AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_hinf_reg_300.orf -o00400_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HI0195.1 26 conserved hypothetical transmembrane protein (aefA) HI1388.1 48 H. influenzae predicted coding region HI1388.1 HI1612 43 conserved hypothetical transmembrane protein Input sequences: #1 HI0205 292 H. influenzae predicted coding region HI0205 #2 HI0206 22 5'-nucleotidase, putative #3 HI0207 284 shikimic acid kinase I (aroK) #4 HI0468 300 ATP phosphoribosyltransferase (hisG) #5 HI0469 92 histidinol dehydrogenase (hisD) #6 HI0470 68 histidinol-phosphate aminotransferase (hisC) #7 HI0658 160 ABC transporter, ATP-binding protein #8 HI0660 269 H. influenzae predicted coding region HI0660 #9 HI0661 300 hemoglobin-binding protein #10 HI0932 120 enolase (eno) #11 HI0936 108 cytochrome C-type biogenesis #12 HI0937 200 extragenic suppressor (suhB) #13 HI0967 25 H. influenzae predicted coding region HI0967 #14 HI0970 57 3-dehydroquinase (aroQ) #15 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #16 HI1129 201 conserved hypothetical protein #17 HI1130 30 conserved hypothetical protein #18 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #19 HI1137 21 cell division protein (ftsW) #20 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #21 HI1140 71 D-alanine--D-alanine ligase (ddlB) #22 HI1143 83 cell division protein (ftsZ) #23 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #24 HI1145 126 chorismate mutase / prephenate dehydratase (pheA) #25 HI1171 41 anthranilate synthase component II (trpG) #26 HI1288 300 ribosome binding factor A (rbfA) #27 HI1290 59 chorismate mutase / prephenate dehydrogenase (tyrA) #28 HI1310 24 H. influenzae predicted coding region HI1310 #29 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #30 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #31 HI1386 300 H. influenzae predicted coding region HI1386 #32 HI1387 105 anthranilate synthase component I (trpE) #33 HI1389 52 anthanilate phosphoribosyltransferase (trpD) #34 HI1389.1 36 indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) #35 HI1430 179 short chain dehydrogenase/reductase #36 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) #37 HI1549 146 ABC transporter, ATP-binding protein #38 HI1556 59 2-hydroxyacid dehydrogenase #39 HI1560 22 H. influenzae predicted coding region HI1560 #40 HI1561 106 peptide chain release factor 1 (prfA) #41 HI1562 252 H. influenzae predicted coding region HI1562 #42 HI1563 32 conserved hypothetical protein #43 HI1564 32 H. influenzae predicted coding region HI1564 #44 HI1564.1 284 H. influenzae predicted coding region HI1564.1 #45 HI1587 300 DNA-binding protein H-NS (hns) #46 HI1588 69 formyltetrahydrofolate deformylase (purU) #47 HI1610 200 tyrosyl tRNA synthetase (tyrS) #48 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #49 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #50 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 GTAAAAATTTACCGCACTTTTGATTTTAGA 8 16 0 ACCGCACTTT 0.998659 -254 GTAAATTTTTACCGCACTTTTTCTTAAGAA 8 34 1 ACCGCACTTT 0.998659 -236 CCAATTTTCCACCGCACTTTAACCATAAAT 12 19 1 ACCGCACTTT 0.998659 -182 GCGAATTTTAACCGCACTTTTAGTTGAGTT 20 91 1 ACCGCACTTT 0.998659 -47 CACGAAATTGACCGCACTTTTAGTACATTC 24 85 0 ACCGCACTTT 0.998659 -42 ATAAAAAAATACCGCACTTTTGTGCTGTAC 36 19 0 ACCGCACTTT 0.998659 -199 ACTCGTTTTAACCGCACTTTAGCGGCAGAT 37 122 0 ACCGCACTTT 0.998659 -25 GTCAAAATTAACCGCACTTTTGATGAAAT 38 10 0 ACCGCACTTT 0.998659 -50 GTTAATTTTGACCGCACTTTGTATATAAAA 38 28 1 ACCGCACTTT 0.998659 -32 TTTAGATCTGACCGCACTTTTAAAGTGCGG 49 18 1 ACCGCACTTT 0.998659 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 49 29 0 ACCGCACTTT 0.998659 -41 GTAAAAAATGACCGCACTTTTTGATGAATA 50 12 1 ACCGCACTTT 0.998659 -127 ********** Masking position 6 Map Score: 59.6587 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 CTAAATGTTTAATTACTAAAAGAATATTCTCAAATT 1 20 1 ATAAAAAATA 0.831436 -273 GCCTCGTATTATATCGTAAAACAAAATAAATTGTGA 1 189 0 AAAAAAAAAA 0.773421 -104 CAAACCTAGGACTAATAACAAAAATAGCGCGTTAAA 3 41 0 ATACAAAATA 0.676851 -244 TGTTCTTTATCTAATTAAATTAAAAGTGAAATAAA 3 260 0 TTAAATAAAA 0.861713 -25 TTAAAAATACACTTTAAAATTAAAAAAAGCAATTTT 4 47 0 ATAATTAAAA 0.712263 -254 GGTTTTCTTTTATCTCAACTTTAAAATAGGAAAAAC 4 272 1 TTACTTAAAA 0.377179 -29 AGCAGTCAAATTTTCATACAACAATACGAAATATGT 6 43 1 TTACAAAATA 0.546629 -26 TATACGTGGCTTTTTTGACTAGAAAATCGATAAAAT 7 66 1 TTACTAAAAA 0.420244 -95 TTATGATTACACATCAAAAATCAATAACTTATTGGT 8 213 1 AAAAATAATA 0.520736 -57 CATAATGATTACTCCTAAAATAAAAAGAAGTACGCA 9 37 1 ATAAATAAAA 0.915369 -264 TTTTGATCAAAATCAAGAAATAAAAACTATTCTCAT 9 230 0 ATAAATAAAA 0.915369 -71 AAGCATACGCATTTTTTACAAGAAAAAATCTYAAAA 10 25 1 ATACAAAAAA 0.846093 -96 AATTAACTTAATTGAGGAAAATAAAA 10 105 1 ATAAAAAAAA 0.928296 -16 AGTATGTTTCATTAATAAAATTAAAAATAGCACCTT 11 37 0 ATAAATAAAA 0.915369 -72 AATGCTAATAAATAAGTAATTGAATAGGTATAAAAG 15 16 0 ATAATTAATA 0.485363 -166 CTATTTCAAATTACGTCAAATCAAAATTGAATTTAA 15 110 0 TAAAATAAAA 0.621641 -72 AGCAACTGATTTTTATCAAAATAAAAAAGCCGTTTG 16 52 0 TTAAAAAAAA 0.881774 -150 AAAAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 20 61 1 AAAAATAAAA 0.740382 -77 CCTTTATTGTAGATGAAAAATTAAAATAA 22 4 0 AAAAATAAAA 0.740382 -80 GAAATATAGCTTTTTCAACAATAAAACAA 24 4 0 TTACAAAAAA 0.760033 -123 AATCATTGGCTTATCAAAAATAAAAATGGAATAACG 29 35 0 TAAAATAAAA 0.62164 -114 CCAAGTCCTTAAAAAGTAAAAGAATAATGCGAAAAA 29 69 0 AAAAAAAATA 0.565316 -80 GCTTCTCTTTTCTCTATAAAATAAAAAACCGAGTAA 29 113 0 TTAAAAAAAA 0.881777 -36 ACGAGATGTAATTATGCAATAGAAAATATTTTTGG 31 10 0 ATAATAAAAA 0.74766 -291 TAATCAAGGTATTATAAAAATGAAAAGGATCTATAC 31 104 1 ATAAATAAAA 0.915369 -197 TTAATCAAAAAGTATAAAAAATAAAAATCAGGCTTG 32 23 1 ATAAAAAAAA 0.928296 -83 TTAACCTCGATCAATTGAAATAAAAATTGGGCAGAT 35 13 1 TAAAATAAAA 0.621641 -167 ATTTAATGACATTTTTAAAATTAAAATGAAATTGCT 35 91 1 ATAAATAAAA 0.915369 -89 TTAAGTAAATAAAAGATAAAAAAATACCGCACTTTT 36 28 0 AAAAAAAATA 0.565316 -190 GATCAGGCTGTTTTGGCAAATCAAAAACACACTAAA 41 192 0 TTAAATAAAA 0.861713 -61 AGTAGTTACTTGAAAATCTTCAAATT 43 17 0 ATACTTAAAA 0.512472 -16 TATTTAGTCCTATAAAAAAAATAATAATAATTCTCA 44 68 1 TTAAAAAATA 0.739699 -217 AAGAAAGGTATTTTCTCACAACAATAAAGATTGATT 44 117 1 TTACAAAATA 0.546836 -168 TTTTGATAAAAATCAAGAAATAAAAACTATTCTTAT 44 152 1 ATAAATAAAA 0.915369 -133 AGCAGGTTTAAATACAGAAAATAATAAGAATAGTTT 44 175 0 ATAAAAAATA 0.831436 -110 ATATAAAGAAAATAAACACAAAAAAATATATCTGTT 45 177 1 ATACAAAAAA 0.846096 -124 TTTATTTAATAATAGAGAAAATAAAATTTATTGTAA 45 239 0 ATAAAAAAAA 0.928296 -62 AATAGGTTCTAGTTTCAAATAGAAAAA 46 2 0 ATAATAAAAA 0.74766 -68 GTGTGCTATGTTTAGATAAAAAAATAGAACCCATAA 46 38 0 TTAAAAAATA 0.739697 -32 AATGAAAATAATTCCTCAAAAAAATA 47 1 0 ATAAAAAATA 0.831436 -200 TAGCCTTGTCAATAGTTAAATGAAAATAATTCCTCA 47 19 0 ATAAATAAAA 0.915369 -182 CTTAGCAATTTGTGAATAAAAAAAAACGCCTATCTG 47 130 0 TTAAAAAAAA 0.881777 -71 TATTTTCTCAATTTTCTAATTAAAAACGTGGCGTAG 48 133 0 ATAATTAAAA 0.712263 -28 ATAAAATCTTTCTTGATAAAATAAAATGACTGAAGT 50 72 1 TTAAAAAAAA 0.881774 -67 * * **** **** Masking position 8 Map Score: 47.8773 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 496 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 3 AAAAAGCCTGCGAATTTTATACTTTTCAAG 1 105 1 CGAATTTTAT 0.821896 -188 TAGAAATGATCGAATTTTATTTCACTTTTA 3 245 1 CGAATTTTAT 0.821896 -40 ATATACAATATGAATTTTATCTGCACTTAC 4 116 1 TGAATTTTAT 0.906188 -185 GCTTTTACACTGATTTTTATTACACTCGGA 4 210 0 TGATTTTTAT 0.961491 -91 ATATTATAAATAGTTTTTATTGCGTCTTAT 7 36 1 TAGTTTTTAT 0.852396 -125 ATAATGAGAATAGTTTTTATTTCTTGATTT 9 227 1 TAGTTTTTAT 0.852396 -74 CATAAAACAGTGGTTTTTATAGGTTTTCAG 12 105 0 TGGTTTTTAT 0.903121 -96 TTGAATTTAAAGATTTTTATAAGATTTGTG 15 90 0 AGATTTTTAT 0.88263 -92 TCAATAAAATTTTATGAAAAAAGCC 16 6 1 AAAATTTTAT 0.643147 -196 TTAAAGCAACTGATTTTTATCAAAATAAAA 16 62 0 TGATTTTTAT 0.961491 -140 TTGTAATGTGTGATTTTTATCGACAATCTT 26 85 1 TGATTTTTAT 0.961491 -216 CTCTGTAAAGTGATTTTTATCGGAAGTTTG 26 157 1 TGATTTTTAT 0.961491 -144 CTGTAATTTTTATCTTACATATA 27 47 0 TAATTTTTAT 0.939273 -13 AAGTCAAGCCTGATTTTTATTTTTTATACT 32 33 0 TGATTTTTAT 0.961491 -73 ATAATCTGCCCAATTTTTATTTCAATTGAT 35 22 0 CAATTTTTAT 0.880798 -158 TTTTATTTCTTGATTTTTATCAAAAATCAA 44 147 0 TGATTTTTAT 0.961491 -138 ATAATAAGAATAGTTTTTATTTCTTGATTT 44 161 0 TAGTTTTTAT 0.852396 -124 AAAGTTTATAAAATTTTTATAAAATCTGTT 45 140 0 AAATTTTTAT 0.823275 -161 ATATTTACAATAAATTTTATTTTCTCTATT 45 235 1 TAAATTTTAT 0.856813 -66 ATCCTAAGCACAATTTTTATAAGAATAGGT 48 17 0 CAATTTTTAT 0.880798 -144 CTTTAAGGATAAAATTTTATCCTAAGCACA 48 35 0 AAAATTTTAT 0.643147 -126 AAAGCGTGGTTAATTTTTATAAAATCTTTC 50 54 1 TAATTTTTAT 0.939273 -85 ********** Masking position 5 Map Score: 30.8249 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 120 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 TCAGGCGTGATTGTATGTTTGGAAGATAATAA 4 171 1 TTGTTGTTGG 0.858153 -130 TGCGTACTTAATGTAGGGTGGGCTTCAGCCCA 9 85 1 ATGTGGGTGG 0.904494 -216 AATCGTAAGATATTTTGGTGGGCTGAAGCCCA 9 103 0 TATTTGGTGG 0.795258 -198 CTTACGATTGTTTGATGGTGGGCTGAAGCCCA 9 126 1 TTTGTGGTGG 0.980555 -175 ATATTAGTAATTGTAGGGTGGGCTTCAGCCCA 9 144 0 TTGTGGGTGG 0.978889 -157 TTTTTCGATTTTTGGTGGTCGAA 14 2 0 TTTGTGGTGA 0.768596 -56 AAAAAGCTATATTTCTGGTGGGAAGTATAGCT 24 25 1 ATTTTGGTGG 0.881724 -102 GGTTGGTTGGTTGGTTGGTTGGTTCATCAGTA 31 137 0 TTGGTGGTGG 0.992181 -164 GGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 31 157 0 TTGGTGGTGG 0.992181 -144 GGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTT 31 169 0 TTGGTGGTGG 0.992181 -132 TTTTATTATTTTGGTTGGTTGGTTGGTTGGTT 31 189 0 TTGGTGGTGG 0.992181 -112 TGATTAGTAGTTGTAGGGTGGGCTTTAGCCCA 44 240 1 TTGTGGGTGG 0.978889 -45 CTCTCGATTGTTTTTTGGTGGGCTAAAGCCCA 44 258 0 TTTTTGGTGG 0.973333 -27 **** **** ** Masking position 9 Map Score: 20.3463 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 108 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 CTTTTCAAGCAAAATTGCAAGTTTTGTATGCAT 1 126 1 AAAATTGCGT 0.750628 -167 AATTTGACCTAAAACAGCTGGATGCCTCGTATT 1 215 0 AAAACAGCGT 0.953023 -78 TTATCAAGCTAAAATACCGCTATACGCGTAAAT 1 245 0 AAAATACCTT 0.771202 -48 AAATAGGCTAAAAATAGCGCGTATTTAACGCGC 3 18 1 AAAATAGCGA 0.853761 -267 ACTAATAACAAAAATAGCGCGTTAAATACGCGC 3 34 0 AAAATAGCGT 0.971658 -251 TAGAGGTTGAAAAATAGGGTGATTTATTGCGAT 3 150 1 AAAATAGGGT 0.734138 -135 TTTAAAATTAAAAAAAGCAATTTTTTTGAAAAA 4 38 0 AAAAAAGCTT 0.896964 -263 TTTTCTAGTCAAAAAAGCCACGTATAATAAGAC 7 59 0 AAAAAAGCCT 0.864728 -102 AAAATATTGCAAAATAGCCTCAAATTAAGACCT 7 128 1 AAAATAGCCA 0.601738 -33 AAAAATAGCGAAAATAGCTTGATTTTCAAGGAG 8 126 0 AAAATAGCGT 0.971658 -144 GCATTATAGGAAACAAGCACGTTTAAATACAGC 9 192 1 AAACAAGCGT 0.763691 -109 AAAAAATCTYAAAATAGCTTTATCATATCGCCT 10 47 1 AAAATAGCTT 0.923564 -74 AATAAAATTAAAAATAGCACCTTGATAGGTGCT 11 27 0 AAAATAGCCT 0.89871 -82 GAGATTTGCCAAAATAACTAGTTGAAAATCATA 12 131 0 AAAATAACGT 0.553669 -70 CCAAAAATCGAAAAAACCAGTATAATGTGCCAC 14 19 1 AAAAAACCTT 0.708324 -39 TTTGAAATAGAATACAGCCGCTTGTTTAGGGCA 15 136 1 AATACAGCCT 0.397785 -46 AAATTTTATGAAAAAAGCCGTTTGAATTGTTTA 16 17 1 AAAAAAGCTT 0.896966 -185 TTATCAAAATAAAAAAGCCGTTTGAATAAACAA 16 43 0 AAAAAAGCTT 0.896966 -159 AAATCTCCACAAAACACCACTTTTCTCCACTTC 16 137 0 AAAACACCTT 0.666056 -65 TAAATATAGCTAGGTTCGCTCTTTC 18 3 1 AATATAGCGT 0.811788 -120 TTACTAACGTAAAAAAGGTCGCTCTTTCAAAAG 18 37 0 AAAAAAGGGT 0.665494 -86 TAAGTTTCAGAAAATACCTAGTAAATGAAGGTA 23 11 1 AAAATACCGA 0.619565 -28 TCCCACCAGAAATATAGCTTTTTCAACAATAAA 24 15 0 AATATAGCTT 0.603196 -112 TAAWTCATTTAAAAATGCTTGTTGTAATGTGTG 26 64 1 AAAAATGCGT 0.68441 -237 TCTATAAAATAAAAAACCGAGTAATGATAATAC 29 104 0 AAAAAACCGA 0.539879 -45 TTGATTTGCCAAAACAGCCTGATCTTCAAGAAA 41 204 1 AAAACAGCGT 0.953023 -49 CGACTCCTAAAAAACCGCAAGATTATA 42 5 0 AAAACCGCGT 0.599539 -28 TTGTTGTGAGAAAATACCTTTCTTCATATAATA 44 108 0 AAAATACCTT 0.771196 -177 GCATTATAGGAAACAAGCAGGTTTAAATACAGA 44 193 0 AAACAAGCGT 0.76369 -92 ******** * * Masking position 2 Map Score: 23.9664 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 364 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 GAAAGCATCTAAATATGGAATAGTTAAAATTCT 3 96 0 AAATGGAAAG 0.830294 -189 AGATCTCCCAAAAAATGGGGTAGATTATCGCAA 3 176 0 AAAAGGGGAG 0.732661 -109 TAATTAAATTAAAAGTGAAATAAAATTCGATCA 3 251 0 AAAAGAAAAA 0.90592 -34 TCTCAACTTTAAAATAGGAAAAACATT 4 284 1 AAAAGGAAAA 0.957005 -17 GAAAATCGATAAAATCGGAATAGACTGTTCCGA 7 87 1 AAAAGGAAAG 0.954096 -74 GACTGTTCCGAGAAAAGAAAAAATATTGCAAAA 7 109 1 AGAAGAAAAA 0.782382 -52 TCGACCACCAAAAATCGAAAAAACCAGTATAAT 14 12 1 AAAAGAAAAA 0.90592 -46 TAAACTTGCCAGAAGTGGAGAAAAGTGGTGTTT 16 126 1 AGAAGGAGAA 0.802583 -76 TCGCTCTTTCAAAAGTGAAAGAGCGAACCTAGC 18 19 0 AAAAGAAAAG 0.899917 -104 TGTCATTGGGAGAAAAGGAAAAATAA 20 122 1 AGAAGGAAAA 0.892594 -16 GCGCTTTTATAAATAAGGAATAACT 26 286 1 AAATGGAAAA 0.839728 -15 CAAGAAAAAATGGAATAGCGAATACGTT 29 6 1 AAAAGGAAAG 0.954096 -143 TATCAAAAATAAAAATGGAATAACGTATTCGCT 29 27 0 AAAAGGAAAA 0.957005 -122 TTTTATAGAGAAAAGAGAAGCAGGGGAAACT 29 128 1 AAAAGAAGAG 0.814769 -21 TGTTTTGATAAGATTAGAAATAAGATTACGAGA 31 40 0 AGATGAAAAA 0.45837 -261 TATACAAAGAAAAACAGGAATAGACT 33 37 1 AAAAGGAAAG 0.954096 -16 CTTTGTATATAAAAAAGGAGCAATTA 38 44 1 AAAAGGAGAA 0.915886 -16 TGGAGGGCTTAAGACTGAAAAAAGTGAGCAATT 41 28 0 AAGAGAAAAA 0.628815 -225 TCTTCAAGAAAAAATTGAAGCAATTAAAGAAGA 41 226 1 AAAAGAAGAA 0.824885 -27 AAGAAGAAAAAAGAAAGGAATAGTTGCCGAAAT 45 19 0 AAGAGGAAAG 0.785255 -282 AAATAACATTAAATGTGGGAAAATTTATTTAAT 45 265 0 AAATGGGAAA 0.585442 -36 TTTTAATTAGAAAATTGAGAAAATAGC 48 144 1 AAAAGAGAAA 0.721868 -17 **** **** ** Masking position 12 Map Score: 22.3886 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 289 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 ATTTCTAATGAAAATAAACTGCGTAAAAATGC 3 220 0 AAAATAACGC 0.925439 -65 TGTTGTATGAAAATTTGACTGCTTACGTGTCG 6 34 0 AAATTTACGC 0.727248 -35 CCGAGAAAAGAAAAAATATTGCAAAATAGCCT 7 116 1 AAAAAAATGC 0.431153 -45 AAGTGCGGTAAAAATTTACCGCACTTTTGATT 8 21 0 AAAATTACGC 0.968907 -249 ACTAATATCAACAATCAACGGCTCGCATTATA 9 168 1 ACAATCACGC 0.888001 -133 CATCAACGAAAAAAACGACGACATT 11 94 1 AAAAACACAC 0.659752 -15 GAAAACCTATAAAAACCACTGTTTTATGATTT 12 107 1 AAAAACACGT 0.506717 -94 ATATAATTTTAAAATTTATAGCAATTAAGAAG 18 94 1 AAAATTATGC 0.756639 -29 AAAATCCCACGAAATTGACCGCACTTTTAGTA 24 90 0 GAAATTACGC 0.798054 -37 ATAAAAGATAAAAAAATACCGCACTTTTGTGC 36 24 0 AAAAAAACGC 0.883674 -194 AAGTGCGGTCAAAATTAACCGCACTTTTGATG 38 15 0 AAAATTACGC 0.968907 -45 GATTTTAGGGAAAATTGACAGCGAAAAGGAAA 40 47 0 AAAATTACGC 0.968907 -60 CTACTAATCAACAATCAACGGCTCGCATTATA 44 218 0 ACAATCACGC 0.888001 -67 AATTTACGAAAAAAACAACCGCACTTTAAAAG 49 34 0 AAAAACACGC 0.951062 -36 TGTAAAAAATGACCGCACTTTTTGAT 50 5 1 AAAAATACGC 0.950179 -134 AGATTTTATAAAAATTAACCACGCTTTGATAT 50 49 0 AAAATTACAC 0.75664 -90 ****** ** ** Masking position 8 Map Score: 12.2964 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 405 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 8 ATTTTAACTATTCCATATTTAGATGCTTTCT 3 99 1 TTCATATTTA 0.799771 -186 AAAGCTATTTTAGATTTTTTCTTGTAAAAA 10 37 0 TAATTTTTT 0.252067 -84 CCTATCAAGGTGCTATTTTTAATTTTATTAA 11 31 1 TGCATTTTTA 0.700864 -78 TACTGGTTTTTTCGATTTTTGGTGGTCGAA 14 10 0 TTCATTTTTG 0.760283 -48 AATCTTTAAATTCAATTTTGATTTGACGTAA 15 105 1 TTCATTTTGA 0.674506 -77 TAAAAATAAGTTCAATTTTTAAGGCGTAAT 16 182 1 TTCATTTTTA 0.948649 -20 AATTTATATTTTATATATTTAGTCAGCTTAT 22 41 1 TTAATATTTA 0.463971 -43 GTATTCGCTATTCCATTTTTTCTTG 29 5 0 TTCATTTTTT 0.911563 -144 GAATACGTTATTCCATTTTTATTTTTGATAA 29 30 1 TTCATTTTTA 0.948652 -119 TATAGATCCTTTTCATTTTTATAATACCTTG 31 108 0 TTTATTTTTA 0.682114 -193 AAAATACAATTTTTAATCAAAAAGT 32 5 1 TACATTTTTA 0.735849 -101 CAAGCCTGATTTTTATTTTTTATACTTTTTG 32 28 0 TTTATTTTTT 0.544867 -78 TTTGTTAATTTTCTATATTTTA 33 2 0 TTCATATTTT 0.690255 -51 AATTAAATAGTTCAATTTTTAATCATTTCAC 41 71 1 TTCATTTTTA 0.948649 -182 CTTTAATTGCTTCAATTTTTTCTTGAAGATC 41 224 0 TTCATTTTTT 0.911563 -29 TTAAAGTTTATAAAATTTTTATAAAATCTGT 45 141 0 TAAATTTTTA 0.372873 -160 TTTATTTTCTTTATATTTTTATTAAAGTTTA 45 162 0 TTAATTTTTA 0.800141 -139 ATTTTATGGGTTCTATTTTTTTATCTAAACA 46 35 1 TTCATTTTTT 0.911563 -35 *** ******* Masking position 6 Map Score: 12.5235 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 159 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 ATGCCTCGTATTATATCGTAAAACAAAATAAA 1 195 0 TTATTCTAAA 0.599912 -98 TACGCGTAAATTTGACCTAAAACAGCTGGATG 1 224 0 TTTGCCAAAA 0.550469 -69 AAAACACAATTTTTTTCAAAAAAATTGCTTTT 4 27 1 TTTTTCAAAA 0.946876 -274 ATTTCTTGATTTTGATCAAAAATACACTTTTA 9 245 1 TTTGTCAAAA 0.792307 -56 TCCACCGCACTTTAACCATAAATGAATGGGTA 12 26 1 TTTACCTAAA 0.588324 -175 TTCAAACGGCTTTTTTCATAAAATTTTATTGA 16 11 0 TTTTTCTAAA 0.912749 -191 AGCAACTGATTTTTATCAAAATAAAAAAGCCG 16 56 0 TTTTTCAAAT 0.499234 -146 AATGTAGTACTTTTATCTTAAATTT 17 16 1 TTTTTCTAAA 0.912749 -15 TAAGTATTTTTTATATCCAAAAGTGCTAATAT 20 43 1 TTATTCAAAA 0.72422 -95 TTTTAAATGATTAGACGAAAAACTTTGGGCA 26 46 0 TTAACAAAA 0.00562209 -255 AATGTGTGATTTTTATCGACAATCTTGGTCGT 26 89 1 TTTTTCACAA 0.61686 -212 TCAGGTGTCATTTTATCGAAAAACAGTATTAA 26 204 1 TTTTTCAAAA 0.946876 -97 CCTGCTTCTCTTTTCTCTATAAAATAAAAAAC 29 120 0 TTTTTCATAA 0.520553 -29 AAATACAATTTTTAATCAAAAAGTATAAAAAA 32 12 1 TTTATCAAAA 0.885547 -94 TTTTTCTCCTAAATCTTGAGCTT 35 167 0 TTTTTCTAAA 0.912749 -13 ATTTGTAGGTTTTATTCTAAAAAAACATATCG 36 117 1 TTTATCAAAA 0.885547 -101 TCGCTGTCAATTTTCCCTAAAATCGGCTAGAA 40 55 1 TTTTCCAAAA 0.854146 -52 ATTGCTTCAATTTTTTCTTGAAGATCAGGCTG 41 218 0 TTTTTCTGAA 0.628442 -35 GGCAAGCACGTTTAATCTAAAATTGGTCATAT 44 39 1 TTTATCAAAA 0.885547 -246 ATTTCTTGATTTTTATCAAAAATCAATCTTTA 44 141 0 TTTTTCAAAA 0.946876 -144 GGTTCTATTTTTTTATCTAAACATAGCACACA 46 43 1 TTTTTCAAAC 0.596379 -27 GGCGTTTTTTTTTATTCACAAATTGCTAAGAA 47 136 1 TTTATCCAAA 0.481778 -65 TATTATTTCCTAAATTATGTTTTA 47 187 0 TTATTCTAAA 0.599912 -14 AGGATAAAATTTTATCCTTAAAGTTGCAATGG 48 42 1 TTTACCTAAA 0.588324 -119 GTGCGGTTGTTTTTTTCGTAAATTTAACGAGA 49 42 1 TTTTTCTAAA 0.912749 -28 AGTCATTTTATTTTATCAAGAAAGATTTTATA 50 71 0 TTTTTCAGAA 0.747657 -68 **** ** **** Masking position 2 Map Score: 22.095 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 241 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 10 CATTCACAATTTATTTTGTTTTACGATATAA 1 186 1 TTATTTTGTT 0.836071 -107 TTTACGCAGTTTATTTTCATTAGAAATGATC 3 225 1 TTATTTTCTT 0.959565 -60 TGTTTATTTTCCTTTGTATCCGTA 5 79 0 TTATTTTCTT 0.959565 -14 TTTTATTTTCCTCAATTAAGTTA 10 108 0 TTATTTTCTC 0.775873 -13 AATGTCGTCGTTTTTTTCGTTGATGCGCAGA 11 88 0 TTTTTTTCTT 0.70021 -21 TTATTTTAATTTTTCATCTAC 22 1 1 TTATTTTATT 0.65155 -83 AACGGTTTTATTATTTTGGTTGGTTGGTTGG 31 195 0 TTATTTTGTT 0.836071 -106 TCTGAGATTCTTAATTTCCTTTTCGCTGTCA 40 33 1 TTAATTTCTT 0.70021 -74 TACGCCGATTTTATTTTCGGTGACTTACAA 40 87 1 TTATTTTCGT 0.882316 -20 AGAATTATTATTATTTTTTTTATAGGACTAA 44 71 0 TTATTTTTTT 0.65155 -214 ACTATTCTTATTATTTTCTGTATTTAAACCT 44 177 1 TTATTTTCGT 0.882316 -108 TTTTTTGTGTTTATTTTCTTTATATTTTTAT 45 171 0 TTATTTTCTT 0.959565 -130 ACAATAAATTTTATTTTCTCTATTATTAAAT 45 241 1 TTATTTTCCT 0.802913 -60 TTTTGAGGAATTATTTTCATTTAACTATTGA 47 16 1 TTATTTTCTT 0.959565 -185 ******** ** Masking position 6 Map Score: 12.7878 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 54 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 AATAGAAACTAAAAATTTGGCGAGATAGTCAT 8 182 0 AAAATTGGCG 0.919486 -88 TACGCATAGAAAGAATTATGCGTACTTAATGT 9 67 1 AAAATATGCG 0.878048 -234 AGGTTTTCAGAAAAACTTTGCGATACAGATCG 12 83 0 AAAACTTGCG 0.958722 -118 TATTAGAAATAAAAACGTTGCGAATTTTAACC 20 72 1 AAAACTTGCG 0.958722 -66 GATTAGACGAAAAACTTTGGGCATCTGCTGA 26 38 0 AAAACTTGGG 0.73063 -263 TGATTTCCAGTAGAATGAGGCGCTTTTATAAA 26 267 1 TAAATAGGCG 0.72841 -34 TAAAAAGTAAAAGAATAATGCGAAAAATCATT 29 64 0 AAAATATGCG 0.878048 -85 CCAAAATAATAAAACCGTTGCGGTAGTGACTT 31 207 1 AAACCTTGCG 0.813916 -94 AAAAACACACTAAAACAAGGCGACAATATGCT 41 174 0 TAAACAGGCG 0.836096 -79 TATAATCTTGCGGTTTTTTAGG 42 1 1 TAAATTTGCG 0.829469 -32 TTTTCTAATTAAAAACGTGGCGTAGAATAGCA 48 126 0 AAAACTGGCG 0.955988 -35 ** *** ***** Masking position 4 Map Score: 6.02772 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 94 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TGCAATTTTGCTTGAAAAGTATAAAATTCG 1 115 0 CTTGAAAAGT 0.634159 -178 TAAAAATACACTTTAAAATTAAAAAAAGCA 4 52 0 CTTTAAAATT 0.632326 -249 GCTTTTTTGACTAGAAAATCGATAAAATCG 7 74 1 CTAGAAAATC 0.801696 -87 GCAAAATCTCCTTGAAAATCAAGCTATTTT 8 119 1 CTTGAAAATC 0.753545 -151 AAAATAACTAGTTGAAAATCATAAAACAGT 12 124 0 GTTGAAAATC 0.543568 -77 TTTTTCTGTTCTTTAAAAGCTGGTGGAAAT 12 181 1 CTTTAAAAGC 0.753545 -20 ATTTGATCCTTATAAAAGTGAGAAT 13 10 1 TTATAAAAGT 0.637869 -16 AATTGAATAGGTATAAAAGCAAAT 15 5 0 GTATAAAAGC 0.611599 -177 GAACTTATTTTTAGAAAATCTCTAAAAATC 16 165 0 TTAGAAAATC 0.757236 -37 TTGCTATAAATTTTAAAATTATATCATTGA 18 88 0 TTTTAAAATT 0.570247 -35 AATCTTAGTATTAGAAAAGTATCATCAGTA 21 31 1 TTAGAAAAGT 0.63878 -41 TATTCCTTATTTATAAAAGCGCCTCATTCT 26 278 0 TTATAAAAGC 0.757236 -23 TTATTGTGGCGTATAAAATTAGCTTTTA 34 9 0 GTATAAAATT 0.469696 -28 TTAATGACATTTTTAAAATTAAAATGAAAT 35 93 1 TTTTAAAATT 0.570247 -87 AGTAGTTACTTGAAAATCTTCAAATTTA 43 15 0 CTTGAAAATC 0.753545 -18 TATAAAATTTTTATAAAATCTGTTGGCATT 45 134 0 TTATAAAATC 0.756509 -167 TTATTAAAGTTTATAAAATTTTTATAAAAT 45 145 0 TTATAAAATT 0.636957 -156 TGGTATTTTCCTATAAAAGCCATTTAGCAA 48 71 1 CTATAAAAGC 0.801696 -90 ACGTTTTTAATTAGAAAATTGAGAAAATAG 48 140 1 TTAGAAAATT 0.637869 -21 AACAACCGCACTTTAAAAGTGCGGTCAGAT 49 23 0 CTTTAAAAGT 0.633243 -47 TGGTTAATTTTTATAAAATCTTTCTTGATA 50 60 1 TTATAAAATC 0.756509 -79 ********** Masking position 2 Map Score: 13.5967 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 183 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 AGTAGGTTGTATTCCTTTTAATTATCATTCAC 1 161 1 ATTCTTTTAT 0.442345 -132 ATAGTTTTTATTGCGTCTTATTATACGTGGCT 7 45 1 TTGCTCTTAT 0.80616 -116 TTATCCTATTTATCTACTTATTTCAATAACCA 8 245 0 TATCACTTAT 0.465423 -25 GGCGTTTATCTATCATCATAATGATTACTCCT 9 21 1 TATCTCATAT 0.465423 -280 ACTTATTTATTAGCATTTTAATGGATGTTTTA 15 35 1 TAGCTTTTAT 0.427384 -147 TTTCTTTCTTCTTAATTGCTATAAAT 18 107 0 TTTCTCTTAT 0.946864 -16 CTATCCTGTTTTTCTTCTTACTGATGATACTT 21 47 0 TTTCTCTTAT 0.946864 -25 GCCCAAAGTTTTTCGTCTAAWTCATTTAAAAA 26 47 1 TTTCTCTAAT 0.7289 -254 CAAAAATCCCTTTCAACTTAATACTGTTTTTC 26 221 0 TTTCACTTAT 0.7289 -80 TTGTTGTTATCCTTTTAATTCAAATCCGA 30 15 0 TATCTTTTAT 0.761791 -19 TATAGATCCTTTTCATTTTTATAATACCTTGA 31 107 0 TTTCTTTTTT 0.458005 -194 TTTTCTTCTTATTGTGGCGTATA 34 24 0 TTTCTCTTAT 0.946864 -13 TTGCAAGCAATTTCATTTTAATTTTAAAAATG 35 100 0 TTTCTTTTAT 0.908054 -80 TACTTAATTATTTCGTTTTATTCAGCTTGCAA 36 57 1 TTTCTTTTAT 0.908054 -161 TCCTTTCTTTTTTCTTCTTCGTTATCCACTCT 45 33 1 TTTCTCTTCT 0.693238 -268 TTGTGTTTATTTTCTTTATATTTTTATTAAAG 45 166 0 TTTCTTATAT 0.598409 -135 GAGGAATTATTTTCATTTAACTATTGACAAGG 47 20 1 TTTCTTTAAT 0.598409 -181 **** ***** * Masking position 12 Map Score: 7.39392 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 118 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 14 ATGTAGGGTGGGCTTCAGCCCACCAAAATAT 9 95 1 GGCTTAGCCC 0.993678 -206 TTGTAGGGTGGGCTTCAGCCCACCATCAAAC 9 135 0 GGCTTAGCCC 0.993678 -166 ACTTTTTTCAGTCTTAAGCCCTCCAATTCCC 41 36 1 GTCTTAGCCC 0.977661 -217 TTGCCGTTAGCCCAAGCATAACG 44 3 1 GCCGTAGCCC 0.96692 -282 TTGTAGGGTGGGCTTTAGCCCACCAAAAAAC 44 250 1 GGCTTAGCCC 0.993678 -35 ***** ***** Masking position 5 Map Score: 5.09377 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 3 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 CTATATTCTCAAATCACTTTCGAATTTGAGAAT 1 45 0 AAATCTTCGA 0.963118 -248 GAAGATAATAAAATATCTTCCGAGTGTAATAAA 4 192 1 AAATCTTCGA 0.963118 -109 ACCCCTCGAAAATTGCCTTCCGAGGGGTATTTA 4 242 0 AATTCTTCGA 0.804555 -59 CAGCCCACCAAAATATCTTACGATTGTTTGATG 9 110 1 AAATCTTCGA 0.963118 -191 CTTTAATGTGGAATTACTTGCAAGTTGAGCGAA 16 86 1 GAATCTTCAA 0.834069 -116 TAGCACGCAAAAATCCCTTTCAACTTAATACTG 26 227 0 AAATCTTCAA 0.960164 -74 ATATTGTAAAAAATTAATTACAAGGAGATTACT 27 17 0 AAATATTCAA 0.702639 -43 AATTAAAATGAAATTGCTTGCAATCAAAATTTA 35 109 1 AAATCTTCAA 0.960164 -71 CTATCTTTACAACTCTCTTGCAAGCTGAATAAA 36 73 0 AACTCTTCAA 0.849204 -145 TGTTTCAGGAAAATGTTTTTCAAGATAACGTT 37 10 0 AAATTTTCAA 0.702639 -137 **** *** *** Masking position 8 Map Score: 4.85684 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802