AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoN_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH130 171 cobalamin biosynthesis protein M #2 MTH132 86 cobalt transport protein Q #3 MTH133 167 cobalt transport ATP-binding protein O #4 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #5 MTH384 249 unknown #6 MTH387 24 conserved protein #7 MTH388 35 unknown #8 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #9 MTH394 55 unknown #10 MTH397 40 formate hydrogenlyase, subunit 7 #11 MTH478 49 sulfate transport system permease protein #12 MTH479 136 conserved protein #13 MTH480 91 unknown #14 MTH604 116 adhesion protein #15 MTH695 248 conserved protein #16 MTH783 83 hydrogenase expression/formation protein HypA #17 MTH1072 67 hydrogenase expression/formation protein HypD #18 MTH1246 30 NADH dehydrogenase I, subunit N #19 MTH1251 147 conserved protein #20 MTH1252 143 conserved protein #21 MTH1253 135 unknown #22 MTH1370 137 ABC transporter (ATP-binding protein) #23 MTH1552 139 formate dehydrogenase, alpha subunit homolog #24 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #25 MTH1570 74 glutamine synthetase #26 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #27 MTH1649 110 hydrogenase expression/formation protein HypC #28 MTH1705 33 cobalt transport membrane protein #29 MTH1707 300 cobalamin biosynthesis protein M Motif number 1 GAATTTATAGAAAACATTATATACCTCAATTT 1 113 1 AAAATTATAT 0.92022 -59 CCTTTTTTAAAAAGATTTATAT 5 238 1 AAATTTATAT 0.963942 -12 CTATCTTAATAAATGTTTATATATTTTATGTT 14 19 1 AAATTTATAT 0.963888 -98 TTTATATTAACAATTATTATATGGTTGCGTTG 14 72 1 CAAATTATAT 0.911504 -45 CGGTAATTAACAATTTTTATATAGATAACTCT 16 25 1 CAATTTATAT 0.959804 -59 TTAGTCTGACAAAATTTTATAATTAGAATTAA 16 58 0 AAATTTATAA 0.801377 -26 ATTTATATAGAAAACTTTATATTATCATAAAT 19 84 1 AAATTTATAT 0.963952 -64 TCAATTCCTGAATTAATTATATGGGGGTCCTT 22 56 0 AATATTATAT 0.727328 -82 TCAAATAGAAAAATATATATATAGGTGTGTGG 24 11 0 AAATATATAT 0.800343 -61 TTTTTGTAGAAAATTATTATATGGACGGCGGC 24 43 1 AAAATTATAT 0.920157 -29 ACAAAAAATATATAAACCAGTAG 25 2 1 CAAAATATAT 0.608471 -73 ATGACCCCCTCATGATTTATATCAACACACAC 26 245 1 CATTTTATAT 0.846702 -56 TGTTTCCCACAAATCTTTATATGTGACGGATC 27 30 1 AAATTTATAT 0.963941 -81 TTAATGATTTATAATGATGTTTTT 29 3 1 AATTTTATAA 0.482735 -298 CGACAATGCACAAAGTTTATATATAGATTCCA 29 42 0 CAATTTATAT 0.959805 -259 ATAATCACTTCAACCTTTATATTATATGAATG 29 232 1 CAATTTATAT 0.959805 -69 TCACTATATCAAACATTCATATAATATAAAGG 29 245 0 AAATTCATAT 0.760944 -56 *** ******* Masking position 9 Map Score: 22.2206 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 20 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 TGATACCTCCAGATGGTGGGCTATGAATTTA 3 55 1 AATGGTGGGC 0.947207 -113 AACCTCCAGGACATGATGGGGTGGGAAT 5 8 0 AATGATGGGG 0.980124 -242 AAGACATGATGTGGAATGAAAATG 9 4 1 AATGATGTGG 0.86186 -52 TGTGGAATGAAAATGGAAGGGATTTAATCAG 9 20 1 AATGGAAGGG 0.978847 -36 GGAGAGAGATATATGGAATGGTGATAAC 13 74 1 AATGGAATGG 0.854118 -18 GGATGATTATATGATGGAGGTTCCTATTA 15 230 0 AATGATGGAG 0.907555 -19 GATCATATATATATGGAGGAGGCCAAAGGAT 17 12 0 AATGGAGGAG 0.966174 -56 ATGATTAAACACTTGAAGGGGAAGAGGCTGC 19 32 0 ATTGAAGGGG 0.891449 -116 ACTGAAGATAACATGAAGGGGACTGTTAAAT 23 81 1 AATGAAGGGG 0.987207 -59 AATTTAGAATAGATGGAAGGGAACTTGAGGC 23 109 1 AATGGAAGGG 0.978847 -31 GAAAATTATTATATGGACGGCGGCTAAATGT 24 51 1 AATGGACGGC 0.80314 -21 TTATGCAAGAACATGAAAGAGGGTTTGA 26 283 1 AATGAAAGAG 0.832086 -18 CCTTTTTAATAAATGGTGGGGATGTGCCAGA 29 95 1 AATGGTGGGG 0.98921 -206 * ********* Masking position 1 Map Score: 18.4881 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 274 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 ATCTTACATATATTATCCTTTCAGAGGCCCCCGCAACCATCA 1 50 1 TTTTCAGCCC 0.970672 -122 AAAAAACCGATGTGAGGATATCAGCAGATCTCAGAGGA 3 7 0 TTTTCAGCTC 0.946815 -161 CTCACATCGGTTTTTTGATTTCTGATACCTCCAGATGGTGGG 3 33 1 TTTTCTGTCC 0.976686 -135 ATGTGTATTCTATATTTAAGTCTGCTTAATCCTATCGGATCG 3 107 0 TTATCTGTCC 0.816787 -61 GAAACTTTTTTTTACTGATATCTGAAGGGTCCCTCTACAGAA 5 124 0 TTTTCTGTCC 0.976686 -126 TATGGCCTTTTTTACTAATATCTGGAGGTTTCTCTACAGAAA 5 162 0 TTTTCTGTTC 0.957508 -88 GAGTAGTCCTTCTTTATCTTTCAGGACGATCCCATGTTCTCA 12 32 1 TTTTCAGTCC 0.984976 -105 TCAGGTCCTTCATTAGAATCTAAGTGTTCTCCTTTTCCAGTC 15 54 1 CTTTAAGTCC 0.685528 -195 GTAATAAAAACATGAGCGTATCAGAATGATTCCATTTATAAG 21 11 0 CTTTCAGTTC 0.946815 -125 TTCCATCTATTCTAAATTTAACAGTCCCCTTCATGTTATCTT 23 85 0 TTTACAGTTC 0.789596 -55 GAAACGTGATTTTTGTTTTTTCAGAAGAATTCATCTTTTCTG 26 29 0 TTTTCAGTTC 0.972425 -272 AACCGAACTGTTTTTCGATTTCAGAATGGCTCCAGAGGACCG 26 103 1 TTTTCAGCTC 0.946815 -198 TGGTAATAATCCTCCGCCTATCTGGCACATCCCCACCATTTA 29 104 0 CTTTCTGTCC 0.95485 -197 * * * **** *** Masking position 3 Map Score: 14.4551 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 131 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 4 AGCCCACCATCTGGAGGTATCAGAAATCAAA 3 46 0 CTGGGGTATC 0.961318 -122 CCATCATGTCCTGGAGGTTCCTATGGAGTCA 5 20 1 CTGGGGTTCC 0.990112 -230 TTACTAATATCTGGAGGTTTCTCTACAGAAA 5 162 0 CTGGGGTTTC 0.984324 -88 TGATTATATGATGGAGGTTCCTATTATAACT 15 225 0 ATGGGGTTCC 0.965817 -24 TTTAAGTGTAATGGTGGTCTT 17 57 1 ATGGGGTCTT 0.938474 -11 AATTAATTATATGGGGGTCCTTTATATATAG 22 47 0 ATGGGGTCCT 0.960512 -91 CAGTCAGCCACTGGAGGTCCCGCTGTAGCGA 22 108 0 CTGGGGTCCC 0.996738 -30 CAGTGGCTGACTGGGGGACTCA 22 126 1 CTGGGGACTC 0.964233 -12 GAGCCTATCACTGGAGATCCTGTGGGAAAGA 26 178 0 CTGGGATCCT 0.882792 -123 ATGACCATTGCCGGGGGTCTCAGGGTGTATA 29 147 0 CCGGGGTCTC 0.975584 -154 **** ****** Masking position 6 Map Score: 15.4918 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 283 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TACATATATTATCCTTTCAGAGGCCCCCGCAAC 1 54 1 ATCCTCAGGG 0.955179 -118 AGTTTCCTTGATGGTTGCGGGGGCCTCTGAAAG 1 67 0 ATGGTCGGGG 0.990383 -105 GTATATATTCATGGAGCCGGTGGCGA 4 60 1 ATGGGCGGGG 0.950965 -16 ATATATACATATCGGTTCTGTGAAGGAATGAGA 12 69 0 ATCGTCTGGA 0.896899 -68 CAATTATTATATGGTTGCGTTGACATAACTTAA 14 82 1 ATGGTCGTGA 0.810111 -35 GGTGAGCAACATCGCTGCAGCGACTCAGAGAAA 20 18 0 ATCGTCAGGA 0.976691 -126 AGGTTAATTGATGCCTGCGGAGGTTTATAA 20 124 1 ATGCTCGGGG 0.964958 -20 TAAAAATGTTATCGCTACAGCGGGACCTCCAGT 22 97 1 ATCGTCAGGG 0.987608 -41 CGAAAAACAGTTCGGTTCAGGGAAGGGGTTTTA 26 87 0 TTCGTCAGGA 0.841877 -214 CGATTTCAGAATGGCTCCAGAGGACCGCCCCAG 26 118 1 ATGGTCAGGG 0.989589 -183 CCATGTCTTTATGTGTTCAGCGACAATGCACAA 29 61 0 ATGTTCAGGA 0.830491 -240 **** * *** ** Masking position 2 Map Score: 11.1672 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 140 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TAGAAGGATTCAAGAAGGTGATAAA 1 157 1 CAAGAGGTGA 0.876466 -15 ACCTCCAGGACATGATGGGGTGGGAAT 5 7 0 CATGTGGGGT 0.727976 -243 AAATCTTTTTAAAAAAGGTGAGTTAGACCTA 5 225 0 AAAAAGGTGA 0.780712 -25 TATATAGATGATTACTGGTGA 6 14 1 ATTATGGTGA 0.707002 -11 AAGACATGATGTGGAATGAAAATGG 9 5 1 CATGTGTGGA 0.623223 -51 GTGGAATGAAAATGGAAGGGATTTAATCAGA 9 21 1 AATGAAGGGA 0.766334 -35 ATTTAATCAGAAAAGAGGGGATTTA 9 41 1 AAAAAGGGGA 0.917676 -15 GAAAAAATACATTATTGGGGAGAGAGATATA 13 56 1 ATTATGGGGA 0.883111 -36 AATGAGGAATCTAACAGGTGAGGAATT 18 14 1 CTAAAGGTGA 0.721332 -17 TGATTAAACACTTGAAGGGGAAGAGGCTGCC 19 31 0 CTTGAGGGGA 0.956923 -117 AAATCGTAATAAAATAGGGGATCCGATGATT 19 57 0 AAAAAGGGGA 0.917676 -91 TGGCGCCGGCCTTACTGGTGAGCAACATCGC 20 36 0 CTTATGGTGA 0.773056 -108 CTGAAGATAACATGAAGGGGACTGTTAAATT 23 82 1 CATGAGGGGA 0.977341 -58 CTTTTTAATAAATGGTGGGGATGTGCCAGAT 29 96 1 AATGTGGGGA 0.953935 -205 ATATTACCACAATATAAGGGAAACCGAAGAT 29 196 1 AATAAAGGGA 0.699085 -105 **** ****** Masking position 10 Map Score: 9.23629 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 683 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 CACTTACCGGTTTCTGTGAATATAATCACG 5 55 1 TTTCTGTGAA 0.946662 -195 GTTCTGGGAATAACTCCCTC 12 1 1 GTTCTGGGAA 0.986304 -136 ATACATATCGGTTCTGTGAAGGAATGAGAA 12 68 0 GTTCTGTGAA 0.978451 -69 TGAATCTGATGTTCAGTGAAAAAATACATT 13 39 1 GTTCAGTGAA 0.965875 -53 TGAGGTTAAATTTCTGGGATTCCAGGGTTT 20 74 1 TTTCTGGGAT 0.834572 -70 AAACAGTTCGGTTCAGGGAAGGGGTTTTAT 26 86 0 GTTCAGGGAA 0.978209 -215 AGATTCTTCAGATCAGTGAAAAGCAGATGT 26 151 0 GATCAGTGAA 0.835316 -150 CATATAAAGATTTGTGGGAAACAATGCCAT 27 23 0 TTTGTGGGAA 0.823301 -88 ********** Masking position 9 Map Score: 7.20055 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 87 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 TCACCTTCTTGAATCCTTCTAAAGTAAACTTTAA 1 144 0 GATCTCTAAG 0.720437 -28 GTACCTCAAAGGATTATTCTGATGATTCACCCCT 2 52 0 GGTTTCTGTG 0.948925 -35 TATGATAATAGAATCATTCCGGTGTTAATGGTGA 8 14 1 GATCTCCGTG 0.887621 -28 TTAAGACCCCGACTTTTTCTGAAG 11 36 1 GATTTCTGAG 0.954638 -14 TGAGAACATGGGATCGTCCTGAAAGATAAAGAAG 12 40 0 GGTCTCTGAA 0.966751 -97 TGGGATTCCAGGGTTTTGATGCTGTATTCTGACT 20 88 1 GGTTTATGTG 0.701555 -56 CTTATAAATGGAATCATTCTGATACGCTCATGTT 21 11 1 GATCTCTGTA 0.930784 -125 GCAGGTATACGGATTTTTCCGGAAGTGGGCCAGC 21 105 1 GGTTTCCGAA 0.831678 -31 CAGAAAAGATGAATTCTTCTGAAAAAACAAAAAT 26 29 1 GATTTCTGAA 0.91883 -272 CGGTCCTCTGGAGCCATTCTGAAATCGAAAAACA 26 111 0 GACCTCTGAA 0.768481 -190 TCCAGTGATAGGCTCATGCTGCAAGCAGATATAA 26 194 1 GGTCTCTGAA 0.966751 -107 AATCATGAGGGGGTCATCCTGTAGGACCACAGCC 26 228 0 GGTCTCTGAG 0.981836 -73 TTAATGATTTATAATGATGTTTTTAATTT 29 6 1 GATTTATGTG 0.629827 -295 ** ** * *** ** Masking position 7 Map Score: 9.5882 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 357 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 GAAAACATTATATACCTCAATTTTAAAGTT 1 122 1 TATACCTCAA 0.82049 -50 TTTGATTTCTGATACCTCCAGATGGTGGGC 3 46 1 GATACCTCCA 0.789313 -122 TTTCTGTAGAGAAACCTCCAGATATTAGTA 5 162 1 GAAACCTCCA 0.899616 -88 TTCTTTACCTCAGCATTTGCTCT 10 28 0 TTTACCTCAG 0.69765 -13 GGTCTTTAACCTCCATTAACTCAGA 12 122 0 TTAACCTCCA 0.968626 -15 TAAATTATTTTTAAGCTCCAGATGACTCTC 15 26 1 TTAAGCTCCA 0.926911 -223 TCTCTGCTCTTTATGCTCCATTCCGTTAAA 15 145 1 TTATGCTCCA 0.721674 -104 TCCATTCCGTTAAAGATCCATAAAAGTCAA 15 161 1 TAAAGATCCA 0.435915 -88 TCCCAGAAATTTAACCTCAAAGTCATTGGC 20 63 0 TTAACCTCAA 0.91618 -81 CAGGCATCAATTAACCTCAAGTCAGAATAC 20 111 0 TTAACCTCAA 0.91618 -33 TTATAAACCTCCGCAGGCATCAA 20 131 0 TAAACCTCCG 0.939709 -13 TCCGGTGAAGTTAAGCTCATGCCATGGAGG 25 47 1 TTAAGCTCAT 0.363546 -28 GGGTTATGCCTCCATGGCATGAGC 25 61 0 TATGCCTCCA 0.689026 -14 ATAATGGTAATAATCCTCCGCCTATCTGGC 29 120 0 TAATCCTCCG 0.760959 -181 ********** Masking position 7 Map Score: 8.08811 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 375 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 TTTATCACCTTCTTGAATCCT 1 161 0 TTATCACCTT 0.784556 -11 AGAATACACATTATTATCATAACGTTTAAG 3 138 1 TTATTATCAT 0.839217 -30 CTCATCACCATTAACACCGGA 8 31 0 TCATCACCAT 0.843683 -11 GTTATCACCATTCCATATATC 13 81 0 TTATCACCAT 0.966285 -11 ATATAAACATTTATTAAGATAGGATCTTCC 14 11 0 TTATTAAGAT 0.654233 -106 AAAGATCTATTTATCACGATCATATATATA 17 30 0 TTATCACGAT 0.971577 -38 ATCCCCTATTTTATTACGATTTATATAGAA 19 66 1 TTATTACGAT 0.935846 -82 GTACCAATAATTAACATGATTATTTATGAT 19 107 0 TTAACATGAT 0.649552 -41 TGGTGAAACTTTATCATGATGCACAGATAA 23 41 0 TTATCATGAT 0.935846 -99 TTAATGATTTATAATGATGTTTTTAATT 29 9 1 TTATAATGAT 0.654234 -292 AGGCGGAGGATTATTACCATTATACACCCT 29 127 1 TTATTACCAT 0.924419 -174 ********** Masking position 6 Map Score: 6.18957 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 34 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 AATTTATCCATTCATGATCTGTTTCATCGATCCGA 3 80 1 TTCATTCTTC 0.981485 -88 TTTAAGGATTTTCATAGTCGTTTTCGTGATTATAT 5 74 0 TTCATTCTTC 0.981485 -176 GGCTTCCATGTTCTCATTCAGGATTATTT 7 5 1 TCCATTCTTC 0.967762 -31 TCAGGACGATCCCATGTTCTCATTCCTTCACAGAA 12 52 1 CCCATTCTTC 0.944441 -85 TTTCCAGTCCTTCAGCTTCCCTTTCTAAGTGGCTA 15 87 1 TTCAGTCTTC 0.981118 -162 TCATGTTATCTTCAGTGTCCTTTTTATGGTGAAAC 23 62 0 TTCAGTCTTT 0.852994 -78 TCCAGGTTCAGCCTCAAGTTCCCTTCCATCT 23 119 0 TTCAGTCTTC 0.981118 -21 GTGATTATTACTAATCTTCGGTTTCCCTTATATTG 29 205 0 CTAATTCTTC 0.77023 -96 ***** ** *** Masking position 4 Map Score: 3.63282 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 131 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 ATGTAAGGACATAAAGTTCAGTAGAGTCGA 1 20 0 ATAAAGTTCA 0.817064 -152 CTGATCTAAATTAAAGTTTCCTTGATGGTT 1 84 0 TTAAAGTTTC 0.670217 -88 TACCTCAATTTTAAAGTTTACTTTAGAAGG 1 134 1 TTAAAGTTTA 0.854281 -38 CATTATTATCATAACGTTTAAGGGATCACG 3 146 1 ATAACGTTTA 0.675872 -22 ATGAAAATCCTTAAAATTTATTACTAAATC 5 94 1 TTAAAATTTA 0.711625 -156 ATATTTTATGTTAAAATTTATTAAATTTTA 14 39 1 TTAAAATTTA 0.711625 -78 AATATAAACGATAAAATTTAATAAATTTTA 14 50 0 ATAAAATTTA 0.866232 -67 TTAAAGATCCATAAAAGTCAACCGCTACCA 15 170 1 ATAAAAGTCA 0.442815 -79 AATTCTAATTATAAAATTTTGTCAGACTAA 16 60 1 ATAAAATTTT 0.591986 -24 TTATGATAATATAAAGTTTTCTATATAAAT 19 84 0 ATAAAGTTTT 0.77515 -64 TGATGCACAGATAAAGGTTATGAGTAGAGA 23 25 0 ATAAAGGTTA 0.866775 -115 GTGCATCATGATAAAGTTTCACCATAAAAA 23 47 1 ATAAAGTTTC 0.842098 -93 TATAGATTCCATAAAATTAAAAACATCATT 29 23 0 ATAAAATTAA 0.407954 -278 GCGACAATGCACAAAGTTTATATATAGATT 29 45 0 ACAAAGTTTA 0.676148 -256 TTCATATAATATAAAGGTTGAAGTGATTAT 29 232 0 ATAAAGGTTG 0.550609 -69 ********** Masking position 4 Map Score: 4.25032 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 28 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 13 AGGATATCAGCAGATCTCAGAGGA 3 5 0 CAGATCTCAG 0.945685 -163 AACCGATGTGAGGATATCAGCAGATCTCAG 3 15 0 AGGATATCAG 0.846273 -153 AGGGACCCTTCAGATATCAGTAAAAAAAAG 5 132 1 CAGATATCAG 0.844604 -118 GAGAAACCTCCAGATATTAGTAAAAAAGGC 5 170 1 CAGATATTAG 0.911558 -80 CAAACTGATAAAGATATCCGGAAG 13 5 0 AAGATATCCG 0.846273 -87 ATGCTGCAAGCAGATATAAGGCTGTGGTCC 26 209 1 CAGATATAAG 0.911558 -92 ********** Masking position 5 Map Score: 0.707408 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 91 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 TTTAATTTAGATCAGAATTTATAGAAAACAT 1 99 1 ATCAGAATTA 0.840464 -73 GGGGTGAATCATCAGAATAATCCTTTGAGGT 2 53 1 ATCAGAATAT 0.727274 -34 ATCTGGAGGTATCAGAAATCAAAAAACCGAT 3 38 0 ATCAGAAATA 0.840464 -130 CCCTTCAGATATCAGTAAAAAAAAGTTTCTG 5 137 1 ATCAGTAAAA 0.727274 -113 AAGGGATTTAATCAGAAAAGAGGGGATTTA 9 36 1 ATCAGAAAAA 0.949879 -20 ATAAAATTTTGTCAGACTAAAGAG 16 70 1 GTCAGACTAA 0.737814 -14 TTAACCTCAAGTCAGAATACAGCATCAAAAC 20 100 0 GTCAGAATAA 0.931005 -44 TTATCCTTAAAACAGAAAAGATGAATTCTTC 26 17 1 AACAGAAAAA 0.749222 -284 TAGGATTAAAGTCAGAATACACTAATGTTTA 27 68 0 GTCAGAATAA 0.931005 -43 TCGACTTCACCAGAAAAAAATTAATTGGG 28 15 0 ACCAGAAAAA 0.815769 -19 ********* * Masking position 4 Map Score: 3.14849 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 = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 ATTTAGATCAGAATTTATAGAAAACATTAT 1 103 1 GAATTTATAG 0.943698 -69 GGTGGGCTATGAATTTATCCATTCATGATC 3 69 1 GAATTTATCC 0.790825 -99 CCGGCTCCATGAATATATACTAGAAGCACC 4 50 0 GAATATATAC 0.838378 -26 GAATATATAGATGATTACTG 6 1 1 GAATATATAG 0.879599 -24 TTTATAATTAGAATTAATAGAGTTATCTAT 16 45 0 GAATTAATAG 0.927656 -39 CAATGCCATTGAATTAATACC 27 2 0 GAATTAATAC 0.889962 -109 AACCCTCTCCAAATTAATAGGATTAAAGTC 27 86 0 AAATTAATAG 0.62654 -25 ********** Masking position 7 Map Score: 0.41881 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 8 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987