AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_bsub_reg_300.orf -o00272_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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 cysE 300 serine acetyltransferase #11 ycgA 300 similar to hypothetical proteins #12 ycgB 115 ycgB #13 amyE 148 alpha-amylase #14 lctE 176 L-lactate dehydrogenase #15 yjcI 300 similar to cystathionine gamma-synthase #16 ykrV 94 similar to aspartate aminotransferase #17 yloU 276 similar to alkaline-shock protein #18 yloW 138 similar to phosphoglycerate dehydrogenase #19 ylpA 25 similar to L-serine dehydratase #20 aspB 22 aspartate aminotransferase #21 ypmA 142 ypmA #22 dinG 125 ATP-dependent helicase #23 panB 245 ketopantoate hydroxymethyltransferase #24 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #25 ypjD 300 alternate gene name: jojD #26 ypcA 155 similar to glutamate dehydrogenase #27 ypbH 158 similar to negative regulation of competence MecA homolog #28 ypbG 85 similar to hypothetical proteins #29 ypbF 62 ypbF #30 ypbD 59 ypbD #31 ypbB 265 ypbB #32 yrhA 64 similar to cysteine synthase #33 yrrT 192 yrrT #34 ytkP 148 similar to cysteine synthase #35 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #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 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 8 27 0 TTTCACTTTT 0.931735 -20 AATCTATCAATTTCAAAATTTTTTGTCAA 9 6 0 TTTCATTTTT 0.949941 -70 GCATTTTAAATGTCATACGTTTTTTCTTAGGCTG 11 92 0 TGTCATTTTT 0.881243 -209 GACCTTCCTCCCGCACTTTTACGAATGGCT 12 96 0 CCTCCCTTTT 0.76544 -20 TTGTGCAACACTTCACAAACTTTTGCAAGAGAAA 14 87 0 CTTCACTTTT 0.828536 -90 TCACAGTTTATTTCAACACTTTTTTCTTCGTGTG 15 48 0 TTTCATTTTT 0.949941 -253 ACCCCAAATTTTTCTTTACTTTTTTCATTTAACC 16 20 1 TTTCTTTTTT 0.618861 -75 TGGACTATCATTTCAAGATTTTTTTAGAAGGTGA 16 65 1 TTTCATTTTT 0.949941 -30 GAAACAATAGTTGCAAACGTTTTTTAGCTGTGGT 17 99 0 TTGCATTTTT 0.829439 -178 CCAGCGATTATTGCCTGGTCTTTTCATAATGGAA 17 203 1 TTGCCCTTTT 0.728267 -74 AAACTGCTGATTTCAGCAGTTTTTTTTCGTTAAA 26 23 1 TTTCATTTTT 0.949941 -133 ACGTTATGTTTTTCCATGTTTTTTAACGAAAAAA 26 44 0 TTTCCTTTTT 0.935652 -112 AAAAAACTCTCCATTCTTTTTAGAACTTATC 28 65 0 TCTCCTTTTT 0.927617 -21 TGATAAGCATTCTCAATCATTTTTCTGTTGAAAT 31 117 0 TCTCATTTTT 0.943583 -149 GGGAGAACGTTCTCCTCCGTTTTTCTCTAAAAAC 32 15 1 TCTCCTTTTT 0.927617 -50 TCTGTGTCACTCCCTTTTTTTGATGGTT 35 5 1 TGTCACTTTT 0.842203 -143 AGCGGAAGTTTCTCCTCGTTTTTTCTTAGCATTC 35 66 1 TCTCCTTTTT 0.927617 -82 GAAATTGAACTGTCAATGTTTTTTGAAAATATTG 36 82 0 TGTCATTTTT 0.881243 -70 CGTGTTACATCCTCATGTATTTTTAGAATGAAAT 37 46 1 CCTCATTTTT 0.855517 -164 CAAAATAATTTTGCATTTGTTTTTTGCGTAAAGA 39 26 1 TTGCATTTTT 0.829439 -201 ACTGAGATGTTTTCAGTCTCTTTTTTTGTGGATT 40 32 1 TTTCACTTTT 0.931735 -145 CTTTTTCACCTCATTGTTTTTTTGGCCGGCTG 40 155 0 CCTCATTTTT 0.855517 -22 AAATGGACGATTTCCCTCTCTTTTTCTAGTAACA 41 81 0 TTTCCCTTTT 0.912727 -220 ***** ***** Masking position 11 Map Score: 30.4626 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 587 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 AATGTCCTCCTCACAATGAGCAGG 4 90 0 TCCTCCTCAC 0.977265 -14 TCCTTACCTCCTCCCACAGTAAGCA 5 83 0 ACCTCCTCCC 0.897594 -15 GACCTTCCTCCCGCACTTTTAC 12 104 0 CCTTCCTCCC 0.9062 -12 TTCTTCCGCTTCCTCCTTTCAAACCGATGT 13 65 0 TCCTCCTTTC 0.770892 -84 AAGGGCCAGTCCCTCCACCTCTCACGATAA 15 126 0 CCCTCCACCT 0.896508 -175 TTGTTTCCCTCCTCACTTGCACAAAA 17 7 1 CCCTCCTCAC 0.976802 -270 GCTATTCCTCCTTATGAACCAGAGC 18 124 0 TCCTCCTTAT 0.804623 -15 AACTGGCTCCTCCTGACCCTTTTCG 19 9 0 TCCTCCTGAC 0.974185 -17 TAAAACACCATCCTACTCCCACACCGCAAA 21 29 0 TCCTACTCCC 0.773809 -114 TTTTTCATCCTCCAGTTTGAACAAATA 21 126 0 TCCTCCAGTT 0.68657 -17 GTTTTCTCCTCCTCATGTTTAGAGGA 23 230 0 TCCTCCTCAT 0.959715 -16 AACGTTCCCTCCTGCCTCTACTTGCA 27 143 0 CCCTCCTGCC 0.983423 -16 CCACCTACATTCTTCCTGACAAAAATCGTT 31 241 0 TCTTCCTGAC 0.843632 -25 ATATGTCCTCCTCCTTAATAGAGGT 32 50 0 TCCTCCTCCT 0.97451 -15 GTCTTGACCCTCCAGCTTTCACAAGTC 33 8 1 CCCTCCAGCT 0.883787 -185 AAATTGTCCTCCTGATCAAAAAGTTG 38 58 0 TCCTCCTGAT 0.954368 -16 AATGAGAATTCCTTCCTGTTTATACAAGGT 41 117 0 CCTTCCTGTT 0.570128 -184 ********** Masking position 4 Map Score: 18.8315 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 275 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 3 AGCGGTTAAGACACCGCCCTTTCACGGCGGT 1 53 1 ACACGCCCTT 0.819311 -248 TCATCCTAACAAATCGGTTTCTCTTGCAGAA 1 109 1 AAACGGTTTC 0.688798 -192 AAAATGAAAAAAATCGGCTTCTGCAAGAGAA 1 127 0 AAACGGCTTC 0.811989 -174 AGCGGTCGTGACATCCCCCTTTGTCACGCGG 11 205 0 ACACCCCCTT 0.892684 -96 TCGGAGTCAAAAATCCCTCTTACTTCATTCT 13 91 0 AAACCCTCTT 0.933792 -58 TTTCAAAATAAAAACCCCTTCTTCATAAGAA 15 262 0 AAACCCCTTC 0.947975 -39 CCACACCGCAAAAGCCGCTTTATGCGGCTT 21 10 0 AAACCGCTTT 0.511201 -133 ACAGAGCGGGAAATCCGCTTTTAAATAAAAC 21 53 0 AAACCGCTTT 0.836563 -90 AAGAAAAGCCCCCTTTATCGGGGGT 22 5 1 AAACCCCCTT 0.964202 -121 ATGGAGCGGCAAAACCGTTTTACTCTCAAAA 22 48 0 AAACCGTTTT 0.507599 -78 AATACCTGTAAAACCGCCCTCAGCCAGATTG 25 49 1 AAACGCCCTC 0.930028 -252 AGCATCACACAAAACCCCTTTTCCTTCCATT 25 167 1 AAACCCCTTT 0.925906 -134 GACAATAAAAAAAGACGTTTCTATCGTTTGA 28 25 0 AAAACGTTTC 0.46603 -61 TATCTACATAACATCCCCCTTAATGATGACT 31 161 1 ACACCCCCTT 0.892684 -105 CCTATAATTAAAAACCCTTTTTAAAGGGTTT 36 27 1 AAACCCTTTT 0.886964 -125 ATACAAACAAAAAAACCCTTTAAAAAGGGTT 36 39 0 AAAACCCTTT 0.816424 -113 AAAAAGCTCTCCGGGAGGCCG 37 1 1 AAAAGCTCTC 0.592197 -209 TAACACGTAAAAAAAGCTCTCCGGCCTCCCG 37 22 0 AAAAGCTCTC 0.592197 -188 TCTTTCTCAAACACCTCTTCCATAATCTT 37 191 0 AAAACCTCTT 0.751401 -19 GAATTATGAAAAAGCGCTTTTTCTGCAGAGG 41 238 1 AAACGCTTTT 0.775093 -63 *** ******* Masking position 10 Map Score: 19.3222 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 528 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 4 TCAAGCGGTTAAGACACCGCCCTTTCACGGC 1 50 1 AAGACACCCC 0.662771 -251 CTAAAAATGAAAAAAATCGGCTTCTGCAAGA 1 130 0 AAAAAATCGC 0.817625 -171 AATATCAAGGCAGAAACCGTCGAAGATTTCT 1 191 1 CAGAAACCTC 0.654736 -110 AACAATACCAAAGAAATCTTCGACGGTTTCT 1 202 0 AAGAAATCTC 0.789687 -99 GAATATCTTTAAAATACCTGCTCATTGTGAG 4 74 1 AAAATACCGC 0.630203 -30 CTTTCTTTCTAAAAAAACTGCCGGCTGACGC 6 15 1 AAAAAAACGC 0.908265 -180 TCATTTACATAAAAAAACTGCCAGCGTCAGC 6 38 0 AAAAAAACGC 0.908265 -157 TTTCTCAAATTAAAAACCCGCTAAAGAGC 8 9 0 TAAAAACCGC 0.60438 -38 CTACCCAATAAAAAAAGCGTCTCTGCATGTA 10 248 0 AAAAAAGCTC 0.643902 -53 CTTCGGAGTCAAAAATCCCTCTTACTTCATT 13 93 0 AAAAATCCTC 0.649404 -56 GACTTACCGAAAGAAACCATCAATGATGGTT 14 27 1 AAGAAACCTC 0.949648 -150 ATGAACAAAAAAGAAACCATCATTGATGGTT 14 41 0 AAGAAACCTC 0.949648 -136 GCTTTTAAATAAAACACCATCCTACTCCCAC 21 37 0 AAAACACCTC 0.823185 -106 AAAATCTTAAAAGAAAACCCCCGATAAAGGG 22 21 0 AAGAAAACCC 0.741862 -105 TTAGAAAGTGAAGAATCCTTCTCGTTGTAAC 23 159 1 AAGAATCCTC 0.692891 -87 TCTGCAAGCCAAAAAACCTTCCGTTACAACG 23 181 0 AAAAAACCTC 0.939334 -65 TGGCTTGCAGAAGAAAACGGCAGATCATCTC 23 201 1 AAGAAAACGC 0.92343 -45 GTGGATGAAAAAGAAAACAGCAAACGTGCTT 25 217 1 AAGAAAACGC 0.92343 -84 TTTTTAACGAAAAAAAACTGCTGAAATCAGC 26 28 0 AAAAAAACGC 0.908265 -128 TTTTTCTCTAAAAACAACCTCTATTAAGGAG 32 34 1 AAAACAACTC 0.671807 -31 TAAGCGCTTTAAAAAATCAGCCCGCCAATTC 40 119 0 AAAAAATCGC 0.817625 -58 ******** ** Masking position 4 Map Score: 21.1649 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 504 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 5 AAGCCGATTTTTTTCATTTTTAGACAACATTC 1 138 1 TTTTCATTTA 0.903037 -163 ATGGTTATTGTTTGTATTGGAATGATTTTCTA 5 30 1 TTTGTATTGA 0.767524 -68 TTTCCGACTATTTGTATTGGTATTATGTATAT 9 40 0 TTTGTATTGA 0.767525 -36 ACCGGCTTGTTTTGCATTTGCAAAGCGCCAAG 15 169 1 TTTGCATTTA 0.797475 -132 GAAGAAGGGGTTTTTATTTTGAAAAGGGAAGG 15 269 1 TTTTTATTTA 0.895672 -32 TTCTTTACTTTTTTCATTTAACCATATATGAT 16 31 1 TTTTCATTTC 0.849155 -64 AGCGGCAATTTTTTCATTTGGCTTGGTTCATT 25 93 0 TTTTCATTTC 0.849155 -208 AAAAACATATTTTTTATTTTAATCGGAGCGGC 25 119 0 TTTTTATTTA 0.895672 -182 CACAATGCAGTTTTTATTGCCATACGGATTTT 27 24 0 TTTTTATTGA 0.886475 -135 GAAACGTCTTTTTTTATTGTCCGTCTTATTGA 28 35 1 TTTTTATTGC 0.825172 -51 GGTATTATTTTTATTTTACGTTCATATAT 29 8 1 TTTTTATTTC 0.838431 -55 ACCTTGTCCATTTTCATTGCTACAATATATGA 29 32 0 TTTTCATTGA 0.894412 -31 TGATTTGCTCTTTTTATTTTAACAGATTTCAA 31 210 0 TTTTTATTTA 0.895672 -56 AGTTTTATTATTTTCATTTAAATCCCATTATA 37 89 0 TTTTCATTTA 0.903032 -121 GATTCTTGCATTTTTATTCATATGCGAAGATA 39 178 1 TTTTTATTCA 0.64163 -49 ********* * Masking position 6 Map Score: 11.3914 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 250 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 AAACAAATATGGTAGCGGCGGAGGGGATC 1 8 0 GGTAGCGCGA 0.760562 -293 ATGGTGCAAACTGCAGAGCCTATGCTT 4 6 1 GCAAACGCGA 0.949004 -98 CATCTCGGAAGCAGGCTGCCGA 5 1 0 GCAGGCGCGA 0.987226 -97 TAAAAAAACTGCCGGCTGACGCTGGCAGTTTT 6 24 1 GCCGGCGAGC 0.922697 -171 AGCCTGTAACGGCGGCGGCCGCCTTTGAATAC 10 145 0 GGCGGCGCGC 0.971037 -156 TGTTTGAAAAGCAGACTTCTGCTCTCCCAACT 10 179 0 GCAGACTCGC 0.590356 -122 ATATGAGTATGCCAGCAGCCGAAACACAGCCT 11 66 1 GCCAGCGCGA 0.975795 -235 CATATATTGTGCCGGCAGGTGAATTTGACCGC 11 177 1 GCCGGCGGGA 0.942841 -124 TTTGAAAGGAGGAAGCGGAAGAATGAAGTAAG 13 72 1 GGAAGCGAGA 0.832549 -77 TGCAAAACAAGCCGGTTGCTGAGGTTTCTAAG 15 153 0 GCCGGTGCGA 0.84358 -148 GACATCTTGCGGAAACAGCAGCGCTATAGTAT 17 157 1 GGAAACGCGC 0.915143 -120 ATATAAAATGGCAAGCGGGCGCGTTACAGCGC 18 58 0 GCAAGCGGGC 0.945844 -81 TTGGATCAAGGCAGACTGCTGCAATGTCTATC 23 90 0 GCAGACGCGC 0.967249 -156 GCTTGCAGAAGAAAACGGCAGATCATCTCCTC 23 203 1 GAAAACGCGA 0.721106 -43 GAATGCAACGGAAAACTGCTGATTTCAGCAGT 26 11 1 GAAAACGCGA 0.721106 -145 TGATTTGTGTGCAAGTAGAGGCAGGAGGGAAC 27 134 1 GCAAGTGAGC 0.508665 -25 AAGCTCTCCGGGAGGCCGGAGAGCTTTTTTTA 37 14 1 GGAGGCGGGA 0.918174 -196 ****** ** ** Masking position 11 Map Score: 15.5075 Number of sites scoring better than the average of aligned sites = 1693 Number in coding regions = 1568 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 GCCAGCGTCAGCCGGCAGTTTTTTTAGAAA 6 20 0 GCCGGCAGTT 0.945428 -175 GCCGGCTGACGCTGGCAGTTTTTTTATGTA 6 34 1 GCTGGCAGTT 0.659244 -161 GCTCTTTAGCGGGTTTTTAATTTGAGAA 8 9 1 GCGGGTTTTT 0.698415 -38 AGATCCATGAGCCGGGTTTTAGAAGTGCGC 10 81 1 GCCGGGTTTT 0.826237 -220 CATATATTGTGCCGGCAGGTGAATTTGACC 11 177 1 GCCGGCAGGT 0.92706 -124 ATTGCTGCCCGCCGGCTTGTACGGCGGGCT 12 13 1 GCCGGCTTGT 0.972794 -103 GGCTTGTACGGCGGGCTTTTGAGTTATTCA 12 26 1 GCGGGCTTTT 0.972345 -90 TTGCAGAAGCGCAGGCTGTTATTGTAACAT 12 56 1 GCAGGCTGTT 0.868603 -60 AACCTCAGCAACCGGCTTGTTTTGCATTTG 15 159 1 ACCGGCTTGT 0.866108 -142 AGCCGCATAAAGCGGCTTTTGCGGTGTGGG 21 12 1 AGCGGCTTTT 0.613374 -131 CCCCGATAAAGGGGGCTTTTCTT 22 4 0 GGGGGCTTTT 0.863325 -122 ACCAAAATCAACGGGCTTGTACCAACACA 23 10 0 ACGGGCTTGT 0.823955 -236 AAAGGAATTGGCGGGCTGATTTTTTAAAGC 40 115 1 GCGGGCTGAT 0.8574 -62 TGTTTTTTTGGCCGGCTGTAATGTAAGCGC 40 143 0 GCCGGCTGTA 0.853509 -34 ********** Masking position 5 Map Score: 9.34376 Number of sites scoring better than the average of aligned sites = 906 Number in coding regions = 807 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 8 ATTGGATGATTGTAAAAGCCGCAGCTGAGCCAATC 6 67 0 TTAAGGCAGC 0.986229 -128 AACTTCAGCCTGTAACGGCGGCGGCCGCCTTTGAA 10 148 0 TTAAGGCGGC 0.98927 -153 TCACATCGGTTTGAAAGGAGGAAGCGGAAGAATGA 13 63 1 TGAAGGAAGC 0.852747 -86 AATTTCTCTCTTTAAACGGTTCGGCACACGAAGAA 15 24 1 TTAAGTCGGC 0.947796 -277 TATGTCTGCTTTTAAGTGCGGCAGCGCTGTAACGC 18 35 1 TTAAGGCAGC 0.986229 -104 ACGTTTTGTACGGAAATGGAGCGGCAAAACCGTTT 22 59 0 CGAAGGCGGC 0.94672 -67 TATTTTTTATTTTAATCGGAGCGGCAATTTTTTCA 25 109 0 TTAAGGCGGC 0.98927 -192 ATATAACTGCTTCAGCATATCATGGT 30 44 0 TTAAGTCAGC 0.933784 -16 CATTTTTCTGTTGAAATGTGGCAGCAACATCATTA 31 99 0 TGAAGGCAGC 0.983353 -167 * *** * ***** Masking position 5 Map Score: 8.83067 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 64 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CAGAATTGGATGATTGTAAAAGCCGCAGCT 6 76 0 TGATTGTAAA 0.657209 -119 TATTGTAGAATGTTTGTAAAAAGTAAAGTA 6 146 1 TGTTTGTAAA 0.885411 -49 GGTTCCACTCTGTTTGAAAAGCAGACTTCT 10 191 0 TGTTTGAAAA 0.95096 -110 CCATCCCCTCTGTTTGAAAATATTAATTAT 11 30 0 TGTTTGAAAA 0.95096 -271 GATGTCTTTTTGTTTGTGAAGTATTTCACA 14 127 0 TGTTTGTGAA 0.878439 -50 ACGTTTCTATCGTTTGAGAAAACGCCCCAT 28 12 0 CGTTTGAGAA 0.773578 -74 AACAGAAAAATGATTGAGAATGCTTATCAC 31 122 1 TGATTGAGAA 0.81823 -144 CGTCGATTTCTGTTTGAAATCTGTTAAAAT 31 197 1 TGTTTGAAAT 0.71139 -69 AGAGGAACAGTGTATGAAAACACTCTCGCA 34 70 1 TGTATGAAAA 0.711385 -79 CTGTCAATGTTTTTTGAAAATATTGATAAT 36 77 0 TTTTTGAAAA 0.604084 -75 ATGGAAGAGGTGTTTGAGAAAGA 37 197 1 TGTTTGAGAA 0.947759 -13 ********** Masking position 9 Map Score: 6.40867 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 124 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 GATTCTCAGATTCATATATTCCCATCTTCG 2 40 0 TTCATATATT 0.866699 -45 GCGCAATCGCTTCATATATTGTGCCGGCAG 11 165 1 TTCATATATT 0.866699 -136 CTTTTTAACATTCATATAATCTTAGATGCT 17 43 1 TTCATATAAT 0.925267 -234 AGTATACACCTTCATATGATCTGTGCATAG 26 83 0 TTCATATGAT 0.740317 -73 GACTCATCATCTCATATAATGTGTTATATG 27 106 1 CTCATATAAT 0.766954 -53 TTATTTTACGTTCATATATTGTAGCAATGA 29 21 1 TTCATATATT 0.866699 -42 GATGGAACAGTTCCTATAATACCACATATT 33 122 0 TTCCTATAAT 0.858329 -71 TAAAACAAGTGTCATATAATATCCTAACAT 34 112 0 GTCATATAAT 0.766954 -37 AGTTTCTAAATTCCTATAATTAAAAACCCT 36 15 1 TTCCTATAAT 0.858329 -137 ********** Masking position 5 Map Score: 4.18741 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 49 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 CCATATTTGTTTGGCCCGTTGGTCAAGCGG 1 28 1 TTGGCCCGTT 0.850848 -273 AATTCCATTGGCCCCTTTACCAAGCTG 3 72 0 TTGGCCCCTT 0.850847 -17 ATTTAGCACCTTGGCGCTTTGCAAATGCAA 15 180 0 TTGGCGCTTT 0.937515 -121 AAGGGCAATTTGCCCTTCTATTCTTATG 18 9 1 TTTGCCCTTC 0.838574 -130 CCAGAGCTTATTAGCGCTTTGCTTCTAGAC 18 101 0 TTAGCGCTTT 0.869411 -38 ACTTTTGCTTTATGCCCTTTTCCACATCAG 25 17 0 TATGCCCTTT 0.873804 -284 AAATCGTTGATTTGCTCTTTTTATTTTAAC 31 219 0 TTTGCTCTTT 0.871715 -47 TTTTGCGTTTTTTGCTCTTTACGCAAAAAA 39 45 0 TTTGCTCTTT 0.871715 -182 GGCTGTAATGTAAGCGCTTTAAAAAATCAG 40 130 0 TAAGCGCTTT 0.648105 -47 TTCGACTTTTTTTGCCCTTTTTTAAAATAG 41 24 1 TTTGCCCTTT 0.961404 -277 ********** Masking position 9 Map Score: 4.26671 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 108 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 CCTTTGAAGAACGTTTTTTGAAATCAGTAT 10 119 1 ACGTTTTTTG 0.951019 -182 ATGCAGAGACGCTTTTTTTATTGGGTAGAG 10 251 1 GCTTTTTTTA 0.402819 -50 TAAATGTCATACGTTTTTTCTTAGGCTGTG 11 90 0 ACGTTTTTTC 0.715435 -211 AATCCAGCAAGCGTTTTTTATGCTTGGAAG 15 207 1 GCGTTTTTTA 0.843336 -94 TAAAAAGTAGATGTTTTGTGCAAGTGAGGA 17 20 0 ATGTTTTGTG 0.662813 -257 ATAGTTGCAAACGTTTTTTAGCTGTGGTAA 17 97 0 ACGTTTTTTA 0.923404 -180 AAAGTGTAACACGTTTTGTACGGAAATGGA 22 74 0 ACGTTTTGTA 0.793689 -52 TTGTAACGGAAGGTTTTTTGGCTTGCAGAA 23 183 1 AGGTTTTTTG 0.654625 -63 AATAAAAAATATGTTTTTTAATCTAATTTC 25 133 1 ATGTTTTTTA 0.792735 -168 ATGTTTTTCCATGTTTTTTAACGAAAAAAA 26 43 0 ATGTTTTTTA 0.792735 -113 AATGTGTTATATGATTTGTGTGCAAGTAGA 27 123 1 ATGATTTGTG 0.207809 -36 GAGCAAATCAACGATTTTTGTCAGGAAGAA 31 232 1 ACGATTTTTG 0.721529 -34 TCTCGCACAAACGTTTATTATGTTAGGATA 34 93 1 ACGTTTATTA 0.463092 -56 ACATTATATCACGTTTTTTGACGAATGCTA 35 92 0 ACGTTTTTTG 0.951019 -56 TGAACTGTCAATGTTTTTTGAAAATATTGA 36 81 0 ATGTTTTTTG 0.860334 -71 AGGCCGGAGAGCTTTTTTTACGTGTTACAT 37 26 1 GCTTTTTTTA 0.402819 -184 AATTTATTTTGCGTTTTTTGCTCTTTACGC 39 51 0 GCGTTTTTTG 0.896584 -176 GGCATCTTCGACTTTTTTTGCCCTTTTTTA 41 18 1 ACTTTTTTTG 0.708704 -283 ATGGAAGTAAATGTTTTTTAAGGAATATTA 41 160 0 ATGTTTTTTA 0.792735 -141 ********** Masking position 5 Map Score: 16.5518 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 474 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 13 TACAGGCTGAAGTTGGGAGAGCAGAAGTCTGC 10 169 1 AGTTGGGAGC 0.82655 -132 CAAAAAATCAAATAAGGAGTGTCAAGA 13 132 1 AATAGGGTGT 0.949302 -17 AGTAAAGAAAAATTTGGGGTGTTAAAAAG 16 8 0 AATTGGGTGT 0.907598 -87 GACGAATTAGGGGGAGTTCAAG 20 6 1 ATTAGGGAGT 0.857449 -17 CTGTGATACTAGTATGGCGTGTCCTGAAATGG 21 80 1 AGTAGGGTGT 0.979551 -63 CACTTTCTAAAGTTCGGCGAGTTTCATCCCTC 23 137 0 AGTTGGGAGT 0.953262 -109 AGTTCTAAAAAGAATGGAGAGTTTTTT 28 69 1 AGAAGGGAGT 0.924737 -17 GGAATTATTAAATATGGAGTGTGACAAAT 33 174 1 AATAGGGTGT 0.949302 -19 TAGCTGTCAAAGAAGGGAGTGTCAGACGG 34 8 0 AGAAGGGTGT 0.938033 -141 **** ** **** Masking position 1 Map Score: 3.85291 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 18 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 GCCGCTACCATATTTGTTTGGCCCGTTGGT 1 21 1 TATTTGTTTG 0.577387 -280 GAGCCTATGCTTCTTCTTTGCTTGGAGGGG 4 26 1 TTCTTCTTTG 0.757996 -78 TCCGAGATGGTTATTGTTTGTATTGGAATG 5 24 1 TTATTGTTTG 0.717993 -74 CAGAGACGCTTTTTTTATTGGGTAGAGGAA 10 254 1 TTTTTTATTG 0.573026 -47 TGTCATACGTTTTTTCTTAGGCTGTGTTTC 11 86 0 TTTTTCTTAG 0.547211 -215 TGTCCTCTTATTTATGATTGCTTTCATTTG 11 136 1 TTTATGATTG 0.357552 -165 GGCTTTTGAGTTATTCATTGCAGAAGCGCA 12 39 1 TTATTCATTG 0.541885 -77 CAATGATGGTTTCTTTTTTGTTCATAAATC 14 47 1 TTCTTTTTTG 0.469147 -130 CTTTGATGTCTTTTTGTTTGTGAAGTATTT 14 131 0 TTTTTGTTTG 0.911015 -46 GCAGGGTATGTTTCTCTTTGATGTCTTTTT 14 146 0 TTTCTCTTTG 0.792812 -31 TTTCAACACTTTTTTCTTCGTGTGCCGAAC 15 42 0 TTTTTCTTCG 0.651494 -259 CGATTTCAATTTTCTGATTGTTTTATATTA 15 89 0 TTTCTGATTG 0.743876 -212 AGAAACGTCTTTTTTTATTGTCCGTCTTAT 28 34 1 TTTTTTATTG 0.573026 -52 TAAACGTCGATTTCTGTTTGAAATCTGTTA 31 193 1 TTTCTGTTTG 0.830248 -73 TTCTCCTCGTTTTTTCTTAGCATTCGTCAA 35 75 1 TTTTTCTTAG 0.547211 -73 TTAAAGGGTTTTTTTGTTTGTATGGGAATA 36 47 1 TTTTTGTTTG 0.911015 -105 GTTAGACAAATTTCTGTTCGATTCAACAAG 39 118 1 TTTCTGTTCG 0.533034 -109 GCCAATTCCTTTCTTCATTGGATTCACCCT 40 97 0 TTCTTCATTG 0.650344 -80 CATTTCCCCCTAATTGATTGTTGAAATTTG 41 279 0 TAATTGATTG 0.167887 -22 ********** Masking position 5 Map Score: 3.76333 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 661 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 15 AAAAATCGGCTTCTGCAAGAGAAACCGATTTGT 1 117 0 TTCGCAGGAA 0.931272 -184 TATTCCCATCTTCGCCAGAAGAAATTTGATTTA 2 21 0 TTCCCAAGAA 0.799633 -64 ATGGATCTCTCTCAGCCAATGAAGATCCTTTCT 10 56 0 CTCGCCAGAA 0.908733 -245 GCAGCCGAAACACAGCCTAAGAAAAAACGTATG 11 80 1 CACGCCAGAA 0.514469 -221 TATGAAGCGATTGCGCAAATGAAAGCAATCATA 11 148 0 TTGGCAAGAA 0.833675 -153 CTTCACAAACTTTTGCAAGAGAAAAGTTTTGTC 14 78 0 TTTGCAGGAA 0.653262 -99 CTTTAAACGGTTCGGCACACGAAGAAAAAAGTG 15 33 1 TTCGCAAGAA 0.977199 -268 TAAAAACCCCTTCTTCATAAGAAGAAGGGGTTT 15 252 0 TTCTCAAGAA 0.753965 -49 AAAGATTATATTCAGCATATGACTGACCATGAT 30 19 1 TTCGCAAGAC 0.955883 -41 TTTGAGAAGCCTCCGCAAAATAATTTTGCATTT 39 11 1 CTCGCAATAA 0.674888 -216 AACAAGTTTTTTCAGCAAAAGACAAGAAAATGG 39 142 1 TTCGCAAGAC 0.955883 -85 TGAAATATATCTTCGCATATGAATAAAAATGCA 39 184 0 CTTGCAAGAA 0.81409 -43 AAAGCGCTTTTTCTGCAGAGGACGCTCTGGCCA 41 248 1 TTCGCAAGAC 0.95581 -53 *** *** * *** Masking position 12 Map Score: 5.78977 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 393 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974