AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_hpyl_reg_300.orf -o02020_hpyl_300.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 HP0012 286 DNA primase (dnaG) #2 HP0014 88 H. pylori predicted coding region HP0014 #3 HP0015 146 H. pylori predicted coding region HP0015 #4 HP0018 251 H. pylori predicted coding region HP0018 #5 HP0019 107 chemotaxis protein (cheV) #6 HP0165 25 H. pylori predicted coding region HP0165 #7 HP0166 235 response regulator (ompR) #8 HP0168 46 H. pylori predicted coding region HP0168 #9 HP0170 74 H. pylori predicted coding region HP0170 #10 HP0171 60 peptide chain release factor RF-2 (prfB) #11 HP0174 300 H. pylori predicted coding region HP0174 #12 HP0246 188 flagellar basal-body P-ring protein (flgI) #13 HP0616 77 chemotaxis protein (cheV) #14 HP0695 300 hydantoin utilization protein A (hyuA) #15 HP0698 187 H. pylori predicted coding region HP0698 #16 HP0699 39 H. pylori predicted coding region HP0699 #17 HP1365 83 response regulator #18 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 TATTATTAGCTTTGTTTTTATGGCTTGACTT 1 98 0 TTTGTTTTAT 0.677775 -189 AACCTTATTTTAAGATTTTATTTATTGAGTA 1 213 1 TAAGTTTTAT 0.879148 -74 TTTTAGGGGTTTTCTTTTTATGCTATAATGG 2 28 1 TTTCTTTTAT 0.573577 -61 TAAGGCTTTTACACTCTTTGG 3 1 1 TAAGCTTTTA 0.907476 -146 CTTTGCTTTTTTACCCTTTTAAAGATAAAAA 3 32 1 TTACCTTTTA 0.760536 -115 AGAGGATTTTTATGGTTTTTTTGAGATAATA 3 85 1 TATGTTTTTT 0.852546 -62 ATTAACTTTATAAGTCTTTATTATCTCAAAA 3 103 0 TAAGCTTTAT 0.856151 -44 AAAACAAAACTAACTTTTTAAAA 4 3 0 TAACTTTTAA 0.846336 -249 AAAATAGTATTAACTTTTTAAAACAAAACTA 4 22 0 TAACTTTTAA 0.846336 -230 AATGAAAACATAAGCTTTTTATGGCTAAAAT 4 172 0 TAAGTTTTTA 0.923007 -80 GAGCGTATCATAACATTTTTAATGAAAACAT 4 192 0 TAACTTTTTA 0.884599 -60 TCTAACCCTTTTAATTGATATTT 4 239 0 TAACCTTTTA 0.862486 -13 CAAAGGAATTTTAGTTTTTAAGTGTCGTTGG 5 26 1 TTAGTTTTAA 0.813479 -82 TAGGTTTTCGTATCGTTTTATAATTATATCG 5 72 0 TATCTTTTAT 0.7265 -36 CTTATTTTTTAATGTTTTTAAACAATTCCTT 7 21 0 AATGTTTTAA 0.658373 -215 CATTAAAAAATAAGACTTTATTTTTCAATAT 7 38 1 TAAGCTTTAT 0.856149 -198 TAACAAAGTTAATCGTTTTTAAAGTTGCAGA 7 190 1 AATCTTTTTA 0.631723 -46 GGTTACTATAAAACGCTTTTTAAAACCAATT 9 40 1 AAACCTTTTT 0.674896 -35 AATGGCTTTTAACAATGCTAT 10 1 1 AATGCTTTTA 0.686971 -60 AATAATATTTATTGTCTTTTTTGGTGTTAGT 11 48 1 ATTGCTTTTT 0.484174 -253 GAATCTTCTTTAACATTTTTTTTCTTTCCAA 11 89 0 TAACTTTTTT 0.86622 -212 ATTCTTTATATTTGGTTTTTTAGCATTGCAT 11 201 1 TTTGTTTTTT 0.745401 -100 TAGCCTTTTATTAGCTTTTTATAAAGTTTCA 12 36 0 TTAGTTTTTA 0.858568 -153 GATTTTAATTTTAGCCTTTTATTAGCTTTTT 12 47 0 TTAGCTTTTA 0.832399 -142 ACTTTAAATCAAAGATTTTAATTTTAGCCTT 12 60 0 AAAGTTTTAA 0.771429 -129 TTAAAGTTTATAAGATTTTTGAGTATAGCAT 12 84 1 TAAGTTTTTG 0.546565 -105 TATTTTAGCATAAGCCTTTTATAAAAACTTT 12 137 0 TAAGCTTTTA 0.907476 -52 ATTTAGTTTAAAAGGTTTTTACAAAC 13 6 0 AAAGTTTTTA 0.824493 -72 TGTTACTACTTTTCACTTTATTACGCCAAAT 14 175 1 TTTCCTTTAT 0.523916 -126 GATTGCTCAATCCTTTTTATGAAAGAGGC 15 9 1 AATCTTTTTA 0.631723 -179 TTAAAAAATTTAAGCTTTTTTCTTTTTTTTT 15 120 1 TAAGTTTTTT 0.910118 -68 TGTAGCGCTAATTGCCTTTATACTAAAAGCG 17 55 0 ATTGCTTTAT 0.402756 -29 TAATACTTCCTATGTTTTTTAAGGAGCGTTA 18 65 0 TATGTTTTTA 0.872534 -236 CCATGCAAAAAAAGATTTTTTTATTAGAAGA 18 130 1 AAAGTTTTTT 0.798706 -171 TAGAAGACGATTACCTTTTAAGCGAGAGCGT 18 154 1 TTACTTTTAA 0.736076 -147 TCTTATTTTTACCTTTTATTAAACTTCAA 18 282 0 TTACTTTTAT 0.701997 -19 **** ****** Masking position 7 Map Score: 37.432 Number of sites scoring better than the average of aligned sites = 1747 Number in coding regions = 1432 Number in noncoding regions = 315 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 2 AATAACAATAAGCGCTAAATTTCTATTTTAT 1 35 0 AGCGCTAATT 0.886307 -252 TCCCTAAAAATGCGCTATAGTTATGTCGCTT 1 66 0 TGCGCTAAGT 0.853983 -221 GTTTTCTTTTTATGCTATAATGGAAAAAGCT 2 36 1 TATGCTAAAT 0.956311 -53 CCTGAAGCGTTACCCTAAAATCCTATTGCAT 4 116 1 TACCCTAAAT 0.76745 -136 AATGTTATGATACGCTCAAATAGTCAAGCAA 4 206 1 TACGCTCAAT 0.912883 -46 TTAATAATAAAATGCTAGAATTAGTCCCCTA 7 153 1 AATGCTAAAT 0.96082 -83 GTGCGCTAAAATGACAGCCGAT 9 2 1 TGCGCTAAAT 0.975665 -73 GGCTTTTAACAATGCTATAATGATAAGTTCA 10 14 1 AATGCTAAAT 0.96082 -47 GATAACATGCAATGCTAAAAAACCAAATATA 11 207 0 AATGCTAAAA 0.663262 -94 AAGCTAATAAAAGGCTAAAATTAAAATCTTT 12 50 1 AAGGCTAAAT 0.866906 -139 AGCGTATTTTTATGCTATACTCAAAAATCTT 12 95 0 TATGCTAACT 0.76151 -94 AGCATAAAAATACGCTCAATTAGGTTTAAAG 12 110 1 TACGCTCATT 0.645218 -79 ATAAAAGGCTTATGCTAAAATAATTAGAATT 12 146 1 TATGCTAAAT 0.956311 -43 TCAAAGATTAAATGCTATAATACTACCCTAA 13 36 0 AATGCTAAAT 0.96082 -42 AAAGGCAATTAGCGCTACAATACCCCC 17 67 1 AGCGCTAAAT 0.978222 -17 TTTTTTAAGGAGCGTTATAATGAAAACGAAC 18 51 0 AGCGTTAAAT 0.690171 -250 CCGCTCATTAAGCGCTACAATACCCCCATGC 18 105 1 AGCGCTAAAT 0.978222 -196 ******* *** Masking position 6 Map Score: 20.2744 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 365 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 AAGGGAGTTTTTGAGGGTTTTA 2 3 1 GGGAGTTTTT 0.889055 -86 TGAGGGTTTTAGGGGTTTTCTTTTTATGCT 2 22 1 AGGGGTTTTC 0.951343 -67 GGTCAAAAGGGGTGGTTTTTATCTTTAAAA 3 48 0 GGTGGTTTTT 0.889055 -99 AATTAAACAGAAGGGTTTTG 3 137 1 AAGGGTTTTG 0.898842 -10 TTCCTTTGGTGGGGGTTTTGAAA 5 4 0 GGGGGTTTTG 0.995821 -104 CCTTTATGAGTGGGGTTTTGAACTTATCAT 10 33 0 TGGGGTTTTG 0.968664 -28 CAATAAAATAAGGGGTTTTTT 16 29 1 AGGGGTTTTT 0.977479 -11 GGGGGTATTGTAGCGCTAAT 17 74 0 GGGGGTATTG 0.989575 -10 TTTTTTGCATGGGGGTATTGTAGCGCTTAA 18 112 0 GGGGGTATTG 0.989575 -189 ACAATGAAATGGGGGTATTTTAAAAAAATG 18 229 0 GGGGGTATTT 0.975909 -72 TTAAACTTCAATGGGTTTTGCATGAAAGAA 18 263 0 ATGGGTTTTG 0.898842 -38 ********** Masking position 6 Map Score: 18.2114 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 387 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 GCTTGACTTATCCCTAAAAATGCGCTATAGT 1 76 0 TCCCTAAAAT 0.804486 -211 AAAAAGAAAACCCCTAAAACCCTCAAAAACT 2 16 0 CCCCTAAACC 0.979994 -73 ACAGCAGAGTCCCCTAATTTCTTGTGTGCCT 4 77 0 CCCCTAATTC 0.943871 -175 CTGAAGCGTTACCCTAAAATCCTATTGCATA 4 117 1 ACCCTAAATC 0.853995 -135 GCTAAAATGATCCCTAAGCTCTTATTTAGAC 4 149 0 TCCCTAAGTC 0.841413 -103 GACTTCCCCTTAATTTAGGTTTTCGT 5 92 0 CCCCTTAATT 0.927684 -16 AACCCCTTAACTCCTTATTAGAA 6 13 0 CCCCTTAATC 0.975474 -13 TAGAATTAGTCCCCTAAAACATTAACAAAGT 7 168 1 CCCCTAAACA 0.89438 -68 AGTCCCTTAATCTTACATAGTAA 11 288 0 TCCCTTAACT 0.865826 -13 CCTTTCTTATTCCCTAAATTCTAATTATTTT 12 162 0 TCCCTAAATC 0.965723 -27 CTATTTTCCCCTAAAGCCCTATCAAAGA 13 60 0 CCCCTAAACC 0.979994 -18 CGCCAAATTTTCCCTTATTACAAACAACTTT 14 198 1 TCCCTTATAC 0.756688 -103 AAAAAACCCCTTATTTTATTGAAAGTA 16 23 0 CCCCTTATTT 0.804629 -17 AAAAAAACACTCCCTTAAAAAAGACACCGCT 17 19 0 TCCCTTAAAA 0.626109 -65 ******** ** Masking position 7 Map Score: 15.8802 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 571 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 AGTCAAGCCATAAAAACAAAGCTAATAATA 1 99 1 TAAAAACAAA 0.755792 -188 TTCAAGCGAGTTAAAACAAGAAAGCAAGAT 1 251 1 TTAAAACAAG 0.930475 -36 TAAGTCTTTATTATCTCAAAAAAACCATAA 3 94 0 TTATCTCAAA 0.779884 -53 TATTAACTTTTTAAAACAAAACTAACTTTT 4 16 0 TTAAAACAAA 0.966756 -236 CAATATTCCATGAAAACAAAGCCTTAAATT 7 63 1 TGAAAACAAA 0.821012 -173 AAAACGCTTTTTAAAACCAATTGGCAAGGA 9 49 1 TTAAAACCAA 0.809245 -26 CTTATAAACTTTAAATCAAAGATTTTAATT 12 68 0 TTAAATCAAA 0.956674 -121 TAAACTGATATTAAATCAAAAGGCGAAATT 14 66 0 TTAAATCAAA 0.956674 -235 AAATTTTCCCTTATTACAAACAACTTTGAA 14 202 1 TTATTACAAA 0.812114 -99 TGGAAATCATTTATTTCAAAGTTGTTTGTA 14 216 0 TTATTTCAAA 0.766466 -85 GAGCAACACTTTAATACAAGGAGTCTAA 14 283 1 TTAATACAAG 0.826335 -18 TTGGGTTGATTTAACTCAAGCAAATTTTCT 15 64 1 TTAACTCAAG 0.79593 -124 ATACCTAGTATTAAATCAAAAAAAAAGAAA 15 138 0 TTAAATCAAA 0.956674 -50 ATAGGAAGTATTATAACAAAGCCCGCTCAT 18 83 1 TTATAACAAA 0.923997 -218 ********** Masking position 3 Map Score: 12.7718 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 214 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 TGTCGCTTAATAACAATAAGCGCTAAATTTC 1 43 0 TAACAATAGC 0.730613 -244 GACTTATCCCTAAAAATGCGCTATAGTTATG 1 72 0 TAAAAATGGC 0.705776 -215 AAAACAAAGCTAATAATATAACTATAAGGAT 1 111 1 TAATAATAAA 0.655456 -176 TTCATTAGTTTAAAAATACAAGGATTAGAGA 1 165 1 TAAAAATAAA 0.871178 -122 TAAAGTTAATTAAAATTAAACAGAAGGGTTT 3 124 1 TAAAATTAAC 0.742388 -23 TAAAAACATTAAAAAATAAGACTTTATTTTT 7 32 1 AAAAAATAGA 0.625907 -204 GAAAATATCTTAAAAATAAAAATTCAAAACA 7 113 0 TAAAAATAAA 0.871178 -123 GTATCTTTAATAATAAAATGCTAGAATTAGT 7 147 1 TAATAAAAGC 0.802536 -89 CATGCAATGCTAAAAAACCAAATATAAAGAA 11 202 0 TAAAAAACAA 0.485163 -99 TATAAAAAGCTAATAAAAGGCTAAAATTAAA 12 44 1 TAATAAAAGC 0.802536 -145 AATAAAAGGCTAAAATTAAAATCTTTGATTT 12 55 1 TAAAATTAAA 0.6412 -134 GAGTATAGCATAAAAATACGCTCAATTAGGT 12 104 1 TAAAAATAGC 0.955329 -85 GATTTCCATTTAAAAATCAGCCTTATACTTC 14 238 1 TAAAAATCGC 0.815312 -63 GTATTAAATCAAAAAAAAAGAAAAAAGCTTA 15 130 0 AAAAAAAAGA 0.530399 -58 TAGGTGGAATTAAAATTATACCTAGTATTAA 15 154 0 TAAAATTAAC 0.742388 -34 TAAAATAAAGCGGTGTCTTTT 17 1 1 TAAAATAAGC 0.792317 -83 AAAGCGGTTATAAAAAAACACTCCCTTAAAA 17 30 0 TAAAAAAAAC 0.880409 -54 AATCGTCTTCTAATAAAAAAATCTTTTTTTG 18 135 0 TAATAAAAAA 0.562398 -166 GGGGGTATTTTAAAAAAATGAGTCAGTCAAG 18 218 0 TAAAAAAAGA 0.899524 -83 TAATAAAAGGTAAAAATAAGA 18 290 1 TAAAAATAGA 0.929883 -11 ******** ** Masking position 5 Map Score: 13.5676 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 585 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 TTTTTATGCTATAATGGAAAAAGCTCTAAT 2 42 1 ATAATGGAAA 0.84901 -47 CATAACATTTTTAATGAAAACATAAGCTTT 4 185 0 TTAATGAAAA 0.80025 -67 TTTTCATGGAATATTGAAAAATAAAGTCTT 7 49 0 ATATTGAAAA 0.922793 -187 ATCATAGTTATTAATGGAAATTTAAGGCTT 7 81 0 TTAATGGAAA 0.69133 -155 TAGAGATTAGGTATTGAAAATGATTAAGAG 8 21 1 GTATTGAAAA 0.736326 -26 TAACAATGCTATAATGATAAGTTCAAAACC 10 20 1 ATAATGATAA 0.839141 -41 TACGAATATTATATTCATAATTGCATCGAG 11 127 0 ATATTCATAA 0.760247 -174 TATGAATATAATATTCGTAATTATTGTTGT 11 138 1 ATATTCGTAA 0.639371 -163 AATCAATCTCATATTGATAAGCTTACTATG 11 266 1 ATATTGATAA 0.861062 -35 TTTTTATGCTATACTCAAAAATCTTATAAA 12 90 0 ATACTCAAAA 0.652959 -99 AGTAACAAATTTATTCAAAACGCTACCGAT 14 152 0 TTATTCAAAA 0.708905 -149 AAGGAGCGTTATAATGAAAACGAACGAAGC 18 46 0 ATAATGAAAA 0.909568 -255 ********** Masking position 3 Map Score: 5.10784 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 262 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 TTTAAACTAATGAAACTTGATACAAATAGACTTAAT 1 143 0 TAAACGTAAA 0.922256 -144 TTTTTATCTTTAAAAGGGTAAAAAAGCAAAGCCAAA 3 27 0 TAAAGTAAAG 0.70939 -120 AAAAATCCTCTAAAAGGGGGTCAAAAGGGGTGGTTT 3 60 0 TAAAGGTAAA 0.967895 -87 GGCATTAAACGCAAACACGATATAATTATAAAACGA 5 55 1 GAAACGTAAT 0.396498 -53 AAAGATACCTTGAAAATATCTTAAAAATAAAAATTC 7 119 0 TAAAATTAAA 0.506819 -117 ATTAGTCCCCTAAAACATTAACAAAGTTAATCGTTT 7 172 1 TAAACTAAAG 0.489926 -64 TTAATCGTTTTTAAAGTTGCAGAAATCATTGAAGGA 7 198 1 TAAAGGAAAT 0.59563 -38 ATGGTTACTATAAAACGCTTTTTAAAACCAATTGGC 9 38 1 TAAACTTAAA 0.869155 -37 ATTCAAAGCGGGTAAAAGTGTTCGCCTC 11 3 1 TAAAGGTAAG 0.939338 -298 AAAAAAAATGTTAAAGAAGATTCAAAAATTCTCGAT 11 97 1 TAAAGGTAAA 0.967895 -204 CAATTTAATTTGAAACTTTATAAAAAGCTAATAAAA 12 26 1 TAAACTTAAA 0.869158 -163 TCAATTAGGTTTAAAGTTTTTATAAAAGGCTTATGC 12 125 1 TAAAGTTAAA 0.944078 -64 TAATTTAGTTTAAAAGGTTTTTACAAAC 13 3 0 TAAAGTTCAA 0.787167 -75 GTAATAAAGTGAAAAGTAGTAACAAATTTATTCAAA 14 163 0 GAAAGGAAAA 0.73034 -138 ATCATTTATTTCAAAGTTGTTTGTAATAAGGGAAAA 14 205 0 TAAAGGTTAA 0.707728 -96 ATCCTTTTTATGAAAGAGGCTTTATGCCTCTTGGTG 15 20 1 TAAAGGTATG 0.525587 -168 GCCTTTATACTAAAAGCGGTTATAAAAAAACACTCC 17 37 0 TAAAGGTAAA 0.967895 -47 CTATGAAAAGGTTTTCTAAAACTTCATAAA 18 5 1 GAAAGTTAAA 0.84344 -296 GGGTTTTGCATGAAAGAATTTTACAATGAAATGGGG 18 245 0 TAAAGTTCAA 0.787167 -56 * **** * * *** Masking position 5 Map Score: 13.4744 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 892 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 9 CTTTGTTTTTATGGCTTGACTTATCCCTAAA 1 89 0 ATGGCTTGAT 0.863338 -198 AGTTATATTATTAGCTTTGTTTTTATGGCTT 1 103 0 TTAGCTTTGT 0.546359 -184 TTTACACTCTTTGGCTTTGCTTTTTTACCCT 3 18 1 TTGGCTTTGT 0.915149 -129 TTGATATTTTTTTGCTTGACTATTTGAGCGT 4 217 0 TTTGCTTGAT 0.89906 -35 AAAAACTAAAATTCCTTTGGTGGGGGTTTTG 5 14 0 ATTCCTTTGT 0.645456 -94 TATATCGTGTTTGCGTTTAATGCCAACGACA 5 48 0 TTGCGTTTAT 0.706407 -60 TTTTTAAACAATTCCTTTGATCGTTTT 7 7 0 ATTCCTTTGT 0.645456 -229 ATGCATTCTCTTTCCTTGGTTACCAGGGTTA 11 168 1 TTTCCTTGGT 0.913362 -133 TTCTAATAGGTTGCCTTGAGCAACACTTTAA 14 266 1 TTGCCTTGAC 0.796901 -35 TGCTAAAAGCTTGGGTTGATTTAACTCAAGC 15 54 1 TTGGGTTGAT 0.793859 -134 TTGAAGAAAATTTGCTTGAGTTAAATCAACC 15 67 0 TTTGCTTGAT 0.89906 -121 GTAGCGCTAATTGCCTTTATACTAAAAGCGG 17 54 0 TTGCCTTTAA 0.587456 -30 AAAATTTAGATTGCCTTGACTGACTCATTTT 18 204 1 TTGCCTTGAT 0.958082 -97 ********* * Masking position 6 Map Score: 4.86163 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 416 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GAGCGTATCATAACATTTTTAATGAAAACA 4 193 0 TAACATTTTT 0.896834 -59 CCCTTTTAATTGATATTTTTTTGCTTGACT 4 227 0 TGATATTTTT 0.926824 -25 TCTTATTTTTTAATGTTTTTAAACAATTCC 7 23 0 TAATGTTTTT 0.782028 -213 GATGTTGTAATAATATTTATTGTCTTTTTT 11 40 1 TAATATTTAT 0.829131 -261 GAATCTTCTTTAACATTTTTTTTCTTTCCA 11 90 0 TAACATTTTT 0.896834 -211 TTAAAGTTTATAAGATTTTTGAGTATAGCA 12 84 1 TAAGATTTTT 0.825302 -105 AATATCAGTTTAATATTTTTCTTCCTATAT 14 84 1 TAATATTTTT 0.938833 -217 TCTTCCTATATGATATTTATATGATATTTT 14 103 1 TGATATTTAT 0.8001 -198 GATATTTATATGATATTTTTGGGTAATTTA 14 114 1 TGATATTTTT 0.926824 -187 ********** Masking position 6 Map Score: 7.12042 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 71 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: 1.48036e-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 12 ********** No masking Map Score: 1.48036e-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 13 ********** No masking Map Score: 1.48036e-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