AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_bsub_reg_100.orf -o00230_bsub_100.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 Purged sequences: rpsE 24 ribosomal protein S5 rpsN 22 ribosomal protein S14 Input sequences: #1 dnaN 188 DNA polymerase III (beta subunit) #2 guaB 120 inositol-monophosphate dehydrogenase #3 dnaX 300 DNA polymerase III (gamma and tau subunits) #4 xpaC 119 xpaC #5 yaaO 81 similar to lysine decarboxylase #6 yaaQ 73 similar to hypothetical proteins #7 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #8 prs 22 phosphoribosyl pyrophosphate synthetase #9 yacA 103 similar to cell-cycle protein #10 rpoB 245 RNA polymerase (beta subunit) #11 rpoC 61 RNA polymerase (beta' subunit) #12 rpsJ 235 ribosomal protein S10 (BS13) #13 rplC 39 ribosomal protein L3 (BL3) #14 rplD 27 ribosomal protein L4 #15 rplB 31 ribosomal protein L2 (BL2) #16 rpsS 57 ribosomal protein S19 (BS19) #17 rpsQ 22 ribosomal protein S17 (BS16) #18 rplN 40 ribosomal protein L14 #19 rplX 37 ribosomal protein L24 (BL23) (histone-like protein HPB12) #20 rplE 26 ribosomal protein L5 (BL6) #21 rpsH 31 ribosomal protein S8 (BS8) #22 rplF 29 ribosomal protein L6 (BL8) #23 rplR 32 ribosomal protein L18 #24 rplO 30 ribosomal protein L15 #25 adk 54 adenylate kinase #26 rpoA 176 RNA polymerase (alpha subunit) #27 yclB 89 similar to phenylacrylic acid decarboxylase #28 guaA 232 GMP synthetase #29 purE 300 phosphoribosylaminoimidazole carboxylase I #30 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #31 purM 101 phosphoribosylaminoimidazole synthetase #32 yfkN 242 similar to 2',3'-cyclic-nucleotide 2'-phosphodiesterase #33 yhcV 136 similar to hypothetical proteins #34 yitA 300 similar to sulfate adenylyltransferase #35 yjbP 234 similar to diadenosine tetraphosphatase #36 adeC 154 adenine deaminase #37 yloD 233 similar to guanylate kinase #38 polC 108 DNA polymerase III (alpha subunit) #39 pnpA 172 polynucleotide phosphorylase (PNPase) #40 ymaA 242 similar to ribonucleoprotein #41 deoD 300 purine nucleoside phosphorylase #42 yosP 300 similar to ribonucleoside-diphosphate reductase (beta subunit) #43 xpt 300 xanthine phosphoribosyltransferase #44 ndk 115 nucleoside diphosphate kinase #45 drm 160 phosphodeoxyribomutase #46 relA 167 GTP pyrophosphokinase #47 yrvE 66 similar to single-strand DNA-specific exonuclease #48 yrvD 75 yrvD #49 yrvC 157 yrvC #50 polA 243 DNA polymerase I #51 pykA 42 pyruvate kinase #52 pfk 183 6-phosphofructokinase #53 dnaE 300 DNA polymerase III (alpha subunit) #54 yunH 174 similar to allantoinase #55 ureA 300 urease (gamma subunit) #56 rpoE 182 RNA polymerase (delta subunit) #57 purA 205 adenylosuccinate synthetase Motif number 1 AGTAAATCCCCCTCTTTTCGGCAAAATATTA 2 99 0 CCTCTTTTCG 0.494327 -22 GGGGCCTACCTCCCTTTTTATCTTCGGAT 11 43 0 CCTCCCTTTT 0.98268 -19 TATTTTCCCTCCTTTTCGCCTACATCAC 12 218 0 CCTCCTTTTG 0.92085 -18 AATCAATTTCCTCCTTTCCTAAGAGAA 14 8 0 CCTCCTTTCT 0.97331 -20 TTTGAATTTCCCTCCTTCTTTTTACAGATAA 15 11 0 CCTCCTTCTT 0.95639 -21 TTTGGAACCTCCCTTCGTGATTGCACTA 16 40 0 CCTCCCTTCT 0.98198 -18 TATTTGTTACCTCCCTTCGGAAAAAGAATT 18 21 0 CCTCCCTTCG 0.943496 -20 GAGATAGACCTCCCTTCCTTTTAATA 20 8 0 CCTCCCTTCT 0.98198 -19 TATATAATTACCTCCTTCCCTTTCTTGGGGA 21 11 0 CCTCCTTCCT 0.954676 -21 ACCAAACACCTCCATTCATGTTAAACTTC 22 11 0 CCTCCATTCT 0.863556 -19 CTAGGTCACTCCTTTCTTCACTTTAAGC 23 15 0 ACTCCTTTCT 0.76135 -18 TTTCCCCCGTCCTCTCTTTATTAAGAGGGAA 25 29 0 CCTCTCTTTT 0.832308 -26 GAAGCTCGCTCCGCCCTCTTTGGCAAGGCCG 28 155 0 CCGCCCTCTT 0.707458 -78 TCATATCTGTCCTCGTTTTTTTCTGTGTCAA 28 184 1 CCTCGTTTTT 0.660826 -49 GATTCATAACCTCCCGCTTTATATGTCTAC 32 10 1 CCTCCCGCTT 0.822265 -233 CTTTCCTCTAACTCCCTTTTTAAACGGCTCG 33 79 1 ACTCCCTTTT 0.832308 -58 ACGTGTTCAACCTCCATTTATACGTTTCCTT 34 89 0 CCTCCATTTT 0.868239 -212 AATCAGAACCTCCTTTTTAAGTCAGGGTT 35 9 1 CCTCCTTTTA 0.690346 -226 ATAGGCCCCTCCTTTTTTTATTATATGG 36 137 0 CCTCCTTTTT 0.974338 -18 AAGCGGGAATCCTCCCGCTTTTTACGA 39 7 0 CCTCCCGCTT 0.822265 -166 ATTACGAACTCCTCTCTTCGTTGTGTGAAAT 39 149 0 CCTCTCTTCT 0.826603 -24 ATGTCCCACCCCTCCTTCCTGCGGTTAGGTT 41 108 1 CCTCCTTCCG 0.86585 -193 CTTGAAAGCCTCCTTTTTTTCTATACGTC 45 142 0 CCTCCTTTTT 0.974338 -19 AGCGCATTCTCCTTTTCTATAAAAACAT 54 8 1 TCTCCTTTTT 0.567952 -167 CGGGACATCACCTCCCTTTCTTCGAGAATGG 55 214 0 CCTCCCTTTT 0.98268 -87 CTGTAGTCCTCCTTCTTTTGTCATATAA 55 283 0 CCTCCTTCTT 0.95639 -18 GGTCGGACACTCCCTTTCTATTACTTATA 56 164 0 ACTCCCTTTT 0.832308 -19 ********* * Masking position 4 Map Score: 46.0305 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 153 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 TTCCCGCTTCCTTGACATGCTCTTGGCTAG 2 54 1 CTTGACATGC 0.850572 -67 TCCTTCCGGACCTGACATGGTTCATGAATT 3 52 0 CCTGACATGG 0.993622 -249 ACCTGAACACCTTGCCATGGCAAAGCGGCC 12 165 0 CTTGCCATGG 0.955531 -71 TATCTTAACAACGGACATGGATAATGTCAA 29 36 0 ACGGACATGG 0.949753 -265 GATCGATAAAACTGACATGGATATATCGCA 29 161 1 ACTGACATGG 0.977758 -140 GCAATACAAACCGGGCATGGTACATGTATC 29 207 0 CCGGGCATGG 0.946764 -94 AAAAAAGCACCCTGACATGGAGTGCTTTTT 46 27 0 CCTGACATGG 0.993622 -141 TGTTACATAAACTGACATGGAAAATCGTCA 54 134 1 ACTGACATGG 0.977758 -41 AAATCGTCATCCTGACATGGGGGGATCAAT 54 155 1 CCTGACATGG 0.993622 -20 CTTCATCAGCCTTGCCATGGTCAACAACCG 55 143 0 CTTGCCATGG 0.955531 -158 ********** Masking position 7 Map Score: 15.0447 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 59 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TATTAAGAGTACAAAAAAAGACCTTTTCAG 4 13 0 ACAAAAAAAG 0.863991 -107 ACAAGACAAAAGAAAAAAGGGTTTCTAATT 10 155 0 AGAAAAAAGG 0.924305 -91 GTTAATCCGAAGATAAAAAGGGAGGTAGGC 11 39 1 AGATAAAAAG 0.724726 -23 CCCCTGTATAATAAAAAAAGTGTGCAAATG 12 35 1 ATAAAAAAAG 0.866327 -201 TTTTTGACACAGAAAAAAACGAGGACAGAT 28 188 0 AGAAAAAAAC 0.848621 -45 AGTGCAGAAAAGAAAACAAGGAAACGTATA 34 72 1 AGAAAACAAG 0.674088 -229 GTACCATATAATAAAAAAAGGAGGGGCCTA 36 134 1 ATAAAAAAAG 0.866327 -21 CTTTAATACGATAAAAAAGCGGGAATCCTC 39 24 0 ATAAAAAAGC 0.625169 -149 CGTTATGAGAATAAAAAAAGCATTGCCCGC 43 269 0 ATAAAAAAAG 0.866327 -32 GTCGCTCTAAACAAAAAAGCCGCAGCCACC 45 16 0 ACAAAAAAGC 0.620466 -145 ATAGACGTATAGAAAAAAAGGAGGCTTTCA 45 139 1 AGAAAAAAAG 0.942228 -22 GCAAAACAATAGGAAAAAAGCACCCTGACA 46 40 0 AGGAAAAAAG 0.674088 -128 TTTACTATCAAGAAAAAAACGAAAGATGTA 46 112 0 AGAAAAAAAC 0.848621 -56 AAGAGAAGACACAAAAAAGGACGGGAACAC 50 119 0 ACAAAAAAGG 0.826273 -125 GCTCAATATGATATAAAAGGTGAGGTGATA 53 175 0 ATATAAAAGG 0.43924 -126 AGAAATTTCCAGAAAAAAAGACATTTGTTA 55 52 1 AGAAAAAAAG 0.942228 -249 ********** Masking position 5 Map Score: 11.5138 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 587 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 4 TTAACCGATGTCACTTGCCTTTATAACTAG 11 14 0 TCACTTGCCT 0.747769 -48 AATCAATTTCCTCCTTTCCTAA 14 16 0 TCAATTTCCT 0.884345 -12 GAGATAGACCTCCCTTCCTTTTAATA 20 7 0 TCCCTTCCTT 0.914486 -20 ATTACCTCCTTCCCTTTCTTGGGGA 21 6 0 TCCCTTTCTT 0.95032 -26 AATGGATAAATCCATTTCCT 25 1 0 TCCATTTCCT 0.934278 -54 AATGGATTTATCCATTCCCTCTTAATAAAG 25 15 1 TCCATTCCCT 0.888233 -40 GTTTTATCGATCACTTTCCTGCATAGTCCG 29 143 0 TCACTTTCCT 0.934278 -158 GAACTGAGCGTCAATTTCTTAAAATTTCAT 36 73 1 TCAATTTCTT 0.846965 -82 TCAATTTCCTCCTAAGAAGC 50 234 0 TCAATTTCCT 0.884345 -10 TTGGTTCACTTCCTTCTGAAATCTT 51 28 0 TCACTTCCTT 0.8519 -15 CTCATTACGATCCATTTCTTCCTTCATTAT 53 267 0 TCCATTTCTT 0.91142 -34 GGACATCACCTCCCTTTCTTCGAGAATGGG 55 213 0 TCCCTTTCTT 0.95032 -88 GGTCGGACACTCCCTTTCTATTACTTATAT 56 163 0 TCCCTTTCTA 0.670582 -20 ********** Masking position 5 Map Score: 13.3131 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 167 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 ACTTCTACTATTTTTTATAAATATATATATTAATACATTATCCGTT 1 141 1 TTTTTAATTC 0.912929 -48 TGAGCAGGTATTTTAAAGATATTCATATCCTAACACTTTCAACCCC 9 52 0 TTTTAAATTC 0.861559 -52 CAAATACCGATTTTATTAGCATTTCCATACTTGTATAATTTATACA 10 89 0 TTTTAAATTT 0.875996 -157 AGAAAAGCTCTTTTTGTATCAGAGAAATCATATCATAAAACCTTTC 33 38 1 TTTTTAATTT 0.922457 -99 GTTAACAGGTTTTTTGGGAGAAAAAGATTATCATTCCGTTGTGAAA 34 262 1 TTTTTAATTC 0.912929 -39 CAGAACCTCCTTTTTAAGTCAGGGTTATGCTAGTTCTCACTCAGAG 35 14 1 TTTTTAATTC 0.912929 -221 CGGGGTGTCGTTTTTAGCCGATGTATATCATAACATGAAAAAAAAC 40 14 0 TTTTTAATTT 0.922457 -229 TATAGATTCGTTTTTATGAAAAATTCATATTTTGATCAAATCAGGC 40 123 0 TTTTTAATTT 0.922457 -120 CAATGATATCTTTTTCAGGTATATGATTGTTCTTTTTTTGGCCGGT 41 37 1 TTTTTATTTT 0.694635 -264 AGCCCGTCCATTTTACAACGAATGTCATGATGAAACAAACTTCAGC 41 232 0 TTTTAAATTC 0.861615 -69 AGACAGTGAATTTTTTAGATAACCTTATATCTTTGTTAGAGAGTAC 42 156 0 TTTTTAATCT 0.698932 -145 ATTCACTGCATTTTTTTCGGAAAAAAATATTTCAATTGAAAGGACA 42 258 1 TTTTTAATTT 0.922457 -43 CGTGTACGGTTTTTTGTGATATCAGCATTGCTTGCTCTTTATTTGA 43 223 1 TTTTTAATCT 0.698932 -78 AAAGCCTCCTTTTTTTCTATACGTCTATTGTATCGCTAAGAGGTCT 45 121 0 TTTTTAATTC 0.912929 -40 CCATAAACACTTTTAACACCATATATATGTTTAAATGTAAGCGTAT 49 91 0 TTTTAAATTT 0.875995 -67 ATTCCTTAAATTTTATTTAAAAACAATTTATTTAATTGTATAATAG 52 51 1 TTTTAATTTT 0.574616 -133 TTTTCATTGTTTTTAGGGCAATGATCATGTTATGTTTAATCATATA 52 127 1 TTTTAAATTT 0.875996 -57 TTATGGTGAATTTTATCAATAGCTACTTCATTGCGTTAGGGGTGCT 53 107 0 TTTTAATTTT 0.574616 -194 CAAATGTTCTTTTTTGACTCATCATCATACTTGTCCTGAAAGCTCA 53 200 0 TTTTTAATTC 0.912929 -101 AAATGTCTTTTTTTCTGGAAATTTCTATAATAACTTGTCTGACTAG 55 32 0 TTTTCAATTT 0.652331 -269 ***** * ** * * Masking position 18 Map Score: 15.6279 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 164 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 AACTCTTTCCCGCTTCCTTGACATGCTCTT 2 48 1 CGCTTCCTTG 0.810264 -73 AACGTGATCTCGTTTACATTATTATATCAA 6 26 0 CGTTTACATT 0.81736 -48 TCGATAATATCGTTGACATTATCCATGTCC 29 24 1 CGTTGACATT 0.673145 -277 AGCCGAACTGCGCTGCCTTTATGTCATTTT 31 18 0 CGCTGCCTTT 0.871308 -84 AGCGCAGTTCGGCTGCCTTTCTCTTTCTGC 31 34 1 GGCTGCCTTT 0.658715 -68 TCCATTTATACGTTTCCTTGTTTTCTTTTC 34 78 0 CGTTTCCTTG 0.696698 -223 CCGTGGGGTTCGTTTCCATTCAACGTGTTC 34 112 0 CGTTTCCATT 0.932773 -189 GCTTATATTTGGTTTACTTTGTAATGCTCT 42 63 0 GGTTTACTTT 0.421179 -238 CGTACACGTGCGGTTCCATTGCTCACCCAT 43 201 0 CGGTTCCATT 0.810222 -100 AAGTATAAACCGTTTTCATTCCCGTTGACA 45 83 0 CGTTTTCATT 0.705758 -78 TAATGACATACGCTTACATTTAAACATATA 49 84 1 CGCTTACATT 0.892704 -74 AGAAGCCTCAGGCTTCCATTCATCTCTTAC 50 210 0 GGCTTCCATT 0.880291 -34 GATACAAAATCGCTTTCATTATTGATAAAA 56 126 1 CGCTTTCATT 0.816824 -57 TATATTCGTTCGCTTCCATTCGTTTTATAA 57 75 0 CGCTTCCATT 0.96268 -131 ********** Masking position 4 Map Score: 7.65514 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 431 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 ACTTCTACTATTTTTTATAAATATATATATTAATA 1 141 1 TTTTTAATAA 0.825045 -48 GTGAGTTTTTTGTTATGTAAAAAGAGCTTTTGGAA 3 221 1 TGTTTAAAAA 0.880036 -80 TTATCTGTAAAAAGAAGGAGGGAAA 15 1 1 TTATTAAAAA 0.907197 -31 CCTCGTTTTTTTCTGTGTCAAAAAACTTAGAGGAG 28 194 1 TTCTTAAAAA 0.746864 -39 CTAATGCTTTTGTTTTCAGAAAATAAAAAATACCC 29 261 0 TGTTTAAAAA 0.707519 -40 CAAAAAGAGCTTTTCTAAAAATAGAAAAGCCCTTG 33 19 0 TTTTTAATAA 0.830779 -118 ATGATAATCTTTTTCTCCCAAAAAACCTGTTAACG 34 261 0 TTTTTAAAAA 0.770941 -40 TTCACTGCATTTTTTTCGGAAAAAAATATTTCAAT 42 259 1 TTTTTAAAAA 0.49741 -42 GAAATACGAATGATATCTAAAAAAACAAAATTAAA 43 31 1 TGATTAAAAA 0.850979 -270 AGTGTTCCTATTATATTGTAATAAATTATATCAAG 43 108 0 TTATTAATAA 0.788546 -193 CAAGCAATGCTGATATCACAAAAAACCGTACACGT 43 222 0 TGATTAAAAA 0.850979 -79 AAGTTTCTCATTATTTCCAAATACATTGTCAACGG 45 57 1 TTATTAATAA 0.786128 -104 ATTCCTTAAATTTTATTTAAAAACAATTTATTTAA 52 51 1 TTTTTAAAAA 0.817735 -133 CGCATTCTCCTTTTCTATAAAAACATTGGTTAAGG 54 13 1 TTTTTAAAAA 0.817735 -162 CGCATCTGCTTTATATGACAAAAGAAGGAGGACTA 55 273 1 TTATTAAAAA 0.907197 -28 **** * **** * Masking position 10 Map Score: 8.36339 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 135 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 8 GGGTTTGCCCTCCTCCGTTATTCATCAT 3 283 0 TGCCCTCCGT 0.959058 -18 CTGTGAAGGCCTCCTTTAGATTGGAA 6 58 0 GGGCCTCCTT 0.897401 -16 GGGGCCTACCTCCCTTTTTATCTTC 11 47 0 GGTCCTCCCT 0.848906 -15 AATCAATTTCCTCCTTTCCTAAGAGA 14 12 0 TATCCTCCTT 0.668723 -16 TTTGAATTTCCCTCCTTCTTTTTACAG 15 15 0 GATCCTCCTT 0.786782 -17 ACCAAACACCTCCATTCATGTTAAA 22 15 0 CACCCTCCAT 0.570221 -15 TAGGACACCTCCTTATCCGATCAA 24 17 0 TGCCCTCCTT 0.970733 -14 TCGGATTTCCCCCGTCCTCTCTTTA 25 40 0 CGTCCCCCGT 0.657303 -15 AAGAAAGCGCCTCCTTATCATACCTT 27 3 1 GACCCTCCTT 0.935456 -87 TCTGTTCCCCACCTTCTAATGCTTT 29 286 0 CGCCCACCTT 0.873429 -15 CAGTTCTCCACCTTTCAACGAAAT 32 229 0 CGCCCACCTT 0.873429 -14 AGCGGTTGATTAATACCCCTCCGTGGGGTTCGTT 34 128 0 TACCCTCCGT 0.848385 -173 GCGGTCTCCTCCTTACCGATTGTT 35 221 0 GGCCCTCCTT 0.983785 -14 ATAGGCCCCTCCTTTTTTTATTAT 36 141 0 AACCCTCCTT 0.58692 -14 TAAGACAGTATCCCTCCCTAAAAACATCA 38 90 0 CGTCCTCCCT 0.848906 -19 TTTACCCATGTCCCACCCCTCCTTCCTGCGGTTA 41 101 1 TCCCCTCCTT 0.81784 -200 CCTGTCTACCTCCGTTATGAGAATA 43 286 0 CGTCCTCCGT 0.915982 -15 CTTGAAAGCCTCCTTTTTTTCTATA 45 146 0 TGACCTCCTT 0.63694 -15 GAACCTATTTGTGTTCCCGTCCTTTTTTGTGTCT 50 109 1 GGCCGTCCTT 0.764912 -135 TTGGTTCACTTCCTTCTGAAATCTT 51 28 0 TGCCTTCCTT 0.545649 -15 GCCCTCCGATGAGTGCGCCCCCGATCAGCACCCC 53 81 1 GGCCCCCCGA 0.297441 -220 AGTCAGGCGGGACATCACCTCCCTTTCTTCGAGA 55 218 0 GCCCCTCCCT 0.74906 -83 CTGTAGTCCTCCTTCTTTTGTCAT 55 287 0 CGGCCTCCTT 0.897408 -14 GTCCGTGCACCTCCGTTAACCTTTCA 57 190 0 CGCCCTCCGT 0.97718 -16 * * * ******* Masking position 8 Map Score: 21.8611 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 208 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 TTAAAACCCTCCTTCAAAACGTCGAAACCTC 26 153 0 CCTTCAAACG 0.938707 -24 ATGTTGGGAATTTTCAAACTGCGGCGGCTTA 30 33 0 TTTTCAAATG 0.655666 -40 GCACGCGCACCCTTCAAAATGGCATGCGGGA 34 166 0 CCTTCAAATG 0.906153 -135 CTCTTTCACAACGGAATGATAAT 34 288 0 CTTTCACACG 0.938707 -13 TATGTATAGGCTTTCACACTGCACACCGAAA 44 74 0 CTTTCACATG 0.906155 -42 ACGTATTTTCCTTTCAAATTGAACTTTGTTA 50 156 1 CTTTCAAATG 0.944604 -88 GGTAAGATGCCTTTCAAAGCGGCATGCCGTT 55 174 0 CTTTCAAACG 0.964345 -127 CTCCGTTAACCTTTCAAAACGATTCTATTCA 57 175 0 CTTTCAAACG 0.964343 -31 ******** ** Masking position 6 Map Score: 4.73325 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 80 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 GATTTGTGGATAAGTTGTGAAAAAGACAGGAAAC 1 91 0 TTGTGAAAAA 0.649246 -98 TTTAACTATGTTAATATTGTAAAATGCCAATGTA 10 19 1 TTTTGTAAAA 0.875811 -227 CCTTTTTTCTTTTGTCTTGTAAAAGTATTTTCTT 10 165 1 TTTTGTAAAA 0.875808 -81 TGTTTCTTTATGATTATTGTAAAAGGGAGAAAAA 32 148 0 TTTTGTAAAA 0.875811 -95 TTTTTCATCATCACCCTTGTTAAAATCGCGTTAT 35 84 0 TCTTGTTAAA 0.782088 -151 TATTTTAACATGTTTTTTGATAAATCGTTATGGT 38 13 0 TTTTGATAAA 0.87581 -96 TATTTTTTGATAGGTCGTGATAAAAC 40 227 1 TTGTGATAAA 0.764448 -16 TCGTTTGCACTTAATTTTGTTAAATTTTCTCATA 42 29 1 TTTTGTTAAA 0.925176 -272 TTTAAACATATATATGGTGTTAAAAGTGTTTATG 49 102 1 TTGTGTTAAA 0.850525 -56 ACAGTGCATGAAGATATTGTTAAACCTTTGTAAA 50 13 0 ATTTGTTAAA 0.548931 -231 CCTTTCAAATTGAACTTTGTTAAAATAAGAGGAG 50 165 1 TCTTGTTAAA 0.782088 -79 CGCAATGAAGTAGCTATTGATAAAATTCACCATA 53 118 1 TTTTGATAAA 0.875811 -183 CTCAGTCGGATCACTCTTGTAAAATTATTTAAAT 56 23 1 TTTTGTAAAA 0.875811 -160 AAAATCGCTTTCATTATTGATAAAACAGATACAT 56 131 1 TTTTGATAAA 0.875811 -52 * * ******** Masking position 12 Map Score: 6.01195 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 147 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 ATCCACATGTGGACAGACTGTGTATGACTT 1 54 0 GGACAGACTG 0.943513 -135 GTCCACATGTGGATAGGCTGTGTTTCCTGT 1 70 1 GGATAGGCTG 0.91368 -119 CAAAGAAGAAGCATAGGCTCTGCAGTTTGC 9 16 0 GCATAGGCTC 0.736196 -88 CGTTTGATTGGCGCAGACTCCGGGCTGACA 37 152 0 GCGCAGACTC 0.85527 -82 TCAGGCAAACGGGCAGACTCATTAGGGCCC 40 99 0 GGGCAGACTC 0.897224 -144 GTTGTAAAATGGACGGGCTGGATGATAATT 41 259 1 GGACGGGCTG 0.889468 -42 CTAATCTCTTGCATAGGCTGAAAATAAAAA 43 75 0 GCATAGGCTG 0.877524 -226 TATTATACTAGAGCAGGCTGAGGGGTTTCA 47 26 0 GAGCAGGCTG 0.881469 -41 GCCCTGCAGAGGACAGCCTGATATTTT 49 8 0 GGACAGCCTG 0.947455 -150 GTCCTCTGCAGGGCAGCCTGTTTTTTGAAG 49 24 1 GGGCAGCCTG 0.960313 -134 TCTTAGTCGAGCGCAGTCTGGAAAACGCGT 55 82 1 GCGCAGTCTG 0.857245 -219 ********** Masking position 9 Map Score: 5.70615 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 351 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 ATGTGCCGCAGGGTTGCCTGGGCCGAGCTA 3 105 1 GGGTTGCCTG 0.85011 -196 TGACATAAGCCTTTTGCCGGCGGTCCTTTT 7 45 1 CTTTTGCCGG 0.81584 -148 TTGGCAAGGCCGTTTGCCGGAGTCAGGCCA 28 137 0 CGTTTGCCGG 0.98066 -96 CGGCAATTTACGGTTGCCGGGTAGAAACTT 29 115 0 CGGTTGCCGG 0.980276 -186 GAGCTTATTGCGATCGGCGGCTACAGCCCG 34 233 1 CGATCGGCGG 0.829505 -68 CGAAATCATCCGATTGGCGGAGATGATATT 37 120 0 CGATTGGCGG 0.85504 -114 TGAGTCTGCCCGTTTGCCTGATTTGATCAA 40 108 1 CGTTTGCCTG 0.955829 -135 CGGACATTTACGGTGCCCGGTAGAAACTTG 43 168 0 CGGTGCCCGG 0.803509 -133 TGTAAGCGGGGGTTCGCCTGCCAAGTATGC 53 46 1 GGTTCGCCTG 0.826773 -255 GGTCAACAACCGTTCCCCTGTCGATCACGG 55 125 0 CGTTCCCCTG 0.826772 -176 ********** Masking position 4 Map Score: 2.73986 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 310 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 GACCCAAACGTCAACACCACTTACTTAAG 3 9 0 TCACACCACT 0.856842 -292 GTCAGCCCTTTCAGCAGTCCTTGCTTTTTGG 7 18 0 TCACAGTCCT 0.755172 -175 TGTCAGCACCCCTTTCAATCATT 33 124 0 TCACACCCCT 0.983885 -13 TTATTTTTCATCATCACCCTTGTTAAAATCG 35 90 0 TCACACCCTT 0.968823 -145 ATTCTCCACCCCATCATTATGTA 44 103 0 TCTCACCCCA 0.75256 -13 CCTTCTGAAATCTTCAGCCTTCAGCTGTACA 51 11 0 TCTCAGCCTT 0.835 -32 GCGCCCCCGATCAGCACCCCTAACGCAATGA 53 95 1 TCACACCCCT 0.983885 -206 TGCCGTTTCTTCATCAGCCTTGCCATGGTCA 55 150 0 TCACAGCCTT 0.941226 -151 AGGCGGGACATCACCTCCCTTTCTTCGAGAA 55 217 0 TCACTCCCTT 0.83047 -84 *** ******* Masking position 1 Map Score: 4.04835 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 76 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 CTTCATGAAGTCTCCTTGAAATCAGAAGATA 7 124 1 TCTCTTGAAA 0.635708 -69 TCCTGATATATCCATATGAAAAATATCTATT 27 58 0 TCCAATGAAA 0.688649 -32 GTGTTACAGCTCCTATTGTAAGAATATTTTG 32 196 0 TCCTTTGTAA 0.817855 -47 TCTTCTACGTTCCCCCTGTAAAATAGACGTC 37 57 0 TCCCCTGTAA 0.879177 -177 CTCATATCCTCCTGTAAATCTAAATTA 41 284 0 TCCTCTGTAA 0.787398 -17 CACACAACCATCCAGTTGAAATGACTGTACT 42 130 1 TCCATTGAAA 0.857991 -171 TTATATCGAATCCCCTTGAAATACGAATGAT 43 14 1 TCCCTTGAAA 0.956799 -287 CCGTTTTCATTCCCGTTGACAATGTATTTGG 45 73 0 TCCCTTGACA 0.806608 -88 TTGGTTCACTTCCTTCTGAAATCTTCAGCCT 51 22 0 TCCTCTGAAA 0.902896 -21 ATCTCCATCCTCCCTATGAAACCTTACCTAT 52 93 0 TCCCATGAAA 0.890205 -91 CCGCTAGAATTCCTATTGAAAATTATTCACC 54 46 0 TCCTTTGAAA 0.918519 -129 **** ****** Masking position 11 Map Score: 3.77706 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 148 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 15 ATAAGGTGTAAGAAGACACATTCAAAGGAT 5 55 1 AGAAGACACA 0.853672 -27 CTCCAAGCAAAGAAGAAGCATAGGCTCTGC 9 23 0 AGAAGAAGCA 0.940272 -81 ATTGCACTTATGAGGAAGCAATACAAACCG 29 224 0 TGAGGAAGCA 0.747768 -77 GCGGCGGCTTAGAAGAAGCCGTAAAAGCTT 30 14 0 AGAAGAAGCC 0.747769 -59 ACAATAATCATAAAGAAACACCTACAAATA 32 162 1 TAAAGAAACA 0.700494 -81 AAATTATAGAAGAAGAATCATTTTCTAAAC 35 141 0 AGAAGAATCA 0.751035 -94 TCATTGCAGCTGAAGAAGCACACGGGAAAG 41 13 0 TGAAGAAGCA 0.940272 -288 ACGAATGTCATGATGAAACAAACTTCAGCA 41 231 0 TGATGAAACA 0.68141 -70 GAACTATAAGAGAAGACACAAAAAAGGACG 50 126 0 AGAAGACACA 0.853672 -118 GCCGGTTTCCAAAAGAAACAAATGTTCTTT 53 234 0 AAAAGAAACA 0.700494 -67 GCAAGGCTGATGAAGAAACGGCATGCCGCT 55 158 1 TGAAGAAACG 0.760194 -143 AGTTTATCAGTGAAGAAACAGAAAGTCAAT 57 136 0 TGAAGAAACA 0.943925 -70 ********** Masking position 6 Map Score: 2.2931 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 425 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035