AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icrp_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 RP053 300 ADP,ATP CARRIER PROTEIN (tlc1) #2 RP054 72 GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT) #3 RP069 266 DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE (dcd) #4 RP070 196 PROTEIN-EXPORT PROTEIN SECB (secB) #5 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #6 RP095 300 ALANINE RACEMASE (alr) #7 RP322 300 unknown #8 RP332 300 unknown #9 RP333 32 CAPD PROTEIN (capD) #10 RP427 121 PETR PROTEIN (ompR) #11 RP449 99 THREONINE DEHYDRATASE (tdcB) #12 RP501 215 TRNA PSEUDOURIDINE 55 SYNTHASE (truB) #13 RP503 21 30S RIBOSOMAL PROTEIN S15 (rpsO) #14 RP504 154 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (pnp) #15 RP505 184 KPSF PROTEIN (kpsF) #16 RP581 114 unknown #17 RP600 195 unknown #18 RP707 194 unknown #19 RP708 300 INTEGRATION HOST FACTOR ALPHA-SUBUNIT (himA) Motif number 1 GATGAAATTTTAATATTTTACCTTCAATAT 1 28 1 TAATATTTTA 0.678149 -273 ATAGTAAATTTATTATTTAAATAATATGGA 3 20 0 TATTATTTAA 0.407468 -247 ACTATTAAATTCTTAATTTTAAGTATATAG 3 128 1 TCTTAATTTT 0.660099 -139 ATCATTAGTTTATTAATTAAATAAAGTTTT 3 243 1 TATTAATTAA 0.683054 -24 CTATTCGCGATCTTAATTTTAAAGCTAATT 4 31 1 TCTTAATTTT 0.660099 -166 ATAAACATCTTATTAATTTTTGCTTTAAAA 4 103 1 TATTAATTTT 0.956348 -94 ATTTTTGCTTTAAAAATTTTTAATTATTAG 4 118 1 TAAAAATTTT 0.91343 -79 GAACAGGCTCTAAAAATTATGTTAAATTTT 4 163 1 TAAAAATTAT 0.718923 -34 AAATCCTTATTAAAAATTTAACATAATTTT 4 175 0 TAAAAATTTA 0.802973 -22 AATTTAATAGTAAAAATTTTATAATTTGAT 5 60 1 TAAAAATTTT 0.91343 -137 ATACGTTCATTAATAATATAAGTAAAGAAT 5 95 0 TAATAATATA 0.541964 -102 TTAACTAAATTATAATTTTTTATCTAGTGC 5 128 0 TATAATTTTT 0.813496 -69 ATAATTTAGTTAATAATTATTAACTAAATT 5 145 1 TAATAATTAT 0.802423 -52 TCAATTTTGATAATAATTTAGTTAATAATT 5 159 0 TAATAATTTA 0.871898 -38 CTCTTGTTTTTACTAATTTTATTTGATTGA 6 36 0 TACTAATTTT 0.896969 -265 CATGTTCTTTTAAAAATTTTTCTGCTTTTA 6 125 0 TAAAAATTTT 0.91343 -176 CTACCAAATTTACAATTTTTTATAAATGGT 6 190 0 TACAATTTTT 0.636247 -111 CTGACTTATCTATAAATTTTCATAATATTA 6 256 1 TATAAATTTT 0.93241 -45 AATCAAGATTTATTATTTTTGATTTGTAAT 7 55 1 TATTATTTTT 0.874848 -246 TACTATAAAATAAAAATTTAGAATTTTTAT 7 83 0 TAAAAATTTA 0.802973 -218 TAGTAAACGCTATAAATTTATCCAGTATTG 7 189 1 TATAAATTTA 0.847098 -112 AATAACTATTATTTTTGACTTAGAAA 7 285 0 TATTATTTTT 0.874848 -16 TGCGATTAAGTAATAATTAAATCTAATGTT 8 98 1 TAATAATTAA 0.622563 -203 GAACTTACAGTATCAATTTTTATTCAAGTA 8 131 1 TATCAATTTT 0.824272 -170 TTACTTTTTATACAAATTTTAATATTTCTA 8 171 0 TACAAATTTT 0.845744 -130 TGTAAAGATATATTATTTATGATAGAAAGG 8 258 1 TATTATTTAT 0.6287 -43 GGTTATATTATTTTTTATCGCACCC 8 286 0 TATTATTTTT 0.874848 -15 TCTAATCTAATATAAATATAACTTA 10 6 0 TATAAATATA 0.492255 -116 ACTATGATATTAATAATTTTGAACCCGTGG 10 73 1 TAATAATTTT 0.943719 -49 CTATAAACTATATAAATTTTTAAAAAGGTT 11 18 0 TATAAATTTT 0.93241 -82 AAGCTACCATTATTAATTATATTT 11 86 1 TATTAATTAT 0.84143 -14 AAACTGTGTCTATCAATTTTGCATTTTATA 12 186 1 TATCAATTTT 0.824272 -30 TTTAATAGAATATAAATTATGAAATGAGAT 14 129 1 TATAAATTAT 0.769683 -26 CAAGAAACTTTACTATTTTAATAAGTTACG 16 70 0 TACTATTTTA 0.530083 -45 AATTTTTTTATAATAATATTATTAAAATAA 17 27 1 TAATAATATT 0.744507 -169 CATAGAACCTTATTATTTTAATAATATTAT 17 39 0 TATTATTTTA 0.738252 -157 GTTTACGGTATAATAATATTAACTCAATTC 18 48 0 TAATAATATT 0.744507 -147 AGCTATAACCTATAAATTTTGCTAATGCTT 19 133 0 TATAAATTTT 0.93241 -168 TCAGGATTTTTAATAATTTTCAATTTTTAC 19 174 0 TAATAATTTT 0.943719 -127 ATAAATTACATAATAATATTTATTTGCACT 19 204 0 TAATAATATT 0.744507 -97 ATTCTACTGTTATTAATATTTTAGTTCTGG 19 243 1 TATTAATATT 0.791984 -58 AAATAATACCAATTTTATATATTATG 19 285 0 TACCAATTTT 0.650826 -16 ********** Masking position 5 Map Score: 45.4986 Number of sites scoring better than the average of aligned sites = 1380 Number in coding regions = 889 Number in noncoding regions = 491 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 2 TGGGATGAAATTTTAATATTTTACCTTCAA 1 25 1 TTTTAATATT 0.884988 -276 TTTATATTTTTTTACAAATT 2 1 0 TTTACAAATT 0.417052 -72 TTTAGAAGCTTTTTTATATTTTTTTACAAA 2 13 0 TTTTTATATT 0.855322 -60 TGAATCTTACTTTTTATAGTTGAGGAGAGT 2 46 1 TTTTTATAGT 0.817739 -27 AAATTTATTATTTAAATAATATGGAATTAT 3 15 0 TTTAAATAAT 0.810931 -252 AAAATTAAGAATTTAATAGTTTCTTATTGT 3 118 0 ATTTAATAGT 0.838637 -149 AAAATTTTTCTTTAAAAAATCTAAAACTAC 3 188 0 TTTAAAAAAT 0.67538 -79 TTGCCTAATAATTAAAAATTTTTAAAGCAA 4 122 0 ATTAAAAATT 0.617085 -75 AAAAATCCTTATTAAAAATTTAACATAATT 4 177 0 ATTAAAAATT 0.617085 -20 TAAAGGTAGAATTTAATAGTAAAAATTTTA 5 51 1 ATTTAATAGT 0.838637 -146 AATAGTAAAAATTTTATAATTTGATTAAAT 5 65 1 ATTTTATAAT 0.558852 -132 TTATAATTTGATTAAATATTCTTTACTTAT 5 78 1 ATTAAATATT 0.768639 -119 ATTTTTCTGCTTTTAATATTGTCATCAATG 6 110 0 TTTTAATATT 0.884988 -191 TCACATGTTCTTTTAAAAATTTTTCTGCTT 6 128 0 TTTTAAAAAT 0.810931 -173 TATCTATAAATTTTCATAATATTATAGTGT 6 262 1 TTTTCATAAT 0.777469 -39 CTAAATTTTTATTTTATAGTAGCATATTTT 7 92 1 ATTTTATAGT 0.78994 -209 ATAGTAGCATATTTTATAGTAAGTTACGTT 7 107 1 ATTTTATAGT 0.78994 -194 AGTCATATAGTTTTAATATTGTAATTACTT 7 148 1 TTTTAATATT 0.884988 -153 TTTGATGTTTTTTAAAAAGTACAGCTAATT 7 226 0 TTTAAAAAGT 0.578864 -75 AAATCTAATTTTTTTATATTTCAGTATTAT 8 61 0 TTTTTATATT 0.855322 -240 AAAAAATTAGATTTTAAAATATGCGATTAA 8 77 1 ATTTTAAAAT 0.467815 -224 TTTATACAAATTTTAATATTTCTAGATTTT 8 165 0 TTTTAATATT 0.884988 -136 ATTAAAACCTTTTTAAAAATTTATATAGTT 11 13 1 TTTTAAAAAT 0.810931 -87 GCAATTTTTAATTATATAATATAGTATCAA 11 47 1 ATTATATAAT 0.467815 -53 ATTGGCTAGAATTATATATTAAAGATTTTC 12 32 1 ATTATATATT 0.700916 -184 TACTCGTTTAATTTTAAAATTGGCTAAGTT 12 81 1 ATTTTAAAAT 0.467815 -135 TATTTATCTCATTTCATAATTTATATTCTA 14 134 0 ATTTCATAAT 0.747437 -21 AAGTTTCTTGATTTAAAATTAGCGGGATAA 16 90 1 ATTTAAAATT 0.768639 -25 TTGCAAAATTTTTTTATAATAATATTATTA 17 21 1 TTTTTATAAT 0.860949 -175 AACCTTATTATTTTAATAATATTATTATAA 17 34 0 TTTTAATAAT 0.898383 -162 TACCGAAATCATTTTAAAATACTTGAATAA 17 99 1 ATTTTAAAAT 0.467815 -97 ACTTCAGGATTTTTAATAATTTTCAATTTT 19 177 0 TTTTAATAAT 0.898383 -124 ACGTTAATAAATTACATAATAATATTTATT 19 210 0 ATTACATAAT 0.586785 -91 TAATACCAATTTTATATATTATGTTGTTTA 19 278 0 TTTATATATT 0.741476 -23 ********** Masking position 6 Map Score: 34.5807 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 753 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 AATTTTAATATTTTACCTTCAATATTTTGTATTGTC 1 33 1 TTTTTTAATT 0.897752 -268 TTTTACTTAATTTTGATTTCTATATATTAACTGTTA 1 144 0 TTTTTTAATA 0.949241 -157 GTAAAAATTGTTTTCTTTTTCACATCCTATAGTTAA 1 174 1 TTTTTTAATC 0.933341 -127 TTAAATTTTCTATTTATTTGAAGATAAACATTATAC 1 273 0 TATTTTAATA 0.905123 -28 AGCTTTTTTATATTTTTTTACAAATT 2 1 0 TATTTTAATT 0.817583 -72 AATAAGAAACTATTAAATTCTTAATTTTAAGTATAT 3 120 1 TATTTTTATT 0.648909 -147 AATACAAAATTTTTCTTTAAAAAATCTAAAACTACT 3 187 0 TTTTTAAATC 0.474544 -80 TAAAGAAAAATTTTGTATTGTAAATAATTATGCGTT 3 204 1 TTTTTTAATA 0.949239 -63 TCTTATTAATTTTTGCTTTAAAAATTTTTAATTATT 4 110 1 TTTTTTAATT 0.897752 -87 ATATTGTTGTTTTTCAATTAAAGGTAGAATTTAATA 5 33 1 TTTTTTAGTA 0.775809 -164 TTACTAATTTTATTTGATTGATAATTTCTTTTCAAT 6 21 0 TATTTTTATT 0.64886 -280 AGATTTATTATTTTTGATTTGTAATAAAAATTCTAA 7 60 1 TTTTTTTATA 0.885043 -241 AAATTCTAAATTTTTATTTTATAGTAGCATATTTTA 7 87 1 TTTTTTTGTA 0.587838 -214 TAACTATTATTTTTGACTTAGAAATATCGATAAAAA 7 273 0 TTTTTTAATA 0.949239 -28 TGTCTATCAATTTTGCATTTTATATCATATATTC 12 192 1 TTTTTTAATC 0.933341 -24 TCATAATTTATATTCTATTAAAGATATCATTCAGTA 14 115 0 TATTTTAATA 0.905239 -40 CATAGAACCTTATTATTTTAATAATATTATTATAAA 17 33 0 TATTTTTATA 0.794539 -163 ATTTACGTTTTTTTCTATTATTGATAATAAAAGTTA 17 170 0 TTTTTTTATA 0.885158 -26 ACTATTATTTTCCATATCAACGTATTAG 18 3 1 TATTTTAATC 0.877338 -192 GTAAGTATCGTTTTAGGTTTTATATCTAGTTTGCAC 19 34 0 TTTTTTAATC 0.933341 -267 AATTTTCAATTTTTACTTTTTACATAAAGCTATAAC 19 154 0 TTTTTTAATA 0.949241 -147 **** ** * *** Masking position 8 Map Score: 26.604 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 244 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 CTTTAAATTGTAAAGGCTTATTTGATATTTCT 1 87 0 TAAACTTATT 0.922361 -214 GAAAGAACTCAATAAACATTTTATTAACTATA 1 201 0 AATACATTTT 0.477352 -100 ATTCAGGTTTTAGAAGCTTTTTTATATTTTTT 2 19 0 TAGACTTTTT 0.875186 -54 TTTAATAATTCCATATTATTTAAATAA 3 6 1 TAATCATATT 0.831843 -261 AAGAATTTAATAGTTTCTTATTGTCAATTCTG 3 110 0 TAGTCTTATT 0.818405 -157 TAAAGCTAATTAAAATCTTTTTAAGTGAGAAA 4 50 1 TAAACTTTTT 0.905776 -147 AAAAATCCTTATTAAAAATTTAA 4 184 0 AAAACTTATT 0.714285 -13 AGTATATACTCATTTTATAACACTAT 6 285 0 TATACATTTT 0.81605 -16 TTTTATTTTATAGTAGCATATTTTATAGTAAG 7 98 1 TAGTCATATT 0.784124 -203 TTTAATATTGTAATTACTTATTGATTTATTTA 7 159 1 TAATCTTATT 0.859893 -142 AATTATTACTTAATCGCATATTTTAAAATCTA 8 84 0 TAATCATATT 0.831837 -217 GAGCTATGTAAAAAACCTTATTGTAAAGATAT 8 237 1 AAAACTTATT 0.712636 -64 TTATACTCATTTTACATCTCGTG 10 109 0 TATACATTTT 0.81605 -13 CAATTAAAACCTTTTTAAAAATTTAT 11 5 1 TAAACTTTTT 0.905776 -95 CTCCTTGCATTATAAACTTTTTGCTCTTGTTG 12 149 1 TATACTTTTT 0.84587 -67 ATCAAACACTTAATCTCATATTGCAATATATA 14 80 0 TAATCATATT 0.831846 -75 TAAGTTACGTTATAGTCATTTTTATTGTTTCT 16 47 0 TATACATTTT 0.81605 -68 ATGATGTTCATAGAACCTTATTATTTTAATAA 17 45 0 TAGACTTATT 0.89787 -151 **** ****** Masking position 9 Map Score: 15.0797 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 185 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 TAAATTTTCATTTAGTTAGTTAACAGTTAA 1 124 1 TTTAGTTAGT 0.828964 -177 GAAAACAATTTTTACTTAATTTTGATTTCT 1 159 0 TTTACTTAAT 0.821093 -142 TTTCACATCCTATAGTTAATAAAATGTTTA 1 191 1 TATAGTTAAT 0.828387 -110 AAACTTTTAGATTAGTTAATTAAATCAACT 3 57 1 ATTAGTTAAT 0.897201 -210 AATCAAAACTTTATTTAATTAATAAACTA 3 248 0 TTTATTTAAT 0.872927 -19 TTATTGGATAATTAGGTAATTTT 5 4 0 ATTAGGTAAT 0.745464 -193 ATAAGTAAAGAATATTTAATCAAATTATAA 5 78 0 AATATTTAAT 0.445199 -119 AAAATTATAATTTAGTTAATAATTATTAAC 5 139 1 TTTAGTTAAT 0.950927 -58 TTGATAATAATTTAGTTAATAATTATTAAC 5 153 0 TTTAGTTAAT 0.950927 -44 TAGATCAGATTTTTGTTAATGATACTCTAG 6 220 1 TTTTGTTAAT 0.624182 -81 TACTTATTGATTTATTTAGTAAACGCTATA 7 173 1 TTTATTTAGT 0.631867 -128 AGATTTAATTATTACTTAATCGCATATTTT 8 92 0 ATTACTTAAT 0.642006 -209 ATGTACTAGATATAGTTAATAAACCACGGT 15 148 1 TATAGTTAAT 0.828387 -37 TAGATGTGAATTGAGTTAATATTATTATAC 18 41 1 TTGAGTTAAT 0.711116 -154 TCTAGGTGATTTTATGTAATAACACATGTA 18 164 1 TTTATGTAAT 0.728152 -31 AATAAATATTATTATGTAATTTATTAACGT 19 210 1 ATTATGTAAT 0.533188 -91 ********** Masking position 7 Map Score: 12.4862 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 152 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 CAAAAACCATATCTCGTGGTATTTTTATCG 7 252 1 ATCTCGTGGT 0.983032 -49 TTAGAAACTCATCCCGTGGTTTGACCACGA 10 31 1 ATCCCGTGGT 0.98403 -91 TTGTTTTTGGCTTTCGTGGTCAAACCACGG 10 44 0 CTTTCGTGGT 0.862164 -78 AATAATTTTGAACCCGTGGTCAAACCACGA 10 84 1 AACCCGTGGT 0.967987 -38 CTCATTTTACATCTCGTGGTTTGACCACGG 10 97 0 ATCTCGTGGT 0.983032 -25 TGGATTGCAACACACGTGGTGACGAAAAAA 18 116 1 CACACGTGGT 0.933022 -79 GATACTTACTATCAGGTGGTGGCACCAAAG 19 61 1 ATCAGGTGGT 0.903954 -240 ********** Masking position 7 Map Score: 6.39039 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 4 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 7 TCATAAGAATATTGACCCCAAGAAATATCAAATAAGC 1 67 1 ATCAAGAAAA 0.785755 -234 ATGTTTATTGAGTTCTTTCTAGAAAAAATCAATTTGT 1 214 1 ATCTAGAAAA 0.958789 -87 AAGATCGCGAATAGGTTCCTACATAAAAAAGAAG 4 8 0 AACTACATAA 0.771711 -189 TAATGAACGTATAAAGCACTAGATAAAAAATTATAAT 5 113 1 AACTAGATAA 0.958789 -84 ATTCAAGTATAGAAAAATCTAGAAATATTAAAATTTG 8 152 1 AACTAGAAAA 0.949708 -149 CCTAATACTAAATATGTACTAGATATAGTTAATAAAC 15 135 1 ATCTAGATAA 0.966196 -50 GAACTTTATTACTTGTTGCTAGAAACAATAAAAATGA 16 27 1 ATCTAGAAAA 0.958789 -88 GTTATTACATAAAATCACCTAGATAAAAGCACATATT 18 150 0 AACTAGATAA 0.958789 -45 AAGATAGTGAAGTGCAAACTAGATATAAAACCTAAAA 19 23 1 ATCTAGATAA 0.966288 -278 * * ******* * Masking position 11 Map Score: 4.7676 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 20 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 AAAGAACTCAATAAACATTTTATTAACTATAGGA 1 198 0 AAAATTTATT 0.905188 -103 TTATTTGAAGATAAACATTATACTAAAATATATG 1 262 0 AAAATATACT 0.914611 -39 TATTATTTAAATAATAAATTTACTATACAAAATA 3 24 1 AAAAATTACT 0.649758 -243 TTTCTCACTTAAAAAGATTTTAATTAGCTTTAAA 4 48 0 AAAATTTAAT 0.570416 -149 TTTGAATAAGATAAACATCTTATTAATTTTTGCT 4 93 1 AAAATTTATT 0.905188 -104 TAATTGAAAAACAACAATATTATTGGATAATTAG 5 19 0 AAAATTTATT 0.907067 -178 TAATCAAATTATAAAATTTTTACTATTAAATTCT 5 58 0 AAATTTTACT 0.496821 -139 ATGATACTCTAGAAGTATCTGACTTATCTATAAA 6 238 1 AAAATTGACT 0.817308 -63 CTCATTTTATAACACTATAATATTATGAAAATTT 6 269 0 ACAATATATT 0.509091 -32 TTACAATATTAAAACTATATGACTAATATACCAA 7 138 0 AAAATTGACT 0.81731 -163 AATAACTATTATTTTTGACTTAGAA 7 286 0 AAAATATTTT 0.410225 -15 TACTTATAGTATAACAATAATACTGAAATATAAA 8 45 1 AAAATATACT 0.916461 -256 ACTGAAATATAAAAAAATTAGATTTTAAAATATG 8 66 1 AAAATAGATT 0.759946 -235 AAAGCCAAAAACAACTATGATATTAATAATTTTG 10 60 1 AAAATATATT 0.897037 -62 TATAAGTATTATACTTATACCGCAA 14 2 1 AAAATATACT 0.916461 -153 AAATTTTTTTATAATAATATTATTAAAATAATAA 17 26 1 AAAATTTATT 0.905391 -170 TTAAATATCCAGAACTAAAATATTAATAACAGTA 19 247 0 AAAAAATATT 0.567955 -54 * ** ** ***** Masking position 4 Map Score: 12.7354 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 172 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 GGTAAAATATTAAAATTTCATCCCATACAAT 1 19 0 TAAATTTCAT 0.892477 -282 TAAAGTTCACTAAATTTTCATTTAGTTAGTT 1 114 1 TAAATTTCAT 0.892477 -187 CAAATAAATAGAAAATTTAATT 1 289 1 GAAATTTAAT 0.529257 -12 TCAACTACGCTAAAATATAATATACTTTGCA 3 81 1 TAAATATAAT 0.880136 -186 CAATTAAAGGTAGAATTTAATAGTAAAAATT 5 47 1 TAGATTTAAT 0.674171 -150 AATTATTAACTAAATTATAATTTTTTATCTA 5 132 0 TAAATATAAT 0.880136 -65 AATTATTAACTAAATTATTATCAAAATTGAA 5 159 1 TAAATATTAT 0.542399 -38 TTTTTCTCCATAAAATTCAATTTTGATAATA 5 174 0 TAAATTCAAT 0.814508 -23 CAGATACTTCTAGAGTATCATTAACAAAAAT 6 228 0 TAGATATCAT 0.476911 -73 GACTTATCTATAAATTTTCATAATATTATAG 6 258 1 TAAATTTCAT 0.892477 -43 ATAAAAATTCTAAATTTTTATTTTATAGTAG 7 83 1 TAAATTTTAT 0.654994 -218 ACAGCTAATTTAAAGTACAATACTGGATAAA 7 205 0 TAAATACAAT 0.73273 -96 TCGCATATTTTAAAATCTAATTTTTTTATAT 8 72 0 TAAATCTAAT 0.631756 -229 ACTTTTTATACAAATTTTAATATTTCTAGAT 8 168 0 CAAATTTAAT 0.529257 -133 AAGGGTGCGATAAAAAATAATATAACC 8 284 1 TAAAAATAAT 0.321395 -17 AGAAAATCTTTAATATATAATTCTAGCCAAT 12 32 0 TAATTATAAT 0.455084 -184 TGTTGATACCTAAATTATCATTGAAAAGAAA 15 98 0 TAAATATCAT 0.838247 -87 CAACAAGTAATAAAGTTCAATATGTATATGT 16 14 0 TAAATTCAAT 0.814508 -101 ATTAAAATAGTAAAGTTTCTTGATTTAAAAT 16 78 1 TAAATTTCTT 0.337859 -37 TTATTGATAATAAAAGTTAATAGAACTTTCC 17 158 0 TAAAGTTAAT 0.529257 -38 TATTATACCGTAAACTTTAATCGAGTGATCT 18 63 1 TAAATTTAAT 0.921635 -132 GGATTTTTAATAATTTTCAATTTTTACTTTT 19 170 0 TAATTTCAAT 0.333079 -131 **** ****** Masking position 11 Map Score: 15.3853 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 257 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 CCTTTACAATTTAAAGTTCACTAAATTTTC 1 103 1 TTAAAGTTCA 0.812362 -198 TTAACTAATCTAAAAGTTTATTTTGTATAG 3 46 0 TAAAAGTTTA 0.733936 -221 AATTCTTAATTTTAAGTATATAGCGTTGTA 3 135 1 TTTAAGTATA 0.602176 -132 TTTAGATTTTTTAAAGAAAAATTTTGTATT 3 193 1 TTAAAGAAAA 0.506919 -74 GATCTTAATTTTAAAGCTAATTAAAATCTT 4 39 1 TTAAAGCTAA 0.474208 -158 TTAAAAATTTTTAAAGCAAAAATTAATAAG 4 111 0 TTAAAGCAAA 0.617818 -86 TCATTAATAATATAAGTAAAGAATATTTAA 5 89 0 TATAAGTAAA 0.681035 -108 GAAAAATTTTTAAAAGAACATGTGATTCAG 6 133 1 TAAAAGAACA 0.762096 -168 ATTATAAGATCAGTATTAAAGA 7 3 1 TATAAGATCA 0.435322 -298 TACAGCTAATTTAAAGTACAATACTGGATA 7 207 0 TTAAAGTACA 0.885847 -94 GATGTTTTTTAAAAAGTACAGCTAATTTAA 7 223 0 AAAAAGTACA 0.467842 -78 TAAAATAAAAGTACAACAATCATTG 8 6 1 TAAAAGTACA 0.916281 -295 ATTGTTATACTATAAGTATAACTAATGCAA 8 33 0 TATAAGTATA 0.680952 -268 TAAGTTGCGGTATAAGTATAATACTTATA 14 10 0 TATAAGTATA 0.680952 -145 TTATTGATAATAAAAGTTAATAGAACTTTC 17 159 0 TAAAAGTTAA 0.734053 -37 GATCACTCGATTAAAGTTTACGGTATAATA 18 63 0 TTAAAGTTTA 0.661784 -132 ATCACCTAGATAAAAGCACATATTCAGTTT 18 144 0 TAAAAGCACA 0.834357 -51 ********** Masking position 5 Map Score: 7.03928 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 226 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 CAAATTGATTTTTTCTAGAAAGAACTCAATAAACATTTT 1 211 0 TTTTGAACAA 0.908795 -90 AGTATAATGTTTATCTTCAAATAAATAGAAAATTTAATT 1 272 1 TTTTCAAAGA 0.666422 -29 AAATTCTACCTTTAATTGAAAAACAACAATATTATTGGA 5 26 0 TTATGAACAA 0.716769 -171 TATTTTTCTCCATAAAATTCAATTTTGATAAT 5 175 0 TTTTCAACAA 0.97714 -22 GATTGATAATTTCTTTTCAATAATGACAATT 6 3 0 TTTTCAACAA 0.974646 -298 CTAGGTATAGTTATATTCATTGATGACAATATTAAAAGC 6 93 1 TTTTCAACAA 0.878921 -208 CAGTATCAATTTTTATTCAAGTATAGAAAAATCTAGAAA 8 138 1 TTTTCAAAAA 0.913834 -163 TACAATAAGGTTTTTTACATAGCTCACAATATGTCATGA 8 223 0 TTTTCACCAA 0.888703 -78 ATATTAAAGATTTTCTACATTTAAGTCAAGGATATACTC 12 47 1 TTTTCAACAA 0.97559 -169 TAGACACAGTTTAATTTCAACAAGAGCAAAAAGTTTATA 12 159 0 TTATCAACAA 0.913988 -57 CTATTAACTTTTATTATCAATAATAGAAAAAAACGTAAA 17 166 1 TTTACAAAAA 0.574046 -30 ** * * ** * *** Masking position 9 Map Score: 5.79655 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 25 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TTCTTATGACAATACAAAATATTGAAGGTAAA 1 44 0 AATACAAATT 0.942635 -257 TTAGTTAGTTAACAGTTAATATATAGAAATCA 1 135 1 AACAGTAATT 0.734613 -166 TCTTCAAATAAATAGAAAATTTAATT 1 285 1 AATAGAAATT 0.871081 -16 GTTTATTTTGTATAGTAAATTTATTATTTAAA 3 29 0 TATAGAAATT 0.539736 -238 GAAACTATTAAATTCTTAATTTTAAGTATATA 3 125 1 AATTCTAATT 0.659042 -142 AATTATTTACAATACAAAATTTTTCTTTAAAA 3 201 0 AATACAAATT 0.942635 -66 AATCTGATCTACTACCAAATTTACAATTTTTT 6 199 0 ACTACAAATT 0.690359 -102 ACAAATCAAAAATAATAAATCTTGATTCATAG 7 50 0 AATAAAAATT 0.564225 -251 TTGTAATAAAAATTCTAAATTTTTATTTTATA 7 78 1 AATTCAAATT 0.740387 -223 TTTTAAAAAGTACAGCTAATTTAAAGTACAAT 7 215 0 TACAGTAATT 0.324512 -86 TATATATAAATACCTAATTTTACAATTAAC 9 13 0 AATACTAATT 0.917609 -20 GTAATCATCAAACACTTAATCTCATATTGCAA 14 86 0 AACACTAATT 0.870666 -69 CGCACTGAGTAACACATAATCTTAGGAATTGA 15 63 0 AACACTAATT 0.870666 -122 AAATACTCCTAATACTAAATATGTACTAGATA 15 128 1 AATACAAATT 0.942635 -57 AAATAATACCAATTTTATATATTATG 19 285 0 AATACAATTT 0.600685 -16 ***** **** * Masking position 8 Map Score: 8.94772 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 106 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 TATTTTATAGTAAGTTACGTTATTGGTATA 7 116 1 TAAGTTACGT 0.967354 -185 TAAGTTATATTTATATTAGA 10 1 1 TAAGTTATAT 0.864269 -121 ATCAAATGGTCAAGTTACGTGCTTACACTA 14 43 0 CAAGTTACGT 0.915501 -112 ACTATTTTAATAAGTTACGTTATAGTCATT 16 59 0 TAAGTTACGT 0.967354 -56 TCTGATACAATAAGTTATATAGATCACTCG 18 84 0 TAAGTTATAT 0.864269 -111 ATTACGTTAATAAATTACATAATAATATTT 19 213 0 TAAATTACAT 0.744588 -88 ********** Masking position 5 Map Score: 0.948127 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 7 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ********** No masking Map Score: -3.90555e-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: -3.90555e-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