AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_synecho_reg_300.orf -o064_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 RCY07838 269 Synechocystis #2 RCY50648 180 Synechocystis #3 RCY10954 211 Synechocystis #4 RCY26047 35 Synechocystis #5 RCY44892 192 Synechocystis #6 RCY43438 300 Synechocystis #7 RCY33884 213 Synechocystis #8 RCY28358 232 Synechocystis #9 RCY44461 245 Synechocystis #10 RCY22265 286 Synechocystis #11 RCY39566 239 Synechocystis #12 RCY11341 81 Synechocystis #13 RCY10798 68 Synechocystis #14 RCY31626 279 Synechocystis #15 RCY15876 126 Synechocystis #16 RCY14629 300 Synechocystis #17 RCY18065 158 Synechocystis #18 RCY45983 163 Synechocystis Motif number 1 GAACGGCCAAATTCCCTCCGCTATGTTGGGG 1 166 1 ATTCCCTCCC 0.741886 -104 ATTTTTCCCCTACATCGAAAATT 2 3 1 TTTTCCCCTC 0.924581 -178 ATATTGCCATTTTACCCCCCAACTCAAATTT 2 94 0 TTTACCCCCA 0.624301 -87 CAGATGAGAGCTTCCCCCCACGGCGATCGCC 3 36 0 CTTCCCCCCC 0.990996 -176 GTTCGCCGCCCTTGCCCCCAATCGGAGAGGG 4 11 1 CTTGCCCCCA 0.946349 -25 AAAGGGCATTCTTTCCCCTGTTTTTTCCTAG 5 75 1 CTTTCCCCTT 0.920785 -118 TTGTTTAAAGCTTCTCCCATTACAGACCATA 5 138 0 CTTCTCCCAT 0.677411 -55 AAAGGGATTTATTGCCCCTTTGATCGTAATT 5 167 1 ATTGCCCCTT 0.914206 -26 TAGCCAAATTCTTGCCCCCAAAAAGTAAAAT 6 80 0 CTTGCCCCCA 0.946349 -221 ATTTGGCTACATTTCCCCAGCATCTAACCCA 6 102 1 ATTTCCCCAC 0.976174 -199 TAGCTACGACATTACCCCACTGTGCAGGCTG 6 165 0 ATTACCCCAT 0.816441 -136 AATTGATCCCATTCACCCCCCATCTAGCTAC 6 189 0 ATTCACCCCC 0.767514 -112 CGACAAATACATTTTCCCAGCAACTTAGTTG 7 39 0 ATTTTCCCAC 0.804568 -175 GTGAAGTTCCATTTCCCCATCCAAGTCCCTT 7 73 0 ATTTCCCCAC 0.976174 -141 AGAAAAACGACTTTCCCCCCCCCTAACCAAT 8 84 1 CTTTCCCCCC 0.987336 -149 ACCAATTTTACGTTCCCCTACAGATCCTTTC 8 109 1 CGTTCCCCTC 0.780337 -124 CCATGCCATGATTACCCCACCCAGCTCACCC 8 146 1 ATTACCCCAC 0.942262 -87 TTACTCACTAATTTCCCCTGCC 10 2 0 ATTTCCCCTC 0.969852 -285 GGCTGGTAGTTTTCCCCCTGAATTTGCCTTG 11 171 1 TTTCCCCCTA 0.76313 -69 CTGAATTTGCCTTGCCCCAATCACGATATAC 11 188 1 CTTGCCCCAT 0.947346 -52 TTTTGCCCCACTCCTTGGAAAA 14 2 1 TTTGCCCCAT 0.83797 -278 AATGTTTAAACTTGCCCCTGCCGAAACAAAG 15 101 1 CTTGCCCCTC 0.981073 -26 GAGCAACTGCATTCTCCCCGCCCTGTCCTCT 18 40 0 ATTCTCCCCC 0.892951 -124 GCGGGGCGGAATTCCCCCATCCTTCCTTTGA 18 129 1 ATTCCCCCAC 0.983004 -35 ********* * Masking position 3 Map Score: 34.0026 Number of sites scoring better than the average of aligned sites = 2305 Number in coding regions = 2064 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 2 TTAAATCGCTTGCCGTGGGGGGTGGTCTCTG 1 73 1 TGCGTGGGGG 0.926724 -197 ATTAACTACTCTGGTTTGGGGACGAGCCATG 1 116 1 CTGTTTGGGG 0.979677 -154 ATTCCCTCCGCTATGTTGGGGGCTGAGCCTT 1 176 1 CTTGTTGGGG 0.937582 -94 AGCCAATTTTCGATGTAGGGGAAAAAT 2 7 0 CGTGTAGGGG 0.89373 -174 TGGCTTTAGCCGTTTTGGGGGATGTCAAAGA 2 37 0 CGTTTGGGGG 0.942293 -144 CAGATAAATTTGAGTTGGGGGGTAAAATGGC 2 89 1 TGGTTGGGGG 0.955237 -92 CGCTGGCGATCGCCGTGGGGGGAAGCTCTCA 3 32 1 CGCGTGGGGG 0.978336 -180 AAGAATGCCCTTTGTTTGGGCTATTTTTTAG 5 57 0 TTGTTTGGGC 0.756643 -136 ACAGCGGCAACGGTGTCGGGGTATGGTCTGT 5 117 1 CGTGTCGGGG 0.754605 -76 GAAAATTTTACTTTTTGGGGGCAAGAATTTG 6 76 1 CTTTTGGGGG 0.93194 -225 AATGTCGTAGCTAGATGGGGGGTGAATGGGA 6 183 1 CTGATGGGGG 0.978408 -118 GGCCAAGGGACTTGGATGGGGAAATGGAACT 7 69 1 CTGGATGGGG 0.950688 -145 AAAGATTAAGCTCGAATGGGGCGGTGAAGTT 7 96 0 CTGAATGGGG 0.903823 -118 GAAAGTCGTTTTTCTTTGGGGCTAGACGACA 8 68 0 TTCTTTGGGG 0.846165 -165 GAACGTAAAATTGGTTAGGGGGGGGGAAAGT 8 93 0 TTGTTAGGGG 0.863708 -140 TTTGGGTGAGCTGGGTGGGGTAATCATGGCA 8 149 0 CTGGTGGGGT 0.931025 -84 TTAAGAAATTTGGCTTTGGGTGAGCTGGGTG 8 163 0 TGCTTTGGGT 0.487855 -70 CATCCCAGGGCGAGTAAGGGCGCAGAAGCAC 8 208 0 CGGTAAGGGC 0.630942 -25 CTTACTCGCCCTGGGATGGGCC 8 221 1 CTGGATGGGC 0.816205 -12 GGATCAAGTTCGCCATTGGGCAATTTTGATA 9 73 0 CGCATTGGGC 0.792783 -173 CGTACAATGGCTAGACGGGGGTTAGGTCCGA 9 182 1 CTGACGGGGG 0.893445 -64 AGCGGCCGGCCGAGAAAGGGGCATAATGTGC 10 42 0 CGGAAAGGGG 0.840313 -245 ATTGCGGTCGCTTGATTGGGTCAGTTTACAG 10 150 0 CTGATTGGGT 0.832317 -137 TTGAGTATATCGTGATTGGGGCAAGGCAAAT 11 192 0 CGGATTGGGG 0.976053 -48 CGGAGAAATGTTCCTTGGGGTTGCGGGAAAA 15 58 1 TTCTTGGGGT 0.514328 -69 ACGGCTTTGTTTCGGCAGGGGCAAGTTTAAA 15 105 0 TTGGCAGGGG 0.630373 -22 ** ******** Masking position 8 Map Score: 28.3765 Number of sites scoring better than the average of aligned sites = 3198 Number in coding regions = 2919 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 3 AGAGCTTCCCCCCACGGCGATCGCCAGCGT 3 31 0 CCCACGGCGA 0.753613 -181 ATCTTATTGGCGAACGGCGGGAGTGAAAGA 3 76 0 CGAACGGCGG 0.851818 -136 CCGATTGGGGGCAAGGGCGGCGAAC 4 6 0 GCAAGGGCGG 0.936157 -30 ATAGCCCAAACAAAGGGCATTCTTTCCCCT 5 64 1 CAAAGGGCAT 0.616976 -129 AAGCTTTAAACAAAGGGATTTATTGCCCCT 5 156 1 CAAAGGGATT 0.585907 -37 AATCAGCCTGCACAGTGGGGTAATGTCGTA 6 162 1 CACAGTGGGG 0.592575 -139 GGCCCATCCCAGGGCGAGTAAGGGCGC 8 216 0 CCCAGGGCGA 0.917278 -17 TTGACCGCTCCCCAGGACGGACTAGCAATA 9 147 0 CCCAGGACGG 0.932418 -99 GCCGGCCGCTCAAACGGATGAGTCACTCAG 10 63 1 CAAACGGATG 0.660876 -224 TGGGTCAGTTTACAGGGCTGATCAGATCTG 10 135 0 TACAGGGCTG 0.606418 -152 CAAATACAAACAAAGGGGGGCTTTGCTGTA 11 44 1 CAAAGGGGGG 0.971892 -196 AGCAAAGGCCGGTCTGCTTATT 12 3 1 CAAAGGCCGG 0.911903 -79 GGTAATTTTTCCAAGGAGTGGGGCAAAA 14 9 0 CCAAGGAGTG 0.483157 -271 GATCATCTCCCACAGGGCGGCATTGTACAG 14 54 0 CACAGGGCGG 0.992121 -226 GGATTTGCGGCCAACGGCGGGAATTTGTGA 14 82 0 CCAACGGCGG 0.967637 -198 CCTTTAACCACAAAGGGATTTTCGGGGAAC 14 128 1 CAAAGGGATT 0.585907 -152 GAAACAGCAGCAAAGGGCGTTTTAATCAGA 16 269 0 CAAAGGGCGT 0.963586 -32 AAAGCCAGAGGACAGGGCGGGGAGAATGCA 18 34 1 GACAGGGCGG 0.944544 -130 AGTGGCTCATCAAAGGAAGGATGGGGGAAT 18 139 0 CAAAGGAAGG 0.792707 -25 ********** Masking position 4 Map Score: 16.1259 Number of sites scoring better than the average of aligned sites = 1770 Number in coding regions = 1611 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 CGTTCAACTGTTGTTTAACTGTCCCATGGC 1 141 0 TTGTTTAACT 0.970059 -129 CCCAGGGTAATTATTTAACCACTGTAGCTG 1 208 0 TTATTTAACC 0.758413 -62 AACTTTAATGTTGTTTAAATATTGCCATTT 2 113 0 TTGTTTAAAT 0.718537 -68 AACATTAAAGTTGTTAAACTCGCCCACATC 2 131 1 TTGTTAAACT 0.928085 -50 TGTGGAGGGCTTCTTTCACTCCCGCCGTTC 3 65 1 TTCTTTCACT 0.859184 -147 ACTTTGCTGCTTGTTTAACTCTAATTATTG 3 167 1 TTGTTTAACT 0.970059 -45 ACTCTAATTATTGTTTAACTACTTAGAAAT 3 184 1 TTGTTTAACT 0.970059 -28 AAAGCCAAATTTCTTAAACTAAGTGCCATC 8 177 1 TTCTTAAACT 0.928085 -56 ACGAAATTTTTCCTTTAACCACAAAGGGAT 14 117 1 TCCTTTAACC 0.792595 -163 CTCTATAGTTTTCTTAAACTGTGCCGAAAC 17 18 0 TTCTTAAACT 0.928085 -141 AGAGTCAATCTTCTTTAACCTTCTCTTAAC 17 122 1 TTCTTTAACC 0.953035 -37 ********** Masking position 8 Map Score: 9.90801 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 83 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 CACTCCCGCCGTTCGCCAATAAGATGGCGGA 3 81 1 GTTCCCAATA 0.813428 -131 TTGTACAAAATTTGACAAAACAGTGCTACCT 6 38 0 TTTGCAAAAC 0.774939 -263 GAACGGAATCTTTGCCCAATCAGCCTGCACA 6 145 1 TTTGCCAATC 0.959505 -156 TTTTTCTCCAATAAAATACGTTG 8 3 1 TTTCCCAATA 0.896228 -230 GGTTCTCAAATCTCAAATAATG 9 2 1 GTTCCAAATC 0.93975 -244 AACACACCAATTTCACTAATCTGTTGGCATT 9 29 0 TTTCCTAATC 0.884025 -217 TAGAGTCTGTTTTCCCAAAACTCCAGTATTG 10 177 0 TTTCCAAAAC 0.908421 -110 TGCCACTCAATTTCACCAATCTTTTCCCC 10 268 1 TTTCCCAATC 0.985562 -19 GCCAGTCACCGTTGGCAAAACCTTAACAAAA 11 143 0 GTTGCAAAAC 0.634749 -97 TGAATTTGCCTTGCCCCAATCACGATATACT 11 189 1 TTGCCCAATC 0.915011 -51 ATAGCAACTTTTTCGCCAATCCCCGCCTCAG 16 232 0 TTTCCCAATC 0.985561 -69 AATGATAGCCTTTAACAAATCTCTATAGTTT 17 37 0 TTTACAAATC 0.729688 -122 CCACTAAGTTTTTCACCTATCCTATCAGTGA 17 75 0 TTTCCCTATC 0.878994 -84 **** ****** Masking position 9 Map Score: 12.1131 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 341 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 TTGTTTAACTGTCCCATGGCTCGTCCCCAAA 1 130 0 GTCCATGGCT 0.989769 -140 TATCGGCCCTATTCCTTGGCCTATTGCTATA 1 242 1 ATCCTTGGCC 0.969968 -28 AGGTCTAGGAATCCCCTGGCTTTAGCCGTTT 2 53 0 ATCCCTGGCT 0.98075 -128 ACATGGAGATATGCCATGGCCAAACTGCCAA 5 11 0 ATCCATGGCC 0.98671 -182 CCCCATCCAAGTCCCTTGGCCGACAAATACA 7 59 0 GTCCTTGGCC 0.976281 -155 TGGGGTAATCATGGCATGGCACCGGGAAAGG 8 134 0 ATGCATGGCA 0.850585 -99 TCAACTTTGCGTACAATGGCTAGACGGGGGT 9 173 1 GTCAATGGCT 0.91586 -73 ATTTAGTAATATAGCATGGCTCCATTTAAAT 14 244 1 ATGCATGGCT 0.958464 -36 TCCCCGCCCTGTCCTCTGGCTTTCATAAACC 18 26 0 GTCTCTGGCT 0.879929 -138 ** ******** Masking position 7 Map Score: 6.64989 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 363 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 7 CAGTTGAACGGCCAAATTCCCTCCGCTATGT 1 161 1 GCCAATTCCC 0.878288 -109 ATGTCAAAGAGCCAATTTTCGATGTAGGGGA 2 16 0 GCCAATTTCG 0.940345 -165 ATATGCCATGGCCAAACTGCCAA 5 3 0 GCCAACTGCC 0.927661 -190 CAAAATCAACGAAAATTTTACTTTTTGGGGG 6 66 1 GAAAATTTAC 0.809386 -235 GGCTGATTGGGCAAAGATTCCGTTCAAAACT 6 139 0 GCAAAATTCC 0.817846 -162 ATAGTCAACAGAAAACCTTCCCCTCAACTAA 7 15 1 GAAAACTTCC 0.927471 -199 GGATACTACGGACAAATTGCCGGGTTCGGAT 7 128 1 GACAATTGCC 0.906945 -86 AGATGGAAGCGAAAATTTTCCTGTGTCGTCT 8 45 1 GAAAATTTCC 0.937998 -188 CTCACCCAAAGCCAAATTTCTTAAACTAAGT 8 170 1 GCCAATTTCT 0.75149 -63 GCCATTGTACGCAAAGTTGACCGCTCCCCAG 9 162 0 GCAAATTGAC 0.79652 -84 CCACTCCTTGGAAAAATTACCAGCTAATTAT 14 18 1 GAAAATTACC 0.710652 -262 GTGGTTAAAGGAAAAATTTCGTCCAGAGGAT 14 108 0 GAAAATTTCG 0.888249 -172 TACGACTAATGCCAAATTTAGGACACTGGAG 16 89 0 GCCAATTTAG 0.788366 -212 CTCCTTCACCGCAAAACTTCCATAGCGATAA 16 171 0 GCAAACTTCC 0.958858 -130 TAGGATAGGTGAAAAACTTAGTGGCCTAATT 17 82 1 GAAAACTTAG 0.554787 -77 ***** ***** Masking position 5 Map Score: 9.34979 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 974 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 8 TAAACAACAGTTGAACGGCCAAATTCCCTC 1 154 1 TTGAACGGCC 0.921697 -116 ACCACTGTAGCTGAAAGGCTCAGCCCCCAA 1 191 0 CTGAAAGGCT 0.826631 -79 TGACATCCCCCAAAACGGCTAAAGCCAGGG 2 41 1 CAAAACGGCT 0.845236 -140 ACTCATCCGTTTGAGCGGCCGGCCGAGAAA 10 56 0 TTGAGCGGCC 0.869545 -231 ATGAGTCACTCAGAATAGCTTCTAGATTTG 10 80 1 CAGAATAGCT 0.776444 -207 TTAGCCAGATCTGATCAGCCCTGTAAACTG 10 130 1 CTGATCAGCC 0.799543 -157 TGGCTTTTTTCAGAACAGCCTTAATCCATT 10 237 0 CAGAACAGCC 0.965668 -50 ACAGAATAAGCAGACCGGCCTTTGCT 12 7 0 CAGACCGGCC 0.968428 -75 TTCCGCCCCGCAGAACGGCTTGACATTTAT 18 110 0 CAGAACGGCT 0.984255 -54 ATCAGAGTGGCTCATCAAAGGA 18 152 0 CAGAGTGGCT 0.874536 -12 ********** Masking position 4 Map Score: 4.31752 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 307 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 ATTTTTCCCCTACATCGAAAATTG 2 5 1 TTCCCCTACA 0.873366 -176 AGATGAGAGCTTCCCCCCACGGCGATCGCC 3 36 0 TTCCCCCCAC 0.955894 -176 GTTCGCCGCCCTTGCCCCCAA 4 2 1 TTCGCCGCCC 0.961633 -34 TTACAGACCATACCCCGACACCGTTGCCGC 5 120 0 TACCCCGACA 0.672454 -73 ATTGATCCCATTCACCCCCCATCTAGCTAC 6 189 0 TTCACCCCCC 0.889618 -112 ACAGAAAACCTTCCCCTCAACTAAGTTGCT 7 22 1 TTCCCCTCAA 0.934385 -192 CAAATACATTTTCCCAGCAACTTAGTTGAG 7 37 0 TTCCCAGCAA 0.723642 -177 GAAATGGAACTTCACCGCCCCATTCGAGCT 7 89 1 TTCACCGCCC 0.958709 -125 AAAAACGACTTTCCCCCCCCCTAACCAATT 8 86 1 TTCCCCCCCC 0.978 -147 CAATTTTACGTTCCCCTACAGATCCTTTCC 8 111 1 TTCCCCTACA 0.873366 -122 ACTCACTAATTTCCCCTGCC 10 1 0 TTCCCCTGCC 0.796534 -286 ATTCCCGCCGTTGGCCGCAAATCCTCTGGA 14 88 1 TTGGCCGCAA 0.448411 -192 CATAAACTTGTTCCCCGAAAATCCCTTTGT 14 137 0 TTCCCCGAAA 0.921203 -143 AATATAATGTTTTCCCGCAACCCCAAGGAA 15 68 0 TTTCCCGCAA 0.736991 -59 AGGACTCTCCTTCACCGCAAAACTTCCATA 16 178 0 TTCACCGCAA 0.899817 -123 CAACTGCATTCTCCCCGCCCTGTCCTCTGG 18 38 0 CTCCCCGCCC 0.942 -126 ********** Masking position 5 Map Score: 17.814 Number of sites scoring better than the average of aligned sites = 1416 Number in coding regions = 1277 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 10 TGGGGGGTGGTCTCTGTTTTTAAGTTAGAT 1 88 1 TCTCTGTTTT 0.802425 -182 TAGATTAACTACTCTGGTTTGGGGACGAGC 1 113 1 ACTCTGGTTT 0.885376 -157 GGGCATTCTTTCCCCTGTTTTTTCCTAGAC 5 78 1 TCCCCTGTTT 0.923555 -115 TCTAACCCACTCCCTAGTTTTGAACGGAAT 6 124 1 TCCCTAGTTT 0.909127 -177 GCGAACTTGATCCCCGGTTTAGCAAAGATT 9 91 1 TCCCCGGTTT 0.987355 -155 AAGGAACATTTCTCCGGTTTTCCTTGGTGG 15 44 0 TCTCCGGTTT 0.974233 -83 TACTTACCCTGCCCTGGTTTGGACTCGGAG 16 122 0 GCCCTGGTTT 0.959425 -179 ********** Masking position 8 Map Score: 2.54205 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 226 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 AGATGAGAGCTTCCCCCCACGGCGATCGCC 3 36 0 TTCCCCCCAC 0.880164 -176 AAAAACGACTTTCCCCCCCCCTAACCAATT 8 86 1 TTCCCCCCCC 0.920948 -147 CCATCGGTGCTTCTGCGCCCTTACTCGCCC 8 202 1 TTCTGCGCCC 0.661485 -31 TCCGGGATCCTTCTGCCCAGAGATATTGCT 9 124 1 TTCTGCCCAG 0.96104 -122 GATATTGCTAGTCCGTCCTGGGGAGCGGTC 9 145 1 GTCCGTCCTG 0.719222 -101 GGCTGGTAGTTTTCCCCCTGAATTTGCCTT 11 171 1 TTTCCCCCTG 0.778828 -69 AATGGTTTTCTGTCCTGATCGTCGCCA 11 223 0 TTCTGTCCTG 0.897285 -17 GGTCTGCTTATTCTGTCCTGTAAGTGTTGT 12 21 1 TTCTGTCCTG 0.897285 -61 TTTTGCCCCACTCCTTGGAA 14 1 1 TTTTGCCCCA 0.432994 -279 AGCTGTACAATGCCGCCCTGTGGGAGATGA 14 52 1 TGCCGCCCTG 0.899106 -228 AAAGGAAAAATTTCGTCCAGAGGATTTGCG 14 103 0 TTTCGTCCAG 0.724093 -177 TTTTGGATAATTCTGCCCACCAAGGAAAAC 15 28 1 TTCTGCCCAC 0.926578 -99 GATGGGGGAATTCCGCCCCGCAGAACGGCT 18 120 0 TTCCGCCCCG 0.986439 -44 ********** Masking position 8 Map Score: 8.67534 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1428 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 12 CTTTCACTCCCGCCGTTCGCCAATAAGATG 3 77 1 CGCCGTTCGC 0.933152 -135 GATTATATCCCACCGTCTCCGCCATCTTAT 3 99 0 CACCGTCTCC 0.821171 -113 GTTCGCCGCCCTTGCCCCCAATCGGA 4 7 1 CGCCCTTGCC 0.918497 -29 CATACCCCGACACCGTTGCCGCTGTAAAGG 5 112 0 CACCGTTGCC 0.990904 -81 GGCGCAGAAGCACCGATGGCACTTAGTTTA 8 191 0 CACCGATGGC 0.949966 -42 ACCAGCCAGTCACCGTTGGCAAAACCTTAA 11 148 0 CACCGTTGGC 0.992643 -92 TTTCTGTCCTGATCGTCGCCATTGAGTATA 11 214 0 GATCGTCGCC 0.779444 -26 CACAAATTCCCGCCGTTGGCCGCAAATCCT 14 83 1 CGCCGTTGGC 0.989698 -197 GGTTAGAGTACATCGTTGACATCGATGGGG 14 192 0 CATCGTTGAC 0.854859 -88 GTAAGTATGGGATCATTGGCAAAAAATTAT 16 145 1 GATCATTGGC 0.49951 -156 ********** Masking position 4 Map Score: 6.03608 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 928 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 13 CGGCGGGAGTGAAAGAAGCCCTCCACAGAT 3 62 0 GAAAGAAGCC 0.912206 -150 GCTGAGGTGCAAACAACGCCCTAGCGAAAG 3 136 0 AAACAACGCC 0.830603 -76 TCCATCCCTAAAAAATAGCCCAAACAAAGG 5 50 1 AAAAATAGCC 0.760454 -143 TAGCCCCAAAGAAAAACGACTTTCCCCCCC 8 75 1 GAAAAACGAC 0.896469 -158 GGGAAAAAAGACGCAAAGTAGG 9 234 0 GAAAAAAGAC 0.938617 -12 GGAGTTTTGGGAAAACAGACTCTAACTTTT 10 184 1 GAAAACAGAC 0.824718 -103 AGGCTGTTCTGAAAAAAGCCATTGCCACTC 10 246 1 GAAAAAAGCC 0.975074 -41 GCCCCTGCCGAAACAAAGCCGTC 15 114 1 AAACAAAGCC 0.896469 -13 ********** Masking position 3 Map Score: 1.47942 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 201 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 TTGCCCCCAATCGGAGAGGGATCT 4 22 1 TCGGAAGGAT 0.698033 -14 AGGAAAAAACAGGGGAAAGAATGCCCTTTGTT 5 72 0 AGGGGAGAAT 0.833648 -121 GCAACGGTGTCGGGGTATGGTCTGTAATGGGA 5 123 1 CGGGGAGGTC 0.835872 -70 GTTCAAAACTAGGGAGTGGGTTAGATGCTGGG 6 117 0 AGGGATGGTT 0.917491 -184 AACTTAGTTGAGGGGAAGGTTTTCTGTTGACT 7 17 0 AGGGGAGTTT 0.865212 -197 TTGTCGGCCAAGGGACTTGGATGGGGAAATGG 7 64 1 AGGGATGGAT 0.938681 -150 GGACAAATTGCCGGGTTCGGATGTTTTATTTG 7 137 1 CCGGGTGGAT 0.911486 -77 TGGCATGGCACCGGGAAAGGATCTGTAGGGGA 8 122 0 CCGGGAGGAT 0.934108 -111 TGTTTGTATTTGGGGTTAGGTTATAGTTGTGT 11 24 0 TGGGGTGGTT 0.905342 -216 CCCATTGGTAAGGGTTTTGGATAATTCTGCCC 15 14 1 AGGGTTGGAT 0.823098 -113 TTGTTTCGGCAGGGGCAAGTTTAAACATTCTC 15 98 0 AGGGGAGTTT 0.865212 -29 AGATTGGTCTAGGGACAAGGATAATCGAAGAC 16 15 0 AGGGAAGGAT 0.954698 -286 ***** * **** Masking position 4 Map Score: 4.74836 Number of sites scoring better than the average of aligned sites = 924 Number in coding regions = 816 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 15 ********** No masking Map Score: 1.67931e-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