AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_hpyl_reg_100.orf -o02010_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0251 300 oligopeptide ABC transporter, permease protein (oppC) #2 HP0298 116 dipeptide ABC transporter, periplasmic dipeptide-binding protein (dppA) #3 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #4 HP0474 21 molybdenum ABC transporter, permease protein (modB) #5 HP0686 247 iron(III) dicitrate transport protein (fecA) #6 HP0807 193 iron(III) dicitrate transport protein (fecA) #7 HP0813 132 conserved hypothetical protein #8 HP0818 68 osmoprotection protein (proWX) #9 HP0890 217 conserved hypothetical protein #10 HP1169 212 glutamine ABC transporter, permease protein (glnP) #11 HP1172 48 glutamine ABC transporter, periplasmic glutamine-binding protein (glnH) #12 HP1253 31 tryptophanyl-tRNA synthetase (trpS) #13 HP1254 116 biotin synthesis protein (bioC) #14 HP1400 300 iron(III) dicitrate transport protein (fecA) #15 HP1466 134 conserved hypothetical integral membrane protein #16 HP1564 139 outer membrane protein #17 HP1574 74 riboflavin synthase alpha subunit (ribC) #18 HP1576 21 ABC transporter, ATP-binding protein (abc) Motif number 1 AGAATGATTATCTTAAAATTAGAAAGTTTCTTTTA 1 7 0 TTAATTATTT 0.972134 -294 AGCAAAATGTTATAATGCTCGCTTAATTTTATTTGGGGT 1 94 1 TTATTCATTT 0.466176 -207 TTAAAGGTTAATTAAACCTTTAGGTGTTTGTGAAACACC 2 19 1 ATAATTTTTT 0.815964 -98 AGGATAGAGATCTAAATTATAAATATTTTATTGCGTTTA 2 60 0 TTAAATATTT 0.959107 -57 CGGTTATTTTTCTAAAAGTTTTAATTTTTTATCAAAGAT 3 51 1 TTAATTTTTT 0.925577 -175 TTTAATTTTTTATCAAAGATGAAGATTTTAGAGTGAAAA 3 70 1 TTAAATATTT 0.959107 -156 CCTATTTGTATCTTAAAAATTTGTATTTTAAAAGTTTGA 3 157 0 TTAAATATTT 0.959107 -69 CATTAGAAATATTAAAAAATTTTTATTTTTCTTCCAATC 5 63 1 ATAAATATTT 0.893178 -185 ATTATTATTTAGATAATATTAATGACTTTTTTATCAAAA 5 132 0 AAAATTATTT 0.756133 -116 TTATCTAAATAATAATTTTTCAAAAATTTAAGCTAAAAC 5 155 1 ATATTTATTT 0.59252 -93 GTGAAATTTATAATAACCATTATTAGTTTTAGCTTAAAT 5 180 0 TAAAATATTT 0.853867 -68 TACCACCTTTTATGAAAAATGTTCTTTTTTACAACAATG 5 218 0 TTAAATTTTT 0.893178 -30 TGAAGTTTGATTTTATTTATTTGCAATTTGTTATCAAAA 6 93 0 TTATATATTT 0.732781 -101 AAATCAAACTTCAAAATTTAAGTTAATTTTAATAATTAT 6 119 1 TAAATAATTT 0.606601 -75 TGTGATAACCTTTCTCATTTAATTCAAACCG 6 173 0 TAAATTATTA 0.406691 -21 GCGCTATTCTAGTCAAAATCGCCTTATTTTTGCGCTATG 7 54 1 ATAATCTTTT 0.486982 -79 GCGCTATGATTTTCAATAATAATGACTTTTTAAAACTAG 7 85 1 TTAAATATTT 0.959107 -48 TCTAATATTCACTCAATATTACTTAATTTTTACTAATAT 9 74 0 ATAATTATTT 0.925577 -144 TAATCATTGTTGTTAATTTCAGCCAGTTTTTTTATTATA 10 34 1 TTAATCATTT 0.881923 -179 AACATGGTGCTTTAAAGCGTCATTAATTTTTAAGGTATA 10 179 1 TTAAGTATTT 0.787201 -34 AATTTTAATATTTTAATTTATCTTAGTTT 12 1 0 TTAATAATTT 0.860822 -31 CGTGATTTTTTCTAAATTTTAGGCATTTAAGGAATCA 13 9 0 TTAATTATTA 0.733294 -108 GCTCGTTGTGTGTCAAAAATGGGGATTTTTCACTAGAGA 14 71 1 TTAAATATTT 0.959107 -230 TTTTTTTTTTTTTTGATTTTGCTGATTTTACTCAATCTC 14 106 0 TTGATTATTT 0.690852 -195 ATTAATCCCATGAAAATCTTTTTTTTTTTTTTTTGATTT 14 126 0 TAAATTTTTT 0.756056 -175 TCATGGGATTAATAAAATTTTAAGAATTTTTATGATAAA 14 152 1 ATAATTATTT 0.925577 -149 TTCCGCACATTATTAAGTTTTTTTTGTTTTTATTACTTA 14 192 1 TTAATTTTTT 0.925482 -109 TTTCAATCTCTCAAAACATTAAGGAGTTT 14 282 1 TAAATTATTT 0.896879 -19 TACTCTGTTTAATAAAGGATTAATTATTTTTAAA 15 6 0 ATAAATTTTT 0.747822 -129 AAAATAGTCGTTTTAACAAACAAAATTTTGTTAATAGAT 15 75 1 TTAAAAATTT 0.806136 -60 AATTAATTTTTTTTAATAAAGGGGTTTTT 16 121 1 TTAAAATTTT 0.597167 -19 * * ** ** * *** Masking position 17 Map Score: 32.0947 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 590 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 ACTTTCTAATTTTAAGATAATCATTCTTAATTTGCTAT 1 19 1 TTTATAATTT 0.939826 -282 GATCGGTTATTTTTCTAAAAGTTTTAATTTTTTATCAA 3 48 1 TTTAAAATAT 0.853757 -178 GCCTCAAACTTTTAAAATACAAATTTTTAAGATACAAA 3 154 1 TTTATACTTT 0.808051 -72 CCATTAGAAATATTAAAAAATTTTTATTTTTCTTCCAA 5 62 1 TATAAAATTT 0.776471 -186 AATGACTTTTTTATCAAAAATACCGATTAATGCGAATG 5 113 0 TTAAAAAGTT 0.836627 -135 TAGCTTAAATTTTTGAAAAATTATTATTTAGATAATAT 5 152 0 TTTAAAATTT 0.98177 -96 CAATGTGAAATTTATAATAACCATTATTAGTTTTAGCT 5 185 0 TTTATAATTT 0.939826 -63 TTACCACCTTTTATGAAAAATGTTCTTTTTTACAACA 5 221 0 TTTAAAATTT 0.98177 -27 CGTTAAGCGCTTTTTAAAACAGAATGTTAGTTTTAGAA 6 19 0 TTTAAACTTT 0.93555 -175 ATCAAAACCATTTGAAAAAAGTTTTTTGCGTTTTTTAA 6 62 0 TTTAAAATTG 0.824158 -132 TTCAAACTAGTTTTAAAAAGTCATTATTATTGAAAATC 7 92 0 TTTAAAGTTT 0.844117 -41 ACCAAACTTATTTGGATAAAGGGGTTTTAAAATGCTAA 8 37 0 TTTTAAATTT 0.759748 -32 TGTTTCTCCTTAATTAAAATTGGTGTTAAAAATGTTT 9 10 1 TTAAAAATTT 0.89772 -208 TGGAATGTTTTTTACAAAAAACATTTTTAACACCAATT 9 28 0 TTTAAAATTT 0.98177 -190 TAAAGCACCATGTTTAAAAACAGCTCTTATTCACCCCA 10 155 0 TGTAAAATTT 0.904533 -58 ATAAAGTTTGCTAAAAAGATGATTCTAATTTCAA 11 7 1 TTTAAAAGTT 0.969157 -42 ATGATTCTAATTTCAAAAAAAGGTGTTTTT 11 29 1 TTTAAAAGTT 0.969157 -20 TGCCTAAAATTTAGAAAAAATCACGCTTGATCTTATCT 13 23 1 TTAAAAAGTT 0.836627 -94 AGGCTCGTTGTGTGTCAAAAATGGGGATTTTTCACTAG 14 69 1 TGTAAAAGAT 0.374704 -232 TGTGCGGAATTTTATCATAAAAATTCTTAAAATTTTAT 14 163 0 TTTATAATTT 0.939826 -138 TAATTAATCCTTTATTAAACAGAGTATTGTTTAACCTT 15 19 1 TTTAAACTTT 0.93555 -116 CAAAATTTTGTTTGTTAAAACGACTATTTTAACACAAT 15 67 0 TTTAAAATTT 0.98177 -68 GAATTAATTTTTTTTAATAAAGGGGTTTTT 16 120 1 TTTATAAGTT 0.901113 -20 *** **** * ** Masking position 1 Map Score: 30.8985 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 489 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 TAATTTTAAGATAATCATTCTTAATTTGCTATTAA 1 25 1 ATAATTTTAT 0.543076 -276 CGAGCATTATAACATTTTGCTTAAAAGATGTCAAT 1 80 0 AACATGTTAA 0.85819 -221 ATACTAGCAAGAAAACGGGTTTGATCCATAAAGAA 1 222 0 GAAAAGTTAT 0.462153 -79 TTTTAGAGTGAAAATGTTGGTTAAATACTAATAAG 3 95 1 AAAATGTTAA 0.949502 -131 TTGTATCTTAAAAATTTGTATTTTAAAAGTTTGAG 3 156 0 AAAATTTTTA 0.525553 -70 AAGGCTAGCCATAAAGGGTTTTTAAGCCCTTTATT 5 12 1 ATAAATTTAA 0.76553 -236 TGGAAGAAAAATAAAAATTTTTTAATATTTCTAAT 5 64 0 ATAAATTTAA 0.757681 -184 TTTTTTATCAAAAATACCGATTAATGCGAATGTTT 5 110 0 AAAATGTTAT 0.849691 -138 TATTATCTAAATAATAATTTTTCAAAAATTTAAGC 5 153 1 ATAATTTTAA 0.798127 -95 TTCTAAAACTAACATTCTGTTTTAAAAAGCGCTTA 6 19 1 AACATGTTAA 0.858168 -175 AAAAAACGCAAAAAACTTTTTTCAAATGGTTTTGA 6 64 1 AAAAATTTAA 0.886777 -130 GCAAATAAATAAAATCAAACTTCAAAATTTAAGTT 6 108 1 AAAATATTAA 0.621827 -86 GCATACTATAAAAATAATTATTAAAATTAACTTAA 6 136 0 AAAATTTTAA 0.904528 -58 ATTTTCAATAATAATGACTTTTTAAAACTAGTTTG 7 93 1 ATAATTTTAA 0.79804 -40 ACTTATTTGGATAAAGGGGTTTTAAAATGCTAAAG 8 35 0 ATAAAGTTAA 0.866211 -34 CTCCTTAATTAAAATTGGTGTTAAAAATGTTTTTT 9 16 1 AAAATTTTAA 0.904528 -202 TGATTGTTTAATCATTGTTGTTAATTTCAGCCAGT 10 26 1 ATCATTTTAT 0.276742 -187 GATTATAATAAAAAAACTGGCTGAAATTAACAACA 10 41 0 AAAAAGCTAA 0.498918 -172 GCTGTTTTTAAACATGGTGCTTTAAAGCGTCATTA 10 169 1 AACATGTTAA 0.85819 -44 GCTTTAAAGCGTCATTAATTTTTAAGGTATAGCGT 10 187 1 GTCATTTTAA 0.189589 -26 AAAGTTTGCTAAAAAGATGATTCTAATTTCAAAAA 11 13 1 AAAAAGTTTA 0.645042 -36 AAATTTAGAAAAAATCACGCTTGATCTTATCTAAA 13 29 1 AAAATGTTAT 0.849393 -88 AGAATACACTAAAATTTAGTTTTAATTTCAAGCGT 13 72 1 AAAATGTTAA 0.9495 -45 TTGTGTGTCAAAAATGGGGATTTTTCACTAGAGAT 14 76 1 AAAATGTTTT 0.39795 -225 AAAAAAAAAAAAAAAAGATTTTCATGGGATTAATA 14 131 1 AAAAATTTAT 0.70193 -170 GAATTTTATCATAAAAATTCTTAAAATTTTATTAA 14 160 0 ATAAATTTAA 0.765625 -141 TTGAGAGATTGAAAAATGGTTTAAATTTTTCAAGT 14 261 0 GAAAAGTTAA 0.740782 -40 CACAATGATAAAACAAAAGGTTAAACAATACTCTG 15 38 0 AAACAGTTAA 0.515986 -97 CATTGTGTTAAAATAGTCGTTTTAACAAACAAAAT 15 66 1 AAATAGTTAA 0.41836 -69 GAAGAATCAAAAAGAAAGGATTTAACCAAGAAAGA 16 39 0 AAAGAGTTAA 0.51598 -101 CCTTTATTAAAAAAAATTAATTCAAAAATGATAAA 16 108 0 AAAAAATTAA 0.576148 -32 ***** * ** ** Masking position 12 Map Score: 25.6966 Number of sites scoring better than the average of aligned sites = 1697 Number in coding regions = 1347 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 4 GCTCAAACTCCCTTGATGAAAAACAAT 1 284 0 ACCCCTTGAT 0.805008 -17 AGAACTCCCTTTGATTAAATGATT 3 212 0 ACCCCTTTGA 0.884659 -14 TGCTCGCCTTTTTTATGCGTT 4 8 0 TCCCTTTTTT 0.661556 -14 AAGGGCTTAAAAACCCTTTATGGCTAGCCTT 5 12 0 AACCCTTTAT 0.932821 -236 AAGGGTTTTTAAGCCCTTTATTTGTTTAAAA 5 25 1 AACCCTTTAT 0.932821 -223 TTTGTTATCAAAACCATTTGAAAAAAGTTTT 6 75 0 AACCATTTGA 0.626859 -119 ACTCCAAACTCCCTTCAAACTAGTTTTA 7 115 0 ACCCCTTCAA 0.554254 -18 AGCATTTTAAAACCCCTTTATCCAAATAAGT 8 39 1 AACCCTTTAT 0.932821 -30 AACATTTTTAACACCAATTTTAATTAAGGAG 9 16 0 ACCCAATTTT 0.765205 -202 TTCTTTTTTCTCGCCCATTATCTAACGCCAA 9 137 0 TCCCCATTAT 0.806469 -81 GTCCTCTCCATTTAATGATTGTTTA 10 5 1 TCCCATTTAA 0.695086 -208 GCTCTTATTCACCCCAATTGTTAGAAGTTTG 10 140 0 ACCCAATTGT 0.807538 -73 AAAAACACCTTTTTTTGAAATTAGA 11 34 0 ACCCTTTTTT 0.830498 -15 TAGTGAAAAATCCCCATTTTTGACACACAAC 14 75 0 TCCCATTTTT 0.811919 -226 CCAATAACGAACGCCAATTATTAAGTAATAA 14 221 0 ACCCAATTAT 0.851059 -80 TGAAAAATTTAAACCATTTTTCAATCTCTCA 14 264 1 AACCATTTTT 0.812468 -37 GAGTATTGTTTAACCTTTTGTTTTATCATTG 15 40 1 TACCTTTTGT 0.501892 -95 AAAAACCCCTTTATTAAAAAAAAT 16 126 0 AACCCTTTAT 0.932821 -14 ** ******** Masking position 8 Map Score: 13.7285 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 846 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 GTCAGGGGTTCGAACCCCCTACACTCCACC 1 173 1 CGAACCCCCT 0.987529 -128 GCTCAAACTCCCTTGATGAAAAA 1 288 0 CAAACTCCCT 0.984314 -13 ACCCACAAAACAAACCGCCTCAAACTTTTA 3 138 1 CAAACCGCCT 0.921497 -88 AGAACTCCCTTTGATTAAAT 3 216 0 AGAACTCCCT 0.969045 -10 ACTCCAAACTCCCTTCAAACTAGT 7 119 0 CAAACTCCCT 0.984314 -14 TTAGCATTTTAAAACCCCTTTATCCAAATA 8 37 1 AAAACCCCTT 0.801236 -32 TTATCTAACGCCAACTCTCTTATTATTTTT 9 121 0 CCAACTCTCT 0.818776 -97 TAACCAAGAAAGAACTCTCTTGGTTAAAAG 16 22 0 AGAACTCTCT 0.860399 -118 AAAAACCCCTTTATTAAAAA 16 130 0 AAAAACCCCT 0.801236 -10 ********** Masking position 4 Map Score: 8.23371 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 275 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 TTGAAACGCTTAATAGCAAATTAAGAATGATTATCT 1 33 0 TAAAAATAAA 0.431094 -268 ACACCCCAAATAAAATTAAGCGAGCATTATAACATT 1 99 0 TAAAAGCAGA 0.843141 -202 GGTTTGATCCATAAAGAAAGAGAATAAGCGTAATAA 1 204 0 ATAAAGAAAA 0.694808 -97 AAATACAAATTTTTAAGATACAAATAGGTATAATCA 3 168 1 TTTAAACAAA 0.22278 -58 AACGCATAAAAAAGGCGAGCA 4 6 1 ATAAAGCAGA 0.515393 -16 TTCAAAAATTTAAGCTAAAACTAATAATGGTTATTA 5 173 1 TAACAACAAA 0.691912 -75 TAACGGCTGTTTAAAAAACGCAAAAAACTTTTTTCA 6 52 1 TTAAAGCAAA 0.921171 -142 ATGGTTTTGATAACAAATTGCAAATAAATAAAATCA 6 89 1 TAAATGCAAA 0.839343 -105 TGTTTTTTGTAAAAAACATTCCAAGAACTATATATT 9 43 1 AAAAATCAAA 0.668975 -175 ATGGGCGAGAAAAAAGAAAGCCAAAAGGTGGCGGTT 9 150 1 AAAAAGCAAA 0.945652 -68 ATAAAGTTTGCTAAAAAGATGATTCT 11 1 1 ATAATGCAAA 0.508287 -48 CTTAAATGCCTAAAATTTAGAAAAAATCACGCTTGA 13 17 1 TAAATGAAAA 0.6522 -100 TAAAATTTGCTAAGAATACACTAAAATTTAGTTTTA 13 60 1 TAAAAACAAA 0.930527 -57 CAGCAAAATCAAAAAAAAAAAAAAAAGATTTTCATG 14 121 1 AAAAAAAAAA 0.722949 -180 AATTATTAAGTAATAAAAACAAAAAAAACTTAATAA 14 201 0 TAAAACAAAA 0.529024 -100 ATTTTTCAAGTAAAATCACACCAATAACGAACGCCA 14 236 0 TAAAAACAAA 0.930527 -65 ACGACTATTTTAACACAATGATAAAACAAAAGGTTA 15 50 0 TAAAAGAAAA 0.92004 -85 ACGAAAACTTTAAAACTAAGCGAAGAATCAAAAAGA 16 59 0 TAAAAGCAAA 0.969749 -81 GATAAAAAGATAAAACGATACGAAAACTTTAAAACT 16 78 0 TAAAAACAAA 0.930527 -62 AAATTAATTCAAAAATGATAAAAAGATAAAACGATA 16 94 0 AAAAAAAAAA 0.722949 -46 ATACTAAATAAAACCATAGGATAAAAGC 17 3 0 AAACAGAAAA 0.511527 -72 ATTTAGTATGTTACAATAATCAAACATTCTAACATA 17 30 1 TTAAATCAAA 0.575774 -45 TCAAACATTCTAACATAAGGAGAATAACAATCAATT 17 49 1 TAAAAGAAAA 0.92004 -26 *** * * ** ** * Masking position 13 Map Score: 15.0853 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 761 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 TAAAAGAAACTTTCTAATTTTAAGATAAT 1 10 1 CTTTCTAATT 0.717601 -291 CGCTTATTCTCTTTCTTTATGGATCAAACC 1 210 1 CTTTCTTTAT 0.838496 -91 AATAAATCCTTCTTGTTGAATTAAAGT 3 8 1 CCTTCTTGTT 0.842462 -218 TTTTTAAGCCCTTTATTTGTTTAAAATTCA 5 30 1 CTTTATTTGT 0.643133 -218 TGTGATAACCTTTCTCATTTAATTCAAAC 6 175 0 CTTTCTCATT 0.790189 -19 CTAACGCCAACTCTCTTATTATTTTTAAAA 9 117 0 CTCTCTTATT 0.873914 -101 CACCTTTTGGCTTTCTTTTTTCTCGCCCAT 9 150 0 CTTTCTTTTT 0.966634 -68 CCATGAAAATCTTTTTTTTTTTTTTTTGAT 14 128 0 CTTTTTTTTT 0.716803 -173 CAAGAAAGAACTCTCTTGGTTAAAAGAATT 16 18 0 CTCTCTTGGT 0.885843 -122 CAAGAGAGTTCTTTCTTGGTTAAATCCTTT 16 30 1 CTTTCTTGGT 0.952871 -110 TGGTTAAATCCTTTCTTTTTGATTCTTCGC 16 46 1 CTTTCTTTTT 0.966634 -94 ********** Masking position 6 Map Score: 5.26117 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 306 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 CTTTCTAATTTTAAGATAATCATTCTTAATTT 1 20 1 TTAGATAACA 0.71951 -281 TATTAAGCGTTTCAAAAAAGCATCAAATTGAC 1 54 1 TTCAAAAACA 0.704766 -247 CAAACTCCCTTGATGAAAAACAATTCCTGAGA 1 276 0 TGAGAAAACA 0.464522 -25 ATTAAAACTTTTAGAAAAATAACCGATCTTAG 3 44 0 TTAAAAAAAA 0.790341 -182 CCTCAAACTTTTAAAATACAAATTTTTAAGAT 3 155 1 TTAAATACAA 0.571575 -71 AATGACTTTTTTATCAAAAATACCGATTAATG 5 119 0 TTACAAAATA 0.461754 -129 AATGTGAAATTTATAATAACCATTATTAGTTT 5 190 0 TTAAATAACA 0.890323 -58 TAACGGCTGTTTAAAAAACGCAAAAAACTTTT 6 52 1 TTAAAAACCA 0.939185 -142 TTGCAATTTGTTATCAAAACCATTTGAAAAAA 6 80 0 TTACAAAACA 0.933745 -114 GATTTTCCTTTCATCAAACTCATCTCAACCAA 7 11 1 TCACAAACCA 0.818886 -122 GGAATGTTTTTTACAAAAAACATTTTTAACAC 9 33 0 TTAAAAAACA 0.949555 -185 AAATTTTGGATTATAATAAAAAAACTGGCTGA 10 52 0 TTAAATAAAA 0.619204 -161 TGTTAGAAGTTTGGAAAACCCAAGCCCTTATT 10 121 0 TTGAAAACCA 0.782809 -92 GCCTAAAATTTAGAAAAAATCACGCTTGATCT 13 24 1 TAGAAAAACA 0.301862 -93 ATATGCGTTCTCAAAACACACAAGACACTCTT 14 37 0 TCAAACACCA 0.487831 -264 TTGAGTAAAATCAGCAAAATCAAAAAAAAAAA 14 110 1 TCACAAAACA 0.846414 -191 AATAGTCGTTTTAACAAACAAAATTTTGTTAA 15 77 1 TTACAAACAA 0.698401 -58 ATTTAGTATGTTACAATAATCAAACATTCTAA 17 30 1 TTAAATAACA 0.890344 -45 *** ***** ** Masking position 1 Map Score: 4.73104 Number of sites scoring better than the average of aligned sites = 789 Number in coding regions = 689 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 TTAATTTTATTTGGGGTGTTAGCTCAGCTG 1 116 1 TTGGGGTGTT 0.960046 -185 CGTAATAATGGTGGAGTGTAGGGGGTTCGA 1 182 0 GTGGAGTGTA 0.891646 -119 ATAACCGATCTTAGGGTGTAACTTTAATTC 3 28 0 TTAGGGTGTA 0.926652 -198 GATGAAGATTTTAGAGTGAAAATGTTGGTT 3 87 1 TTAGAGTGAA 0.85949 -139 AATATTTCTAATGGGGTGAATTTTAAACAA 5 46 0 ATGGGGTGAA 0.91979 -202 TGGGATTGGGTTGGAGTGTGCGTTA 9 203 1 TTGGAGTGTG 0.907225 -15 CTTCTAACAATTGGGGTGAATAAGAGCTGT 10 144 1 TTGGGGTGAA 0.982218 -69 GCGTTCGTTATTGGTGTGATTTTACTTGAA 14 238 1 TTGGTGTGAT 0.821572 -63 ********** Masking position 7 Map Score: 3.9992 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 117 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 CAATTCCTGAGATTATAATTAATTATGGGTA 1 257 0 GATTATATTA 0.888092 -44 TGGAATTGGTGATTATACCTATTTGTATCTT 3 182 0 GATTATACTA 0.914162 -44 TTTGAAGTTTGATTTTATTTATTTGCAATTT 6 103 0 GATTTTATTA 0.969682 -91 AAAATAAGGCGATTTTGACTAGAATAGCGCT 7 53 0 GATTTTGCTA 0.899511 -80 TTTTAACACCAATTTTAATTAAGGAGAAACA 9 11 0 AATTTTATTA 0.71592 -207 GATCAAGCGTGATTTTTTCTAAATTTTAGGC 13 24 0 GATTTTTCTA 0.857945 -93 AATCACGCTTGATCTTATCTAAAATTTGCTA 13 41 1 GATCTTACTA 0.889905 -76 TGATTTTGCTGATTTTACTCAATCTCTAGTG 14 101 0 GATTTTATCA 0.857616 -200 TTATTGGTGTGATTTTACTTGAAAAATTTAA 14 245 1 GATTTTATTG 0.857616 -56 TTTGTTAATAGATTTTACCTAATCTGAGAGA 15 101 1 GATTTTACTA 0.977232 -34 TTTATCCTATGGTTTTATTTAGTATGTTACA 17 14 1 GGTTTTATTA 0.857616 -61 ******* *** Masking position 6 Map Score: 5.91704 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 118 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 TAATTTTAAGATAATCATTCTTAATTTGCTA 1 25 1 ATATCATTCT 0.739719 -276 AAGCGAGCATTATAACATTTTGCTTAAAAGA 1 87 0 TAAACATTTT 0.724962 -214 GATCTAAATTATAAATATTTTATTGCGTTTA 2 60 0 ATAATATTTT 0.66471 -57 TTTATCAAAGATGAAGATTTTAGAGTGAAAA 3 78 1 ATAAGATTTT 0.75573 -148 TTAGTATTTAACCAACATTTTCACTCTAAAA 3 95 0 ACAACATTTT 0.89051 -131 TGGAAGAAAAATAAAAATTTTTTAATATTTC 5 68 0 ATAAAATTTT 0.84438 -180 TATTATCTAAATAATAATTTTTCAAAAATTT 5 153 1 ATATAATTTT 0.659428 -95 TGTTGTAAAAAAGAACATTTTTCATAAAAGG 5 221 1 AAAACATTTT 0.927295 -27 GCATTCTAAAACTAACATTCTGTTTTAAAAA 6 16 1 ACAACATTCT 0.828003 -178 AAAAAACGCAAAAAACTTTTTTCAAATGGTT 6 64 1 AAAACTTTTT 0.418233 -130 GTTAATTTTAATAATTATTTTTATAGTATGC 6 140 1 ATATTATTTT 0.409804 -54 GTTTTTTACAAAAAACATTTTTAACACCAAT 9 29 0 AAAACATTTT 0.863338 -189 AAAAAAAAAAAAAAAGATTTTCATGGGATTA 14 132 1 AAAAGATTTT 0.611109 -169 TCATGGGATTAATAAAATTTTAAGAATTTTT 14 152 1 AAAAAATTTT 0.844631 -149 GAATTTTATCATAAAAATTCTTAAAATTTTA 14 164 0 ATAAAATTCT 0.763818 -137 CGTTTTAACAAACAAAATTTTGTTAATAGAT 15 83 1 AAAAAATTTT 0.844631 -52 TAAAATATAATTCTCTCTCAGATT 15 121 0 AAATAATTCT 0.545267 -14 GTTTTATCTTTTTATCATTTTTGAATTAATT 16 98 1 TTATCATTTT 0.494477 -42 GTTACAATAATCAAACATTCTAACATAAGGA 17 39 1 TCAACATTCT 0.494179 -36 ** ******** Masking position 8 Map Score: 12.2006 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 401 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 12 ATAGAGATCTAAATTATAAATATTTTATTG 2 66 0 AAATTATAAA 0.540113 -51 AAACCGCCTCAAACTTTTAAAATACAAATT 3 149 1 AAACTTTTAA 0.513502 -77 TTTAAAATACAAATTTTTAAGATACAAATA 3 164 1 AAATTTTTAA 0.797232 -62 CTAATGGGGTGAATTTTAAACAAATAAAGG 5 39 0 GAATTTTAAA 0.84173 -209 ACCCCATTAGAAATATTAAAAAATTTTTAT 5 59 1 AAATATTAAA 0.771806 -189 GTTTTAGCTTAAATTTTTGAAAAATTATTA 5 164 0 AAATTTTTGA 0.778316 -84 AAATTAACTTAAATTTTGAAGTTTGATTTT 6 118 0 AAATTTTGAA 0.809318 -76 AATATTGAGTGAATATTAGAGGAATTTTAA 9 93 1 GAATATTAGA 0.523469 -125 AATATTAGAGGAATTTTAAAAATAATAAGA 9 104 1 GAATTTTAAA 0.84173 -114 CTATTCAAAGAAATTTTGGATTATAATAAA 10 64 0 AAATTTTGGA 0.791235 -149 AGATAAATTAAAATATTAAAATTAG 12 17 1 AAATATTAAA 0.771806 -15 TTAAATGCCTAAAATTTAGAAAAAATCACG 13 18 1 AAAATTTAGA 0.693828 -99 TATTCTTAGCAAATTTTAGATAAGATCAAG 13 48 0 AAATTTTAGA 0.928862 -69 AATTAAAACTAAATTTTAGTGTATTCTTAG 13 69 0 AAATTTTAGT 0.527688 -48 GGGATTAATAAAATTTTAAGAATTTTTATG 14 156 1 AAATTTTAAG 0.64966 -145 TTTTACTTGAAAAATTTAAACCATTTTTCA 14 257 1 AAAATTTAAA 0.717335 -44 AACGATACGAAAACTTTAAAACTAAGCGAA 16 71 0 AAACTTTAAA 0.796973 -69 ********** Masking position 7 Map Score: 12.0157 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 609 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 13 ********** No masking Map Score: 3.05066e-12 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 14 ********** No masking Map Score: 3.05066e-12 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 15 ********** No masking Map Score: 3.05066e-12 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