AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_ecoli_reg_300.orf -o00061_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rpsB 300 30S ribosomal subunit protein S2 #2 tsf 257 protein chain elongation factor EF-Ts #3 pyrH 146 uridylate kinase #4 frr 291 ribosome releasing factor #5 yaeM 91 putative ATP-binding component of a transport system #6 yaeS 185 orf, hypothetical protein #7 cdsA 120 CDP-diglyceride synthetase #8 yaeT 29 orf, hypothetical protein #9 hlpA 121 histone-like protein, located in outer membrane or nucleoid #10 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #11 dnaE 36 DNA polymerase III, alpha subunit #12 fabA 68 beta-hydroxydecanoyl thioester dehydrase, trans-2-decenoyl-ACP isomerase #13 b0955 185 putative ATP-dependent protease #14 yceD 159 orf, hypothetical protein #15 rpmF 51 50S ribosomal subunit protein L32 #16 plsX 110 glycerolphosphate auxotrophy in plsB background #17 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #18 acpP 210 acyl carrier protein #19 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #20 fabI 300 enoyl-[acyl-carrier-protein] reductase (NADH) #21 ydbO 284 orf, hypothetical protein #22 atoS 214 sensor protein AtoS for response regulator AtoC #23 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #24 atoB 30 acetyl-CoA acetyltransferase #25 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #26 dedA 82 orf, hypothetical protein #27 usg 65 putative PTS system enzyme II A component #28 pdxB 98 erythronate-4-phosphate dehyrogenase #29 fabB 98 3-oxoacyl-[acyl-carrier-protein] synthase I #30 yqeF 251 putative acyltransferase #31 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #32 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 GACCCCAAAGGGCACCCCGGAATATGTGCC 1 226 0 GGCACCCCGG 0.795839 -75 AAAAAGAAGCCGCCCTCAGGCGGCTCCTTT 3 18 0 CGCCCTCAGG 0.886187 -129 GCAGTTTGGTCACGGCCAGCGCGCAGCAAC 4 94 1 CACGGCCAGC 0.905925 -198 GGATGGCGAGCACTGCCCGGGGCCAAAATG 4 146 1 CACTGCCCGG 0.915856 -146 CACTGTGTGTGACTGTCTGGTCTGACTGAG 4 249 1 GACTGTCTGG 0.66044 -43 AAAAGCAAAACGCCGCCAGCCGATCCGCAA 5 46 0 CGCCGCCAGC 0.96154 -46 GTACCGTAAACCCTGTCAGGGAATAAAAAA 6 163 1 CCCTGTCAGG 0.750751 -23 CAGTTCTTTGCGTGGCCCGGCGATCTTATA 9 65 0 CGTGGCCCGG 0.573461 -57 CAAAGAACTGCACCCTCCGGTGCAAATGGG 9 85 1 CACCCTCCGG 0.821411 -37 ACAATAATAACACGGCCTGCCGCAATCGTA 10 55 0 CACGGCCTGC 0.946063 -50 CAAAGAAAAAGGCAGCCTGTGGTTGCCTTT 14 105 0 GGCAGCCTGT 0.545175 -55 AAGGTATCGTCGCCGCCCGGTTTGGTCTTT 16 63 0 CGCCGCCCGG 0.981723 -48 CAGGACGCTGCCAGCGAACTCGCAG 17 6 1 CGCTGCCAGC 0.908549 -62 TCATGTTGCGCGCAGTCTGCGTGGTTATGA 18 31 1 CGCAGTCTGC 0.883398 -180 GCGGTCGAACGACCGCCTGGAGATGTTCAC 19 11 0 GACCGCCTGG 0.932829 -77 ATCATTTTTTCCCTCCCTGGAGGACAAAC 19 69 1 CCCTCCCTGG 0.881147 -19 CGGTCCCCTCGCCCCTCTGGGGAGAGGGTT 20 106 1 GCCCCTCTGG 0.679594 -195 GGGAAAAGCGCCCCCCCTGCCGCAGCCTGC 20 144 1 CCCCCCCTGC 0.909578 -157 CCCCCCCTGCCGCAGCCTGCTCCGGTCGGA 20 154 1 CGCAGCCTGC 0.955547 -147 TATAGCTACTCACAGCCAGGTTGATTATAA 20 193 1 CACAGCCAGG 0.9178 -108 GCCATAATCTCGCGGCCAGGCATACTTGCG 28 36 0 CGCGGCCAGG 0.97209 -63 GTCTAACATTGACACTCTGGGGCAAAATAG 31 161 1 GACACTCTGG 0.524078 -140 AGACCGGCGTCCCGGCCTGCTGGAATTTAT 31 189 1 CCCGGCCTGC 0.939391 -112 GGCGTTTCACCGCCGTCTGTAAAGCGTATG 31 242 0 CGCCGTCTGT 0.734996 -59 CGGCAGAAATCACGCTCTGGATGAACGATG 32 57 0 CACGCTCTGG 0.845298 -133 ********** Masking position 7 Map Score: 29.334 Number of sites scoring better than the average of aligned sites = 4889 Number in coding regions = 4663 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 2 GGTATAAAGCGCGCCGGACTTCCGATCCATTTCGTA 1 135 1 GCGCCGTCGT 0.96721 -166 TTCATATTTCGCGCCGCAGATGCGTTATCTTCGCTC 2 108 0 GCGCCGTCGT 0.96721 -150 CCGCCCTCAGGCGGCTCCTTTTTGATAA 3 3 0 GCGGCTTTGT 0.808806 -144 AAGTATCGCGGGGGCGTAAGTCTGGTTATAAGGCGT 4 47 1 GGGGCGTTGT 0.965511 -245 CGCTCCGGTTGCTGCGCGCTGGCCGTGACCAAACTG 4 95 0 GCTGCGGCCT 0.868992 -197 GATCTACTGAGCGGCGTTTTTGTCGTTCAAGAAA 5 9 0 GCGGCGTTCT 0.984699 -83 GGATCGGCTGGCGGCGTTTTGCTTTTTATTCTGTCT 5 50 1 GCGGCGGTTT 0.898976 -42 CGTCGTCATCGCGGCGTTGTTTCTGTTGCCGCCGGT 7 64 1 GCGGCGTCTT 0.972209 -57 TGTTGTCAAAGCCGCGATTATACCGTAACCGGCACT 13 142 0 GCCGCGTCCT 0.96767 -44 ACCAAACCGGGCGGCGACGATACCTTGACACGTCTA 16 67 1 GCGGCGTCCT 0.993504 -44 TCTCCCCAGAGGGGCGAGGGGACCGTATTGTGCAAA 20 95 0 GGGGCGGCCT 0.971921 -206 TGCGGCAGGGGGGGCGCTTTTCCCCTCACCCTAACC 20 132 0 GGGGCGTCCT 0.982838 -169 GTATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACC 22 50 1 GGGGCGTCGC 0.94696 -165 AGTATGCCTGGCCGCGAGATTATGGCACACTTGTCC 28 40 1 GCCGCGTTGC 0.797079 -59 CGGACATTGTGCAGCGATCTGCTGCTATCCTCCGGC 31 121 0 GCAGCGGTGT 0.76429 -180 ****** * ** * Masking position 5 Map Score: 18.3986 Number of sites scoring better than the average of aligned sites = 1403 Number in coding regions = 1159 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 AGTCCGGCGCGCTTTATACCACAAATACGTCGT 1 122 0 GCTTAACCCA 0.982541 -179 GATCTGCCCGGCATTAAACCGCACAGATATAAA 2 215 0 GCTTAACCCA 0.982541 -43 ATTGTACGTCGCTTTTCAGCGCAGCCCCACAAG 3 75 0 GCTTTAGCCA 0.975975 -72 CAGAATATCAGCTTTTTAGGCCAGTGAAGAAAA 13 42 1 GCTTTAGGCA 0.81203 -144 CCTGGCATGGGCGTTAAAGCTCACAGGATGGAG 13 79 0 GCTTAAGCCA 0.975975 -107 ACCGTAACCGGCACTACAGCACACGTAGAAAGC 13 124 0 GCCTAAGCCA 0.884394 -62 CGAAAATAAAGCAGTAACCCGCAATGTGTGCGA 14 62 1 GCGTACCCCA 0.855592 -98 TTATTTTGAGGCCTTACCCCCCAATAACGCAAA 18 82 0 GCTTACCCCA 0.969194 -129 CAGGGGGGGCGCTTTTCCCCTCACCCTAACCCT 20 130 0 GCTTTCCCCA 0.969194 -171 AGCGGTAAAAGCGTGTTACCGCAATGTTCTCTC 22 105 1 GCTGTACCCA 0.913779 -110 ATTGTGACAGGCGTTTCACCGCCGTCTGTAAAG 31 248 0 GCTTTACCCC 0.9062 -53 TTAAGTCTCCGCATCTTAGCACATCGTTCATCC 32 36 1 GCTCTAGCCA 0.884394 -154 ** *** *** ** Masking position 2 Map Score: 12.5455 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 103 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 GAGAATCATTCTGAATTTCGCCAAACGTGCCACTGAAGGTTTTCT 1 21 1 CGTTGCAGAG 0.971705 -280 CAGTAAGTGACCGGGATGAGCGAGCGAAGATAACGCATCTGCGGC 2 87 1 CGAGGCAGAG 0.948738 -171 GTTAGGGGGCCTGCATATGGCCCCCTTTTTCACTTTTATATCTGT 2 181 1 CGTTGCCTAT 0.695962 -77 TCAGTCAGACCAGACAGTCACACACAGTGGAAGTGTGCTAAGTAT 4 233 0 CGATACCGAG 0.896706 -59 AATCCGGCTACAGAGAGTCGCGCTATTTGTTAGCGTAGGGCTTCA 6 15 1 CGATGCCGAG 0.993037 -171 GAAAATAAAGCAGTAACCCGCAATGTGTGCGAATTATTGGCAAAA 14 63 1 CGACGCAGAT 0.897326 -97 CGGTTATATACCGTCACTTGCAAACTGCGAGTTCGCTGGCAGCGT 17 15 0 CGATGCAGTG 0.963356 -53 CCGCGATTTGCACAAAATGCTCATGTTGCGCGCAG 18 1 1 CGATGCCGCG 0.980169 -210 ATCAACCTGGCTGTGAGTAGCTATAGTTGCCAGGTCCGACCGGAG 20 173 0 CGATGCAGAT 0.982273 -128 ACTTGCTATGCAGAAATTTGCACAGTGCGCAATTTTCTGCATAGC 23 18 1 CGATGCCGAT 0.985368 -178 TGGGTACAGTCAGGCAATAGCAAGGGGAGTGCCAGAATGAGATTA 23 134 0 CGATGCAGCG 0.973536 -62 CGGAACATTTCAGGCTGTAGCCAACGTAGTTACAGCCTGAAAGAT 26 24 1 CGTTGCAGAG 0.9717 -59 TCAATACCTCTGTAAGTCGCACATAGAGTAAGTTTCGAATGCAC 29 65 0 CGATGCCGAT 0.985368 -34 GCTGCCAATTGCTACGAAATCGTTATAATGTGCGAC 31 2 1 CGATGCATTT 0.59049 -299 * * * * ** * * * * Masking position 11 Map Score: 14.7586 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 476 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 AGATTGTCGCTTCCGTCCAGTCTGTGTATAC 1 168 0 TTCGTCCAGT 0.78815 -133 GGCGTTATTGTTGCAGGCAGTTTGGTCACGG 4 78 1 TTCAGGCAGT 0.948026 -214 TCGCCAAACTTTACGGCCTGTCTCATTCTTA 10 26 1 TTCGGCCTGT 0.97991 -79 ATATCAGCTTTTTAGGCCAGTGAAGAAAAGA 13 46 1 TTAGGCCAGT 0.765592 -140 AATGCTCATGTTGCGCGCAGTCTGCGTGGTT 18 26 1 TTCGCGCAGT 0.951669 -185 CATGAAAGGGTTAGGGGCTGTATGAGCCTGT 20 44 1 TTGGGGCTGT 0.932212 -257 ATGCAGAAAATTGCGCACTGTGCAAATTTCT 23 29 0 TTCGCACTGT 0.788996 -167 TTATCCAAAGTTTCGGGCTGTTATGTTTTAA 25 39 1 TTCGGGCTGT 0.989545 -117 GCTCGGAACATTTCAGGCTGTAGCCAACGTA 26 21 1 TTCAGGCTGT 0.963905 -62 ACTCGTCATCTTTCAGGCTGTAACTACGTTG 26 45 0 TTCAGGCTGT 0.963905 -38 ** ******** Masking position 2 Map Score: 8.11929 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 312 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TTACAAGATGGGCACAAAAAGAAGCCGCCC 3 33 0 GGCACAAAAA 0.93078 -114 AGCACTGCCCGGGGCCAAAATGGCAAATAA 4 154 1 GGGGCCAAAA 0.922041 -138 TGATTCTAGTGGGACAAAAAGATAAAACTC 19 43 0 GGGACAAAAA 0.958462 -45 GTTTGTTGCTGGGGTAACAATATTTGCACA 20 73 1 GGGGTAACAA 0.906922 -228 CTGATTTTCAGGCACAACAAGCATCAACAA 20 267 1 GGCACAACAA 0.893865 -34 GTATGCAAGAGGGATAAAAA 23 186 1 GGGATAAAAA 0.851094 -10 TGGTCTGTTGGGGGCAAAAATGGCATTATG 25 83 1 GGGGCAAAAA 0.984327 -73 CCTTTTCCGCAGCGCAAAAACTGCGTCAGG 31 56 0 AGCGCAAAAA 0.849363 -245 AGGTGACATTGGCGCAACGAAGGTATATTT 31 83 1 GGCGCAACGA 0.811919 -218 TTGACACTCTGGGGCAAAATAGACCGGCGT 31 169 1 GGGGCAAAAT 0.888641 -132 AAAAAACAGAAGGGTAAAAA 32 1 0 AGGGTAAAAA 0.705596 -189 ********** Masking position 7 Map Score: 7.28293 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 387 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 ACAAATACGTCGTGGACACCAATAATTGTTGGCGCTGTGTACA 1 92 0 CCCATGTTGC 0.98141 -209 GCTCGCTCATCCCGGTCACTTACTGATGTAAGCTCCCGGGAAT 2 69 0 CCCATGTAGC 0.996083 -189 CAGTGCTCGCCATCCTCACGTACTTTTGTACGCTCCGGTTGCT 4 118 0 CCCATGTAGC 0.996083 -174 TTGAAGCACGCAGGATAGCTAACACGTGTACGCTGAACAAGTC 12 14 0 CACATGTAGC 0.98579 -55 CTATTGCCTGACTGTACCCACAACGGTGTATGCAAGAGGGATA 23 159 1 ACCATGTAGC 0.970575 -37 GTTTCGAATGCACAATAGCGTACACTTGTACGCCGAACAAGTC 29 35 0 CACATGTAGC 0.98579 -64 GTCTGTAAAGCGTATGCCCCGACAGCTGTATGCATAGCGATAA 31 215 0 CCCATGTAGC 0.996083 -86 * * * * **** ** Masking position 12 Map Score: 6.51496 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 3 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ATCAAAAAGGAGCCGCCTGAGGGCGGCTTC 3 13 1 AGCCGCCTGA 0.900161 -134 TGGCAAATAAAATAGCCTAATAATCCAGAC 4 174 1 AATAGCCTAA 0.623347 -118 TTTGCTGAAGTATCGCCTGATATCTGCTTT 7 22 1 TATCGCCTGA 0.961791 -99 ATCTTATATTGATCGCCTAAAGTCATCGCT 9 43 0 GATCGCCTAA 0.824039 -79 GCGGTCGAACGACCGCCTGGAGATGTTCAC 19 11 0 GACCGCCTGG 0.915881 -77 GCGGTCGTTCGACCGCCTGAGTTTTATCTT 19 25 1 GACCGCCTGA 0.982998 -63 TAAAACGACGAATCGCCTGATTTTCAGGCA 20 251 1 AATCGCCTGA 0.961791 -50 CTCCCCTTGCTATTGCCTGACTGTACCCAC 23 150 1 TATTGCCTGA 0.765538 -46 ATTAAAACATAACAGCCCGAAACTTTGGAT 25 41 0 AACAGCCCGA 0.793716 -115 CTACGTTGGCTACAGCCTGAAATGTTCCGA 26 23 0 TACAGCCTGA 0.95334 -60 CCAACGTAGTTACAGCCTGAAAGATGACGA 26 44 1 TACAGCCTGA 0.95334 -39 ********** Masking position 6 Map Score: 8.5946 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 697 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 9 GCTTGCCGCCTTTCTGCAACTCGAACTATTTT 2 31 0 TTTCGCACTC 0.94082 -227 GCGGCTTCTTTTTGTGCCCATCTTGTAAATTC 3 35 1 TTTGGCCATC 0.86983 -112 GTACGTCGCTTTTCAGCGCAGCCCCACAAGGG 3 73 0 TTTCGCGAGC 0.963317 -74 ACATGAGCATTTTGTGCAAATCGCGG 18 5 0 TTTGGCAATC 0.908529 -206 ACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 23 12 0 TTTCGCAAGC 0.986265 -184 AGTGCGCAATTTTCTGCATAGCCGCTCATTCT 23 41 1 TTTCGCAAGC 0.986265 -155 AATGTCACCTTTTCCGCAGCGCAAAAACTGCG 31 61 0 TTTCGCACGC 0.976001 -240 CAGAGCGTGATTTCTGCCGAGCGTGATCAGAT 32 68 1 TTTCGCCAGC 0.979645 -122 **** *** *** Masking position 3 Map Score: 6.75389 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 159 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 GCGCAGCAACCGGAGCGTACAAAAGTACGT 4 114 1 CGGAGCGTAC 0.922016 -178 GTGTGACTGTCTGGTCTGACTGAGACAAGT 4 255 1 CTGGTCTGAC 0.794048 -37 TCTGCGCCATCTGATCGTAAGTAGTTGGCT 6 69 1 CTGATCGTAA 0.676272 -117 CGAAAAGTGACTGAGCGTAC 17 58 1 CTGAGCGTAC 0.943199 -10 ATGGCTGGGACGGTTCAGACCTTGCCGAAT 20 11 0 CGGTTCAGAC 0.700933 -290 GCAGCCTGCTCCGGTCGGACCTGGCAACTA 20 165 1 CCGGTCGGAC 0.912631 -136 AACCGTTTATCTGTTCGTACTGTTTACTAA 20 224 1 CTGTTCGTAC 0.953186 -77 TACCTTGCTTCTTTTCGTACAACCCTGAAA 22 23 0 CTTTTCGTAC 0.616023 -192 TATTAAATGGCTGATCGGACTTGTTCGGCG 29 18 1 CTGATCGGAC 0.961232 -81 ATACAGCTGTCGGGGCATACGCTTTACAGA 31 227 1 CGGGGCATAC 0.764255 -74 GCAAGGTGATCTGGTCGTACCAGATGAGTC 32 153 0 CTGGTCGTAC 0.976773 -37 ********** Masking position 9 Map Score: 5.21712 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 348 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 GTACACGTTTGGTTAGGGGGCCTGCATATG 2 170 1 GGTTAGGGGG 0.96181 -88 CCCTGACAGGGTTTACGGTACTCAGGAATA 6 154 0 GTTTACGGTA 0.847663 -32 CTGTAGTGCCGGTTACGGTATAATCGCGGC 13 138 1 GGTTACGGTA 0.944377 -48 GCCATGAAAGGGTTAGGGGCTGTATGAGCC 20 42 1 GGTTAGGGGC 0.877342 -259 CTGGGGAGAGGGTTAGGGTGAGGGGAAAAG 20 122 1 GGTTAGGGTG 0.980961 -179 GATGGAGTGTGGTTAAGGTAGCGGTAAAAG 22 86 1 GGTTAAGGTA 0.916501 -129 GATTATCAGAGGTTAAGGTGATGATTTCTC 22 162 0 GGTTAAGGTG 0.945681 -53 ACTTAACCTGGTTTATGGTAAATTGCCCTC 30 46 0 GTTTATGGTA 0.671057 -206 CGTACTCTTTGTTTAGTGTGATTGTGACAG 31 271 0 GTTTAGTGTG 0.623414 -30 ********** Masking position 5 Map Score: 3.6956 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 101 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 TAACAACACACACGTATCGGCACATATTCCG 1 208 1 CACGTATCGC 0.882135 -93 GAGCGAAGATAACGCATCTGCGGCGCGAAAT 2 108 1 AACGCATCGC 0.86962 -150 CTATACTTAGCACACTTCCACTGTGTGTGAC 4 231 1 CACACTTCAC 0.934858 -61 AGCCGATCCGCAAGGATCTACTGAGCGGCGT 5 28 0 CAAGGATCAC 0.779571 -64 AACAGACTAAAAAACATCAACT 13 174 1 AAAACATCAC 0.663475 -12 GTGCTGATAACAAACATCAACCTGCAAAACG 14 27 0 CAAACATCAC 0.927522 -133 TCACGCATCTGCGTGATGAAGC 16 2 1 CACGCATCGC 0.977424 -109 TCAGGCACAACAAGCATCAACAATAAGGATT 20 274 1 CAAGCATCAC 0.960537 -27 ATTGCGGTAACACGCTTTTACCGCTACCTTA 22 99 0 CACGCTTTAC 0.682608 -116 GCGCACTGTGCAAATTTCTGCATAGCAAGTT 23 17 0 CAAATTTCGC 0.549517 -179 ACACAAAATACACACTTCGACTCATCTGGTA 32 135 1 CACACTTCAC 0.934858 -55 ******** ** Masking position 2 Map Score: 3.40527 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 587 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 AAATATGAAGGGGGAGAGCCCTTATAGACCA 2 135 1 GGGGAAGCCC 0.986145 -123 TGCCGCCGGTGGGGTTCGCCATTGTAACGCT 7 90 1 GGGGTCGCCA 0.913645 -31 CCGATCCAACGGGGAGCACCAA 15 2 0 GGGGACACCA 0.916485 -50 CCGTTGGATCGGGGATAAACCGTAATTGAGG 15 21 1 GGGGAAAACC 0.92749 -31 CCAGTTGCCTGGGGAAAATCCTCACTAAGCT 16 30 0 GGGGAAATCC 0.92749 -81 CCAGGCAACTGGGGAAAGACCAAACCGGGCG 16 49 1 GGGGAAGACC 0.975067 -62 GCGTTATTGGGGGGTAAGGCCTCAAAATAAC 18 85 1 GGGGTAGGCC 0.912051 -126 GCAATAGCAAGGGGAGTGCCAGAATGAGATT 23 135 0 GGGGATGCCA 0.9244 -61 ACACCGTTGTGGGTACAGTCAGGCAATAGCA 23 157 0 GGGTAAGTCA 0.662173 -39 ***** ***** Masking position 10 Map Score: 3.49753 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 142 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 TCGTATACACAGACTGGACGGAAGCGACAA 1 166 1 AGACTGGACG 0.908902 -135 TTCGAGTTGCAGAAAGGCGGCAAGCTCGAG 2 38 1 AGAAAGGCGG 0.824619 -220 TTATAAGGTCAGATATGCCGTGGTTTTACA 6 99 1 AGATATGCCG 0.947118 -87 CGTAAGAATGAGACAGGCCGTAAAGTTTGG 10 29 0 AGACAGGCCG 0.988223 -76 AATCGTGGTAAGACCTGCCGGGATTTAGTT 18 120 1 AGACCTGCCG 0.95084 -91 ATAGAGGGGTAGATAGGGCGTTAATCTCCC 30 78 0 AGATAGGGCG 0.86691 -174 TGTCAATGTTAGACTTGACGGACATTGTGC 31 145 0 AGACTTGACG 0.862828 -156 AAAAGATTAAAGAAATGCCGATCTGATCAC 32 90 0 AGAAATGCCG 0.947118 -100 ********** Masking position 3 Map Score: 2.00564 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 166 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 CTTCAGATTCCGGTTTACTTAATCTC 11 21 0 GATTCCGTTT 0.979256 -16 TGCTTTTTATGATTCGCGATTTAACTATTAG 21 43 0 GATTCGGATT 0.907845 -242 AAAACAATGTGATTCGTGTTTTTAATTAATT 21 234 1 GATTCGGTTT 0.970071 -51 TCACCTTTACGATTCCAGTTTTCGTGAATTA 21 260 0 GATTCCGTTT 0.979259 -25 AACCTGGTTCGATGCCAGTTTTATCTTTGGG 25 117 0 GATGCCGTTT 0.955094 -39 ****** **** Masking position 3 Map Score: 0.582046 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555