AlignACE version 2.2 July 7, 1998 AlignACE -jPET.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 YBL080C 563 bp YBL080C PET112 1-1626 62-kDa protein #2 YBL030C 600 bp YBL030C pet9 1-957 mitochondrial ADP\/ATP translocator #3 YCR020C 300 bp YCR020C PET18 1-648 Transcription regulator #4 YDR079W 300 bp YDR079W PET100 1-336 cytochrome c oxidase-specific assembly factor #5 YER058W 600 bp YER058W PET117 1-324 cytochrome c oxidase assembly factor #6 YER153C 300 bp YER153C pet122 1-765 translational activator of cytochrome c oxidase subunit III #7 YGR222W 300 bp YGR222W pet54 1-882 translational activator of cytochrome c oxidase subunit III #8 YJL023C 538 bp YJL023C PET130 1-1044 Nuclear gene encoding mitochondrial protein #9 YJR034W 300 bp YJR034W PET191 1-327 Required for assembly of active cytochrome c oxidase #10 YLR067C 300 bp YLR067C PET309 1-2898 Involved in expression of mitochondrial COX1 by regulating translation of COX1 mRNA and by affecting transcription or stability of COX1 mRNAs #11 YMR257C 588 bp YMR257C pet111 1-2403 translational activator of cytochrome c oxidase subunit II #12 YNL003C 344 bp YNL003C pet8 1-855 Member of family of mitochondrial carrier proteins #13 YNR045W 300 bp YNR045W pet494 1-1470 translational activator of cytochrome c oxidase #14 YOR017W 327 bp YOR017W pet127 1-2403 Mitochondrial membrane protein #15 YOR158W 412 bp YOR158W pet123 1-957 Mitochondrial ribosomal protein of small subunit #16 YOR201C 300 bp YOR201C pet56 1-1239 Ribose methyltransferase for mitochondrial 21S rRNA Motif number 1 TAATGTCCCATCTCGAAAAATTGTTTTTTTTTTTACAAATAAAG 1 132 1 TTAATTTTTT 0.79719 -432 AGATTAACTTTCTGATTTTAGGTTTATTATTTTTTTGTTGTATG 1 357 1 TTTTTTTTTT 0.96903 -207 GTTGGGCTGCTTTTGTCGTAAGTTTTGTTGTTCTTGAATGACTT 2 74 0 TTTTTTTTTT 0.96903 -527 CTTTTCTTCCTCTTATATATGTATTTATATATATGTGTTCACTA 2 136 1 TTTATTTATT 0.828082 -465 GGAGCCCCTCTATATTATTTATATTTGTCGTTGTTCTTTTTTGT 2 514 1 TTTTTTTTTT 0.96903 -87 CCTTGTGACTTGTTCTTTTCTCCCTATTTCTTCTTCATCACCAA 4 123 1 TTTTCTTTTT 0.833647 -178 CTCCTATATATTTTAAAATACTTTTCTTTCTTTTTGTTTTAAAA 7 66 0 TTATTTTTTT 0.915132 -235 AATTTTCAATTTTTTTTTTCATATTCGTTAATCGTGATGAGAAT 7 174 1 TTTTTTTATG 0.76344 -127 CTATTAACCTTCTTAATCTTTTCTTTCTTCATCTGCCATCGCCT 8 493 0 TTATTTTATT 0.819938 -46 TATTTGTGTCTATTCTGTTCCGATTAATTGTTATGGCAGCCTTT 9 237 0 TTTTTTTTTT 0.96903 -64 CGCGATGAGGTTTGATTTTGAAATTTTTCATTGTTTGAAGGAAA 10 84 1 TTTTTTTTTT 0.96903 -217 CACTACATGATTTTTTATTTTTATTTCTCTATTGGCCCGAAAAG 10 133 0 TTTTTTTATG 0.76344 -168 CTTATGTACATTTGTTGAAGGAGTTCGTATATATACAGCCAGTT 11 35 1 TTTATTTATT 0.828082 -554 ATAATTATATTTTACTATTGCATTTCATAATTATTACCCGGACC 11 84 1 TTTTTTTTTT 0.96903 -505 TACAGAAGCTTGTTCATTTCAGTTTTTTCATTGTCTCTTCCTTC 11 178 0 TTATTTTTTT 0.915132 -411 ACGGTTGTTATTTATTGTTTGGACTTCTTGTTGTTAGGCTTTAT 11 241 1 TTTTCTTTTT 0.833647 -348 TTTAAAATTGTATAGTACATAGGTTGTTAGTTATCTAATGCCAT 12 23 1 TTTATTTTTT 0.919393 -322 AGAATATACGTATTTTGGCAAGTTTATTGGTTTTTAGTTTATGT 12 121 1 TTTCTTTTTT 0.778251 -224 TTGTTATCCGTTTGTTTTATACTTTCCTTATTTTGTAATTTACT 13 218 0 TTTATTTTTT 0.919393 -83 ATGGACTACTTTTTTTTCACTGTTTCCTGTTTTTTGACGTGATA 14 164 0 TTTATTTTTT 0.919393 -164 TCAAGTGCCCTGTTTATATTATATTTTTACATATTTGTTTCTTT 14 243 0 TTATTTTATT 0.819938 -85 ATTATTAGTTTATCCTTTTCATCTTTCTTTTTGGTATTTTGCCA 15 123 1 TTTTTTTTTG 0.884288 -290 AAATAATCCATATGTAGATTCTCTTCTTTATTCTACTCCTCTTG 15 323 0 TTATTTTTTT 0.915132 -90 CTTTCTGCTCTGTCATCTTTGCCTTCGTTTATCTTGCCTGCTCA 16 58 1 TTTTTTTATT 0.929645 -243 * * * * ** * ** * Masking position 15 Map Score: 20.6836 Number of sites scoring better than the average of aligned sites = 4612 Number in coding regions = 1603 Number in noncoding regions = 3009 Number of orfs with sites within 600 bp upstream = 1313 Fraction of orfs with sites within 600 bp upstream = 0.21089 Motif number 2 TTTATTATTTTTTTGTTGTATGCCCTTGTTAAAAATT 1 379 1 TTTTTTTCTT 0.933352 -185 AACGAAATAATTTCCTTTTCTTCCTCTTATATATGTA 2 122 1 TTTCTTTCCT 0.962887 -479 TGTCGTTGTTCTTTTTTGTGTGCTCTTTTATACTTCA 2 539 1 CTTTTTTCTT 0.824986 -62 AGTGATTACTTTTGTTTGTCAGCCCTTATTAAATTGT 4 260 0 TTTGTTTCTT 0.802565 -41 GCTCACGTGGTTTCATTATAACTCCTTTCTCCATAGC 5 110 0 TTTCTTTTTT 0.831357 -491 AATAATCATTCTTCTTATTTCACCATTTTAACCATTC 5 187 0 CTTCTATCTT 0.724056 -414 TTAAAATACTTTTCTTTCTTTTTGTTTTAAAACCTGC 7 61 0 TTTCTTTTTT 0.831357 -240 TAAATGTTTCTTTCCTCCTATATATTTTAAAATACTT 7 87 0 TTTCTCTTTT 0.626291 -214 ATGCTTTCGATTTCATCATTTTCCTTTCGCATTTTCT 8 42 1 TTTCTCTCTT 0.86541 -497 GAATCCTACCTTTCGTTTTGAGCCGCTCAAATAAGAC 8 162 0 TTTCTTTCCT 0.962887 -377 GATTTGGTTTTTCTATTAACCTTCTTAATCTTTTC 8 514 0 TTTTTATCCT 0.887858 -25 ATTTCAGTTTTTTCATTGTCTCTTCCTTCGGTATGCC 11 170 0 TTTCTTTTCT 0.871168 -419 TTTATTATCGTTTTATTCTCTTCCTTTTTTATAAAAT 11 431 1 TTTTTTTCTT 0.933352 -158 GGGCGCCTCTTTTTTTCCTCGCTTACTGAGCGCTGTT 12 179 1 TTTTTCTTCT 0.629914 -166 TTTATTAAAGTTTTATTTTAAACCGTTCTAGTGACTT 13 159 1 TTTTTTTCTT 0.933352 -142 ACTTTCCTTATTTTGTAATTTACTATTGGATGTATCT 13 205 0 TTTTTATCTT 0.85233 -96 CGGAAACGCGCTTTATTATGGACTACTTTTTTTTCAC 14 188 0 CTTTTTTCCT 0.866059 -140 CATCTTTCTTTTTGGTATTTTGCCACTCGGCCGGGTT 15 142 1 TTTGTATCCT 0.696795 -271 TGGGAATCACTTTCCTACTCGGCGACTTCAGGGTTCT 15 288 0 TTTCTATCCT 0.914479 -125 AGATTCTCTTCTTTATTCTACTCCTCTTGGGAATCAC 15 315 0 CTTTTTTCCT 0.866059 -98 TGCCTGCTCATTTTTTAGTATATTCTTCGAAGAAATC 16 92 1 TTTTTATTTT 0.600695 -209 GATGACTCTTTTTTTTTCTTAGCGATTGGCATTATCA 16 161 0 TTTTTTTCTT 0.933352 -140 ATGATTTTCATTTTTTTTTTTCCACCTAGCGGATGAC 16 192 0 TTTTTTTCCT 0.950519 -109 TTCCCGCAATTTTCTTTTTCTATTACTCTTGGCCTCC 16 263 0 TTTCTTTTCT 0.871168 -38 **** ** * * ** Masking position 9 Map Score: 16.6214 Number of sites scoring better than the average of aligned sites = 3237 Number in coding regions = 1653 Number in noncoding regions = 1584 Number of orfs with sites within 600 bp upstream = 1156 Fraction of orfs with sites within 600 bp upstream = 0.185673 Motif number 3 GCCTGTTCTGCAGGAGCTTACTGCGAATAAA 3 83 1 CAGGGCTTAC 0.933852 -218 TCCATAGTAACAATTGCTTGGCAAAAAAGGT 3 161 1 CAATGCTTGG 0.934267 -140 TTTTGTAGGTCAGCAGCTCGCGCTATGGAGA 5 89 1 CAGCGCTCGC 0.975365 -512 AAAATTTAACCAGTGGCTCGCCCTCTATACG 6 142 0 CAGTGCTCGC 0.987805 -159 TTGATCTGTAAAGCTGCTTGCAGGTTTTAAA 7 42 1 AAGCGCTTGC 0.88944 -259 TTTACTTTCTCAATTGTTTGCGGTGTTCTTA 9 108 1 CAATGTTTGC 0.822815 -193 TGATTTTGCTCAGTTGCTTACTTGACCACCT 10 16 1 CAGTGCTTAC 0.981534 -285 TAAATTTAAACAATTGCTTACGAGAACTTA 11 569 1 CAATGCTTAC 0.93749 -20 CCATCATGGCAGTTGCTTGCAATGTAATTT 13 10 1 CAGTGCTTGC 0.99472 -291 CGGATAACAACAGTAGCTTGGAGACAGCAAA 13 252 1 CAGTGCTTGG 0.980534 -49 **** ****** Masking position 8 Map Score: 5.36419 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 250 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CAAGGGTTATTTAAATTTTTAACAAGGGCA 1 399 0 TTAAATTTTT 0.925841 -165 CGGCTTGACCTTAAATGGTTATTTTTTCCC 4 181 1 TTAAATGGTT 0.926368 -120 TCAGCCCTTATTAAATTGTTATAGAACAGA 4 249 0 TTAAATTGTT 0.966952 -52 GAGCCACTGGTTAAATTTTTCATGGCTCGG 6 154 1 TTAAATTTTT 0.925841 -147 AGACTTTTTGTTAAATGTTTCTTTCCTCCT 7 105 0 TTAAATGTTT 0.842988 -196 CACTCCTACCCTAAATTGTTAACTTCCTAT 7 237 0 CTAAATTGTT 0.872388 -64 TCCACTTGTTGTAAATTGTTTGGCGATTTT 12 276 1 GTAAATTGTT 0.872388 -69 TATAAATGAATTAAATTGTTCTGATATTAA 13 45 0 TTAAATTGTT 0.966952 -256 AGCGTTTTCATTACATTGTTGTATTTTTAT 13 96 0 TTACATTGTT 0.859195 -205 TAGTAAAGCGTTAAATTTTTTCAGGAATAC 15 55 0 TTAAATTTTT 0.925841 -358 ********** Masking position 5 Map Score: 5.20926 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 107 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GAGAAGTAATAAACGCACTCTGCTTTTTTGT 1 27 1 AAACGCACTT 0.940693 -537 GAAAGGCGGTAAATGCGCTATGCTGATTGGT 2 278 1 AAATGCGCTT 0.981198 -323 GAACTTTACTAAAGGCTCTTTTCGGGGTTAC 5 462 1 AAAGGCTCTT 0.932121 -139 GAGTATACTGAAACACGCTTTTTGGCCATT 10 281 1 AAACACGCTT 0.949647 -20 ATCAACATAAAAATGCTCTATACCAGATAGA 11 468 0 AAATGCTCTT 0.970499 -121 TACAATTTTAAAATACTCTCTTAA 12 4 0 AAATACTCTT 0.88266 -341 CGATGAACTAAAATTCGCTTTGAAAAGTTTG 12 322 1 AAATTCGCTT 0.871234 -23 AATGTAATGAAAACGCTCTCTATTGATATGT 13 109 1 AAACGCTCTT 0.981195 -192 GCATTGACGGAAACGCGCTTTATTATGGACT 14 201 0 AAACGCGCTT 0.98805 -127 ********* * Masking position 3 Map Score: 4.05316 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 96 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ACTGCCCCATATGCAATTGGCGACAAGATTTT 2 20 1 ATGCATTGCG 0.971603 -581 ATCAGTTGGGCTGCTTTTGTCGTAAGTTTTGT 2 90 0 CTGCTTTGCG 0.975077 -511 AGAGGGTGAGGTGCGATTATCGGGGACATGTC 2 343 1 GTGCATTACG 0.852385 -258 ACAACTTGGGATACTATTGACGGCGGTAAGAT 8 203 0 ATACATTGCG 0.883469 -336 TAAATTTGCAGTGCGTTTGTAGATATCAAAGA 9 279 1 GTGCTTTGAG 0.979261 -22 CATTTCTTATGTACATTTGTTGAAGGAGTTCG 11 30 1 GTACTTTGTG 0.848241 -559 TAGTTATCTAATGCCATTGAAGGAGCAGATAT 12 50 1 ATGCATTGAG 0.936037 -295 AGAGGCGCCCGTGCTTTTGCCGATACATAAAC 12 157 0 GTGCTTTGCG 0.991051 -188 TTGTATATAAATACATTTGCAGTGGGGTGCAC 12 216 1 ATACTTTGAG 0.812797 -129 GCCTGCTCGGGTGCCTTTGCTGTCTCCAAGCT 13 266 0 GTGCTTTGTG 0.962022 -35 TATTTCCCAGCTGCCTTTGAAGTAGTTTCACG 14 64 0 CTGCTTTGAG 0.94344 -264 ACTCAAAGATGAGCGATTGACGATCTGAGAAT 14 131 0 GAGCATTGCG 0.903113 -197 **** **** ** Masking position 7 Map Score: 5.57465 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 501 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 AAGGGCATACAACAAAAAAATAATAAACCTAAAATCA 1 369 0 AAAAAATATA 0.773075 -195 GAACACATATATATAAATACATATATAAGAGGAAGAA 2 139 0 AAAAACAATA 0.640134 -462 ACGACAACCCACTCAAAAAAGTATATATTCACTGTTA 2 441 1 AAAAAAGATA 0.66648 -160 TTCGAAAGATATATAAACGAATATGAACTGGACTGAA 3 197 1 AAAAGAAATA 0.884618 -104 TTTAGTTAATACAGAAAAAAATATCTAAGTTCAGTCC 3 226 0 AAAAAAAATA 0.961569 -75 ATTTAGCGCAAATAATAACAATATCAACAATATCTGC 3 263 1 AATACAAATA 0.65894 -38 AAACTGGTTAACACAAACGATGATACAAAACTGGATG 4 41 0 AAAAGATATA 0.510741 -260 TGTGCCTTGAATATATATAAATATATATATTGCTATA 5 297 1 AATAAAAATA 0.923449 -304 AAATATATAGGAGGAAAGAAACATTTAACAAAAAGTC 7 97 1 GAAAAAAATA 0.779361 -204 ATTAACGAATATGAAAAAAAAAATTGAAAATTTTGTA 7 169 0 AAAAAAAATA 0.961569 -132 TCTGTAGAAGAGTTATGAAAATATACACTTAAACTAT 8 86 0 AATGAAAATA 0.620969 -453 CTACAGAAGAAACTATACAAAGATTAAACAACCGTTT 8 116 1 AATAAAAATA 0.923449 -423 AAAGGTTGAAATTAATACGAACTTTGACCTGGCCTTA 8 391 1 AATAGAATTA 0.334798 -148 ATGGCAGATGAAGAAAGAAAAGATTAAGAAGGTTAAT 8 498 1 AAAGAAAATA 0.772625 -41 ACAATTGAGAAAGTAAACAAACGTGCACACGCAAAGG 9 88 0 AAAAAAAGTA 0.66648 -213 AACAGAATAGACACAAATAAATTTGCAGTGCGTTTGT 9 262 1 AAAAAAATTA 0.773075 -39 TCGGGCCAATAGAGAAATAAAAATAAAAAATCATGTA 10 137 1 AAAAAAAATA 0.961569 -164 AAAGGAAGAGAATAAAACGATAATAAAAGGAAAGACA 11 421 0 AAAAGATATA 0.510741 -168 TTTAATAGGTAGTGATAAAAAATTTGACGATATCAAA 11 536 0 AATAAAATTA 0.621571 -53 AATTTAATTCATTTATATAAACATATACAATCAATCG 13 58 1 AATAAAAATA 0.923449 -243 ATATACAATCAATCGAATAAAAATACAACAATGTAAT 13 80 1 AGAAAAAATA 0.640134 -221 GTTGGTTAATAAAGAAACAAATATGTAAAAATATAAT 14 233 1 AAAAAAAATA 0.961569 -95 TGGCAAAATACCAAAAAGAAAGATGAAAAGGATAAAC 15 130 0 CAAAAAAATA 0.65746 -283 GCGTATTACAAATGAAACCAAGATTCAGATTGCGATC 16 11 0 AAAACAAATA 0.80029 -290 CCAATCGCTAAGAAAAAAAAAGAGTCATCCGCTAGGT 16 169 1 AAAAAAAAGA 0.772625 -132 TCCGCTAGGTGGAAAAAAAAAAATGAAAATCATTACC 16 196 1 GAAAAAAATA 0.779361 -105 ATCATTACCGAGGCATAAAAAAATATAGAGTGTACTA 16 224 1 AATAAAAATA 0.923449 -77 GGAGGCCAAGAGTAATAGAAAAAGAAAATTGCGGGAA 16 263 1 AATAAAAAGA 0.620969 -38 * *** *** ** * Masking position 17 Map Score: 8.98586 Number of sites scoring better than the average of aligned sites = 2458 Number in coding regions = 995 Number in noncoding regions = 1463 Number of orfs with sites within 600 bp upstream = 906 Fraction of orfs with sites within 600 bp upstream = 0.145519 Motif number 8 GCACGAAGGATTGTTACTTTATTTGTAAAA 1 162 0 TTGTTACTTT 0.856268 -402 GTTTTCCCTTTTGTTATGATAATAGTAGTT 1 444 1 TTGTTATGAT 0.909943 -120 ATATTTGTCGTTGTTCTTTTTTGTGTGCTC 2 534 1 TTGTTCTTTT 0.856268 -67 TGCCAAGCAATTGTTACTATGGAAACTATT 3 154 0 TTGTTACTAT 0.909943 -147 ATTGTTGATATTGTTATTATTTGCGCTAAA 3 264 0 TTGTTATTAT 0.941631 -37 CCCTTGTGACTTGTTCTTTTCTCCCTATTT 4 122 1 TTGTTCTTTT 0.856268 -179 TGACCTTAAATGGTTATTTTTTCCCGTATA 4 186 1 TGGTTATTTT 0.784973 -115 GGCAAACCGTTTGTTACGATTGCTCAAAAA 8 278 0 TTGTTACGAT 0.863545 -261 CTGAAATATATGGTTATTATTCGAAGAACT 11 133 0 TGGTTATTAT 0.860949 -456 ATGAATTAAATTGTTCTGATATTAACTGAA 13 40 0 TTGTTCTGAT 0.863545 -261 TCAATTATCCTTGTTATTATTGTTGTTGAC 15 390 0 TTGTTATTAT 0.941631 -23 ********** Masking position 5 Map Score: 3.85233 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 489 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 9 ACGCACTCTGCTTTTTTGTTCGCTTGTCAGA 1 39 1 CTTTTTTTTC 0.949559 -525 AAAAATTGTTTTTTTTTTTACAAATAAAGTA 1 147 1 TTTTTTTTAC 0.79719 -417 CCCAAATATCCTCTTCTTTACTTTGAAATGT 1 258 0 CTCTTCTTAC 0.873143 -306 TTTTTGTGTGCTCTTTTATACTTCAGAATCA 2 551 1 CTCTTTTTAC 0.912128 -50 AAATTTTCAATTTTTTTTTTCATATTCGTTA 7 173 1 TTTTTTTTTC 0.869566 -128 TTATTTGTGTCTATTCTGTTCCGATTAATTG 9 251 0 CTATTCTTTC 0.849674 -50 TATTATCGTTTTATTCTCTTCCTTTTTTATA 11 433 1 TTATTCTTTC 0.66685 -156 GCACGGGCGCCTCTTTTTTTCCTCGCTTACT 12 175 1 CTCTTTTTTC 0.946252 -170 TATTTGGGAACTCTTCTCTGCTTTGAAGACA 14 98 0 CTCTTCTTGC 0.892609 -230 GCGTTTGGCTCTTTTTTGTGCTCTCTCAAGT 14 281 0 CTTTTTTTGC 0.930573 -47 TCACTCAATTCTATTTTCTACAATCAGGTTT 15 13 1 CTATTTTTAC 0.834049 -400 GCGGATGACTCTTTTTTTTTCTTAGCGATTG 16 170 0 CTTTTTTTTC 0.949559 -131 TGATTTTCATTTTTTTTTTTCCACCTAGCGG 16 197 0 TTTTTTTTTC 0.869566 -104 ACACTCTATATTTTTTTATGCCTCGGTAATG 16 226 0 TTTTTTTTGC 0.825988 -75 ******* *** Masking position 5 Map Score: 6.35057 Number of sites scoring better than the average of aligned sites = 1590 Number in coding regions = 719 Number in noncoding regions = 871 Number of orfs with sites within 600 bp upstream = 682 Fraction of orfs with sites within 600 bp upstream = 0.109541 Motif number 10 ATCATGGTCCATTGCAAACATTTCAAAGTA 1 241 1 ATTGCAAACA 0.914483 -323 TTAGAATCTCATTGGAAACAATCCTCGTTT 1 291 1 ATTGGAAACA 0.972305 -273 CTTGTTCTCCATTGGAAACAGTGCTCGTGC 2 247 0 ATTGGAAACA 0.972305 -354 TCGCTTTTTCGTGGAAACCAAATATCAAA 5 10 1 CGTGGAAACC 0.887357 -591 AATTACTACTCTTGGAAACAGCGGGATCAT 5 333 0 CTTGGAAACA 0.98571 -268 ACAATTTCCCCTTGGAAGCATTGGGTAAA 8 10 0 CTTGGAAGCA 0.971195 -529 TGAAAATTACATTGCAAGCAACTGCCATGA 13 14 0 ATTGCAAGCA 0.839411 -287 ACAACAGTAGCTTGGAGACAGCAAAGGCAC 13 258 1 CTTGGAGACA 0.941576 -43 CCCGAGCAGGCGTGGAAACACACG 13 287 1 CGTGGAAACA 0.971195 -14 ********** Masking position 6 Map Score: 5.22693 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 245 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 GTGTTGGTGATGAAGAAGAAATAGGGAGAAA 4 139 0 TGAGAAGAAA 0.915051 -162 ATCCGTTTGATAATGAAGTAAATTAGTATTT 5 57 1 TAAGAAGTAA 0.872911 -544 GCTGCTGACCTACAAAAGAAATACTAATTTA 5 75 0 TACAAAGAAA 0.916796 -526 TAGCCAGCAGTACGGAAGTAATCCGAGCCAT 6 175 0 TACGAAGTAA 0.916621 -126 GATAAGAAAATGCGAAAGGAAAATGATGAAA 8 52 0 TGCAAAGGAA 0.882032 -487 ATAACTCTTCTACAGAAGAAACTATACAAAG 8 107 1 TACGAAGAAA 0.954457 -432 TATCATGGAGTGATGAAGAAAAATTCAAACT 8 313 0 TGAGAAGAAA 0.915051 -226 CGCAAACAATTGAGAAAGTAAACAAACGTGC 9 99 0 TGAAAAGTAA 0.748164 -202 TCAACAAATGTACATAAGAAATGTTTATCAC 11 22 0 TACTAAGAAA 0.731063 -567 AAGGTAGGCATACCGAAGGAAGAGACAATGA 11 164 1 TACGAAGGAA 0.945313 -425 TAGAATTTTATAAAAAAGGAAGAGAATAAAA 11 441 0 TAAAAAGGAA 0.850264 -148 TGCCGTTGGTTAATAAAGAAACAAATATGTA 14 229 1 TAAAAAGAAA 0.873165 -99 *** ******* Masking position 6 Map Score: 2.52984 Number of sites scoring better than the average of aligned sites = 1318 Number in coding regions = 962 Number in noncoding regions = 356 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 12 TTCACTAATATGTTCAGAATTCTACAATAT 1 102 1 TGTTCAGAAT 0.732386 -462 TATATATATGTGTTCACTATAACCATACAT 2 161 1 TGTTCACTAT 0.844767 -440 TGATGTTATTTGTTACGTATGGAAAAATCG 2 213 0 TGTTACGTAT 0.778108 -388 TGTATTGCAATGTTCCGTATAACTAACAGT 2 471 0 TGTTCCGTAT 0.978024 -130 TTAGATATTTTTTTCTGTATTAACTAAAAT 3 235 1 TTTTCTGTAT 0.78284 -66 ACTTGTTCTTTTCTCCCTATTTCTTCTTCA 4 130 1 TTCTCCCTAT 0.586688 -171 ATATCAAAGTTGTTCCTTATCATGTATCCG 5 32 1 TGTTCCTTAT 0.761525 -569 GATTATTGTGTGCTCAGTATCGGTTGAAAC 5 217 1 TGCTCAGTAT 0.927515 -384 TACCCCTAAATTTTCAGTATTTGATTTGTA 5 490 1 TTTTCAGTAT 0.90781 -111 AGAAACGGAGTGCTCAGTATAAAAAGCGCA 7 140 0 TGCTCAGTAT 0.927515 -161 CCTTTCTATGTTTTCCGTATTTCTTCCCCG 8 466 0 TTTTCCGTAT 0.940337 -73 TACTGAGCGCTGTTTTGTATATAAATACAT 12 202 1 TGTTTTGTAT 0.669596 -143 ATTAGGGCCATGTTTCGTATTTTATAACCC 15 174 0 TGTTTCGTAT 0.898584 -239 GCCTGCTCATTTTTTAGTATATTCTTCGAA 16 93 1 TTTTTAGTAT 0.662213 -208 ********** Masking position 9 Map Score: 3.48123 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 531 Number in noncoding regions = 248 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 13 ATCTAGTTCCTACTCTGGTCTTTTTGGAC 1 545 0 CCTACTCTGT 0.908082 -19 GGGCTCCAGTAGTAGAATGATGG 3 3 1 GCTCCAGTGT 0.936966 -298 TTGGCGCTTGACTCCACTCGTGAGTCATGTT 5 255 1 ACTCCACTGT 0.958055 -346 TCTAGTAATTACTACTCTTGGAAACAGCGGG 5 338 0 ACTACTCTGG 0.866905 -263 TTATTCTGTGGCTCCGCTTGTACGTGAACAG 6 108 1 GCTCCGCTGT 0.963436 -193 ATTTACAATTGCTGCACTAGGTCTACACTTT 11 346 1 GCTGCACTGG 0.88891 -243 GATCATTAAAGCTCCACTTGTTGTAAATTGT 12 264 1 GCTCCACTGT 0.983189 -81 CTGTCTCCAAGCTACTGTTGTTATCCGTTTG 13 248 0 GCTACTGTGT 0.861108 -53 TCTTTATTCTACTCCTCTTGGGAATCACTTT 15 312 0 ACTCCTCTGG 0.952473 -101 TTACTCTTGGCCTCCTCTAGTACACTCTATA 16 247 0 CCTCCTCTGT 0.967388 -54 ******** ** Masking position 8 Map Score: 2.09497 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 262 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 CTTAGTCGTACCACCTAGTAATAGTGTTATTG 1 502 1 CCACTAGAAT 0.902172 -62 TATTAAAAACTCAAATGGTATTTATATTGTGC 2 399 0 TCAATGGATT 0.868145 -202 AACAGCGGGATCATATAGCAATATATATATTT 5 315 0 TCAATAGAAT 0.958112 -286 CACCACGAACTCAAATAGGAAGTTAACAATTT 7 223 1 TCAATAGAAG 0.842374 -78 TTCTTTAAACTCAGATAGTATTAGAATCGATA 8 430 0 TCAATAGATT 0.96573 -109 TGCGTTAGCGTCACCTAGAAATCCCACTTTAA 10 181 0 TCACTAGAAT 0.917901 -120 TCTCAAAGTATCAGATAGTATTATGCACGGTA 11 286 0 TCAATAGATT 0.96573 -303 ATGCTCTATACCAGATAGAATTTTATAAAAAA 11 455 0 CCAATAGATT 0.958753 -134 AGAAGAGTTCCCAAATAGAATTCTCAGATCGT 14 112 1 CCAATAGATT 0.958753 -216 *** **** *** Masking position 6 Map Score: 1.08814 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 135 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 ********** No masking Map Score: 1.76523e-11 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