AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_ecoli_bsub_300.orf -o060_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 b0024 102 orf, hypothetical protein #2 ileS 42 isoleucine tRNA synthetase #3 slpA 29 probable FKBX-type 16KD peptidyl-prolyl cis-trans isomerase (a rotamase) #4 yaaF 65 orf, hypothetical protein #5 dapB 166 dihydrodipicolinate reductase #6 usg 65 putative PTS system enzyme II A component #7 pdxB 98 erythronate-4-phosphate dehyrogenase #8 dapA 79 dihydrodipicolinate synthase #9 lysC 300 aspartokinase III, lysine sensitive #10 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #11 nusA 34 nusA #12 truB 81 tRNA pseudouridine 55 synthase #13 rpsO 156 ribosomal protein S15 (BS18) #14 pnpA 172 polynucleotide phosphorylase (PNPase) #15 ylxY 117 alternate gene name: ymxI; similar to deacetylase #16 ymxG 39 similar to processing protease #17 ymxH 77 similar to hypothetical proteins #18 spoVFA 185 dipicolinate synthase subunit A #19 asd 125 aspartate-semialdehyde dehydrogenase #20 dapG 91 aspartokinase I (alpha and beta subunits) #21 dapA 30 dihydrodipicolinate synthase #22 ypjD 300 alternate gene name: jojD #23 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #24 ask 94 ask #25 uvrC 135 excinuclease ABC (subunit C) #26 trxA 300 thioredoxin Motif number 1 AATCCATTGACAAAAGAAGGCTAAAAGGGC 1 63 0 CAAAAGAAGG 0.900952 -40 TGCAAATTAACAAAAGAGAATAGCT 5 152 1 CAAAAGAGAA 0.867458 -15 CTGTTCAATACAAAAGAGCGGGTTTCCCCA 10 165 0 CAAAAGAGCG 0.983632 -136 AACCCTGCTTCAAAAGAGCAGGGGCTAAAA 10 228 0 CAAAAGAGCA 0.963532 -73 AAAAAGAGAGGATAGGCGTA 12 1 1 AAAAAGAGAG 0.943406 -81 TTATAAACGAAGAAAGAGGACAGACGATAT 12 30 0 AGAAAGAGGA 0.839209 -52 GAAAAAAACTCAAAAGAAGGAGTGAAAGGC 12 60 1 CAAAAGAAGG 0.900952 -22 TCGTAAAAAGCGGGAGGATTCCCG 14 5 1 AAAAAGCGGG 0.963132 -168 TAATACGATAAAAAAGCGGGAATCCTCCCG 14 21 0 AAAAAGCGGG 0.963132 -152 TGAAGCTTTTCAAAAGCAGGCGGGTTCTAC 15 54 1 CAAAAGCAGG 0.823694 -64 TTTTATATGGAAAAAGCGCATCTTTTATAT 18 81 1 AAAAAGCGCA 0.938262 -105 ATAGTGGATGAAAAAGAAAACAGCAAACGT 22 214 1 AAAAAGAAAA 0.59479 -87 TGTCCACAATAAAAAAAGCAATGAGAGGAA 23 104 0 AAAAAAAGCA 0.73389 -72 GCGGGTGAGGAGAAAGAGCGCTTTGTCCAC 23 127 0 AGAAAGAGCG 0.940141 -49 ATTGGCGAATAAAAAAAGCGATCCCTCAAT 25 43 0 AAAAAAAGCG 0.862494 -93 TTAAAACCTGAAAAAGAGCGCCGGCATG 26 9 0 AAAAAGAGCG 0.985358 -292 TGTGTTTTAAAAAAAGAGCATATCCCATTC 26 157 1 AAAAAGAGCA 0.967308 -144 ********** Masking position 5 Map Score: 22.2183 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 494 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 CAGAGAGCATGAAGAAGAGA 6 1 0 GAAGAAGAGA 0.757135 -65 GCGCAGGCCAGAAGAGGCGCGTTGCCCAAG 9 20 1 GAAGAGGCGC 0.863847 -281 GATAACACCTGAGGGGGTGCATCGCCGAGG 9 77 1 GAGGGGGTGC 0.958189 -224 TGGCACAAGGGAAGAGCGGAAGACGGGTGG 9 247 0 GAAGAGCGGA 0.892161 -54 CTTTTGTATTGAACAGGAGAATTTTGTCTC 10 179 1 GAACAGGAGA 0.838392 -122 TGCTTCAAAAGAGCAGGGGCTAAAAAGTAA 10 223 0 GAGCAGGGGC 0.790511 -78 ACAAATGTTTTAAGGGGGGAGACCGTTAA 11 16 1 TAAGGGGGGA 0.819284 -19 AAACTCAAAAGAAGGAGTGAAAGGCAA 12 65 1 GAAGGAGTGA 0.833694 -17 TTCACACAACGAAGAGAGGAGTTCGTAATT 14 151 1 GAAGAGAGGA 0.752051 -22 AATGTGAGGTGAGGGGGGGACAGAAC 15 102 1 GAGGGGGGGA 0.985032 -16 TACATAGTACAAGGGGGTGACAGAC 17 63 1 AAGGGGGTGA 0.700144 -15 ATCATAAGATGAAGGGGAGCTTAACAACTA 18 130 1 GAAGGGGAGC 0.965401 -56 ATTGAATCATGATGAGGTGAATAAA 21 16 1 GATGAGGTGA 0.798796 -15 GAGGGGCTGATGTGGAAAAG 22 1 1 GAGGGGCTGA 0.872638 -300 ACATGACAGTGAAGAGGAGATGTGATCTTA 26 66 1 GAAGAGGAGA 0.968988 -235 TAGCGTGAACGAATGGGAGATGCTATACTA 26 248 1 GAATGGGAGA 0.753598 -53 ********** Masking position 2 Map Score: 13.7665 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 682 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 CTTCGCAAGTATGCCTGGCCGCGAGATTAT 7 33 1 ATGCCTGGCC 0.911769 -66 TTGTCACCAGAAGCGTTCGCAGTCGGGCGT 9 161 1 AAGCGTTCGC 0.628587 -140 GATCCATTTTCAGCCTTGGCACAAGGGAAG 9 263 0 CAGCCTTGGC 0.769509 -38 CAAAATAAAGAAGCCGGGTCTCCCAGGCTC 15 26 0 AAGCCGGGTC 0.943313 -92 AAAGGAAAGCCTGCCCCATAATGGAG 17 7 1 AAGCCTGCCC 0.952483 -71 GGATTAAAAAATGCCTGCTCCATTATGGGG 17 24 0 ATGCCTGCTC 0.960273 -54 ATTGACTGTGAAGCGGGCTCTAAAGAAAAC 18 19 1 AAGCGGGCTC 0.874019 -167 GAAACATCGGCTGCCGGAGCCGATGTTTTT 18 53 1 CTGCCGGAGC 0.953503 -133 AAGGCGCTATCAGCCTGCTCTCTTCTGTTA 20 46 1 CAGCCTGCTC 0.951814 -46 CGCTGCTTACATGCCAGAGCGATTCCGATT 25 16 1 ATGCCAGAGC 0.794085 -120 CATGCCGGCGCTCTTTTTCAG 26 2 1 ATGCCGGCGC 0.986957 -299 TTACCATGCCCTGCCGGAGCTGTTTTAAAA 26 33 0 CTGCCGGAGC 0.953503 -268 ********** Masking position 4 Map Score: 9.83526 Number of sites scoring better than the average of aligned sites = 1641 Number in coding regions = 1556 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 CCCAAATGTGTTCTATATGGACAATTCAAAGGC 1 20 1 TTCTTTGGAA 0.874495 -83 TAACGGCGCTTATTTGCACAAATCCATTGA 1 83 0 GCTTTTGCAA 0.951724 -20 GTTACCGGCATTTTTTATGGAGAAAAC 4 49 1 TTTTTTGGAA 0.920176 -17 ATTCTCTTTTGTTAATTTGCATAGACCGTTTTC 5 140 0 GTTATTGCAA 0.909373 -27 GGGCCATCCTCTGTGCAAACAAGTGTCTC 8 61 0 TCCTTTGCAA 0.866995 -19 GCTTCTATGCATACATAAGCGCA 10 1 1 GCTTTTGCAA 0.951724 -300 CATAACCATATTTTTATTGCAAATGGATATACG 10 89 0 TTTTATGCAA 0.779134 -212 TTATGGTATAGTTTTATTGGAAATGCTAACGAT 10 117 1 GTTTATGGAA 0.849986 -184 TTGAAGCAGGGTTTTTATGCAGAGTGACGAGAC 10 245 1 GTTTTTGCAA 0.960005 -56 TAAAAATCGTGCCTATATGCAAATATTTTAGAA 13 33 0 GCCTTTGCAA 0.922579 -124 GCCGATGTTTTTTTATATGGAAAAAGCGCATCT 18 71 1 TTTTTTGGAA 0.920175 -115 GAGGGGCTGATGTGGAAAAGGGCATAAA 22 6 1 GCTGTTGGAA 0.76522 -295 CTTGGTTCATTTCAATATGCAGAACAATCTGGC 22 71 0 TTCATTGCAA 0.768409 -230 CATTGCTTTTTTTATTGTGGACAAAGCGCTCTT 23 111 1 TTTATTGGAA 0.828149 -65 AAACGTTCGTGTTAAACTGGAAATAAAGGATTA 25 93 1 GTTAATGGAA 0.703145 -43 **** * **** * Masking position 11 Map Score: 12.1122 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 109 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 TATCACAGGACTGGCTCCTCCAACACCGTTA 9 50 0 CTGGCCCTCC 0.87291 -251 TGAATCCCCTGGGTTGTCACCAGAAGCGTTC 9 148 1 GGGTTTCACC 0.815698 -153 TACTTCGCTACTATTTTCACCCAGAAGTGCT 9 205 0 CTATTTCACC 0.879468 -96 TACAAAAGAGCGGGTTTCCCCACTCTTTGCC 10 156 0 CGGGTTCCCC 0.918994 -145 TTAACGGTCTCCCCCCTTAAAACAT 11 20 0 CGGTCCCCCC 0.990839 -15 GTTCTGTCCCCCCCTCACCTCACA 15 104 0 CTGTCCCCCC 0.99143 -14 GTCTGTCACCCCCTTGTACTATG 17 65 0 CTGTCCCCCC 0.99143 -13 CTAAAAAATTCGGTCATCACCCGCATATTCT 19 34 1 CGGTCTCACC 0.980602 -92 ACGAAACCTCCTATCATCCTCTTACATGTTA 22 277 0 CTATCTCCTC 0.713913 -24 GTATTACCACCCTTTACATTT 23 165 0 GTATTCCACC 0.700008 -11 GTTCGCACCTCTATCTTCACCATATAACACG 24 40 0 CTATCTCACC 0.952061 -55 ***** ***** Masking position 8 Map Score: 7.221 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 634 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GCATTTTCGCATAACTTAGGCTGCTAATGAC 4 9 0 ATACTTGGCG 0.898994 -57 GCTCTCTGCTGTAACATTGGCAGGGAGCTTTGC 6 23 1 GTACATGGCG 0.777857 -43 CTCCAACACCGTTACTTGGGCAACGCGCCTCTT 9 31 0 GTACTTGGCA 0.970596 -270 CAGCCGTTCAATCACCTCGGCGATGCACCCCCT 9 88 0 ATACCTGGCA 0.963833 -213 GTAGCCGATGATGAACGTGGCCAGCCGTTCAAT 9 109 0 ATAACGGGCA 0.906719 -192 AATGCTAACGATTACCGAGGCAAAGAGTGGGGA 10 138 1 ATACCGGGCA 0.97701 -163 CGGTTGCTAGGTAACTGGGGCTAAATATGATTT 13 120 1 GTACTGGGCA 0.981357 -37 CCGCTTCACAGTCAATTGGGCTAT 18 2 0 GTAATTGGCA 0.883042 -184 CATTTTAATGATTATTGGGGCAATTGTAGTGAT 26 106 1 ATATTGGGCA 0.883042 -195 GGCAATTGTAGTGATCGGGGCCATTATCAGATT 26 124 1 GTATCGGGCA 0.939398 -177 ** **** *** * Masking position 4 Map Score: 7.11843 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 241 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 7 GGAGGGATATCAGTGAAAGGCATGAGTCGAT 5 42 0 CAGTGAAGGC 0.973062 -125 GCCTGGCCGCGAGATTATGGCACACTTGTCC 7 45 1 GAGATATGGC 0.959175 -54 CTTGTTTGCACAGAGGATGGCCC 8 67 1 CAGAGATGGC 0.984561 -13 TCAAAAGAAGGAGTGAAAGGCAA 12 69 1 GAGTGAAGGC 0.964914 -13 CAGATGAAGGCAGCTTGTCTT 16 1 1 CAGATAAGGC 0.97573 -39 ACGAATAGAAGAGAGTAAGGCGCTATCAGCC 20 30 1 GAGAGAAGGC 0.984428 -62 AAACACAAATCTGATAATGGCCCCGATCACT 26 133 0 CTGATATGGC 0.865048 -168 ***** ***** Masking position 7 Map Score: 5.9793 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 78 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 CCCAAATGTGTTCTATATGGACAATTCAAA 1 20 1 TTCTATATGG 0.928551 -83 GTTACCGGCATTTTTTATGGAGAAAAC 4 49 1 TTTTTTATGG 0.953312 -17 GGATTCCCGCTTTTTTATCGTATTAAAGCG 14 26 1 TTTTTTATCG 0.771661 -147 GCCGATGTTTTTTTATATGGAAAAAGCGCA 18 71 1 TTTTATATGG 0.963752 -115 ATCACCCGCATATTCTATGGTAAAATAAAA 19 49 1 TATTCTATGG 0.797983 -77 TCTCATTGCTTTTTTTATTGTGGACAAAGC 23 108 1 TTTTTTATTG 0.695135 -68 AGTTAGATCGTGTTATATGGTGAAGATAGA 24 32 1 TGTTATATGG 0.875958 -63 ACGTTTGTTTTTCTCTATGGTTCACAATTG 25 69 0 TTCTCTATGG 0.915069 -67 GTTTACTCATTTTTATATGGTTGAATGGGA 26 179 0 TTTTATATGG 0.963752 -122 ********** Masking position 6 Map Score: 5.82234 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 60 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 GTTTTTGGCTGGCGGCGTAGCGATGCGCTGG 5 102 1 GGCGCGTAGC 0.94272 -65 AACATTGGCAGGGAGCTTTGCTATTTCTGGA 6 35 1 GGGGCTTTGC 0.987978 -31 AGGCCAGAAGAGGCGCGTTGCCCAAGTAACG 9 24 1 AGGGCGTTGC 0.912611 -277 ACACCTGAGGGGGTGCATCGCCGAGGTGATT 9 81 1 GGGGCATCGC 0.967201 -220 GTTCGCAGTCGGGCGTTTCGCAAGTGGTGGA 9 175 1 GGGGTTTCGC 0.952273 -126 GAAGACGGGTGGGCGCAGAGCGATACTTCGC 9 228 0 GGGGCAGAGC 0.779332 -73 AATAAAATTTGCGTGCGTTGCAAG 13 4 0 GCGGCGTTGC 0.941703 -153 TTTCTTTAGAGCCCGCTTCACAGTCAATTGG 18 16 0 GCCGCTTCAC 0.733116 -170 TAAGATGAAGGGGAGCTTAACAACTAGAGAT 18 134 1 GGGGCTTAAC 0.949549 -52 GATTGGCGGAAGGAGTTTTACAG 19 113 1 AGGGTTTTAC 0.535364 -13 TCTGGCTGAGGGCGGTTTTACAGGTATTACA 22 46 0 GGCGTTTTAC 0.744447 -255 *** ******* Masking position 11 Map Score: 4.17204 Number of sites scoring better than the average of aligned sites = 1089 Number in coding regions = 1001 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 AAAATCCTTAAATATAAGAGCAAACCTGC 3 11 1 AATATAAGAG 0.942063 -19 TATGCAAATTAACAAAAGAGAATAGCT 5 150 1 AACAAAAGAG 0.715297 -17 TTACTCCAGAAATAGCAAAGCTCCCTGCCA 6 40 0 AATAGCAAAG 0.720011 -26 TCTGGGTGAAAATAGTAGCGAAGTATCGCT 9 211 1 AATAGTAGCG 0.690725 -90 GTGCCATCGTAATATTAGAGTTTCTGTCAC 10 38 1 AATATTAGAG 0.818838 -263 TCTCCTGTTCAATACAAAAGAGCGGGTTTC 10 169 0 AATACAAAAG 0.757629 -132 ATGAAAACATAAAAGGAGCCTGGGA 15 6 1 AACATAAAAG 0.84263 -112 AATACCGGTGAATATAAAAGATGCGCTTTT 18 92 0 AATATAAAAG 0.895277 -94 TCTAAAGACGAATAGAAGAGAGTAAGGCGC 20 23 1 AATAGAAGAG 0.954408 -69 ATTCGGACGTAACAGAAGAGAGCAGGCTGA 20 55 0 AACAGAAGAG 0.929135 -37 CATCCACTATAATATAAACGCTATCTAATG 22 194 0 AATATAAACG 0.766415 -107 ********** Masking position 4 Map Score: 4.25862 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 58 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 GGTAACAAGACCGGCATTTTCGCATAACTT 4 25 0 CCGGCATTTT 0.97513 -41 GGTCTTGTTACCGGCATTTTTTATGGAGAA 4 43 1 CCGGCATTTT 0.97513 -23 CGTTCGCAGTCGGGCGTTTCGCAAGTGGTG 9 174 1 CGGGCGTTTC 0.92913 -127 CATAATGGAGCAGGCATTTTTTAATCCCTT 17 27 1 CAGGCATTTT 0.858474 -51 GCTCCGGCAGCCGATGTTTCAGATGTTTTC 18 43 0 CCGATGTTTC 0.883072 -143 GCTGCCGGAGCCGATGTTTTTTTATATGGA 18 62 1 CCGATGTTTT 0.862145 -124 TTTATATTCACCGGTATTTCCTTTTGATCA 18 104 1 CCGGTATTTC 0.958204 -82 ********** Masking position 7 Map Score: 2.95037 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 316 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 AAAAGAGAGGATAGGCGTATATCGTCTGTC 12 12 1 ATAGGCGTAT 0.881823 -70 TTCGTTCATAATAGGAGTAATTGATTATTT 14 123 1 ATAGGAGTAA 0.893961 -50 TTGTCTTTGAATAGGAGGAACAAAT 16 25 1 ATAGGAGGAA 0.961465 -15 AATGAAGCTGATTGGCGGAAGGAGTTTTAC 19 104 1 ATTGGCGGAA 0.958566 -22 TAAGAGGATGATAGGAGGTTTCGTTCA 22 284 1 ATAGGAGGTT 0.799122 -17 ATGGTTCACAATTGGCGAATAAAAAAAGCG 25 53 0 ATTGGCGAAT 0.771174 -83 ATCATTTCACATTGGAGGAATTCAATA 26 284 1 ATTGGAGGAA 0.950401 -17 ********** Masking position 1 Map Score: 1.52277 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GCGCATCGCTACGCCGCCAGCCAAAAACGCTGAT 5 96 0 ACGCCGCCAA 0.989936 -71 AGAAATAGCAAAGCTCCCTGCCAATGTTACAGCA 6 29 0 AAGCCGCCAA 0.979435 -37 AGTGTGCCATAATCTCGCGGCCAGGCATACTTGC 7 37 0 AATCCGCCAG 0.964072 -62 ATGGCATTAAAAGCAAGCAGACAGAACCGTTCTG 8 12 0 AAGCCGACAG 0.927318 -68 CTGTAAAACTCCTTCCGCCAATCAGCTTCAT 19 105 0 ACTCCGCCAA 0.964072 -21 AGAGAGTAAGGCGCTATCAGCCTGCTCTCTTCTG 20 39 1 GCGCCGCCTG 0.939105 -53 ACCTGTAAAACCGCCCTCAGCCAGATTGTTCTGC 22 52 1 CCGCCGCCAG 0.986713 -249 **** * ***** Masking position 8 Map Score: 1.44443 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 625 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 TGATAAACAGGGAGGGATATCAGTGAAAGGC 5 52 0 GGAGGGAATC 0.974647 -115 GACAGCACAAGGAGGAAGAAC 10 290 1 GGAGGAAAAC 0.966269 -11 AATATGATTTGGAGGTGAAACAGG 13 143 1 GGAGGTGAAC 0.916189 -14 TCTTTGAATAGGAGGAACAAAT 16 28 1 GGAGGAAAAA 0.787943 -12 CGAATAATTTGGAGTGAAAACA 20 80 1 GGAGTGAAAC 0.921423 -12 GCTATCTAATGGAAGGAAAAGGGGTTTTGTG 22 174 0 GGAAGGAAAG 0.821983 -127 TCATTTTCTTGGAGGGCTATCTCGTTGTTCA 23 34 1 GGAGGGCATC 0.933583 -142 TTAAACATAAGGAAGGGTAACAT 25 123 1 GGAAGGGAAC 0.941733 -13 ******* *** Masking position 3 Map Score: 1.01359 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 97 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 15 ACGGTCTATGCAAATTAACAAAAGAGAATAGC 5 144 1 CAATAACAAA 0.800259 -23 TTTCTTCGTTTATAAGAAAAAAACTCAAAAGA 12 45 1 TAAGAAAAAA 0.802154 -37 CGAAAACTATCATACTAAAAATCGTGCCTATA 13 49 0 CAATAAAAAT 0.839463 -108 TTCGCTTTAATACGATAAAAAAGCGGGAATCC 14 26 0 TAGTAAAAAA 0.644573 -147 TGAAAAGCTTCAAAATAAAGAAGCCGGGTCTC 15 34 0 CAATAAAGAA 0.800259 -84 GCGCTTTTTCCATATAAAAAAACATCGGCTCC 18 68 0 CAAAAAAAAA 0.766569 -118 AAATCTTTCCCAAACTAAAAAATTCGGTCATC 19 20 1 CAATAAAAAA 0.958913 -106 TGAACCAAGCCAAATGAAAAAATTGCCGCTCC 22 95 1 CAAGAAAAAA 0.899571 -206 CCGCTCCGATTAAAATAAAAAATATGTTTTTT 22 120 1 TAATAAAAAA 0.913525 -181 TTGGAGAAATTAGATTAAAAAACATATTTTTT 22 136 0 TAATAAAAAA 0.913525 -165 GCGCTTTGTCCACAATAAAAAAAGCAATGAGA 23 108 0 CAATAAAAAA 0.958913 -68 TGGGAGATGCTATACTAAAAATCATCATTTCA 26 261 1 TAATAAAAAT 0.702992 -40 ** * ******* Masking position 7 Map Score: 8.08872 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 46 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789