AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_synecho_ctra_300.orf -o250_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 RCY09804 120 Synechocystis #2 RCY32573 300 Synechocystis #3 RCY06805 249 Synechocystis #4 RCY30145 114 Synechocystis #5 RCY33828 162 Synechocystis #6 RCY50530 178 Synechocystis #7 RCY34375 180 Synechocystis #8 RCY13890 300 Synechocystis #9 RCY29867 300 Synechocystis #10 RCY07516 147 Synechocystis #11 RCY07197 190 Synechocystis #12 RCY48903 300 Synechocystis #13 RCY14422 284 Synechocystis #14 RCY11010 269 Synechocystis #15 RCY50049 71 Synechocystis #16 RCY41758 300 Synechocystis #17 RCY40119 90 Synechocystis #18 RCY41993 184 Synechocystis #19 RCT00257 300 Chlamydia_trachomatis #20 RCT00260 277 Chlamydia_trachomatis #21 RCT00725 300 Chlamydia_trachomatis #22 RCT00726 208 Chlamydia_trachomatis #23 RCT00795 132 Chlamydia_trachomatis #24 RCT00796 300 Chlamydia_trachomatis Motif number 1 TATTTTTACCCTCCACTCCAGCCATTCTC 3 4 1 TTTTCCTCCC 0.947332 -246 GAATCTGAGCTTTTTCCCTCTATCACGGGAGAATGG 3 32 0 TTTTCCTCTC 0.960038 -218 CTGTGGTTGCTTTTGCGCCCTAAGAATTTGCTCATT 3 197 1 TTTTCCCCTA 0.94608 -53 AATTTGCTCATTTTGCTCCCCTAATACTTCCCCCCT 3 221 1 TTTTCCCCCA 0.92927 -29 TTGCACCAGCTTTTCCCCGTTACCTCCACTGGCTGT 8 69 1 TTTTCCGTTC 0.862766 -232 CTAGCATGGATTTTCCTCCCTTTTTCCACAGGGGCC 8 140 1 TTTTCCCCTC 0.974718 -161 AGTAAAATTTTTTGTCCCCCTACAGCTAAGGCTACC 8 182 0 TTTGCCCCTC 0.945101 -119 GGACAAAAAATTTTACTCCCGGCAACCTTGTCACGA 8 201 1 TTTTCCCCGC 0.94664 -100 CTCCGCCATATTTTTCACTCCTATTCTTTCCCATGA 9 162 1 TTTTCCTCCC 0.947332 -139 GTATTAACGGTTTTTCGCGTTTTTCCATTGACAGGC 12 60 0 TTTTCCGTTC 0.862766 -241 GGAAATTGTCTTTGTCGCACTTCTCCACTGAATTTA 13 188 0 TTTGCCACTC 0.772204 -97 GGTGGGAATCTTTTTCCCTTTCTCTCCGTCGCTGTT 14 115 1 TTTTCCTTTC 0.898269 -155 CGAGCCAAATTTTTTCTCTTTTTATAATCCTCTTCA 16 71 0 TTTTCCTTTA 0.800755 -230 TTGGATGGAATTTTCCCCACGAGCCAAATTTTTTCT 16 90 0 TTTTCCACGA 0.613922 -211 CAACAGCGGCTTTTCCGCCTGGGATCTCTACTTTGG 16 135 0 TTTTCCCTGC 0.867037 -166 GGACTAAAGTTTTGTCACGTCCCTGACGAAATTCTT 16 254 1 TTTGCCGTCA 0.488923 -47 GAACTCGTCTTTTTACTCTTTCACAAAAAAAGTAAC 19 148 0 TTTTCCTTTA 0.800755 -153 CATACTTGACTTTTTCCCTCCCCCGATTATGATTGA 20 37 0 TTTTCCTCCA 0.89115 -241 TTCCTTCCATTTTGGCGCCCTAAGAAAGGAGGAAAG 24 220 1 TTTGCCCCTA 0.886817 -81 **** * **** * Masking position 3 Map Score: 18.8894 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 539 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 2 GAGCCATGGACTCCTCCCACCCAAAACTAAATT 1 18 1 CTCCCCACCA 0.931677 -103 TATTTTTACCCTCCACTCCAGCCATTCTCCCGT 3 11 1 CTCCTCCGCC 0.895597 -239 ACAGAGATCCCCTCGCCCAAGCACAAATCCCAG 3 115 0 CCTCCCAGCA 0.916685 -135 TCCCCTAATACTTCCCCCCTGCA 3 237 1 CTTCCCCGCA 0.975964 -13 ATCAAGGACTCTAAGCACCGCCCTAGGGTTTAT 4 49 0 CTACACCCCC 0.704487 -66 CTCCACGGAACTTATCCCCGGCAAAGTAATTCA 5 101 0 CTTCCCCGCA 0.975964 -62 CCATGTCCCCCTTGCCCCCTGCCGTTGGCCTGA 6 22 0 CTTCCCCGCC 0.96628 -157 GCCAACTAACCAAAACCCCCCCAGGGATAAAGC 7 58 0 CAACCCCCCA 0.828343 -123 CCAGCTTTTCCCCGTTACCTCCACTGGCTGTTA 8 74 1 CCCTACCCCA 0.528321 -227 AAACTTAGTCCCCAACCCTAGCATGGATTTTCC 8 123 1 CCCCCCTGCA 0.885014 -178 TGAGCAGTTGCCCATTCCCACCATTGGCATTGG 13 32 1 CCCTCCCCCA 0.886808 -253 AACAACCGCCCTTTGCTCCGGCCTATCTGAATT 13 127 1 CTTCTCCGCC 0.842139 -158 TAGTTTGTTCCCTAACCCCGCCGGGGAAATTGT 13 215 0 CCTCCCCCCG 0.855642 -70 AACAGGCTGCCCAGGCTCCAGCAATGACCATAA 13 258 1 CCACTCCGCA 0.850892 -27 AGCAAAAACTCTACCCCCAGGCATAGACAAAAC 14 166 0 CTACCCAGCA 0.856127 -104 AGCAACGCTCCTCACAAGCCATAAATGTTA 14 250 0 CTCCACAGCC 0.601747 -20 ACGGAGGAATCCTGACCCACCCAAAGATGGTTA 18 55 0 CCTCCCACCA 0.909251 -130 ATCAAAATGTCCAATCCCCCGCATAACGGAGGA 18 80 0 CCACCCCGCA 0.968408 -105 CCATACTTGACTTTTTCCCTCCCCCGATTATGA 20 41 0 CTTTCCCCCC 0.744272 -237 GCTTTACGTTCTCCCCTCTACCATACTTGACTT 20 61 0 CTCCTCTCCA 0.524793 -217 TTAGAAGATGCACTCCCCCGCCATCTCCTAAAA 21 218 0 CACCCCCCCA 0.923917 -83 *** **** *** Masking position 8 Map Score: 22.6005 Number of sites scoring better than the average of aligned sites = 2154 Number in coding regions = 1982 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 GGACGATAGACCGCTGGGATTTGTGCTTGGGCGAGG 3 102 1 CCCTGGGTTC 0.988081 -148 GCAAAAGCAACCACAGGGAGAGCAACGCTTCCGAAG 3 177 0 CCCAGGGGGC 0.983006 -73 AGAAAATAAACCCTAGGGCGGTGCTTAGAGTCCTTG 4 44 1 CCTAGGGGTT 0.598033 -71 ACCAAAACCCCCCCAGGGATAAAGCCGGGATATTTC 7 47 0 CCCAGGGTAC 0.820649 -134 AAAGGGAACGCCCCTGGCATCGATGTCGCACCATTT 7 111 0 CCCTGGCTGT 0.893032 -70 CCCGTTACCTCCACTGGCTGTTACCCAATGGAACCA 8 84 1 CCCTGGCGTC 0.98191 -217 CTCCCTTTTTCCACAGGGGCCTGTGCAGGTAGCCTT 8 155 1 CCCAGGGCTC 0.871 -146 GATGCAAGCACCCATGGGAGGTGATCTAGATCACAG 9 74 1 CCATGGGGTC 0.893585 -227 TAAGGTTTTGCCACTGGGGTTTTTCCAACTGGGAAG 11 147 0 CCCTGGGTTC 0.988081 -44 TTTTCTGGTTACTCTGGGGGAGGAACTTTCGTGGTT 12 193 0 ACCTGGGGGC 0.897252 -108 CCCATTCCCACCATTGGCATTGGGGCAGGGCCCCAG 13 42 1 CCTTGGCTGC 0.927609 -243 TTTACCGTGGCCTCTGGGTTTTGTCTATGCCTGGGG 14 149 1 CCCTGGGTTT 0.927277 -121 GCGGCTTTTCCGCCTGGGATCTCTACTTTGGAGGCT 16 130 0 CGCTGGGTTC 0.866571 -171 AATACCCCACCCGCTGGCGGAGTAACAAATCAAAAT 18 105 0 CCCTGGCGGC 0.987118 -80 CTTTTTGAAGCCCTTGTGTGCGTGTCTTAGGGATCT 19 272 1 CCTTGTGGGC 0.673362 -29 AACAGATCCCTTGGCTTCGTGCCGAATACCAAC 21 278 0 CCTTGGCTGC 0.927609 -23 ** ***** * * * Masking position 6 Map Score: 16.2277 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 971 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 TCCCAGCGGTCTATCGTCCCTACACTAGGCA 3 90 0 CTACGTCCCT 0.849735 -160 TGGTTATTAGCTCACGTCCCTTAAGCGGC 5 9 0 CTCCGTCCCT 0.94604 -154 TAATTGCCTTGGTGCGTCCCACTGTTATCTA 6 58 0 GGTCGTCCCA 0.844916 -121 GGCAATCCCCTGAAAAATTAA 6 168 0 GGCATCCCCT 0.870919 -11 GGGCAAAAAGGGAACGCCCCTGGCATCGATG 7 122 0 GGACGCCCCT 0.96624 -59 CGGTTAAGACGGCGATCGCCTAGGATAGAAG 8 268 1 GGCATCGCCT 0.528356 -33 CAAAATCTTCGTCCCTTCCCAGTTGGAAAAA 11 133 1 GTCCTTCCCA 0.867666 -58 CATAGTAACACGTTCTCCCCTCGGCTGGGGA 12 136 1 CGTCTCCCCT 0.88802 -165 TTGCTTAGACGGCTCGTGCCTATAGCTTATA 12 240 1 GGCCGTGCCT 0.931419 -61 CTAAAGTTTTGTCACGTCCCTGACGAAATTC 16 257 1 GTCCGTCCCT 0.97177 -44 CTTTGCTTTACGTTCTCCCCTCTACCATACT 20 67 0 CGTCTCCCCT 0.88802 -211 ATTTCTTATAGGAGCTTCCCATAATAAAACG 22 116 1 GGACTTCCCA 0.834033 -93 CTTGGACGGAGTCGCTTCCCTTACTCTGTCA 23 56 0 GTCCTTCCCT 0.960606 -77 TTGGGCTTGTGTCGCTTCCCTTGAACAGTCA 23 92 1 GTCCTTCCCT 0.960606 -41 AAAAAACTCTCGATCGCCCCTGGTAAACAGG 24 147 1 CGACGCCCCT 0.935803 -154 *** ******* Masking position 9 Map Score: 14.3058 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 487 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 TCATCCTATTCACCCGAAAGCGACTAGGCGCATG 5 38 0 CCAAAGCGAC 0.973424 -125 GGCGGTGATCCCCCTCAAAGCTAAAATGGTGCGA 7 88 1 CCAAAGCTAA 0.72603 -93 AATTTTTTGTCCCCCTACAGCTAAGGCTACCTGC 8 179 0 CCACAGCTAA 0.891494 -122 ACGGGGCGACCCATTGACAGCGACACCAACATTC 10 33 0 CTACAGCGAC 0.986102 -115 CCAGAGGCCACGGTAAACAGCGACGGAGAGAAAG 14 132 0 CTACAGCGAC 0.986102 -138 TTTGCCCAGACCATGAAAAGCGAACTGGGGCAGA 16 36 1 CTAAAGCGAA 0.834762 -265 TATTGACCTCCACTCAACAGCGGCTTTTCCGCCT 16 151 0 CTACAGCGGC 0.924129 -150 GCTGCACACTCATCCCAAAGCAACAGACCTCAAC 19 16 0 CCAAAGCAAC 0.923104 -285 CTTCAATACACCTCAAACAGCAACTTATTACATC 20 113 0 CCACAGCAAC 0.973835 -165 ACTAAACATGCGATACACTGCAACCTTCTGCTTT 20 160 1 CTACTGCAAC 0.838972 -118 TTAAAAAGAGCATCTTACAGCGACTTGAAAGTTA 22 48 0 CCACAGCGAC 0.991271 -161 CTCCGCTCTAGACTGCTACATGGTACCTA 24 6 1 CTACTGCTAC 0.838972 -295 * * ******** Masking position 7 Map Score: 11.2688 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 93 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 CCAATTCATCTCCCTTTACCAAGCATATTTCCCGTCA 1 60 1 TCCTTTCCAA 0.97066 -61 CTCCACTCCAGCCATTCTCCCGTGATAGAGGGAAAAA 3 21 1 GCCTTCCGAA 0.841115 -229 GGGTATTGAAGCCTTTTTACGACGACAGAGATCCCCT 3 135 0 GCCTTTCGAA 0.971068 -115 TAAGCTTAGATCGGTTTATCTCGCATAGCCTATCACA 6 134 0 TCGTTTCCAA 0.959818 -45 ACACCAACATTCCCTTTGGTCAGGATAGTTTAAC 10 8 0 TCCTTTTGAA 0.580048 -140 CGATCGCCAATCCGTTTATCTTTCATAGAAGCCGGGA 10 93 1 TCCTTTCCAA 0.970668 -55 CCTTTGGCTGTCGATTTTGCTGACAGATTTAAATATC 11 18 0 TCGTTTCCAA 0.959818 -173 TTGATCAATGACGTTTTCTCCATCAGACTAGCATCAA 11 64 0 ACGTTTCCAA 0.83219 -127 ACGGTTTTTCGCGTTTTTCCATTGACAGGCATTTCTC 12 53 0 GCGTTTCGAA 0.960361 -248 GCGGATTTACTCGGTTTGACAGTCAAACAACCGCCCT 13 102 1 TCGTTTCCAA 0.959818 -183 AAAGCTAAAAGCCATTTTCCTCGCAAAACGTCCCCCC 16 204 1 GCCTTTCCAA 0.98147 -97 TCTTGTCTTTGCTCTTTCTCTGACAGATGACGTAGTT 19 184 1 GCTTTTCCAA 0.855379 -117 ACTACAATAAGCCGCTTAGCTGCGAAAGTACAGCTTT 20 214 0 GCCCTTCGAA 0.841115 -64 *** *** * ** * Masking position 15 Map Score: 11.0634 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 51 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TTTGCACTAGCAAAACTGTCCATCTCGAACC 2 122 1 CAAACTGTCC 0.898733 -179 CTCAAAGACCCAATTCTGTCCCATTGCCGTT 2 228 1 CAATCTGTCC 0.911358 -73 GGTGCAAAGCCAATACTGTCCCGCAACTGTG 8 45 0 CAATCTGTCC 0.911358 -256 TTTTTCACTCCTATTCTTTCCCATGAACTCC 9 172 1 CTATCTTTCC 0.948429 -129 CCCATGAACTCCAAACTTTCCCTATTTGACA 9 191 1 CCAACTTTCC 0.968934 -110 TTGTCTGTTACCAATCTTTCCGAGGATATAC 9 248 1 CCAACTTTCC 0.968934 -53 AGCAATGGTACCATTCTTTTCTGGTTACTCT 12 214 0 CCATCTTTTC 0.740057 -87 ATAGCTTATACCAACCTTTACCTAACTCAAA 12 261 1 CCAACTTTAC 0.812506 -40 AATTTTCGAGCTTAGCTTTCC 12 290 1 CTTACTTTCC 0.880228 -11 AATCTTTTTCCCTTTCTCTCCGTCGCTGTTT 14 121 1 CCTTCTCTCC 0.777205 -149 CATTAGTCTTCAAACCTTTCCAGC 18 4 0 CAAACTTTCC 0.94074 -181 CCTTAAAAACCTTTGCTTTACGTTCTCCCCT 20 77 0 CTTTCTTTAC 0.541899 -201 AAAAGATTCTCTTTTCTTTCCTCTACTAGCA 21 190 0 CTTTCTTTCC 0.89489 -111 **** ****** Masking position 7 Map Score: 10.3936 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 368 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 CGTCAGGAAAGGCACAGACAAAAAACCCAACAA 1 92 1 GGCAAGCAAA 0.992081 -29 GGGGGACATGGGCATAGATAACAGTGGGACGCA 6 44 1 GGCAAGTAAA 0.924711 -135 GAAAAGCTGGTGCAAAGCCAATACTGTCCCGCA 8 51 0 TGCAAGCAAA 0.93329 -250 GGAAAGATTGGTAACAGACAATAGACAACTTTC 9 236 0 GTAAAGCAAA 0.73368 -65 TTTTGCGTTGGCCATAGTCAAAAAATTAGTTCA 11 105 0 GCCAAGCAAA 0.953992 -86 TCTACCCCCAGGCATAGACAAAACCCAGAGGCC 14 157 0 GGCAAGCAAA 0.992081 -113 AGGCCGTCGTGGCAACGGCAAAATTGAAACAGT 17 30 0 GGCACGCAAA 0.966966 -61 TCAGAGAAAGAGCAAAGACAAGAGAACTCGTCT 19 174 0 AGCAAGCAAA 0.93329 -127 GATGTTATGAGGAAAAGTCAATAACAGTGTGCA 21 33 1 GGAAAGCAAA 0.961044 -268 **** ** *** * Masking position 4 Map Score: 7.72568 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 119 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 CCCTGTTGTTGGGTTTTTTGTCTGTGCCTTTCC 1 97 0 GGGTTTGTCT 0.959756 -24 AAGGTGCGGTGGGTGAATTGTCTTCACTTTAAC 2 256 0 GGGATTGTCT 0.965917 -45 CACCGCCCTAGGGTTTATTTTCTTAACTAATCT 4 34 0 GGGATTTTCT 0.968055 -81 GCACAAAAAGGGGAATTTTTTCTGTAACTGACA 6 90 1 GGGTTTTTCT 0.962265 -89 TTATCCCTGGGGGGGTTTTGGTTAGTTGGCGGT 7 61 1 GGGTTTGGTT 0.702498 -120 TAACCCCGCCGGGGAAATTGTCTTTGTCGCACT 13 203 0 GGGATTGTCT 0.965916 -82 CTATGCCTGGGGGTAGAGTTTTTGCTATGATGT 14 173 1 GGGAGTTTTT 0.750028 -97 CCAGCGGGTGGGGTATTTTTTTTGTGGGCTTAT 18 124 1 GGGTTTTTTT 0.930593 -61 GTCAATAACAGTGTGCATTTTCTGGGATCTTTT 21 49 1 GTGATTTTCT 0.704816 -252 TGCATTTTCTGGGATCTTTTTTTTGTAAGCAGG 21 62 1 GGGTTTTTTT 0.930593 -239 AAAAGCTTCAGGAAAAATTTTTTCTTCATCCTG 21 91 0 GGAATTTTTT 0.556608 -210 *** ******* Masking position 9 Map Score: 5.90643 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 287 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 10 GATTCATCCATCTGGGCTAAAGAAT 2 6 0 TCTGGGCTAA 0.788029 -295 CGGGATCGTTTGGGGACGTAG 5 152 1 TGGGGACGTA 0.840044 -11 TATTGAAAGTTGGGGGCAAAAAGGGAACGC 7 136 0 TGGGGGCAAA 0.975606 -45 ATGCTAGGGTTGGGGACTAAGTTTAGTTGG 8 117 0 TGGGGACTAA 0.954603 -184 CTTAGCTGTAGGGGGACAAAAAATTTTACT 8 188 1 GGGGGACAAA 0.780675 -113 GACAAAATGATGGGGGGTTAACCGACGGTT 8 243 1 TGGGGGGTTA 0.813366 -58 CATTACTCTATGGGGGCATAGTAACACGTT 12 120 1 TGGGGGCATA 0.964686 -181 CTTTTCATGGTCTGGGCAAATTAAAACCAT 16 26 0 TCTGGGCAAA 0.751084 -275 GTGCGTAAAATGGGGACTAAAGTTTTGTCA 16 241 1 TGGGGACTAA 0.954603 -60 GTATTTTTTTTGTGGGCTTATCAAAGGCTT 18 136 1 TGTGGGCTTA 0.904728 -49 ********** Masking position 10 Map Score: 4.95696 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 629 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 11 TTAATGAATTTTTTTAAAGCTAAAAGCCAT 16 189 1 TTTTTAAAGC 0.791448 -112 GTTACTTTTTTTGTGAAAGAGTAAAAAGAC 19 148 1 TTGTGAAAGA 0.903733 -153 AGTAAACTATTTGAGAAAGCTTTTTGAAGC 19 253 1 TTGAGAAAGC 0.880317 -48 CAAGGGAATTTTTTGAAAGCTGTACTTTCG 20 199 1 TTTTGAAAGC 0.971418 -79 GGGATCTTTTTTTTGTAAGCAGGATGAAGA 21 72 1 TTTTGTAAGC 0.858975 -229 TTAACTTGCCTTTTGAAAGCTTAAGTTTAA 22 78 1 TTTTGAAAGC 0.971418 -131 CTAACGTATGTTGTGAAAGCCTTTTCTATT 22 165 1 TTGTGAAAGC 0.976216 -44 GTCATTATTTTTATGAAAGAGCGGACCTGT 24 173 0 TTATGAAAGA 0.702634 -128 ********** Masking position 7 Map Score: 4.17144 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 GTTTTGGGTGGGAGGAGTCCATGGCTCGAA 1 15 0 GGAGGAGTCC 0.932238 -106 TAGCCCAGATGGATGAATCCAAGAATGGTA 2 17 1 GGATGAATCC 0.738261 -284 AACAGCCAGTGGAGGTAACGGGGAAAAGCT 8 76 0 GGAGGTAACG 0.767776 -225 TTACATTGGAGGAGAAATAGATACAGAAAA 9 42 0 GGAGAAATAG 0.743784 -259 AAAATATGGCGGAGGAAAACTGAGTTAGAA 9 146 0 GGAGGAAAAC 0.868372 -155 CTAGTCTGATGGAGAAAACGTCATTGATCA 11 70 1 GGAGAAAACG 0.902147 -121 CTCAGTTTTTGGAGAAAATC 12 1 0 GGAGAAAATC 0.700372 -300 GGGTGATTTCGGAGAAATGCCTGTCAATGG 12 42 1 GGAGAAATGC 0.927448 -259 TAAATTCAGTGGAGAAGTGCGACAAAGACA 13 188 1 GGAGAAGTGC 0.815867 -97 CCCGCATAACGGAGGAATCCTGACCCACCC 18 66 0 GGAGGAATCC 0.975357 -119 CGGGAGATATCCGAGTGTACGC 21 3 1 GGAGATATCC 0.83762 -298 CCCTAAGAAAGGAGGAAAGGCTGAGCCTTC 24 237 1 GGAGGAAAGG 0.883783 -64 ********** Masking position 3 Map Score: 6.52278 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 461 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 GTTAGGACTACAAAGGTGCGGTGGGTGAATT 2 270 0 CAAAGGTGCG 0.897414 -31 GGATTTACCGGACAGTTGGTGAAGATTAGTT 4 12 1 GACAGTTGGG 0.919765 -103 AAAAACTATTGAAAGTTGGGGGCAAAAAGGG 7 141 0 GAAAGTTGGG 0.952927 -40 CTGGGCCCATCACAGTTGCGGGACAGTATTG 8 35 1 CACAGTTGCG 0.949111 -266 CCTTTCGTGACAAGGTTGCCGGGAGTAAAAT 8 210 0 CAAGGTTGCG 0.975474 -91 TGACCAAAGGGAATGTTGGTGTCGCTGTCAA 10 23 1 GAATGTTGGG 0.860198 -125 AGACTAGCATCAAGGTTGCTGGCCTTTGGCT 11 46 0 CAAGGTTGCG 0.975474 -145 AGCTAAAGCAGAAGGTTGCAGTGTATCGCAT 20 167 0 GAAGGTTGCG 0.975474 -111 ********* * Masking position 2 Map Score: 3.88728 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 49 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 AACTGTGATGGGCCCAGGCCCTAAGTCAGG 8 22 0 GGCCCAGGCC 0.905058 -279 TAAGGCTACCTGCACAGGCCCCTGTGGAAA 8 162 0 TGCACAGGCC 0.950192 -139 TGCCCAGAGCAGGATTAGTA 11 181 0 TGCCCAGAGC 0.830322 -10 GTCACACTGGGGCCCTGCCCCAATGCCAAT 13 54 0 GGCCCTGCCC 0.899517 -231 AACCGCCCTTTGCTCCGGCCTATCTGAATT 13 130 1 TGCTCCGGCC 0.927576 -155 GCCAACAGGCTGCCCAGGCTCCAGCAATGA 13 255 1 TGCCCAGGCT 0.959814 -30 GGTTTTAATTTGCCCAGACCATGAAAAGCG 16 28 1 TGCCCAGACC 0.971108 -273 GATGATTGTAAGCTCAGGCCGTCGTGGCAA 17 48 0 AGCTCAGGCC 0.922117 -43 GTAATACGAAGGCTCAGCCTTTCCTCCTTT 24 244 0 GGCTCAGCCT 0.797167 -57 ********** Masking position 5 Map Score: 5.5468 Number of sites scoring better than the average of aligned sites = 713 Number in coding regions = 673 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 15 GATGTCAATAAATTGGGGATCACTTATTAT 2 68 0 AATTGGGGAT 0.808527 -233 TTACCCTGGGAAGGCGGGATCGTTTGGGGA 5 138 1 AAGGCGGGAT 0.975368 -25 CCCAGGGATAAAGCCGGGATATTTCGGCTC 7 42 0 AAGCCGGGAT 0.975292 -139 CCCAGGCCCTAAGTCAGGATGCCCGCCAA 8 10 0 AAGTCAGGAT 0.826336 -291 TCTTTCATAGAAGCCGGGATTTATCAGCTA 10 111 1 AAGCCGGGAT 0.975292 -37 CCCCCTTTGAAATTCGGGATCTAAGTGTTC 14 85 0 AATTCGGGAT 0.909148 -185 CCGAATTTCAAAGGGGGGGTGGGAATCTTT 14 98 1 AAGGGGGGGT 0.837177 -172 ********** Masking position 2 Map Score: 2.59539 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 72 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234