the average of aligned sites = 1939 Number in coding regions = 1810 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 GGAATGATTTGCCCCCCAACGTCTTTGGTTG 4 26 1 GCCCCCCACG 0.949313 -139 ATGGAAAGGAGCCCTCCGGCAAACGTGATAT 4 79 1 GCCCTCCGCA 0.981608 -86 CACTAAATAAAAGCTCCGACAATATTAAAGG 6 27 0 AAGCTCCGCA 0.775827 -145 GGCCACAGAAACCCACCGCCATCTTCGTTAA 7 29 0 ACCCACCGCA 0.940264 -96 TCATTCTATGGCCCCACACCATTGCGTTAAA 10 214 0 GCCCCACACA 0.88683 -53 GTTGGGACAAACCCCCCGGCAGTGATTCCAG 12 178 0 ACCCCCCGCA 0.992955 -123 CAAGGAAGCAAATCCCCAACAAACTCAAATC 15 126 0 AATCCCCACA 0.916626 -121 AGAAATTCTAAATCCCCAACATTCACTCTGC 18 189 1 AATCCCCACA 0.916626 -91 GCGAAACTGTGATCTCCAACACCAATGGCGA 19 14 1 GATCTCCACA 0.80631 -264 GGAGGACTTGAACCCCCGACATCAGGTTTTG 19 162 0 AACCCCCGCA 0.986686 -116 TGGCATTTCTGCCCCCCGCCAAATTTTCCTC 22 177 0 GCCCCCCGCA 0.994741 -65 ******** ** Masking position 7 Map Score: 11.4526 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 696 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GTTATCGACAACCAAAGACGTTGGGGGGCAA 4 34 0 ACCAAGACGT 0.611764 -131 CTTTCTGCAATCCAATGCCGATGATAACGCG 6 100 0 TCCAAGCCGA 0.849329 -72 GATCAAAACAGCCAAAAACGAGAAAACGAAG 7 71 0 GCCAAAACGA 0.758538 -54 CCCATGGCTAGCCAATGGCGATCGTAAAGAT 10 182 1 GCCAAGGCGA 0.987602 -85 ACCTTATTCGGCCAAGGCTCAGAATGTATGA 12 142 0 GCCAAGCTCA 0.88217 -159 TACCAAGGACGACTCCTGTGAT 12 289 0 ACCAAGACGA 0.941211 -12 AAAATAACCAATGCTGACTGACCAGTC 13 190 0 ACCAAGCTGA 0.839613 -17 AACTGGCTATGCCAAAGACCGCAGGAGCAAT 15 52 1 GCCAAGACCG 0.860079 -195 CCCGGCGATCGCCAAGGGGCATTTTTATTGT 15 182 1 GCCAAGGGCA 0.858836 -65 TCCCTACTTCGCCAGTACCCAAGGAGTTACC 16 60 1 GCCAGACCCA 0.65377 -51 GATCTCCAACACCAATGGCGATCGCCATCGA 19 24 1 ACCAAGGCGA 0.977567 -254 CTAATTTGCTGCCAATTCCCATCGATGGCGA 19 45 0 GCCAATCCCA 0.732507 -233 CGTAAAGCAGACCAAGGGTGACCCCGGTAAA 21 172 1 ACCAAGGTGA 0.87882 -129 AAATGCCTACACCAGCGGCCATAATTTTGTT 21 223 1 ACCAGGGCCA 0.930225 -78 CCATTGCCAGACCAGAGGCCAAACCAATGAA 22 60 0 ACCAGGGCCA 0.930225 -182 AGGATTTGCGGCCAACGGCGGGAATTTGTGA 23 82 0 GCCAAGGCGG 0.955327 -198 ***** ***** Masking position 4 Map Score: 15.0821 Number of sites scoring better than the average of aligned sites = 1788 Number in coding regions = 1669 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 6 TTAACCCTCCCTGTCCCAACCTATCGAATA 2 163 1 CTGTCCCAAC 0.934682 -33 TTTCCCATGGCTGACCCCACCAATCGAGAC 3 22 1 CTGACCCCAC 0.941881 -77 GTCGGCCACAGAAACCCACCGCCATCTTCG 7 33 0 GAAACCCACC 0.831747 -92 TTTTCGCTTGTAAACCCAACATTACCTACA 10 31 0 TAAACCCAAC 0.844446 -236 GATTTTGGGCCAATCCCAACGATAAAGCAC 12 42 0 CAATCCCAAC 0.962401 -259 ACCGTTGGGACAAACCCCCCGGCAGTGATT 12 182 0 CAAACCCCCC 0.969142 -119 GTGATGATGTCTAACCGAACCCGGACGGAA 12 264 0 CTAACCGAAC 0.789355 -37 TTAATGCTTGCTATCCCAACCCCAAGGAGG 15 217 1 CTATCCCAAC 0.962401 -30 TAACGGCGATCAAACCCACCGCGGGGAGCG 17 42 0 CAAACCCACC 0.974475 -60 GGATTGCCGGCAATCCCCCCAGTCAATATT 18 244 1 CAATCCCCCC 0.958007 -36 TCAAGCTGATCTAACCCATCTTCAGGTTAA 21 130 0 CTAACCCATC 0.928057 -171 TGCCCCTAATTTGTCCCCTCC 22 231 1 TTGTCCCCTC 0.399013 -11 ********** Masking position 5 Map Score: 9.17814 Number of sites scoring better than the average of aligned sites = 879 Number in coding regions = 793 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TGTTCACTATTTTTCAACCTCTGTAACTTTTG 1 168 1 TTTTACCTCT 0.91147 -24 TTAGCTAAGCTTTTAACCCTCCCTGTCCCAAC 2 151 1 TTTTCCCTCC 0.966352 -45 AGGGGGCTTTTTTTCAACCTTTTTCTTTTTTG 3 74 0 TTTTACCTTT 0.612934 -25 TATTATCGTTTTTTGCTCCTCTCACCGTGAGC 5 27 1 TTTTTCCTCT 0.942911 -74 CTTCAGGAAGTTTTTGTCCCCTGGGCTGACTC 5 58 1 TTTTTCCCCT 0.865927 -43 TTATTGGGAATTTTCCCCTTTTCT 6 158 1 TTTTCCTTTT 0.515103 -14 GGAACAAATTTTAGCCCTTTCCGTTCCCGT 9 9 1 TTTTCCCTTT 0.888317 -88 AAAGCACCGATTTTTCCCTTCTGGAAGTGGTT 12 17 0 TTTTCCTTCT 0.873525 -284 GGTTGTTTTCACCCTGTTCACCCCAAA 14 6 1 TTTTCCCTGT 0.895685 -82 CCTTGACAGCTTTTGATCCTCTGCTTCAGCCC 15 152 1 TTTTTCCTCT 0.942911 -95 TTTTTTATTTTTTCGATCCTGTTGAAGTTTTA 18 158 1 TTTCTCCTGT 0.390253 -122 CAAAAGTTGCTTTTTTCCCACTTGCCTTGCTG 20 70 0 TTTTCCCACT 0.899751 -68 AATTGACTAGTTTTTGCCCCCAAGAACTGGTT 21 11 1 TTTTCCCCCA 0.682741 -290 GCGGCCATAATTTTGTTCCTCGCTTTGATAAA 21 237 1 TTTTTCCTCG 0.722612 -64 GGTAACGATGTTTTTTACTTCCTTGACTAACC 22 145 1 TTTTACTTCC 0.432986 -97 TGTATTGGCATTTCTGCCCCCCGCCAAATTTT 22 181 0 TTTCCCCCCC 0.723834 -61 CTGCCCCTAATTTGTCCCCTCC 22 230 1 TTTGCCCTCC 0.78458 -12 TTTTGCCCCACTCCTTGGAAAA 23 1 1 TTTTCCCACT 0.899751 -279 **** ****** Masking position 3 Map Score: 11.8479 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 768 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 8 CCGATGCGTTGCCGAACCCTAGGGGGCAAATTGGCTTCGG 1 112 1 GGACGGGAAA 0.896781 -80 TAAAAGCTTAGCTAAAGGTCTGACAGTAAATGCGGACTCG 2 126 0 GAAGGCGAAA 0.955724 -70 AGTCTCTGTGGAAAAAACCTAGGCTGTAAAGTATTGGGCG 4 135 0 GAACGCGAAA 0.989081 -30 TTTATTTAGTGCCAAGTTTTGGCCGGGAAACTAAAACTTT 6 47 1 GAGTGCGAAA 0.77938 -125 AGCCAAAAACGAGAAAACGAAGAAGGCATAGTCGGCCACA 7 53 0 GAACGAGATA 0.802969 -72 GGGGAGAGCGAGTAAATTGCAGGCCGAAAATCCGAGAGAA 10 84 0 AAATGCGAAA 0.59567 -183 GCCATGGGAAGCTAAAATACAGGCCGGATAACCCCATTTA 10 150 0 GAATGCGATA 0.818801 -117 GCCCAAAATCGGTGGATCTCTGTCCGAAAAAATTGTGTTA 12 62 1 GGACGCGAAA 0.986737 -239 ACGGGCCAAGGAAATATCCTAGCCCGAAAAAGAAATTATT 13 106 0 GAACGCGAAA 0.989081 -101 GATCGCCGGGGCTGAAGCAGAGGATCAAAAGCTGTCAAGG 15 152 0 GGACGACAAA 0.77603 -95 AAATATCGAGGGCGTAGCTGAGAAATAAAAATCTTATTTT 18 121 0 GGACGATAAA 0.55953 -159 AGTTCAGTTGGTAGAACGCAGGTCTCCAAAACCTGATGTC 19 136 1 GGAGGCCAAA 0.761056 -142 GAGAAAATCTGGAACATCACCGAACGCAAAGTCGAATAAT 19 237 0 GAACGAGAAA 0.959153 -41 AGATCAGCTTGACAAACCGCAGACCGTAAAGCAGACCAAG 21 148 1 GAACGCGAAA 0.989081 -153 GGAGGGGACAAATTAGGGGCAGGGAAGACCAAGCTA 22 216 0 GAATGCGGAA 0.77938 -26 * * * * * * * *** Masking position 20 Map Score: 9.45608 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 589 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 TAACAACAAAATTAAGCTGGGGGAGCCGGA 6 131 0 ATTAAGCTGG 0.815506 -41 ATGAGAGGGTATTTAGCCTGGGGCAGTATG 8 43 1 ATTTAGCCTG 0.965564 -69 TCATACTGTAGTTTAGCCTGAGTTGCCCCA 8 71 0 GTTTAGCCTG 0.867573 -41 TTGCCTAATTATTTAGCCGGTCATTTACTT 13 31 1 ATTTAGCCGG 0.973045 -176 GAGTCTAATAATTTAGCTTCCAAAAAAAGT 13 68 0 ATTTAGCTTC 0.759877 -139 GCCACTATTTATTTAACTGGCTATGCCAAA 15 38 1 ATTTAACTGG 0.846659 -209 AGGGTTGCTTAATTAACCTGCCGAGGTTGA 15 84 1 AATTAACCTG 0.635673 -163 TGCCAATACAATTTAGCTTGGTCTTCCCTG 22 203 1 ATTTAGCTTG 0.956101 -39 CAGCTACGATAATTAGCTGGTAATTTTTCC 23 27 0 AATTAGCTGG 0.898587 -253 ********** Masking position 5 Map Score: 3.84449 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 165 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 GTCTTTCCCTCCAATGGTAATGGTGATTCCCGA 1 34 1 CCAAGTAAGG 0.949816 -158 ACTCGAAAAGCCGATGCTAATGCTAATTTTAAC 2 98 0 CCGAGTAAGC 0.985693 -98 CAATCCAATGCCGATGATAACGCGAGGGCCTGT 6 91 0 CCGAGTAAGC 0.985693 -81 CAGTTTCCCCCCAGGGCTGAGGATTATCGTGAT 7 99 0 CCAGGTGAGA 0.869559 -26 TGGGCCAATCCCAACGATAAAGCACCGATTTTT 12 34 0 CCAAGTAAGC 0.981657 -267 AAAATAACCAATGCTGACTGACCAGTCTCT 13 187 0 CCAAGTGATG 0.805975 -20 AATTAACCTGCCGAGGTTGAAGCCTGAATCAAG 15 94 1 CCGAGTGAGC 0.992667 -153 TTGGCGATCGCCGGGGCTGAAGCAGAGGATCAA 15 164 0 CCGGGTGAGC 0.985112 -83 GTAAAGCAGACCAAGGGTGACCCCGGTAAAAAC 21 173 1 CCAAGTGACC 0.945658 -128 **** * *** ** Masking position 8 Map Score: 6.86528 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 191 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 TTCAACCTCTGTAACTTTTGCC 1 180 1 GTAATTTTGC 0.831225 -12 CTCAGAATTTGTAAATTTTCGTTAACAAAGT 2 17 1 GTAATTTTCG 0.831126 -179 TTGGTTGTCGATAACTTTCCCTTTTCGTGAT 4 50 1 ATAATTTCCC 0.920815 -115 GTTGTTATTGGGAATTTTCCCCTTTTCT 6 154 1 GGAATTTCCC 0.905678 -18 CTGAGGCAGTGTACTTTTTCCTGCTGCTTCC 8 11 0 GTACTTTTCC 0.888055 -101 CATCATACAGGTTATTTTCCCTGGTACGGGA 9 35 0 GTTATTTCCC 0.852922 -62 TGGGCTAAAAATAAATTTCCCTAGCCCCCTC 12 113 1 ATAATTTCCC 0.920812 -188 CCTAGACCCAATAAGTTTTCCATTTATTTCG 16 20 1 ATAATTTTCC 0.914771 -91 TAATTAGCTGGTAATTTTTCCAAGGAGTGGG 23 17 0 GTAATTTTCC 0.974224 -263 TCCTCTGGACGAAATTTTTCCTTTAACCACA 23 109 1 GAAATTTTCC 0.856935 -171 **** ****** Masking position 6 Map Score: 5.01591 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 429 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 TTAAGCTAGGGAACGCCGATGCGTTGCCGA 1 97 1 GAACGCCGAT 0.857313 -95 AAAGATCGCAGTTTGGTATTATC 5 4 1 GATCGCAGTT 0.978683 -97 ATATCTTTACGATCGCCATTGGCTAGCCAT 10 185 0 GATCGCCATT 0.918837 -82 CCCCGGCAGTGATTCCAGTTCAAACCTTAT 12 166 0 GATTCCAGTT 0.7072 -135 GCCCCTTGGCGATCGCCGGGGCTGAAGCAG 15 172 0 GATCGCCGGG 0.887657 -75 CGGTGGGTTTGATCGCCGTTAATTCACATC 17 51 1 GATCGCCGTT 0.986575 -51 TGGTGTTGGAGATCACAGTTTCGCTGA 19 8 0 GATCACAGTT 0.800451 -270 CATCGATGGCGATCGCCATTGGTGTTGGAG 19 27 0 GATCGCCATT 0.918837 -251 TCAGTTGGTAGAACGCAGGTCTCCAAAACC 19 139 1 GAACGCAGGT 0.937165 -139 TTGGCCGCTAGAATGCAGTTTTGCTGGATC 20 26 0 GAATGCAGTT 0.840161 -112 GTTGCTAGGCGATCGCCTGTTGAAATTAAC 22 90 1 GATCGCCTGT 0.800844 -152 TCACTGGTTCGAATCCAGTTACGTCCATAA 23 162 0 GAATCCAGTT 0.556088 -118 ********** Masking position 2 Map Score: 8.63439 Number of sites scoring better than the average of aligned sites = 2340 Number in coding regions = 2127 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 13 TCGGTGCTTTATCGTTGGGATTGGCCCAAA 12 39 1 ATCGTTGGGA 0.863097 -262 CCCCTTGGCGATCGCCGGGGCTGAAGCAGA 15 171 0 ATCGCCGGGG 0.939136 -76 AATAAAAAATATCGAGGGCGTAGCTGAGAA 18 137 0 ATCGAGGGCG 0.963377 -143 GCCAATTCCCATCGATGGCGATCGCCATTG 19 36 0 ATCGATGGCG 0.983163 -242 TTGCGTAACAATCGTTGGCGAGGTAATTGG 19 208 0 ATCGTTGGCG 0.976049 -70 CATCGTTGACATCGATGGGGTCACTGGTTC 23 182 0 ATCGATGGGG 0.983163 -98 ********** Masking position 2 Map Score: 3.48846 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 78 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 AAAGTTAACAATTGGTCAATAATAATTGCC 2 43 1 ATTGGTCAAT 0.891156 -153 GACCAACAGGACTGGGCAATTATTATTGAC 2 57 0 ACTGGGCAAT 0.956079 -139 GCTGTAAAGTATTGGGCGATAAATTTCGTT 4 123 0 ATTGGGCGAT 0.872703 -42 CGGCTAAATAATTAGGCAAATAGCAAATAT 13 20 0 ATTAGGCAAA 0.685056 -187 AAAATAAGAGACTGGTCAGTCAGCATTGGT 13 181 1 ACTGGTCAGT 0.910306 -26 GTCAAAGCTTATTGGGCAGTAATTTACCGA 18 33 0 ATTGGGCAGT 0.930782 -247 TTTGAGCAAGACTGGGCAGAGTGAATGTTG 18 205 0 ACTGGGCAGA 0.935458 -75 GGGGGCAAAAACTAGTCAATT 21 2 0 ACTAGTCAAT 0.786119 -299 ********** Masking position 1 Map Score: 2.54896 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 403 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 15 CCAATCGAGACCGTCTTCCTTTTGAGCGGAA 3 41 1 CCTCTTCCTT 0.944921 -58 TTTTTTTCAACCTTTTTCTTTTTTGATTTCC 3 68 0 CCTTTTCTTT 0.880401 -31 CGATAACTTTCCCTTTTCGTGATGGAAAGGA 4 58 1 CCTTTTCGTG 0.933539 -107 AAACCCACCGCCATCTTCGTTAATCTTCGTG 7 21 0 CCTCTTCGTT 0.983715 -104 GCCGACTATGCCTTCTTCGTTTTCTCGTTTT 7 57 1 CCTCTTCGTT 0.983715 -68 CAAATTTTAGCCCTTTCCGTTCCCGTACCAG 9 15 1 CCTTTCCGTT 0.933539 -82 ** ******** Masking position 6 Map Score: 1.38455 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 41 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467