AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR_rpxx_opreg_300.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP025 90 unknown #2 RP069 266 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (dcd) #3 RP070 196 PROTEIN-EXPORT PROTEIN SECB (secB) #4 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #5 RP076 75 unknown #6 RP122 98 HFLK PROTEIN (hflK) #7 RP123 143 HFLC PROTEIN (hflC) #8 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #9 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #10 RP317 138 PROTEIN KINASE C INHIBITOR 1 (pkcI) #11 RP318 264 unknown #12 RP427 121 PETR PROTEIN (ompR) #13 RP696 300 PROBABLE TRANSPORT ATP-BINDING PROTEIN MSBA (msbA2) #14 RP755 282 PROLINE/BETAINE TRANSPORTER (proP5) #15 RP756 300 unknown #16 RP780 245 unknown #17 RP782 175 unknown #18 RP784 254 VIRB4 PROTEIN PRECURSOR (virB4) #19 RP785 112 unknown #20 RP822 300 unknown #21 RP852 211 PROLINE/BETAINE TRANSPORTER (proP6) #22 RP854 163 unknown #23 RP855 190 unknown #24 RP881 300 PROLINE/BETAINE TRANSPORTER (proP7) Motif number 1 GTATATATTTTTATTGAAATAAAATTGATAC 1 30 1 TATTGAAATA 0.744956 -61 TAATTCCATATTATTTAAATAATAAATTTAC 2 16 1 TATTTAAATA 0.916712 -251 TTAGCGTAGTTGATTTAATTAACTAATCTAA 2 63 0 TATTTAATTA 0.832333 -204 AATCAAAACTTTATTTAATTAATAAACTAAT 2 246 0 TATTTAATTA 0.737135 -21 GATGTTTATCTTATTCAAAAAACTTCATAAT 3 81 0 TATTCAAAAA 0.776133 -116 ATTCTACCTTTAATTGAAAAACAACAATATT 4 32 0 TATTGAAAAA 0.844413 -165 TAAAAAATTATAATTTAGTTAATAATTATTA 4 136 1 TATTTAGTTA 0.699813 -61 ATTTTGATAATAATTTAGTTAATAATTATTA 4 155 0 TATTTAGTTA 0.699813 -42 AATCTTAAAATAATATAAAAAAGCAA 6 83 1 TATATAAAAA 0.957682 -16 TGTTTGATTTTATTTAAAAAAATTATAGAA 9 10 1 TATTTAAAAA 0.952134 -80 TTTAAAAAAATTATAGAAAAAGTTTATTTTA 9 23 1 TATAGAAAAA 0.865227 -67 CAGTTGATCTTCATATAATAATCATTCTACT 11 72 0 TATATAATAA 0.910248 -193 GTTTCTAATCTAATATAAATATAACTTA 12 8 0 TATATAAATA 0.92473 -114 GTCAAGAATATTATATAGAAAATATGAATTT 13 19 0 TATATAGAAA 0.912815 -282 TCTAAGATTTTGATATAATTATCTTTTAATT 15 223 0 TATATAATTA 0.846292 -78 TTTAAAAATTTAATATAAAAATCACAAAAAA 16 13 0 TATATAAAAA 0.957682 -233 ATATAACGTATAATTTAAAAATTTAATATAA 16 26 0 TATTTAAAAA 0.953044 -220 CAAAGATCCATAATATAAAAAGCTGAAGCTG 16 115 1 TATATAAAAA 0.957682 -131 CATTAAACTATTATACAAAAAACTTTACCTT 18 33 0 TATACAAAAA 0.815046 -222 ATCGGTGCAATAATATAGTAAAAAATCTATA 18 216 1 TATATAGTAA 0.824318 -39 TTTTCAAAGATGATATAGAAAATTTTCAAGC 21 17 0 TATATAGAAA 0.912815 -195 GTTACTTTATTTATTTAAAAAGATAATAAAA 21 188 0 TATTTAAAAA 0.952134 -24 AAAACTTAGTTTATATAAAAAAGTAGTATGG 24 31 1 TATATAAAAA 0.95767 -270 * ********* Masking position 4 Map Score: 23.9467 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 333 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 TATTTCAATAAAAATATATACTTTATAATAGAAGC 1 16 0 AAATATATTA 0.835582 -75 CCATATTATTTAAATAATAAATTTACTATACAAAA 2 21 1 TAATAAATTA 0.891031 -246 GTAGTTGATTTAATTAACTAATCTAAAAGTTTATT 2 54 0 TAATAAATTA 0.913047 -213 TCAATTCTGCAAAGTATATTATATTTTAGCGTAGT 2 84 0 AAATATTTTT 0.714331 -183 TTTAATTAATAAACTAATGATTATAACGCATAATT 2 229 0 AAATAAATTA 0.913051 -38 ATTTTAAAGCTAATTAAAATCTTTTTAAGTGAGAA 3 46 1 TAATAATTTT 0.837503 -151 TTTAAGTGAGAAATTATGAAGTTTTTTGAATAAGA 3 69 1 AAATATATTT 0.819446 -128 AAAGCAAAAATTAATAAGATGTTTATCTTATTCAA 3 94 0 TTATAATTTA 0.837503 -103 TTTTGCCTAATAATTAAAAATTTTTAAAGCAAAAA 3 119 0 TAATAAATTT 0.903417 -78 TGTTAAATTTTTAATAAGGATTTTT 3 182 1 TTATAAATTT 0.892845 -15 GTAGAATTTAATAGTAAAAATTTTATAATTTGATT 4 56 1 ATATAAATTA 0.903419 -141 ATTAATAATATAAGTAAAGAATATTTAATCAAATT 4 82 0 TAATAAATTT 0.903419 -115 ATTATTAACTAAATTATAATTTTTTATCTAGTGCT 4 127 0 AAATATTTTT 0.714486 -70 TATAGTACTTATAATAATTTCTATAATTTCACTTA 5 49 0 ATATAATTTA 0.837692 -27 TTGACGTTATATACTATTATATATATAATCACTTA 6 49 1 ATATATTTTA 0.71463 -50 ATATTATAAAATAATAAGGAATATTAA 7 127 1 ATATAAATTT 0.892845 -17 ATTTTCGTTTATACTAACATATATATGATCTAAAA 9 49 0 ATATAATTTA 0.837694 -41 ATTAAGTTGTTAATTAAGTACTATAACATAATATT 11 28 1 TAATAAATTA 0.913051 -237 TGATCTTCATATAATAATCATTCTACTTTAGAATA 11 64 0 ATATAAATTA 0.903419 -201 TAATTCAATTTAATTAATTATTGTTCCTTGAATTT 11 220 1 TAATAAATTT 0.903419 -45 ATAATTAATGTAACTAATTAATCTTAAGCAAAAAT 15 72 1 TAATAAATTT 0.903415 -229 CTTTAATATTTTATTATCCATTTTTGCTTAAGATT 15 91 0 TTATATATTT 0.801698 -210 ATCTTAGATCAAATTAAAATTTATATTAATGAACT 15 246 1 AAATAATTTA 0.852813 -55 TGGTAATGTATTAATATACACTCTACTCCTCGTAT 17 88 1 TTATATATTA 0.819448 -88 AATTTGGAAAATAGTAATCAGTCTATAATACGAGG 17 115 0 ATATAAATTA 0.903419 -61 AAAACGCTGTAAATTAAAAATTTTTACTGGATTAC 18 151 1 AAATAAATTT 0.903417 -104 GTGCAATAATATAGTAAAAAATCTATAATTTAAAT 18 220 1 ATATAAATTA 0.903419 -35 TGACGATAGTTTATTATGAATTATAAAAACAACGA 19 70 1 TTATATATTA 0.819448 -43 CACAGTGCAAAAAGTATATTATCTTTATATAGTTT 20 65 1 AAATATTTTT 0.714331 -236 ATAGGATCTTTTATTATTTTTTGTAAAAAAGTTGC 20 141 0 TTATATTTTA 0.714632 -160 AAACAATAAAATACTAAAAACTATTAATATATCTG 22 46 1 ATATAAATTT 0.892845 -118 GCAATAACATTAAATAATATATCTTACC 23 4 0 TAATAATTTT 0.81754 -187 CCATATATCATAAATATTTTATGTTTATAGCAATG 24 72 0 TAATATTTTT 0.681394 -229 ATAATAATAATTAGTAATTAATTTATTTTAAATTC 24 275 1 TTATAAATTA 0.903415 -26 *** *** * * ** Masking position 6 Map Score: 37.6281 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 435 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 AATTAACTAATCTAAAAGTTTATTTTGTATAGT 2 45 0 TCTAAAGTAT 0.839979 -222 GCGATCTTAATTTTAAAGCTAATTAAAATCTTT 3 37 1 TTTTAAGTAT 0.962372 -160 AATTTCTCACTTAAAAAGATTTTAATTAGCTTT 3 51 0 TTAAAAGTTT 0.549838 -146 AAGTGAGAAATTATGAAGTTTTTTGAATAAGAT 3 72 1 TTATAAGTTT 0.766988 -125 AAAGCAAAAATTAATAAGATGTTTATCTTATTC 3 96 0 TTAAAAGTTT 0.549838 -101 TAAATTTCCTTTTTAAAGCTCTTTAAGCTGGTA 6 14 1 TTTTAAGTTT 0.89869 -85 TCTTTGCTCTTTTTGAAGTTGATCTTCTTACAA 7 79 1 TTTTAAGTAT 0.962372 -65 ACGAAAATAGTTTTTCAGGTTATT 9 76 1 TTTTCAGTAT 0.947508 -14 ACTACTATCTTTTTGCAGTTGATCTTCATATAA 11 85 0 TTTTCAGTAT 0.947509 -180 CAACGCAAATTTTTGAAGTTTATCAAGCATACT 11 183 1 TTTTAAGTAT 0.962372 -82 TCGCCCCATGTTTTACAGTTGTTATGTGATTAC 13 161 1 TTTTCAGTTT 0.86227 -140 GAGTAAGGCGTCTTGCAGCTTATAACAGAAGCG 14 199 1 TCTTCAGTAT 0.908957 -84 GAGTAAGGCGTCTTGCAGCTTATAATACTCACG 14 244 0 TCTTCAGTAT 0.908957 -39 CTGCAATAATTCATCAAGTTTATGCTCAACTTC 15 138 0 TCATAAGTAT 0.839979 -163 TTTCTTTATTTCTTCAAGTTCATTAATATAAAT 15 264 0 TCTTAAGTAT 0.933976 -37 CTTTGGTTCTTTCTGAAGTTGATTCTTATACTA 16 87 0 TTCTAAGTAT 0.776295 -159 ATCCAATAATTTTCAAAGATGATATAGAAAATT 21 24 0 TTTCAAGTAT 0.776295 -188 AGCTTGCTTTTTTAAAAGTTGATCCTCATCTAT 21 101 1 TTTAAAGTAT 0.904676 -111 CTTTATTTATTTAAAAAGATAATAAAAGGAATA 21 182 0 TTAAAAGTAT 0.778841 -30 CAATTTTCAATTTTCCAGCTCATGACGAAAATA 23 52 0 TTTTCAGTAT 0.947509 -139 **** *** * ** Masking position 10 Map Score: 22.4461 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 165 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 AAGTAGTTTTAGATTTTTTAAAGAAAAATT 2 186 1 AGATTTTTTA 0.789813 -81 TTTTAAAGAAAAATTTTGTATTGTAAATAA 2 201 1 AAATTTTGTA 0.678606 -66 CTAATAATTAAAAATTTTTAAAGCAAAAAT 3 118 0 AAAATTTTTA 0.745591 -79 AAAATTATGTTAAATTTTTAATAAGGATTT 3 175 1 TAAATTTTTA 0.793838 -22 ATCAAATTATAAAATTTTTACTATTAAATT 4 60 0 AAAATTTTTA 0.745591 -137 AACTAAATTATAATTTTTTATCTAGTGCTT 4 126 0 TAATTTTTTA 0.927468 -71 TTGCTTTTTTATATTATTTTA 6 88 0 TGCTTTTTTA 0.669013 -11 ACTTTTTCTATAATTTTTTTAAATAAAATC 9 16 0 TAATTTTTTT 0.54878 -74 TACTATAACATAATATTTTATTCTAAAGTA 11 46 1 TAATATTTTA 0.640881 -219 ACAACAACGCAAATTTTTGAAGTTTATCAA 11 179 1 AAATTTTTGA 0.678608 -86 TTAATCTCTTTAATATTTTATTATCCATTT 15 103 0 TAATATTTTA 0.640881 -198 TTTCGTTTTGTAATTTTTTTACTTCATTGT 15 187 0 TAATTTTTTT 0.54878 -114 AATTATCTTTTAATTTTTTATTTTCGTTTT 15 208 0 TAATTTTTTA 0.927468 -93 ATTTTTATATTAAATTTTTAAATTATACGT 16 22 1 TAAATTTTTA 0.793838 -224 TAGTACTGCGTACTTTTTTAGGATGACTTA 16 158 1 TACTTTTTTA 0.835691 -88 TAATCCAGTAAAAATTTTTAATTTACAGCG 18 155 0 AAAATTTTTA 0.745591 -100 TCAAAACTGATAATTTTTGATGACTAGGTA 18 187 1 TAATTTTTGA 0.740812 -68 TTTAAATTATAGATTTTTTACTATATTATT 18 224 0 AGATTTTTTA 0.789813 -31 GTAGAAGTTAAAATTTTTTACGTGAATAAG 19 28 0 AAATTTTTTA 0.904358 -85 CGTCATCCCGTAAATTTGTAGAAGTTAAAA 19 45 0 TAAATTTGTA 0.469107 -68 AAGTAATAGCAACTTTTTTACAAAAAATAA 20 133 1 AACTTTTTTA 0.789812 -168 AGAGATAGCTTGCTTTTTTAAAAGTTGATC 21 95 1 TGCTTTTTTA 0.669013 -117 ATGACAAAATAAATTTTTGATTCTTGCTGC 22 103 1 AAATTTTTGA 0.678608 -61 AACTAAGTTTTGATTTTGTAAAGCTTTATC 24 12 0 TGATTTTGTA 0.531783 -289 TAAACCATACTACTTTTTTATATAAACTAA 24 36 0 TACTTTTTTA 0.835691 -265 CATATATCATAAATATTTTATGTTTATAGC 24 76 0 AAATATTTTA 0.572799 -225 ********** Masking position 6 Map Score: 24.5876 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 474 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 TATTATAAAGTATATATTTTTATTGAAATAAAATTG 1 21 1 TTATATATGA 0.795808 -70 AATACAACGCTATATACTTAAAATTAAGAATTTAAT 2 131 0 TTATATATTA 0.875066 -136 ATTAAAAATTTTTAAAGCAAAAATTAATAAGATGTT 3 106 0 TTAAAAATTA 0.547711 -91 GCGAACAGGCTCTAAAAATTATGTTAAATTTTTAAT 3 161 1 TTAAATTTTA 0.609885 -36 TAGTAAAAATTTTATAATTTGATTAAATATTCTTTA 4 67 1 TTATATATAA 0.885787 -130 TATCTAGTGCTTTATACGTTCATTAATAATATAAGT 4 102 0 TTATATATAA 0.8858 -95 TATAATAATTTCTATAATTTCACTTAAATGTCTTGA 5 39 0 TTATATATTA 0.875066 -37 TATATAGTACTTATAATAATTTCTAT 5 60 0 TTATAATTAA 0.857309 -16 TATACTATTATATATATAATCACTTAATCTTAAAAT 6 58 1 TTATAAATTA 0.84437 -41 ATAAACTTTTTCTATAATTTTTTTAAATAAAATCAA 9 14 0 TTATATTTAA 0.885694 -76 TCAAGAATATTATATAGAAAATATGAATTTATACAA 13 13 0 TTATAATTGA 0.752053 -288 ATATTCCAAGTGTATACCTCAAATAAATGAAGAGTA 16 53 1 TTATATATAA 0.8858 -193 ATCTGAATATTATAAACCTTTTTTAATAATTG 17 7 0 TTAAATTTAA 0.633866 -169 TAGTAAAAAATCTATAATTTAAATCAGGTTATTT 18 231 1 TTATATATCA 0.593614 -24 TTTGGTACTGTATATAACATGTATAAAGCTGAGGCA 20 25 1 TTATAATTAA 0.857312 -276 ATATTATCTTTATATAGTTTATATAATGTACCTTAT 20 80 1 TTATATTTAA 0.8858 -221 ATAGTCAAACTATATAGGATCTTTTATTATTTTTTG 20 153 0 TTATAATTTA 0.84437 -148 GTACTCATTGTGTATATTAGTACTAATACCCGTGGC 20 211 1 TTATAAATAA 0.857309 -90 TTGAAAATTTTCTATATCATCTTTGAAAATTATTGG 21 19 1 TTATAATTGA 0.752053 -193 ATATTTTATGTTTATAGCAATGCTTAGATAAACCAT 24 58 0 TTATAAGTTA 0.482239 -243 ATTTATAAAGTGTAAATATCATTTTAACTAAGAATA 24 225 0 TTAAATTTTA 0.609885 -76 ATATTTACACTTTATAAATGATGTAAATTGTCTATA 24 242 1 TTATATTTAA 0.8858 -59 ATGTAAATTGTCTATAATAATAATTAGTAATTAATT 24 262 1 TTATAAATTA 0.844364 -39 * **** * * *** Masking position 3 Map Score: 17.234 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 370 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 ATTTATTCCTTTTGACTATTAACCATTCTACA 1 69 0 TTTTTGTTAA 0.361839 -22 ATCTAAAAGTTTATTTTGTATAGTAAATTTATTATT 2 33 0 TTTTTGTGAA 0.4553 -234 CAACGCTATATACTTAAAATTAAGAATTTAATAGTT 2 127 0 TTTAAATAAA 0.517728 -140 GTATTGTAAATAATTATGCGTTATAATCATTAGTTT 2 218 1 TTTATGTAAA 0.665855 -49 AATCAAAACTTTATTTAATTAATAAACTAATGATT 2 242 0 TATTTATAAA 0.721522 -25 TAAAAAGATTTTAATTAGCTTTAAAATTAAGATCGC 3 37 0 TATTAGTAAA 0.506389 -160 CTAATTAAAATCTTTTTAAGTGAGAAATTATGAAGT 3 55 1 TTTTTATAAA 0.940539 -142 ACATCTTATTAATTTTTGCTTTAAAAATTTTTAATT 3 107 1 ATTTTGTAAA 0.596761 -90 GTTCGCAATTTTATTTTGCCTAATAATTAAAAATTT 3 131 0 TTTTTGTAAA 0.929782 -66 TATTAAATTCTACCTTTAATTGAAAAACAACAATAT 4 33 0 TCTTTATAAA 0.682358 -164 AAAGATAGAATTCTTTTATGTTAAAAGTCAAGACAT 5 12 1 TTTTTATAAA 0.940527 -64 ATATATATAATCACTTAATCTTAAAATAATATAAAA 6 67 1 TCTTAATAAA 0.498177 -32 AACATCGTAGTACTTTAGCATGATATATCTAATT 7 9 0 TTTTAGTAAT 0.672796 -135 GATGTTCACATCATTTAGGATAAGATTTTATCTCAT 7 39 1 TTTTAGTAAT 0.672796 -105 CTTACAAGGCTTTTTTAGTATGATATTATAAAATAA 7 105 1 TTTTAGTAAT 0.672781 -39 TGTTTGATTTTATTTAAAAAAATTATAGAA 9 5 1 TTTTTATAAA 0.940451 -85 TAGAAAAAGTTTATTTTAGATCATATATATGTTAGT 9 36 1 TTTTTATAAT 0.838537 -54 TGCAGCATCTAAATTTTACCTCACAATGATGATAAT 10 33 0 ATTTTATAAA 0.633346 -106 ATAATCATTCTACTTTAGAATAAAATATTATGTTAT 11 50 0 TTTTAGTAAT 0.672795 -215 TAAGTTATATTTATATTAGATTAGAAACTCATCCCG 12 11 1 TTATTATAAA 0.39073 -111 ATATAAATTTTAATTTGATCTAAGATTTTGATATAA 15 236 0 TTTTGATAAT 0.311279 -65 TATAATTTAAAAATTTAATATAAAAATCACAAAAAA 16 13 0 ATTTAATAAA 0.443877 -233 TCAGATATACTTGTTTAATATGAAAAATTGATACCA 17 37 1 TTTTAATAAA 0.879477 -139 TTTACCTTATTATTTATATTTAATAAAGAA 18 5 0 TTTATATAAA 0.692506 -250 TTTTGTATAATAGTTTAATGTAAAATTAGCTATGTA 18 44 1 TTTTAATAAT 0.705882 -211 ATGCTCGTTGTTTTTATAATTCATAATAAACTATCG 19 73 0 TTTATATAAA 0.698893 -40 GGATCTTTTATTATTTTTTGTAAAAAAGTTGCTATT 20 137 0 TTTTTTTAAA 0.492847 -164 ACTATAGAGTTTTTTTTGCTTTATAATGTACTCATT 20 184 1 TTTTTGTAAA 0.930957 -117 ATTTGGGTTATGTTTTTACTTGAGAAAGTACACTAT 21 149 1 TTTTTATAAA 0.940538 -63 TCAGTTACTTTATTTATTTAAAAAGATAATAAAA 21 188 0 TATTTATAAA 0.721239 -24 AAATCAAAACTTAGTTTATATAAAAAAGTAGTATGG 24 26 1 TGTTTATAAA 0.538478 -275 AGTGTAAATATCATTTTAACTAAGAATAAGAAAGTT 24 217 0 TTTTTATAAA 0.940538 -84 TAATTAGTAATTAATTTATTTTAAATTCA 24 282 1 TATTTATAAT 0.459681 -19 * ***** * * ** Masking position 11 Map Score: 21.8682 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 411 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 7 TTAAATATTCTTTACTTATATTATTAATGA 4 89 1 TTTACTTATA 0.584974 -108 TATATAGTACTTATAATAATTTCTA 5 61 0 AGTACTTATA 0.954749 -15 TTACACGTATATTACGTATACGCTATGTTC 11 130 0 ATTACGTATA 0.676271 -135 CGGGTTCAAAATTATTAATATCATAGTTGT 12 70 0 ATTATTAATA 0.522563 -52 TCTTTTCACAATTACTAATAATTAGTAATC 13 188 0 ATTACTAATA 0.815451 -113 AAAACAATTAGTACTTATATCGATTATGA 15 10 1 AGTACTTATA 0.954749 -291 ATACATTACCAGTACTTATAGGACCTTGGT 17 69 0 AGTACTTATA 0.954749 -107 ACTTTACCTTATTATTTATATTTAATAAAG 18 13 0 ATTATTTATA 0.733181 -242 TGTGTATATTAGTACTAATACCCGTGGCTT 20 219 1 AGTACTAATA 0.893663 -82 TTGTAATGACAGTTCTTATACCCATGCAGA 23 140 1 AGTTCTTATA 0.728325 -51 AATGGTTTTAAGTATTTATAATCTAGTTTA 24 165 0 AGTATTTATA 0.839392 -136 ********** Masking position 8 Map Score: 7.09343 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 36 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TAGAAACTCATCCCGTGGTTTGACCACGAA 12 32 1 TCCCGTGGTT 0.97705 -90 TGTTTTTGGCTTTCGTGGTCAAACCACGGG 12 43 0 TTTCGTGGTC 0.756853 -79 ATAATTTTGAACCCGTGGTCAAACCACGAG 12 85 1 ACCCGTGGTC 0.991338 -37 TCATTTTACATCTCGTGGTTTGACCACGGG 12 96 0 TCTCGTGGTT 0.920755 -26 CGGGATTCGAACCCGTGGCCCTCAGAACCA 13 127 0 ACCCGTGGCC 0.987185 -174 TAGTACTAATACCCGTGGCTTGACCACCGG 20 228 1 ACCCGTGGCT 0.973796 -73 AAGACTGGATACCGGTGGTCAAGCCACGGG 20 239 0 ACCGGTGGTC 0.956561 -62 ********** Masking position 6 Map Score: 5.21332 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 2 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAGAAGATCAACTTCAAAAAGAGCAAAGATC 7 77 0 ACTCAAAAAG 0.973112 -67 ATGAAGATCAACTGCAAAAAGATAGTAGTTC 11 89 1 ACTCAAAAAG 0.973112 -176 TGCTTGATAAACTTCAAAAATTTGCGTTGTT 11 181 0 ACTCAAAAAT 0.899642 -84 TCTGTTATAAGCTGCAAGACGCCTTACTCTT 14 197 0 GCTCAAGACG 0.877364 -86 AGTATTATAAGCTGCAAGACGCCTTACTCTT 14 248 1 GCTCAAGACG 0.877364 -35 AAGTAAAAAAATTACAAAACGAAAATAAAAA 15 193 1 ATTCAAAACG 0.893572 -108 ATAAGAATCAACTTCAGAAAGAACCAAAGAT 16 91 1 ACTCAGAAAG 0.87204 -155 CTCAGATAGAACTCCAAAAATTTGCTAAGTC 16 182 0 ACTCAAAAAT 0.899646 -64 CTTTTCCTGGATTGCAAAACGTAGTATATGA 18 116 0 ATTCAAAACG 0.893572 -139 TTACTGGATTACTTCAAAACTGATAATTTTT 18 174 1 ACTCAAAACT 0.923253 -81 GCAGTATCACAGTGCAAAAAGTATATTATCT 20 58 1 AGTCAAAAAG 0.840221 -243 *** ******* Masking position 6 Map Score: 7.084 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 33 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 AACCTGAAAAACTATTTTCGTTTATACTAA 9 67 0 ACTATTTTCG 0.884359 -23 TGGAAAACACACTATTTTTCATTCTGTGTC 13 233 1 ACTATTTTTC 0.837657 -68 AAGACGCCTTACTCTTTTCCAAATCCAACG 14 183 0 ACTCTTTTCC 0.981289 -100 AAGACGCCTTACTCTTTTCCAAATCCAACT 14 263 1 ACTCTTTTCC 0.981289 -20 TAGACTGATTACTATTTTCCAAATTAAACT 17 125 1 ACTATTTTCC 0.970891 -51 CAGCGTTTTTATTCTTTTCCTGGATTGCAA 18 130 0 ATTCTTTTCC 0.890271 -125 ********** Masking position 5 Map Score: 2.87975 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TAATCTAAAAGTTTATTTTGTATAGTAAATT 2 40 0 GTTTTTTTGT 0.739311 -227 TATAGAAAAAGTTTATTTTAGATCATATATA 9 34 1 GTTTTTTTAG 0.713443 -56 TAATATCATAGTTGTTTTTGGCTTTCGTGGT 12 54 0 GTTGTTTTGG 0.954437 -68 ATGTATACTCGTTGGATTTGGAAAAGAGTAA 14 174 1 GTTGATTTGG 0.962698 -109 AGTTGGATTTGGAAAAGAGTAA 14 271 0 GTTGATTTGG 0.962698 -12 GATAGGTGGAGTTTAATTTGGAAAATAGTAA 17 133 0 GTTTATTTGG 0.969029 -43 TGACTATAGAGTTTTTTTTGCTTTATAATGT 20 182 1 GTTTTTTTGC 0.807813 -119 CTACTCTCTTATTTTATTTGGGTTATGTTTT 21 134 1 ATTTATTTGG 0.754141 -78 GAATAAGAAAGTTTTATTAGGAATGATTACA 24 199 0 GTTTATTAGG 0.831434 -102 **** ****** Masking position 7 Map Score: 2.60247 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 CACTCTTATTGTAGAATGGTTAATAGTCAA 1 60 1 GTAGAATGGT 0.95683 -31 TTATTCTAAAGTAGAATGATTATTATATGA 11 63 1 GTAGAATGAT 0.933756 -202 ATAATGAAAAGTAGATAGGTGGAGTTTAAT 17 147 0 GTAGATAGGT 0.922356 -29 GTGTCACCACGTAGATTGATCAGGTTGTCC 20 275 0 GTAGATTGAT 0.933756 -26 AAATAAGAGAGTAGATAGATGAGGATCAAC 21 118 0 GTAGATAGAT 0.883105 -94 ATATAAAAAAGTAGTATGGTTTATCTAAGC 24 43 1 GTAGTATGGT 0.845394 -258 ********** Masking position 3 Map Score: 1.5383 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 5 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 CTTTGCAGAATTGACAATAAGAAACTATTAA 2 105 1 TTACAATAAG 0.600693 -162 CGCTATATACTTAAAATTAAGAATTTAATAG 2 129 0 TTAAATTAAG 0.847386 -138 TTAATTAGCTTTAAAATTAAGATCGCGAATA 3 32 0 TTAAATTAAG 0.847386 -165 TTATATTATTTTAAGATTAAGTGATTATATA 6 70 0 TTAGATTAAG 0.823543 -29 ATAAAATTTATTGATATTAAGTTGTTAATTA 11 13 1 TTATATTAAG 0.957226 -252 AAGATAGTAGTTCACATCAAGAGGAACATAG 11 107 1 TTACATCAAG 0.865337 -158 TAGTCCTAGGTTAATATTAAGCTCACGCACC 14 32 0 TTATATTAAG 0.957226 -251 GAAGTCCACCTTTACATCAAGGTCTTTGAAG 14 117 1 TTACATCAAG 0.865337 -166 ATGTAACTAATTAATCTTAAGCAAAAATGGA 15 79 1 TTATCTTAAG 0.739452 -222 CAAATTAAAATTTATATTAATGAACTTGAAG 15 255 1 TTATATTAAT 0.59578 -46 TTTTGTGATTTTTATATTAAATTTTTAAATT 16 15 1 TTATATTAAA 0.786989 -231 GCTTCAGCTTTTTATATTATGGATCTTTGGT 16 113 0 TTATATTATG 0.656931 -133 GTATCAATTTTTCATATTAAACAAGTATATC 17 40 0 TTATATTAAA 0.788308 -136 ATATGAAAAATTGATACCAAGGTCCTATAAG 17 54 1 TTATACCAAG 0.542826 -122 CATAGCTAATTTTACATTAAACTATTATACA 18 47 0 TTACATTAAA 0.731954 -208 TGTTAAATGTTTTATATTAAGATTCGTAACA 24 129 0 TTATATTAAG 0.957196 -172 ** ******** Masking position 4 Map Score: 10.9665 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 47 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 ********** No masking Map Score: 8.44368e-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: 8.44368e-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