AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_bsub_reg_100.orf -o00240_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: yncF 29 similar to deoxyuridine 5'-triphosphate pyrophosphatase Input sequences: #1 dnaN 188 DNA polymerase III (beta subunit) #2 dnaX 300 DNA polymerase III (gamma and tau subunits) #3 xpaC 119 xpaC #4 yaaO 81 similar to lysine decarboxylase #5 yaaQ 73 similar to hypothetical proteins #6 rpoB 245 RNA polymerase (beta subunit) #7 rpoC 61 RNA polymerase (beta' subunit) #8 rpoA 176 RNA polymerase (alpha subunit) #9 ybxA 127 alternate gene name: ybaD; similar to ABC transporter (ATP-binding protein) #10 yfkN 242 similar to 2',3'-cyclic-nucleotide 2'-phosphodiesterase #11 pyrB 145 aspartate carbamoyltransferase #12 polC 108 DNA polymerase III (alpha subunit) #13 pnpA 172 polynucleotide phosphorylase (PNPase) #14 ymaA 242 similar to ribonucleoprotein #15 yncE 300 yncE #16 thyA 300 thymidylate synthase A #17 deoD 300 purine nucleoside phosphorylase #18 yosS 45 similar to deoxyuridine 5'-triphosphate nucleotidohydrolase #19 yosR 300 similar to thioredoxin #20 yosP 300 similar to ribonucleoside-diphosphate reductase (beta subunit) #21 thyB 83 thymidylate synthase B #22 ypjP 259 ypjP #23 ndk 115 nucleoside diphosphate kinase #24 cmk 78 cytidylate kinase #25 ypfB 44 alternate gene name: jofB #26 ypfA 92 alternate gene name: jofA #27 ypeB 34 alternate gene name: joeB, yzuA; similar to hypothetical proteins #28 sleB 138 spore cortex-lytic enzyme #29 drm 160 phosphodeoxyribomutase #30 cdd 118 cytidine/deoxycytidine deaminase #31 comEB 66 alternate gene name: comD #32 comEA 83 integral membrane protein #33 yrrM 151 similar to caffeoyl-CoA O-methyltransferase #34 polA 243 DNA polymerase I #35 dnaE 300 DNA polymerase III (alpha subunit) #36 trxB 205 thioredoxin reductase #37 upp 134 uracil phosphoribosyltransferase #38 tdk 88 thymidine kinase #39 rpmE 118 ribosomal protein L31 #40 ctrA 241 CTP synthetase #41 rpoE 182 RNA polymerase (delta subunit) #42 pdp 29 pyrimidine-nucleoside phosphorylase #43 nupC 115 pyrimidine-nucleoside transport protein Motif number 1 CGATTCCAAAAGCTCTTTTTACATAACAAA 2 229 0 AGCTCTTTTT 0.85945 -72 GGGTTTGCCCTCCTCCGTTATTCAT 2 286 0 TGCCCTCCTC 0.869039 -15 GGGGCCTACCTCCCTTTTTATCTTCGG 7 45 0 ACCTCCCTTT 0.887918 -17 GAAACTGTCCCGCCCTTCTTTAGATACACA 9 22 0 CGCCCTTCTT 0.790323 -106 ACTGGATCTATGCCCTTTTTTTAGATACTG 9 54 1 TGCCCTTTTT 0.805602 -74 GTTCTTTCCCCTCTCTTTTCAACTTAAG 11 128 0 CCCTCTCTTT 0.885728 -18 AATTACGAACTCCTCTCTTCGTTGTGTGAA 13 151 0 TCCTCTCTTC 0.836765 -22 ATTCTCGTTCTGCTCTCTTTTTTGGGCCCT 14 76 1 TGCTCTCTTT 0.942124 -167 GAATTTCCTCAGCCCTTCTCATTTAAAAGG 15 171 0 AGCCCTTCTC 0.713695 -130 AGGAGTTAATCCCCCTCTTTTACACCTGTA 16 155 0 CCCCCTCTTT 0.840075 -146 CCCATGTCCCACCCCTCCTTCCTGCGGTTA 17 105 1 ACCCCTCCTT 0.915731 -196 TATGTATTAGCTCCTTTTAATTCAAGTT 18 28 0 AGCTCCTTTT 0.805602 -18 TGGATTAACATCCTCTTCTTCAAACCAATG 19 147 0 TCCTCTTCTT 0.857619 -154 AATTCCTCTCCTTGCTCTTTTCT 24 66 0 TCCTCTCCTT 0.941296 -13 TTATCACACCTCTTTTTATGCTTTCTC 27 18 0 ACCTCTTTTT 0.814512 -17 TGGTTTCCCCTCCTTTGAGCTATTA 32 6 1 TCCCCTCCTT 0.915731 -78 GAGAGCTTTTTGCTCTCCTT 33 1 0 TGCTCTCCTT 0.957135 -151 GAGAGCAAAAAGCTCTCCTTTTGTTCGCTT 33 14 1 AGCTCTCCTT 0.957135 -138 CATAGTCATTAGCTCCTCTTATTTTAACAA 34 181 0 AGCTCCTCTT 0.850399 -63 ACTGTGTTTCAGCTCCTTTTTTATTGTCCC 37 115 0 AGCTCCTTTT 0.805602 -20 AGGCTTCGCTCCCCTCTCTCTGCCAG 38 73 0 CGCTCCCCTC 0.814818 -16 TAGTACGTTATGCTCCCTTTCAAGAAATTG 40 100 1 TGCTCCCTTT 0.916887 -142 AAAATAAGAAAGCTCCCTTTCAATTTCTTG 40 120 0 AGCTCCCTTT 0.916887 -122 TTCGTTTGCTCCTCTCTTCGCTCTTAGCT 40 223 0 TCCTCTCTTC 0.836765 -19 ********** Masking position 9 Map Score: 26.5925 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 528 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 ACTTCTACTATTTTTTATAAATATATATAT 1 141 1 TTTTTTATAA 0.780593 -48 CAAAAGCTCTTTTTACATAACAAAAAACTC 2 223 0 TTTTACATAA 0.52853 -78 TTTAACATGTTTTTTGATAAATCGTTATGG 12 14 0 TTTTTGATAA 0.634913 -95 TAAAGCGAAATTTCTTATAACAAATCATTG 13 49 1 TTTCTTATAA 0.864011 -124 AAAATATGAATTTTTCATAAAAACGAATCT 14 136 1 TTTTTCATAA 0.898846 -107 TTTGTTAAATTTTCTCATAAGAGCATTACA 20 44 1 TTTCTCATAA 0.940718 -257 TCGTAACATCTTTCTGATAATTAATCAATC 23 44 0 TTTCTGATAA 0.756433 -72 TTTTTCACCCTTTTTCATAAAGTTCGTGAT 24 22 1 TTTTTCATAA 0.898846 -57 TCTTTTCCTTTTTTTCATTACGTGCTTTAA 26 34 1 TTTTTCATTA 0.701329 -59 CTTTTTATGCTTTCTCATATCTG 27 4 0 TTTCTCATAT 0.807446 -31 AATATTGAAGTTTCTCATTATTTCCAAATA 29 50 1 TTTCTCATTA 0.807446 -111 TCACTTTATATTTTACATAATCGCGCGCTT 30 63 0 TTTTACATAA 0.52853 -56 CCCGATATATTTTATCATAAAACCTTGCGG 33 45 0 TTTATCATAA 0.555622 -107 CTATCACCTCTTTCTCATTACGATCCATTT 35 280 0 TTTCTCATTA 0.807446 -21 GTTTGGGCTCTTTCTTATAAGATAAGAATC 36 157 0 TTTCTTATAA 0.864011 -49 GTCTTGCCTGTTTTTTATATTGTCTAAAAC 38 39 1 TTTTTTATAT 0.484582 -50 CTGATATAATTTTCTCATATGCGTTTCGGA 39 37 1 TTTCTCATAT 0.807446 -82 GAAAGGGAGCTTTCTTATTTTCACCCCTCA 40 129 1 TTTCTTATTT 0.307322 -113 ACCCCTCATTTTTCTTATAAATCATTTAAA 40 151 1 TTTCTTATAA 0.864011 -91 GGCTAAATGATTTTTTATAAAATAGTACAT 40 182 1 TTTTTTATAA 0.780593 -60 ********** Masking position 3 Map Score: 17.6305 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 279 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 GAGATAATCGACTCCTGTGTCTATACTC 3 102 0 TAAACTCCTT 0.641942 -18 CTGTGAAGGCCTCCTTTAGATTGGAAA 5 57 0 TGACCTCCTT 0.973218 -17 TTAGAAACTGTCCCGCCCTTCTTTAGATACACAA 9 21 0 TCCCCTTCTT 0.530718 -107 TGTGAAATAATCAATTACTCCTATTATGAACGAA 13 123 0 TCAACTCCTT 0.932533 -50 ACAATTACGAACTCCTCTCTTCGTTGTG 13 155 0 TTAACTCCTT 0.759698 -18 TGAGAAGGGCTGAGGAAATTCTGTAAAAGATAAT 15 180 1 TGAAATTCTT 0.346428 -121 TAAAAGAGGGGGATTAACTCCTCTTTAAACACAC 16 163 1 GGAACTCCTT 0.882532 -138 GACTATTCATATCCTTCTTTCATTTTCAGT 16 281 0 TCACCTTCTT 0.845647 -20 CTCATATCCTCCTGTAAATCTAAAT 17 286 0 TCACCTCCTT 0.952611 -15 TGAATACATCCTTTCTCGGTAAAA 19 287 0 TGACATCCTT 0.738797 -14 AAAGCTGAATTGACAGACTCCTATATTACTGTCA 20 221 0 TGAACTCCTT 0.961519 -80 TCAATCATGCGGAAAGCCTCCTTTCATGAAATAT 22 98 1 GGACCTCCTT 0.916152 -162 TGGAGCACCTCCATTACAAATAGTA 25 30 0 GGACCTCCAT 0.579563 -15 AGACATTTAGTCCTTTCCTCCTGTTT 26 3 0 TCCCCTCCTT 0.805805 -90 TTGGAAATAATGAGAAACTTCAATATTTTCTGTC 29 43 0 TGAACTTCAT 0.462122 -118 CTTGAAAGCCTCCTTTTTTTCTATAC 29 145 0 TGACCTCCTT 0.973218 -16 CGCATAAGACTGGGGCACTCCTTTTTAGAACGGG 33 116 1 TGGACTCCTT 0.737025 -36 TCTTACATAGTCATTAGCTCCTCTTATTTTAACA 34 182 0 TCAGCTCCTT 0.72245 -62 CCATCAACAATTACACACTTCTATTGATTCTACA 37 83 0 TTAACTTCTT 0.462837 -52 ATTATATCAGTGATTTACTTCTTTTGCAAATACA 39 13 0 TGAACTTCTT 0.871959 -106 *** ****** * Masking position 9 Map Score: 16.1751 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 236 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 4 CTCAAATCATGCGTATTATATGTGTAATAAGC 6 213 0 GCGTATTTAG 0.575835 -33 GATTCTATTCGAGGTTTCGACGTTTTGAAGGA 8 143 1 GAGGTTTGAG 0.674215 -34 CGTTTTGAAGGAGGGTTTTAAGTA 8 163 1 GAGGGTTTAG 0.968907 -14 GGCTGGGGTAGAGTGTTTTATGTAGACATATA 10 30 0 GAGTGTTTAG 0.797683 -213 AAAGTCCAGAGAGGCTTGGAAGGGTTATGAAG 11 23 1 GAGGCTTGAG 0.94102 -123 CGGGATACATGAGGCTTGTAAGTGGGGTGTTA 15 17 1 GAGGCTTTAG 0.97874 -284 TAACATTGTTGAGGATTATACGAAATGGTTTG 16 58 0 GAGGATTTAG 0.913267 -243 CAGCAACCGTGCGGCTTTTTTGTGTGCAGTTT 28 19 1 GCGGCTTTTG 0.95598 -120 GCAGGTGGCTGCGGCTTTTTTGTTTAGAGCGA 29 13 1 GCGGCTTTTG 0.95598 -148 AGAAAAAAAGGAGGCTTTCAAG 29 149 1 GAGGCTTCAG 0.896583 -12 ATGGAAGCCTGAGGCTTCTTAGGAGGAAATTG 34 221 1 GAGGCTTTTG 0.955182 -23 ATAAGCCCAAGCGGGTTTTAGGATC 37 4 0 GCGGGTTTAG 0.969469 -131 CTTATGCCCGGCGGGTTTTTTGACGATGTTCT 37 31 1 GCGGGTTTTG 0.936307 -104 ******* ** * Masking position 6 Map Score: 12.7701 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 105 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ACTTTCCCCGATTGATCCCCGGTCCTG 1 8 0 ATTGATCCCC 0.621671 -181 GGGTTTGCCCTCCTCCGTTATTC 2 288 0 TTTGCCCTCC 0.821609 -13 CTGATTCACCCCTCAAATCATGC 6 233 0 ATTCACCCCT 0.771285 -13 GTTCTTTCCCCTCTCTTTTCAACT 11 132 0 TTTCCCCTCT 0.897046 -14 TAAGACAGTATCCCTCCCTAAAAACATCA 12 90 0 ATCCCTCCCT 0.85472 -19 AGAGGAGTTAATCCCCCTCTTTTACACCTG 16 157 0 ATCCCCCTCT 0.885982 -144 GACTGCTTATTCCTCTCTATTTTATTGT 22 242 0 ATTCCTCTCT 0.922183 -18 AATTCCTCTCCTTGCTCTTTT 24 68 0 ATTCCTCTCC 0.943596 -11 GTGTACATTCCTCTCTTACCTATAAT 30 103 0 ATTCCTCTCT 0.922183 -16 TGGTTTCCCCTCCTTTGAGCTAT 32 4 1 TTTCCCCTCC 0.924812 -80 AGGAGAGCTTTTTGCTCTCCTT 33 3 0 TTTGCTCTCC 0.809365 -149 TCAGGCTTCCATTCATCTCTTACATAGTCA 34 203 0 ATTCATCTCT 0.791009 -41 AGGCTTCGCTCCCCTCTCTCTGCC 38 75 0 TTCGCTCCCC 0.678223 -14 TGTATCCATCTCCTTCCGCCCTG 39 106 0 ATCCATCTCC 0.763572 -13 GCTTTCTTATTTTCACCCCTCATTTTTCTT 40 137 1 TTTCACCCCT 0.695642 -105 ********** Masking position 2 Map Score: 9.35778 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 245 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 6 TATTAAGAGTACAAAAAAAGACCTTTTCAGGT 3 6 0 AAAAAAATTT 0.8737 -114 GTAGATAATAATAATAAAACTGAGTATAGACACAGGA 3 81 1 AAAAAAATAT 0.808992 -39 ACCACATCCAAAAACAAATACCGATTTTATTAGCATT 6 112 0 AAAAAATTTT 0.797824 -134 TTTACAAGACAAAAGAAAAAAGGGTTTCTAATTAAGA 6 151 0 AAAAAAATTT 0.873759 -95 TTTCTTCCAAAGAAAGAAAATACTTTTACAAGACAAA 6 175 0 AAAGAAATTT 0.917481 -71 ATGATTTGTTATAAGAAATTTCGCTTTAATACGATAA 13 40 0 AAAAAATTTT 0.717914 -133 ATTTTTCATAAAAACGAATCTATATATTGTGTTTTTG 14 145 1 AAAGAATTAT 0.795222 -98 AAAATGTCCCAAAACAAATAATCATTTTTGTAATCCT 15 65 0 AAAAAATTTT 0.797847 -236 CACCGGCCAAAAAAAGAACAATCATATACCTGAAAAA 17 47 0 AAAGAACTAT 0.723323 -254 GAACTTTACGAAAATGAATTGGAGTATACAGAAGATG 19 24 1 AAAGAATTAT 0.795222 -277 GTAGTGTAACACAATAAAAAATCATTTCTGAACCCAG 21 28 0 AAAAAAATTT 0.87376 -56 CGTAATGAAAAAAAGGAAAAGACATTTAGTCCTTTCC 26 19 0 AAAGAAATTT 0.917558 -74 CTGAGGGATAACAAGGAAAGAGTGTATAAAAATAACC 28 58 1 AAAGAAATAT 0.871988 -81 TGATGAGTCAAAAAAGAACATTTGTTTCTTTTGGAAA 35 222 1 AAAGAACTTT 0.810237 -79 CATTATAAACAAAATAAAACAGAATATGCTACCCTTA 41 66 0 AAAAAAATAT 0.809018 -117 TGTTTTATCAATAATGAAAGCGATTTTGTATCGTTCT 41 121 0 AAAGAAATTT 0.917529 -62 * ** **** *** Masking position 8 Map Score: 10.3072 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 347 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 7 TACTACGTTCAATCCTTAAACAAGTTTCATCT 3 52 0 AATCCTAACA 0.58238 -68 AAGAAAACCACATCCAAAAACAAATACCGATT 6 123 0 CATCCAAACA 0.776932 -123 TACTTAAAACCCTCCTTCAAAACGTCGAAACC 8 155 0 CCTCCTAAAA 0.76759 -22 AGACAGTATCCCTCCCTAAAAACATCATAAGT 12 85 0 CCTCCTAAAA 0.76759 -24 TTATGATATACATCGGCTAAAAACGACACCCC 14 27 1 CATCGCAAAA 0.912478 -216 TCGGTCGCCGCATCCATTAACACCCCACTTAC 15 34 0 CATCCTAACA 0.951065 -267 GTAACCGGATCACCGGCCAAAAAAAGAACAAT 17 62 0 CACCGCAAAA 0.767105 -239 GTGCCTAACAGATCCTCGAACATTTCTTTTTT 17 177 1 GATCCCAACA 0.705383 -124 TTTTTTCATCCTTTAAAAGTAGTCTTCT 21 66 0 CATCCTAAAA 0.912695 -18 TCATGGAGGTCACCGATTAACAGAAAGCCCGT 22 19 0 CACCGTAACA 0.840921 -241 ACATCGGCAAACACTTCCATACT 25 2 1 CATCGCAACA 0.950939 -43 CATCATGATACATCGGTAAACAACCCGATATA 33 66 0 CATCGTAACA 0.943606 -86 GTTTCAAGAACATCGTCAAAAAACCCGCCGGG 37 37 0 CATCGCAAAA 0.912478 -98 ***** * **** Masking position 9 Map Score: 5.29343 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 205 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TCTGTCCACATGTGGATAGGCTGTGTTTCCTG 1 67 1 TGTGGATGCT 0.954946 -122 CCTGTGGATTTGTGGATAAGTTGTGAAAAAGA 1 99 0 TGTGGATGTT 0.833433 -90 GTGCACCTTCTGTCGATTCGCTACCCTAAGCG 2 148 0 TGTCGATGCT 0.639963 -153 ATTATACAAGTATGGAAATGCTAATAAAATCG 6 96 1 TATGGAAGCT 0.831685 -150 CAACGAAATTTGTGTTACAGCTCCTATTGTAA 10 206 0 TGTGTTAGCT 0.730155 -37 ATCTATATATTGTGTTTTTGCTAGAGGGTAGT 14 162 1 TGTGTTTGCT 0.840095 -81 TATGTATTAGCTCCTTTTAATT 18 34 0 TATGTATGCT 0.898416 -12 ACTTGCATGTTTTGGATGTGCTAAAATAAGAG 22 203 1 TTTGGATGCT 0.856743 -57 CATCATTATGTATGTATAGGCTTTCACACTGC 23 83 0 TATGTATGCT 0.898416 -33 TTACAAATAGTATGGAAGTGTTTGCCGATGT 25 10 0 TATGGAAGTT 0.538421 -35 GTTGGCAAGCTTTGTAATGGCTGTAAGCGGGG 35 25 1 TTTGTAAGCT 0.739541 -276 TCAATAGAAGTGTGTAATTGTTGATGGGACAA 37 90 1 TGTGTAAGTT 0.703755 -45 ACTGTGTTTCAGCTCCTTTTTTAT 37 121 0 TGTGTTTGCT 0.840095 -14 CTATTACTTATATGTATCTGTTTTATCAATAA 41 144 0 TATGTATGTT 0.676146 -39 TTCTCCTTTATTTGTATTCGCTTACAATTACT 43 88 0 TTTGTATGCT 0.84646 -28 ******* *** Masking position 3 Map Score: 9.09889 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 245 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 ATCCGAAGATAAAAAGGGAGGTAGGCCCC 7 43 1 AAAAAGGGAG 0.922463 -19 GTAGACATATAAAGCGGGAGGTTATGAATC 10 11 0 AAAGCGGGAG 0.960669 -232 ATGATTATTGTAAAAGGGAGAAAAATGAGT 10 143 0 TAAAAGGGAG 0.79392 -100 TAAGTTGAAAAGAGAGGGGAAAGAAC 11 130 1 AGAGAGGGGA 0.793035 -16 TCGTAAAAAGCGGGAGGATTCCCGCT 13 7 1 AAAGCGGGAG 0.960669 -166 ATACGATAAAAAAGCGGGAATCCTCCCGCT 13 19 0 AAAGCGGGAA 0.867042 -154 TACAGGTGTAAAAGAGGGGGATTAACTCCT 16 155 1 AAAGAGGGGG 0.941425 -146 GAACTTTATGAAAAAGGGTGAAAAATTGAT 24 17 0 AAAAAGGGTG 0.579479 -62 TGCTTTAATAAAAACGTGAGTATATTGAAT 26 56 1 AAAACGTGAG 0.55786 -37 ATTGAATGCGAAAGAGTGAAGTCA 26 79 1 AAAGAGTGAA 0.348189 -14 AAATATGACGAAAGCGGGGAACATGCACG 32 65 1 AAAGCGGGGA 0.830003 -19 ACTCCTTTTTAGAACGGGAGGCTGTTTGTA 33 132 1 AGAACGGGAG 0.923594 -20 GTAATGGCTGTAAGCGGGGGTTCGCCTGCC 35 38 1 TAAGCGGGGG 0.855529 -263 CAGCTGGCAGAGAGAGGGGAGCGAAGCCT 38 70 1 AGAGAGGGGA 0.793035 -19 TTCAATTTCTTGAAAGGGAGCATAACGTAC 40 102 0 TGAAAGGGAG 0.774782 -140 TTCAAGAAATTGAAAGGGAGCTTTCTTATT 40 118 1 TGAAAGGGAG 0.774782 -124 TATAAGTAATAGAAAGGGAGTGTCCGACC 41 164 1 AGAAAGGGAG 0.913969 -19 ********** Masking position 3 Map Score: 18.1595 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 485 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 10 CTCTCATGTGCCGCAGGGTTGCCTGGGCCGA 2 100 1 CCGCAGGTTG 0.991937 -201 CCTAATGAGTCTGCCCGTTTGCCTGATTTGA 14 103 1 CTGCCGTTTG 0.882716 -140 CTCATAGTTACCGCCAGTTTGGTACATACAC 16 96 0 CCGCCGTTTG 0.970504 -205 GTCATTTCAACTGGATGGTTGTGTGATAGGC 20 124 0 CTGGAGGTTG 0.908749 -177 AGGAGGCTTTCCGCATGATTGACGCTCTGTT 22 89 0 CCGCAGATTG 0.950097 -171 CACAAAAAAGCCGCACGGTTGCTGTGCGGCT 28 12 0 CCGCAGGTTG 0.991937 -127 TGTTCGCTTTCCGCAAGGTTTTATGATAAAA 33 35 1 CCGCAGGTTT 0.965693 -117 GGGCTTATGCCCGGCGGGTTTTTTGACGATG 37 28 1 CCGGCGGTTT 0.907075 -107 ***** ***** Masking position 9 Map Score: 5.23068 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 96 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TGGATAAGTTGTGAAAAAGACAGGAAACACAGCCTAT 1 82 0 GAAAAACAGA 0.927749 -107 TTCTTTCTTTGGAAGAAATGCTTATTACACATATAAT 6 194 1 GGAAAGCTTA 0.482127 -52 TTAATCCGAAGATAAAAAGGGAGGTAGGCCCC 7 40 1 GAAAAGGAGG 0.816712 -22 ACTTTTAATAGAGAGAAAAGCAGAGCATTAGCTGAGA 9 86 1 GGAAAGCAGA 0.963454 -42 TCAGCCTTAAGTTGAAAAGAGAGGGGAAAGAAC 11 123 1 GAAAAAGAGA 0.827825 -23 CTCCTATTATGAACGAAATGAATTGAACATATCAATG 13 103 0 GGAAAGAATA 0.594574 -70 ACTCATTAGGGCCCAAAAAAGAGAGCAGAACGAGAAT 14 76 0 GAAAAAGAGA 0.827825 -167 AAGATAATCGGTTGAAAAGGCAGTCGATTCCTTGTTC 15 206 1 GAAAAGCAGA 0.958625 -95 GGTGGGACATGGGTAAAAAACATCGTAACCGGATCAC 17 81 0 GAAAAACATA 0.849527 -220 CATTCGAAAGGAATGAAAGACAGTGAATTTTTTAGAT 20 182 0 GGAAAACAGA 0.93594 -119 ATTTTTTTCCGAAAAAAATGCAGTGAATTTAAAAGCT 20 249 0 GAAAAGCAGA 0.958625 -52 TTAGAAATGGGCGTGAAAAAAAGCGCGCGATTATGTA 30 43 1 GGAAAAAAGG 0.48704 -76 TTATAATGAAGGAAGAAATGGATCGTAATGAGAAAGA 35 265 1 GGAAAGGATA 0.812739 -36 TTTTTATATTGTCTAAAACACAGCTGGCAGAGAGAGG 38 50 1 GAAAAACAGG 0.868338 -39 TCGGAGCATTGTCCGAAACGCATATGAGAAAATTATA 39 41 0 GGAAAGCATA 0.920578 -78 TTTTTGAAGAGCCCAAAATACATACTACATAGTTCGA 40 50 0 GAAAAACATA 0.849527 -192 AAGGAGAAAATGCATCAGGCGGAGACAAC 43 3 1 GAAAAGCATG 0.839544 -113 * **** **** * Masking position 8 Map Score: 9.92497 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 550 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 CAAAAAAAGACCTTTTCAGGT 3 1 0 CCTTTTCAGT 0.683258 -119 CTTTCCCCTCTCTTTTCAACTTAAGGCTGAA 11 122 0 TCTTTTCAAT 0.902102 -24 GAATCGACTGCCTTTTCAACCGATTATCTTT 15 205 0 CCTTTTCAAC 0.699914 -96 TCCCATGACTTCTTTTCAACTAAAGGGAATG 19 210 1 TCTTTTCAAT 0.902102 -91 GAGAGTACAGTCATTTCAACTGGATGGTTGT 20 133 0 TCATTTCAAT 0.622832 -168 TGTCTTTCATTCCTTTCGAATGTTTGACAGT 20 197 1 TCCTTTCGAT 0.865355 -104 TTAATCATGTCCTTTCAATTGAAATATTTT 20 281 0 TCCTTTCAAT 0.927172 -20 TCACGTATTTTCCTTTCAAATTGAACTTTGT 34 154 1 TCCTTTCAAT 0.927172 -90 TAACATATACCCTTTTCGAATACATTTAATC 36 56 1 CCTTTTCGAT 0.881869 -150 CCTTAAACCATCTTTTCAAGTTTGGGCTCTT 36 175 0 TCTTTTCAAT 0.902102 -31 ACGTTATGCTCCCTTTCAAGAAATTGAAAGG 40 104 1 CCCTTTCAAA 0.684958 -138 TAAGAAAGCTCCCTTTCAATTTCTTGAAAGG 40 115 0 CCCTTTCAAT 0.953338 -127 GTCGGACACTCCCTTTCTATTACTTATATGT 41 161 0 CCCTTTCTAT 0.721909 -22 GGTCACCGATCCTTTTCGATTAAGT 42 5 0 CCTTTTCGAT 0.881869 -25 ********* * Masking position 6 Map Score: 13.4854 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 96 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 CAATCGGGGAAAGTGTGAATAACTTTTCGGAA 1 24 1 AAGTTGAAAA 0.771602 -165 GTATAATGGGAATGATGAATAACGGAGGAGGG 2 272 1 AATGTGAAAA 0.771602 -29 ACGATATAATAAGGTGTAAGAAGACACATTCA 4 47 1 AAGGGTAAAA 0.749986 -35 ATTATTGTAAAAGGGAGAAAAATGAGTATTAT 10 138 0 AAGGAGAAAA 0.860638 -105 AGAGGCTTGGAAGGGTTATGAAGAGAAGGAAG 11 32 1 AAGGTTATAA 0.640342 -114 TTTTCAACTTAAGGCTGAAAAAAAACCCCGGT 11 109 0 AAGGTGAAAA 0.9718 -37 ACTACTTTTAAAGGATGAAAAAA 21 71 1 AAGGTGAAAA 0.9718 -13 CTTTATGAAAAAGGGTGAAAAATTGATGAATA 24 12 0 AAGGTGAAAA 0.9718 -67 TGTTTACAAAGGTTTAACAATATCTTCATG 34 9 1 AAGGTTAAAA 0.91866 -235 **** **** ** Masking position 8 Map Score: 2.55092 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 = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 TGAAAAGGTCTTTTTTTGTACTCTTAATAAT 3 14 1 TTTTTTTGTC 0.704391 -106 GTTTGTATAGATTTTGTGTCCCTGTCAATAA 8 14 1 ATTTTGTGTC 0.762936 -163 TCACATATTTTTGTGTATCTAAAGAAGG 9 8 1 TTTTTGTGTT 0.896831 -120 CAAATAATCATTTTTGTAATCCTCGGTCGCC 15 57 0 TTTTTGTAAC 0.551511 -244 ACTTAAACGATTTTTGTGAATACGAGTATAA 15 269 0 TTTTTGTGAT 0.639699 -32 AATAGTCAGGTGTTTGTGTATACC 16 4 0 TGTTTGTGTT 0.620786 -297 ACTATTTGAATTTTTATGTACCGCAATATCA 16 29 1 TTTTTATGTC 0.80776 -272 CACTGTTGCTTTTTTGTATCCATTCCCTTTA 19 230 0 TTTTTGTATC 0.857566 -71 CCGTGCGGCTTTTTTGTGTGCAGTTTTTATG 28 25 1 TTTTTGTGTC 0.967992 -114 TTGTGTGCAGTTTTTATGTTCTGAGGGATAA 28 38 1 TTTTTATGTC 0.80776 -101 GGCGGGAACCTATTTGTGTTCCCGTCCTTTT 34 104 1 TATTTGTGTC 0.871396 -140 TTCCCGTCCTTTTTTGTGTCTTCTCTTATAG 34 122 1 TTTTTGTGTT 0.896831 -122 GTTTCTCCTTTATTTGTATTCGCTTACAATT 43 91 0 TATTTGTATC 0.574284 -25 ********* * Masking position 5 Map Score: 4.34995 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 248 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 CCCATTGCGCAGGACCCAAACGTCAACACC 2 22 0 AGGACCCAAA 0.942022 -279 CAGACTCATTAGGGCCCAAAAAAGAGAGCA 14 86 0 AGGGCCCAAA 0.984745 -157 CTTATAAGAAAGAGCCCAAACTTGAAAAGA 36 166 1 AGAGCCCAAA 0.976599 -40 TCGTTTTTGAAGAGCCCAAAATACATACTA 40 60 0 AGAGCCCAAA 0.976599 -182 ********** Masking position 8 Map Score: 0.78861 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467