AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -irpoH_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 RP036 300 CLPB PROTEIN (clpB) #2 RP039 300 30S RIBOSOMAL PROTEIN S6 (rpsF) #3 RP040 24 30S RIBOSOMAL PROTEIN S18 (rpsR) #4 RP042 158 CELL CYCLE PROTEIN MESJ (mesJ) #5 RP043 50 CELL DIVISION PROTEIN FTSH (ftsH) #6 RP162 114 N UTILIZATION SUBSTANCE PROTEIN B (nusB) #7 RP184 122 DNAJ PROTEIN (dnaJ) #8 RP185 287 DNAK PROTEIN (dnaK) #9 RP319 264 HEAT SHOCK PROTEIN HSLV (hslV) #10 RP450 99 ATP-DEPENDENT PROTEASE LA (lon) #11 RP520 152 ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT (clpP) #12 RP521 249 30S RIBOSOMAL PROTEIN S1 (rpsA) #13 RP522 300 CYTIDYLATE KINASE (cmk) #14 RP615 90 RIBOSOMAL PROTEIN S21 (rpsU) #15 RP627 300 10 KD CHAPERONIN (groES) #16 RP629 211 GRPE PROTEIN (grpE) #17 RP692 114 ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX (clpX) #18 RP694 300 unknown #19 RP839 300 unknown #20 RP840 157 HEAT SHOCK PROTEIN HTPG (htpG) #21 RP860 270 unknown Motif number 1 CTTTAGTAACATTTAATTTTTTATAAGCATT 1 67 1 ATTTATTTTT 0.791447 -234 TGAGATCTCTTTTTGATTTTTCAATATTTCA 1 163 1 TTTTATTTTT 0.944525 -138 TCTCTTGTTATTTTAATTAAAAATCATTATA 1 225 1 TTTTATTAAA 0.536241 -76 AAATAACATATTTTCATTAATAAAGTGCAAT 1 278 0 TTTTATTAAT 0.920866 -23 GTCTTTGTTTATTTAATTTTTTATGTCATTT 2 101 1 ATTTATTTTT 0.791447 -200 TATCAAACACTTTTAAATAATCTGTTGATTA 2 139 1 TTTTAATAAT 0.608194 -162 TTAATAAGATTTTTAATTTTTGAAGATAATA 2 207 1 TTTTATTTTT 0.944525 -94 TATTATGACTTTTTATTTGATATAGTGCTGC 8 15 0 TTTTTTTGAT 0.488347 -273 TCAACAAGCCCTTTAATTATTGTATTATGAC 8 37 0 CTTTATTATT 0.823014 -251 CTCGTTTTCTTTTTGTTTATTATTAGCGTTG 8 260 0 TTTTTTTATT 0.907933 -28 GACTAATTCAATTTAATTAATTATTGTTCCT 9 38 0 ATTTATTAAT 0.721701 -227 TTATAGCAATTTTTAATTATATAATATAGTA 10 48 0 TTTTATTATA 0.785457 -52 CTATTCTAGCTTTTGATTATTATCTCACGCG 11 24 1 TTTTATTATT 0.973575 -129 AAGACTAACATTGTTATTATTTTTGATCTCA 11 62 0 TTGTATTATT 0.669517 -91 TTCTCCCAAAATTTGATTAATTAAAGATGTT 11 125 0 ATTTATTAAT 0.721737 -28 CTGATTACTGTTTTAGTTATTTTATGGATGT 12 104 1 TTTTGTTATT 0.828191 -146 TCTTGATACGTTTTCTTTACTTGGGTGTTTG 13 26 0 TTTTTTTACT 0.572524 -275 TACATCATATCTTTAATTGTTTGCATCGTTA 13 171 1 CTTTATTGTT 0.587615 -130 AATAATTAATTTTTGATTATATAATAGGCTT 13 221 1 TTTTATTATA 0.785457 -80 CTTTGCCACTTTTTAATTACTTAATATATAT 15 40 0 TTTTATTACT 0.833435 -261 AAAATAAAAATTTTTTTTATTAGAGATATAT 15 209 0 TTTTTTTATT 0.907933 -92 ATAAAAAAAATTTTTATTTTTCCCCCTTGAA 15 220 1 TTTTATTTTT 0.944525 -81 TACTATATATATTTTATTTTTGTTAGTTCAA 15 246 0 ATTTATTTTT 0.791447 -55 TTGCTACGTTATTTTATTTTTCGTACTAAAT 16 103 0 ATTTATTTTT 0.791447 -109 AATATTTTTTATATTAGTGTTCTTT 16 197 0 TTTTTATATT 0.568128 -15 TAATTTTCTTTTTTTAGTTTATAC 17 101 0 TTTTTTTTTT 0.820057 -14 GTTTCTCTAATTTTCATTATTACTAAAATTT 18 61 1 TTTTATTATT 0.973575 -240 TTCCTTTTGTTTTTAAATTTTAGTAATAATG 18 75 0 TTTTAATTTT 0.694302 -226 TAAAACTAATTTTTGATTATTATTGCATCTA 19 18 0 TTTTATTATT 0.973575 -283 AAACGCTTTATTTTATTTGTTGTATCTGCAG 19 72 1 TTTTTTTGTT 0.751359 -229 CCATTCTTCATTTTTGTTATTTTTAAACATA 19 108 0 TTTTGTTATT 0.828191 -193 ATTTATTACATTTTTATTATTTCTAATAAGA 19 269 0 TTTTATTATT 0.973575 -32 AGTTATTTTTAATTTATTACATTTTTA 19 284 0 TTTTATTTAT 0.843203 -17 TAGTATACTATTTTCAATAATATTGATTTCA 21 39 1 TTTTAATAAT 0.608197 -232 AAATAAGCCTTTTTAATTATTTAGTGTTTCC 21 100 1 TTTTATTATT 0.973575 -171 AATTTGAGTATTTTAATTGTTATCTAGACAC 21 180 0 TTTTATTGTT 0.91863 -91 **** ****** Masking position 4 Map Score: 37.0227 Number of sites scoring better than the average of aligned sites = 902 Number in coding regions = 535 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 TATGTATATCATATAAAATCTTTAGTAACATTT 1 48 1 ATATAATTTT 0.899605 -253 ATTTAATTTTTTATAAGCATTTTGAATACAATT 1 77 1 TTATAAATTT 0.911171 -224 CATCAAAGTAATATTATCAATTTTATCTTTCAT 1 123 1 ATATTAATTT 0.814358 -178 GACTATTTTCATATAATGATTTTTAATTAAAAT 1 234 0 ATATAAATTT 0.905454 -67 ATAAATAACATATTTTCATTAATAA 1 286 0 AAATAATTTT 0.813502 -15 ATCAACAAATTAATAAGATTTTTAATTTTTGAA 2 198 1 TAATAATTTT 0.871892 -103 ATATAAAACCTAATAAAAATTTTATCGGTACTA 5 26 0 TAATAAATTT 0.879348 -25 ATTAGTAAACTTATAAAATTTTT 6 1 0 TTATAATTTT 0.905549 -114 ATAAGTTTACTAATAAATTATTTTAAGATATAA 6 20 1 TAATAATTTT 0.820743 -95 AAATTATGTTATAATAGTTGTTTTATACGACGA 7 99 0 ATAATATTTT 0.573165 -24 AAAAAACAACTTATAATTTATTTCTAGATCCTG 8 169 1 TTATAATTTT 0.904907 -119 CAATTAAAACCTTTTTAAAAATTTAT 10 84 0 TTAAAATTTT 0.758538 -16 GTGCATAAGCTAATAAAAATTTTTTAAAGGTTA 12 202 0 TAATAAATTT 0.879348 -48 GGGTGTTTGATAATAACTTTTTTG 13 2 0 TAATAATTTT 0.853707 -299 ATCAAGATTAAAATAAGCTTTTTAAAAAAGTAT 13 68 0 AAATAATTTT 0.846147 -233 CTAAAACTGCAAATAATTAATTTTTGATTATAT 13 210 1 AAATAAATTT 0.521712 -91 CAAGTTACAAATAATAATTATTTATATTTAATA 13 259 0 ATAATATTTT 0.539197 -42 AATTGCAAAATTATAATAACTTTTATGCTGTAT 15 74 1 TTATAAATTT 0.911172 -227 AAAGTGGTATTTATAATGATTTTTTGTACTTTA 15 125 1 TTATAAATTT 0.911171 -176 CAAGGGGGAAAAATAAAAATTTTTTTTATTAGA 15 216 0 AAATAAATTT 0.863454 -85 TAACCTCCAATTATTAAATCTTTAAATGTACAT 15 276 0 TTATTATTTT 0.814642 -25 ATATATATAGATATAATAAATTTTTTTTCAACG 16 158 0 ATATAAATTT 0.905255 -54 TATTATATAGAAAATATGAATTTATACAACAAT 18 15 1 AAAATAATTT 0.490722 -286 AAAAAGTTTGATAAAACTAATTTTTGATTATTA 19 27 0 ATAAAAATTT 0.73667 -274 TTTTCCATTTTTAAAAAAAGTTTGATAAAACTA 19 41 0 TTAAAAATTT 0.770695 -260 TATTTTTAATTTATTACATTTTTATTATTTCTA 19 275 0 TTATTATTTT 0.81464 -26 ATAGTTTTATTACATTTTTCTTCTGTCGT 20 7 1 TTATTATTTT 0.81464 -151 GATCCATGTAAAAATACAAATTTGAGTATTTTA 21 196 0 AAAATAATTT 0.490722 -75 ATGTAGCAATAAATTAGTAATTTT 21 257 1 AAATTAATTT 0.470622 -14 ****** * *** Masking position 6 Map Score: 33.1857 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 471 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 3 AAATTTACTATGATTATGTATATCATATAAAATCTTTAGTAA 1 34 1 TATGATTTAA 0.70441 -267 TGTTTACAGTAAACCTTGTATAACATCAACAAATTAATAAGA 2 174 1 AATGATTAAA 0.786641 -127 TATTGTAAAATATTCGTGAATACTGTGATCAAACATAGTATG 4 108 0 TTTGATTAAA 0.969967 -51 TGAGTGATAATTTTTCTGGATACCTTCGTCAAGTTACGGT 6 85 1 TTTGATTGAA 0.921549 -30 AGCGTGCGTTTTTTACTGGATGACGTGGTTAAGCCATGGTAT 7 53 1 TTTGATTGAA 0.92155 -70 TTATAAGTTGTTTTTTTGAATACCGTGGACAAGCTGCGATGT 8 143 0 TTTGATTGAA 0.92155 -145 GAAATCCAGTTGATACTATATTATATAATTAAAAATTGCTAT 10 35 1 TATAATTAAA 0.776622 -65 TAAAATTGGATGTTATTGCATCAATTGAGAAACAAACGTGTT 12 159 0 TTTGATTAAA 0.969967 -91 TAATATTAGCTGAAAGTGCATAAGCTAATAAAAATTTTTTAA 12 208 0 TATGATTAAA 0.963007 -42 TTAGTAATAATCTATATATATTAAGTAATTAAAAAGTGGCAA 15 27 1 TTTAATTAAA 0.811799 -274 TTTTTCGTACTAAATATGTATGTTGTGATCAATAAAACATTT 16 76 0 TATGATTAAA 0.963007 -136 AAATTTATTATATCTATATATATCTTAAAAAAGAACACTAAT 16 168 1 TTTAATTAAA 0.811782 -44 AAGTGGGATTACAATATGTATAAACTAAAAAAAGAAAATTA 17 84 1 AATGATTAAA 0.786641 -31 TATAAATGGTTATGAGTGTATTACTTTAGCAAAGTCTAGGCA 18 209 1 TTTGATTAAA 0.969967 -92 TTAGAAATAATAAAAATGTAATAAATTAAAAATAACT 19 274 1 TATGAATAAA 0.663307 -27 ATATTTACCATATTTCTGGATACCGTAAGGAATATGAGACGA 20 36 0 TTTGATTAAA 0.969967 -122 AAATTATATTGTATAGATTTAGTAATTTTAGTATA 21 4 1 TATGATTAAA 0.963005 -267 AATTTGTATTTTTACATGGATCTCATAATAAATTACATGATG 21 207 1 TTTGATTAAA 0.969967 -64 * * ** ** * * ** Masking position 7 Map Score: 24.5757 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 50 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 CTTTGTAACTTTTGACAAATTTACTATGATTAT 1 18 1 TTTGAATTTA 0.938096 -283 ATTAATAAGATTTTTAATTTTTGAAGATAATAC 2 206 1 TTTTATTTTG 0.719721 -95 AAAAATTTTATAAGTTTACTAATAAATT 6 6 1 TTTTAATTTA 0.952316 -109 ACAACGCAAATTTTTGAAGTTTATCAAGCATAC 9 71 0 TTTTAATTTA 0.952316 -194 ATTAAAACCTTTTTAAAAATTTATATAGTTTAT 10 75 0 TTTTAATTTA 0.952316 -25 TGATTACTGTTTTAGTTATTTTATGGATGTATT 12 105 1 TTTATATTTA 0.530175 -145 TAATAAAAATTTTTTAAAGGTTAATAAAATTGG 12 192 0 TTTTAAGTTA 0.787032 -58 CTGTTTTACATCTTTATTAGTAATAA 15 4 1 TTTTATTTTA 0.866703 -297 GTTATTATAATTTTGCAATTTTACTTTGCCACT 15 61 0 TTTTAATTTA 0.952316 -240 TTATAATGATTTTTTGTACTTTAAAATAGAAGT 15 135 1 TTTTTATTTA 0.866703 -166 CATTTTGCTCTTTTTGAAATTTGCTTTCGTATA 16 48 0 TTTTAATTTG 0.887481 -164 AATCATTTAATTTGAAAAATTTGCTACGTTATT 16 121 0 TTTGAATTTG 0.856833 -91 TAATTTTCTTTTTTTAGTTTATACATATTGT 17 94 0 TTTTTATTTA 0.866703 -21 CTTCCTTTTGTTTTTAAATTTTAGTAATAATGA 18 74 0 TTTTAATTTA 0.952316 -227 AATAAAGCGTTTTTCCATTTTTAAAAAAAGTTT 19 51 0 TTTTATTTTA 0.866703 -250 ATTCTTCATTTTTGTTATTTTTAAACATATCAA 19 104 0 TTTGATTTTA 0.83147 -197 ATGGTAAATATTTGATAACGTTGACAAGACATG 20 67 1 TTTGAAGTTG 0.525493 -91 ATTGTATAGATTTAGTAATTTTAGTATACTATT 21 18 1 TTTAAATTTA 0.776092 -253 AAAAGGCTTATTTGACAAATTTAACTATTACAA 21 80 0 TTTGAATTTA 0.938096 -191 AAATAAGCCTTTTTAATTATTTAGTGTTTCCCT 21 100 1 TTTTTTTTTA 0.679163 -171 AAAATACAAATTTGAGTATTTTAATTGTTATCT 21 186 0 TTTGTATTTA 0.83147 -85 **** ** **** Masking position 3 Map Score: 27.1532 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 115 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 ATTAAAAGAAATGACATAAAAAATTAAATAAAC 2 107 0 ATGACATAAA 0.485451 -194 TAAACCTTGTATAACATCAACAAATTAATAAGA 2 183 1 ATAACATAAA 0.749139 -118 ATATTCGTGAATACTGTGATCAAACATAGTATG 4 108 0 ATACTGTAAA 0.623565 -51 ATTTTTCTGGATACCTTCGTCAAGTTACGGT 6 94 1 ATACCTTGAA 0.803247 -21 TTTTTACTGGATGACGTGGTTAAGCCATGGTAT 7 62 1 ATGACGTGAA 0.888205 -61 GTTTTTTTGAATACCGTGGACAAGCTGCGATGT 8 143 0 ATACCGTGAA 0.97906 -145 TTTGATTTAGATACCATTGACAATGGATGGTAT 11 92 1 ATACCATGAA 0.911672 -61 GCGTCATGCAATAACGCAATAAAATAACAGAGC 12 17 0 ATAACGCAAA 0.810384 -233 GAAAAATAAAATAACGTAGCAAATTTTTCAAAT 16 112 1 ATAACGTGAA 0.961759 -100 TTAAATGATTATACCGTTGAAAAAAAATTTATT 16 144 1 ATACCGTGAA 0.97906 -68 TCGTCCTGAGATACCGCTACCAAGTAGCGGAAT 17 22 0 ATACCGCAAA 0.888212 -93 ATATTTCTGGATACCGTAAGGAATATGAGACGA 20 36 0 ATACCGTAAA 0.961759 -122 TAAATATTTGATAACGTTGACAAGACATGAGAT 20 71 1 ATAACGTGAA 0.961757 -87 ******* * ** Masking position 12 Map Score: 10.128 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 34 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATAATGATTTTTAATTAAAATAACAAGAGATAC 1 222 0 TTTTAAATAA 0.607076 -79 TTGATTAATATTGTTTACAGTAAACCTTGTATA 2 163 1 TTTTAAGTAA 0.69128 -138 CCAATAAACAAACTTTAAAATAAAGGTATTTAT 2 263 0 AATTAAATAA 0.705338 -38 TATTCACGAATATTTTACAATACTAACATCCTT 4 128 1 TATTAAATAC 0.910212 -31 CCCGGTATTAAATTATAGTACCGATAAAATT 5 9 1 TATTAAGTAC 0.935692 -42 TTGCAACTTATATCTTAAAATAATTTATTAGTA 6 27 0 TATTAAATAA 0.911828 -88 GAAATTATGTTATAATAGTTGTTTTATA 7 105 0 TATTAAATAG 0.660887 -18 CACACTGGAATAATATAGAATACAACGCTAATA 8 238 1 TAATAAATAC 0.4488 -50 ATAATCATTCTACTTTAGAATAAAATATTATGT 9 200 1 TATTAAATAA 0.911884 -65 AATAAAATATTATGTTATAGTACTTAATTAACA 9 218 1 TATTAAGTAC 0.935692 -47 AAAATTTATATAGTTTATAGCAATTTTTAATTA 10 60 0 TATTAAGCAA 0.638751 -40 TTTCTGCATCAAGATTAAAATAAGCTTTTTAAA 13 75 0 AATTAAATAA 0.705339 -226 AAGTTAATTATAAGTTATAGTACAATAAACCAC 14 42 1 TATTAAGTAC 0.935692 -49 GTAAAATTGCAAAATTATAATAACTTTTATGCT 15 70 1 AATTAAATAA 0.705339 -231 GTTTTACTTCTATTTTAAAGTACAAAAAATCAT 15 140 0 TATTAAGTAC 0.935691 -161 CTTTTGTTTTTAAATTTTAGTAATAATGAAAAT 18 70 0 TATTTAGTAA 0.543998 -231 AGGGTGCACGTAGTTTACAGTAAACCTTATATC 19 206 1 TATTAAGTAA 0.936918 -95 ** *** ***** Masking position 6 Map Score: 13.2515 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 47 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 AATATTATCAATTTTATCTTTCATATTTTTTTGAG 1 132 1 ATTTATTCTA 0.858087 -169 TAAATCCTTCTATTTATGCTTATTAAGCCTTTGTC 2 69 1 TTTTATTATA 0.930802 -232 AAAATAAAGGTATTTATAGCAACTAAAACTATTAA 2 245 0 TTTTATAATA 0.464563 -56 GTTTCTTTATTGTTACTATTGTCAAAAT 4 4 1 TTTTATTATA 0.930804 -155 CCTAATAAAAATTTTATCGGTACTATAATTTAATA 5 16 0 ATTTATTATA 0.94677 -35 TTCCTCGTTTTCTTTTTGTTTATTATTAGCGTTGT 8 259 0 TTTTTTTATA 0.629228 -29 ATATAAAATTTATTGATATTAAGTTGTTAAT 9 244 0 ATTTATTATA 0.94677 -21 AAATAATAATTATTTATATTTAATACAGAATTAAG 13 249 0 TTTTATTATA 0.930048 -52 CTGTTTTACATCTTTATTAGTAATAATCTATATAT 15 11 1 TTTTATTATA 0.930786 -290 TATAAATACCACTTTATATGTAGTAAAACAATGAT 15 105 0 ATTTATTATA 0.94677 -196 TTTGCAAAAAAATATATCTCTAATAAAAAAAATTT 15 198 1 ATATATTATA 0.762771 -103 TACTATATATATTTTATTTTTGTTAGTTCAAGGGG 15 242 0 ATTTATTGTA 0.692839 -59 GTATACCGATTCTTTAATATTATTAGGAGTACAAA 16 18 0 TTTTAATATA 0.464564 -194 TTGCTACGTTATTTTATTTTTCGTACTAAATATGT 16 99 0 ATTTATTCTA 0.858087 -113 ATTTATTATATCTATATATATCTTAAAAAAGAACA 16 170 1 TTATATTCTA 0.452561 -42 TTCTTTTTTTAGTTTATACATATTGTAATCCCACT 17 85 0 ATTTATTATG 0.629674 -30 ATAAATTCATATTTTCTATATAATATTCT 18 5 0 ATTTCTTATA 0.653506 -296 TGATAAAACTAATTTTTGATTATTATTGCATCTAA 19 17 0 ATTTTTTATA 0.69173 -284 AAAACGCTTTATTTTATTTGTTGTATCTGCAGTTT 19 71 1 ATTTATTTTA 0.728529 -230 ATTTATTACATTTTTATTATTTCTAATAAGAAAAG 19 265 0 TTTTATTTTA 0.669925 -36 GATTTCAGCAAGTATATTTGTAATAGTTAAATTTG 21 63 1 ATATATTATA 0.762771 -208 * ***** ** ** Masking position 5 Map Score: 16.1081 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 147 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 TTTACTGTAAACAATATTAATCAACAGATT 2 157 0 ACAATATTAA 0.808584 -144 CTATATTTTGACAATAGTAACAATAAAGAA 4 13 0 ACAATAGTAA 0.920141 -146 ATTCAATTAAACAATAATAATGCTATATTT 4 35 0 ACAATAATAA 0.959303 -124 CGAATATTTTACAATACTAACATCCTTCAA 4 134 1 ACAATACTAA 0.943767 -25 AAGTCATAATACAATAATTAAAGGGCTTGT 8 35 1 ACAATAATTA 0.828014 -253 AATTCAAGGAACAATAATTAATTAAATTGA 9 32 1 ACAATAATTA 0.828014 -233 AGTGAGATCAAAAATAATAACAATGTTAGT 11 60 1 AAAATAATAA 0.824343 -93 ATGATCCAGTAAAATACTAAACTGATTACT 12 83 1 AAAATACTAA 0.769657 -167 TGCGCAAGTTACAATAGTAAGAATGCAAAG 13 139 1 ACAATAGTAA 0.920141 -162 CCTTGAACTAACAAAAATAAAATATATATA 15 244 1 ACAAAAATAA 0.714976 -57 AATTTATACAACAATCCTAAATGATTATGT 18 33 1 ACAATCCTAA 0.725811 -268 TAGTTTAGATGCAATAATAATCAAAAATTA 19 13 1 GCAATAATAA 0.881616 -288 TTTCTTATTAGAAATAATAAAAATGTAATA 19 267 1 GAAATAATAA 0.5972 -34 ********** Masking position 4 Map Score: 8.57289 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 68 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 TATAATATTCTATATGCAGTTATGTATCTCT 1 199 1 TATTGCAGTT 0.950135 -102 TAAAAATCATTATATGAAAATAGTCTAGTTA 1 242 1 TATTGAAAAT 0.604548 -59 AGATTTTTAATTTTTGAAGATAATACTTGAA 2 213 1 TTTTGAAGAT 0.863042 -88 ACAACGCAAATTTTTGAAGTTTATCAAGCAT 9 73 0 TTTTGAAGTT 0.923152 -192 AACTACTATCTTTTTGCAGTTGATCTTCATA 9 167 1 TTTTGCAGTT 0.939268 -98 GAATGATTATTATATGAAGATCAACTGCAAA 9 179 0 TATTGAAGAT 0.885892 -86 AAAAATTAATTATTTGCAGTTTTAGTGTATT 13 204 0 TATTGCAGTT 0.950135 -97 CATTTTGCTCTTTTTGAAATTTGCTTTCGTA 16 50 0 TTTTGAAATT 0.702842 -162 TTATTTGTTGTATCTGCAGTTTGATATGTTT 19 84 1 TATTGCAGTT 0.950135 -217 *** ******* Masking position 5 Map Score: 5.95748 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 55 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 AAACAAAGACAAAGGCTTAATAAGCATAAAT 2 80 0 AAAGGCTTAT 0.849373 -221 CTTGAATTTAATAGTTTTAGTTGCTATAAAT 2 238 1 ATAGTTTTAT 0.908781 -63 TTGCAAGGTTATAGGTATAATTTAGTCATTA 6 54 1 ATAGGTATAT 0.704916 -61 TATCAAATAAAAAGTCATAATACAATAATTA 8 24 1 AAAGTCATAT 0.414641 -264 TGATTATATAATAGGCTTAATTCTGTATTAA 13 234 1 ATAGGCTTAT 0.892702 -67 ATGCTGTATCATTGTTTTACTACATATAAAG 15 98 1 ATTGTTTTAT 0.728175 -203 AATCTAATATTTAGTTTTACTTCTATTTTAA 15 155 0 TTAGTTTTAT 0.633573 -146 ATGTACATTTAAAGATTTAATAATTGGAGGT 15 276 1 AAAGATTTAT 0.680897 -25 AAAAGAGCAAAATGTTTTATTGATCACAACA 16 67 1 AATGTTTTAT 0.644838 -145 TAAGCTGATATAAGGTTTACTGTAAACTACG 19 214 0 TAAGGTTTAT 0.618188 -87 ATCAGCTTAAATAGTTTTATGCAAGGATTCT 19 236 1 ATAGTTTTAG 0.574782 -65 ATAGTTTTATTACATTTTTCT 20 1 1 ATAGTTTTAT 0.908781 -157 GAATTTATAAATTGGTTTAGT 20 147 1 ATTGGTTTAT 0.787282 -11 ATTATATTGTATAGATTTAGTAATTTTAGTA 21 13 1 ATAGATTTAT 0.758935 -258 AAATAATTAAAAAGGCTTATTTGACAAATTT 21 91 0 AAAGGCTTAT 0.849373 -180 ********* * Masking position 9 Map Score: 4.47268 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 201 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 AATATTATAATGCTTGAAATATTGAAAAAT 1 178 0 TGCTTGAAAT 0.748862 -123 TATTTAAAAGTGTTTGATATTAAAAGAAAT 2 128 0 TGTTTGATAT 0.927801 -173 TGACATACTATGTTTGATCACAGTATTCAC 4 105 1 TGTTTGATCA 0.707596 -54 TATGACTTTTTATTTGATATAGTGCTGCTT 8 13 0 TATTTGATAT 0.664402 -275 TAGTCAAGTATGCTTGATAAACTTCAAAAA 9 64 1 TGCTTGATAA 0.923182 -201 TAATAATGGTAGCTTGAAATCCAGTTGATA 10 20 1 AGCTTGAAAT 0.637434 -80 TTTACTTGGGTGTTTGATAATAACTTTTTT 13 12 0 TGTTTGATAA 0.927801 -289 TGACCACTCAAGCTTGATACACACGCTTAG 18 278 0 AGCTTGATAC 0.721517 -23 TTTTAAAAAAAGTTTGATAAAACTAATTTT 19 36 0 AGTTTGATAA 0.883405 -265 TTGTATCTGCAGTTTGATATGTTTAAAAAT 19 91 1 AGTTTGATAT 0.883405 -210 ATATGGTAAATATTTGATAACGTTGACAAG 20 65 1 TATTTGATAA 0.664402 -93 ********** Masking position 7 Map Score: 3.807 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 79 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 TATGTATATCATATAAAATCTTTAGTAACA 1 48 1 ATATAAAATC 0.733253 -253 AGTAAACCTTGTATAACATCAACAAATTAA 2 181 1 GTATAACATC 0.955472 -120 TTAAGCCATGGTATGACATCGTCGTATAAA 7 81 1 GTATGACATC 0.868464 -42 ACAATGGATGGTATAACATCTTTAATTAAT 11 111 1 GTATAACATC 0.955472 -42 TTTTAAAAAAGTATAAATTCCATTTTCTTG 13 52 0 GTATAAATTC 0.931675 -249 TAGGATTGTTGTATAAATTCATATTTTCTA 18 22 0 GTATAAATTC 0.931675 -279 CTAAACCAATTTATAAATTCTTGTTTTTAG 20 137 0 TTATAAATTC 0.678568 -21 ********** Masking position 6 Map Score: 1.16272 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 12 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 ATAAAATCTTTAGTAACATTTAATTTTTTA 1 60 1 TAGTAACATT 0.782715 -241 ATTTGTAAGAATTAAGGTTAAA 3 3 1 TTGTAAGAAT 0.712066 -22 ATTTTGACAATAGTAACAATAAAGAAAC 4 9 0 TAGTAACAAT 0.952609 -150 AGATCAAAAATAATAACAATGTTAGTCTTT 11 64 1 TAATAACAAT 0.691803 -89 CAAGTTACAATAGTAAGAATGCAAAGCGTA 13 143 1 TAGTAAGAAT 0.932431 -158 ACATCTTTATTAGTAATAATCTATATATAT 15 18 1 TAGTAATAAT 0.927449 -283 TTTTAAATTTTAGTAATAATGAAAATTAGA 18 66 0 TAGTAATAAT 0.927449 -235 CTTTTCTTATTAGAAATAATAAAAATGTAA 19 265 1 TAGAAATAAT 0.69613 -36 ********** Masking position 5 Map Score: 1.75347 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 55 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 AACTTTTGACAAATTTACTATGATTATGTAT 1 24 1 AAATTTACTT 0.810905 -277 TAAAATTGATAATATTACTTTGATGAATTGC 1 117 0 AATATTACTT 0.810885 -184 TCTAGTTAAAAATATTGCACTTTATTAATGA 1 265 1 AATATTGCAT 0.533043 -36 ATTAAACAATAATAATGCTATATTTTGACAA 4 29 0 AATAATGCTT 0.643583 -130 TATATAATTAAAAATTGCTATAAACTATATA 10 56 1 AAAATTGCTT 0.903198 -44 AAAAGTGCTCTGTTATTTTAT 12 1 1 AAAAGTGCTT 0.660538 -249 TTGCATCGTTAAAAATACACTAAAACTGCAA 13 191 1 AAAAATACAT 0.581564 -110 TAAAATTACTCTCCTAAAAAGA 14 79 0 AAAATTACTT 0.911175 -12 ATAATTTTGCAATTTTACTTTGCCACTTTTT 15 57 0 AATTTTACTT 0.641909 -244 GCTCTTTTTGAAATTTGCTTTCGTATACCGA 16 44 0 AAATTTGCTT 0.795936 -168 AATCCACATGAAAAATACTGTAAGAATTACA 18 148 1 AAAAATACTT 0.826057 -153 ATAGTATACTAAAATTACTAAATCTATACAA 21 19 0 AAAATTACTA 0.658119 -252 CAATACAACAAAATATACAGTCAATCACAAT 21 143 0 AAATATACAT 0.367494 -128 AAAATTACTAATTTATTGCTA 21 260 0 AAAATTACTA 0.658119 -11 ********* * Masking position 2 Map Score: 3.23126 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 256 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 ********** No masking Map Score: 8.17367e-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