AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gltJ 169 glutamate/aspartate transport system permease #2 ybeJ 249 putative periplasmic binding transport protein #3 trs5_3 300 IS5 transposase #4 artP 217 ATP-binding component of 3rd arginine transport system #5 ybjP 125 putative enzyme #6 fliY 87 putative periplasmic binding transport protein #7 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #8 BIME89 108 BIME #9 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #10 hisQ 89 histidine transport system permease protein #11 hisJ 220 histidine-binding periplasmic protein of high-affinity histidine transport system #12 argT 265 lysine-, arginine-, ornithine-binding periplasmic protein #13 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #14 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #15 cvpA 165 membrane protein required for colicin V production #16 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #17 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #18 dedA 82 orf, hypothetical protein #19 usg 65 putative PTS system enzyme II A component #20 pdxB 98 erythronate-4-phosphate dehyrogenase #21 yhdW 300 putative periplasmic binding transport protein #22 yhdX 49 putative transport system permease protein #23 yhdY 98 putative transport system permease protein #24 livH 47 high-affinity branched-chain amino acid transport system; membrane component #25 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein Motif number 1 GGAACGACCATCAGGCGTATAGTCTGTCCGT 1 60 0 TCAGGCTATA 0.813336 -110 TCAATAGCTATCAGACTGCCAGTATACGAGT 4 193 1 TCAGACGCCA 0.86951 -25 AAAAGCATTATCAGACTGATACGCTATTATT 5 45 1 TCAGACGATA 0.971021 -81 CAGGTAAATTCCAGGCAGAAAAAAACCCCGC 7 54 0 CCAGGCGAAA 0.874909 -125 AAACGGATAATCATGCCGATAACTCATATAA 7 142 1 TCATGCGATA 0.739628 -37 GCTGCGCTTATCAGGCCTACAAGTTGAATTG 8 63 1 TCAGGCTACA 0.83464 -46 TTTGCGCAATTCAGACCGATAACCCCGGTAT 9 45 0 TCAGACGATA 0.971021 -221 AGTCAGGGTGCCAGACCGGCACCCTCAGCGA 13 16 0 CCAGACGGCA 0.901781 -79 AGTTGCCCTGTCAGACTTGCAGGCAGACTTT 13 70 0 TCAGACTGCA 0.806008 -25 TTAAAACATAACAGCCCGAAACTTTGGATAA 17 39 0 ACAGCCGAAA 0.83833 -117 CGAACCAGGTTCAGACAGAAAGGTCCCTA 17 137 1 TCAGACGAAA 0.960537 -19 TACGTTGGCTACAGCCTGAAATGTTCCGAGC 18 21 0 ACAGCCGAAA 0.83833 -62 CAACGTAGTTACAGCCTGAAAGATGACGAGT 18 45 1 ACAGCCGAAA 0.83833 -38 AACTCTCGTCTCATACAGGTAACACAAAC 20 80 1 TCATACGGTA 0.700449 -19 GAGGATGGCCACAGACAGGTAAAAGACGTTT 21 129 1 ACAGACGGTA 0.905306 -172 AGCGAGATAGTCAGGCTGATAATCAGATAGA 23 26 0 TCAGGCGATA 0.968231 -73 AACCCCTTAATCAGACAGGCAAAAACAGTGC 25 202 1 TCAGACGGCA 0.966735 -99 ****** **** Masking position 3 Map Score: 18.5334 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 1105 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 2 CCCTAACAGGCACAACACTGCACAATAAAGT 2 155 1 CACAACCTGC 0.943301 -95 TAAACACAAAAACAACTCCGCTACATCTTAT 6 17 0 AACAACCCGC 0.943301 -71 CCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 7 44 0 AAAAACCCGC 0.964942 -135 TCGTCCGATTAAAAACCCTGCAGAAACGGAT 7 119 1 AAAAACCTGC 0.965633 -60 GATAAACAGCCCTGCGTTATATGAG 7 164 0 AACAGCCTGC 0.809189 -15 CATCGGTGAAAGAAAGCCCGCTCCCTTCGGG 10 15 1 AGAAAGCCGC 0.777346 -75 GCCATTCAATCGAAACGCTGCGATTCAACCG 12 76 1 CGAAACCTGC 0.964237 -190 CAACTCCCGCCGAAATCCTGCAAAGTCTGCC 13 49 1 CGAAATCTGC 0.919005 -46 GCGCATCAATAAAAATGGCGCTGAAAAAATA 15 58 0 AAAAATGCGC 0.875562 -108 AAAGTAACTCCGCGGTTCGACCA 17 3 1 AGTAACCCGC 0.757454 -153 AACAGCGCCCCGCAATGGTGCGAAAATGAAA 21 21 0 CGCAATGTGC 0.806432 -280 AGGAAATAATAAAAACAGCGCCCCGCAATGG 21 34 0 AAAAACGCGC 0.943566 -267 TATTGCGACGCGAAATCGTGCGCAAAAGCTG 21 79 1 CGAAATGTGC 0.873297 -222 TCTTATAAGCAAAAGTAGTGCCAGCTTTTGC 21 100 0 AAAAGTGTGC 0.64203 -201 GCTATTATCACAAAATACTGCGCTAACCCCT 25 178 1 CAAAATCTGC 0.920527 -123 TCAGACAGGCAAAAACAGTGCAGTATAAAAA 25 212 1 AAAAACGTGC 0.944654 -89 ****** **** Masking position 4 Map Score: 15.0961 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 674 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 AACAATCGAGAGGGCTGGAATTTCCGCCCCTGGTTCT 1 16 0 AGGGCGGTGC 0.962153 -154 ACAATCTTCGAGGGTAGCAGTTAACGCTGCTACCCTC 1 124 1 AGGGTGCTGC 0.951832 -46 GCTTCGGAATGGTGCGGCGCATCTCGCAAAAACAAAC 3 194 1 GGTGCGCTGC 0.882552 -107 AAATAACGGGGGCGGTGGTCGGCGAGCATAAATGTCG 4 65 0 GGCGGGGGGC 0.952339 -153 TTCCTTATAAGCGATCGCTCTGAAAGCGTTCTACGAT 5 93 0 GCGATGCGGC 0.80914 -33 AAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGA 7 29 0 GCCGGGGGGC 0.938635 -150 AGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGT 8 44 0 AGCGCGCTGC 0.979452 -65 TTCACCACACACGACAGGACAGGCAGC 10 73 1 ACGACGGGGC 0.773687 -17 TACGTCTAACGGGGCGGGATATTTTGCCTTGATGGTC 11 123 1 GGGGCGGTGC 0.976122 -98 TGCCTTCGCTGAGGGTGCCGGTCTGGCA 13 2 1 GCCTTGCGGC 0.734222 -93 TAACTGATAAGGGCAGGGCCACTGGCTCTGCCCTTT 16 10 1 AGGGCGGAGC 0.889164 -60 CAGCACGCTGGCGGCAGCCAGTGTGGCTATCATCATC 21 212 0 GCGGCGCTGC 0.979982 -89 CGTGCTGCTTGCCGTTGCAAATCAGGCGCTGCTGGCG 21 242 1 GCCGTGCTGC 0.965828 -59 AACGGCATCAAGCGTCGCGCCAGCAGCGCCTGATTTG 21 259 0 AGCGTGCAGC 0.876011 -42 TGAGGTAACGAGCGTCGCTACGGCGGCGCTCTCTTCA 22 18 1 AGCGTGCGGC 0.972807 -32 AATATCTATAACCGCCGCATCGCGATCGTTGAACGCT 23 64 1 ACCGCGCGTC 0.759824 -35 ***** ** * ** Masking position 7 Map Score: 13.3265 Number of sites scoring better than the average of aligned sites = 3963 Number in coding regions = 3781 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 4 CAGCGTATTGCGGTTTTCAGGCCCGATGGGGAACGAC 1 83 0 CGTTTGCCCT 0.975904 -87 CCTATTTAGACCGTTTCTTCGCCATTTAAGGCGTTAT 2 20 0 CGTTTGCCAT 0.972193 -230 AAGAATTTCCCCGCTTATTCGCACCTTCCCTAACAGG 2 128 1 CGCTTGCACT 0.974279 -122 ATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATG 3 179 0 CATTCGCAAT 0.73268 -122 ACATAAAGCGCAATTTGTCAGCAACGTGCTTCCCCGC 7 12 1 CATTTGCAAT 0.896646 -167 AATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCG 8 62 0 CACTTGCCTT 0.661153 -47 CCATCAGGTACAGCTTCCCAGCGACGTA 11 2 0 CGCTTGCGAT 0.896748 -219 TGGTGCACGCCAGGTTTGTTGCACTATCGTGGTGCAT 11 50 1 CGGTTGCACT 0.966486 -171 CCTTGATGGTCAATTTTATGGCACGATAAGTGTAACA 11 149 1 CATTTGCACT 0.9095 -72 CGCTGTTGCCCTGTTTCAGGGCAATTTTGCAACCGCG 12 14 1 CGTTTGCAAT 0.967929 -252 CTCTTTCATGCAGGTCTTATGCCATCTTGACGACAAC 12 179 0 CGGTCGCCAT 0.901096 -87 CTGTCTGAACCTGGTTCGATGCCAGTTTTATCTTTGG 17 118 0 CGGTTGCCAT 0.966486 -38 AAAGTAGTGCCAGCTTTTGCGCACGATTTCGCGTCGC 21 83 0 CGCTTGCACT 0.974279 -218 * **** **** * Masking position 5 Map Score: 11.4012 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 357 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 AAATCTACTCCAGAAAAAAGAGGGTAGCAG 1 150 0 CAGAAAAAAG 0.963896 -20 GCATTTACGGGAGAAAAAATCGGCTCAAAC 2 67 1 GAGAAAAAAT 0.570637 -183 TAACGCAGAAGATAAAGGAGTTGGAT 2 234 1 GATAAAGGAG 0.579005 -16 AAATTCCAGGCAGAAAAAAACCCCGCCGGT 7 50 0 CAGAAAAAAA 0.637477 -129 ATAAGGGGCAGAGAAAAGAGTATTTCGGCG 9 109 1 GAGAAAAGAG 0.930457 -157 TAACCGGAGGGAGACAAGAGGCGGTAATTC 10 46 1 GAGACAAGAG 0.678484 -44 ATAAGACCTGCATGAAAGAGCCTGCAAACA 12 196 1 CATGAAAGAG 0.806084 -70 CAATACACAACATAAAAAAGCCATTTTCAC 12 233 1 CATAAAAAAG 0.904348 -33 GTGGCTTAACGAGGAAAAAGACGT 14 23 1 GAGGAAAAAG 0.930457 -14 CGAAACTTTGGATAAAAAAGTGGTCGAACC 17 24 0 GATAAAAAAG 0.877236 -132 CAGCAGAGAGCATGAAGAAGAGA 19 4 0 CATGAAGAAG 0.645351 -62 TGGCCACAGACAGGTAAAAGACGTTTCCCA 21 134 1 CAGGTAAAAG 0.653241 -167 TGATGCCGTTCAGAAAAAAGGTTTT 21 286 1 CAGAAAAAAG 0.963896 -15 GATAGATAAACAGAAAAAAGTGCCTTTGTC 25 93 0 CAGAAAAAAG 0.963896 -208 ********** Masking position 6 Map Score: 10.8518 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 411 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 ATGGTCGTTCCCCATCGGGCCTGAAAACCG 1 80 1 CCCATCGGGC 0.631094 -90 GTGCCTGTTAGGGAAGGTGCGAATAAGCGG 2 138 0 GGGAAGGTGC 0.950203 -112 GCCGCATCCGGTGAGCGTGCCGAAATAT 3 9 0 GTGAGCGTGC 0.941749 -292 ATTTTGCTTCGGAATGGTGCGGCGCATCTC 3 189 1 GGAATGGTGC 0.893055 -112 ATGTTACCTAAGGAAGGTGCGAACAAGTCC 3 268 1 AGGAAGGTGC 0.808146 -33 GCAATTTGTCAGCAACGTGCTTCCCCGCCA 7 21 1 AGCAACGTGC 0.815174 -158 GTTACCCGAAGGGAGCGGGCTTTCTTTCAC 10 20 0 GGGAGCGGGC 0.95692 -70 TGGAATGATCATCATGGTGCACGCCAGGTT 11 36 1 ATCATGGTGC 0.774746 -185 TGCCTTCGCTGAGGGTGCCGGTCTGGCA 13 9 1 CTGAGGGTGC 0.835998 -86 GGAGTTGCAAGTCAGGGTGCCAGACCGGCA 13 26 0 GTCAGGGTGC 0.967356 -69 ATGCCTTTGCGGCATCGGGCAATGCGT 15 8 0 GGCATCGGGC 0.941793 -158 CTGTAACATTGGCAGGGAGCTTTGCTATTT 19 31 1 GGCAGGGAGC 0.911099 -35 ACAGCGCCCCGCAATGGTGCGAAAATGAAA 21 21 0 GCAATGGTGC 0.787456 -280 ACTGGCTGCCGCCAGCGTGCTGCTTGCCGT 21 227 1 GCCAGCGTGC 0.963594 -74 ********** Masking position 4 Map Score: 10.8099 Number of sites scoring better than the average of aligned sites = 1137 Number in coding regions = 1067 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TTCTCCCGTAAATGCCTTGAATCAGCCTAT 2 52 0 AATGCCTTGA 0.81002 -198 TGGCACATCTATTGCTTTGTTATACAAGGC 3 81 1 ATTGCTTTGT 0.835116 -220 TGTTTCAGGGTTTGCCTTGTATAACAAAGC 3 94 0 TTTGCCTTGT 0.962577 -207 GGCGGGATATTTTGCCTTGATGGTCAATTT 11 135 1 TTTGCCTTGA 0.930999 -86 CTCCGCTGTTGCCCTGTTTCAGGGCAA 12 8 1 GTTGCCCTGT 0.970897 -258 CGGTTGCAAAATTGCCCTGAAACAGGGCAA 12 19 0 ATTGCCCTGA 0.917554 -247 AAATAGTTGCCCTGTCAGACTTGCA 13 80 0 GTTGCCCTGT 0.970897 -15 ATTTGCCTATGCCTTGTACTCGTCATC 18 66 0 TATGCCTTGT 0.890448 -17 GTGATGTTGTGTTGCTTTGTTTTTATGTGT 25 263 0 GTTGCTTTGT 0.888445 -38 ********** Masking position 3 Map Score: 8.16189 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 106 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 AAACTGGGGATAACGCCTTAAATGGC 2 6 1 GGGGATACGC 0.948576 -244 GACAATTTACGGGGTTTATTGGTTGATCAAG 4 14 0 GGGGTTTTTG 0.960916 -204 CGCCACCGGCGGGGTTTTTTTCTGCCTGGAA 7 46 1 GGGGTTTTTT 0.791819 -133 GGGTTATTTGGGGGTTACAGGTAAATTCCAG 7 71 0 GGGGTTAAGG 0.906303 -108 GGTGAAATGAGGGGTTATTTGGGGGTTACAG 7 82 0 GGGGTTATTG 0.960916 -97 AACGAATACCGGGGTTATCGGTCTGAATTGC 9 40 1 GGGGTTACGG 0.980574 -226 GGTGGTTTACTCCAGAAATAGC 19 54 0 GTGGTTTCTC 0.690646 -12 CTATCATTCAGGGGATTATGCTGGACATTTT 25 26 0 GGGGATTTGC 0.93478 -275 GTCTGATTAAGGGGTTAGCGCAGTATTTTGT 25 187 0 GGGGTTACGC 0.976032 -114 CATCACGAATGGGGATTTTTGACT 25 287 1 GGGGATTTTG 0.917578 -14 ******* *** Masking position 6 Map Score: 6.25153 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 210 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 CGCTATACCTGCTATCTTCAACTTCAGGAC 12 105 1 GCTATCTTCA 0.959742 -161 CAGGTCTTATGCCATCTTGACGACAACAGT 12 176 0 GCCATCTTGA 0.846719 -90 ACATAAAAAAGCCATTTTCACTTGAGGGTT 12 242 1 GCCATTTTCA 0.959742 -24 TTTTTTCAGCGCCATTTTTATTGATGCGCG 15 60 1 GCCATTTTTA 0.700342 -106 CAGTGGCCCTGCCCTTATCAGTTA 16 5 0 GCCCTTATCA 0.864679 -65 CTGCCCTTTTGCTATTCTCACCGTAACGAA 16 38 1 GCTATTCTCA 0.909581 -32 CCTGTCTGTGGCCATCCTCTTATAAGCAAA 21 118 0 GCCATCCTCT 0.782594 -183 AGCCAGTGTGGCTATCATCATCTTTTTCAT 21 204 0 GCTATCATCA 0.936951 -97 CTACGGCGGCGCTCTCTTCAGCGTT 22 35 1 GCTCTCTTCA 0.911117 -15 GATTTTAATCGCTATTATCACAAAATACTG 25 168 1 GCTATTATCA 0.903089 -133 ********** Masking position 5 Map Score: 5.44294 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 487 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 TACAAGAACCAGGGGCGGAAATTCCAGCCC 1 12 1 AGGGGCGGAA 0.983486 -158 ACAAAATAACGGGGGCGGTGGTCGGCGAGC 4 75 0 GGGGGCGGTG 0.9122 -143 AGCGGGAATAAGGGGCAGAGAAAAGAGTAT 9 102 1 AGGGGCAGAG 0.975921 -164 GATTGAGCCGACGGGTGGAAACCCAATACG 9 213 1 ACGGGTGGAA 0.731147 -53 GAGGGAGACAAGAGGCGGTAATTCACCACA 10 52 1 AGAGGCGGTA 0.753852 -38 GTTTCGATTGAATGGCAGAAACAAAATGTC 12 62 0 AATGGCAGAA 0.611019 -204 TAACTGATAAGGGCAGGGCCACTGGCTC 16 9 1 AAGGGCAGGG 0.887163 -61 AGAATAGCAAAAGGGCAGAGCCAGTGGCCC 16 26 0 AAGGGCAGAG 0.962338 -44 CCCGCATTTTACGGGCGGTGGGATGA 24 7 0 ACGGGCGGTG 0.963016 -41 TAACGGCACAAAGGGCGGAATAATTCACTA 25 54 0 AAGGGCGGAA 0.974057 -247 ********** Masking position 5 Map Score: 6.9094 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 322 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 TGTTATCCGGATAATGCACTGATGCCGCAT 3 32 0 ATAATGCACT 0.966439 -269 CAAAATTCTTAAAATGCACTCTTTTAGTGC 3 165 0 AAAATGCACT 0.926076 -136 TGTTTATTGAATAATGCGCTTTGCTTTTAA 4 109 1 ATAATGCGCT 0.972047 -109 CGTTGCTGACAAATTGCGCTTTATGTT 7 8 0 AAATTGCGCT 0.821367 -171 AAAGGGCGGAATAATTCACTATCATTCAGG 25 45 0 ATAATTCACT 0.788817 -256 TTATCACAAAATACTGCGCTAACCCCTTAA 25 182 1 ATACTGCGCT 0.966476 -119 TTCTTTTTTTATACTGCACTGTTTTTGCCT 25 218 0 ATACTGCACT 0.959797 -83 ********** Masking position 3 Map Score: 4.81653 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 74 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 AAATGTCGGCATTCCTCACGAAATGCCGGAC 4 42 0 ATTCTCACGA 0.860821 -176 GCCGACATTTATGCTCGCCGACCACCGCCCC 4 63 1 ATGCCGCCGA 0.985389 -155 ATTCACCCCGAATGTTGTTAT 6 77 0 ATTCCCCCGA 0.985751 -11 AGAAACGGATAATCATGCCGATAACTCATAT 7 140 1 AATCTGCCGA 0.77531 -39 ATGCATTTCAATGCACCACGATAGTGCAACA 11 66 0 ATGCCCACGA 0.961682 -155 CTGACTTGCAACTCCCGCCGAAATCCTGCAA 13 41 1 ACTCCGCCGA 0.928995 -54 TTCTGTTAGAATGCGCCCCGAACAGGATGAC 15 121 1 ATGCCCCCGA 0.990969 -45 AAATGGCATTATGCGTCCCCAAAGATAAAAC 17 100 1 ATGCTCCCCA 0.876526 -56 **** ****** Masking position 1 Map Score: 4.02339 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 168 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 AATTTCCGCCCCTGGTTCTTGTAA 1 3 0 CCTGTTTTGT 0.847254 -167 AGACTATACGCCTGATGGTCGTTCCCCATCGG 1 66 1 CCTGTGTCGT 0.846633 -104 ACCAATAAACCCCGTAAATTGTCCGGCATTTC 4 22 1 CCCGAATTGT 0.908914 -196 CGTAAATTGTCCGGCATTTCGTGAGGAATGCC 4 34 1 CCGGATTCGT 0.905729 -184 ACCACCGCCCCCGTTATTTTGTGCTATGTTTA 4 83 1 CCGTATTTGT 0.499029 -135 ATTCACCCCGAATGTTGTTATGTCTGTT 6 70 0 CCCGATTTGT 0.908914 -18 CCTCATTTCACCCACTAATCGTCCGATTAAAA 7 101 1 CCCATATCGT 0.837223 -78 GACCGATAACCCCGGTATTCGTTTTACGTGTC 9 31 0 CCCGTATCGT 0.978752 -235 TCGCCGTCAACCCTGTTATCGTCTGTCGTAAA 9 183 0 CCCTTTTCGT 0.928558 -83 AATATCCCGCCCCGTTAGACGTATTATTTTTC 11 114 0 CCCGTAACGT 0.854079 -107 TTTGCCTATGCCTTGTACTCGTCATCTTTCAG 18 60 0 CCTTTATCGT 0.809878 -23 **** ** **** Masking position 12 Map Score: 2.99026 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 383 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 TAAATGCCTTGAATCAGCCTATTTAGACCGT 2 43 0 GATCAGCCTA 0.928175 -207 ATTTCTTCATGTTTGAGCCGATTTTTTCTCC 2 76 0 GTTGAGCCGA 0.970586 -174 TGAAATGACTGAGTCAGCCGAGAAGAATTTC 2 106 1 GATCAGCCGA 0.990061 -144 GGTTGACGGCGATTGAGCCGACGGGTGGAAA 9 203 1 GATGAGCCGA 0.986988 -63 GAAACGCTGCGATTCAACCGCTATACCTGCT 12 87 1 GATCAACCGC 0.79905 -179 TCACCGTAACGAATCAGCGGATACC 16 55 1 GATCAGCGGA 0.95038 -15 TGTGTTACCTGTATGAGACGAGAGTTAACCG 20 75 0 GTTGAGACGA 0.81061 -24 ** ******** Masking position 6 Map Score: 2.49894 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 146 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 GATCGATCTCCTTGTTTGCTAAG 5 4 1 CGATCTCCTT 0.956353 -122 ACGATAATAATGATATCCTTTCAATAATAG 5 68 0 TGATATCCTT 0.905279 -58 AATGATTTCCTTATAAGCGATC 5 114 0 TGATTTCCTT 0.960236 -12 GCGATTTCCTTTTATCTTTCG 9 2 1 CGATTTCCTT 0.973927 -264 GTTTGCGTAGGGATTTCCTTCCCGCGCATC 15 82 0 GGATTTCCTT 0.953045 -84 ********** Masking position 6 Map Score: 1.38046 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 22 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678