AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iphoB_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0301 48 conserved hypothetical protein #2 MJ0302 117 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) #3 MJ0303 44 riboflavin synthase beta chain (ribH) #4 MJ0304 89 ferripyochelin binding protein (fbp) #5 MJ1009 51 phosphate transport system regulatory protein (phoU) #6 MJ1010 300 M. jannaschii predicted coding region MJ1010 #7 MJ1012 30 phosphate specific transport complex component (pstB) #8 MJ1014 164 phosphate transport system permease protein C (pstC) #9 MJ1015 230 periplasmic phosphate-binding protein (pstS) #10 MJ1027 125 formate hydrogenlyase, subunit 5 #11 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #12 MJ1266 189 high-affinity branched-chain amino acid transport protein (braC) #13 MJ1267 96 high-affinity branched-chain amino acid transport ATP-binding protein (braF) #14 MJ1368 122 sulfate transport system permease protein (cysT) Motif number 1 TACAATCTTTTTTTATTTTTAAAACTGAA 1 10 1 TTTTTATTTT 0.762498 -39 TAAAAATTTTTTATAATTTTAGAAGACA 2 9 0 TTATAATTTT 0.937202 -109 TTCAATTTCATAAAAATTTTTTATAATTTT 2 19 0 TAAAAATTTT 0.868669 -99 AGTGTCTTTCAAAACATTTTGTAATAACTA 2 81 0 AAAACATTTT 0.511144 -37 TCACATTTTTTATACTTTTTTAAATGTTA 4 10 1 TTATACTTTT 0.894796 -80 AAATAACATAAAAAACTTTTTGGTGAAATA 4 70 1 AAAAACTTTT 0.694964 -20 CTATACTTTATTTTACTTTTATATTGCCAA 5 11 1 TTTTACTTTT 0.805324 -41 ATTTCCCTCCATATAATTTTTTGGCAATAT 5 31 0 ATATAATTTT 0.900274 -21 GAAGATGTGTTTATAGTTTTTGCAAAAGTT 6 51 1 TTATAGTTTT 0.827685 -250 TTTTAATTTTAATAACTTTTGCAAAAACTA 6 64 0 AATAACTTTT 0.526149 -237 AAATTTTTATTTTTAATTTTAATAACTTTT 6 74 0 TTTTAATTTT 0.878915 -227 AGTGGGGGCGTTCAAATTTTTATTTTTAAT 6 87 0 TTCAAATTTT 0.789005 -214 TAGTTTTTGCAAAACATTTTGAAATATATA 6 138 0 AAAACATTTT 0.511144 -163 AATAGCAACATTATAGTTTTTGCAAAACAT 6 151 0 TTATAGTTTT 0.827685 -150 CGCATCTTTCTAAATATTTTCCTATATTGG 6 194 0 TAAATATTTT 0.735645 -107 TAGAAAAGAGATATACTTTTTAATTACTGG 6 243 1 ATATACTTTT 0.837263 -58 TATATATTTCATATCATTTTTTTGCCAGTA 6 267 0 ATATCATTTT 0.819573 -34 CTATCCCTTTTTTATATTTTATAAAATT 7 9 0 TTTATATTTT 0.79641 -22 ATCTAATTTTTTAATATTTT 8 1 1 ATCTAATTTT 0.649913 -164 ATCTAATTTTTTAATATTTTTTAAATCCAA 8 11 1 TTAATATTTT 0.889324 -154 ATATTTGGGAATAATATTTTTATTAAGCAA 8 61 1 ATAATATTTT 0.818529 -104 CAAAGAAGTGTTTTACTTTTTATATTGAGT 9 18 1 TTTTACTTTT 0.805324 -213 TGAATTAAAGTTCATATTTTATGAACATTC 9 65 0 TTCATATTTT 0.623203 -166 ATAAAGGTATATAAAGTTTTCTATTTTGAA 9 91 0 ATAAAGTTTT 0.779607 -140 AAGAAGGCGTTCAAAATTTTCATTAGTAGA 9 170 0 TCAAAATTTT 0.696523 -61 TTAACCTTTTATATAGTTTTGTTTTAATAA 10 21 0 ATATAGTTTT 0.743952 -105 GATAATTAGCTTAACCTTTTATATAGTTTT 10 31 0 TTAACCTTTT 0.839112 -95 TTTGTTACATTATTTATTTTACTGATATTT 11 40 1 TATTTATTTT 0.539001 -21 AACAATATTATCATTATTTTTAATAACTTC 12 79 0 TCATTATTTT 0.454487 -111 ATGAGCAATATTTAAATTTTTCGAGATAGA 12 116 0 TTTAAATTTT 0.898419 -74 TGTTATGGCAATTTCATTTTTTATATATGA 12 142 0 ATTTCATTTT 0.688444 -48 TGAAATTGCCATAACATTTTGAGGTGATAC 12 156 1 ATAACATTTT 0.843316 -34 TTATTCTTTTAATGGTATCA 12 180 0 TTATTCTTTT 0.79 -10 AAAGAGTTATTTAAAGTTTTAGGAATTTT 13 10 0 TTAAAGTTTT 0.85407 -87 ATAACTCTTTTTTAAATTTTTAAGATATGC 13 30 1 TTTAAATTTT 0.898419 -67 GTTCTAAGATTATAAATTTTATTCTTTAAA 13 62 1 TATAAATTTT 0.763086 -35 ATTTTATTCTTTAAACTTTTTATCATTTTT 13 77 1 TTAAACTTTT 0.911998 -20 TTTAATAAATTTTTAATGAAAAT 14 4 1 AATAAATTTT 0.660722 -119 ATTTGATAGTATAATATTTTCATTAAAAAT 14 19 0 ATAATATTTT 0.818529 -104 TAATCAATCTTAATCATTTTTAAGGTAATT 14 94 0 TAATCATTTT 0.732258 -29 ********** Masking position 7 Map Score: 50.3188 Number of sites scoring better than the average of aligned sites = 3037 Number in coding regions = 2022 Number in noncoding regions = 1015 Number of orfs with sites within 600 bp upstream = 609 Fraction of orfs with sites within 600 bp upstream = 0.0978156 Motif number 2 CCTTTCTTTGGAAGGCATTCAATTTCATAAA 2 35 0 GAGGCATTCA 0.988989 -83 CCTTCCAAAGAAAGGTGTTCATTAGTGCCTT 2 51 1 AAGGTGTTCA 0.893725 -67 CCTTATCCATAGTGTCTTTCAAAACATTTTG 2 90 0 AGGTCTTTCA 0.808671 -28 GCCCCCAAGTGGGGGCGTTCAAATTTTTATT 6 93 0 GGGGCGTTCA 0.998089 -208 GCCCCCACTTGGGGGCGTTCATATATATCCT 6 108 1 GGGGCGTTCA 0.998089 -193 TGTAAATTATGGTGTCATTCAAAAATAACAA 9 137 1 GGGTCATTCA 0.970225 -94 CCTTCTAAAAGAAGGCGTTCAAAATTTTCAT 9 177 0 GAGGCGTTCA 0.996972 -54 CCTTCTTTTAGAAGGCGTTCATCTATACCTT 9 193 1 GAGGCGTTCA 0.996972 -38 ** ******** Masking position 11 Map Score: 15.5119 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 11 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TACAATCTTTTTTTATTTTTAAAACT 1 7 1 CTTTTTTTAT 0.900216 -42 ATTGATGATTCAGTTTTAAAAATAAAAAAA 1 18 0 CAGTTTTAAA 0.533515 -31 CCTCCTGCTATATTGATGATTCAGTTT 1 32 0 CTATATTGAT 0.661719 -17 TCACATTTTTTATACTTTTTTAA 4 4 1 CATTTTTTAT 0.82102 -86 ATTTTTTATACTTTTTTAAATGTTATATGT 4 15 1 CTTTTTTAAA 0.949736 -75 CTATACTTTATTTTACTTTTATATT 5 6 1 CTTTATTTTA 0.330626 -46 TATAATGTTGCTATTGTGAATGAGCTAACC 6 166 1 CTATTGTGAA 0.492643 -135 AAGTATATCTCTTTTCTAAAGTCATTTGCA 6 231 0 CTTTTCTAAA 0.60145 -70 TTCTATCCCTTTTTTATATTTTATAAAA 7 13 0 CTTTTTTATA 0.777464 -18 ATCTAATTTTTTAATATTTTTTAAA 8 6 1 ATTTTTTAAT 0.515032 -159 ATTTTTTAATATTTTTTAAATCCAAATTTA 8 16 1 ATTTTTTAAA 0.515032 -149 TTTATAAGTTCTATTTTAATAAGACTTTCG 8 119 0 CTATTTTAAT 0.922744 -46 CCTTTTTTAATCCTTATCTTA 8 154 0 CTTTTTTAAT 0.949736 -11 TATGAACATTCAATTTTAATAGTTAAAAAC 9 46 0 CAATTTTAAT 0.85862 -185 ATAAAGTTTTCTATTTTGAATTAAAGTTCA 9 81 0 CTATTTTGAA 0.868528 -150 ATCTTACAATCTATTGTAAATTATGGTGTC 9 123 1 CTATTGTAAA 0.637099 -108 AACTTTTTTAATGATTTAAGGT 9 219 0 CTTTTTTAAT 0.949736 -12 CTCGATAACTTTATTAAAACAAAACTAT 10 9 1 CTTTATTAAA 0.848367 -117 AGCTAATTATCATTATTAATTATGATAAAT 10 50 1 CATTATTAAT 0.739908 -76 ATTAACTAAACTATTTTTAAACT 11 4 0 CTATTTTTAA 0.85081 -57 TAGTTAATTTCTATTTTGTTACATTATTTA 11 26 1 CTATTTTGTT 0.54985 -35 TATTTTGTTACATTATTTATTTTACTGATA 11 37 1 CATTATTTAT 0.575965 -24 TATATATGAGCAATATTTAAATTTTTCGAG 12 121 0 CAATATTTAA 0.461966 -69 ATGGCAATTTCATTTTTTATATATGAGCAA 12 138 0 CATTTTTTAT 0.82102 -52 TTAAATAACTCTTTTTTAAATTTTTAAGAT 13 26 1 CTTTTTTAAA 0.949736 -71 CAAATGTCATCAATTTTGTTTAACACAAAT 14 44 1 CAATTTTGTT 0.383127 -79 CAATCTTAATCATTTTTAAGGTAATTAAAT 14 90 0 CATTTTTAAG 0.583589 -33 ********** Masking position 4 Map Score: 25.7212 Number of sites scoring better than the average of aligned sites = 2184 Number in coding regions = 1797 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 323 Fraction of orfs with sites within 600 bp upstream = 0.0518792 Motif number 4 TTATGAAATTGAATGCCTTCCAAAGAAAGG 2 36 1 GAATGCCTTC 0.757492 -82 AGGCACTAATGAACACCTTTCTTTGGAAGG 2 51 0 GAACACCTTT 0.900739 -67 ATAAAAATTTGAACGCCCCCACTTGGGGGC 6 94 1 GAACGCCCCC 0.995166 -207 GGATATATATGAACGCCCCCAAGTGGGGGC 6 108 0 GAACGCCCCC 0.995166 -193 TGAAAATTTTGAACGCCTTCTTTTAGAAGG 9 178 1 GAACGCCTTC 0.767577 -53 AGGTATAGATGAACGCCTTCTAAAAGAAGG 9 193 0 GAACGCCTTC 0.767577 -38 ********** Masking position 3 Map Score: 12.0134 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 8 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 TACAATCTTTTTTTATTTTTAAAACTGA 1 8 1 TTTTTTATTT 0.714819 -41 TCATAAAAATTTTTTATAATTTTAGAAGACA 2 11 0 TTTTTTAATT 0.814506 -107 ATAAAAAATTTTTATGAAATTGAATGCCTTC 2 25 1 TTTATAAATT 0.878484 -93 TTCAAAGGATTTTTGTTATTTCTATTTAGTT 3 17 0 TTTTGTATTT 0.826674 -28 TTATGTTATTTTTAGATATTTATCTTTATAC 4 50 0 TTTAGTATTT 0.90855 -40 TTCAAATTTTTATTTTTAATTTTAATAACTT 6 76 0 TATTTTAATT 0.588933 -225 ATATGAAATATATAGTAAATTTGAGGAG 6 283 1 TATAGAAATT 0.818018 -18 TTTTTTATATTTTATAAAATT 7 1 0 TTTATAAATT 0.878484 -30 AAATTTAAAGATAAGAAATTTTATATTTGGG 8 39 1 ATAAGAATTT 0.450429 -126 CTTTCGCAGGATTAAATAATTGTAACATTGT 8 94 0 ATTAATAATT 0.297245 -71 TCTTACAATCTATTGTAAATTATGGTGTCAT 9 124 1 TATTGAAATT 0.683236 -107 CATTAGTAGATTTTGTTATTTTTGAATGACA 9 149 0 TTTTGTATTT 0.826674 -82 CAAAATCTACTAATGAAAATTTTGAACGCCT 9 165 1 TAATGAAATT 0.360662 -66 ATATAAAAGGTTAAGCTAATTATCATTATTA 10 37 1 TTAAGTAATT 0.819835 -89 TAAGGTAATGAATAGATAATTTATCATAATT 10 67 0 AATAGTAATT 0.694236 -59 TTAAAAATAGTTTAGTTAATTTCTATTTTGT 11 14 1 TTTAGTAATT 0.945666 -47 ATTTTGTTACATTATTTATTTTACTGATATT 11 38 1 ATTATTATTT 0.675798 -23 CGCTTTTGATATTATATAATTACTATTATTA 12 19 1 ATTATTAATT 0.785024 -171 TATTTAAAGTTTTAGGAATTTT 13 2 0 TTTAGAATTT 0.887033 -95 TAAATAACTCTTTTTTAAATTTTTAAGATAT 13 27 1 TTTTTAAATT 0.776264 -70 AAGTTCTAAGATTATAAATTTTATTCTTTAA 13 60 1 ATTATAATTT 0.622275 -37 TTTAATAAATTTTTAATGAAAA 14 2 1 TTAATAATTT 0.518977 -121 ATTACCTAATTATATAAAATTTGTGTTAAAC 14 61 0 TATATAAATT 0.702544 -62 ATTTTATATAATTAGGTAATTTAATTACCTT 14 72 1 ATTAGTAATT 0.874192 -51 TTAATCATTTTTAAGGTAATTAAATTACCTA 14 84 0 TTAAGTAATT 0.819835 -39 ***** ***** Masking position 10 Map Score: 24.1026 Number of sites scoring better than the average of aligned sites = 2115 Number in coding regions = 1627 Number in noncoding regions = 488 Number of orfs with sites within 600 bp upstream = 387 Fraction of orfs with sites within 600 bp upstream = 0.0621587 Motif number 6 AATCTTTTTTTATTTTTAAAACTGAATCAT 1 14 1 TATTTTTAAA 0.803107 -35 AGGCATTCAATTTCATAAAAATTTTTTATA 2 24 0 TTTCATAAAA 0.532673 -94 AATAACAAAAATCCTTTGAAGTAAAAG 3 28 1 ATCCTTTGAA 0.370553 -17 TTTAGATATTTATCTTTATACAAACTACAT 4 41 0 TATCTTTATA 0.690555 -49 TAAAGATAAATATCTAAAAATAACATAAAA 4 53 1 TATCTAAAAA 0.491703 -37 TCTTGCTAAGTATCTTTGAAACTCTTCATA 6 12 0 TATCTTTGAA 0.935497 -289 TAAAATTTCTTATCTTTAAATTTGGATTTA 8 32 0 TATCTTTAAA 0.971902 -133 TACCTTTATGTATCTTACAATCTATTGTAA 9 112 1 TATCTTACAA 0.629319 -119 TAGATTTTGTTATTTTTGAATGACACCATA 9 144 0 TATTTTTGAA 0.631182 -87 CTATACCTTAAATCATTAAAAAAGTT 9 215 1 AATCATTAAA 0.851957 -16 TTAACTAAACTATTTTTAAACT 11 3 0 TATTTTTAAA 0.803107 -58 TAAATATCAGTAAAATAAATAATG 11 47 0 TATCAGTAAA 0.531116 -14 CCGTATCAAAAAGCTTTAAAGTATTAGTAA 12 50 0 AAGCTTTAAA 0.677862 -140 ATATATGAGCAATATTTAAATTTTTCGAGA 12 120 0 AATATTTAAA 0.45224 -70 TTTGAGGTGATACCATTAAAAGAATAA 12 173 1 TACCATTAAA 0.782318 -17 AAAATTCCTAAAACTTTAAATAACTCTTTT 13 11 1 AAACTTTAAA 0.586736 -86 AGAACTTGCATATCTTAAAAATTTAAAAAA 13 37 0 TATCTTAAAA 0.934449 -60 TAAAATTTATAATCTTAGAACTTGCATATC 13 53 0 AATCTTAGAA 0.753309 -44 TATAAATTTTATTCTTTAAACTTTTTATCA 13 72 1 ATTCTTTAAA 0.814856 -25 AGTATAATATTTTCATTAAAAATTTATTAA 14 12 0 TTTCATTAAA 0.735248 -111 GTAATTTAATTACCTTAAAAATGATTAAGA 14 87 1 TACCTTAAAA 0.819846 -36 ********** Masking position 10 Map Score: 11.807 Number of sites scoring better than the average of aligned sites = 1808 Number in coding regions = 1569 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 7 CACTATGGATAAGGGATATCT 2 107 1 AAGGGATATC 0.948021 -11 GACTTTAGAAAAGAGATATACTTTTTAATT 6 238 1 AAGAGATATA 0.840035 -63 AAATATAAAAAAGGGATAGAA 7 20 1 AAGGGATAGA 0.979956 -11 AAGATACATAAAGGTATATAAAGTTTTCTA 9 98 0 AAGGTATATA 0.951459 -133 TTAATGATTTAAGGTATAGATGAACGCCTT 9 204 0 AAGGTATAGA 0.959468 -27 AACATGATAATAGGTATATGACTCACTAAG 10 94 0 TAGGTATATG 0.876075 -32 TAAGATTGATTAGGGATAGGC 14 112 1 TAGGGATAGG 0.946331 -11 ********** Masking position 6 Map Score: 4.36296 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 80 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TAAAACTGAATCATCAATATAGCAGGAGG 1 30 1 TCTCAATATA 0.740462 -19 ATATAATTTTTTGGCAATATAAAAGTAAAAT 5 20 0 TTGCAATATA 0.922615 -32 TTGAAATATATAGGATATATATGAACGCCCC 6 119 0 TAGATATATA 0.770414 -182 TGCAAAACATTTTGAAATATATAGGATATAT 6 130 0 TTGAAATATA 0.902539 -171 GTGAATGAGCTAACCAATATAGGAAAATATT 6 181 1 TACCAATATA 0.920409 -120 AAAAAAATGATATGAAATATATAGTAAATTT 6 274 1 TAGAAATATA 0.955099 -27 AATTTTATAAAATATAAAAAAGGGAT 7 6 1 TAAAAATATA 0.766301 -25 AAAATATTATTCCCAAATATAAAATTTCTTA 8 50 0 TCCAAATATA 0.858044 -115 ATATTTTTATTAAGCAATATACAATGTTACA 8 74 1 TAGCAATATA 0.964795 -91 ** ******** Masking position 7 Map Score: 4.71393 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 125 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TACAATCTTTTTTTATTTTTAAAACTGAATC 1 11 1 TTTTATTTTA 0.936238 -38 CATAAAAATTTTTTATAATTTTAGAAGACA 2 10 0 TTTTATATTT 0.825157 -108 TCACATTTTTTATACTTTTTTAAATGTT 4 8 1 TTTTATCTTT 0.620583 -82 ATTTTTAGATATTTATCTTTATACAAACTAC 4 43 0 ATTTATTTTA 0.563163 -47 AAGTTTTTTATGTTATTTTTAGATATTTATC 4 57 0 TGTTATTTTA 0.63609 -33 CTATACTTTATTTTACTTTTATATTGCCAAA 5 11 1 TTTTACTTTA 0.510738 -41 GCGTTCAAATTTTTATTTTTAATTTTAATAA 6 79 0 TTTTATTTTA 0.936238 -222 ATATATTTCATATCATTTTTTTGCCAGTAAT 6 265 0 TATCATTTTT 0.756399 -36 TCTATCCCTTTTTTATATTTTATAAAATT 7 9 0 TTTTATTTTT 0.88188 -22 TCTAATTTTTTAATATTTTTTAAATCCAAAT 8 12 1 TAATATTTTT 0.571685 -153 ATATAAAATTTCTTATCTTTAAATTTGGATT 8 34 0 TCTTATTTTA 0.63609 -131 AGATAAGAAATTTTATATTTGGGAATAATAT 8 47 1 TTTTATTTTG 0.608917 -118 TATTTGGGAATAATATTTTTATTAAGCAATA 8 62 1 TAATATTTTA 0.723943 -103 GTGTTTTACTTTTTATATTGAGTTTTTAACT 9 25 1 TTTTATTTGA 0.666014 -206 CGTTCAAAATTTTCATTAGTAGATTTTGTTA 9 162 0 TTTCATAGTA 0.302725 -69 TTAAGCTAATTATCATTATTAATTATGATAA 10 47 1 TATCATATTA 0.794244 -79 ATATACCTATTATCATGTTTATAATTGTTGG 10 105 1 TATCATTTTA 0.859289 -21 TTCTATTTTGTTACATTATTTATTTTACTGA 11 34 1 TTACATATTT 0.467579 -27 GCTTTTGATATTATATAATTACTATTATTAT 12 20 1 TTATATATTA 0.724143 -170 ATATAATTACTATTATTATTACTAATACTTT 12 32 1 TATTATATTA 0.854198 -158 TAACCAACAATATTATCATTATTTTTAATAA 12 83 0 TATTATATTA 0.854379 -107 GTTATGGCAATTTCATTTTTTATATATGAGC 12 140 0 TTTCATTTTT 0.830855 -50 GAAATTGCCATAACATTTTGAGGTGATACCA 12 157 1 TAACATTTGA 0.190001 -33 AGATTATAAATTTTATTCTTTAAACTTTTTA 13 68 1 TTTTATCTTT 0.620583 -29 TCTTTAAACTTTTTATCATTTTT 13 84 1 TTTTATATTT 0.825157 -13 GATAGTATAATATTTTCATTAAAAATTTATT 14 14 0 TATTTTATTA 0.219626 -109 AACACAAATTTTATATAATTAGGTAATTTAA 14 65 1 TTATATATTA 0.724143 -58 AATCAATCTTAATCATTTTTAAGGTAATTAA 14 92 0 AATCATTTTA 0.34903 -31 ****** **** Masking position 5 Map Score: 22.2528 Number of sites scoring better than the average of aligned sites = 2106 Number in coding regions = 1460 Number in noncoding regions = 646 Number of orfs with sites within 600 bp upstream = 468 Fraction of orfs with sites within 600 bp upstream = 0.0751686 Motif number 10 TTTTACTTCAAAGGATTTTTGTTATTTCTAT 3 23 0 AAGATTTTTG 0.976527 -22 AATAACATAAAAAACTTTTTGGTGAAATA 4 71 1 AAACTTTTTG 0.884197 -19 ACTTAGCAAGAAAGATTTTTGAAGATGTGTT 6 31 1 AAGATTTTTG 0.976498 -270 TTTTAATTTTAATAACTTTTGCAAAAACTAT 6 63 0 AAAACTTTTG 0.884088 -238 AAATTCTGCAAATGACTTTAGAAAAGAGATA 6 225 1 AAGACTTTAG 0.924124 -76 AACTTTTTTAATGATTTAAGGTATAGATGA 9 211 0 AAGATTTAAG 0.78981 -20 CTAATACTTTAAAGCTTTTTGATACGGAAGT 12 53 1 AAGCTTTTTG 0.965512 -137 ** ******** Masking position 2 Map Score: 3.92439 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 70 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ********** No masking Map Score: -7.15216e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: -7.15216e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -7.15216e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0