AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_ecoli_opreg_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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 pflA 191 pyruvate formate lyase activating enzyme 1 #3 pflB 54 formate acetyltransferase 1 #4 focA 300 probable formate transporter (formate channel 1) #5 ndh 300 respiratory NADH dehydrogenase #6 narK 300 nitrite extrusion protein #7 narG 300 nitrate reductase 1, alpha subunit #8 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #9 ansB 175 periplasmic L-asparaginase II #10 yggN 182 orf, hypothetical protein #11 yggH 160 orf, hypothetical protein #12 yhfC 270 putative transport #13 nirB 261 nitrite reductase (NAD(P)H) subunit #14 nirC 300 nitrite reductase activity #15 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #16 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #17 nrfE 79 formate-dependent nitrite reductase; possible assembly function Motif number 1 TACTTTATTCGCCTGATGCTCCCTTTTAATT 4 67 1 GCCTGATGCC 0.988356 -234 ATGCCTGATGCGCTTCTTATCAG 5 3 1 GCCTGATGCC 0.98833 -298 CGTTCGGTAGGCCTGATAAGAAGCGCATCAG 5 15 0 GCCTGATAAA 0.751788 -286 TCCTGTGGGAGCCTGTCGGCCCTCTGATAAA 7 272 0 GCCTGTCGGC 0.935507 -29 ACGCACCACTGCCTGACAGGCCAGTTAAAAA 8 65 0 GCCTGACAGC 0.536029 -167 ATGCAAAACTGCCTGATGCGCTACGCTTATC 10 33 1 GCCTGATGCC 0.98833 -150 ATCTTTCCAGGCCTGATAAGCGTAGCGCATC 10 47 0 GCCTGATAAC 0.903037 -136 CGTTTTCCATGCCGGATGCGGCGTAAACACC 10 101 0 GCCGGATGCG 0.953801 -82 AAAGTTAGTTGCCGGATGCAAGCATGATAAG 11 94 0 GCCGGATGCA 0.961394 -67 AATATATGTAACCTGACGATCACTTTTTATT 12 111 1 ACCTGACGAC 0.871001 -160 TTGCTCATGCCGGACGGCACTATCGTCGT 13 9 1 GCCGGACGGA 0.964349 -253 AGAGGAAAAGGCCGGACGACGATAGTGCCGT 13 24 0 GCCGGACGAG 0.933946 -238 CGCATTGCACGCCTGTCGGCAAATAACCCGC 14 101 1 GCCTGTCGGA 0.847909 -200 TGAACTGTTCACCGGACACACC 14 289 1 ACCGGACACC 0.788609 -12 ********* * Masking position 3 Map Score: 18.1868 Number of sites scoring better than the average of aligned sites = 2072 Number in coding regions = 1527 Number in noncoding regions = 545 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 TTCAGCCAATTTGATCGAGAACAATTTATCT 1 6 0 TTGAGACAAT 0.968225 -295 TTTGCATTTTTCGACGGTGATCAATTTATAGCTAAA 1 51 0 TCGAGACAAT 0.805231 -250 AGATGAGAAATTGATATAGATCATATCTCGCCTGGC 4 225 0 TTGATACATT 0.93394 -76 CATACCAAAATTGATGTTAATCAAGTTTTGTTGCTG 5 149 0 TTGATACAAT 0.973753 -152 TTATCTATCATTGATATTTATCATTACCCATAGTGA 6 188 0 TTGATACATA 0.843447 -113 ATCTTATCGTTTGATTTACATCAAATTGCCTTTAGC 6 228 1 TTGATACAAT 0.973753 -73 CCCATCACTCTTGATCGTTATCAATTCCCACGCTGT 7 196 1 TTGAGACAAT 0.968225 -105 GAGCGTTACCTTGCCCTTAAACATTAGCAATGTCGA 7 236 1 TTGCTACATA 0.712588 -65 TCTACCGCTATTGAGGTAGGTCAATTTGCGAAGGCG 8 99 1 TTGATGCAAT 0.834263 -133 CTGAATCTTTTTGCGCGAAATCAAAAAGAACATCTG 8 152 0 TTGCGACAAA 0.842361 -80 TATGGGAAATTTGACGTTAAACAATTTACAACGTGA 9 103 0 TTGATACAAT 0.973753 -73 TAGCAACCGATTGCAATAAAACATTTAAACAGATCA 12 174 1 TTGCTACATT 0.866774 -97 ACCCCGCTTATTGATGTAAATCAAATTCACCTTTAT 13 188 0 TTGATACAAT 0.973753 -74 AGGGTAATTTTTGAAGGTCAGCAACAAAAGTTGATT 15 44 1 TTGAGACAAA 0.920709 -257 ACTGTGAATGTTGTCTTTAATCAATTGTAAGTGCAT 15 158 0 TTGTTACAAT 0.811218 -143 **** * * *** * Masking position 13 Map Score: 18.0049 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 46 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 CCACGTATATATTACGCCGCAAAATCCTTA 1 114 0 ATTACGCCGC 0.964177 -187 GCAACCTTTCTTTACGCCGTTTTTGTGTGC 1 173 1 TTTACGCCGT 0.9821 -128 GGATTTTTTATTTACTGCGTACTTCGACAA 3 14 0 TTTACTGCGT 0.901959 -41 ATGAGTTGAATTTTTTCCGCATCCTCCGCT 4 107 0 TTTTTTCCGC 0.691192 -194 TAATCAAATATTTACTCCGTATTTGCATAA 4 169 1 TTTACTCCGT 0.971755 -132 TTTCAGGGGTATTACTGCGCGAGGAAACTA 8 199 0 ATTACTGCGC 0.818616 -33 ATAAAAAAGTATTATGCCGTCTTAAAATAG 9 15 0 ATTATGCCGT 0.913808 -161 ATAATACTTTTTTATGCCGTTTAATTCTTC 9 30 1 TTTATGCCGT 0.95904 -146 GGATAAGGTGTTTACGCCGCATCCGGCATG 10 95 1 TTTACGCCGC 0.983455 -88 ACGATCACTTTTTATTCCGTGATCAAAATC 12 126 1 TTTATTCCGT 0.936234 -145 ********** Masking position 3 Map Score: 11.1114 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 341 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 CAGCCAATTTGATCGAGAACAATTTATCT 1 8 0 GATGAAACAA 0.840897 -293 GCTATAAATTGATCACCGTCGAAAAATGCAAA 1 55 1 GATACGTCGA 0.609707 -246 TTTACTGTACGATTTCAGTCAAATCTAA 2 7 0 GATTCGTCAA 0.863278 -185 TTAAAGTATAGATAGCTGACAAAAAAGGCTCT 2 85 0 GATGCGACAA 0.761195 -107 GGCGAGATATGATCTATATCAATTTCTCATCT 4 229 1 GATTAATCAA 0.912812 -72 AACAAAACTTGATTAACATCAATTTTGGTATG 5 153 1 GATAAATCAA 0.946686 -148 TATGGGTAATGATAAATATCAATGATAGATAA 6 192 1 GATAAATCAA 0.946686 -109 CTTATCGTTTGATTTACATCAAATTGCCTTTA 6 230 1 GATTAATCAA 0.912812 -71 CGTGGGAATTGATAACGATCAAGAGTGATGGG 7 196 0 GATACATCAA 0.921716 -105 GTTGTAAATTGTTTAACGTCAAATTTCCCATA 9 107 1 GTTAAGTCAA 0.613837 -69 GCTGGCCCCAGATTGATAACAAAGTACGCGTT 10 128 0 GATGAAACAA 0.840897 -55 TTTATTCCGTGATCAAAATCACCTCTTAAAAT 12 136 1 GATAAATCAC 0.721467 -135 AGGTGAATTTGATTTACATCAATAAGCGGGGT 13 192 1 GATTAATCAA 0.912812 -70 ACTTACAATTGATTAAAGACAACATTCACAGT 15 162 1 GATAAGACAA 0.870995 -139 *** ** ***** Masking position 3 Map Score: 10.5524 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 183 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TAACTGTTTTAGCGGAGGATGCGGAAAAAAT 4 97 1 AGCGGAGATG 0.793186 -204 CTATAAGCCAGGCGAGATATGATCTATATCA 4 219 1 GGCGAGTATG 0.816067 -82 GCTCTGAAACAGCGTGGGAATTGATAACGAT 7 209 0 AGCGTGGAAT 0.864627 -92 AATTTGCGAAGGCGGATTATTTTGTGGCAAA 8 121 1 GGCGGATATT 0.628401 -111 CGATCGAGTAGGCGGGATAAGGTGTTTACGC 10 81 1 GGCGGGTAAG 0.97036 -102 GCCGGATGCAAGCATGATAAGGCCGTGGCTG 11 84 0 AGCATGTAAG 0.655984 -77 GCAGAAAAAAAGCAAGTGAAGAGATTCTAAA 12 32 1 AGCAAGGAAG 0.510144 -239 ATATGCCGCGAGCGGGCGATTTTAGGTGATT 12 213 0 AGCGGGGATT 0.951329 -58 AAAATGGCATAGCGGGATATGCCGCGAGCGG 12 229 0 AGCGGGTATG 0.972272 -42 AGATGCACGTAGCGGGGGAAGAGAGGAAAAG 13 45 0 AGCGGGGAAG 0.975972 -217 AGACAAAATGAGCGGGTTTATAGAAATAGAT 13 72 0 AGCGGGTTAT 0.666243 -190 TTTGCCGACAGGCGTGCAATGCGCGCAGCGT 14 93 0 GGCGTGAATG 0.697074 -208 CCAAAAGCCGAGCGGGTTATTTGCCGACAGG 14 112 0 AGCGGGTATT 0.95045 -189 CAAATTACCGAGCGTGAAAATCAGGATGATC 14 181 0 AGCGTGAAAT 0.635349 -120 GCAAATAAACGGCAGGGTAATTTTTGAAGGT 15 31 1 GGCAGGTAAT 0.748781 -270 ****** **** Masking position 3 Map Score: 9.92063 Number of sites scoring better than the average of aligned sites = 1672 Number in coding regions = 1537 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 CCGCAAAATCCTTACAATAAACAGGTTTTTG 1 97 0 CTACAATAAA 0.884673 -204 TGACTGAAATCGTACAGTAAAAAGCGTACAA 2 18 1 CTACAGTAAA 0.657008 -174 CAGTAAAAAGCGTACAATAAAGGCTCCACGA 2 32 1 CTACAATAAA 0.88468 -160 AAAATAAATTTTAAAAATTAACAAATGAGTT 4 130 0 TAAAAATTAA 0.603607 -171 GATTATCCAAATAAAAATAAATTTTAAAAAT 4 143 0 AAAAAATAAA 0.691523 -158 GCTCAAATAATAAACAATAAACTCTGTTTTT 5 87 1 TAACAATAAA 0.885265 -214 GTGATGGGGATGAAAAATAAAGTAAATTCCT 7 173 0 TAAAAATAAA 0.85962 -128 TCTCTTGCCGTTAAAAATTAAGCTGAATTTT 8 26 1 TAAAAATTAA 0.603607 -206 CGCGAGGAAACTAACAGTAAAATTCTGAATC 8 181 0 CAACAGTAAA 0.803086 -51 ATTATGCCGTCTTAAAATAGAGGA 9 4 0 CTAAAATAGA 0.704209 -172 TGGCCTGCGTTCAAAAATAAAATGGCATAGC 12 247 0 TAAAAATAAA 0.859617 -24 CATGTTTGTGCAAAAAATAGACAAAATGAGC 13 90 0 CAAAAATAGA 0.83528 -172 AAAATAAAAACAAAAAATAAAACAAAAAGTT 14 13 0 CAAAAATAAA 0.928406 -288 GATTATCCTTTAAAAAATAAAAACAAAAAAT 14 26 0 TAAAAATAAA 0.85962 -275 TTTACATGCACTTACAATTGATTAAAGACAA 15 153 1 CTACAATTGA 0.427263 -148 ACTGTCGTGAAAAACAATAAAAACCGCCATT 15 249 1 AAACAATAAA 0.738541 -52 * ********* Masking position 6 Map Score: 7.23598 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 193 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 CTTTCTTTACGCCGTTTTTGTGTGCATTCA 1 178 1 GCCGTTTTTG 0.917494 -123 CCCATCTGAGGCCGTGTTGGTGCGCAGCTC 2 150 0 GCCGTGTTGG 0.782811 -42 AGTCTGTTATGTGGTGGCTGTTAATTATCC 7 129 1 GTGGTGGCTG 0.885865 -172 TTTACACCCTGCCGTCGCTGTGCTGCAATC 11 41 0 GCCGTCGCTG 0.961427 -120 GCATGATAAGGCCGTGGCTGCGGAAAGTTC 11 74 0 GCCGTGGCTG 0.988734 -87 ATCAATAAGCGGGGTTGCTGAATCGTTAAG 13 209 1 GGGGTTGCTG 0.927733 -53 GGTCAGCTCCGCCATGGCGGGCGCGTATGT 14 142 1 GCCATGGCGG 0.808646 -159 GGTGATTATCGCCGGTTCTGAACTGTTCAC 14 271 1 GCCGGTTCTG 0.855464 -30 CAGTGTAGGTGCGGTTACTGTCGTGAAAAA 15 233 1 GCGGTTACTG 0.842796 -68 TCCGAATTGCGCCATTGTTGCAATGGCGGT 15 271 0 GCCATTGTTG 0.807892 -30 CAGAAAAGAGGTGGTTTCTGGACGTATTCC 17 13 1 GTGGTTTCTG 0.753037 -67 TCGGTTTTCTGGCGTTGTTGTTAAGTCTCG 17 52 1 GGCGTTGTTG 0.890032 -28 ********** Masking position 1 Map Score: 6.642 Number of sites scoring better than the average of aligned sites = 2320 Number in coding regions = 2247 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 TTGCAAACATGTTAATAAAAACTCAAATTGATCCC 1 142 0 GTTAATAACA 0.834757 -159 CGCTAAAACAGTTAATTAAAAGGGAGCATCAGGCG 4 76 0 GTTAATAAGA 0.968179 -225 TCGTCGCCGACTTAATAAAGAGAGAGTTAGT 4 280 1 CTTAATAAGA 0.732977 -21 ATCAAGTTTTGTTGCTGAAAAGATAGGCGACTTTA 5 131 0 GTTGCTAAGA 0.913537 -170 GTAACCTGTTGTTAATTAAGAGCTATGTTAATAAC 5 236 1 GTTAATAAGA 0.968179 -65 TTAACCAATTGTTAATTAATGGTTATTAACATAGC 5 257 0 GTTAATAAGA 0.968179 -44 GCAATTTGATGTAAATCAAACGATAAGATAACTTT 6 222 0 GTAAATAAGA 0.735819 -79 ACCCCTTTAGGATAATTAACAGCCACCACATAACA 7 133 0 GATAATAAGA 0.840776 -168 TGACAGGCCAGTTAAAAAAATGCTATAAAATTCAG 8 48 0 GTTAAAAAGA 0.840776 -184 ATTGCAATCGGTTGCTAAATTGCATTTTAAGAGGT 12 156 0 GTTGCTAAGT 0.739649 -115 AATAAGCGGGGTTGCTGAATCGTTAAGGTAGGCGG 13 212 1 GTTGCTAAGA 0.913537 -50 TTTTTTAAAGGATAATCAAATGTTTACAGACACTA 14 40 1 GATAATAAGT 0.586751 -261 AGCAACAAAAGTTGATTAATTCTTTGAGGAACATG 15 63 1 GTTGATAACT 0.52733 -238 TATGCATGCTGTTGAAAAAGAGGAAGATACTGACT 15 102 1 GTTGAAAAGA 0.812629 -199 GAATGTTGTCTTTAATCAATTGTAAGTGCATGTAA 15 154 0 TTTAATAAGA 0.649377 -147 ****** ** * * Masking position 8 Map Score: 8.91581 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 182 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 GGCTGAAAGGCGGTAATTTAGCTATAAATT 1 35 1 CGGTAATTTA 0.872572 -266 GGTTAAATATCGGTAATTTGTATTTAATAA 4 21 1 CGGTAATTTG 0.98141 -280 AGCTCTGTATGGGAAATTTGACGTTAAACA 9 116 0 GGGAAATTTG 0.878088 -60 AAAGCCGAGCGGGTTATTTGCCGACAGGCG 14 110 0 GGGTTATTTG 0.961618 -191 TTTTCACGCTCGGTAATTTGCTCGATCCAT 14 192 1 CGGTAATTTG 0.98141 -109 ATTACCCTGCCGTTTATTTGCACAATTCTA 15 22 0 CGTTTATTTG 0.786085 -279 ATAAACGGCAGGGTAATTTTTGAAGGTCAG 15 35 1 GGGTAATTTT 0.839054 -266 ATTCACAGTGTGGTTATTTGTTACACATAG 15 185 1 TGGTTATTTG 0.863124 -116 ********** Masking position 6 Map Score: 4.33071 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 105 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ACTCTGTTTTTTGATCTCACCCGGTAAAGTCGCCTA 5 107 1 TTTCCCGGTA 0.753863 -194 AAATAAGGAGTAACTCTTTCCGGGTATGGGTATACT 6 65 0 TATCCGGGTA 0.948947 -236 TTAGTCGCTTTACATCGGTAAGGGTAGGGATTTTAC 6 110 1 TATCAGGGTA 0.984749 -191 TGAAGTCACTGTACTCACTATGGGTAATGATAAATA 6 174 1 GTTCAGGGTA 0.957616 -127 TAAGGTGGCAGACATCGAAACGAGTATCAGAGGTGT 6 273 1 GATCAGAGTA 0.644285 -28 GTATTAAGGAGTATTCCCCATGGGTAACATATTAAT 7 33 0 GTTCAGGGTA 0.957616 -268 TATTAAGATTTTTATGCAGATGGGTATTAAGGAGTA 7 56 0 TTTGAGGGTA 0.815821 -245 TGGCTGTTAATTATCCTAAAGGGGTATCTTAGGAAT 7 143 1 TTCCAGGGTA 0.932799 -158 GGCCCTCTGATAAATCGACATTGCTAATGTTTAAGG 7 250 0 TATCATGCTA 0.61744 -51 CAAATTGACCTACCTCAATAGCGGTAGAAAAACGCA 8 91 0 TATCACGGTA 0.932157 -141 CATTATCCCTTAGCTCTGTATGGGAAATTTGACGTT 9 121 0 TATCAGGGAA 0.863608 -55 AGGGATGGCCTTGTTCTTGAAGGCTATTTAGAATCT 12 53 0 TTTCAGGCTA 0.898168 -218 CACCTTTATATACTCCTTAATGGGTATATTGCTGAT 13 161 0 TACCAGGGTA 0.9343 -101 AGATACTGACTAACTCTAAAGTGGTATTTTACATGC 15 126 1 TATCATGGTA 0.899411 -175 ** ** * ***** Masking position 16 Map Score: 8.25611 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 229 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 GCTATCTATACTTTAAGGTGACTGCCAAAACAGACTCG 2 101 1 CTTTCTGCCA 0.946102 -91 TAGCGAAGAACATTTTCATTGCTGTAACCTGTTGTTAA 5 213 1 CTTTCTGTAC 0.865757 -88 CTCTGATACTCGTTTCGATGTCTGCCACCTTAGTGTCT 6 267 0 CTTTCTGCCC 0.986085 -34 TGTTTCAGAGCGTTACCTTGCCCTTAAACATTAGCAAT 7 229 1 CTTTCCTTAA 0.440603 -72 TTTAATTCTTCGTTTTGTTACCTGCCTCTAACTTTGTA 9 49 1 CTTTCTGCCC 0.986085 -127 GCAGCCACGGCCTTATCATGCTTGCATCCGGCAACTAA 11 83 1 CTTTTTGCAC 0.694625 -78 CGTCGTCCGGCCTTTTCCTCTCTTCCCCCGCTACGTGC 13 34 1 CTTTCTTCCC 0.963012 -228 GCCTCGATTTCTTTTCTATTACCGCCTACCTTAACGAT 13 230 0 CTTTCCGCCA 0.959278 -32 ACCCGCTCGGCTTTTGGGTCAGCTCCGCCATGGCGGGC 14 126 1 CTTTGCTCCC 0.81898 -175 TGGGCGCGACCTTTGGTATCGCCTTAACGCTGGTGATT 14 240 1 CTTTCCTTAC 0.760751 -61 TCCATTGTGTTTTCCGCCCCTTGCGAGGCG 16 19 0 CTTTCCGCCC 0.989594 -20 * ** * ***** * Masking position 9 Map Score: 4.89964 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 581 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 AAATTGATCACCGTCGAAAAATGCAAATTT 1 60 1 CCGTCGAAAA 0.86442 -241 TTTTACAGCACCGTGAAAAATCTCATAATT 6 140 1 CCGTGAAAAA 0.949472 -161 GTCTCTCTTGCCGTTAAAAATTAAGCTGAA 8 23 1 CCGTTAAAAA 0.892932 -209 GCAGTAATACCCCTGAAAAAAGAGGAAAGC 8 211 1 CCCTGAAAAA 0.907591 -21 AGTCTTCCCTCAAGAAAAATCAGGCC 10 167 0 CCCTCAAGAA 0.872947 -16 TTCTAAATAGCCTTCAAGAACAAGGCCATC 12 56 1 CCTTCAAGAA 0.892329 -215 GATTGGCCTGCGTTCAAAAATAAAATGGCA 12 251 0 CGTTCAAAAA 0.713942 -20 ATTTGATTATCCTTTAAAAAATAAAAACAA 14 31 0 CCTTTAAAAA 0.840196 -270 TTGTTGCTGACCTTCAAAAATTACCCTGCC 15 41 0 CCTTCAAAAA 0.950675 -260 GCGGTTACTGTCGTGAAAAACAATAAAAAC 15 243 1 TCGTGAAAAA 0.621456 -58 ********** Masking position 4 Map Score: 5.07079 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 199 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 CCCCACTTTCGTGGAGCCTTTATTGTACGC 2 41 0 GTGGAGCCTT 0.946343 -151 CTCCACGAAAGTGGGGCCTTTTTTAGCGCG 2 55 1 GTGGGGCCTT 0.965487 -137 AACAGACTCGACGTAGCCTTCGAGCTGCGC 2 129 1 ACGTAGCCTT 0.636127 -63 AGGGGTGTATGCAGGGCGTTCGGTAGGCCT 5 32 0 GCAGGGCGTT 0.813084 -269 CTGTTTCAGAGCGTTACCTTGCCCTTAAAC 7 228 1 GCGTTACCTT 0.64961 -73 CTGTCAGGCAGTGGTGCGTTTTTCTACCGC 8 77 1 GTGGTGCGTT 0.864837 -155 AAGGGATAATGCGTAGCGTTCACGTAACTG 9 146 1 GCGTAGCGTT 0.931247 -30 CACTATCGTCGTCCGGCCTTTTCCTCTCTT 13 28 1 GTCCGGCCTT 0.755776 -234 CGTGCAATGCGCGCAGCGTTAGCCGCACAC 14 82 0 GCGCAGCGTT 0.955153 -219 TTGGTGATGGGCGCGACCTTTGGTATCGCC 14 233 1 GCGCGACCTT 0.89613 -68 ********** Masking position 9 Map Score: 1.70544 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 900 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 14 CACACGCATGCCCCAATAGAAATTTGTTTGA 1 227 0 CCCCATAGAA 0.907698 -74 CGAGAGTGAACCCCGTTAGAAAGGGTCACAC 1 253 0 CCCCTTAGAA 0.935055 -48 AATAAAGGCTCCACGAAAGTGGGGCCTTTTT 2 47 1 CCACAAAGTG 0.87049 -145 AATAAAAAATCCACTTAAGAAGGTAGGTGTT 3 32 1 CCACTAAGAA 0.930017 -23 TATACCCATACCCGGAAAGAGTTACTCCTTA 6 67 1 CCCGAAAGAG 0.860368 -234 TCGATGTCTGCCACCTTAGTGTCTGTAGCTA 6 260 0 CCACTTAGTG 0.907753 -41 TTAACAGCCACCACATAACAGACTGTAAATT 7 122 0 CCACTAACAG 0.801283 -179 TCCTAAGATACCCCTTTAGGATAATTAACAG 7 146 0 CCCCTTAGGA 0.792644 -155 ATGTAAAATACCACTTTAGAGTTAGTCAGTA 15 129 0 CCACTTAGAG 0.968885 -172 GCCAGAAAAGAGGTGGTTTCTG 17 2 1 CCAGAAAGAG 0.850467 -78 **** ****** Masking position 8 Map Score: 1.79152 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 161 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 TTATAAGGTTAAATATCGGTAATTTGTATT 4 15 1 AAATATCGGT 0.530321 -286 AATAAAGTAACAATATCGATCGTATTTATT 4 46 0 CAATATCGAT 0.81825 -255 ATGTTATTCTCAATAGCGAAGAACATTTTC 5 200 1 CAATAGCGAA 0.917694 -101 ATACTTCAGCCAATAGCCGAGAATACTGCC 6 40 0 CAATAGCCGA 0.805618 -261 TAAACATTAGCAATGTCGATTTATCAGAGG 7 253 1 CAATGTCGAT 0.852857 -48 TGACCTACCTCAATAGCGGTAGAAAAACGC 8 92 0 CAATAGCGGT 0.972331 -140 TACGCGCCCGCCATGGCGGAGCTGACCCAA 14 139 0 CCATGGCGGA 0.895617 -162 GCCATTGTTGCAATGGCGGTTTTTATTGTT 15 261 0 CAATGGCGGT 0.978375 -40 GCCATTGCAACAATGGCGCAATTCGGATGA 15 274 1 CAATGGCGCA 0.893844 -27 ********** Masking position 4 Map Score: 2.89311 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 788 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529