AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_ecoli_reg_100.orf -o03010_ecoli_100.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 rpsT 102 30S ribosomal subunit protein S20 #2 rpsB 300 30S ribosomal subunit protein S2 #3 rpsA 110 30S ribosomal subunit protein S1 #4 yceD 159 orf, hypothetical protein #5 rpmF 51 50S ribosomal subunit protein L32 #6 rpsV 101 30S ribosomal subunit protein S22 #7 rplT 52 50S ribosomal subunit protein L20, and regulator #8 rpmI 96 50S ribosomal subunit protein A #9 thrS 300 threonine tRNA synthetase #10 rplY 124 50S ribosomal subunit protein L25 #11 rplS 41 50S ribosomal subunit protein L19 #12 trmD 30 tRNA methyltransferase; tRNA (guanine-7-)-methyltransferase #13 rpsP 248 30S ribosomal subunit protein S16 #14 rpsU 237 30S ribosomal subunit protein S21 #15 rpsO 148 30S ribosomal subunit protein S15 #16 rplU 258 50S ribosomal subunit protein L21 #17 rplM 218 50S ribosomal subunit protein L13 #18 rplQ 40 50S ribosomal subunit protein L17 #19 rpoA 25 RNA polymerase, alpha subunit #20 rpsD 33 30S ribosomal subunit protein S4 #21 rpsM 146 30S ribosomal subunit protein S13 #22 rpmJ 31 50S ribosomal subunit protein L36 #23 rpsH 33 30S ribosomal subunit protein S8, and regulator #24 rplN 164 50S ribosomal subunit protein L14 #25 rplC 32 50S ribosomal subunit protein L3 #26 rpsJ 237 30S ribosomal subunit protein S10 #27 rpsG 96 30S ribosomal subunit protein S7, initiates assembly #28 rpsL 125 30S ribosomal subunit protein S12 #29 rpmB 216 50S ribosomal subunit protein L28 #30 rpmH 300 50S ribosomal subunit protein L34 #31 rpmE 202 50S ribosomal subunit protein L31 #32 rplK 157 50S ribosomal subunit protein L11 #33 rplJ 300 50S ribosomal subunit protein L10 #34 rplL 66 50S ribosomal subunit protein L7/L12 #35 rpsF 300 30S ribosomal subunit protein S6 #36 rplI 41 50S ribosomal subunit protein L9 Motif number 1 ACCAATAATTGTTGGCGCTGTGTACAGCATCAGA 2 84 0 GGGCGTGTTA 0.8704 -217 CTCCATGCCGGATGGGGTTGTTTAACATACCCGC 3 51 0 GGGGGTGTTA 0.884395 -60 ACTTTTATAAGGGTGAGGAGTATACACGAGGCTT 14 90 0 GTGAGAGTTA 0.482636 -148 TTCAAAAAAGGCCGCGGTGCTTTACAAAGCAGCA 14 128 1 GGCGGGCTTA 0.774613 -110 ATTTCAAAATGGTGCGGAATTTTACTGCAATTGC 14 162 0 GGCGGATTTA 0.975439 -76 GCGACGTTAAGCGGCAGTATTCTACTCGTAGCGA 15 35 0 GGCAGATTTA 0.927586 -114 AGAATGAAAGGACGCCGATCTCTAATTCAGCGAT 15 105 0 GGCCGTCTTA 0.736493 -44 GGTGTGCGCGGAAGCGGAGTTTTAT 16 244 1 GGCGGGTTTA 0.908396 -15 GTAACGTGGGGTCGCAGGATTATAGAGAAGTCGG 17 50 0 GGCAGATTTA 0.927586 -169 CCATATCGAGGGCGCGGCATTATAACACCGCTTC 24 81 0 GGCGGATTTA 0.975439 -84 ACTACGACAAGCCCGCGCATTATACATACTTAAC 26 55 0 GCGCGATTTA 0.652251 -183 CATTACGATTGATGGGAGAGTGTAACCGTTCTTA 26 163 0 GGGGAAGTTA 0.74308 -75 ACAATATGAGGACGCCGAATTTTAGGGCGATGCC 28 46 0 GGCCGATTTA 0.972118 -80 GATTCTCAAAGGTGGCGTAGTATACGCTGACTCA 29 66 0 GGGCGAGTTA 0.966706 -151 TGGCGCGCCGGGTGGAGGATTATACGGGCTGATG 30 67 0 GGGAGATTTA 0.903618 -234 AAAGAGAATTGACTCCGGAGTGTACAATTATTAC 30 172 1 GTCCGAGTTA 0.776246 -129 GGTGATTAAAGAGGCCGGATTGTAATAATTGTAC 30 193 0 GGCCGATTTA 0.972118 -108 CTTGAAATTCGGTGGGTTAGTATACACATTGCCG 31 24 1 GGGGTAGTTA 0.621241 -179 AAAAACAAAAGGCGCGAAATTGTATTCCAATCTC 32 55 0 GGCGAATTTA 0.776437 -103 * **** *** ** Masking position 11 Map Score: 18.5878 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 237 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 GACAATTCAAAGGCCGAGGAATATGCCCTT 1 55 0 AGGCCGAGGA 0.814998 -48 TTTGTGGTATAAAGCGCGCCGGACTTCCGA 2 130 1 AAAGCGCGCC 0.830789 -171 AGGGCGCGCATATTAACTTT 4 150 0 AGGGCGCGCA 0.991659 -10 TTGGTGCCGGAGTGCGCGCAGTCACCGGAG 13 77 0 AGTGCGCGCA 0.894076 -172 GACTTTTATAAGGGTGAGGAGTATACACGA 14 95 0 AGGGTGAGGA 0.78638 -143 CTTTCAAAAAAGGCCGCGGTGCTTTACAAA 14 126 1 AGGCCGCGGT 0.936473 -112 TTATTTCAAAATGGTGCGGAATTTTACTGC 14 168 0 ATGGTGCGGA 0.841924 -70 TATTCACAATAGGGCGCGAATATTACGCAA 16 186 0 AGGGCGCGAA 0.976803 -73 TCAATGATTCAGAGTGCGCTATAAATATTC 16 211 0 AGAGTGCGCT 0.668361 -48 CCCCATATCGAGGGCGCGGCATTATAACAC 24 87 0 AGGGCGCGGC 0.990385 -78 AACTACGACAAGCCCGCGCATTATACATAC 26 60 0 AGCCCGCGCA 0.787418 -178 GGAAACCAGCATGGCGCGCCGGGTGGAGGA 30 82 0 ATGGCGCGCC 0.907736 -219 TCCCTGCGAAAAGGTGCGGAAAAGCGCGGT 30 134 1 AAGGTGCGGA 0.924489 -167 AAGGTGCGGAAAAGCGCGGTAAATAAGGAA 30 144 1 AAAGCGCGGT 0.75879 -157 TTGCCGTAGAAGAGTGCGGATCAGTTTGCA 31 52 1 AGAGTGCGGA 0.901207 -151 ATTTCGTACGAAGGCGCGAAATCATACAGA 31 96 0 AAGGCGCGAA 0.924751 -107 CCTCGGTTTAAGGCCGCGTCGCTCTTCCAG 31 176 0 AGGCCGCGTC 0.749065 -27 ATAAAAACAAAAGGCGCGAAATTGTATTCC 32 61 0 AAGGCGCGAA 0.924751 -97 ********** Masking position 1 Map Score: 19.1192 Number of sites scoring better than the average of aligned sites = 1511 Number in coding regions = 1404 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 ACACACGTATCGGCACATATTCCGGGGTGCCCTTT 2 215 1 CGCCTATTCG 0.926936 -86 GCGACCGAATTTGCAGTACCCCCGTT 3 2 1 CGCGATTTCG 0.889694 -109 TTAAACTATGCGCTTCGTTTTGCAGGTTGATGTTT 4 12 1 CGTCTTTTCG 0.949454 -148 TATAGAATCTCGCCCGCTTTTGCATACGCAAAGCA 10 44 1 CGCGTTTTCT 0.822606 -81 AGCGCCGTCTTTTACCGTTTATCCGGT 12 14 0 CGCTTTTTCG 0.953754 -17 GGAGTATACACGAGGCTTTCTCCAGGGGCGAACAA 14 73 0 CGGCTTCTCG 0.786541 -165 GGTCAAAGATCGACCCCTTTTTGTGATTTGTGACA 17 15 0 CGCCTTTTGG 0.98078 -204 CGCCTCGTTTTCCAGGTTTGTTGGA 20 1 1 CGCCTTTTCG 0.993309 -33 AAAAAATAAACGGCTCATTTCTGAGCCGTTTATTC 24 32 0 CGCCTTTCGG 0.92723 -133 GGATTTTTAACGACCTGATTTTCGGGTCTCAGTAG 24 115 1 CGCTATTTCG 0.781657 -50 AATATGAGGACGCCGAATTTTAGGGCGATGCCGAA 28 43 0 CGCATTTTGG 0.800622 -83 ATTGGCGCCTCGTCAGGCTTTACAGCCCGGTCATC 29 148 0 CGCGCTTTCG 0.87146 -69 CGCGCTTTTCCGCACCTTTTCGCAGGGAAAATGTA 30 127 0 CGACTTTCCG 0.726766 -174 CGGTGTCCATCGTTTCATTTTTCGGCGGATATCCA 30 235 1 CGTCTTTTCG 0.949454 -66 ACGATTAAATCGCCGCTTTTTTGATCGCTGGG 32 8 0 CGCCTTTTGT 0.835837 -150 AGTACTATAACGCGTCATTTTTCAGCCGACCTTTA 35 205 1 CGGCTTTTCG 0.966728 -96 ** * * **** * * Masking position 2 Map Score: 14.9868 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 577 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AACAAACATCAACCTGCAAAACGAAGCGCATAG 4 17 0 ACCGAAAACG 0.95306 -143 AACGAAAATAAAGCAGTAACCCGCAATGTGTGC 4 60 1 AGCGAACCCG 0.911708 -100 GTAGTGAGTACACCAGCAAAACGCTTAAAGAAC 9 43 0 CCCGAAAACG 0.980662 -258 GCTACAGGCGACCCAGCAACAGGTAAGTGATCT 10 78 0 ACCGAACAGG 0.847852 -47 TCTTAAATTAATCCTGCTACAGGCGACCCAGCA 10 93 0 ACCGTACAGG 0.530717 -32 ACCACCGGATAAACGGTAAAAGACG 12 3 1 CCCGTAAACG 0.911437 -28 GCGCGCACTCCGGCACCAAACTGGCTGCACCGC 13 88 1 CGCCAAACTG 0.623971 -161 GTTGCTAACTCTGCTGTAAAAGGCCGTCGGCGG 13 117 0 CGCGAAAAGG 0.954979 -132 GCGTTGATGCCAGCGGCAAACCGAATTAATCAA 14 202 1 CGCGAAACCG 0.97757 -36 GAGTAGAATACTGCCGCTTAACGTCGCGTAAAT 15 42 1 CGCGTTAACG 0.553293 -107 TTCTCCAACAAACCTGGAAAACGAGGCG 20 6 0 ACCGAAAACG 0.95306 -28 CCATTTGAGTATCCTGAAAACGGGCTTTTCAGC 21 90 1 ACCGAAACGG 0.899742 -57 TATTGGATATCCGCCGAAAAATGAAACGATGGA 30 240 0 CGCGAAAATG 0.892375 -61 AAGAGCGACGCGGCCTTAAACCGAGGTTTTCCC 31 180 1 CGCTAAACCG 0.697304 -23 TTTATGGCCTTGCCCGTAAAACGATTTTTTATA 32 86 1 TCCGAAAACG 0.784418 -72 ACTCACTTCACTCCTCCAAACGGAGAGAGCGTC 33 238 0 CCCCAAACGG 0.824779 -63 TTTCGCAATTAACCTCTAACACGCTGATTTGAA 35 126 0 ACCCAACACG 0.716166 -175 TGTTAAAGGTCGGCTGAAAAATGACGCGTTATA 35 210 0 CGCGAAAATG 0.892375 -91 CTGTCTGGGTCAGCCGAATCCCGGGGAGGCAAG 35 248 0 CGCGATCCCG 0.774861 -53 * ** * ****** Masking position 4 Map Score: 15.2682 Number of sites scoring better than the average of aligned sites = 2434 Number in coding regions = 2292 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 GGAAGTCCGGCGCGCTTTATACCACAAATACGTC 2 124 0 CGCGCTTCCA 0.713601 -177 TCAAGTAGCACTGTCTGTGGAGCCTTCGGGCTTC 8 16 1 CTGTCTGGCC 0.899103 -81 GTGGAGCCTTCGGGCTTCACAGGCTTTGTTCGCC 8 32 1 CGGGCTTGGC 0.969411 -65 TCGGCCTGGCTTGTTTGCCATTTTGGCAC 13 6 1 CTGGCTTGCC 0.988837 -243 CGGCACCAAACTGGCTGCACCGCCGACGGCCTTT 13 98 1 CTGGCTGGCC 0.981666 -151 TTGAAATAAGCTGGCGTTGATGCCAGCGGCAAAC 14 189 1 CTGGCGTGCC 0.959647 -49 CGCAAAAGCCGGGCTTTTCGCCCCGATTACCTT 16 10 1 CGGGCTTCCC 0.976946 -249 ATCCTGAAAACGGGCTTTTCAGCATGGAACGTAC 21 100 1 CGGGCTTGCA 0.982861 -47 CTGTCTTTACTCCCGTGATTCAAT 23 20 0 CTGTCTTCCC 0.794153 -14 CTGCGATGACCGGGCTGTAAAGCCTGACGAGGCG 29 144 1 CGGGCTGGCC 0.989887 -73 GAGGATTATACGGGCTGATGGGTAAAGCGCAAGG 30 53 0 CGGGCTGGTA 0.814322 -248 CCTTATTTACCGCGCTTTTCCGCACCTTTTCGCA 30 138 0 CGCGCTTGCA 0.904956 -163 TTAATCACCCATGGCTTCGGTGTCCATCGTTTCA 30 218 1 ATGGCTTGTC 0.388071 -83 CGCGTGGTGTCTGGCGTTAGGGCTGGAAGAGCGA 31 154 1 CTGGCGTGCT 0.67508 -49 GAAACTCCTGCGGTCTTCGACGGAGGCCTGGATA 33 116 0 CGGTCTTGGA 0.651301 -185 ******* *** Masking position 5 Map Score: 12.9461 Number of sites scoring better than the average of aligned sites = 1278 Number in coding regions = 1189 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 CCAAAGGGCACCCCGGAATATGTGCCGATAC 2 221 0 CCCCGAATAT 0.902934 -80 TAAAGCAGTAACCCGCAATGTGTGCGAATTA 4 68 1 ACCCGAATGT 0.790934 -92 CTTTCAGACGCACCGTGATGTTATCAGTTGT 9 14 1 CACCGGATGT 0.950525 -287 GCCCCCGAGATATCAGTTTACCC 11 3 1 CCCCGGATAT 0.981755 -39 GCCATTTTGGCACCGGGATGTGCTCGTCATC 13 27 1 CACCGGATGT 0.950525 -222 CTGTCTTTACTCCCGTGATTCAATTGGTGAC 23 13 0 TCCCGGATTC 0.810549 -21 CAAATGCCAAACCCGAGATTCTCAAAGGTGG 29 85 0 ACCCGGATTC 0.882964 -132 ACGCCAGACACCACGCGATGTTAAAAGTATA 31 140 0 CCACGGATGT 0.906627 -63 CTGAGAGGCTCCCCGTGATATAAAAAATCGT 32 106 0 CCCCGGATAT 0.981755 -52 TTCCTTGCCTCCCCGGGATTCGGCTGACCCA 35 245 1 CCCCGGATTC 0.974563 -56 ***** ***** Masking position 8 Map Score: 8.27994 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 103 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AGGGCGCGCATATTAACTTTGT 4 148 0 GGCGCGCATA 0.925605 -12 AGCACATCCCGGTGCCAAAATGGCAAACAA 13 21 0 GGTGCCAAAA 0.904363 -228 GCTTTCTCCAGGGGCGAACAAAGTTTTACA 14 64 0 GGGGCGAACA 0.910092 -174 ATTTCAAAATGGTGCGGAATTTTACTGCAA 14 166 0 GGTGCGGAAT 0.885398 -72 TAAGGTAATCGGGGCGAAAAGCCCGGCTTT 16 15 0 GGGGCGAAAA 0.970499 -244 TTCACAATAGGGCGCGAATATTACGCAAAA 16 184 0 GGCGCGAATA 0.981567 -75 AGCCTGACGAGGCGCCAATACCCCATACGA 29 164 1 GGCGCCAATA 0.926954 -53 CCTGCGAAAAGGTGCGGAAAAGCGCGGTAA 30 136 1 GGTGCGGAAA 0.944636 -165 TTCGTACGAAGGCGCGAAATCATACAGAAA 31 94 0 GGCGCGAAAT 0.972453 -109 AAAAACAAAAGGCGCGAAATTGTATTCCAA 32 59 0 GGCGCGAAAT 0.972453 -99 CTATGTGACTGGTGCGAATGAAGGAAGCCA 33 28 1 GGTGCGAATG 0.878034 -273 ********** Masking position 8 Map Score: 10.7655 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 512 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 AGTAACCCGCAATGTGTGCGAATTATTGGC 4 74 1 AATGTGTGCG 0.580382 -86 CCCCGATCCAACGGGGAGCACCAA 5 5 0 ACGGGGAGCA 0.780146 -47 AACCGGGTGGAAGGTGAGAGGTTAATGTCT 9 148 1 AAGGTGAGAG 0.914745 -153 CAGTTTGGTGCCGGAGTGCGCGCAGTCACC 13 81 0 CCGGAGTGCG 0.706617 -168 CCATCGAGGAACGGAGTCCGGTGTCATATT 13 196 0 ACGGAGTCCG 0.824773 -53 GAATTAATCAAAGGTGAGAGGCAC 14 224 1 AAGGTGAGAG 0.914745 -14 GCACTTGTCAAAGGCGTGCGTTTTGCGTAA 16 164 1 AAGGCGTGCG 0.9174 -95 AATCATTGAAAAGGTGTGCGCGGAAGCGGA 16 232 1 AAGGTGTGCG 0.957845 -27 CGATGCCGAAAAGGTGTCAAGAAATATACA 28 23 0 AAGGTGTCAA 0.378479 -103 ATCGTTGCACAAGGCGTGAGATTGGAATAC 32 38 1 AAGGCGTGAG 0.839862 -120 TTTTTATATCACGGGGAGCCTCTCAGAGGC 32 111 1 ACGGGGAGCC 0.675479 -47 CCCTGCGTAGACGGTGACAGAACGCTAAGA 33 165 1 ACGGTGACAG 0.830756 -136 CGTCTTAATTACGGTGAGCAGAAACAAGCC 33 212 0 ACGGTGAGCA 0.878928 -89 ACTCCTCCAAACGGAGAGAGCGTCTTAATT 33 232 0 ACGGAGAGAG 0.886321 -69 ********** Masking position 6 Map Score: 6.94651 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 825 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 ACATCAACCTGCAAAACGAAGCGCATAGTT 4 15 0 GCAAAACGAA 0.948303 -145 CGAATTATTGGCAAAAGGCAACCACAGGCT 4 92 1 GCAAAAGGCA 0.965957 -68 TAGAGTCAAAGAAAAAGGCAGCCTGTGGTT 4 111 0 GAAAAAGGCA 0.786344 -49 GAGTACACCAGCAAAACGCTTAAAGAACAA 9 41 0 GCAAAACGCT 0.966945 -260 GATGCCAGCGGCAAACCGAATTAATCAAAG 14 207 1 GCAAACCGAA 0.849495 -31 CGAATATTACGCAAAACGCACGCCTTTGAC 16 170 0 GCAAAACGCA 0.985346 -89 TACTTTACTAGCAATACGCTTGCGTTCGGT 26 24 1 GCAATACGCT 0.858618 -214 ********** Masking position 4 Map Score: 2.70223 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 281 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 CCCGATCCAACGGGGAGCACCAA 5 4 0 CGGGGAGCAC 0.955634 -48 TTGCCGATCAAGCATAGCACC 6 2 0 AGCATAGCAC 0.916616 -100 ATATAGATACAGGAGAGCACAT 7 41 1 AGGAGAGCAC 0.986122 -12 GCATACGCAAAGCAGATCACTTACCTGTTG 10 65 1 AGCAGATCAC 0.916616 -60 AGTTGACATTAGCGGAGCACTAAA 24 151 1 AGCGGAGCAC 0.983308 -14 ATCATCACAGAGGAGAGCACA 35 2 0 AGGAGAGCAC 0.986122 -299 ********** Masking position 6 Map Score: 4.33418 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ATTTAGGGGTTTAGCACGTGTTTCTTCGCTACGGCG 6 36 1 TTGCTGTTTT 0.9663 -66 ACAGGCTTTGTTCGCCTTTGTTTCGTTTATTAACAA 8 50 1 TTGCTGTTTT 0.9663 -47 GCGAACCAATTTAGCATTTGTTGGCTAGATGGTTTC 9 197 1 TTGCTGTTGT 0.978675 -104 AGCAGATCACTTACCTGTTGCTGGGTCGCCTGTAGC 10 75 1 TTCCTGCTGT 0.849707 -50 TACAGCAGAGTTAGCAACTGTTGATTGCAATTCCCG 13 132 1 TTGCTGTTGT 0.978675 -117 TTTTACTGCAATTGCTGCTGCTTTGTAAAGCACCGC 14 141 0 ATGCTGCTTT 0.793698 -97 TTTTTTCGCATATTTTTCTTGCAAAGTTGG 21 5 1 TTGCTTTTTT 0.863571 -142 TGAACCTCAGTTAGCCGAATTTGGCTACCTAACAAT 26 106 1 TTGCATTTGT 0.715403 -132 GCTCCTGGTTTTAGCTTTTGCTTCGTAAACACGTAA 28 94 0 TTGCTGCTTT 0.970774 -32 AAAAATCAAATTAGCTCGAGCTTCGTATGGGGTATT 29 180 0 TTGCAGCTTT 0.891792 -37 TGCGGATCAGTTTGCATACGCTGGTTAATTTCTGTA 31 66 1 TTGCCGCTGT 0.917267 -137 GGAATACAATTTCGCGCCTTTTGTTTTTATGGCCTT 32 61 1 TTGCTTTTGT 0.910162 -97 ** ** ***** * Masking position 12 Map Score: 6.76359 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 177 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 TTATATTTAACGTCCACCTGGCTCCATGCCGG 3 74 0 CTCCACCGGC 0.989705 -37 TTTAATAACTTCCACTTCGCATTGTTAATA 8 77 0 CTCCACTCGC 0.983769 -20 AACCTCTCACCTTCCACCCGGTTGAGCGATGT 9 139 0 CTCCACCGGT 0.925761 -162 CCGCATTGGTCCTACACTGCGCGGTAATAAAG 14 27 0 CTACACTCGC 0.974498 -211 CTTTGCGTAACGTACACTGGGATCGCTGAATT 15 84 1 CTACACTGGA 0.832117 -65 GCTGAGTCAGCGTATACTACGCCACCTTTGAG 29 64 1 CTATACTCGC 0.810144 -153 CCCGTATAATCCTCCACCCGGCGCGCCATGCT 30 73 1 CTCCACCGGC 0.989705 -228 GCCCTAACGCCAGACACCACGCGATGTTAAAA 31 145 0 CGACACCCGC 0.941516 -58 * ****** *** Masking position 6 Map Score: 3.92024 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 247 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 CGGGCAAATTGAGAATCATTCTGAATT 2 8 1 ATTGAGAATC 0.855233 -293 CTACAAACGAATTGCGAATCGAATCAATGT 9 72 1 ATTGCGAATC 0.962725 -229 TGTGTACCTGATTGCGAACCAATTTAGCAT 9 184 1 ATTGCGAACC 0.938081 -117 TTAACAGTTCATTGCGAAACCATCTAGCCA 9 218 0 ATTGCGAAAC 0.971075 -83 TGTTTAACACTTTGCGTAACGTACACTGGG 15 75 1 TTTGCGTAAC 0.723868 -74 CTACGCCACCTTTGAGAATCTCGGGTTTGG 29 80 1 TTTGAGAATC 0.719888 -137 GATTAAGTTTCTTGCGAAACTCCTGCGGTC 33 135 0 CTTGCGAAAC 0.924502 -166 TTAGAGGTTAATTGCGAAAGGGGAGATTTA 35 140 1 ATTGCGAAAG 0.847437 -161 ********** Masking position 8 Map Score: 2.48032 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 99 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 GGCTTCACAGGCTTTGTTCGCCTTTGTTTCG 8 44 1 GCTTTGTCGC 0.814776 -53 TTGGCACCGGGATGTGCTCGTCATCCTCACG 13 33 1 GATGTGTCGT 0.725324 -216 ACATCAACCCGCATTGGTCCTACACTGCGCG 14 36 0 GCATTGTCCT 0.941778 -202 GGGCTTTTCAGCATGGAACGTACATATTAAA 21 111 1 GCATGGACGT 0.811803 -36 TGGGTAAAGCGCAAGGATCGTCCTGGATCTT 30 38 0 GCAAGGTCGT 0.922328 -263 GCCTTCGTACGAAATGATCGTATTGAAGCTA 31 111 1 GAAATGTCGT 0.874462 -92 CACATAGTTAGCTATGCTCCTGGC 33 4 0 GCTATGTCCT 0.902891 -297 GGATAGAAAAGATTTGTTCGTTGGAGCCTGG 33 83 1 GATTTGTCGT 0.895637 -218 TAGCTTTGCTCCTGGATGTTTGC 33 288 0 GCTTTGTCCT 0.931564 -13 TCCCGGGGAGGCAAGGAACGTGTTAAAGGTC 35 232 0 GCAAGGACGT 0.746602 -69 CGAATTGCTCCTTACGGATTAT 35 289 0 GAATTGTCCT 0.85597 -12 ****** **** Masking position 9 Map Score: 2.35493 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 243 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 TTTATCCCCGATCCAACGGGGAGCACCAA 5 10 0 ATCCAACGGG 0.913311 -42 CTGTCTGTGGAGCCTTCGGGCTTCACAGGC 8 26 1 AGCCTTCGGG 0.99048 -71 TAAAGTAAACAGCCTTCGGG 26 1 0 AGCCTTCGGG 0.99048 -237 GCTATGCGCGATCCTTCGGGATCTTTGTCT 29 14 1 ATCCTTCGGG 0.985351 -203 ********** Masking position 1 Map Score: 1.38218 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185