AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_synecho_ctra_300.orf -o071_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 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 #21 RCT00164 300 Chlamydia_trachomatis #22 RCT00312 295 Chlamydia_trachomatis Motif number 1 TAAAATAGGGTTTTCTGTGGATTAACCACGGACG 3 198 1 TTTCTTGTTA 0.802173 -54 CACGGACGATTTTCCCGTCGATTACATAGAGAGA 3 224 1 TTTCCTGTTA 0.840141 -28 AGGGGCCAGCGTTGCCCTCAATTTTTACCATTGG 5 13 1 GTTCCTATTT 0.77911 -87 AGAAAACTAATTGCCCCTTATTTTACGGGGTTAG 7 259 0 TTGCCTATTT 0.938341 -42 GGGCAATTAGTTTTCTCGTATTTTTTCCATTGTT 7 277 1 TTTCTGATTT 0.842156 -24 ATTTCAACAATTTTCCTAAAATTTAGAACATTTC 11 29 1 TTTCCAATTT 0.717133 -72 AGGGCAAATTTCCTGGGGATTTTAGGTTGAAT 11 79 0 TTTCTGGTTT 0.814033 -22 TCTGCCCCTTTTTGCTATAAATTATTCGAGAGTT 12 37 1 TTTCTTATTA 0.831719 -195 TATGTTACCATTGACCCTAAATTTGGCAAATATT 12 110 1 TTGCCTATTT 0.938341 -122 AACTATTGCCTTGGCCATAGCTTTGTAACAAAAC 12 158 1 TTGCCTGTTT 0.925846 -74 TAATAAACACTTACCTGTTACTTTAAGGGACTGC 13 238 1 TTACTTATTT 0.692307 -63 TGTTTTTGCCCTTGCCATAGATTTTT 14 205 1 CTTCCTGTTT 0.743179 -16 ATGTAACTTATTTCCTGTCAATTTAGTCAGTGCA 17 13 1 TTTCTTATTT 0.95809 -189 ATCCCTTGCATTGACCGTCAATTT 20 287 1 TTGCCTATTT 0.938341 -14 GTCGCCAGTTTTTTCTATGATTTTAACACTATAA 21 262 1 TTTCTTATTT 0.95809 -39 TTGGAAATGGTTTTCTGTGAGTTTCTTTGTCTGT 22 70 1 TTTCTTATTT 0.95809 -226 ATATGATTTATTTTCTATTGCTTTGATATAAATC 22 195 1 TTTCTTGTTT 0.949381 -101 TGTCTTACTTTTTTCTGTGAATTTGCTTAAATAG 22 250 1 TTTCTTATTT 0.95809 -46 *** ** * * *** Masking position 12 Map Score: 18.3634 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 267 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 AATTCTGCTCCCCAGGACAATGGGTAGAGCATC 1 77 0 CCCGGCAAGG 0.982844 -119 GGGGAGCAGAATTTGGTGAAATGTTACAGTTCT 1 97 1 ATTGGGAATG 0.495689 -99 GTATAAACAGATTTGGCGATCGCCGCTTGACCG 3 133 1 ATTGGGATGC 0.597285 -119 TCGCCGCTTGACCGGGGGAATGGTATCTCTCGC 3 152 1 ACCGGGAAGG 0.972975 -100 CGCCACCAAACTTGGGAGATCGGGCGGTTTAGC 4 43 0 CTTGGGATGG 0.956335 -72 TTTGGTGGCGCTTTGGTCAATTGGGATCAACTG 4 66 1 CTTGGCAATG 0.62057 -49 ATACGCACGGGAAAAGGGGGGAAAGAAA 5 82 0 CACGGAAAGG 0.843716 -18 TGAGCAAATCCTTTGGGGATTGGCCATGGGACT 6 13 1 CTTGGGATGG 0.956335 -131 TGAAATCATTACCCGGTCAAAGGGACGGGGATA 7 135 0 ACCGGCAAGG 0.958557 -166 ACTGTTATTTACCTGGAAATTGGAAATTCTGTC 7 205 1 ACCGGAATGG 0.896162 -96 TTCTGTCATTCCCACGGGAAAGGCCGCCCTAAC 7 231 1 CCCCGGAAGG 0.851414 -70 GGAAAATCCCCCGCTGATGGGATTGTGGCAA 9 9 1 CCCGCGATGG 0.878927 -61 TGGAACTCCAACCCTGGCATTGGTGTTGT 10 11 1 ACCTGCATGG 0.561349 -19 ACCTAAAATCCCCAGGAAATTTGCCCT 11 84 1 CCCGGAATTG 0.774499 -17 CATATAATACATCGGGGCATAGGTCTGCCCCTT 12 14 1 ATCGGCATGG 0.92069 -218 TCAACTATTGCCTTGGCCATAGCTTTGTAACAA 12 156 1 CCTGGCATGC 0.8665 -76 CCCCAATGGCCACCGGCGATCGCCTTCT 14 6 0 CACGGGATGC 0.873498 -215 ATCCAGGTTACATAGGAGAATTGTTCTGTCGAC 15 19 1 CATGGGAATG 0.681734 -46 TAGATCACTCCATTGGGCAACGGCGTTAATGCA 17 43 0 CATGGCAAGG 0.899484 -159 ATTTATAGACCACTGGCGATCGGCATGGTAACA 17 110 0 CACGGGATGG 0.975226 -92 GCGCTTATCTACTTGGCGATAGGCCTAATTAAG 21 161 1 ACTGGGATGG 0.957041 -140 *** ** *** ** Masking position 9 Map Score: 21.8615 Number of sites scoring better than the average of aligned sites = 4163 Number in coding regions = 3808 Number in noncoding regions = 355 Number of orfs with sites within 600 bp upstream = 355 Fraction of orfs with sites within 600 bp upstream = 0.057019 Motif number 3 TTTAGGGAATCCTACCACTGACCTACGGTT 1 147 0 CCTACCACTG 0.926503 -49 TAGCTTTGGTGCTACCATTTATCGCCTCCT 3 20 0 GCTACCATTT 0.844443 -232 ATGGGTCCTTCCTAGCTTTGGTGCTACCAT 3 32 0 CCTAGCTTTG 0.918187 -220 CTTCCCTTAGCCTAACATTGACCATAATCA 3 67 0 CCTAACATTG 0.772612 -185 GGAAAGAAACCCTACCATTTTAGGGAGGTT 5 61 0 CCTACCATTT 0.960235 -39 CAACAATAAGCCTTGCTCTGAGCCTCACAT 6 56 0 CCTTGCTCTG 0.653946 -88 CCCAATCCCACCTTCCTTTTTGTCCTAGCC 6 114 1 CCTTCCTTTT 0.783546 -30 AAATACCTAGCCTCGCACTTTTCAAACACT 7 77 1 CCTCGCACTT 0.830795 -224 GGTCTATCCCCGTCCCTTTGACCGGGTAAT 7 131 1 CGTCCCTTTG 0.474951 -170 CAATTGCTTCCCTAGCATTTTGCCACAATC 9 31 0 CCTAGCATTT 0.960235 -39 GAACTCCAACCCTGGCATTGGTGTTGT 10 13 1 CCTGGCATTG 0.878464 -17 GTATGGCCATCCTCCCATTGTATGTATAGT 12 190 0 CCTCCCATTG 0.950923 -42 CGCCGGGCAAGCTTGCATTTTGCAAAATTC 14 125 1 GCTTGCATTT 0.715351 -96 TGGGTAATTCCGTAGCATTTCCAGAATATT 17 166 1 CGTAGCATTT 0.776858 -36 CTTTGTCTGGGCTACCATTTGGTGCGCTTT 20 33 0 GCTACCATTT 0.844443 -268 ACGATTCCATCCTACTATTTAAAATTGGAA 20 226 1 CCTACTATTT 0.544945 -75 CAAAAATATCCCTTGCATTGACCGTCAATT 20 280 1 CCTTGCATTG 0.941331 -21 ********** Masking position 3 Map Score: 16.0279 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 369 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 ATTAACCCTGTTTTACCGCTGACAAGGGCCA 3 100 1 TTTTACCCTG 0.916362 -152 CTGTTTATACTTTGGCCCTTGTCAGCGGTAA 3 112 0 TTTGGCCTTG 0.88765 -140 TGCCCTCAATTTTTACCATTGGTCAAGTCTT 5 25 1 TTTTACCTTG 0.951758 -75 GCCTCACATATTTTGCCATAGTCCCATGGCC 6 34 0 TTTTGCCTAG 0.973016 -110 CCACCTTCCTTTTTGTCCTAGCCTAGCCTGC 6 121 1 TTTTGTCTAG 0.627484 -23 GCCTAAAAAATTTTACCTATGCTGAAATCAT 7 159 0 TTTTACCATG 0.78733 -142 TTTCTCGTATTTTTTCCATTGTT 7 288 1 TTTTTCCTTG 0.899328 -13 GTTGCTGCTTTTTTGCCCCTGGTTCCT 8 7 0 TTTTGCCCTG 0.952444 -139 TTCCCTAGCATTTTGCCACAATCCCATCAGC 9 23 0 TTTTGCCCAA 0.727741 -47 CTACAACAATTGCTTCCCTAGCATTTTGCCA 9 36 0 TGCTTCCTAG 0.483191 -34 AATAGTTCTATGTTACCATTGACCCTAAATT 12 102 1 TGTTACCTTG 0.904076 -130 AATGGTTGAATTTTTCCTTAGCGACAGAACT 13 207 1 TTTTTCCTAG 0.899328 -94 ACCGGTGGAATTTTACCCCAATGGCCACCGG 14 23 0 TTTTACCCAA 0.594035 -198 AAACGATTGTTTTTGCCCTTGCCATAGATTT 14 198 1 TTTTGCCTTG 0.973019 -23 CCCGTCCACATTTGACCGTAAAGGAGCATTC 16 13 1 TTTGACCTAA 0.365982 -24 GAGATGGTGTTGTTACCGTAGTATTCTCCCT 18 56 0 TGTTACCTAG 0.904076 -24 GATTGTCTTGTTCTGCCTTTGTCTGGGCTAC 20 48 0 TTCTGCCTTG 0.88765 -253 TCGTTAATTTTGTTGCCCAAGCTCCTCCGGC 20 199 0 TGTTGCCAAG 0.763761 -102 ******* *** Masking position 1 Map Score: 17.1937 Number of sites scoring better than the average of aligned sites = 1472 Number in coding regions = 1270 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 5 AATCTCCTTGCCAAAACTCCTATGATTCTA 1 11 1 CCAAAACTCC 0.85193 -185 CTGCCAATTGTGCAAGTTCCGCAAGCAAGT 2 22 0 TGCAAGTTCC 0.557267 -100 CATAATTTCCCTAAAGTTCCGTCGGCTAAA 4 19 1 CTAAAGTTCC 0.720479 -96 GGCTAAACCGCCCGATCTCCCAAGTTTGGT 4 42 1 CCCGATCTCC 0.599809 -73 TCCCAATTGACCAAAGCGCCACCAAACTTG 4 62 0 CCAAAGCGCC 0.807098 -53 TTGAGGGCAACGCTGGCCCCTAC 5 4 0 CGCTGGCCCC 0.581588 -96 ACATATTTTGCCATAGTCCCATGGCCAATC 6 30 0 CCATAGTCCC 0.87397 -114 GAATCAACGTCGAAAGTCCCCCTTTTTAAG 7 16 1 CGAAAGTCCC 0.807836 -285 AATCTCCTCACTAAAGCTCCGGCTTAAAAA 7 38 0 CTAAAGCTCC 0.789412 -263 ATTTATCCCCCCAAATCTCCTCACTAAAGC 7 51 0 CCAAATCTCC 0.851929 -250 TGACAGAATTTCCAATTTCCAGGTAAATAA 7 209 0 TCCAATTTCC 0.55129 -92 GGAAAGGCCGCCCTAACCCCGTAAAATAAG 7 247 1 CCCTAACCCC 0.809584 -54 GCTTTTTTGCCCCTGGTTCCT 8 2 0 CCCTGGTTCC 0.7921 -144 ACTATTCAACCTAAAATCCCCAGGAAATTT 11 76 1 CTAAAATCCC 0.386929 -25 TTGAATAGTTCCAAGTTCCGGATTGATTT 13 10 1 TCCAAGTTCC 0.838826 -291 TCCCCTGGCTCCCAATCCCTAG 18 3 1 CCCTGGCTCC 0.847119 -77 ATAAAACTTTCCCAATTCCCTTCCTGACTG 19 55 1 CCCAATTCCC 0.879921 -23 TCGCTCAAAATCCCAACAGAGTAA 20 5 1 TCAAAATCCC 0.416434 -296 AATTTTGTTGCCCAAGCTCCTCCGGCCAGC 20 195 0 CCCAAGCTCC 0.97754 -106 ********** Masking position 9 Map Score: 12.092 Number of sites scoring better than the average of aligned sites = 2880 Number in coding regions = 2502 Number in noncoding regions = 378 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 6 CAAGAACTGTAACATTTCACCAAATTCTGC 1 102 0 AACATTTCAC 0.611589 -94 GGCGAGAGATACCATTCCCCCGGTCAAGCG 3 156 0 ACCATTCCCC 0.783568 -96 TTCCTTGCCATAATTTCCCTAAAGTTCCG 4 10 1 ATAATTTCCC 0.837915 -105 TGGGATTGGGATCATCTCCCTGGAACGGAC 6 94 0 ATCATCTCCC 0.821806 -50 CTATGCTGAAATCATTACCCGGTCAAAGGG 7 144 0 ATCATTACCC 0.732571 -157 TGGGAATGACAGAATTTCCAATTTCCAGGT 7 215 0 AGAATTTCCA 0.816408 -86 TAAAATTTAGAACATTTCCATCTGTTTATT 11 45 1 AACATTTCCA 0.938361 -56 GTAATTCCGTAGCATTTCCAGAATATTTCC 17 169 1 AGCATTTCCA 0.926237 -33 GCATTTCCAGAATATTTCCAGAAAATTACC 17 180 1 AATATTTCCA 0.570821 -22 ATATTTCCAGAAAATTACCAT 17 191 1 AAAATTACCA 0.5029 -11 CGGTAACAACACCATCTCCCC 18 69 1 ACCATCTCCC 0.878815 -11 CAAAAGTGAAAAAATTTCCCCGTGAATCCA 20 138 0 AAAATTTCCC 0.907877 -163 CTTAGCCGCAAAAATATCCCTTGCATTGAC 20 272 1 AAAATATCCC 0.668087 -29 CTCACAGAAAACCATTTCCAACTTGGGCCC 22 61 0 ACCATTTCCA 0.926237 -235 CAAGAAGATTAGCATATCCAAGAGATTTAT 22 222 0 AGCATATCCA 0.719469 -74 ********** Masking position 4 Map Score: 8.34145 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 908 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 7 TTACCGCTGACAAGGGCCAAAGTATAAACA 3 112 1 CAAGGGCCAA 0.963573 -140 AAGACTTGACCAATGGTAAAAATTGAGGGC 5 26 0 CAATGGTAAA 0.862878 -74 TGCCATAGTCCCATGGCCAATCCCCAAAGG 6 22 0 CCATGGCCAA 0.917048 -122 GGCCATGGGACTATGGCAAAATATGTGAGG 6 34 1 CTATGGCAAA 0.942095 -110 AACAATGGAAAAAATACGAGAA 7 289 0 CAATGGAAAA 0.781115 -12 AGGAACCAGGGGCAAAAAAGCAGCAA 8 7 1 CAGGGGCAAA 0.796751 -139 ATAGGCTCAACAATCGCAAA 11 1 0 CAATCGCAAA 0.897735 -100 AATTTAGGGTCAATGGTAACATAGAACTAT 12 103 0 CAATGGTAAC 0.685623 -129 TGTTACAAAGCTATGGCCAAGGCAATAGTT 12 158 0 CTATGGCCAA 0.949614 -74 AATTTTACCCCAATGGCCACCGGCGATCGC 14 16 0 CAATGGCCAC 0.942524 -205 AAATCTATGGCAAGGGCAAAAACAATCGTT 14 199 0 CAAGGGCAAA 0.958045 -22 TTAATTAGGCCTATCGCCAAGTAGATAAGC 21 163 0 CTATCGCCAA 0.801999 -138 ********** Masking position 9 Map Score: 12.7033 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 930 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 TTCCTGGCTCTACTTGCTTGCGGAACT 2 6 1 GGCCACTTGC 0.982231 -116 TCTACTTGCTTGCGGAACTTGCACAATTGGCA 2 19 1 TGCGACTTGC 0.768278 -103 AAACAGATTTGGCGATCGCCGCTTGACCGGGG 3 137 1 GGCACGCCGC 0.81685 -115 GTAGGGGCCAGCGTTGCCCTCAATTTT 5 6 1 GGCACGTTGC 0.980291 -94 ATTGTTGTAGGGCGGGCCTTGCT 9 57 1 GGCGCCTTGC 0.964309 -13 AGTAATGAAAGGCGCCAGTTGCGTAATAGTTC 12 78 1 GGCCAGTTGC 0.985605 -154 ATATCACCATGGCAATATTTGCCAAATTTAGG 12 125 0 GGCAATTTGC 0.915301 -107 CTATGGCCAAGGCAATAGTTGATATCACCATG 12 146 0 GGCAAGTTGA 0.872583 -86 ATGGGAGGATGGCCATACCTGCTCCATTACCC 12 202 1 GGCAACCTGC 0.960395 -30 GGAGAAGGTGGGCCCAAGTTGGAAATGGTTTT 22 52 1 GGCCAGTTGG 0.908665 -244 *** * ****** Masking position 3 Map Score: 5.89532 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 206 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 AGTGGTAGGATTCCCTAAAATACCTTATGAA 1 158 1 TTCCCTAAAT 0.949754 -38 TTGCCATAATTTCCCTAAAGTTCCGTCGGCT 4 15 1 TTCCCTAAAT 0.949754 -100 TTTTCCTAACCTCCCTAAAATGGTAGGGTTT 5 54 1 CTCCCTAAAT 0.977921 -46 TTGGGATCATCTCCCTGGAACGGACAGAGCA 6 88 0 CTCCCTGGAC 0.811429 -56 CCCAAATCTCCTCACTAAAGCTCCGGCTTAA 7 41 0 CTCACTAAAC 0.767025 -260 CAACAATTGCTTCCCTAGCATTTTGCCACAA 9 33 0 TTCCCTAGCT 0.810274 -37 TTTCAACAATTTTCCTAAAATTTAGAACATT 11 30 1 TTTCCTAAAT 0.622842 -71 TGCAAAATTCCTCACTAGAGTTAGGGAAGCT 14 145 1 CTCACTAGAT 0.892421 -76 CCGTAGTATTCTCCCTAGATTGTGCCATATT 18 41 0 CTCCCTAGAT 0.979586 -39 CTTTTCTCCATAAAATTATAGTGTTA 21 285 0 CTCCATAAAT 0.794648 -16 ********* * Masking position 6 Map Score: 4.81428 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 172 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 10 CTTGCGGAACTTGCACAATTGGCAGAAGTTTA 2 27 1 TTGCCAATGG 0.98413 -95 TGGTGGCGCTTTGGTCAATTGGGATCAACTGG 4 68 1 TTGGCAATGG 0.92261 -47 CATAGAACTATTACGCAACTGGCGCCTTTCAT 12 82 0 TTACCAATGG 0.980898 -150 GTAGCATAGCTTACTCAAATGGTTGAATTTTT 13 190 1 TTACCAATGG 0.980898 -111 CGGTGGAATTTTACCCCAATGGCCACCGGCGA 14 20 0 TTACCCATGG 0.97705 -201 TTCACTAACTTTGCACGACTGGGCCCTAACCC 14 56 0 TTGCCGATGG 0.96544 -165 TCTAACTAGATCACTCCATTGGGCAACGGCGT 17 50 0 TCACCCATGG 0.92907 -152 **** *** *** Masking position 8 Map Score: 5.44542 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 107 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 AATCTCCTTGCCAAAACTCCTATG 1 5 1 TCCTTGCCAA 0.883335 -191 CACTACTGAACCTTTGACAGTTCGCTCTTT 2 83 1 CCTTTGACAG 0.816023 -39 AAAACCTTTGCCAACATTGAAAGA 2 108 0 CCTTTGCCAA 0.915507 -14 TATACTTTGGCCCTTGTCAGCGGTAAAACA 3 108 0 CCCTTGTCAG 0.955189 -144 TTCCTTGCCATAATTTCCCTA 4 2 1 TCCTTGCCAT 0.933893 -113 TCAACTATTGCCTTGGCCATAGCTTTGTAA 12 156 1 CCTTGGCCAT 0.791978 -76 ATTGTTTTTGCCCTTGCCATAGATTTTT 14 203 1 CCCTTGCCAT 0.974652 -18 TCTTGTTCTGCCTTTGTCTGGGCTACCATT 20 44 0 CCTTTGTCTG 0.816984 -257 GCAAAAATATCCCTTGCATTGACCGTCAAT 20 279 1 CCCTTGCATT 0.70234 -22 TCTGTGAGTTTCTTTGTCTGTAAACATGAG 22 83 1 TCTTTGTCTG 0.621223 -213 AAATAAGCCTTCCTTGCAAGAAATCGAGTA 22 163 0 TCCTTGCAAG 0.810463 -133 ********** Masking position 4 Map Score: 5.15143 Number of sites scoring better than the average of aligned sites = 1252 Number in coding regions = 1112 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 12 AAATTCTGCTCCCCAGGACAATGGGTAGAG 1 81 0 CCCCAGGACA 0.846758 -115 CGTGGTTAATCCACAGAAAACCCTATTTTA 3 198 0 CCACAGAAAA 0.948329 -54 TCTATGTAATCGACGGGAAAATCGTCCGTG 3 224 0 CGACGGGAAA 0.916433 -28 GCGGTTTAGCCGACGGAACTTTAGGGAAAT 4 23 0 CGACGGAACT 0.763661 -92 CCCGTGGGAATGACAGAATTTCCAATTTCC 7 219 0 TGACAGAATT 0.383357 -82 TCTGTCATTCCCACGGGAAAGGCCGCCCTA 7 232 1 CCACGGGAAA 0.904226 -69 AACCTAAAATCCCCAGGAAATTTGCCCT 11 83 1 CCCCAGGAAA 0.855251 -18 TTTTCCTTAGCGACAGAACTTAATAAACAC 13 218 1 CGACAGAACT 0.864877 -83 GCAGTGTAGTCGACAGAACAATTCTCCTAT 15 30 0 CGACAGAACA 0.952237 -35 CTGACTAAATTGACAGGAAATAAGTTACAT 17 13 0 TGACAGGAAA 0.861959 -189 AAAAAACTGGCGACAGAATAATCCTGCGCA 21 246 0 CGACAGAATA 0.870746 -55 ACAAAGAAACTCACAGAAAACCATTTCCAA 22 70 0 TCACAGAAAA 0.840651 -226 TTAAGCAAATTCACAGAAAAAAGTAAGACA 22 250 0 TCACAGAAAA 0.840651 -46 ********** Masking position 8 Map Score: 9.96125 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 286 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 TAACATTTCACCAAATTCTGCTCCCCAGGACAA 1 90 0 CCATTCTGCC 0.961536 -106 TTATGAAATTCCATTTTCATCCCT 1 182 1 CCATTCATCC 0.827811 -14 CCATTTATCGCCTCCTCCTCCTCCA 3 3 0 CCTTCCTCCC 0.834673 -249 CTAACATTGACCATAATCAGCTCCATGGGTCCT 3 53 0 CCAATCAGCC 0.916909 -199 TATTTATCCCCCCAAATCTCCTCACTAAAGCTC 7 49 0 CCCATCTCCC 0.942551 -252 TAGCATTTTGCCACAATCCCATCAGCGGGGGAT 9 16 0 CCAATCCCAC 0.778278 -54 CATACCTGCTCCATTACCCCCCCGCCA 12 215 1 CCAACCCCCC 0.944745 -17 CTAGATTGTGCCATATTCTCCGCTTCTAGGGAT 18 25 0 CCATTCTCCC 0.989416 -55 TACGGTAACAACACCATCTCCCC 18 67 1 ACAATCTCCC 0.861087 -13 TTGGAATGAGCTAATTTCACCTCTTAGCCGCAA 20 250 1 CTATTCACCC 0.794408 -51 CAACTTGGGCCCACCTTCTCCACTCTGAGCCAT 22 40 0 CCATTCTCCC 0.989416 -256 *** ****** * Masking position 8 Map Score: 5.95602 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 772 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 14 CCAGTAGGTTGGTGTAATCGAGATAGAATCATA 1 31 0 GGTTAATCGA 0.76931 -165 CAAAAAGGAAGGTGGGATTGGGATCATCTCCCT 6 103 0 GGTGGATTGA 0.827501 -41 AATAGTGGGAGGACTGATCCCGTTTAAAACTCA 8 38 1 GGATGATCGT 0.943102 -108 TTAAAACTCAGACCTGATTCAGATCTAAACTGT 8 61 1 GACTGATTGA 0.819337 -85 TCCAAGTTCCGGATTGATTTTGACTTGAGCAAA 13 20 1 GGATGATTGA 0.97456 -281 CTGCCTACTCGGCATGATTCTGTAAATTCTTTT 13 268 1 GGCTGATTGT 0.960423 -33 GTTGCCCAATGGAGTGATCTAGTTAGAATCAAT 17 55 1 GGATGATCGT 0.943102 -147 AATCCACTGTGGAGTGATTACGAAAAAGTACTT 20 111 0 GGATGATTGA 0.97456 -190 CTTGGCGATAGGCCTAATTAAGAAGCCTTTTAT 21 172 1 GGCTAATTGA 0.901082 -129 *** ***** ** Masking position 7 Map Score: 1.88623 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 140 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 GGAGCTGATTATGGTCAATGTTAGGCTAAG 3 62 1 ATGGTCAATG 0.954889 -190 GCGGTAAAACAGGGTTAATTTCCTTCCCTT 3 89 0 AGGGTTAATT 0.769 -163 TGGTGGCGCTTTGGTCAATTGGGATCAACT 4 68 1 TTGGTCAATT 0.746606 -47 TAGGCTAAGTATGGACAATGACTGTTATTT 7 185 1 ATGGACAATG 0.791377 -116 CCGTAAAATAAGGGGCAATTAGTTTTCTCG 7 265 1 AGGGGCAATT 0.900193 -36 TGCCAAATTTAGGGTCAATGGTAACATAGA 12 108 0 AGGGTCAATG 0.977638 -124 ATGCTCCTTTACGGTCAAATGTGGACGGGG 16 12 0 ACGGTCAAAT 0.736698 -25 GTTTTATGGTCGGGTCAATTTGTAACAGCT 19 32 0 CGGGTCAATT 0.900193 -46 AAATTGACGGTCAATGCAAGGGATAT 20 285 0 ACGGTCAATG 0.958072 -16 ********** Masking position 7 Map Score: 3.08684 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 290 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331