AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_ecoli_reg_300.orf -o00910_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 Purged sequences: BIME145 77 BIME Input sequences: #1 cynT 108 carbonic anhydrase #2 cynS 30 cyanate aminohydrolase, cyanase #3 fdrA 300 involved in protein transport; multicopy suppressor of dominant negative ftsH mutants #4 ylbE 266 orf, hypothetical protein #5 asnB 247 asparagine synthetase B #6 BIME40 115 BIME #7 nagD 47 N-acetylglucosamine metabolism #8 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #9 nagB 300 glucosamine-6-phosphate deaminase #10 dadA 300 D-amino acid dehydrogenase subunit #11 narG 300 nitrate reductase 1, alpha subunit #12 narZ 81 cryptic nitrate reductase 2, alpha subunit #13 narU 300 nitrite extrusion protein 2 #14 gdhA 235 NADP-specific glutamate dehydrogenase #15 sppA 160 protease IV, a signal peptide peptidase #16 ansA 166 cytoplasmic L-asparaginase I #17 napF 300 ferredoxin-type protein: electron transfer #18 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #19 ansB 175 periplasmic L-asparaginase II #20 yggN 71 orf, hypothetical protein #21 yggH 160 orf, hypothetical protein #22 metC 103 cystathionine beta-lyase (beta-cystathionase) #23 gltB 300 glutamate synthase, large subunit #24 yhfC 270 putative transport #25 nirB 261 nitrite reductase (NAD(P)H) subunit #26 rpmH 300 50S ribosomal subunit protein L34 #27 yidC 223 60 KD inner-membrane protein #28 thdF 105 GTP-binding protein in thiophene and furan oxidation #29 tnaL 242 tryptophanase leader peptide #30 tnaA 205 tryptophanase #31 asnA 151 asparagine synthetase A #32 glnA 300 glutamine synthetase #33 aspA 300 aspartate ammonia-lyase (aspartase) Motif number 1 AGGCGCTGGCAATACTGGAGCAGGGGAA 4 249 1 AAAGGCGGGG 0.970993 -18 ACCTGTTAAAAACCGCGTCGCCGGAGAATTTTTTTC 10 42 1 AACGGCGGAG 0.986862 -259 ATCCCAATTCATTCCTGGAGCAGGAGTCATGTC 12 59 1 ATCGGCGGAG 0.988638 -23 TCTGCTACTGATAACGGTAGCCGGGTGGCAAAACTT 14 35 1 ATAGGCGGGT 0.946102 -201 GCAAAAGTATATACGTGAGGCAGGGGGAGCGCACCT 16 114 0 ATCGGCGGGG 0.991751 -53 TAGCAGGATCAAAAGAGTGGCGGGAAGCGTGGCAAA 17 139 0 AAAGGCGGAA 0.730142 -162 GATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTG 17 156 0 AACGGCGGAT 0.97143 -145 GCATTATCCAAAGTTAGTTGCCGGATGCAAGCATGA 21 98 0 AATGGCGGAT 0.769235 -63 ATAGAAATAGATGCACGTAGCGGGGGAAGAGAGGAA 25 48 0 ATCGGCGGGG 0.991751 -214 GTGGAGGATTATACGGGCTGATGGGTAAAGCGCAAG 26 54 0 ATCGGAGGGT 0.781873 -247 GCCATGGGTGATTAAAGAGGCCGGATTGTAATAATT 26 197 0 ATAGGCGGAT 0.927035 -104 TAATCATAAGCAACAGGACGCAGGAGTATAAAAA 31 128 1 CACGGCGGAG 0.922166 -24 TTCGCAACCCATTCAGGTAGCCGGGGTTAACCGGCT 33 39 0 ATCGGCGGGG 0.991751 -262 ** * * ** **** Masking position 7 Map Score: 16.3639 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 264 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 TTGTTGTTTTAAAAATCAGGTTAAAAGTGAGCGG 3 110 0 AAAAAGGTAA 0.9418 -191 GAATTCAAATAACCACCAGGCTATTACTCATTAT 3 157 0 AACAAGGCAT 0.586564 -144 AACAAGCAACAAATACCAGGTTAACGGAGAAGGT 5 223 1 AAAAAGGTAA 0.9418 -25 GATGGGGATGAAAAATAAAGTAAATTCCTAAGAT 11 168 0 AAAAAAGTAA 0.799713 -133 TACTAAATGTAACTAACAAGCTAACCTTCAAACG 13 107 0 AACAAAGCAA 0.803583 -194 AAAAAAGACAAAACACGAGGTAAGGCGCAATAGC 13 246 0 AAAAAGGTAG 0.790652 -55 GCGGATAAGGAAATATGGGGCGAAACAGCGGGAA 16 72 0 AAAAGGGCAA 0.858809 -95 TTTAACACTAAAAGAGCAGGTAAAATTGTCTG 17 9 0 AAAAAGGTAA 0.9418 -292 ACAGACTGTTAACCATAAGGTAAAATTGATCATC 18 150 0 AACAAGGTAA 0.911467 -151 TTCCCTCAAGAAAAATCAGGCCAGCATTTGCTGG 20 44 0 AAAAAGGCAG 0.858809 -28 CGAAAAGGACAACAAGGGGGCGAATCGGAGGCGC 23 273 1 AACAGGGCAA 0.794653 -28 CAGAGCAGAAAAAAAGCAAGTGAAGAGATTCTAA 24 28 1 AAAAAAGTAA 0.799713 -243 TTCAGATACGTAAAATTAGGTAAAGGGATGGCCT 24 78 0 TAAAAGGTAA 0.550492 -193 ATGTTTGTGCAAAAAATAGACAAAATGAGCGGGT 25 86 0 AAAAAGACAA 0.549003 -176 TACGAAAAGAAAAAAGGCGGTCAACTGACCGCCC 28 35 0 AAAACGGTAA 0.672367 -71 CAGGAGTGGTAACAATGAAGCGAAGCCGCATCTG 29 40 0 AACAAAGCAA 0.803583 -203 TGATTCATTAAAAAAGAAGGCTAAAATAGAATGA 31 37 0 AAAAAGGCAA 0.963048 -115 TCGCCGTAAAAAAGATAAAGCGAAATCTGTGCCA 32 212 0 AAAAAAGCAA 0.865422 -89 *** * **** ** Masking position 5 Map Score: 12.4714 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 212 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 GAGTAAATAAGGTGATGAATATCACACAGGAATTAT 3 199 0 GGTGATCACA 0.644048 -102 AACGATATTTGGTGACAAAACTCACAAAAGACACGC 9 126 0 GGTGATCACA 0.644048 -175 GCTTTTTTATGGTGAGCTGGCTCACATCTCCCTGAC 10 188 0 GGTGATCACA 0.644048 -113 CCCAACTTAAGGTCACACCTGTCACAGGCGCAATAG 15 128 0 GGTCATCACA 0.951168 -33 GGTCACCGAATTCACTGTTGTTGGGG 21 1 1 GGTCATCACT 0.882836 -160 CATTTTAAGAGGTGATTTTGATCACGGAATAAAAAG 24 133 0 GGTGATCACG 0.867003 -138 CCCGAACGATTGTGATTCGATTCACATTTAAACAAT 29 152 1 TGTGATCACA 0.499209 -91 AGAGTCCCTTTGTGATCGCTTTCACGGAGCATAAAA 32 35 1 TGTGATCACG 0.540611 -266 ATCCCAAAGCGGTGATCTATTTCACAAATTAATAAT 33 143 1 GGTGATCACA 0.644048 -158 ***** ***** Masking position 5 Map Score: 11.359 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 45 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CATGTTTACATCAGTGGCGCAAGCCAATGC 4 19 1 TCAGTGGCGC 0.904262 -248 AAAGGGGCGTGCGTGGGCGCATGTCTGTTC 4 194 1 GCGTGGGCGC 0.934966 -73 GAAAGATGAAGCGCAGGCGCTGGCAATACT 4 235 1 GCGCAGGCGC 0.645806 -32 CACCGCCAAATCGCTTGCGCACAGTGCTGC 5 163 1 TCGCTTGCGC 0.693041 -85 TGATGCCTTGTCGGATGCGACACGGTTGTA 12 28 0 TCGGATGCGA 0.74425 -54 GTCACACCTGTCACAGGCGCAATAGATGTG 15 123 0 TCACAGGCGC 0.952788 -38 CCGCATAGTATCAGGTGCGCTCCCCCTGCC 16 102 1 TCAGGTGCGC 0.900786 -65 GCATGAATATTCGCGGGCGCATCCTGAAGA 22 44 0 TCGCGGGCGC 0.979696 -60 AGGGGGCGAATCGGAGGCGCGCGT 23 287 1 TCGGAGGCGC 0.989032 -14 GCTTTGTGTGGCGGATGCGCGGTGCTTATC 28 74 0 GCGGATGCGC 0.758002 -32 GAATGCGGCTTCGTAAGCGCGG 29 3 0 TCGTAAGCGC 0.778142 -240 ********** Masking position 8 Map Score: 10.6958 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 839 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 CAATGCGCTGGCAGGAGATGACCGGACCCAT 4 162 1 GCAGGAGTGA 0.956597 -105 TCAATATATTGCAGGAGCTGCGTAGGCCTGA 6 81 0 GCAGGAGTGC 0.961528 -35 AGGAGCCAGGGCAGGGATAACAA 8 3 0 GCAGGGAAAC 0.701281 -57 AGGGCGTTCAGCAGGAGATACTAAAGACGCC 10 144 1 GCAGGAGTAC 0.952158 -157 ACAGGCTCCCACAGGAGAAAACCG 11 287 1 ACAGGAGAAA 0.690602 -14 AAGCGTAACCGCGGGGGCAGAATGGGGATTA 13 158 0 GCGGGGGAGA 0.897468 -143 AAATATCACGACAGGAGTTAATCAA 15 5 0 ACAGGAGTAA 0.714342 -156 GTACTTGTCAGCAGGAATTGCGGACTGTGCT 15 71 0 GCAGGAATGC 0.744417 -90 TATACGTGAGGCAGGGGGAGCGCACCTGATA 16 110 0 GCAGGGGAGC 0.96222 -57 AAAACCTGTAGCAGGATCAAAAGAGTGGCGG 17 152 0 GCAGGATAAA 0.722091 -149 CACAGCGACGGCAGGGTGTAAACCGGAACTT 21 49 1 GCAGGGTTAA 0.7681 -112 AAATGGCATAGCGGGATATGCCGCGAGCGGG 24 228 0 GCGGGATTGC 0.620063 -43 GATGCACGTAGCGGGGGAAGAGAGGAAAAGG 25 44 0 GCGGGGGAGA 0.897468 -218 GCAACAGGACGCAGGAGTATAAAAA 31 137 1 GCAGGAGATA 0.687189 -15 GGCTGCTATTACAGGAGAAACCTTTGCGCTG 33 12 0 ACAGGAGAAC 0.717493 -289 CATTCAGGTAGCCGGGGTTAACCGGCTGCTA 33 35 0 GCCGGGGTAA 0.7438 -266 TTCGGTCGATGCAGGGGATAATCGTCGGTCG 33 253 1 GCAGGGGTAA 0.952158 -48 ******* *** Masking position 5 Map Score: 12.4279 Number of sites scoring better than the average of aligned sites = 1380 Number in coding regions = 1285 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 GCAGTACAATTTGCAGCAAAATAAAAATACGG 9 19 0 TTGCACAAAT 0.816721 -282 CCTTTTTATCCAGCATAAAATTCCGTTCAGAA 10 115 0 CAGCAAAATT 0.703922 -186 CTCCCTGACTCTGCGGCAATATGGCGTCTTTA 10 165 0 CTGCGCAAAT 0.919996 -136 TAATACCCATCTGCATAAAAATCTTAATAGTT 11 63 1 CTGCAAAAAT 0.930923 -238 GAGAGCAAACCAGCAGAAATATCTCTGGTGAA 17 52 1 CAGCAAAAAT 0.837017 -249 AAGGCCGTGGCTGCGGAAAGTTCCGGTTTACA 21 65 0 CTGCGAAATT 0.898035 -96 GCCATTTGCGAAAATTTTCTGCTTTAT 22 6 1 TTGCGAAATT 0.828119 -98 AAATGTGCTTTAGCGCAAAATTCTTTATTAAA 23 102 0 TAGCGAAATT 0.647395 -199 ATCTCAATTACTGCATAAATATGATGAGCAGG 23 216 0 CTGCAAAAAT 0.930923 -85 TGTCTATTTTTTGCACAAACATGAAATATCAG 25 98 1 TTGCAAAAAT 0.880558 -164 TACATTTTCCCTGCGAAAAGGTGCGGAAAAGC 26 127 1 CTGCGAAAGT 0.879541 -174 CCAAAGGTCATTGCACCAACATGGTGCTTAAT 32 79 1 TTGCACAAAT 0.816721 -222 GATGTGAATGTTGCACCAATATAGTGCTTCAA 32 118 0 TTGCACAAAT 0.816721 -183 CCAGCGCAAAGGTTTCTCCTGTA 33 2 1 CAGCGAAAGT 0.735622 -299 CCAAAAATAGTTGCGCAAACATCTTGAAATTT 33 106 0 TTGCGAAAAT 0.912337 -195 ***** *** ** Masking position 8 Map Score: 10.9392 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 225 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 ACTGCTTCACGCCGGGCCGCCAATGCGCTG 4 142 1 GCCGGGCCGC 0.97371 -125 GCACAGTGCTGCTTTGCGGCATTTTTTTAA 5 181 1 GCTTTGCGGC 0.780281 -67 TCGGATTGACGCCTGTCTGCGCAAATCCAG 9 222 1 GCCTGTCTGC 0.846703 -79 TCCTGTGGGAGCCTGTCGGCCCTCTGATAA 11 273 0 GCCTGTCGGC 0.897205 -28 GATAACGGTAGCCGGGTGGCAAAACTTTAG 14 44 1 GCCGGGTGGC 0.97509 -192 TCCTCTTCCCGCTGTTTCGCCCCATATTTC 16 67 1 GCTGTTTCGC 0.674949 -100 AGATATTTCTGCTGGTTTGCTCTCTCATTA 17 46 0 GCTGGTTTGC 0.819975 -255 CATTGAATAAGCGGGGCTGACAACTTTTTC 18 273 0 GCGGGGCTGA 0.654818 -28 CCCTGCCGTCGCTGTGCTGCAATCTTGCCC 21 35 0 GCTGTGCTGC 0.89564 -126 TTGCTCATGCCGGACGGCACTATCGTCG 25 9 1 GCCGGACGGC 0.641236 -253 ACATCAATAAGCGGGGTTGCTGAATCGTTA 25 207 1 GCGGGGTTGC 0.885215 -55 AGCATGGCGCGCCGGGTGGAGGATTATACG 26 75 0 GCCGGGTGGA 0.82425 -226 TATTTACCGCGCTTTTCCGCACCTTTTCGC 26 139 0 GCTTTTCCGC 0.532698 -162 AATTATTTTGGCCGTGTCGCCGTAAAAAAG 32 232 0 GCCGTGTCGC 0.919385 -69 ********** Masking position 2 Map Score: 9.21724 Number of sites scoring better than the average of aligned sites = 2367 Number in coding regions = 2268 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 8 TAAATGAGACTTTTACCTTATGACAATCGG 1 46 1 TTTTACCTTA 0.819735 -63 AATCCAGATATTTTCCCTGTATGTTAATTG 3 32 0 TTTTCCCTGT 0.819373 -269 AACTATATTTTTTTGCCTGTCTGGATCACA 3 63 0 TTTTGCCTGT 0.897984 -238 TCCGCTCACTTTTAACCTGATTTTTAAAAC 3 109 1 TTTAACCTGA 0.795889 -192 TGAAGCAGTGTTTTGCCTTCGTTTAGTTCG 4 121 0 TTTTGCCTTC 0.909549 -146 CAGACAATTTTACCTGCTCTTTTAGTG 17 8 1 TTTTACCTGC 0.937222 -293 TGATGATCAATTTTACCTTATGGTTAACAG 18 149 1 TTTTACCTTA 0.819735 -152 AATCGTTCTCTTTTGCCTGAACTTACCACC 18 187 0 TTTTGCCTGA 0.92799 -114 TTCTTCGTTTTGTTACCTGCCTCTAACTTT 19 54 1 TGTTACCTGC 0.788484 -122 CGACTTCCCTTTTAGCCTTAAAGATAAAAT 23 54 1 TTTAGCCTTA 0.724245 -247 AAGCTTGCCATTTGACCTGTATCAGCTTTC 23 144 1 TTTGACCTGT 0.688285 -157 CTGAAATATATGTAACCTGACGATCACTTT 24 107 1 TGTAACCTGA 0.493323 -164 AGGTCGTACATTTTCCCTGCGAAAAGGTGC 26 121 1 TTTTCCCTGC 0.914013 -180 TTTGCCCTTCTGTAGCCATC 30 1 1 TTTGCCCTTC 0.642347 -205 TATATCTTAATTTTGCCTTTTGCAAAGGTC 30 75 1 TTTTGCCTTT 0.811012 -131 TTCATTCTATTTTAGCCTTCTTTTTTAATG 31 36 1 TTTAGCCTTC 0.807829 -116 ********** Masking position 3 Map Score: 8.65671 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 703 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 CACCAATCGACAATCACCATTACGTTTTTT 5 126 1 CAATCACCAT 0.785384 -122 GTTTCAAGCCGTATTTTTATTTTG 9 5 1 CAAGCCGTAT 0.86268 -296 TCACCATAAAAAAGCCGCATGTTGAATAAT 10 209 1 AAAGCCGCAT 0.874921 -92 TCTGGCTACTTAATCCCCATTCTGCCCCCG 13 148 1 TAATCCCCAT 0.759627 -153 AGCGACCAAATAAACCGCATAATTAATAAG 17 244 0 TAAACCGCAT 0.634059 -57 CCGCGCTTACGAAGCCGCATTCTGACTGTC 29 11 1 GAAGCCGCAT 0.965267 -232 ACAATGAAGCGAAGCCGCATCTGACAGTCA 29 33 0 GAAGCCGCAT 0.965267 -210 GATATATATGCAAGCACCATCATTTACTAA 30 127 0 CAAGCACCAT 0.936602 -79 AATGAATCATCAATCCGCATAAGAAAATCC 31 12 0 CAATCCGCAT 0.918034 -140 ATGGAAACATTAAGCACCATGTTGGTGCAA 32 89 0 TAAGCACCAT 0.852394 -212 TGTTTCCATTGAAGCACTATATTGGTGCAA 32 110 1 GAAGCACTAT 0.557843 -191 TAGAAATCCTCAAGCAGCATATGATCTCGG 33 220 1 CAAGCAGCAT 0.953416 -81 ********** Masking position 3 Map Score: 6.93538 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 255 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 AGACTACTCGCCGATTGTCATAAGGTAAAAGTC 1 53 0 CGATGTATAA 0.96593 -56 GTTCTGTAATCAGATTGTTAGATCATCTGCTAC 9 55 1 CGATGTAGAT 0.92022 -246 TCATCTGCTACAGAGTGTGTGAAAATTTAATTC 9 77 1 CGATGTTGAA 0.851941 -224 GGGTGAAGTGCTGATTGAAAGAATAGATAAGAA 13 188 0 CGATGAAGAA 0.867395 -113 CAGTCAATTCCTGACTGTCATAAAGGTGTGTTA 23 12 0 CGATGTATAA 0.96593 -289 AATTTAGCAACCGATTGCAATAAAACATTTAAA 24 170 1 CGATGCATAA 0.882771 -101 TTAAAGAGGCCGGATTGTAATAATTGTACACTC 26 189 0 CGATGTATAA 0.96593 -112 AAGCCGCATTCTGACTGTCAGATGCGGCTTCGC 29 22 1 CGATGTAGAT 0.92022 -221 GACAAAAACTCTGAGTGTAATAATGTAGCCTCG 29 197 1 CGATGTATAA 0.96593 -46 * ** *** **** Masking position 6 Map Score: 6.05957 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 GACCGGACCCATGAAAGGGGCGTGCGTGGGCG 4 181 1 AAAAGGGGCG 0.947693 -86 TTGCTTGTTTAAAAAAATGCCGCAAAGCAGCA 5 187 0 AAAAATGCCG 0.912496 -61 TGGTTTAGCCAGTAAAAGGGAGTGATAATAAC 9 159 0 AAAAAGGGAG 0.507745 -142 ATTTCTTATTATCAGAGTGCCACTAATCCGCT 10 84 1 AAGAGTGCCA 0.422946 -217 TTTATGCTGGATAAAAAGGGCGTTCAGCAGGA 10 128 1 AAAAAGGGCG 0.956679 -173 CCAGCTCACCATAAAAAAGCCGCATGTTGAAT 10 204 1 AAAAAAGCCG 0.792427 -97 ATGTCGATTTATCAGAGGGCCGACAGGCTCCC 11 265 1 AAGAGGGCCG 0.912078 -36 TTGAAATGTGAGCAAAAGCCCGTTTTTGCCAC 17 115 1 AAAAAGCCCG 0.65542 -186 TAGCAGGATCAAAAGAGTGGCGGGAAGCGTGG 17 143 0 AAGAGTGGCG 0.75987 -158 GGATGCAAGCATGATAAGGCCGTGGCTGCGGA 21 80 0 AATAAGGCCG 0.889396 -81 CGAAAAGGACAACAAGGGGGCGAATCGGAGGC 23 273 1 AAAGGGGGCG 0.670207 -28 ATAGCCTTCAAGAACAAGGCCATCCCTTTACC 24 62 1 AACAAGGCCA 0.467543 -209 TGCGTTCAAAAATAAAATGGCATAGCGGGATA 24 241 0 AAAAATGGCA 0.609417 -30 AGGCCGGACGACGATAGTGCCGTCCGGCATGA 25 15 0 AATAGTGCCG 0.714601 -247 GGGGGAAGAGAGGAAAAGGCCGGACGACGATA 25 31 0 AAAAAGGCCG 0.964883 -231 TGAAACGCGTATTAAAATGCCACCCTTTACAC 27 146 1 AAAAATGCCA 0.660014 -78 AGTTTTCGCTAAAATAAGGGCGGTCAGTTGAC 28 18 1 AATAAGGGCG 0.866005 -88 CCCTACGAAAAGAAAAAAGGCGGTCAACTGAC 28 40 0 AAAAAAGGCG 0.754197 -66 * ********* Masking position 4 Map Score: 10.7571 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 509 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 12 GGTGCAATTTTTAAGGAGTTGTT 3 288 1 TTAAGGAGTT 0.923926 -13 CAGATGGGTATTAAGGAGTATTCCCCATGG 11 46 0 TTAAGGAGTA 0.957735 -255 TTAATTATCCTAAAGGGGTATCTTAGGAAT 11 149 1 TAAAGGGGTA 0.822527 -152 GACAATAACGTTAAGGAGTTCCCT 14 5 0 TTAAGGAGTT 0.923926 -231 AATATACCCATTAAGGAGTATATAAAGGTG 25 167 1 TTAAGGAGTA 0.957735 -95 AAATTAATAATTAAGGGGTAAAAACCGACA 33 168 1 TTAAGGGGTA 0.94946 -133 ********** Masking position 4 Map Score: 3.41636 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 TTAAAAGTGAGCGGATTATCAAATAAATTC 3 94 0 GCGGATTATC 0.79565 -207 CGTTTAGTTCGCTGATAAGTGAAGAAGCCG 4 102 0 GCTGATAAGT 0.787203 -165 TAAGCCGTTGGCGGATTAGGCATCTTTAAG 9 258 0 GCGGATTAGG 0.943691 -43 CCGTTCAGAAGCGGATTAGTGGCACTCTGA 10 95 0 GCGGATTAGT 0.952863 -206 CTGATACTATGCGGATAAGGAAATATGGGG 16 86 0 GCGGATAAGG 0.952188 -81 AAAGCTTCCAGCGGATTTCCAACTTATCGG 23 174 0 GCGGATTTCC 0.808814 -127 TGGGTATATTGCTGATTTGTATAAATTTTC 25 147 0 GCTGATTTGT 0.553678 -115 GCGAAAAGGTGCGGAAAAGCGCGGTAAATA 26 139 1 GCGGAAAAGC 0.857082 -162 TCATTTTTCGGCGGATATCCAATAAAGCCA 26 249 1 GCGGATATCC 0.834086 -52 TTTTCGTAGGGCGGATAAGCACCGCGCATC 28 61 1 GCGGATAAGC 0.979032 -45 CGTGTCTTGCGAGGATAAGTGCATT 29 228 1 GAGGATAAGT 0.654328 -15 ********** Masking position 5 Map Score: 3.9255 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 534 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 TCGTGCAATTGCCATGGGTGCAATTTTTAA 3 272 1 GCCATGGGTG 0.97224 -29 CACGTCCGCAGACGTGGTTGCTAT 6 5 0 GACGTGGTTG 0.970099 -111 CACGTCTGCGGACGTGGTTGGCTCTGATGA 6 19 1 GACGTGGTTG 0.970099 -97 TGTCGGATGCGACACGGTTGTACATCAGGC 12 20 0 GACACGGTTG 0.828574 -62 TTTACACCCTGCCGTCGCTGTGCTGCAATC 21 41 0 GCCGTCGCTG 0.932912 -120 GCATGATAAGGCCGTGGCTGCGGAAAGTTC 21 74 0 GCCGTGGCTG 0.986364 -87 GGACACCGAAGCCATGGGTGATTAAAGAGG 26 213 0 GCCATGGGTG 0.97224 -88 ********** Masking position 9 Map Score: 3.62665 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 167 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 15 GTGGAACTCCTGATGGTTTAAAAATAAGG 2 6 0 TATTTAAAAA 0.915209 -25 ACTTTTAACCTGATTTTTAAAACAACAACGCTTA 3 116 1 TATTTAAACA 0.649451 -185 CTATTACTCATTATTTTTTAATAAGCGTTGTTGT 3 137 0 TATTTAATAA 0.823203 -164 CCGTAAAATATAAACATTCAATAAAACCCGCTAA 5 45 1 TAATTAATAA 0.347158 -203 TTGTTGTGTTTGCTTGTTTAAAAAAATGCCGCAA 5 194 0 TCTTTAAAAA 0.773245 -54 AAAACTTATTTTATCATTCAAAAAATCAGGTCGG 9 192 1 TATTTAAAAA 0.915203 -109 ATAAAAATCTTAATAGTTTAAATAACTACAGGTA 11 77 1 TATTTAAATA 0.555599 -224 TCACATTAGCTTATGGTTAAAAAATGCAAAAATC 18 118 0 TATTTAAAAA 0.915203 -183 CTTGTCCTCATTGAATAAGCGGGGCTGA 18 283 0 TCTTTAATAA 0.612205 -18 GTAAGAATTTTAATGTTTAAAAAAAGGGTTGAGG 29 79 0 TATTTAAAAA 0.91521 -164 ACGTAATTTATAATCTTTAAAAAAAGCATTTAAT 29 111 1 TATTTAAAAA 0.91521 -132 AACTCACTTTTGATTCATTAAAAAAGAAGGCTAA 31 47 0 TATATAAAAA 0.533265 -105 ACACATGCAATAATCATTCAATAAAAAGCCTAAC 31 78 0 TATTTAATAA 0.833221 -74 * ** ** ***** Masking position 10 Map Score: 4.19486 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 33 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269