AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_rpxx_reg_100.orf -o00300_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP148 240 DIHYDRODIPICOLINATE REDUCTASE (dapB) #3 RP194 82 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE (dapD) #4 RP317 138 PROTEIN KINASE C INHIBITOR 1 (pkcI) #5 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #6 RP371 252 LYSYL-tRNA SYNTHETASE (lysS) #7 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #8 RP429 222 DIHYDRODIPICOLINATE SYNTHASE (dapA) #9 RP596 106 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMYL- 2,6-DIAMINOPIMELATE--D-ALANYL-D-ALANYL LIGASE (murF) #10 RP597 120 UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE-- 2,6-DIAMINOPIMELATE LIGASE (murE) #11 RP719 300 unknown #12 RP753 250 ASPARTOKINASE (lysC) #13 RP874 300 SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE (dapE) Motif number 1 GAGAAATTTAAATTAATAATATTGATTTATTTGAG 1 85 0 ATTAATATGA 0.882419 -216 AAAAATACTAATATAGTAATTTTAAACTAAATTTG 1 157 0 ATTAATTTAA 0.747612 -144 TATTTTTTAAAAATAATTATAATTAAT 3 3 0 ATTTATATTA 0.570788 -80 TTAACTGTTTTATTGCTAATAATGATAAATGATAT 3 53 0 TTTAATATGA 0.922474 -30 TACCTCACAATGATGATAATATTGGTACATCCATT 4 18 0 TTTAATATGG 0.762414 -121 TTATTTACTCATTATATTTAAACTTGCTGA 5 6 1 TTTTATATTA 0.94414 -70 AGGTTTTTATTTTTATTAGGAGCGA 6 1 1 ATTTATTTTA 0.871096 -252 ACGACTTAATTACTTCTTATAATGACAGTGCGAGA 6 59 0 TTTTATATGA 0.939949 -194 TACTGCGTAATGCTCCTTATAATGACTGAGCTTAA 6 158 1 TTTTATATGA 0.941576 -95 GCAATGATTATTATCTTTATTTTTGTCTTACTGCA 7 140 1 TTTTATTTTG 0.742364 -161 TTTTTTAAAATACTAGTTATTGTGAAGTAATAAGA 7 177 1 TTTTATTTGA 0.910604 -124 TTTTATCCTCAATTCATTATAGTAAATTTAAAGAA 7 239 1 ATTTATATAA 0.863907 -62 ATGAGAACAAAAATACTAATATTAATAATATTTTA 8 64 1 ATTAATATAA 0.82397 -159 ACAAGTGATTTTGTTGTTATACTTTTGCTTTATCA 8 121 0 TTTTATATTT 0.790558 -102 AATTATTACGTTATTGTTATACTAAGATTTTTATG 8 183 0 TTTTATATAA 0.908508 -40 GATTTTCCTTATTTTAATTATTACGTTATTGTT 8 200 0 TTTAATTTTA 0.803694 -23 ATACAAATAGAGTTTTTTATTTTTATTACTTAAGC 10 53 0 ATTTATTTTA 0.871096 -68 AAGATGTAAGAGTTAATAATTATGGGAATTGTATT 11 74 1 ATTAATTTGG 0.561834 -227 AGCTTATAATAGTAAGCCTAATAGA 12 236 0 ATTAATATAA 0.824232 -15 ATCACCATACTAATCTTAATAATTTGTTTAACTTT 13 24 1 TTTAATATTT 0.734292 -277 TTTGTTTAACTTTTTATAATTCTAAACAAATTGAA 13 46 1 TTTAATTTAA 0.823097 -255 GTTGGTTTTATATTTCTTATTGTTAAAGTAAAAAC 13 123 1 TTTTATTTTA 0.914441 -178 CAGTTAAATGTATTAATTATTGTTTTTACTTTAAC 13 144 0 TTTTATTTTT 0.704188 -157 TAATACATTTAACTGATTATATTTATATGTGATTT 13 164 1 ATTTATATTA 0.914453 -137 GTGATTTCTATGTTAGTTATAATAACATAAAGTTA 13 192 1 TTTTATATAA 0.909417 -109 AGTAATAAATTTATAGTAATAATTTTTTTTGTACT 13 242 1 TTTAATATTT 0.704734 -59 * * ***** *** Masking position 7 Map Score: 22.2331 Number of sites scoring better than the average of aligned sites = 1057 Number in coding regions = 627 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 2 GTGACTTGACTATAAAAATACTAATATAGT 1 175 0 TATAAAAATA 0.876776 -126 AGCAGTTTGATATACAAATTACTTAGAGTG 2 87 1 TATACAAATT 0.892092 -154 ACCTTGCTCTTTTACAAATTAAACTTTGTC 2 201 1 TTTACAAATT 0.85625 -40 TCAAATATTTTTTAAAAATAATTATAATTA 3 13 0 TTTAAAAATA 0.836784 -70 CACACATATCTTAAAATATTGATTAGATTG 4 67 1 TTAAAATATT 0.647854 -72 TTTCAGCAAGTTTAAATATAATGAGTAAAT 5 13 0 TTTAAATATA 0.684043 -63 TATTATTTTGTAAACAAATAATCGATAAAA 5 56 1 TAAACAAATA 0.875392 -20 ATTCGCTCCTAATAAAAATAAAAACCT 6 8 0 AATAAAAATA 0.750307 -245 TCGTGTAATTTAAAAAAATAAAACATTATA 6 100 1 TAAAAAAATA 0.858089 -153 AATTTGATATTTTACAAATAAATAAATTTA 6 191 1 TTTACAAATA 0.85625 -62 AACTAGTATTTTAAAAAATTTGCAGTAAGA 7 165 0 TTAAAAAATT 0.81331 -136 TGAATTGAGGATAAAATATAGACTATTATA 7 225 0 ATAAAATATA 0.437228 -76 AATTTGCTATAATACAAATTTTTAATATGT 7 273 1 AATACAAATT 0.777347 -28 AATGTTTTACATATTAAAAATTTGT 7 286 0 TTTACATATT 0.715537 -15 TAAACAAATTTTAAAATATTATTAATATTA 8 80 0 TTAAAATATT 0.647854 -143 AGAATCCCATTAAACAAATTTTAAAATATT 8 90 0 TAAACAAATT 0.875392 -133 TTGCTTAAGTAATAAAAATAAAAAACTCTA 10 51 1 AATAAAAATA 0.750307 -70 GATCCAAAATAATACAAATAGAGTTTTTTA 10 69 0 AATACAAATA 0.777342 -52 ATTTACAGCAATTAAAAATAAAGTCAAACA 11 273 0 ATTAAAAATA 0.68405 -28 ATGTGGTTGATAAAAATATTTATTGAAAAG 12 103 1 TAAAAATATT 0.718584 -148 TATAAAAAGTTAAACAAATTATTAAGATTA 13 34 0 TAAACAAATT 0.875392 -267 TTTATAATTCTAAACAAATTGAATATATAT 13 58 1 TAAACAAATT 0.875392 -243 AGAAATCACATATAAATATAATCAGTTAAA 13 171 0 TATAAATATA 0.749693 -130 ATAAAAGTACAAAAAAAATTATTACTATAA 13 252 0 AAAAAAAATT 0.718587 -49 ********** Masking position 9 Map Score: 22.4339 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 630 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 3 AGTTATGCTTTTATTATGCAATAAAATTGT 1 242 0 TTATTATGCA 0.707482 -59 TAGATAAGTGTAAATGAGCAGTTTGATATA 2 71 1 TAAATGAGCA 0.925028 -170 TCTAGTAGTTTAATAGAGCAATTGATACAA 2 133 1 TAATAGAGCA 0.963343 -108 GTTTAATTTGTAAAAGAGCAAGGTGTATTA 2 195 0 TAAAAGAGCA 0.963343 -46 TGATTATTAATTAAAGTGCAAGAAAAATAA 6 233 1 TTAAAGTGCA 0.892286 -20 TAATAAAGTCTAATAAAACACCAATACTTA 7 63 0 TAATAAAACA 0.779812 -238 TGGGATTCTATGATAAAGCAAAAGTATAAC 8 111 1 TGATAAAGCA 0.754753 -112 TCTATTGCTTTTAAAAAGCATCTAGTGTCA 9 70 0 TTAAAAAGCA 0.893811 -37 GTTTTATTATGCAGAGAAAAAAC 10 4 1 TTATTATGCA 0.707482 -117 GATTACAAGCTAAAAAAGCAGTGTAGATAT 11 18 1 TAAAAAAGCA 0.94234 -283 ATATTTCGTTTAAATGAGCATATTTCGTAA 11 123 0 TAAATGAGCA 0.925028 -178 TTATATTAGATAATAAAGCAATAAATATGT 11 246 1 TAATAAAGCA 0.94234 -55 TAGTATATGATTAAAGTGCAATAC 12 5 0 TTAAAGTGCA 0.892286 -246 ATAGTAAGCCTAATAGAACATTCACCATTA 12 223 0 TAATAGAACA 0.850633 -28 TACAAACTTATAAAAGTACAAAAAAAATTA 13 261 0 TAAAAGTACA 0.777057 -40 TTACTTCTTTTAATTATACAAACTTATAAA 13 277 0 TAATTATACA 0.504372 -24 ********** Masking position 3 Map Score: 15.6842 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 269 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TGAACTTGTCTTTTTTCCACTTCCCTTTATAG 2 17 0 TTTTTTACTT 0.940714 -224 ACGGTAATACTTTGTATCAATTGCTCTATTAA 2 142 0 TTTGTAAATT 0.619269 -99 AATCAAATATTTTTTAAAAATAATTATAATTA 3 13 0 TTTTTAAATA 0.632084 -70 TAATGTTTTATTTTTTTAAATTACACGAACTC 6 96 0 TTTTTTAATT 0.940472 -157 TTCTGGATTGTTTCATCGAATTACTGCGTAAT 6 137 1 TTTCATAATT 0.492723 -116 TTATTTTTCTTGCACTTTAATTAATAA 6 236 0 TTTCTTACTT 0.84361 -17 CGTGTTTAGCTTTTTAGCACTAACAACATGAA 7 25 0 TTTTTAACTA 0.635318 -276 GTATTGGTGTTTTATTAGACTTTATTATATCA 7 66 1 TTTATTACTT 0.575858 -235 TTACTGCAAATTTTTTAAAATACTAGTTATTG 7 167 1 TTTTTTAATA 0.794457 -134 TTATAGCAAATTTCTTTAAATTTACTATAATG 7 253 0 TTTCTTAATT 0.843088 -48 ATATTAATAATATTTTAAAATTTGTTTAATGG 8 82 1 TATTTTAATT 0.502966 -141 TATACTAAGATTTTTATGAATACATAAATAGG 8 169 0 TTTTTAAATA 0.634387 -54 GAGTTTTTTATTTTTATTACTTAAGCAAATGA 10 47 0 TTTTTAACTT 0.874949 -74 ATGTTTGACTTTATTTTTAATTGCTGTAAATC 11 272 1 TTATTTAATT 0.530688 -29 TTATCTTGTGTTTTTCAAAATTATGATGCATA 12 66 1 TTTTTCAATT 0.68194 -185 ATCTTAATAATTTGTTTAACTTTTTATAATTC 13 36 1 TTTGTTACTT 0.787382 -265 TATATTCAATTTGTTTAGAATTATAAAAAGTT 13 53 0 TTGTTTAATT 0.75516 -248 TAAAACCAACTTTTATACAATTACAGTTATTT 13 101 0 TTTTATAATT 0.740741 -200 GTATTAATTATTGTTTTTACTTTAACAATAAG 13 138 0 TTGTTTACTT 0.755889 -163 ATTTATTACTTTTTAATAAATTCAATAACTTT 13 220 0 TTTTAAAATT 0.557483 -81 AGTAATAATTTTTTTTGTACTTTTATAAGTTT 13 256 1 TTTTTTACTT 0.940714 -45 ****** **** Masking position 11 Map Score: 13.5819 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 496 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 TGTCATACAGTGACTTGACTATAAAAATACTAATAT 1 178 0 TGTAATAAAA 0.973473 -123 ACTTACAATTTTATTGCATAATAAAAGCATAACTTA 1 238 1 TTTAATAAAA 0.724499 -63 AATTAAACTTTGTCTATATTATAATATTACCAAT 2 217 1 TGTAATAATA 0.969398 -24 AAAAAATATTTGATTCCATGATAATATCATTTATCA 3 30 1 TGTAATAATA 0.969398 -53 TAATTCAGTGTGCAATTACCATAAAACTACAGGATA 4 107 1 TGAAATAAAA 0.921761 -32 ATCGATTATTTGTTTACAAAATAATACATCATGCTA 5 46 0 TGTAATAATA 0.969398 -30 ATAAGAAGCATGAAATTAGTATAATAGTCTATATTT 7 206 1 TGAAATAATA 0.910476 -95 TTTACTATAATGAATTGAGGATAAAATATAGACTAT 7 229 0 TGTAATAAAA 0.973474 -72 CACGTAGTGTTGTTTATATAATATTAGATAAATTAC 9 30 1 TGTAATATTA 0.785826 -77 ATATGTTTTTTCTCTGCATAATAAAAC 10 2 0 TCTAATAAAA 0.796028 -119 CTTTGTCATTTGCTTAAGTAATAAAAATAAAAAACT 10 42 1 TGTGATAAAA 0.852686 -79 AGGTATTGATTACAAGCTAAAAAAGCAGTGTA 11 7 1 TGTACTAAAA 0.852686 -294 GTGAATATATGGAATCACCATACTAATCTTAATAA 13 10 1 TGAAATACTA 0.635819 -291 ** * * ****** Masking position 13 Map Score: 9.03333 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 75 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TCTACTTCAATTAATAACTTGAATCTCAAA 1 131 1 TTAATAACTT 0.687763 -170 AACTTACAATTTTATTGCATAATAAAAGCA 1 237 1 TTTATTGCAT 0.862728 -64 TTTTAACTGTTTTATTGCTAATAATGATAA 3 60 0 TTTATTGCTA 0.554898 -23 CTCCTACGACTTAATTACTTCTTATAATGA 6 69 0 TTAATTACTT 0.904969 -184 TGAATTGATTTTATTTCATGTTGTTAGTG 7 10 1 TTTATTTCAT 0.589743 -291 TAATCATTGCTAAATAACATTTTAATTGAT 7 120 0 TAAATAACAT 0.26583 -181 TTTCATGCTTCTTATTACTTCACAATAACT 7 191 0 CTTATTACTT 0.615215 -110 TAATATTAGATAAATTACATTATGACACTA 9 48 1 TAAATTACAT 0.610193 -59 TACGTGTTGTTCTATTGCTTTTAAAAAGCA 9 80 0 TCTATTGCTT 0.821526 -27 GTTTTTTATTTTTATTACTTAAGCAAATGA 10 47 0 TTTATTACTT 0.930705 -74 GTCAAACATATTTATTGCTTTATTATCTAA 11 251 0 TTTATTGCTT 0.935774 -50 GACTTTATTTTTAATTGCTGTAAATCATAA 11 278 1 TTAATTGCTG 0.567113 -23 AATCATATACTATATTACATAGCACAAAAT 12 23 1 TATATTACAT 0.68826 -228 ACATTCACCATTAATTGCTTTTTGTTCTTA 12 206 0 TTAATTGCTT 0.911742 -45 AAGTTGGTTTTATATTTCTTATTGTTAAAG 13 121 1 TATATTTCTT 0.559461 -180 TTTAATAAATTCAATAACTTTATGTTATTA 13 211 0 TCAATAACTT 0.410341 -90 TTACTATAAATTTATTACTTTTTAATAAAT 13 231 0 TTTATTACTT 0.930705 -70 ********** Masking position 5 Map Score: 8.83474 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 432 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 7 ATTTCTCACATTACATGTTCTACTTCAATTA 1 113 1 TTACTGTTCT 0.90353 -188 ATCTTTTAACTGTTTTATTGCTAATA 3 67 0 TTAATGTTTT 0.907559 -16 TACGACTTAATTACTTCTTATAATGACAGTG 6 64 0 TTACTCTTAT 0.763758 -189 ATTGATTTTATTTCATGTTGTTAGTGCTAAA 7 14 1 TTTCTGTTGT 0.792518 -287 TTTACTATTTCTACTTCTTGTCGTGTAGAAA 8 29 1 CTACTCTTGT 0.743346 -194 TGTGATTTACGTGTTGTTCTATTGCTT 9 90 0 TTACTGTTGT 0.970569 -17 TTATTAACTCTTACATCTTTTCAAGAATTTC 11 62 0 TTACTCTTTT 0.939659 -239 TTCCGTATCATTACCTGTTTTTCCTTGTATA 11 196 0 TTACTGTTTT 0.968192 -105 GACTTTATTTTTAATTGCTGTAAATCATAAA 11 278 1 TTAATGCTGT 0.786615 -23 ACATTCACCATTAATTGCTTTTTGTTCTTAT 12 205 0 TTAATGCTTT 0.772859 -46 ATATAATCAGTTAAATGTATTAATTATTGTT 13 155 0 TTAATGTATT 0.532089 -146 AATGTTACTTCTTTTAATTATACAA 13 286 0 TTACTCTTTT 0.939659 -15 **** ****** Masking position 6 Map Score: 5.57233 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 93 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 CTTTGAATAGCTAAGGTTTTTGTGTAGTTCTTT 1 46 0 CTAAGTTTTT 0.900497 -255 ATTGATTTATTTGAGATTCATCTTTGAATAGCT 1 67 0 TTGAGTTATT 0.931748 -234 TAAACTAAATTTGAGATTCAAGTTATTAATTGA 1 137 0 TTGAGTTAAT 0.634314 -164 CAATAAAATTGTAAGTTTTATATGGCAAAAACG 1 221 0 GTAAGTTATT 0.893996 -80 ATAATATAGACAAAGTTTAATTTGTAAAAGAGC 2 206 0 CAAAGTTATT 0.832188 -35 CTTATAATGACTGAGCTTAATTTGATATTTTAC 6 173 1 CTGAGTTATT 0.964056 -80 AATAAGTATCCTAAGATTGATATAATAAAGTCT 7 82 0 CTAAGTTATT 0.95235 -219 TATTGTTATACTAAGATTTTTATGAATACATAA 8 174 0 CTAAGTTTTT 0.900493 -49 ATAATACAAATAGAGTTTTTTATTTTTATTACT 10 58 0 TAGAGTTTTT 0.605329 -63 ATAAAATTAAGTGAGGTTAATTTATCAGTATAC 11 168 1 GTGAGTTATT 0.918816 -133 AAACAAATTATTAAGATTAGTATGGTGATTCCA 13 20 0 TTAAGTTGTT 0.729871 -281 ***** ** ** * Masking position 4 Map Score: 4.17641 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 71 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 GCTTAGGTAGTTTCTCCTGTATAATACACCT 2 174 1 TTTCTCCTGA 0.935533 -67 TTCTTTTATCCTGTAGTTTTATGGT 4 124 0 TTTATCCTGA 0.907333 -15 CATTATAGCATTTTTTCTGGATTGTTTCATC 6 123 1 TTTTTTCTGA 0.948547 -130 TTATTTTTCTTGCACTTTAATTAA 6 239 0 TTTTTCTTGA 0.948547 -14 GCCATATGTTTTTTCTCTGCATAATAAAAC 10 10 0 TTTTCTCTGA 0.912583 -111 CACTTAATTTTATTTCCTGCATTAACTAATA 11 150 0 TATTTCCTGA 0.894201 -151 CATTACCTGTTTTTCCTTGTATACTGATAAA 11 188 0 TTTTCCTTGA 0.912583 -113 ATAGTAATAATTTTTTTTGTACTTTTATAAG 13 254 1 TTTTTTTTGA 0.87814 -47 ********* * Masking position 11 Map Score: 2.79566 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 98 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ATCTCAAATTTAGTTTAAAATTACTATATT 1 153 1 TAGTTTAAAA 0.792267 -148 TACACCTTGCTCTTTTACAAATTAAACTTT 2 198 1 TCTTTTACAA 0.64378 -43 GAATCAAATATTTTTTAAAAATAATTATAA 3 16 0 TTTTTTAAAA 0.902788 -67 TATCGATTATTTGTTTACAAAATAATACAT 5 53 0 TTGTTTACAA 0.88011 -23 TAATGTTTTATTTTTTTAAATTACACGAAC 6 98 0 TTTTTTTAAA 0.559899 -155 CTTAATTTGATATTTTACAAATAAATAAAT 6 188 1 TATTTTACAA 0.754823 -65 TTACTGCAAATTTTTTAAAATACTAGTTAT 7 167 1 TTTTTTAAAA 0.902788 -134 ATATTAATAATATTTTAAAATTTGTTTAAT 8 82 1 TATTTTAAAA 0.807272 -141 ACACTAGATGCTTTTTAAAAGCAATAGAAC 9 72 1 CTTTTTAAAA 0.655887 -35 AGGTATTGATTACAAGCTAAAAAAG 11 6 1 TTGATTACAA 0.620089 -295 TTATCTTGTGTTTTTCAAAATTATGATGCA 12 66 1 TTTTTCAAAA 0.651734 -185 TATATTCAATTTGTTTAGAATTATAAAAAG 13 55 0 TTGTTTAGAA 0.712381 -246 ATAACTGTAATTGTATAAAAGTTGGTTTTA 13 103 1 TTGTATAAAA 0.401585 -198 AGTTATTGAATTTATTAAAAAGTAATAAAT 13 222 1 TTTATTAAAA 0.708609 -79 ********** Masking position 9 Map Score: 5.64484 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 298 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 TATCGTATCTATGAATACTAAGTAATC 1 7 1 ATCTTGAATA 0.945336 -294 ATACTAAGTAATCTCTAAATAAAAGAACTAC 1 25 1 ATCTTAAATA 0.930711 -276 TTTGAGATTCATCTTTGAATAGCTAAGGTTT 1 60 0 ATCTTGAATA 0.945335 -241 CTGCACACATATCTTAAAATATTGATTAGAT 4 64 1 ATCTAAAATA 0.915986 -75 TATTATATCAATCTTAGGATACTTATTTATA 7 88 1 ATCTAGGATA 0.788505 -213 ATTTTAATTGATATATAAATAAGTATCCTAA 7 101 0 ATATTAAATA 0.599999 -200 CATTAAACAAATTTTAAAATATTATTAATAT 8 82 0 ATTTAAAATA 0.549043 -141 ATTCATAAAAATCTTAGTATAACAATAACGT 8 180 1 ATCTAGTATA 0.715543 -43 ACACAATAATATCTGTAAGTAAGCTAGATAA 12 178 1 ATCTTAAGTA 0.758361 -73 **** ****** Masking position 4 Map Score: 1.09715 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 42 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 ********** No masking Map Score: 1.36667e-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 13 ********** No masking Map Score: 1.36667e-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 14 ********** No masking Map Score: 1.36667e-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