AlignACE version 2.2 July 7, 1998 AlignACE -jRRP.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YCL031C 365 bp YCL031C RRP7 1-894 #2 YCR035C 300 bp YCR035C RRP43 1-1185 Component of the exosome 3->5 exoribonuclease complex with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p). #3 YDL111C 401 bp YDL111C RRP42 1-798 Component of the exosome 3->5 exoribonuclease complex with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p). #4 YDR087C 300 bp YDR087C RRP1 1-837 involved in processing rRNA precursor species to mature rRNAs #5 YDR280W 326 bp YDR280W RRP45 1-918 Putative 3'->5' exoribonuclease\; component of exosome complex of 3'->5' exonucleases #6 YGR095C 300 bp YGR095C RRP46 1-771 Putative 3'->5' exoribonuclease\; component of exosome complex of 3'->5' exonucleases #7 YHR065C 300 bp YHR065C RRP3 1-1632 RRP3 is a DEAD box gene homologous to eIF-4a which encodes an RNA-dependent ATPase possessing helicase activity which is not specific for RNA #8 YHR069C 300 bp YHR069C RRP4 1-1080 3->5 exoribonuclease\; Component of the exosome 3->5 exonuclease complex with Rrp41p, Rrp42p, Rrp43p and Dis3p (Rrp44p). #9 YMR229C 600 bp YMR229C RRP5 1-5190 Protein required for processing of pre-rRNA #10 YOR001W 300 bp YOR001W RRP6 1-2202 Ribosomal RNA Processing Motif number 1 AGAAATAAGCAGGAAAAAGAAGAGAACATT 1 268 1 AGGAAAAAGA 0.97386 -98 ATAAAAAAAGAAAGAAAAATCTTATACTTT 2 188 0 AAAGAAAAAT 0.709166 -113 TCTGAATATTAGAAAAAAATTTCGCCAACT 3 260 0 AGAAAAAAAT 0.900278 -142 TCTAATATTCAGAAAAAAGAAACGTAGAGC 3 277 1 AGAAAAAAGA 0.969262 -125 TAAAGAATTTAGAAAAAAAAATGCGATGAG 4 168 1 AGAAAAAAAA 0.96052 -133 AATTCGAGAAAGGAAAAAAAAGGTAGCCCA 5 105 0 AGGAAAAAAA 0.966381 -222 TCTCGAATTCAAGAAAAAATTAACAACTTT 5 126 1 AAGAAAAAAT 0.900278 -201 AACATCATCGAGGGAAAAGTTGTTAATTTT 5 141 0 AGGGAAAAGT 0.815211 -186 TTAGGAAGTTAGAAAAAAAACTTGAAAGTT 5 229 0 AGAAAAAAAA 0.96052 -98 AAGTAGTAAAAAGAAAAAGAGAGGTACATA 6 226 0 AAGAAAAAGA 0.969262 -75 TGCGCTTAAAAGGAAAAAAAAAGTAGTAAA 6 246 0 AGGAAAAAAA 0.966381 -55 AGAGAAGACAAAAGAAAAGAACACATGCAC 7 103 0 AAAGAAAAGA 0.894924 -198 AAAAAAAAAAAAAAAAAAAAGTAGACGAAG 7 245 0 AAAAAAAAAA 0.953687 -56 TTTTTCACTGAAAAAAAAAAAAAAAAAAAA 7 255 0 AAAAAAAAAA 0.953687 -46 AAGAAAAAGAAAAAAAAAGATTCACTGAGG 8 144 0 AAAAAAAAGA 0.963885 -157 CATACTGAGGAAGAAAAAGAAAAAAAAAGA 8 154 0 AAGAAAAAGA 0.969262 -147 AGGTGAAAAAAAAAAAAAAATTAAGAAAAC 8 196 1 AAAAAAAAAA 0.953687 -105 ACAAAAGTAGAAGAAAAATATCCTTCCTTA 8 230 1 AAGAAAAATA 0.755581 -71 TTTTGCATTTAAAAAAAAGTAAAAACTATT 10 138 0 AAAAAAAAGT 0.908287 -163 ********** Masking position 5 Map Score: 27.0458 Number of sites scoring better than the average of aligned sites = 13079 Number in coding regions = 2156 Number in noncoding regions = 10923 Number of orfs with sites within 600 bp upstream = 2399 Fraction of orfs with sites within 600 bp upstream = 0.38532 Motif number 2 GACCAAAAAGTGAAAAATTTTCCAATTTAA 1 233 0 TGAAAAATTT 0.978559 -133 ATGGAGTTATTGAAATATTTATACGAAGAG 3 74 0 TGAAATATTT 0.806879 -328 TGCGATGAGCTGAAAAAAATTGTCAAATAT 4 189 1 TGAAAAAAAT 0.739025 -112 ATGTATATTCTGAACAATTTTGCAATCACT 5 292 0 TGAACAATTT 0.924542 -35 GAAAAAAGAGTGGAAAATTTGTTAG 6 286 1 TGGAAAATTT 0.860966 -15 TTTTTTTCAGTGAAAAATTTCAATTTCGTC 7 268 1 TGAAAAATTT 0.978559 -33 TGCCAGTATTCCAAAAATTTAATAGATTGA 8 46 0 CCAAAAATTT 0.915706 -255 TTTCATGCAATGAAAAATATCCTTACCTTT 8 83 1 TGAAAAATAT 0.968685 -218 CAAAAGTAGAAGAAAAATATCCTTCCTTAA 8 231 1 AGAAAAATAT 0.813175 -70 AACGTAAATCCCAACAATATGTATTACGCA 9 98 1 CCAACAATAT 0.664044 -503 TTTCTGATTCCGAAAAATTTTGAAAAATTT 9 422 1 CGAAAAATTT 0.976477 -179 CGAAAAATTTTGAAAAATTTTAAGATGAGA 9 432 1 TGAAAAATTT 0.978559 -169 ATATGACTTCCGAAAAATATATATTTGATA 10 55 0 CGAAAAATAT 0.965678 -246 AATATTTTACCCAAAAATATGAGGGCATCG 10 191 1 CCAAAAATAT 0.880422 -110 TATTCATTACTGAAAAATTTTCCGATGCCC 10 213 0 TGAAAAATTT 0.978559 -88 ********** Masking position 4 Map Score: 16.6586 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 627 Number in noncoding regions = 552 Number of orfs with sites within 600 bp upstream = 548 Fraction of orfs with sites within 600 bp upstream = 0.088018 Motif number 3 ATCCTTATTGTCATCACTTCGAACGACGTAA 1 201 1 TCACACTTCG 0.948425 -165 CTTCACCATATAAGCTCTACGTTTCTTTTTT 3 289 0 TAACTCTACG 0.861205 -113 ACAATTTTTTTCAGCTCATCGCATTTTTTTT 4 181 0 TCACTCATCG 0.995884 -120 AGACATTTGTTAACATCATCGAGGGAAAAGT 5 151 0 TAAATCATCG 0.913507 -176 TTTTTCCTTTTAAGCGCATCGGATTGTGGAA 6 258 1 TAACGCATCG 0.96678 -43 ACGAAGAAGCTCATCTCATCGCGATATTAGT 7 220 0 TCACTCATCG 0.995884 -81 TTTTTTTTTTTCACCTCATCGCTCAATCCAT 8 181 0 TCACTCATCG 0.995884 -120 AGGGTTTAGCTCATCTCATCTTAAAATTTTT 9 444 0 TCACTCATCT 0.964311 -157 *** ******* Masking position 3 Map Score: 6.1437 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 153 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 GTATTGCTACACAAATAAGTTTGACAGTAGTT 2 257 1 ACAAAAGTTT 0.987403 -44 TCTGAATATTAGAAAAAAATTTCGCCAACTAG 3 258 0 AGAAAAATTT 0.835323 -144 ACGGCGCCAGCCAACAAAGTTTTCCACGCGGC 6 58 1 CCAAAAGTTT 0.977973 -243 GAATGGTTGGCCAAAGAAGTTTGACCCACTCT 7 24 1 CCAAAAGTTT 0.977973 -277 GATATAGCAGACAATAAAATTTCAAGATGGCC 7 134 0 ACAAAAATTT 0.968398 -167 GGATATTTGAACAAACCAGTTTAAACCATAAG 8 114 0 ACAACAGTTT 0.954181 -187 TACCGCGGCAACAAGTAAGTTTACGTCTACTA 9 312 0 ACAAAAGTTT 0.987403 -289 ATACTGAACAATGAAATTTCAATATCGCA 10 8 1 ACAAAAATTT 0.968375 -293 **** ****** Masking position 8 Map Score: 5.29765 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 160 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TTTGTTTGATATATATATGTATATATACATATT 1 48 0 ATAATAGTAA 0.846799 -318 TAAGCAGGAAAAAGAAGAGAACATTGAGAGGAT 1 273 1 AAAAAGGAAA 0.91665 -93 TCAAACGGGAATAAAAGGGTTTATATCCGAAGG 2 125 0 ATAAAGGTTA 0.902484 -176 TATTCAGAAAAAAGAAACGTAGAGCTTATATGG 3 282 1 AAAAAAGTAA 0.951537 -120 ATTTAGAAAAAAAAATGCGATGAGCTGAAAAAA 4 174 1 AAAATGGATA 0.552601 -127 AATGCGCAAGATATATACGTATACTTAAGAATG 4 225 0 ATAATAGTAA 0.846799 -76 AAATGTCTGAATATAAAGGAATAGGAAACGGTT 5 174 1 ATAAAAGAAA 0.90299 -153 CATTCAAAGTACATAAATGTTGATATGTTCAAA 6 123 0 ACAAAAGTTA 0.830682 -178 CGGATTGTGGAAAAAAGAGTGGAAAATTTGTTA 6 277 1 AAAAAGGTGA 0.771895 -24 AGAGAAGACAAAAGAAAAGAACACATGCACAGC 7 100 0 AAAAAAGAAA 0.90299 -201 ATGTTTAATAATAAAAGAGTATAATCCAGATAT 7 161 0 ATAAAGGTAA 0.958674 -140 AAAAAAAAAAAAAAAAAAGTAGACGAAGAAGCT 7 240 0 AAAAAAGTAA 0.951537 -61 AAGAAAACTAAAACAAAAGTAGAAGAAAAATAT 8 218 1 AAAAAAGTAA 0.951537 -83 TTGCGTAGTCACACAAGCGTAAACAGAT 8 283 1 ACAAAGGTAA 0.935606 -18 CAGGATATTTATAAAAGAGTTTAACAACAGAGT 9 152 0 ATAAAGGTTA 0.902484 -449 ATTGGTAAGTACATATAGGAAAACATTATTCTG 9 233 1 ACAATAGAAA 0.621388 -368 CTGCTAATGTATAGAAGGGTTTAGCTCATCTCA 9 457 0 ATAAAGGTTA 0.902484 -144 ATAGCTTTAAATAAAAATGAATAGACGAACCTT 9 509 0 ATAAAAGAAA 0.90299 -92 TTTTGCATTTAAAAAAAAGTAAAAACTATTTGC 10 135 0 AAAAAAGTAA 0.951537 -166 *** *** *** * Masking position 5 Map Score: 16.8063 Number of sites scoring better than the average of aligned sites = 1412 Number in coding regions = 595 Number in noncoding regions = 817 Number of orfs with sites within 600 bp upstream = 632 Fraction of orfs with sites within 600 bp upstream = 0.10151 Motif number 6 CTTATTTCTTAGGTGACCAAAAAGTGAAAAA 1 246 0 AGGGACCAAA 0.980264 -120 TTATATCCGAAGGTGGCCAGAACAATCATGA 2 107 0 AGGGGCCAGA 0.87967 -194 TTCAAATCACAGTCGACGAAAGTATAAGATT 2 170 1 AGTGACGAAA 0.977209 -131 TTTGAACCCTAGTTGGCGAAATTTTTTTCTA 3 250 1 AGTGGCGAAA 0.978953 -152 AATAGTCTGTAGACGGCAAAAGGCATTCTTT 3 335 1 AGAGGCAAAA 0.929612 -67 GCCAAGTTAAAGGTGACAAAATAGCGCCTTT 6 179 1 AGGGACAAAA 0.968892 -122 TTCAGAGAATGGTTGGCCAAAGAAGTTTGAC 7 18 1 GGTGGCCAAA 0.863217 -283 TGGTAATCAGAGTGGGTCAAACTTCTTTGGC 7 33 0 AGTGGTCAAA 0.854757 -268 GATGGCCAAGAGAAGACAAAAGAAAAGAACA 7 110 0 AGAGACAAAA 0.924096 -191 TAAAATTTCAAGATGGCCAAGAGAAGACAAA 7 121 0 AGAGGCCAAG 0.849715 -180 AAAAAAAAAAAGTAGACGAAGAAGCTCATCT 7 235 0 AGTGACGAAG 0.920068 -66 ATTTCGTCTAAGGCGATAAAA 7 290 1 AGGGATAAAA 0.7976 -11 TTGAGCGATGAGGTGAAAAAAAAAAAAAAAT 8 186 1 AGGGAAAAAA 0.7976 -115 CTAAAACAAAAGTAGAAGAAAAATATCCTTC 8 225 1 AGTGAAGAAA 0.844357 -76 ACAAATTATTAGTAGACGTAAACTTACTTGT 9 303 1 AGTGACGTAA 0.79696 -298 *** ******* Masking position 5 Map Score: 7.55751 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 944 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 7 ACACTAACGAAAATAATATGTATATATACAT 1 34 1 AAATAATTGT 0.896827 -332 AACTCGCTATTAATAATTTATCTCCGAAAGC 3 181 1 TAATAATTAT 0.830354 -221 ACAATGATACTAATAGTCTGTAGACGGCAAA 3 324 1 TAATAGTTGT 0.932634 -78 GAGAGGTACATAATAGTCTTTATGAAGAAAA 6 207 0 TAATAGTTTT 0.943335 -94 CATCTGGCCAGAATAATGTTTTCCTATATGT 9 243 0 GAATAATTTT 0.878446 -358 TTACGTCTACTAATAATTTGTTGAATAAAGT 9 293 0 TAATAATTGT 0.951083 -308 ATATCGCATATAATAATTTTTGTTATCAAAT 10 32 1 TAATAATTTT 0.958859 -269 TAATTTTTAAAAATAATGTTTTAATTATTTA 10 89 0 AAATAATTTT 0.911069 -212 ATATTTTAGCAAATAGTTTTTACTTTTTTTT 10 127 1 AAATAGTTTT 0.884319 -174 GTGATATTATTAATAATATTTTACCCAAAAA 10 177 1 TAATAATTTT 0.944657 -124 ******* *** Masking position 5 Map Score: 5.31425 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 264 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 ATTAATAAATGAATATCCTTATTGTCATCA 1 187 1 GAATATCCTT 0.948985 -179 CCCATCTTTGAAATATGCTGTTGGAACTTT 2 28 1 AAATATGCTG 0.92653 -273 ATGCAATGAAAAATATCCTTACCTTTACTT 8 87 1 AAATATCCTT 0.980617 -214 TGGTTTGTTCAAATATCCTCAGTGAATCTT 8 128 1 AAATATCCTC 0.967578 -173 AGTAGAAGAAAAATATCCTTCCTTAAGTAC 8 235 1 AAATATCCTT 0.980617 -66 ACTCTTTTATAAATATCCTGCTCGTTATTT 9 165 1 AAATATCCTG 0.982137 -436 ********** Masking position 5 Map Score: 3.43838 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 197 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 GTGTATCTCTATTCATTCAAGACTGTATTTTGTT 1 75 0 ATTCAAAACT 0.662372 -291 TTACGTTACCATTCATTACATAGTGTATCTCTAT 1 97 0 ATTCACAAGT 0.945537 -269 ACTACCTCTCTTTTAATCCAAAATTACAATTTTT 1 129 0 TTTTACAAAT 0.914069 -237 GTTTGTTGTCTTTCATCCCAAAGTTCCAACAGCA 2 43 0 TTTCACAAGT 0.978524 -258 CTGGAGAGATTTTCAAATCACAGTCGACGAAAGT 2 159 1 TTTCACAAGT 0.978524 -142 TTCTTTCTTTTTTTATGACATAGTATATAACAAT 2 202 1 TTTTACAAGT 0.936291 -99 TGCGCATCATTTTCACGTCATACTCTTTGTCTCT 3 31 1 TTTCACAACT 0.941591 -371 TATCTTGCGCATTCACGGCATAATACACTAAATA 4 245 1 ATTCACAAAT 0.926274 -56 CCTTTCTCGAATTCAAGAAAAAATTAACAACTTT 5 122 1 ATTCAAAAAT 0.800532 -205 TTTTTTTTTTTTTCAGTGAAAAATTTCAATTTCG 7 262 1 TTTCAAAAAT 0.913263 -39 TATAAAAGAGTTTAACAACAGAGTTCAGGATTGA 9 142 0 TTTAACAAGT 0.91861 -459 TGTATGATTTTTCAACTACATAATTGGTAAGTAC 9 211 1 TTCAACAAAT 0.525707 -390 AAAAAATATATTTTAGCAAATAGTTTTTACTTTT 10 120 1 TTTTAAAAGT 0.82437 -181 TTTACTTTTTTTTAAATGCAAAATAAGTTCACGT 10 145 1 TTTAACAAAT 0.890939 -156 ATTAATAATATTTTACCCAAAAATATGAGGGCAT 10 185 1 TTTTAAAAAT 0.772591 -116 ***** ** *** Masking position 5 Map Score: 7.64841 Number of sites scoring better than the average of aligned sites = 999 Number in coding regions = 689 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 10 TATTTTCGTTAGTGTTCGGTTTCCAAGTTAGAAATAAT 1 11 0 ATTCGTCCGT 0.969978 -355 TATCTGAGGTTGTTATCTGTTACCTAGTTCGTTCGCCC 1 326 0 TTACGTCCGT 0.854154 -40 TCTTTGTCTCTCTGTTCTATCTCTTCGTATAAATATTT 3 54 1 TTTCATCTGT 0.98033 -348 CTTCGTATAAATATTTCAATAACTCCATTTGTCTATTC 3 76 1 AATCATCTAT 0.670573 -326 ACTCCATTTGTCTATTCTATCTACCCGTTCTATCCTTA 3 97 1 TTTCATACGT 0.819346 -305 AGGGTGTGCTTTTCTTCCGTGCCCTAGTCTATTATTTT 3 215 1 TTTCGTCCGT 0.980606 -187 ATATCATTTGAATTTCCAATATCCTAGTCACGGAGCAC 4 124 1 ATTCATCCGT 0.977778 -177 AACAGCAATTTGAATGCTATAACTCGGTGGTGATGACC 5 26 1 TATCATCTGT 0.94118 -301 ATTCTGAACAATTTTGCAATCACTACGTCCTGTTGATT 5 278 0 ATTCATCTGT 0.969543 -49 GAAATTTTATTGTCTGCTATATCTGGATTATACTCTTT 7 143 1 TTTCATCTAT 0.908447 -158 CATCGCGATATTAGTTCGATATCTGGGTTTGAGTGAGT 7 197 0 TATCATCTGT 0.94118 -104 CAGGATTGAATATTCTCAGTAACTGCGTAATACATATT 9 113 0 TTCCGTCTGT 0.862688 -488 TTACTGAAAAATTTTCCGATGCCCTCATATTTTTGGGT 10 199 0 ATTCATCCAT 0.89754 -102 * * * * ** ** ** Masking position 10 Map Score: 3.6723 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 576 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 11 GACTGTATTTTGTTTGATATATATATGTATAT 1 57 0 TGTTTTATAT 0.908003 -309 GCCAATAAGATGTTTGTTGTCTTTCATCCCAA 2 56 0 TGTTTTGTCT 0.909286 -245 AATTTGTCCATTATTGTTATATACTATGTCAT 2 216 0 TTATTTATAT 0.739342 -85 ACTGTCAAACTTATTTGTGTAGCAATACTCAT 2 253 0 TTATTTGTAG 0.406203 -48 TAATAGCGAGTTTTTTTTGTATTTACTTATTT 3 161 0 TTTTTTGTAT 0.958187 -241 TCTACGTTTCTTTTTTCTGAATATTAGAAAAA 3 273 0 TTTTTTGAAT 0.865793 -129 CATCGCATTTTTTTTTCTAAATTCTTTACCTC 4 164 0 TTTTTTAAAT 0.739342 -137 TTTAAGTGTCTATTTAGTGTATTATGCCGTGA 4 257 0 TATTTTGTAT 0.880341 -44 GGCTACCTTTTTTTTCCTTTCTCGAATTCAAG 5 107 1 TTTTTTTTCT 0.446368 -220 AGTTGTTAATTTTTTCTTGAATTCGAGAAAGG 5 122 0 TTTTTTGAAT 0.865793 -205 TACGTCCTGTTGATTAATGTATCGAGACTGAA 5 261 0 TGATTTGTAT 0.863378 -66 CATGTGTTCTTTTCTTTTGTCTTCTCTTGGCC 7 106 1 TTTCTTGTCT 0.678686 -195 GAAATTTTATTGTCTGCTATATCTGGATTATA 7 143 1 TGTCTTATAT 0.670766 -158 CCTTAAACCCTGTTTAATATCTGTTTAGCAAA 9 61 0 TGTTTTATCT 0.81506 -540 TATAGTGCTATTATTTGTGTATGATTTTTCAA 9 194 1 TTATTTGTAT 0.865793 -407 AGTACAGGTGTGTTTTTTATATTAAACGGTCC 9 570 0 TGTTTTATAT 0.908003 -31 ATGTTTTAATTATTTAATGTATATGACTTCCG 10 73 0 TATTTTGTAT 0.880341 -228 TAGTTTTTACTTTTTTTTAAATGCAAAATAAG 10 140 1 TTTTTTAAAT 0.739342 -161 TTGTTGTTCCTATTTCGTCTATCTTCAGATGA 10 250 0 TATTTTCTAT 0.462125 -51 ***** ***** Masking position 5 Map Score: 3.81696 Number of sites scoring better than the average of aligned sites = 2190 Number in coding regions = 1025 Number in noncoding regions = 1165 Number of orfs with sites within 600 bp upstream = 772 Fraction of orfs with sites within 600 bp upstream = 0.123996 Motif number 12 TGACAATCTTGGGCTGCTTGGTTT 4 5 0 GGGCTGCTTG 0.992486 -296 CGCCGTATCCGGGCTGCTTGCCCGTAGCAT 6 34 0 GGGCTGCTTG 0.992486 -267 GGGCAAAATGTGGCCGCGTGGAAAACTTTG 6 72 0 TGGCCGCGTG 0.993035 -229 TCTGGCCAGATGGATGCTTGTTTCTGGGCT 9 262 1 TGGATGCTTG 0.959093 -339 AGTCATTCAATGCCCGCGTGCAAAGTGATC 9 385 1 TGCCCGCGTG 0.9759 -216 ********** Masking position 9 Map Score: 1.39248 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 32 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 GATTAATAAATGAATATCCTTATTGTCATC 1 186 1 TGAATATCCT 0.88481 -180 TACCATCCTCTCAATGTTCTCTTCTTTTTC 1 280 0 TCAATGTTCT 0.94306 -86 ATTTGCTTCATGATTGTTCTGGCCACCTTC 2 100 1 TGATTGTTCT 0.920305 -201 ACTCTTTGTCTCTCTGTTCTATCTCTTCGT 3 52 1 TCTCTGTTCT 0.874238 -350 TAACTCCATTTGTCTATTCTATCTACCCGT 3 95 1 TGTCTATTCT 0.925243 -307 TGTGAATGTTCTCACTCGATTT 4 289 0 TGAATGTTCT 0.977601 -12 TTTAATCTAATGTATATTCTGAACAATTTT 5 301 0 TGTATATTCT 0.94683 -26 AGTTCAGGATTGAATATTCTCAGTAACTGC 9 125 0 TGAATATTCT 0.930563 -476 ********** Masking position 5 Map Score: 1.43073 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 419 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 14 CTCTTGCTACTACCTCTCTTTTAATCCAAAA 1 140 0 TACCCTCTTT 0.98587 -226 GCTATTTGATACCCACTCTTGCTACTACCTC 1 155 0 ACCCCTCTTG 0.752126 -211 CCCGTAACACTCTATCTGAGGTTGT 1 351 0 TAACCTCTAT 0.640795 -15 ATTACTGTAATACCCATCTTTGAAATATGCT 2 16 1 TACCATCTTT 0.833502 -285 CATTTTCACGTCATACTCTTTGTCTCTCTGT 3 38 1 TCATCTCTTT 0.883082 -364 CTAAATTCTTTACCTCTCGTGCTCCGTGACT 4 149 0 TACCCTCGTG 0.893392 -152 TCTTAACGAGTCCTCCTCTTTGAACATATCA 6 105 1 TCCTCTCTTT 0.971603 -196 GACTATTATGTACCTCTCTTTTTCTTTTTAC 6 220 1 TACCCTCTTT 0.98587 -81 TTTTTCTTTTTACTACTTTTTTTTTCCTTTT 6 238 1 TACTCTTTTT 0.693812 -63 CTAACAAATTTTCCACTCTTTTTTCCACAAT 6 280 0 TTCCCTCTTT 0.962323 -21 TATATCTGGATTATACTCTTTTATTATTAAA 7 160 1 TTATCTCTTT 0.718481 -141 TTTATAAATATCCTGCTCGTTATTTATAGTG 9 170 1 TCCTCTCGTT 0.922227 -431 **** ****** Masking position 7 Map Score: 3.017 Number of sites scoring better than the average of aligned sites = 1697 Number in coding regions = 1179 Number in noncoding regions = 518 Number of orfs with sites within 600 bp upstream = 417 Fraction of orfs with sites within 600 bp upstream = 0.0669772 Motif number 15 ********** No masking Map Score: -1.80235e-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