AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -isoxS_ecoli_bsub_300.orf -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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 fumC 142 fumarase C= fumarate hydratase Class II; isozyme #4 fumA 198 fumarase A = fumarate hydratase Class I; aerobic isozyme #5 zwf 300 glucose-6-phosphate dehydrogenase #6 yeiH 98 orf, hypothetical protein #7 nfo 73 endonuclease IV #8 ompC 300 outer membrane protein 1b (Ib;c) #9 sodA 284 superoxide dismutase, manganese #10 soxS 85 regulation of superoxide response regulon #11 yqjJ 226 similar to glucose-6-phosphate 1-dehydrogenase (pentose phosphate) #12 sodA 178 superoxide dismutase #13 yqgC 109 yqgC #14 yqfR 168 similar to ATP-dependent RNA helicase #15 yrpD 300 similar to hypothetical proteins from B. subtilis #16 araA 207 L-arabinose isomerase #17 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #18 ysdC 183 similar to endo-1,4-beta-glucanase #19 citG 300 fumarate hydratase Motif number 1 GTAGCCGCATCCGGTATGTAACGCCTG 1 6 1 CGCATCGGTT 0.96471 -279 GCGTCAGCGTCGCATCAGGCGTTACATACCGG 1 21 0 CGCATCGGCT 0.997596 -264 GCTGACGCGTCTTATCTGGCCTACACGCTGCG 1 45 1 CTTATCGGCT 0.991741 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 74 0 CTTATCGGCT 0.991741 -211 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 91 1 CGCATCGGCT 0.997596 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 106 0 CGCATCGGCT 0.997596 -179 GCTGGCGCGTCTTATCAGGCCTACGCGCTGCG 1 130 1 CTTATCGGCT 0.991741 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 159 0 CTTATCGGCT 0.991741 -126 ATAAGCAAAGCGCATCCGGCATTCAACGCCTG 1 176 1 CGCATCGGCT 0.997596 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCCGG 1 191 0 CGCATCGGCT 0.997596 -94 GCTGGCGCGTCTTATCAGGCCTACACGCTGCG 1 215 1 CTTATCGGCT 0.991741 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATCGC 1 244 0 CTTATCGGCT 0.991741 -41 ATAAGCAAAGCGCATCCGGCACGAAGGAGTCA 1 261 1 CGCATCGGCC 0.984954 -24 ****** *** * Masking position 4 Map Score: 48.4132 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 61 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 ACGCGTCTTATCTGGCCTACACGCTGCGAT 1 49 1 TCTGGCCTAC 0.977223 -236 GCTTTGCTTATCCGGCCTACAAAATCGCAG 1 72 0 TCCGGCCTAC 0.996363 -213 GCAAAGCGCATCCGGCATTCAACGCCTGAT 1 95 1 TCCGGCATTC 0.97953 -190 GCGCGTCTTATCAGGCCTACGCGCTGCGAT 1 134 1 TCAGGCCTAC 0.977042 -151 GCTTTGCTTATCCGGCCTACAAAATCGCAG 1 157 0 TCCGGCCTAC 0.996363 -128 GCAAAGCGCATCCGGCATTCAACGCCTGAT 1 180 1 TCCGGCATTC 0.97953 -105 GCGCGTCTTATCAGGCCTACACGCTGCGAT 1 219 1 TCAGGCCTAC 0.977042 -66 GCTTTGCTTATCCGGCCTACAAAATCGCAG 1 242 0 TCCGGCCTAC 0.996363 -43 ACAGAGCCGCCCTTCGGGGCGGTTT 3 6 1 GCCGCCCTTC 0.9743 -137 TTAACAATCGGCCGCCCGACAATACTGGAG 9 259 1 GCCGCCCGAC 0.932555 -26 TGGAGCTCGGGCTGGCCGTCCTATTGAATA 16 13 1 GCTGGCCGTC 0.853235 -195 AGATTATTTATCCTCCCTTCCTGTCAAATC 17 136 0 TCCTCCCTTC 0.904976 -61 CCTTCATCAGTCCTGCATTCTTATTATACA 18 152 0 TCCTGCATTC 0.858289 -32 ********** Masking position 6 Map Score: 26.329 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 218 Number in noncoding regions = 339 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 CCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACC 2 113 0 TCAAGCTAAG 0.899343 -226 CAAAGCCATGACAAAAACGCGTAACAAAAGTGTCTATAAT 2 155 1 AAAAGCAAAG 0.965298 -184 AAAAGTTGCTTAACGAAAGCAAAACAGAAAGAAAAAATTA 3 94 1 TAAAGCAAAA 0.820648 -49 GCCGTGTTAATGACAAAAGCAGATAAAAAAGTTGTTATTT 5 56 1 TAAAGCAAAA 0.820648 -245 CACGAATATGATACTAAAACTTTTAAGATGTTTCATTTAT 8 157 0 AAAAACTAAG 0.693927 -144 ATAAAAAAGCAAATAAAGGCATATAACAGAGGGTTAATAA 8 270 1 AAAAGCAAAA 0.898828 -31 TGAATTAACGAACTGAACACTGAAAAGAGGCAGATTT 10 59 1 ACAAACAAAG 0.71034 -27 CCCTTTTTTAAGCAGAATGCTGAAAAAATGTTTCTAGCAC 11 102 0 ACAAGCAAAG 0.958065 -125 GGGGTGTACTAAAATAAAGCTTCGAATAAAGTGAGGTACT 11 193 1 AAAAGCCAAA 0.674873 -34 TAACTGAATAAAACAAACGCCTTGCAAACGTGGTGTTTTT 14 76 1 AAAAGCTAAG 0.954796 -93 TTTTATTGAAATAGAAAAGCTATAGAGAGGGGGGAGAAAT 15 66 0 AAAAGCTAAG 0.954796 -235 TCTGATGTAATACGAAAAGCATAGAAAAAGGTTTCACTTT 18 41 1 TCAAGCAAAG 0.921671 -143 CACTTTTTCTAAAAGAAAGCTGTAAAAACATATACCCGAT 18 75 1 AAAAGCTAAA 0.8709 -109 GTAAGTTTTTTTATGAAAGCGGAGGATACGAAGTGGCACA 19 27 1 TAAAGCAAAG 0.934753 -274 TATAAGAGACATCATAATGCTGTTCAAATGATCTAATGAG 19 104 0 ACAAGCTAAG 0.945498 -197 * * ** ** * * * * Masking position 7 Map Score: 14.5375 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 105 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 CTGGCCTACACGCTGCGATTTTGTAGGCCG 1 60 1 CGCTGCGATT 0.972547 -225 ATGCCGGATGCGCTTTGCTTATCCGGCCTA 1 83 0 CGCTTTGCTT 0.926429 -202 CAGGCCTACGCGCTGCGATTTTGTAGGCCG 1 145 1 CGCTGCGATT 0.972547 -140 ATGCCGGATGCGCTTTGCTTATCCGGCCTA 1 168 0 CGCTTTGCTT 0.926429 -117 CAGGCCTACACGCTGCGATTTTGTAGGCCG 1 230 1 CGCTGCGATT 0.972547 -55 GTGCCGGATGCGCTTTGCTTATCCGGCCTA 1 253 0 CGCTTTGCTT 0.926429 -32 TGGACTTTTCTGCCGTGATTATAGACACTT 2 182 0 TGCCGTGATT 0.949048 -157 TTATCAGTTTTGCCGCACTTTGCGCGCTTT 5 151 1 TGCCGCACTT 0.852734 -150 ACCCACTTAATGCCGTGATTGCCAGTAAAT 9 110 0 TGCCGTGATT 0.949048 -175 TGATTATCAATGCCGTACTTTTCGTAAGGG 9 180 0 TGCCGTACTT 0.860949 -105 GTAGTCACTATGCTGTAATTTGTACAGACA 17 53 0 TGCTGTAATT 0.831465 -144 ********** Masking position 9 Map Score: 12.6644 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 724 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGT 1 31 0 AAAGCTCGGG 0.987214 -254 TAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 116 0 AAAGCCCGGG 0.988943 -169 GGCGCGTCTTATCAGGCCTACGCGCTGCGATTTTGTA 1 133 1 ATAGCTAGGG 0.898014 -152 TAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 201 0 AAAGCCCGGG 0.988943 -84 GAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAAT 2 269 0 AAAGCTCGTG 0.972183 -70 CTATTAAAGCAAGAATCCTACGGGAAGTAACCTGGAG 4 46 1 AAATCTAGGG 0.896646 -153 TTTGTCAGATATTACGCCTGTGTGCCGTGTTAATGAC 5 33 1 ATAGCTGGGG 0.914039 -268 GTTTTGCAGGAAAATGCCCGAGATGTGAAGCAAATCA 9 139 0 AAAGCCGGTG 0.961367 -146 GTAATCAATGAAAAAGCTCACGATTTGGCTCATTTCA 12 69 0 AAAGCCAGTG 0.953718 -110 CTGCTATTAGAATATGCATGGGCTGCGGTATTTGCTT 14 35 1 AAAGCTGGTG 0.955519 -134 CGCAATCGTGAAAAATCTCCTGTGAAGTGTAAATGTT 15 133 0 AAATCCCGGG 0.951795 -168 TTTCAAGTGAAATAGTCGTATGGTTAGCGCCATGTTT 18 115 1 AAATCTAGTG 0.797033 -69 ** * ** ** * * * Masking position 4 Map Score: 14.4932 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 197 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ACTTTTCATACTCCCACCATTCAGAGAAGAAACCAATT 2 10 1 ACCCCATTAA 0.894134 -329 CCAACCGGTAACCCCGCTTATTAAAAGCATTCTGTAACA 2 107 1 ACCGTATTAA 0.910508 -232 CTGTTTCTCCATACCCGTTTTTTTGGATGGAGTGAAACG 2 310 1 ACCCTTTTTG 0.806908 -29 GATCAATCCCTGTTTTAATGTGGAAATTAATCC 4 5 1 ACCCTTTTAG 0.949112 -194 TGTGGAAATTAATCCCACTATTAAAGCAAGAATCCTACG 4 29 1 ACCCTATTAA 0.952326 -170 ACAATATCCTACACACTTTTTTAACAAAAACTGAGACTA 4 99 0 ACACTTTTAA 0.709093 -100 ATTTACTGGCAATCACGGCATTAAGTGGGTGATTTGCTT 9 110 1 ACACCATTAG 0.426802 -175 ATGATTATCAATGCCGTACTTTTCGTAAGGGTATGGTTT 9 172 0 ACCGCTTTCG 0.669704 -113 GCAAACATTTAAGCCCTTTTTTAAGCAGAATGCTGAAAA 11 116 0 ACCCTTTTAA 0.957821 -111 ATTTTAGTACACCCCGTATATTTCCTTCATTTTAAATCT 11 169 0 ACCGTATTCA 0.837032 -58 TCATCACATTATACCCGATTTTGCTTAAAAACACCACGT 14 103 0 ACCCTTTTCA 0.919768 -66 CCGGGGGCAGAGCCCGGCTTTTTATTCAATAGGACGGCC 16 26 0 ACCGTTTTAA 0.92042 -182 GATACGGAAGAATCCGCCTATTGAGGTGGATTCTATTTT 17 12 1 ACCGTATTAG 0.89312 -185 AATTTTCGGTATCCCCTTTATTGTAGTCACTATGCTGTA 17 66 0 ACCCTATTTA 0.817374 -131 GTAAAAACATATACCCGATTTTCAAGTGAAATAGTCGTA 18 96 1 ACCCTTTTAA 0.957821 -88 * *** **** * * Masking position 1 Map Score: 10.0797 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 186 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 AACGCCTGATGCGACGCTGACGCGTCTTATCT 1 30 1 GACGCTGACG 0.986035 -255 AACGCCTGATGCGACGCTGGCGCGTCTTATCA 1 115 1 GACGCTGGCG 0.997293 -170 AACGCCTGATGCGACGCTGGCGCGTCTTATCA 1 200 1 GACGCTGGCG 0.997293 -85 TCATTAACACGGCACACAGGCGTAATATCTGA 5 37 0 GACACAGGCG 0.968305 -264 GAAATGCTGGCGGCAGGTTTAA 12 1 1 GATGCTGGCG 0.982759 -178 GACGATATACGATACGCAGTCGATTTGACAGG 17 115 1 GACGCAGTCG 0.974255 -82 * ********* Masking position 4 Map Score: 7.39878 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 151 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 GAATGCTTTTAATAAGCGGGGTTACCGGTTG 2 108 0 AAAAGCGGGG 0.9379 -231 AGCATTCTGTAACAAAGCGGGACCAAAGCCA 2 132 1 AAAAAGCGGG 0.964556 -207 CACTCCATCCAAAAAAACGGGTATGGAGAAA 2 313 0 AAAAAACGGG 0.870816 -26 TAATTTCCACATTAAAACAGGGATTGATC 4 9 0 ATAAAACAGG 0.366203 -190 GAAAACGGTAATGATAGCGGGTTAACAGGAG 7 25 0 ATATAGCGGG 0.8423 -49 AAATGAAGGAAATATACGGGGTGTACTAAAA 11 176 1 AAATACGGGG 0.841409 -51 AAGACAGAGTAAAATGGGAGGATGGAAGCT 13 90 1 AAATGGGAGG 0.651841 -20 AGGGGGGAGAAATAAGAGGGGAAAGAGAGAA 15 48 0 AAAAGAGGGG 0.8797 -253 TCTAATTATAATGATAGGGGGAAATAATG 15 282 1 ATATAGGGGG 0.8423 -19 CCTATTGAATAAAAAGCCGGGCTCTGCCCCC 16 32 1 AAAAGCCGGG 0.9379 -176 TTTCTTTTAAAAAAAGCCGGGGGCAGAGCCC 16 50 0 AAAAGCCGGG 0.9379 -158 TAGTGACTACAATAAAGGGGATACCGAAAAT 17 73 1 AAAAAGGGGA 0.744968 -124 CGCTTTCTAAAATAAAGGAGGTTGAACAAAA 17 176 1 AAAAAGGAGG 0.819135 -21 TGCAGGACTGATGAAGGAGGGTTTGGAAC 18 165 1 ATAAGGAGGG 0.629336 -19 AAGTTTTTTTATGAAAGCGGAGGATACGAAG 19 29 1 ATAAAGCGGA 0.600711 -272 ** ******** Masking position 4 Map Score: 10.0926 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 448 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 9 CCATGTAAAAAAACCGCCCCGAAGGGCGGC 3 16 0 AAACCGCCCC 0.939003 -127 ATTGGGTAAAAATCTGACACTGATCATGTT 5 104 0 AATCTGACAC 0.731184 -197 CGGCATTAACAATCGGCCGCCCGACAATAC 9 254 1 AATCGGCCGC 0.95383 -31 AAATCTGCCTCTTTTCAGTGT 10 75 0 AATCTGCCTC 0.980184 -11 TGCCCCATTAAACCTGCCGCCAGCATTTC 12 10 0 AACCTGCCGC 0.947843 -169 TTTAACCGATAATCTGCCCCATTAAACCTG 12 24 0 AATCTGCCCC 0.987306 -155 ATGGACACATAATGTGCCGCTTTAAGGAGC 14 141 1 AATGTGCCGC 0.900826 -28 GTAAACTGCCCCTTTCTCATAA 16 196 0 AAACTGCCCC 0.955794 -12 GATACGGAAGAATCCGCCTATTGAGGTGGA 17 12 1 AATCCGCCTA 0.844379 -185 AAAAAAATAGAATCCACCTCAATAGGCGGA 17 24 0 AATCCACCTC 0.735102 -173 TTAAAATTAAAATCTGCCAAGATCGAAAAA 19 212 1 AATCTGCCAA 0.841729 -89 ********** Masking position 2 Map Score: 7.58616 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 530 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 GCCTACAAAATCGCAGCGTGTAGGCCAGATA 1 57 0 TCGCAGCGGT 0.991492 -228 GCCTACAAAATCGCAGCGCGTAGGCCTGATA 1 142 0 TCGCAGCGGT 0.991473 -143 GCCTACAAAATCGCAGCGTGTAGGCCTGATA 1 227 0 TCGCAGCGGT 0.991492 -58 TGCTATGGCATAGCAAAGTGTGACGCCGTGC 2 224 0 TAGCAAAGGT 0.762582 -115 GTTGCCCTGTTAAAAGCGAGTAACAATATCC 4 129 0 TAAAAGCGGT 0.762582 -70 TAAAGGCATATAACAGAGGGTTAATAAC 8 283 1 TAACAGAGGT 0.918322 -18 AAATGACGCTTCACAGCGAGCCTTTCTTCAT 12 129 0 TCACAGCGGC 0.933501 -50 CATATTCTAATAGCAGAGAGAGCTGAAAGGA 14 20 0 TAGCAGAGGA 0.856557 -149 ******** ** Masking position 5 Map Score: 4.80234 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 287 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 CCAGATAAGACGCGTCAGCGTCGCATCAGG 1 34 0 CGCGTCAGCG 0.972666 -251 CCTGATAAGACGCGCCAGCGTCGCATCAGG 1 119 0 CGCGCCAGCG 0.991447 -166 CCTGATAAGACGCGCCAGCGTCGCATCAGG 1 204 0 CGCGCCAGCG 0.991447 -81 TTGTTAATGCCGCGTAAGCAGTTGGTTCAT 9 236 0 CGCGTAAGCA 0.924907 -49 ********** Masking position 7 Map Score: 3.97579 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 152 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 TCCCACCATTCAGAGAAGAAACCAATTGTCC 2 22 1 CAGAAAGAAA 0.835107 -317 GACCAAAGCCATGACAAAAACGCGTAACAAA 2 152 1 ATGAAAAAAC 0.684201 -187 GAAAGCAAAACAGAAAGAAAAAATTAATCAG 3 108 1 CAGAAGAAAA 0.920769 -35 CTGAAAGAAATCGAAATGCAG 5 1 1 CTGAAGAAAT 0.631083 -300 ATGACAAAAGCAGATAAAAAAGTTGTTATTT 5 65 1 CAGAAAAAAA 0.909357 -236 TGATCATGTTATGAAAAAAAATAACAACTTT 5 83 0 ATGAAAAAAA 0.862096 -218 TGCGGCAAAACTGATAAAAAAATCATCGTTT 5 137 0 CTGAAAAAAA 0.920774 -164 AATCTTGCCTCTGAAAAGAACAATCCTTTCG 11 72 1 CTGAAAGAAC 0.670336 -155 TAAGAGGGGAAAGAGAGAAAACACTGTAATC 15 36 0 AAGAAGAAAA 0.862088 -265 ATACGTACTAATGATAGGAAAATAAACCTAT 16 140 0 ATGAAGGAAA 0.785212 -68 GTAATTTGTACAGACAAAAAAATAGAATCCA 17 38 0 CAGAAAAAAA 0.909357 -159 AAAATCTGCCAAGATCGAAAAATAAAAAGGA 19 220 1 AAGACGAAAA 0.496458 -81 TAATTCGCCAATGACACAAAAAATCCTTTTT 19 243 0 ATGAACAAAA 0.624119 -58 **** ****** Masking position 4 Map Score: 3.37875 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 303 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 13 AGTAACCTGGAGCCGCAAAAAGTCGTACTAG 4 71 1 AGCCGAAAAA 0.832706 -128 GCGCGCAAAGTGCGGCAAAACTGATAAAAAA 5 147 0 TGCGGAAAAC 0.887578 -154 TCGGGCATTTTCCTGCAAAACCATACCCTTA 9 155 1 TCCTGAAAAC 0.811994 -130 TTAAGCAGAATGCTGAAAAAATGTTTCTAGC 11 104 0 TGCTGAAAAA 0.958486 -123 TTCAGCATTCTGCTTAAAAAAGGGCTTAAAT 11 118 1 TGCTTAAAAA 0.8197 -109 TACCCGATTTTGCTTAAAAACACCACGTTTG 14 100 0 TGCTTAAAAC 0.854083 -69 CGCTTTAAGGAGCTGGGAAAA 14 158 1 AGCTGGAAAA 0.814075 -11 TCTAAAAGAAAGCTGTAAAAACATATACCCG 18 82 1 AGCTGAAAAA 0.949342 -102 AGGTAAGGCTAGCTGGAAAACAAGAAGAAAT 19 66 1 AGCTGAAAAC 0.960202 -235 ***** ***** Masking position 8 Map Score: 2.49904 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 759 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 14 AGAGCCAGTAAAAGACGCAGTGACGGCAATG 2 66 0 AAAGCGCAGT 0.899161 -273 GGGTTAGCGAGAAGAGCCAGTAAAAGACGCA 2 78 0 GAAGGCCAGT 0.85717 -261 TGAACACTGAAAAGAGGCAGATTT 10 72 1 AAAGGGCAGA 0.983715 -14 CGGCAGGTTTAATGGGGCAGATTATCGGTTA 12 21 1 AATGGGCAGA 0.92612 -158 CCAGCTCCTTAAAGCGGCACATTATGTGTCC 14 143 0 AAAGGGCACA 0.962242 -26 ATTTTATGAGAAAGGGGCAGTTTAC 16 193 1 AAAGGGCAGT 0.978876 -15 CGGAGGATACGAAGTGGCACAGGTAAGGCTA 19 46 1 GAAGGGCACA 0.94491 -255 **** ****** Masking position 9 Map Score: 2.41174 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 155 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 GCAGCGCGTAGGCCTGATAAGACGCGCCAG 1 131 0 GGCCTGATAA 0.92566 -154 GCAGCGTGTAGGCCTGATAAGACGCGCCAG 1 216 0 GGCCTGATAA 0.92566 -69 GTGTTCCGTTGCCCTGTTAAAAGCGAGTAA 4 137 0 GCCCTGTTAA 0.980215 -62 ACGCCTGTGTGCCGTGTTAATGACAAAAGC 5 46 1 GCCGTGTTAA 0.891303 -255 GTAACCTTATGCCCGGTTAAAGGAGAGGGT 6 78 1 GCCCGGTTAA 0.929374 -21 CTACATCTTGCTCCTGTTAACCCGCTATCA 7 15 1 CTCCTGTTAA 0.950899 -59 GCGAGGACTCCTGTTAAACCCGCTGGA 7 57 0 CTCCTGTTAA 0.950899 -17 CGTGAAAAATCTCCTGTGAAGTGTAAATGT 15 134 0 CTCCTGTGAA 0.837233 -167 ********** Masking position 9 Map Score: 3.85624 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 107 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401