AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_bsub_reg_300.orf -o00950_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 yclB 89 similar to phenylacrylic acid decarboxylase #6 yerQ 300 similar to hypothetical proteins #7 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #8 ykrV 94 similar to aspartate aminotransferase #9 aspB 22 aspartate aminotransferase #10 ypmA 142 ypmA #11 dinG 125 ATP-dependent helicase #12 panB 245 ketopantoate hydroxymethyltransferase #13 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #14 ypjD 300 alternate gene name: jojD #15 trpE 215 anthranilate synthase #16 aroB 61 3-dehydroquinate synthase #17 aroF 69 chorismate synthase #18 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #19 ndk 115 nucleoside diphosphate kinase #20 gerCA 162 heptaprenyl diphosphate synthase component I #21 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #22 mtrA 187 GTP cyclohydrolase I #23 hbs 300 non-specific DNA-binding protein HBsu #24 yqeT 24 similar to ribosomal protein L11 methyltransferase #25 dnaJ 199 heat-shock protein #26 dnaK 23 class I heat-shock protein (chaperonin) #27 grpE 71 heat-shock protein #28 hrcA 119 transcriptional regulator #29 hemN 52 coproporphyrinogen III oxidase #30 lepA 133 GTP-binding protein #31 spoIIP 62 spoIIP #32 gpr 203 spore protease #33 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #34 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #35 prfA 125 peptide chain release factor 1 #36 ywfB 151 alternate gene name: ipa-80d #37 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #38 rocB 73 alternate gene name: ipa-77d #39 rocA 226 pyrroline-5 carboxylate dehydrogenase #40 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #41 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis Motif number 1 TCAGAATGTCAAAAAGCTCCCGCCCAAAGG 1 266 0 AAAAAGCTCC 0.934087 -35 AAGTGAAAAACTCCTTTCTTGTCG 2 65 0 GAAAAACTCC 0.92574 -14 CAAAAAACGCTAGCGGGTTTT 3 2 1 AAAAAACGCT 0.839633 -154 CGCTGTAAGGGACAAGCTCTTACAAAACCC 3 25 0 GACAAGCTCT 0.815471 -131 AACTTTTATAGAAAAACGCTGTAAGGGACA 3 41 0 GAAAAACGCT 0.92002 -115 AACAGAGGGCGCAAAACCCTCTGAATACAT 4 20 0 GCAAAACCCT 0.789341 -125 TCAGCTTGTTGAAAAACCCTCGCATTCGTT 6 20 1 GAAAAACCCT 0.947787 -281 AAGAAAAGCCCCCTTTATCGGG 11 3 1 GAAAAGCCCC 0.98506 -123 AATCTTAAAAGAAAACCCCCGATAAAGGGG 11 20 0 GAAAACCCCC 0.875185 -106 CAAGCATCACACAAAACCCCTTTTCCTTCC 14 165 1 ACAAAACCCC 0.712672 -136 TTTCTTCACAGAAAAGCCCCTTTCTAAGGG 22 55 1 GAAAAGCCCC 0.98506 -133 CTTGAAATATGAAAAGCCCCTTAGAAAGGG 22 72 0 GAAAAGCCCC 0.98506 -116 ACTCACCCAAAAAAAGCGCCAAAAACTTCA 28 15 0 AAAAAGCGCC 0.950045 -105 GTAATTACTAGACAAGCGCTGGAGGGATTC 31 42 1 GACAAGCGCT 0.85571 -21 ATCCCAGCTGGAAAAGCTCCCTCTGCTATA 35 31 0 GAAAAGCTCC 0.968882 -95 CATACAAACAAAAAAACCCTTTAAAAAGGG 36 41 0 AAAAAACCCT 0.892034 -111 AAAAAGCTCTCCGGGAGGCC 37 1 1 AAAAAGCTCT 0.906927 -209 TAACACGTAAAAAAAGCTCTCCGGCCTCCC 37 23 0 AAAAAGCTCT 0.906927 -187 TCCTCTGCAGAAAAAGCGCTTTTTCATAAT 41 240 0 AAAAAGCGCT 0.92896 -61 ********** Masking position 5 Map Score: 27.5486 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 400 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 GTCGTATATAATCAAATGAAATAAAAAACTTTGGTTC 1 57 0 ATAAAAAAAA 0.873323 -244 CCTGAAAAAGAATAATTAAAATTAAAAATCTTTAATG 1 126 0 AAAATAAAAA 0.574647 -175 CTATGAGTTAAAAAAATCGCAACAAAATGTACATAAT 6 213 0 AAAAAGAAAA 0.894054 -88 TGGTTAAATGAAAAAAGTAAAGAAAAATTTGGGGTGT 8 18 0 AAAAAAAAAA 0.961643 -77 GTGATGCTTGGAGAAATTAGATTAAAAAACATATTTT 14 138 0 GAAAAAAAAA 0.80061 -163 AATACTATATAACAAATAAACCCAAAAGAAAGACTTC 15 138 0 AAAAAAAAAA 0.961643 -78 TGTAAACCTTTACAAAACAGAACAAAAACCGGCGGCG 18 49 0 TAAAAAAAAA 0.595486 -188 GGATGAAAAAAGGAAAAAAAGGAATATTC 23 3 1 ATAAAAAAAA 0.873323 -298 CTGAACTGTGAAGAAATGATAATAAACGAACTGAATG 23 248 1 AAAAAAAAAC 0.894054 -53 TATCCCGGGCAAGAAAAAAAGTCAAAGCCAAGAGATG 25 100 0 AAAAAAAAAG 0.705595 -100 CTTGCCCGGGATAAAAGGAATTGAAAAATCATAATTC 25 124 1 ATAAAAAAAA 0.873323 -76 AACTCACCCAAAAAAAGCGCCAAAAACTTCATTGC 28 9 0 AAAAAGAAAC 0.739615 -111 TAACAAAAGTATCAAACCACAAGAAAAATGTCAATTA 28 47 0 ATAAAAAAAA 0.873323 -73 ATTCAATGTAAAACAAGAAAGAGAAAAGTTCCCTATC 30 41 0 AACAAAAAAA 0.889414 -93 CCATTTGCTGAATAAATCATGCTAAAAAGAGAACCTT 32 140 0 AAAAAAAAAA 0.961643 -64 TCAGGGCATAATACAACCATCAAAAAAAGGGAGTGAC 33 16 0 ATCAAAAAAA 0.688634 -132 GAATGCTAAGAAAAAACGAGGAGAAACTTCCGCTAGA 33 63 0 AAAAAAAAAC 0.894054 -85 CCATACAAACAAAAAAACCCTTTAAAAAGGGTTTTTA 36 35 0 AAAAACAAAA 0.705595 -117 GTAAATAGAGAAAAAACAATGCTAAACTATAATACAA 37 142 1 AAAAAAAAAC 0.894054 -68 CTCTTTACGCAAAAAACAAATGCAAAATTATTTTGCG 39 24 0 AAAAAAAAAA 0.961643 -203 TTTGCGTAAAGAGCAAAAAACGCAAAATAAATTTGCG 39 48 1 GACAAAAAAA 0.562961 -179 AAGTTTTTTCAGCAAAAGACAAGAAAATGGCATGATT 39 145 1 AGAAAAAAAA 0.715974 -82 TGAATCCACAAAAAAAGAGACTGAAAACATCTCAGTC 40 31 0 AAAAAGAAAA 0.894054 -146 CCGGCCAAAAAAACAATGAGGTGAAAAAG 40 158 1 AACAAAAAAA 0.889414 -19 ATCCTATTTTAAAAAAGGGCAAAAAAAGTCGAAGATG 41 20 0 AAAAAGAAAA 0.894054 -281 ** *** * **** Masking position 5 Map Score: 23.145 Number of sites scoring better than the average of aligned sites = 893 Number in coding regions = 696 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 ACATGCTTTCTTCTCCTCATAGGATAGGTT 3 73 1 TTCTCCTCAT 0.949603 -83 GTTTTCTCCTCCTCATGTTTAGA 12 233 0 TTCTCCTCCT 0.984974 -13 CATCTTCTCATTCTCCTTGCCATAAGGAGT 15 189 1 TTCTCCTTGC 0.738231 -27 TTTTCTCATATTCTCCACATTTTCTCTAAT 16 25 0 TTCTCCACAT 0.779532 -37 GACTTCTTCTCCCTTCATCGCAT 17 57 0 TTCTTCTCCC 0.800938 -13 ATTAAGAAATTTCTCCGCCCCGGATTGATT 19 22 1 TTCTCCGCCC 0.918138 -94 ATTCTCCACCCCATCATTATG 19 105 0 TTCTCCACCC 0.930284 -11 GCCTTTCACCTCCTCCCAAAAGGA 23 287 0 TTCACCTCCT 0.971232 -14 GCACCTGTCCTTCTCCTTACACTTTGAGGG 27 41 1 TTCTCCTTAC 0.772816 -31 TGTGTTCACCTCCCTCAAAGTGTA 27 58 0 TTCACCTCCC 0.973421 -14 CGGATTCACCTTCTTTACAGAAAG 29 39 0 TTCACCTTCT 0.848912 -14 GTGTTTCACCTCCTAAGATACAAC 32 5 1 TTCACCTCCT 0.971232 -199 TAGCGGAAGTTTCTCCTCGTTTTTTCTTAG 33 65 1 TTCTCCTCGT 0.939835 -83 AAATTGTCCTCCTGATCAAAAAG 38 61 0 TTGTCCTCCT 0.846088 -13 CTTTTTCACCTCATTGTTTTTTTG 40 163 0 TTCACCTCAT 0.906581 -14 ********** Masking position 2 Map Score: 19.5883 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 192 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 TCTTTAATGAAAATAAAAAAAGTCTGTTCGTGTCGA 1 99 0 AAAAAAGTTG 0.736841 -202 TGATAAACAAAAGGTGTTTCACGTGTAA 2 3 1 AAAAAGGTTT 0.957612 -76 TTTCTTGTCGAAACACAAAAGGTGTTCGACGAATTG 2 39 0 AAAAAGGTTT 0.957612 -40 TTTCGTTATAATAGACAAAGTGCATTTTCTGCTTAT 4 52 1 AAAAATGCTT 0.694615 -93 AGTTTCATGAATATACAAAAGTTTTTATTTTGTCTT 4 109 1 AAAAAGTTTT 0.69269 -36 TCTATAATTAATACCTAAAAGGTATGATAAGGAGGC 5 19 0 AAAAAGGTTG 0.956766 -71 CCCCCTTCCTAGACTACAAGGGTTTTCAATCAAGCT 6 104 1 AACAAGGTTT 0.926178 -197 AACTCATAGTATAATTAAAGGTTGTTAGTGTAAAAA 6 241 1 AAAAAGTTTT 0.69269 -60 CAAAATCCTAAAACGAAAACTGTTTTAGGATTTTGT 7 44 0 AAAAATGTTT 0.803757 -212 CGCCCTTCCTAGACTTCAAAGGTTTTCAATCACGCT 7 90 0 AACAAGGTTT 0.926178 -166 TAAGATTTTGAGAGTAAAACGGTTTTGCCGCTCCAT 11 43 1 AAAAAGGTTT 0.957612 -83 TTTTCTGTGAAGAAATAAAGTGTATGTAAGCTAGAT 22 34 0 AAAAATGTTG 0.800483 -154 GGGGCTTTTCATATTTCAAGAGCATGGGCTTCCTGA 22 82 1 AACAAAGCTG 0.463388 -106 TAAGAGAAAGACAATTAAACGGCTTTTTAAGAAAAA 23 173 0 AAAAAGGCTT 0.926178 -128 AGATTTCTTGACATTGCAAAGGTGTGAATCAA 33 126 1 AACAAGGTTG 0.924754 -22 TCAGCAAAAGACAAGAAAATGGCATGATTCTTGCAT 39 153 1 AAAAAGGCTG 0.924754 -74 * * *** *** ** Masking position 8 Map Score: 13.2155 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 200 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 CTTGAAACCTCCTAATCAGAATGTCAAAAAGC 1 279 0 CTCCTTCAAT 0.785275 -22 ATGCTTTCTTCTCCTCATAGGATAGGTTTGTCGA 3 75 1 CTCCTTAATA 0.899475 -81 CTATTCTCACCTTCTAAAAAAATCTTGAAAT 8 74 0 CACCTTAAAA 0.958704 -21 CTGCGAACTGCACCTATTATTAAAATAGATAGAC 12 63 1 CACCTTAAAA 0.958704 -183 GCCTTTCACCTCCTCCCAAAAGGATACATT 23 281 0 CACCTTCAAA 0.965771 -20 AACTACCAACTCCTCATCCAATAA 24 2 0 CTCCTTCATA 0.915786 -23 TTGAATAACCTCCTGCTATGTAA 26 1 0 CTCCTTATAA 0.861964 -23 AATCTATCACTCCTACTATTAAACGCAAAATAC 30 111 0 CTCCTTAAAA 0.968328 -23 GTGTTTCACCTCCTAAGATACAACCTGTAG 32 7 1 CACCTTAATA 0.8717 -197 CTTCCATAATCTTCTTATCATAAAGTTGTATTAT 37 170 0 CTTCTTCAAA 0.69342 -40 CTTTCTCAAACACCTCTTCCATAATCTTCTTATC 37 185 0 CACCTTCTAA 0.852129 -25 AAATTGTCCTCCTGATCAAAAAGTTGAAATCG 38 52 0 CTCCTTCAAA 0.973793 -22 GAAAGGTGATCACCTGTTAGACAAATTTCTGTTC 39 103 1 CACCTTACAA 0.799413 -124 TGTAGTCCCCCTCGTGTTATGAAATATATCTTCG 39 202 0 CTCGTTAAAA 0.733926 -25 ***** ** *** Masking position 8 Map Score: 10.1982 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 79 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 TATTATAACGAAAAAAACAGAGGGCGCAAA 4 35 0 AAAAAAACAG 0.799443 -110 GCCGAACTTTAGAAAGTGAAGAATCCTTCT 12 151 1 AGAAAGTGAA 0.739522 -95 TGTTTCAATAAAAAAATCAGCTTTTCAGCT 18 153 0 AAAAAATCAG 0.689817 -84 ATACTAGGACAAAAAGACAGCGAGACTGGG 18 208 1 AAAAAGACAG 0.865373 -29 TTATAGCATAAAAAAAAGAATTGGCTGTAT 20 59 0 AAAAAAAGAA 0.817227 -104 GGATGAAAAAAGGAAAAAAAGGAAT 23 6 1 AAAAAAGGAA 0.672948 -295 AGCAAGTAAGAGAAAGACAATTAAACGGCT 23 185 0 AGAAAGACAA 0.806922 -116 CTGTCTCAGAAAAAAATGAGAGCAAGTAAG 23 205 0 AAAAAATGAG 0.730304 -96 TTCAATGATTAGAAAGTCAAAGTCAGGCAT 25 73 1 AGAAAGTCAA 0.699849 -127 CGGGCAAGAAAAAAAGTCAAAGCCAAGAGA 25 102 0 AAAAAGTCAA 0.767644 -98 TACGTGAAAGAGAAAAGCAACCCAGATATG 30 12 1 AGAAAAGCAA 0.543929 -122 ATGTAAAACAAGAAAGAGAAAAGTTCCCTA 30 43 0 AGAAAGAGAA 0.835763 -91 AAATCATGCTAAAAAGAGAACCTTCAATGA 32 134 0 AAAAAGAGAA 0.878202 -70 CAACCATCAAAAAAAGGGAGTGACACAGA 33 10 0 AAAAAGGGAG 0.782695 -138 TCAAGATCGGAAAAAGAGAAAGGTGATCAC 39 86 1 AAAAAGAGAA 0.878202 -141 TTGAATCCACAAAAAAAGAGACTGAAAACA 40 39 0 AAAAAAAGAG 0.829165 -138 TAAGCGCTTTAAAAAATCAGCCCGCCAATT 40 120 0 AAAAAATCAG 0.689817 -57 ACAGCCGGCCAAAAAAACAATGAGGTGAAA 40 154 1 AAAAAAACAA 0.785964 -23 ATGTTACTAGAAAAAGAGAGGGAAATCGTC 41 80 1 AAAAAGAGAG 0.886709 -221 TTAATTTTTAAGAAAAAGAACTGGTAATTC 41 206 1 AGAAAAAGAA 0.759364 -95 ********** Masking position 5 Map Score: 18.6855 Number of sites scoring better than the average of aligned sites = 942 Number in coding regions = 678 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 7 GCTATTATCCTACTAAAAATCCTTTTAAATCAAG 1 17 1 TTAAAATCCT 0.761539 -284 AGAATAATTAAAATTAAAAATCTTTAATGAAAAT 1 121 0 ATAAAAATCT 0.584886 -180 GAATTGTTACACGTGAAACACCTTTTGTTTATCA 2 11 0 ATAAACACCT 0.775152 -68 GTGTAACAATTCGTCGAACACCTTTTGTGTTTCG 2 33 1 TTGAACACCT 0.695714 -46 GCTTTCAGCTTGTTGAAAAACCCTCGCATTCGTT 6 16 1 TTAAAAACCT 0.951885 -285 TCTTTCAGCTTGATTGAAAACCCTTGTAGTCTAG 6 112 0 TTGAAAACCT 0.870559 -189 CTTTTCAGCGTGATTGAAAACCTTTGAAGTCTAG 7 84 1 TTGAAAACCT 0.870559 -172 ATCCGCTTTTAAATAAAACACCATCCTACTCCCA 10 38 0 ATAAACACCT 0.775152 -105 TGGAGAAATTAGATTAAAAAACATATTTTTTATT 14 133 0 ATAAAAAACT 0.793762 -168 AGAGTAACACATATAAAAAGCCATATCAAGCATT 23 90 0 ATAAAAGCCT 0.716885 -211 GTGCAGTTTTTCTTAAAAAGCCGTTTAATTGTCT 23 167 1 TTAAAAGCCT 0.831646 -134 GGATAAAAGGAATTGAAAAATCATAATTCAAAAT 25 132 1 ATAAAAATCT 0.584886 -68 TTCTTAGCATTCGTCAAAAAACGTGATATAATGT 33 88 1 TTAAAAAACT 0.88247 -60 TAAATTCCTATAATTAAAAACCCTTTTTAAAGGG 36 21 1 TTAAAAACCT 0.951885 -131 ATTATCAATATTTTCAAAAAACATTGACAGTTCA 36 77 1 TTAAAAAACT 0.88247 -75 CTATATTTCATTCTAAAAATACATGAGGATGTAA 37 50 0 TTAAAATACT 0.547931 -160 TCTTGTCTTTTGCTGAAAAAACTTGTTGAATCGA 39 135 0 TTAAAAAACT 0.88247 -92 GTGTTAATATTCCTTAAAAAACATTTACTTCCAT 41 156 1 TTAAAAAACT 0.88247 -145 * * ******* * Masking position 4 Map Score: 14.4841 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 271 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 AACGAAAAAAACAGAGGGCGCAAAACCCTCT 4 28 0 ACAGAGGCGC 0.960771 -117 TGTAGTCTAGGAAGGGGGAGCATTGGAGCGG 6 91 0 GAAGGGGAGC 0.709667 -210 GAGCACCGAAGCACAGGCCTGACAACGAATG 7 157 1 GCACAGGCTG 0.813641 -99 AAGGACTGGGACAGAGGGATGAAACTCGCCG 12 124 1 ACAGAGGATG 0.904236 -122 GAACAATCTGGCTGAGGGCGGTTTTACAGGT 14 52 0 GCTGAGGCGG 0.871035 -249 GTTGGGAAAGGCAGAGGTCTGATGCACACTG 18 111 0 GCAGAGGCTG 0.960477 -126 ATGCTCGCAAACAGCGGGAGGATACAGCCAA 20 38 1 ACAGCGGAGG 0.820699 -125 ACAGGGGCCTCCTTCACATTA 32 193 0 ACAGGGGCTC 0.732631 -11 TACCAATAGCAAAGAGGTAGGAAA 34 4 0 AAAGAGGAGG 0.828589 -188 ACATACTAATGCAGATGAAGGAGATGTCAAG 34 168 1 GCAGATGAGG 0.774627 -24 TTCCAGTATAGCAGAGGGAGCTTTTCCAGCT 35 25 1 GCAGAGGAGC 0.977103 -101 GAGCAGAGGCATCTTCGACTTTT 41 3 1 GCAGAGGATC 0.937937 -298 AACCTTGTATAAACAGGAAGGAATTCTCATT 41 116 1 AAACAGGAGG 0.464794 -185 CGCTTTTTCTGCAGAGGACGCTCTGGCCAAA 41 252 1 GCAGAGGCGC 0.981084 -49 ******* *** Masking position 7 Map Score: 9.25925 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 481 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 ATTAAAAATCTTTAATGAAAATAAAAAAAGT 1 112 0 TTAATGAAAA 0.947141 -189 TAGATAAAGGATAAATATAAATAATATTCAT 1 206 1 ATAATATAAA 0.436517 -95 TTCTTTCAGCTTGATTGAAAACCCTTGTAGT 6 116 0 TTATTGAAAA 0.638184 -185 TCATATATGGTTAAATGAAAAAAGTAAAGAA 8 31 0 TTAATGAAAA 0.947149 -64 TCTCAAAATCTTAAAAGAAAACCCCCGATAA 11 25 0 TTAAAGAAAA 0.638185 -101 CTTTATTCACTTTAATGTAAACCTTTACAAA 18 70 0 TTAATGTAAA 0.910523 -167 ATTGTATTGTTTCAATAAAAAAATCAGCTTT 18 159 0 TTAATAAAAA 0.764646 -78 AGATTAAGAAATAAATGTGAATTTGGGGACA 20 130 1 ATAATGTGAA 0.553631 -33 ATTGTAAAGATTCAATGTAAAACAAGAAAGA 30 56 0 TTAATGTAAA 0.91078 -78 AGATTGCAATATAAATGTAAAGTATTTTTCA 32 106 1 ATAATGTAAA 0.810354 -98 AAAGAGAACCTTCAATGAAAAATACTTTACA 32 121 0 TTAATGAAAA 0.947147 -83 ATAATGGGATTTAAATGAAAATAATAAAACT 37 90 1 TTAATGAAAA 0.947149 -120 ATCTTCGCATATGAATAAAAATGCAAGAATC 39 178 0 ATAATAAAAA 0.575955 -49 ACACTTGGAATTCAATGAGAATTCCTTCCTG 41 129 0 TTAATGAGAA 0.838757 -172 ** ******** Masking position 4 Map Score: 8.58382 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 234 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 10 GAATTCGTGAGCACCGACGCGCAGACCTGACA 6 49 0 GCACCACGCC 0.985736 -252 CATTCGCTCCGCTCCAATGCTCCCCCTTCCTA 6 83 1 GCTCCATGCC 0.984438 -218 AGGTGAAAACGCACAAAAGCTCAAAACTGATT 6 176 0 GCACAAAGCC 0.969881 -125 CATTCGCTGTGCTCCGATGCTCGCCCTTCCTA 7 115 0 GCTCCATGCC 0.984438 -141 GAATTCGTGAGCACCGAAGCACAGGCCTGACA 7 149 1 GCACCAAGCC 0.991601 -107 TGTTCGCCCCCAAGCACATCATGATCA 13 15 0 GCCCCAAGCC 0.981547 -17 TTCGATTCTAGCACATATGCCCCGCTAAAAGC 22 133 0 GCACAATGCC 0.968326 -55 ***** **** * Masking position 7 Map Score: 7.50037 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 21 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 AATTATTCTTTTTCAGGGCGTATGTATATA 1 146 1 TTTCAGGGCG 0.875522 -155 CTGAGGCTTTCAGCTTGTTGAAAAACC 6 8 1 TTTCAGCTTG 0.899797 -293 CTTAACATTCTTTCAGCTTGATTGAAAACC 6 124 0 TTTCAGCTTG 0.899797 -177 TTTGTCATCTTTTCAGCGTGATTGAAAACC 7 76 1 TTTCAGCGTG 0.960694 -180 TCAAGCCAAGTTTCAGCGTGTAGGCAAACC 7 192 0 TTTCAGCGTG 0.960694 -64 AAAATCAGCTTTTCAGCTGATTTTAGATCG 18 141 0 TTTCAGCTGA 0.779159 -96 TTCACTTTGCTTTTAGCGGGGCATATGTGC 22 125 1 TTTTAGCGGG 0.905687 -63 GAATTGACAATTTCAGGGCATAATACAACC 33 35 0 TTTCAGGGCA 0.635336 -113 AAATTGTCAATTCTAGCGGAAGTTTCTCCT 33 52 1 TTCTAGCGGA 0.477245 -96 GTTGGTTACATTTTAGCGCGGTTGAAAAAG 34 81 1 TTTTAGCGCG 0.879679 -111 GAGGGAGCTTTTCCAGCTGGGATTGAAATG 35 38 1 TTCCAGCTGG 0.845358 -88 ********** Masking position 5 Map Score: 6.0498 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 641 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 12 TGTAGAATTCGTGAGCACCGACGCGCAGAC 6 55 0 GTGAGCACCG 0.959933 -246 TGTTGAATTCGTGAGCACCGAAGCACAGGC 7 145 1 GTGAGCACCG 0.959933 -111 AAAACGGCAGATCATCTCCTCTAAACATGA 12 214 1 ATCATCTCCT 0.644061 -32 CCTTTTCCACATCAGCCCCTC 14 2 0 ATCAGCCCCT 0.841857 -299 TCTTTTTAGTGTCAGCCCCGCTTCCGGAGC 25 13 1 GTCAGCCCCG 0.952604 -187 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGC 25 27 0 GTCAGCTCCG 0.928538 -173 TTTATCGAAGGGCAGCACCTGTCCTTCTCC 27 27 1 GGCAGCACCT 0.89218 -45 TGTGTTCACCTCCCTCAAAGT 27 61 0 GTGTTCACCT 0.769715 -11 CATCATCACCTCTGTTAGCAC 28 109 0 ATCATCACCT 0.851325 -11 GGTCTTCACCTCTGTTTTCCT 35 115 0 GTCTTCACCT 0.851537 -11 AAAGAGAAAGGTGATCACCTGTTAGACAAA 39 98 1 GTGATCACCT 0.930896 -129 ********** Masking position 6 Map Score: 6.054 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 328 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 ACAGACTTTTTTTATTTTCATTAAAGATTTT 1 108 1 TTTTTTTCAT 0.546299 -193 CAGTGTCCTCTTCATTATCCTGAAATACACT 3 130 0 TTCTTATCCT 0.756328 -26 AAGAAAGCGCCTCCTTATCATACCTTTTAGG 5 11 1 CTCTTATCAT 0.714109 -79 GTTTTGAGCTTTTGTCATCCTTAACATTCTT 6 142 0 TTTTCATCCT 0.830606 -159 TATCTCATCATCCTACTTAAGAGT 6 287 0 CTCTCATCCT 0.839073 -14 GAAATGATAGTCCATCATCATATATGGTTAA 8 48 0 TCCTCATCAT 0.721512 -47 TTTTTCATCCTCCAGTTTGAA 10 132 0 TTTTCATCCT 0.830606 -11 TCACACAAAACCCCTTTTCCTTCCATTAGAT 14 171 1 CCCTTTTCCT 0.681413 -130 GTTTGCTGTTTTCTTTTTCATCCACTATAAT 14 211 0 TTCTTTTCAT 0.49695 -90 AACGAAACCTCCTATCATCCTCTTACATGTT 14 278 0 CCTTCATCCT 0.868279 -23 ACGAATATTCCTTTTTTTCCTTTTTTCATCC 23 11 0 CTTTTTTCCT 0.715378 -290 ATTCAGTTCGTTTATTATCATTTCTTCACAG 23 253 0 TTTTTATCAT 0.701406 -48 GGTCTTCACCTCTGTTTTCCTGTGCGTAACA 35 105 0 TCTTTTTCCT 0.667934 -21 CTTCCATAATCTTCTTATCATAAAGTTGTAT 37 173 0 CTTTTATCAT 0.752753 -37 TGGATTCACCCTTATCATCATGCAAGATCCG 40 78 0 CTTTCATCAT 0.797816 -99 CCCGCCAATTCCTTTCTTCATTGGATTCACC 40 99 0 CCTTCTTCAT 0.677209 -78 ACATTTTATATCTTTTATCCTATTTTAAAAA 41 42 0 TCTTTATCCT 0.796916 -259 TAAAAATTAATCTATCATCATTTTCCATGGA 41 185 0 TCTTCATCAT 0.759493 -116 *** ******* Masking position 5 Map Score: 11.183 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 614 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 14 TGTTGAAAAACCCTCGCATTCGTTGTCAGGT 6 26 1 CCCCGCATTC 0.961329 -275 CGCGTCGGTGCTCACGAATTCTACATTCGCT 6 60 1 CTCCGAATTC 0.965562 -241 ACATTCGCTCCGCTCCAATGCTCCCCCTTCC 6 82 1 CGCCCAATGC 0.794745 -219 TGCTTCGGTGCTCACGAATTCAACATTCGCT 7 139 0 CTCCGAATTC 0.965562 -117 TGTAGGCAAACCTTCGCATTCGTTGTCAGGC 7 173 0 CCTCGCATTC 0.640762 -83 CTTGAACTCCCCCTAATTCGTC 9 4 0 CCCCTAATTC 0.875495 -19 ACGGTTTTGCCGCTCCATTTCCGTACAAAAC 11 61 1 CGCCCATTTC 0.889123 -65 TCGCTTCACTCTCCCGAATTTCTCACATAAA 25 178 0 CTCCGAATTT 0.795733 -22 CATCCCTCCTCGAATTCCAGTATAGCA 35 7 1 TCCCGAATTC 0.837309 -119 GCTAAAGAATCGCACGATTTTATTTCTCTCA 38 13 0 CGCCGATTTT 0.740966 -61 TTTAGCGGATCGCACGATTTCAACTTTTTGA 38 38 1 CGCCGATTTC 0.953678 -36 AAAAAATCAGCCCGCCAATTCCTTTCTTCAT 40 109 0 CCCCCAATTC 0.965443 -68 *** ******* Masking position 9 Map Score: 5.84902 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 112 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 GATTATATACGACAAAATTCGACACGAACA 1 81 1 GACAAAATTC 0.951015 -220 TCAGAATGTTGACAAAATCCTAAAACAGTT 7 33 1 GACAAAATCC 0.916625 -223 CTGAAAAGATGACAAAATCCTAAAACGAAA 7 62 0 GACAAAATCC 0.916625 -194 GCCTATTCAAGCCAAGTTTCAGCGTGTAGG 7 198 0 GCCAAGTTTC 0.834832 -58 ATCCGGGGCGGAGAAATTTCTTAATATCTA 19 17 0 GAGAAATTTC 0.762634 -99 GATAAAATTTGCCAAAATTCCC 27 3 0 GCCAAAATTC 0.950075 -69 TCACCTGTTAGACAAATTTCTGTTCGATTC 39 112 1 GACAAATTTC 0.950987 -115 GGACGCTCTGGCCAAATTTCAACAATCAAT 41 267 1 GCCAAATTTC 0.950073 -34 ********** Masking position 5 Map Score: 4.39894 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802