AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_synecho_ctra_300.orf -o056_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 RCY49813 300 Synechocystis #2 RCY16771 300 Synechocystis #3 RCY45318 279 Synechocystis #4 RCY38307 300 Synechocystis #5 RCY09567 185 Synechocystis #6 RCY39101 220 Synechocystis #7 RCY53266 81 Synechocystis #8 RCY00014 284 Synechocystis #9 RCY28909 136 Synechocystis #10 RCY17336 228 Synechocystis #11 RCY26444 227 Synechocystis Motif number 1 AATTTTAACTCAATCGGCGATGGGCTCCCTATGGC 1 238 0 CAGGCATGGC 0.984187 -63 CAAAATATTGCCGGTGGCCATGGGCAAGAAAAAGA 2 171 0 CCGGCATGGC 0.998848 -130 GAAACTTCAGCCACTGGCGATCGCCTCCCACCTCC 3 148 0 CCGGCATCGC 0.998184 -132 TTATTGAGATCCTGGGGGGAGGGGAAGCTTTTGAA 4 63 1 CCGGGAGGGA 0.949332 -238 GTCGAGTTTGCCGACGGAGATGGTCAGGCTTATGC 4 98 1 CCGGAATGGC 0.98558 -203 AAAAATCTATGGCAAGGGCAAAAACAATCG 6 6 1 TCGGCAGGGA 0.851681 -215 GCAAGCTTGCCCGGCGGGCATGGTAGGATATAAGG 6 101 1 CCGGGATGGA 0.973763 -120 ACCCCAATGGCCACCGGCGATCGCCTTCT 6 202 1 CCGGCATCGC 0.998184 -19 AGTGGGTTTCCGGACGGCGATCGCCTAGATGGAGT 8 222 1 CGGGCATCGC 0.983181 -63 AGAATATTCACCGTTGACCATGAACTAATATTGCC 9 95 1 CCGACATGAC 0.878476 -42 CTGAAAACTCCCTCTGGCCCGCGACAAAGATTTGA 10 20 0 CCGGCCGCGC 0.977662 -209 CATTCATTTTCCCTCGGCGATCGCCCTGTCTAGAC 10 197 1 CCGGCATCGC 0.998184 -32 GGGGAATAAACCATCGACAATGGACAGAAGCATAG 11 178 1 CCGACATGGC 0.990971 -50 ** *** **** * Masking position 6 Map Score: 26.4215 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 1341 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 2 ATGTTCATCTATCTAAACCCAGGTCCCAGTAAATACTAGTCTTTA 1 143 1 ACCCACCAAA 0.988535 -158 TAAGTTTGTTAACTTTTCCTCTTTTGCCATAGGGAGCCCATCGCC 1 213 1 ACCCCTCAGA 0.739403 -88 CTTGGTAATCATCGCCGCCAACCAAGCCTGACAGTTTTTTAATCC 2 116 0 ACCCAACAAT 0.953153 -185 TTTTTGCCATCAATTCCAAGAAAGCTCTTTAAAAACTCTCTTT 3 9 1 ACCCAACTAA 0.946128 -271 GCCACTGGCGATCGCCTCCCACCTCCCAGCAAATACCCTTCCCCC 3 129 0 ACCCACCAAA 0.988535 -151 AGCTTGTGGAATCCATTCCCAAAGCCCGTTTAAATTTACTTATTT 3 215 1 ACCCACCTAT 0.963295 -65 ACCAGCCAATAACTAAACCTAACCTCCAATTGAGTACTGCCTAAC 4 195 0 ACCCATCTAT 0.925335 -106 GTGCGCTTAAATCCCCGCCCATTTTACCGGAGATACCAGCCAATA 4 229 0 ACCCATCAAA 0.976028 -72 ACAAACTTCGACATTGGCCAAACTCCCTACAAAGTGCGCTTAAAT 4 262 0 AACCACCAAT 0.899031 -39 GGGGAAACCAATCGCTACCGATTTTACCTCTTCAAAGTATGCCAA 5 82 1 ACCCATCTCA 0.883596 -104 TACACAGTTGCCCAAAAAGCCAAAAATAAGTCTGAAAT 8 4 1 AACCAACAAA 0.856289 -281 GACAATGCTAAGCAATTCCCAGCCATCTTGCCAAAGCTCATCGTC 8 117 1 ACCCAACCAA 0.843848 -168 TCCTAAAGTTAGACATTCCCCCCCTGCCCCTCAATGGAGAGCAGA 8 160 1 AACCCTCTAT 0.525387 -125 TCCTCTTTACAACAAAACCAATACCACCATAACAAACTCCATCTA 8 247 0 ACCCACCACA 0.969098 -38 GTTTGTCGGTAACTTATCCTGTTCCCCTGCATAAAATAGAATATT 9 58 1 ACCCGCCAAA 0.958587 -79 AGCTTGTCTGAAAACTCCCTCTGGCCCGCGACAAAGATTTGATTA 10 17 0 AACCCCCAAA 0.885076 -212 TCTGAGTGACATCCTAGCCTAATTTCCCAGACTTTAAGACCAAAT 10 61 1 ACCCATCATT 0.688795 -168 TCACCATCTTAGCCTGACCTGACAACCTGAACCTAGGAACAATAA 10 124 0 ACCCGACACA 0.769873 -105 AGTCGCTACGACCACCACCCCATTCTCCATTCATTTTCCCTCGGC 10 170 1 ACCCCCCTAT 0.930939 -59 * * ** * * * * * * Masking position 1 Map Score: 19.394 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 464 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 GTTCATCTATCTAAACCCAGGTCCCAGTAAATACTA 1 145 1 CACCCGTCCA 0.948835 -156 AATTAGAAGACTTAGCCTACGCTTCCTAAAGCGATT 1 269 1 CACCTGCTCC 0.949334 -32 GCGATGATTACCAAGGCTTTGTCGCTCTTTTTCTTG 2 146 1 CAGCTGTCCT 0.768401 -155 CACCTCCCAGCAAATACCCTTCCCCCAATAATTTAG 3 119 0 CAACCTCCCC 0.905251 -161 CACTGGCGATCGCCTCCCACCTCCCAGCAAATACCC 3 136 0 CCCCCCTCCA 0.921864 -144 AACTCGACTTCAAAAGCTTCCCCTCCCCCCAGGATC 4 70 0 CAGCTCCCCC 0.96514 -231 CAGCCAATAACTAAACCTAACCTCCAATTGAGTACT 4 202 0 CACCTCCTCA 0.884515 -99 GCGCTTAAATCCCCGCCCATTTTACCGGAGATACCA 4 236 0 CCCCCTTTCC 0.904842 -65 GCCCTTTCTTCTCCCCCTCTGCTTCCCTAGCCC 5 8 0 CCCCTGCTCC 0.934287 -178 AGCAAAGGCCGGTCTGCTTATTCTGTCC 7 64 0 CAGCCTCTCT 0.810903 -18 TGAAATTTGCCGGCTGCCATTTCGCCCCTGGTTTAT 8 43 1 CCGCCTTCCC 0.943685 -242 AGCCATCTTGCCAAAGCTCATCGTCCTAAAGTTAGA 8 137 1 CAGCTTCGCC 0.742889 -148 GTTAGACATTCCCCCCCTGCCCCTCAATGGAGAGCA 8 167 1 CCCCTCCCCA 0.935547 -118 GATCGCCGTCCGGAAACCCACTTTCACAGAATTCTA 8 208 0 CAACCCTTCA 0.4638 -77 TTAAATTTTTCTGACGCCACGCCCCAAACCGTTTGT 9 28 1 CAGCCGCCCA 0.966384 -109 TTGTCGGTAACTTATCCTGTTCCCCTGCATAAAATA 9 60 1 CACCTTCCCT 0.89474 -77 TGAGTGACATCCTAGCCTAATTTCCCAGACTTTAAG 10 63 1 CACCTTTTCC 0.87527 -166 TCGCTACGACCACCACCCCATTCTCCATTCATTTTC 10 172 1 CCCCCTTCCC 0.959594 -57 TTCCCCTTTGCTCAAGCCTGGCCACAAAAAGTCAAC 11 148 0 CAGCCGCCCA 0.966384 -80 * * *** *** ** Masking position 7 Map Score: 18.7031 Number of sites scoring better than the average of aligned sites = 3045 Number in coding regions = 2841 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 4 GGCTTGAAATGGGCGATAGCAATGTTTCCC 2 51 1 GGGCGATAGC 0.991504 -250 GGGAGGTGGGAGGCGATCGCCAGTGGCTGA 3 147 1 AGGCGATCGC 0.995195 -133 AGAAGGCGATCGCCGGTGGCCAT 6 208 0 AGGCGATCGC 0.995195 -13 AACTCCATCTAGGCGATCGCCGTCCGGAAA 8 228 0 AGGCGATCGC 0.995195 -57 AAGGGAGATCACTGCTATTAAA 9 3 1 GGGAGATCAC 0.937933 -134 AGTCTAGACAGGGCGATCGCCGAGGGAAAA 10 203 0 GGGCGATCGC 0.997663 -26 AGTCAACTTAGGGAGATAGAACCTAAGTTT 11 125 0 GGGAGATAGA 0.805045 -103 ********** Masking position 6 Map Score: 15.6102 Number of sites scoring better than the average of aligned sites = 5982 Number in coding regions = 5447 Number in noncoding regions = 535 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 5 CCGGAGGAACTTTGGCGGGTAGCCTGCA 1 8 0 TTTGCGGGTA 0.837829 -293 AAAGACTAGTATTTACTGGGACCTGGGTTTA 1 156 0 ATTTCTGGGA 0.942251 -145 GGGGAAGGGTATTTGCTGGGAGGTGGGAGGC 3 130 1 ATTTCTGGGA 0.942251 -150 ACGCAATAGAATTGGCTGGCTTGTCAGAAAA 4 13 0 ATTGCTGGCT 0.929131 -288 GCCATTAATTTTTCTCTGGGAACCGCCAACA 4 135 0 TTTCCTGGGA 0.837525 -166 AGGTTTAGTTATTGGCTGGTATCTCCGGTAA 4 220 1 ATTGCTGGTA 0.948209 -81 CTCCGGTAAAATGGGCGGGGATTTAAGCGCA 4 242 1 ATGGCGGGGA 0.958469 -59 CCCCTGGTTTATTGGCGGGGTCAAACCAGAG 8 67 1 ATTGCGGGGT 0.985452 -218 ATTGCTTAGCATTGTCGGAGAAGTGTTAATC 8 102 0 ATTGCGGAGA 0.948753 -183 TCTGCTCTCCATTGAGGGGCAGGGGGGGAAT 8 174 0 ATTGGGGGCA 0.792514 -111 ATGAACTAATATTGCCGGAGAGAGAACCATC 9 114 1 ATTGCGGAGA 0.948752 -23 TTAAGACCAAATTGACTGGATTTTTCTCCAT 10 94 1 ATTGCTGGAT 0.827778 -135 TTATACGCATATTCTCTGGGTGCGACAACCA 11 63 1 ATTCCTGGGT 0.92116 -165 **** ****** Masking position 2 Map Score: 11.4994 Number of sites scoring better than the average of aligned sites = 929 Number in coding regions = 845 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 GGTGGCCATGGGCAAGAAAAAGAGCGACAA 2 164 0 GGCAAGAAAA 0.624289 -137 GCCCAACTCTGGGGAGCAAAGAGAGTTTTT 3 41 0 GGGGAGCAAA 0.846341 -239 TAGTGGATTGGGGACGCAGATTAGAAACTT 3 176 0 GGGACGCAGA 0.92954 -104 CACTACACTGGGGAAGCTTGTGGAATCCAT 3 201 1 GGGAAGCTTG 0.931338 -79 GGGACAAGTTGGGACAATTATTGAGATCCT 4 46 1 GGGACAATTA 0.422424 -255 CTGGGGGGAGGGGAAGCTTTTGAAGTCGAG 4 74 1 GGGAAGCTTT 0.677252 -227 GGGCTAGGGAAGCAGAGGGGGAGAAG 5 7 1 GGGAAGCAGA 0.97317 -179 GGAAGCAGAGGGGGAGAAGAAAGGGCAATG 5 18 1 GGGGAGAAGA 0.93256 -168 AAAGGGCAATGGGACGATAAAGCAAATTAC 5 37 1 GGGACGATAA 0.694787 -149 ACTAGAGTTAGGGAAGCTGAAGAGTAGTCC 6 54 0 GGGAAGCTGA 0.980827 -167 ATGCCCGCCGGGCAAGCTTGCATTTTGCAA 6 92 0 GGCAAGCTTG 0.835498 -129 ATAAACCAGGGGCGAAATGGCAGCCGGCAA 8 49 0 GGCGAAATGG 0.522679 -236 TCAAACCAGAGGAAAGATTAACACTTCTCC 8 87 1 GGAAAGATTA 0.559543 -198 GATGAGCTTTGGCAAGATGGCTGGGAATTG 8 129 0 GGCAAGATGG 0.888249 -156 GCCCCTCAATGGAGAGCAGATAATAGAATT 8 185 1 GGAGAGCAGA 0.759435 -100 ATTTTATGCAGGGGAACAGGATAAGTTACC 9 65 0 GGGGAACAGG 0.789087 -72 CGATCGCCGAGGGAAAATGAATGGAGAATG 10 190 0 GGGAAAATGA 0.850259 -39 ********** Masking position 2 Map Score: 12.4434 Number of sites scoring better than the average of aligned sites = 2241 Number in coding regions = 1947 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 7 ACGATACCGCCATTAGGAAATATATCACCCCTACCG 1 36 0 CATAGAATAC 0.593582 -265 CTTAACAATTCAACGGGAAACATTGCTATCGCCCAT 2 59 0 CAAGGAACAC 0.946366 -242 GAGAGATTAACAAGGGATTAAAAAACTGTCAGGCTT 2 102 1 CAAGGTAAAC 0.95034 -199 GAGAACCGCACAAAAGACAAAATATTGCCGGTGGCC 2 187 0 CAAAGAAAAT 0.738293 -114 CCTAAAGTTTCCTCGGTTAAAAGGTCGGTAATCCGG 2 225 0 CCTGGAAAAC 0.919154 -76 CAAACTTCGACATTGGCCAAACTCCCTACAAAGTGC 4 270 0 CATGGAAACC 0.85105 -31 CGCACCTTTTCAAGGGTGAAAAAGACACAGATAGAT 5 154 0 CAAGGAAAAC 0.98944 -32 AAATCTATGGCAAGGGCAAAAACAATCGTTTAAGAT 6 13 1 CAAGGAAAAT 0.960458 -208 CGCCGGTGGCCATTGGGGTAAAATTCCACCGGTCTG 6 185 0 CATGGTAAAC 0.888888 -36 CGCCAATAAACCAGGGGCGAAATGGCAGCCGGCAAA 8 48 0 CCAGGGAAAC 0.823596 -237 AGTTCATGGTCAACGGTGAATATTCTATTTTATGCA 9 85 0 CAAGGAATAT 0.886338 -52 CTAGGAACAATAATGGAGAAAAATCCAGTCAATTTG 10 101 0 TAAGGAAAAC 0.850823 -128 CAGGCTTGAGCAAAGGGGAATAAACCATCGACAATG 11 164 1 CAAGGAATAC 0.967826 -64 AAACCATCGACAATGGACAGAAGCATAGATTCGCTA 11 185 1 CAAGGAGAAT 0.779889 -43 *** ** **** * Masking position 6 Map Score: 9.16922 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 843 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 8 ATAGGCTCGTTTTGACCTACTTTGATTTGG 2 7 0 TTTCACTTTG 0.989985 -294 TAACTCCGATTTTGCCCAACTCTGGGGAGCAAAG 3 50 0 TTTCACTCTG 0.958499 -230 AATCTAGACGTTTTCTTCACTTTATGTACCCTTT 3 83 1 TTTTACTTTA 0.793087 -197 ATAAGTAAATTTAAACGGGCTTTGGGAATGGATT 3 224 0 TTACGCTTTG 0.892436 -56 GGGCGGGGATTTAAGCGCACTTTGTAGGGAGTTT 4 254 1 TTACACTTTG 0.968967 -47 CTATTTAGACGTTGGCATACTTTGAAGAGGTAAA 5 104 0 GTTCACTTTG 0.958499 -82 TATCAACGAATTTCACTAACTTTGCACGACTGGG 6 143 1 TTTCACTTTG 0.989985 -78 CCTAGCCTAATTTCCCAGACTTTAAGACCAAATT 10 73 1 TTTCACTTTA 0.951136 -156 TTGTCGATGGTTTATTCCCCTTTGCTCAAGCCTG 11 164 0 TTTTCCTTTG 0.837927 -64 *** * ****** Masking position 11 Map Score: 3.80104 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 181 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 CTTCCTAAAGCGATTTGTCCA 1 290 1 CGATTTGTCC 0.953166 -11 TTAATAGGCTCGTTTTGACCTACTTTGATT 2 14 0 CGTTTTGACC 0.878578 -287 AGATTAACTCCGATTTTGCCCAACTCTGGG 3 58 0 CGATTTTGCC 0.982393 -222 ATAATTGTCCCAACTTGTCCCTGACGCAAT 4 37 0 CAACTTGTCC 0.632782 -264 CTTTTGAAGTCGAGTTTGCCGACGGAGATG 4 90 1 CGAGTTTGCC 0.928758 -211 AAATCCCCGCCCATTTTACCGGAGATACCA 4 236 0 CCATTTTACC 0.847793 -65 CAATCGCTACCGATTTTACCTCTTCAAAGT 5 90 1 CGATTTTACC 0.948151 -96 CTTAAACGATTGTTTTTGCCCTTGCCATAG 6 17 0 TGTTTTTGCC 0.521723 -204 TAACTTTGCACGACTGGGCCCTAACCCAGA 6 159 1 CGACTGGGCC 0.878124 -62 TTGCCGGCTGCCATTTCGCCCCTGGTTTAT 8 49 1 CCATTTCGCC 0.861385 -236 AAAATCCAGTCAATTTGGTCTTAAAGTCTG 10 88 0 CAATTTGGTC 0.57993 -141 ********** Masking position 5 Map Score: 2.72669 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 814 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 10 ATCTAAACCCAGGTCCCAGTAAATACTAGTCT 1 153 1 AGTCCCAGAA 0.96484 -148 ATTGTTAAGTAGCTCCGAGAGATTAACAAGGG 2 86 1 AGTCCGAGGA 0.985526 -215 ATCGCCTCCCACCTCCCAGCAAATACCCTTCC 3 132 0 ACTCCCAGAA 0.799488 -148 CCATGTTGGCGGTTCCCAGAGAAAAATTAATG 4 132 1 GGTCCCAGGA 0.963923 -169 ATTTTACCGGAGATACCAGCCAATAACTAAAC 4 222 0 AGTACCAGCA 0.914445 -79 CAATCGTTTAAGATCCGACGGACTACTCTTCA 6 35 1 AGTCCGACGA 0.898137 -186 AATGCTAAGCAATTCCCAGCCATCTTGCCAAA 8 120 1 AATCCCAGCA 0.858385 -165 TTTTCAGACAAGCTCTGAGTGACATCCTAGCC 10 48 1 AGTCTGAGGA 0.856094 -181 TTTTGGTTGTCGCACCCAGAGAATATGCGTAT 11 65 0 CGACCCAGGA 0.873717 -163 AGCATAGATTCGCTACGAGACAGGAGAGAACA 11 206 1 CGTACGAGCA 0.779565 -22 ** ****** ** Masking position 8 Map Score: 2.27358 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 225 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 TATCACCCCTACCGGAGGAACTTTGGCGGG 1 20 0 ACCGGAGGAA 0.984133 -281 CCGGTGGAGAACCGCACAAAAGACAAAATA 2 199 0 ACCGCACAAA 0.68072 -102 CGCCCATTTTACCGGAGATACCAGCCAATA 4 229 0 ACCGGAGATA 0.936071 -72 CCTAACCCAGACCGGTGGAATTTTACCCCA 6 178 1 ACCGGTGGAA 0.907212 -43 TACAACACTTACAGGACAGAATAAGCAGAC 7 51 1 ACAGGACAGA 0.820886 -31 GCGGGGTCAAACCAGAGGAAAGATTAACAC 8 81 1 ACCAGAGGAA 0.924317 -204 AACTAATATTGCCGGAGAGAGAACCATCCC 9 117 1 GCCGGAGAGA 0.973925 -20 TTTGTCGCGGGCCAGAGGGAGTTTTCAGAC 10 27 1 GCCAGAGGGA 0.904479 -202 TCGCTACGAGACAGGAGAGAACA 11 215 1 ACAGGAGAGA 0.937682 -13 ********** Masking position 10 Map Score: 4.86542 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 524 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 TCGCCCATTTCAAGCCCACCCGCTTAATAGG 2 36 0 CAAGCCACCC 0.972251 -265 CGCCGCCAACCAAGCCTGACAGTTTTTTAAT 2 118 0 CAAGCCGACA 0.970006 -183 CTTTTTCTGACAAGCCAGCCAATTCTATTGC 4 11 1 CAAGCCGCCA 0.972251 -290 CAACATGGCATAAGCCTGACCATCTCCGTCG 4 109 0 TAAGCCGACC 0.985641 -192 AGCCAATAACTAAACCTAACCTCCAATTGAG 4 206 0 TAAACCAACC 0.655024 -95 TTGCAAAATGCAAGCTTGCCCGGCGGGCATG 6 92 1 CAAGCTGCCC 0.956124 -129 GACTGGGCCCTAACCCAGACCGGTGGAATTT 6 170 1 TAACCCGACC 0.968209 -51 TCCTCTGGTTTGACCCCGCCAATAAACCAGG 8 69 0 TGACCCGCCA 0.630243 -216 CCTGACCTGACAACCTGAACCTAGGAACAAT 10 126 0 CAACCTAACC 0.688521 -103 TATCACCATCTTAGCCTGACCTGACAACCTG 10 140 0 TTAGCCGACC 0.90618 -89 CCCCTTTGCTCAAGCCTGGCCACAAAAAGTC 11 151 0 CAAGCCGGCC 0.975712 -77 ****** **** Masking position 3 Map Score: 9.6734 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 530 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 13 CGGTATCGTTTTTTGGGCTAGTTAATAAAT 1 63 1 TTTTGGGCTA 0.914267 -238 ACTTACATCATTTAGGTCAACTGAAGTAAA 1 188 0 TTTAGGTCAA 0.905789 -113 CCGAGGAAACTTTAGGGTAAAGTGAGAGCC 2 245 1 TTTAGGGTAA 0.926744 -56 CCCCCAATAATTTAGGGAAAGGGTACATAA 3 104 0 TTTAGGGAAA 0.926479 -176 ATTTTTGGCTTTTTGGGCAACTGTGTA 8 8 0 TTTTGGGCAA 0.972284 -277 ********** Masking position 3 Map Score: 0.054818 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 165 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 ********** No masking Map Score: -1.49681e-12 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: -1.49681e-12 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