AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_hinf_reg_100.orf -o00030_hinf_100.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: HI0052 26 conserved hypothetical protein HI1604 24 phosphate permease, putative Input sequences: #1 HI0050 74 conserved hypothetical transmembrane protein #2 HI0051 38 conserved hypothetical transmembrane protein #3 HI0053 109 zinc-type alcohol dehydrogenase #4 HI0464 132 ribose 5-phosphate isomerase A (rpiA) #5 HI0501 167 high affinity ribose transport protein (rbsD) #6 HI0505 97 ribokinase (rbsK) #7 HI0524 110 fructose-bisphosphate aldolase (fba) #8 HI0553 300 6-phosphogluconate dehydrogenase, decarboxylating (gnd) #9 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #10 HI0559 194 sulfite synthesis pathway protein (cysQ) #11 HI0566 116 ribulose-phosphate 3-epimerase (dod) #12 HI0982 95 6-phosphofructokinase (pfkA) #13 HI0985 300 DNA processing chain A (dprA) #14 HI1023 128 transketolase 1 (tktA) #15 HI1116 110 deoxyribose-phosphate aldolase (deoC) #16 HI1125 295 transaldolase B (talB) #17 HI1573 300 pyruvate kinase, type II (pykA) #18 HI1574 33 replicative DNA helicase (dnaB) #19 HI1576 54 glucose-6-phosphate isomerase (pgi) #20 HI1603 207 conserved hypothetical protein #21 HI1605 65 conserved hypothetical protein #22 HI1607 62 hemM protein (hemM) #23 HI1645 233 fructose-1,6-bisphosphatase (fbp) Motif number 1 TTTTAGACTCCTTATATGCCATTGACA 3 93 0 TTTTCTTATT 0.986378 -17 ATTTCTTAGTTGTTTTTCTATTTTTGTTATCTATATT 5 100 1 TGTTCTTTTT 0.796297 -68 ACATTCGCCCTTTTAATCTACATATAATTGAT 8 6 0 TTTTCATATA 0.794787 -295 ACATTCGCCCTTTTAATCTACATATAATTAATCTTGT 8 171 0 TTTTCATATA 0.794787 -130 CGGAATGGTATTTTATGCTCTATTTGTAATGCCGTGG 10 18 1 TTTTCATTTT 0.79484 -177 ATTTTCGTCTATTTATATTCATGACTGA 11 2 1 TTTTCTTATT 0.986378 -115 GCCCTTTCTTTGTTTATCTTGTTATTTCATATAAGGA 11 53 1 TGTTCTTATT 0.944134 -64 GTCAAACTATTTTTTGGCATTTTATATTAAAAATAAA 13 27 1 TTTTCTTATT 0.986378 -274 ATTTTTTCCTTTTTATTTGAAAATCTAG 13 283 0 TTTTCTTATT 0.986378 -18 TATTTTCCTCCTTTTATTTATGTTTTACC 15 92 0 TTTTCTTATT 0.986378 -19 AAAACTCAATTTTTCTTCAAATAATTTCCTGACAAAT 16 88 0 TTTTCTAATT 0.94366 -208 TTTAGCAATTTTTTTAGCGATTTATTAGACACAACTC 16 127 0 TTTTCTTATA 0.94366 -169 TTTTGTTTACTTTTTTGCCAGTTATATCGGGTTTTAA 17 139 0 TTTTCTTATT 0.986378 -162 TTTCCAAAAGTTTTAAGCGTATAATGTGCACCGATTT 17 204 1 TTTTCTAATT 0.94366 -97 AATTACAAAATTTTAAAGGTGTTATTTTACTTCGCTA 17 258 0 TTTTGTTATT 0.912587 -43 GCGCACGAATTTTTAACCCCTTAATTTGGAGTAAATC 20 177 1 TTTTCTAATT 0.94366 -31 TTTGAATAAATTTTGGAGTGTTTTTATGCATTTGCGC 23 65 0 TTTTGTTTTT 0.707159 -169 **** * **** * Masking position 4 Map Score: 24.3063 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 154 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 ACACCAAGAAATAACAATAAGAATAAACTA 1 39 0 ATAACAATAA 0.745612 -36 TCGTAATAAAGTAACACAATCGTTTACTTA 4 95 1 GTAACACAAT 0.752924 -38 TGGGATATTGATCACAAAATTTCTAGATAG 5 62 0 ATCACAAAAT 0.885182 -106 ACAAATATAGATAACAAAAATAGAAAAACA 5 110 0 ATAACAAAAA 0.956453 -58 AAACGTTTCGATAAGACAAATATAGATAAC 5 125 0 ATAAGACAAA 0.766857 -43 AAACGTTTCGATAACAAAAAGGAGCTTTTA 5 147 1 ATAACAAAAA 0.956453 -21 AAAAAATCCAATAAGAAAAATTTGTTGATT 13 139 0 ATAAGAAAAA 0.911562 -162 CATTTTCAAAATAAGAAAAATTTTGCAATT 13 170 1 ATAAGAAAAA 0.911562 -131 TGCGATGCAGATCGCAAAAATTCTTTTTAA 13 209 0 ATCGCAAAAA 0.888414 -92 TGCGATCTGCATCGCAAAATGCTTTTAAAT 13 223 1 ATCGCAAAAT 0.854011 -78 GCAAATACTTGTAACAATATCTTGCAAGGT 14 56 0 GTAACAATAT 0.560315 -73 GATTAGGAAAATAACAAAATATTCACAGGA 14 102 1 ATAACAAAAT 0.941649 -27 TTTACCTATTGTAGCAAAAATTCTTTATTT 15 68 0 GTAGCAAAAA 0.907935 -43 AATATTTACAATAGGAAAAATCAATACATC 16 193 0 ATAGGAAAAA 0.886635 -103 GGTAATTTATGTAGGAAAATATTTACAATA 16 210 0 GTAGGAAAAT 0.772753 -86 TCAGGTTACGATAGCACAATTAGCATTAAA 16 242 0 ATAGCACAAT 0.796224 -54 TCCGTCAATAATTACAAAATTTTAAAGGTG 17 274 0 ATTACAAAAT 0.596336 -27 AAAAAAATTTGTAAGAAAAAAGGTTTATCT 20 111 0 GTAAGAAAAA 0.859142 -97 TGAGATCTTTATCACAAAAAATTCACATTT 23 134 0 ATCACAAAAA 0.912988 -100 ********** Masking position 2 Map Score: 17.5006 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 298 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 GTTATATCACATTATGGGGCAAATTATATTTGTC 6 31 1 ATAGGGGAAT 0.939772 -67 TGTAGATAAATTGTAGGAGGGAATTACATTCGCC 8 34 0 TGTGGAGAAT 0.977801 -267 ATAGACAAACATGTAGGGGCTAATTATATTAGCC 8 70 1 AGTGGGGAAT 0.989828 -231 TCTTTGTTTATGGTGGGGGCTAATATAATTAGCC 8 87 0 TGTGGGGAAT 0.989828 -214 TGTAGATAAATTGTAGGAGGGAATTACATTCGCC 8 199 0 TGTGGAGAAT 0.977801 -102 TAGACAAAACATGTAGGGGCTAATTATATTAGCC 8 236 1 AGTGGGGAAT 0.989828 -65 ATCTTTGTTTATGATGGGGCTAATATAATTAGCC 8 253 0 AGAGGGGAAT 0.98605 -48 TATGGAAAAAACGAGGGAGAGAAACGATTAATTT 13 249 0 AGAGGAGAAA 0.877583 -52 CACCTTGACATGGTGGGGGTCACTGGTTCGAGTC 17 21 0 TGTGGGGACT 0.943519 -280 TTTGTAATTATTGACGGAGTAAATA 17 286 1 TGAGGAGAAT 0.969693 -15 TTAACCCCTTAATTTGGAGTAAATCACTT 20 189 1 ATTGGAGAAT 0.906746 -19 TGTTGTGATGTTTAAGGGGAAAAA 21 52 1 TTAGGGGAAA 0.777588 -14 * ** **** *** Masking position 12 Map Score: 16.4378 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 49 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TCTAGATAGGATAAAAAATTCTCCGACCAAA 5 40 0 AAAAAAATTC 0.89767 -128 GGATATTGATCACAAAATTTCTAGATAGGAT 5 59 0 CCAAAATTTC 0.800909 -109 AAATATAGATAACAAAAATAGAAAAACAACT 5 107 0 ACAAAAATAG 0.805612 -61 TGATGGTGGCATCAAAAATGCCATCATCAAT 7 35 1 ACAAAAATGC 0.895392 -76 CAACAGTTTTATCAAAAACAGGTTCATGTTG 10 151 1 ACAAAAACAG 0.607436 -44 TGTAGATCAAAATCCCGTCAAATTTT 12 6 1 ACAAAATCCC 0.649843 -90 AATCTGCTCTAGCAAAATTTGACGGGATTTT 12 19 0 ACAAAATTTG 0.89158 -77 GAATAAAAAACTGGCTGTCAAAC 13 3 1 AAAAAAACTG 0.766098 -298 ATATAAAATGCCAAAAAATAGTTTGACAGCC 13 23 0 CAAAAAATAG 0.55672 -278 AAATCCAATAAGAAAAATTTGTTGATTAGGG 13 135 0 AAAAAATTTG 0.83591 -166 TTTTTAATGAATAAAAAATTGCAAAATTTTT 13 185 0 AAAAAAATTG 0.89767 -116 CGATGCAGATCGCAAAAATTCTTTTTAATGA 13 206 0 CCAAAAATTC 0.873855 -95 TACCTATTGTAGCAAAAATTCTTTATTTTTG 15 65 0 ACAAAAATTC 0.934041 -46 TATTTATTAGCTCAAAAATTCATTTTTGTAA 16 55 1 CCAAAAATTC 0.873855 -241 ATAAATCGCTAAAAAAATTGCTAAAAGTGAT 16 139 1 AAAAAATTGC 0.754853 -157 ACTTTTGGAAATCAAAAACGGCTCAGTTATT 17 184 0 ACAAAAACGG 0.761668 -117 TATTAGCCAGATAAAAAATCGGTGCACATTA 17 225 0 AAAAAAATCG 0.841331 -76 ATTCTCCCTAATAAAAATTCCAGAAA 19 39 1 AAAAAATTCC 0.754853 -16 AAAATTTTTCAAAAAAATTTGTAAGAAAAAA 20 120 0 AAAAAATTTG 0.83591 -88 TTTAACTATCAACAAAAATCGGGTAATATGC 20 148 1 ACAAAAATCG 0.895392 -60 GCGATAGTTTCTAAAAATTGCAGTAATAAAT 23 107 1 CAAAAATTGC 0.601007 -127 GATCTTTATCACAAAAAATTCACATTTATTA 23 130 0 AAAAAAATTC 0.89767 -104 * ********* Masking position 6 Map Score: 19.3733 Number of sites scoring better than the average of aligned sites = 637 Number in coding regions = 508 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 TCATAATCATATCATAGTTAAACATAACAAGT 3 51 1 ACATATTAAA 0.932734 -59 CGATAAGACAAATATAGATAACAAAAATAGAA 5 115 0 ATATAATAAC 0.513452 -53 ATTTATCTACATCATAGACAAACATGTAGGGG 8 57 1 ACATAACAAA 0.967003 -244 ATTAGCCCCCACCATAAACAAAGATTCAGTAT 8 97 1 ACATAACAAA 0.967003 -204 CAGATTTATGAATATATTCAAAATAATCCTAT 8 130 1 ATATATCAAA 0.815847 -171 ATTTATCTACATCATAGACAAAACATGTAGGG 8 222 1 ACATAACAAA 0.967003 -79 TATTAGCCCCATCATAAACAAAGATTTAGTAA 8 262 1 ACATAACAAA 0.967003 -39 TTCAGTCATGAATATAAATAGACGAAAAT 11 8 0 ATATAATAGA 0.513452 -109 ATGAAATAACAAGATAAACAAAGAAAGGGCTC 11 51 0 AGATAACAAA 0.773877 -66 CCTACTTTTAACCATAATTGAAAATGGGCATA 12 68 0 ACATATTGAA 0.669174 -28 TAATAAAATTAGCATATTTAACCAATACAACC 13 105 1 ACATATTAAC 0.800992 -196 TGAGCGTAAAACCATAGTCAAAAATAAAGAAT 15 47 1 ACATATCAAA 0.956994 -64 CAATAGGTAAAACATAAATAAAAGGAGGAAAA 15 87 1 ACATAATAAA 0.948083 -24 CTTTTATTTTAACATATTTAGATTGTTGA 18 8 0 ACATATTAGA 0.800992 -26 * **** ***** Masking position 6 Map Score: 10.8785 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 64 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TGCTTGAGAAAAACGCCTGTTAAAAATTACA 4 46 1 AACGCCTGTT 0.806454 -87 CTAAAAGCTCCTTTTTGTTATCGAA 5 153 0 AACTCCTTTT 0.784551 -15 AGGGAATTACATTCGCCCTTTTAATCTACAT 8 20 0 ATCGCCCTTT 0.971295 -281 AGGGAATTACATTCGCCCTTTTAATCTACAT 8 185 0 ATCGCCCTTT 0.971295 -116 AAGGGCACCAAAGAGCCCTTTCTTTGTTTAT 11 39 1 AAAGCCCTTT 0.954392 -78 CGATTAATTTAAAAGCATTTTGCGATGCAGA 13 228 0 AAAGCATTTT 0.774127 -73 CGCCTCTCATATCATCACTTTTAGCAATTTT 16 152 0 ATATCACTTT 0.508598 -144 GGTTAAAATTAACCGCACTTTTTATTGAGAT 21 14 0 AACGCACTTT 0.979072 -52 GGTTAATTTTAACCGCACTTTTGTTGTGATG 21 31 1 AACGCACTTT 0.979072 -35 GGGCTACCATAACCGCACTTTATTAAGCCAA 23 21 0 AACGCACTTT 0.979072 -213 ** ******** Masking position 10 Map Score: 9.15765 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 417 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 7 GTAATTCCCTCCTACAATTTATCTACATCATAGA 8 41 1 CTACATTACT 0.947292 -260 TTTTAATCTACATATAATTAATCTTGTTCCCATA 8 164 0 CTATATTACT 0.9185 -137 GTAATTCCCTCCTACAATTTATCTACATCATAGA 8 206 1 CTACATTACT 0.947292 -95 CGCTAACGAACATTTACTTAACCAAGTATTGCTG 10 90 1 CTTTATTACA 0.944446 -105 GTGTTGTCTTCTTTCAATTCAACATGAACCTGTT 10 167 0 CTTCATTACA 0.964413 -28 AATTTACCTACTTTTAACCATAATTGAAAA 12 76 0 CTACTTTACA 0.848139 -20 AATAAACCTACTTACACTTCATCAAATATACATT 13 58 1 CTACATTACA 0.975425 -243 CGCTCTTTTATTTTAACATATTTAGATT 18 16 0 CTTTATTACA 0.944446 -18 CTCCAGATTCCCTATAATTGATCAACGTATTATG 23 192 1 CTATATTACA 0.961373 -42 AATTTCCTTTTAGTTTTTCATAATACGTTG 23 214 0 CTTTATTTCA 0.705201 -20 * **** ** * ** Masking position 8 Map Score: 8.573 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 47 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AACTACACAAAATAATAGTAACATTATAAGC 1 13 0 AAAATAGTAA 0.647709 -62 ACCAAGAAATAACAATAAGAATAAACTACAC 1 36 0 AAAATAAGAA 0.626064 -39 TTTACTTATTAAGATAAGGAAAAGAA 4 117 1 AAATAAGGAA 0.947025 -16 CCCGCTAAACATAAAAAGGAAACACAAGT 7 92 1 ATAAAAGGAA 0.916849 -19 GGCATTTTATATTAAAAATAAACCTACTTAC 13 42 1 ATAAAAATAA 0.402909 -259 TTACATTTTCAAAATAAGAAAAATTTTGCAA 13 167 1 AAATAAGAAA 0.584818 -134 TTTTTTATTCATTAAAAAGAATTTTTGCGAT 13 198 1 ATAAAAAGAA 0.722452 -103 AGATTTTCAAATAAAAAGGAAAAAAT 13 285 1 ATAAAAGGAA 0.916849 -16 ACTTTCGGTCAAGATTAGGAAAATAACAAAA 14 90 1 AAATTAGGAA 0.82779 -39 TCATCTCAACAAGATAAGGAATAAATAAA 15 9 0 AAATAAGGAA 0.947025 -102 ACCATAGTCAAAAATAAAGAATTTTTGCTAC 15 57 1 AAATAAAGAA 0.808436 -54 GTAAAACATAAATAAAAGGAGGAAAATA 15 93 1 AAAAAAGGAG 0.781599 -18 CTAGTGTGGTAAGATAAGTAACTCAATACAC 20 50 0 AAATAAGTAA 0.822517 -158 CAAATAAAAGTAACTTTACTCAA 22 3 1 AAAAAAGTAA 0.872411 -60 ATTATGAAAAACTAAAAGGAAATT 23 220 1 ACAAAAGGAA 0.832417 -14 ** ******** Masking position 7 Map Score: 9.67101 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 230 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 9 CGCCTGTTAAAAATTACACTTGTTTATTAAATA 4 59 1 AATTACACGT 0.712023 -74 AATATATTCAAAATAATCCTATTTTATGGGAAC 8 140 1 AATAATCCTT 0.728175 -161 CGTCAGCATAAAATTATTCTCTTGTTTTTGGCA 10 59 0 AATTATTCTT 0.809583 -136 TTAGTTTACTCACTTAACGTCAAAA 11 102 0 ATTTACTCTT 0.84932 -15 AATGGGCATAAGATTACATCATTCAAAGAATCT 12 45 0 AATTACATTT 0.66171 -51 AATTTACCTACTTTTAACCATAA 12 83 0 ATTTACCTTT 0.586391 -13 AAATGCTTTTAAATTAATCGTTTCTCTCCCTCG 13 239 1 AATTAATCTT 0.694981 -62 GGTGGCAGCTATTTTATACTATTCTGCCT 14 7 0 ATTTATACTT 0.666236 -122 TTTCCTACATAAATTACCCTTTTAATGCTAATT 16 222 1 AATTACCCTT 0.971957 -74 AAATCGGTGCACATTATACGCTTAAAACTTTTG 17 208 0 AATTATACTT 0.839695 -93 TAGCGAAGTAAAATAACACCTTTAAAATTTTGT 17 258 1 AATAACACTT 0.830506 -43 ACACTAGGAAATATTACCCAGTTGCTTACTTAG 20 74 1 AATTACCCTT 0.971957 -134 ACTTAGTCGAAGATAAACCTTTTTTCTTACAAA 20 101 1 AATAAACCTT 0.589451 -107 ATTCGTGCGCATATTACCCGATTTTTGTTGATA 20 154 0 AATTACCCTT 0.971957 -54 AATAAAAGTAACTTTACTCAATTAAACTAAATC 22 13 1 ATTTACTCTT 0.849316 -50 * ******* ** Masking position 6 Map Score: 7.64202 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 125 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 GTTATATCACATTATGGGGCAAATTATATT 6 31 1 ATTATGGGGC 0.95454 -67 ATAGACAAACATGTAGGGGCTAATTATATT 8 70 1 ATGTAGGGGC 0.976333 -231 ATCTTTGTTTATGGTGGGGGCTAATATAAT 8 92 0 ATGGTGGGGG 0.977492 -209 TAGACAAAACATGTAGGGGCTAATTATATT 8 236 1 ATGTAGGGGC 0.976333 -65 ATCTTTGTTTATGATGGGGCTAATATAATT 8 257 0 ATGATGGGGC 0.987175 -44 CCACCTTGACATGGTGGGGGTCACTGGTTC 17 26 0 ATGGTGGGGG 0.977492 -275 TTTACTCCAAATTAAGGGGTTAAAAATTCG 20 182 0 ATTAAGGGGT 0.755502 -26 ********** Masking position 1 Map Score: 6.68735 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 29 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 AACTGAGCTATAGTCGCACTGTGTGAAGTA 17 66 1 TAGTCGCACT 0.917641 -235 GTTACTTATCTTACCACACTAGGAAATATT 20 59 1 TTACCACACT 0.882596 -149 CGGTTAAAATTAACCGCACTTTTTATTGAG 21 16 0 TAACCGCACT 0.992312 -50 CGGTTAATTTTAACCGCACTTTTGTTGTGA 21 30 1 TAACCGCACT 0.992312 -36 TGGGCTACCATAACCGCACTTTATTAAGCC 23 23 0 TAACCGCACT 0.992312 -211 ********** Masking position 8 Map Score: 4.36844 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 283 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 12 GTAGATTAAAAGGGCGAATGTAATTCCCTC 8 22 1 AGGGCGAATG 0.986542 -279 GTAGATTAAAAGGGCGAATGTAATTCCCTC 8 187 1 AGGGCGAATG 0.986542 -114 CATTACTCGGAAGCCGAATAAGGAATAATT 9 56 1 AAGCCGAATA 0.8917 -20 AGGCAGAATAGTATAAAATA 14 1 1 AGGCAGAATA 0.93938 -128 AAGTCCATTCAAGGAGAATACA 16 284 1 AAGGAGAATA 0.909241 -12 AATTTTTATTAGGGAGAATGACTCCCTCTG 19 28 0 AGGGAGAATG 0.979 -27 ********** Masking position 7 Map Score: 3.94879 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 9 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 GAATGTAATTCCCTCCTACAATTTATCTAC 8 37 1 CCCTCCTACA 0.921626 -264 TAATATAATTAGCCCCTACATGTTTGTCTA 8 71 0 AGCCCCTACA 0.975361 -230 AATTATATTAGCCCCCACCATAAACAAAGA 8 91 1 GCCCCCACCA 0.93716 -210 GAATGTAATTCCCTCCTACAATTTATCTAC 8 202 1 CCCTCCTACA 0.921626 -99 TAATATAATTAGCCCCTACATGTTTTGTCT 8 237 0 AGCCCCTACA 0.975361 -64 TAATTATATTAGCCCCATCATAAACAAAGA 8 256 1 AGCCCCATCA 0.902348 -45 CGAACCAGTGACCCCCACCATGTCAAGGTG 17 25 1 ACCCCCACCA 0.970679 -276 ********** Masking position 10 Map Score: 3.40737 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 AGGTACACCAAGAAATAACAATAAGAATAAA 1 42 0 AGAATAACAA 0.678162 -33 TATGATTATGAAACATAAAAACTCTTTTTGG 3 31 0 AAAATAAAAA 0.940667 -79 TATCATAGTTAAACATAACAAGTAATTTTAT 3 60 1 AAAATAACAA 0.939505 -50 TAGATAACAAAAATAGAAAAACAACTAAGAA 5 102 0 AAAAGAAAAA 0.682648 -66 TAAGACAAATATAGATAACAAAAATAGAAAA 5 113 0 ATAATAACAA 0.587069 -55 TAGAAAGAAAAAATATAACAATACAGGATAA 6 73 1 AAAATAACAA 0.939505 -25 TTATCCCGCTAAACATAAAAAGGAAACACAA 7 88 1 AAAATAAAAA 0.940667 -23 CTTATTTTGAAAATGTAAAAAATCCAATAAG 13 154 0 AAAGTAAAAA 0.9223 -147 TTTCAAATAAAAAGGAAAAAAT 13 289 1 AAAGAAAAAA 0.52076 -12 TCAAGATTAGGAAAATAACAAAATATTCACA 14 98 1 GAAATAACAA 0.663245 -31 AACCATAGTCAAAAATAAAGAATTTTTGCTA 15 56 1 AAAATAAAGA 0.69813 -55 ACAATAGGTAAAACATAAATAAAAGGAGGAA 15 86 1 AAAATAAATA 0.609435 -25 TAACTGGCAAAAAAGTAAACAAAACCAGCTT 17 152 1 AAAGTAAACA 0.633905 -149 AGAAAATTTGAAAGGTAAAAAA 20 2 0 AAAGTAAAAA 0.9223 -206 TTTTCCCCTTAAACATCACAACAAAAGTGCG 21 44 0 AAAATCACAA 0.663245 -22 TATTAAGCCAAAAGGTAAAAA 23 1 0 AAAGTAAAAA 0.9223 -233 *** ******* Masking position 8 Map Score: 10.8318 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 133 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 CGATTCCGATTGAATGTAAATTTGGTCGGAGA 5 20 1 TGAATGTATT 0.901809 -148 ATCAATTATATGTAGATTAAAAGGGCGA 8 7 1 TATATGTATT 0.855855 -294 ATCTGTATACTGAATCTTTGTTTATGGTGGGG 8 103 0 TGAATCTGTT 0.796086 -198 AATATATTCATAAATCTGTATACTGAATCTTT 8 116 0 TAAATCTATA 0.604184 -185 CAAGATTAATTATATGTAGATTAAAAGGGCGA 8 172 1 TATATGTATT 0.855855 -129 GTTGGATTACTAAATCTTTGTTTATGATGGGG 8 268 0 TAAATCTGTT 0.888727 -33 CTTGGTTAAGTAAATGTTCGTTAGCGTCAGCA 10 84 0 TAAATGTGTT 0.939387 -111 GTTTATTAGTTAAATGTATATTTGATGAAGTG 13 72 0 TAAATGTATT 0.949466 -229 ATTGCAGTAATAAATGTGAATTTTTTGTGATA 23 123 1 TAAATGTATT 0.949467 -111 ******* *** Masking position 7 Map Score: 2.04331 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 22 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