AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_hpyl_reg_100.orf -o00300_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 HP0180_HP0181 257 HP0180: apolipoprotein N-acyltransferase (cute), HP0181: H. pylori predicted coding region HP0181 #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0213 95 glucose inhibited division protein (gidA) #4 HP0282 50 H. pylori predicted coding region HP0282 #5 HP0289 66 toxin-like outer membrane protein #6 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #7 HP0506 203 conserved hypothetical secreted protein #8 HP0510 21 dihydrodipicolinate reductase (dapB) #9 HP0566 115 diaminopimelate epimerase (dapF) #10 HP0625 119 protein E (gcpE) #11 HP0820 173 H. pylori predicted coding region HP0820 #12 HP1010 300 polyphosphate kinase (ppk) #13 HP1011 36 dihydroorotate dehydrogenase (pyrD) #14 HP1190 61 histidyl-tRNA synthetase (hisS) #15 HP1228 150 invasion protein (invA) #16 HP1492 138 conserved hypothetical nifU-like protein Motif number 1 GGTAGTTTTTTTTAAGTTGTGTTATTATTTTCAAAT 1 150 0 TTTAGTTATT 0.836861 -108 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTGT 1 166 0 TTTAGTTTTT 0.981813 -92 TTTTAGTGTATTATAGCTATATTTTAATTTAAGAAT 1 206 0 TTAAGTTTTA 0.858181 -52 ATTTTGAGTTTTTAGGAGCAGTTTTT 2 1 0 TTTGGTTTTT 0.967446 -214 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGG 2 21 0 TTTAGTTTTG 0.844431 -194 TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGCG 2 48 0 TTAGGTTTTT 0.910668 -167 TTCTACTACATTTGAAATAATTTTTCTTATAAACAA 2 74 1 TTTAATTTTC 0.860613 -141 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAATT 2 92 0 TTTGGTTTAT 0.795354 -123 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATTTA 2 114 0 TTTAATTTTT 0.970902 -101 GGGCTATTGTTTAAAATTTACATTTTTTAAACGCTA 2 141 1 TTAAAATTTT 0.599499 -74 AAAATCTTAGTTTTGAAAAAGTTTTATTGTAGCATG 3 41 0 TTTGATTTTA 0.85719 -55 CTTTTTCCTATTTTGATATGATTTTTCTAAAATCTT 3 69 0 TTTGATTTTT 0.948369 -27 CGTTTAAGCCTTAATCTTGGATATAATG 4 3 1 TTTAGATCTT 0.50925 -48 CGTTCAAATTTTATGGTTAGGTTTTTCT 6 30 1 TTAGGTTTTT 0.910668 -18 ATTTGATAATTTTTGGTTCAGTTTAATGGGGATAAT 9 14 0 TTTGGTTTAA 0.559472 -102 TTTTTTATCCTTAAAAGAGCGTTTTTTAGCTAACAT 9 48 0 TTAAATTTTT 0.919651 -68 TAATTATAAGTTAAAAGAGGTTTTTTATCCTTAAAA 9 68 0 TTAAATTTTT 0.919597 -48 TTTTAAGGCTGATTTAAAAATTCTGGC 11 2 1 TTTAGTTTAA 0.696912 -172 TTTGAAGTTTTTTTAGCGGGTTTTTCATTGAATGGA 11 80 1 TTTAGTTTTC 0.909003 -94 AAACTGATCTTAACATGCTTTTTAGCGCTTGTA 11 151 0 TCTAATTTTT 0.703457 -23 CTAAAAAAATTTTAAGCGATCTTTTAGGGTTAAATG 12 16 1 TTTAGTTTTA 0.945547 -285 TTAGTTGTTGTTTAAAAACTCTTTTTTGTAAAACTT 12 71 0 TTTAATTTTT 0.970893 -230 TTTTAAAGATTTTAAGCTAAAATTTTAGCATACAAA 14 22 1 TTTAGATTTT 0.87593 -40 ACCCTCTCCGTTTTAATAGCGTTATTTGGGCGCTAT 15 11 1 TTTAATTATT 0.760228 -140 TTAAAATGAGTTTCAAGCCCTTTTTTCTTAATTTTT 15 46 1 TTTAATTTTT 0.970902 -105 TAATTTTTGATTTTAATGGCATTCTTAAAGCTAGTA 15 74 1 TTTAATTCTT 0.830634 -77 AAGACCACTATTAGAACAAGGTTTTTATGACGAT 16 9 0 TTAAATTTTT 0.919652 -130 AAAGTAAAATTTTAAAGAGAGTTTTAAAAA 16 119 1 TTTAATTTTA 0.91598 -20 *** ** ***** Masking position 13 Map Score: 34.5733 Number of sites scoring better than the average of aligned sites = 2732 Number in coding regions = 2172 Number in noncoding regions = 560 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 2 TGTTTTAGTGTATTATAGCTATATTTTAAT 1 214 0 TATTATAGCT 0.904572 -44 CCTTATTATATCTAATAGCGTTTAAAAAAT 2 162 0 TCTAATAGCG 0.944316 -53 ACGATCCTTATTTTATAGGTGGTAACTATC 2 192 0 TTTTATAGGT 0.718097 -23 TAATCTTGGATATAATGGCGTAATCATTTT 4 22 1 TATAATGGCG 0.927172 -29 TTCGTTCAAATTTTATGGTTAGGTTTTTCT 6 28 1 TTTTATGGTT 0.593691 -20 TTTTATCTCGTCTTATAGCGTTGGGTATTT 7 36 0 TCTTATAGCG 0.952937 -168 CTGGCCTTGTTTTTATAGCTTTATGAAGCG 7 101 0 TTTTATAGCT 0.952369 -103 ATCGTTTTTCTTTAATGGCTTATGTTATAC 7 144 1 TTTAATGGCT 0.912046 -60 TTTGGTTCAGTTTAATGGGGATAATTTC 9 9 0 TTTAATGGGG 0.773818 -107 TAAAAGAGCGTTTTTTAGCTAACATTTGAT 9 43 0 TTTTTTAGCT 0.866838 -73 CAAGAAAGAGTATAATAGCGCATAAGAATT 10 81 1 TATAATAGCG 0.953617 -39 TGTTTGAAGTTTTTTTAGCGGGTTTTTCAT 11 78 1 TTTTTTAGCG 0.944003 -96 TCTTAACATGCTTTTTAGCGCTTGTAGCAA 11 147 0 CTTTTTAGCG 0.605672 -27 CGCTTAAAATTTTTTTAGCGTTT 12 4 0 TTTTTTAGCG 0.944003 -297 CCCTCTCCGTTTTAATAGCGTTATTTGGGC 15 12 1 TTTAATAGCG 0.977461 -139 TGAAACTCATTTTAATAGCGCCCAAATAAC 15 31 0 TTTAATAGCG 0.977461 -120 AATTTTTGATTTTAATGGCATTCTTAAAGC 15 75 1 TTTAATGGCA 0.620447 -76 TATTATAGTGTATACTAGCTTTAAGAATGC 15 92 0 TATACTAGCT 0.485882 -59 ATTAAGATGGTATTATAGTGTATACTAGCT 15 102 0 TATTATAGTG 0.743392 -49 AGGTCTTTATTTTAGCTCTTTCTTGTT 15 134 0 TATTTTAGCT 0.755267 -17 AGAACAAGGTTTTTATGACGAT 16 3 0 TTTTATGACG 0.548515 -136 AAAACCTTGTTCTAATAGTGGTCTTATTCT 16 20 1 TCTAATAGTG 0.666822 -119 ********** Masking position 6 Map Score: 26.9141 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 1009 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 3 ATAGTCATAGCGTCTTAAAACAAACACCCA 1 79 1 CGTCTTAAAA 0.461899 -179 AAAAAAACTACCCTTAAAAAAATCAATCTA 1 174 1 CCCTTAAAAA 0.925827 -84 AAAAACTGCTCCTAAAAACTCAAAATTA 2 9 1 CTCCTAAAAA 0.714063 -206 AAGGGGCTATTGTTTAAAATTTACATTTTT 2 138 1 TGTTTAAAAT 0.86995 -77 TATCTAATAGCGTTTAAAAAATGTAAATTT 2 154 0 CGTTTAAAAA 0.923401 -61 TTTATTTTACCCTTTAAAATTACTAACCTC 3 11 1 CCTTTAAAAT 0.846746 -85 TGATATGATTTTTCTAAAATCTTAGTTTTG 3 62 0 TTTCTAAAAT 0.463739 -34 ACTTCCTAAAAAATGATTACGC 4 39 0 TTCCTAAAAA 0.661514 -12 TGATACGGATTGATTAAAAAGAAAATACCC 7 14 1 TGATTAAAAA 0.797549 -190 GCGCTTTCCTTGCTTTAAATC 8 2 0 TGCTTTAAAT 0.667306 -20 AGGTTTTTTATCCTTAAAAGAGCGTTTTTT 9 57 0 TCCTTAAAAG 0.570161 -59 TTTTAAGGCTGATTTAAAAATTCTGGCGT 11 10 1 TGATTTAAAA 0.444177 -164 ATGAAAAACCCGCTAAAAAAACTTCAAACA 11 78 0 CGCTAAAAAA 0.658376 -96 AAACGCTAAAAAAATTTTAAGCG 12 4 1 CGCTAAAAAA 0.658376 -297 CCTAAAAGATCGCTTAAAATTTTTTTAGCG 12 14 0 CGCTTAAAAT 0.926753 -287 GCTTAGTTGTTGTTTAAAAACTCTTTTTTG 12 79 0 TGTTTAAAAA 0.870134 -222 CGACCATGACTTTTTAAAAAAGCTTCAATG 12 212 1 TTTTTAAAAA 0.481161 -89 TAAATCATCATGTTTAAAAATCAGTTTGTT 12 270 0 TGTTTAAAAA 0.870134 -31 TAGAAATCCTTTAAATCATCATGTTT 12 285 0 TCCTTTAAAT 0.563087 -16 TAGCTTAAAATCTTTAAAAAAGGGCTATTG 14 11 0 TCTTTAAAAA 0.829642 -51 TATTTGGGCGCTATTAAAATGAGTTTCAAG 15 33 1 CTATTAAAAT 0.567631 -118 TTTAAGAATGCCATTAAAATCAAAAATTAA 15 73 0 CCATTAAAAT 0.678203 -78 CCTTGAGCCACTCTTAAAAAGCGTTGTTTG 16 61 1 CTCTTAAAAA 0.880166 -78 TTTAAAACTCTCTTTAAAATTTTACTTTAA 16 117 0 TCTTTAAAAT 0.811658 -22 TTTTTAAAACTCTCTTTAAA 16 129 0 TTTTTAAAAC 0.336141 -10 ********** Masking position 7 Map Score: 20.5899 Number of sites scoring better than the average of aligned sites = 2915 Number in coding regions = 2387 Number in noncoding regions = 528 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 4 TAAAAAAATCAATCTAAAATTCTTAAATTA 1 188 1 AATCTAAAAT 0.943769 -70 ACTCAAAATTAACCTAAAATCGCTTGACGC 2 28 1 AACCTAAAAT 0.970588 -187 TTATAAACAAAACCTAAATTGAGAAAAAAT 2 100 1 AACCTAAATT 0.822775 -115 CATTAAACTGAACCAAAAATTATCAAATGT 9 22 1 AACCAAAAAT 0.957522 -94 TTATAATTAAAATCAAAAAGGCTTATCATA 9 95 1 AATCAAAAAG 0.890936 -21 TAGTTAATCTTACCTAAAATTTAAGCGTTA 10 37 1 TACCTAAAAT 0.822808 -83 ACTTCATTTAACCCTAAAAGATCGCTTAAA 12 26 0 ACCCTAAAAG 0.830516 -275 CATACTCCGCAATCAAAAAGGGAGATTGTA 12 119 0 AATCAAAAAG 0.890936 -182 TAAAGATTTTAAGCTAAAATTTTAGCATAC 14 25 1 AAGCTAAAAT 0.883269 -37 ATGCCATTAAAATCAAAAATTAAGAAAAAA 15 66 0 AATCAAAAAT 0.919826 -85 ********** Masking position 6 Map Score: 10.0308 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 120 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 AGGTTTGGGTTTAGGGTTTGAATTATATTGATT 1 22 0 TTGGTTTGAT 0.96139 -236 TTAAGAGTAATGGGTGTTTGTTTTAAGACGCTA 1 86 0 TGGGTTTGTT 0.965753 -172 AATTTAAGAATTTTAGATTGATTTTTTTAAGGG 1 184 0 TTTGATTGTT 0.797193 -74 ATTTTGAAACCTTGAGATTGTTTTAGTGTATTA 1 229 0 CTGGATTGTT 0.951233 -29 TTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 2 94 0 TTGTTTTGTT 0.770665 -121 ACAATAGCCCCTTTGAATTGAATTTTTTCTCAA 2 118 0 CTTAATTGAT 0.530966 -97 GCCAAAAACTCTCTCATTTGATTAAATCAAAGG 5 13 0 CTTATTTGTT 0.814243 -54 GTGCTGTTGGTGGGCGTTTGCATAGAAGAATTA 11 41 1 TGGGTTTGAT 0.953454 -133 GAGATTGTAGCGCGAGTTTGCTTAGTTGTTGTT 12 95 0 CGGGTTTGTT 0.978324 -206 TGGGTGAGGTCGTGGGTTTGAATCCCGCTACTC 12 179 1 CGGGTTTGAT 0.970402 -122 TCCATTTCCTTGTATTTGTATGCTAAAATTT 14 41 0 CTGATTTGAT 0.90802 -21 TTTTAGCTCTTTCTTGTTTGATTAAGATGGTAT 15 119 0 TTTGTTTGTT 0.917055 -32 ** * ***** ** Masking position 8 Map Score: 8.15626 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 352 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 GTAATGGGTGTTTGTTTTAAGACGCTATGA 1 83 0 TTTGTTTTAA 0.729364 -175 TTCTACTACATTTGAAATAATTTTTCTTAT 2 74 1 TTTGAAATAA 0.881123 -141 CAATAGCCCCTTTGAATTGAATTTTTTCTC 2 120 0 TTTGAATTGA 0.719862 -95 TTAAACGCTATTAGATATAATAAGGGATAG 2 167 1 TTAGATATAA 0.744598 -48 TTTTTCCTATTTTGATATGATTTTTCTAAA 3 74 0 TTTGATATGA 0.897747 -22 AGCCTTAATCTTGGATATAATGGCGTAATC 4 17 1 TTGGATATAA 0.888894 -34 TCCCTTTGATTTAATCAAATGAGA 5 5 1 TTTGATTTAA 0.961669 -62 CTTTTTTGCTATAATGCTTCGTTC 6 5 1 TTTGCTATAA 0.799829 -43 AAAATACAGATTTGATTGAAGGCATTAAAC 7 178 1 TTTGATTGAA 0.897675 -26 GATAAGCCTTTTTGATTTTAATTATAAGTT 9 92 0 TTTGATTTTA 0.850212 -24 AACTTCATTTTTTGAATAAAACTTCATTTA 12 46 0 TTTGAATAAA 0.624025 -255 TTTCTTAATTTTTGATTTTAATGGCATTCT 15 69 1 TTTGATTTTA 0.850212 -82 CAAGGGCTAATTGGATAGAATAAGACCACT 16 36 0 TTGGATAGAA 0.735019 -103 AAAAGCGTTGTTTGATAAAAATGGCTCATT 16 77 1 TTTGATAAAA 0.847497 -62 ********** Masking position 10 Map Score: 9.76709 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 539 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 TCAATTCAAAGGGGCTATTGTTTAAAATTT 2 130 1 GGGGCTATTG 0.9667 -85 AGATATAATAAGGGATAGTTACCACCTATA 2 179 1 AGGGATAGTT 0.910283 -36 TCAGTTTAATGGGGATAATTTC 9 3 0 GGGGATAATT 0.890388 -113 AGGGCTACTTTAATCTTAAA 10 1 1 AGGGCTACTT 0.95445 -119 GCAATCAAAAAGGGAGATTGTAGCGCGAGT 12 111 0 AGGGAGATTG 0.865361 -190 TCTTTAAAAAAGGGCTATTG 14 1 0 AGGGCTATTG 0.977345 -61 GAGTGGCTCAAGGGCTAATTGGATAGAATA 16 44 0 AGGGCTAATT 0.961437 -95 ********** Masking position 7 Map Score: 3.65943 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 136 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ATTGGCATGATTTAAGAGTAATGGGTGTTTGT 1 98 0 TTAAGGTAAT 0.940963 -160 ATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 1 128 0 TTAAGCTAAA 0.915319 -130 GATTGATTTTTTTAAGGGTAGTTTTTTTTAAG 1 170 0 TTAAGGTAGT 0.684332 -88 GTTAGTAATTTTAAAGGGTAAAATAAA 3 6 0 TTAAGGTAAA 0.914842 -90 CGTTTAAGCCTTAATCTTGGATAT 4 3 1 TTAAGCTTAA 0.907726 -48 TCGTTTTTCTTTAATGGCTTATGTTATACTAA 7 145 1 TTATGCTTAT 0.658256 -59 AAAACGCTCTTTTAAGGATAAAAAACCTCTTT 9 59 1 TTAAGATAAA 0.710843 -57 ACTATTCCATTTTAAGATTAAAGTAGCCCT 10 9 0 TTAAGTTAAA 0.482155 -111 TTACCTAAAATTTAAGCGTTATGGTATGAAAC 10 46 1 TTAAGGTTAT 0.954045 -74 TCTTCATCAGTTAAATTCTTATGCGCTATTAT 10 92 0 TTAATCTTAT 0.832412 -28 TTTTAAGGCTGATTTAAAAATTC 11 2 1 TTAAGCTGAT 0.83097 -172 AACCGCAAGCTTGAATGGTTATTGCTACAAGC 11 126 1 TTAATGTTAT 0.832423 -48 TTAAGCGATCTTTTAGGGTTAAATGAAGTTTT 12 27 1 TTTAGGTTAA 0.566264 -274 TTAAAAAAGCTTCAATGATTATCATTTCATTA 12 225 1 TTAATATTAT 0.531866 -76 TTAAATCCTTATCTTTTATGAT 13 25 0 TTAATCTTAT 0.83175 -12 ** *** ***** Masking position 9 Map Score: 8.81283 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 402 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 AAAATTACTAACCTCCATGCTACAATAAAACTTTTT 3 26 1 ACCCAGCAAT 0.995718 -70 TTTATGAGAAACCACCATGCATCAATAAAACGCGCT 7 69 1 ACCCAGCAAT 0.995718 -135 CTATAAAAACAAGGCCAGGCTTTAAACTTGTATCGT 7 113 1 AGCCAGCAAA 0.902726 -91 GTGGTTTCATACCATAACGCTTAAATTTTAGGTAAG 10 45 0 ACTAAGCAAT 0.823504 -75 ATGGTATGAAACCACCAAGAAAGAGTATAATAGCGC 10 66 1 ACCCAGAAGT 0.902726 -54 GCCCACCAACAGCACCACGCCAGAATTTTTAAATCA 11 20 0 ACCCAGCAAT 0.995718 -154 GGGGCTTTATAACCGCAAGCTTGAATGGTTATTGCT 11 116 1 ACGCAGCAAT 0.981589 -58 * * *** ** *** Masking position 7 Map Score: 2.51609 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 118 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 GTGTTATTATTTTCAAATTTCAAGTCTAAAGA 1 136 0 TTTCAAATTA 0.952688 -122 AATCTCAAGGTTTCAAAATTTAGCC 1 243 1 TTTCAAAATA 0.944275 -15 AGAAAAATTATTTCAAATGTAGTAGAATTAAG 2 69 0 TTTCAAATTG 0.791322 -146 AGGGGCTATTGTTTAAAATTTACATTTTTTAA 2 139 1 GTTTAAAATA 0.757314 -76 AATAAAACTTTTTCAAAACTAAGATTTTAGAA 3 49 1 TTTCAAAATA 0.944275 -47 ATAATGCTTCGTTCAAATTTTATGGTTAGGTT 6 21 1 GTTCAAATTA 0.949576 -27 AACCAAAAATTATCAAATGTTAGCTAAAAAAC 9 32 1 TATCAAATTA 0.718984 -84 TTGAAGCTTTTTTAAAAAGTCATGGTCGGAGT 12 208 0 TTTAAAAATA 0.769413 -93 AAATCATCATGTTTAAAAATCAGTTTGTTTGG 12 267 0 GTTTAAAATA 0.757314 -34 GGGTTATCGTTCAAATCATAAAAGATAAGG 13 9 1 GTTCAAATAA 0.705256 -28 TAAAACTCTCTTTAAAATTTTACTTTAAGATA 16 113 0 TTTAAAATTA 0.798596 -26 ******** * * Masking position 6 Map Score: 6.61813 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 114 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 ATGGGTGTTTGTTTTAAGACGCTATGACTA 1 80 0 GTTTTAAGAC 0.759353 -178 AACGATACAAGTTTAAAGCCTGGCCTTGTT 7 120 0 GTTTAAAGCC 0.97745 -84 GCAGTTGTTTAATGCCTTCAATCAAA 7 188 0 GTTTAATGCC 0.950059 -16 TTTCTTGGTGGTTTCATACCATAACGCTTA 10 58 0 GTTTCATACC 0.935236 -62 CTTAGTTGTTGTTTAAAAACTCTTTTTTGT 12 78 0 GTTTAAAAAC 0.784173 -223 GGAGTAGCGGGATTCAAACCCACGACCTCA 12 183 0 GATTCAAACC 0.873069 -118 ATTAAAATGAGTTTCAAGCCCTTTTTTCTT 15 45 1 GTTTCAAGCC 0.985469 -106 ********** Masking position 6 Map Score: 4.96104 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 130 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 ********** No masking Map Score: 6.36889e-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: 6.36889e-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: 6.36889e-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