AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_mpneu_reg_300.orf -o00561_mpneu_300.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: C12_orf65 21 rpmB; 50S ribosomal protein L28. [SP:RL28_MYCPN] C12_orf681 30 dnaX; DNA polymerase III subunits gamma and tau. [EC:2.7.7.7] Input sequences: #1 C09_orf223 300 hypothetical protein. #2 D09_orf508 300 glpK; glycerol kinase (ATP:glycerol 3-phosphotransferase) #3 E30_orf184 76 frr; ribosome recycling factor (ribosome releasing factor) (RRF). #4 E30_orf352 300 hypothetical protein. #5 C12_orf172 134 hypothetical protein. #6 C12_orf141 43 hypothetical protein. #7 C12_orf450 157 deaD; ATP-dependent RNA helicase. #8 C12_orf561 45 hypothetical protein. #9 C12_orf132 300 rpsI; 30S ribosomal protein S9. [SP:RS9_MYCPN] #10 H03_orf351 203 adh; probable NADP-dependent alcohol dehydrogenase. [EC:1.1.1.2] #11 H03_orf213 53 udk; uridine kinase (uridine monophosphokinase). [EC:2.7.1.48] #12 H03_orf612 27 gidA; glucose inhibited division protein. [SP:GIDA_MYCPN] #13 H03_orf537 42 argS; arginyl-tRNA synthetase (arginine--tRNA ligase) (argRS). #14 G12_orf326 54 hypothetical protein. #15 G12_orf218 60 hypothetical protein. #16 G12_orf122 37 rplL; 50S ribosomal protein L7/L12. [SP:RL7_MYCPN] #17 G12_orf161 117 rplJ; 50S ribosomal protein L10. [SP:RL10_MYCPN] #18 G12_orf140b 300 hypothetical protein. #19 G12_orf348 300 hypothetical protein. #20 H08_orf150 300 hypothetical protein. #21 A05_orf241a 51 glpQ; glycerophosphoryl diester phosphodiesterase. [EC:3.1.4.46] #22 A05_orf900 300 alaS; alanyl-tRNA synthetase (alanine--tRNA ligase) (alaRS). #23 H10_orf149 206 hypothetical protein. #24 H10_orf220L 48 hypothetical protein. #25 H10_orf206 38 hypothetical protein. #26 H10_orf145L 138 hypothetical protein. #27 H10_orf187V 89 hsdS1B; #28 A65_orf787o 300 hypothetical protein. #29 K04_orf430 21 pgi; glucose-6-phosphate isomerase (GPI) (phosphoglucose isomerase) #30 K04_orf726 273 vacB; vacB protein homolog. [SP:VACB_MYCPN] #31 G07_orf479 197 hypothetical protein. #32 G07_orf240 24 ung; uracil-DNA glycosylase. [EC:3.2.2.-] [SP:UNG_MYCPN] #33 G07_orf417 300 hypothetical protein. Motif number 1 TTCATTTTTCTTATTTTTATTCTGCTTATC 2 114 0 TTATTTTTAT 0.595112 -187 CCCCACGGGGTGGTTTTAGTTAGTCTCAAT 2 251 0 TGGTTTTAGT 0.930559 -50 AGGCGTTAAATTATTTTAATGGAAAGCGGT 3 47 0 TTATTTTAAT 0.819464 -30 ATAAAGTGTTCGATTTTAATGCCGCGACCA 4 94 0 CGATTTTAAT 0.630219 -207 TTGAATTGTTTTGATGCTACCTTCC 4 286 0 TTGTTTTGAT 0.635769 -15 CTTAAGGTGGTTGTTTTGGTTTATTTATTA 7 94 0 TTGTTTTGGT 0.636682 -64 TTAGTCTTATTGATTTTAGTACTAGGGTCA 8 14 1 TGATTTTAGT 0.947086 -32 AAGCTGGTAGTGTTTTTTATCGTAACGGTC 9 13 0 TGTTTTTTAT 0.687497 -288 TAAAGGATTGTGATTTTAATGGAGAGTACG 9 67 0 TGATTTTAAT 0.946888 -234 TCTCCTGGATTGTTTTTGATATATAGTTTG 9 147 1 TGTTTTTGAT 0.777257 -154 TGAGCTCGCTTGGTTTTAATTTTCGTATTG 10 14 1 TGGTTTTAAT 0.930304 -190 CTTACTAACCTGGTTTTAATAACCAACATA 10 46 0 TGGTTTTAAT 0.930304 -158 TCAAAGTTAATGCTTTTAGT 19 291 1 TGCTTTTAGT 0.754458 -10 TTTTAGGCATTGATTTTGGTTTGAAGAGAA 22 272 0 TGATTTTGGT 0.901894 -29 AAAAACCTGCTGATTTTAGTAAGAAAAAGA 26 66 1 TGATTTTAGT 0.947086 -73 TTTGAAATTTTGATTTTTATTGAAATTTGA 28 104 0 TGATTTTTAT 0.852355 -197 CCAAGCTCATTGATTTTAATCTCCAGTTTT 28 151 1 TGATTTTAAT 0.946888 -150 GATCAAAATTTGTTTTTAATAGTTTCGATT 28 196 1 TGTTTTTAAT 0.871694 -105 AAATCCTTTTTTTAGTTGATT 29 6 0 TTTTTTTAGT 0.63458 -16 ATTACGATGTTTATTTTAGTAGTGCTTTTT 30 208 1 TTATTTTAGT 0.820047 -66 ATTTTTCTTATGATTTTTATTCCGCTTGTA 31 68 1 TGATTTTTAT 0.852355 -130 ********** Masking position 5 Map Score: 20.3517 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 138 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 TAAATTTAAGTAAAAATTAAATATGCTTAA 2 41 1 TAAAAATTAA 0.898683 -260 AGGTTAGTTCTTAAAATTAAAAACTACCCC 2 277 0 TTAAAATTAA 0.918683 -24 TAGAGTTAAATTAAACTTAAATCCATATAG 6 19 1 TTAAACTTAA 0.942332 -25 ATCAACACAGTAAAACTTAATCTCCTTTAA 9 231 1 TAAAACTTAA 0.93404 -70 CACTTAATCTTTAAACTTAAAGGAGATTAA 9 247 0 TTAAACTTAA 0.942332 -54 TGTTAATTATTTAAAATTAATCGAATTTAC 11 11 0 TTAAAATTAA 0.918683 -43 GATAACTTTTTTAAAGTTAAAAACTCGTTA 17 57 0 TTAAAGTTAA 0.798522 -61 CAATGAGTGCTAAAACTTCATATATTGTGG 18 37 1 TAAAACTTCA 0.878047 -264 TTAAGAAGTTTAAAACTTCAAAGCTTTATT 19 164 0 TAAAACTTCA 0.878047 -137 TTTTACATTTTTAAAATTAAGCTCATCAAG 25 11 0 TTAAAATTAA 0.918683 -28 GTTTAATTCCTAAAAATTCAGTGATTAAAG 28 235 0 TAAAAATTCA 0.818136 -66 AGCATTAGTTTAAAATTAACACACATTAA 30 10 1 TTAAAATTAA 0.918683 -264 GCTAGCATCAATAAACTTAAGTGGTTTTGA 33 214 1 ATAAACTTAA 0.703494 -87 ********** Masking position 5 Map Score: 13.0457 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 49 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TGGAAAGCGGTTGCGGAAATTCAACGACAATGTAAAACACGGAC 3 14 0 TTGATTCATA 0.895933 -63 GGCATTAAAATCGAACACTTTATCCAAAACGAAAGTAAGGAAAA 4 101 1 TCGTTTCAAA 0.83628 -200 AAAACAGCAATTGCATCCTTTAAACCAGTGCCAAACTTACCAAT 4 164 0 TTGTTTCAAA 0.967473 -137 ATTTCTTATTTTGTTATAATTCAACAAGTATTAATTC 7 4 0 TTGATTCAAA 0.955775 -154 ATCTTTGATTTTGAAACGTTTAATCAACACAGTAAAACTTAATC 9 209 1 TTGTTTCATA 0.92219 -92 ACCTTAATCATTGTCTTTTTTGTACTAGCTTCAATCATCATTAT 18 147 1 TTGTTTCAAA 0.959416 -154 AAAGACAATTTTGTCCCAATTGCTCGATTTAGAAATTTCGTCAA 20 187 1 TTGATTCAAA 0.95578 -114 CTAAAACTTTTTGAGCTATTTCTCCCAGCTTGTAATATTTATTT 26 13 0 TTGTTTCATA 0.92219 -126 AGGTCAAGATTTGGAAATTTTTCGCAAAACCAAAGACCGCGGAA 30 147 1 TTGTTTCAAA 0.96748 -127 GACCGCGGAATTGTCAAAATTCTCCAAATTACGATGTTTATTTT 30 181 1 TTGATTCAGA 0.834709 -93 ACTGGTGTACTTGAAACAATTCCCCAACTGCAAAAGGAAATAAA 33 14 1 TTGATTCAAA 0.95578 -287 GCTAGTTTGTTTGAACAGTTTCAGCTAGCATCAATAAACTTAAG 33 191 1 TTGTTTCAAA 0.96748 -110 *** *** * * ** Masking position 17 Map Score: 13.5883 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTAGTTTAGGTTAATAAATTTAAGTAAAAATTA 2 27 1 TTAATAATTA 0.502169 -274 TAAGTAAAAATTAAATATGCTTAATTGATTTAA 2 47 1 TTAAATAGTA 0.699993 -254 AAGTCTTGAATTATTAATGTTGAGCTTGAATTG 4 61 0 TTATTAAGTA 0.623231 -240 GGTCGCGGCATTAAAATCGAACACTTTATCCAA 4 95 1 TTAAAATGAA 0.608499 -206 TCAGCAACAGTTAATAACGGTGAAATCGGTAAG 9 98 0 TTAATAAGTA 0.953698 -203 TCTACCGCGTTTAATATCGCAAATATCTTTGAT 9 185 1 TTAATATGAA 0.524265 -116 ATTTAATATCGTTTAAATTGTAATT 13 3 1 TTAATATGTA 0.826515 -40 GTTTTTAACTTTAAAAAAGTTATCGAGGATTAT 17 63 1 TTAAAAAGTT 0.814224 -55 AACACAGGCGTTAATAATGATGATTGAAGCTAG 18 171 0 TTAATAAGTA 0.953694 -130 CTTTAAATCCTTAAAAAGGGTATTAACGGCTTG 22 162 1 TTAAAAAGTT 0.814235 -139 AAGATTGAAGTTAAAAACGATGATTTAGAGTTA 23 16 1 TTAAAAAGTA 0.966722 -191 AGAGTTAGCTTTAAAAAAGTTTAAACGGGTTTC 23 42 1 TTAAAAAGTA 0.966708 -165 GAGCTTAATTTTAAAAATGTAAAATAACGGCC 25 17 1 TTAAAAAGAA 0.870302 -22 AAACAAAACCTTAAAAATGTTTAATGAAAGAAA 27 51 1 TTAAAAAGTA 0.966538 -39 TTTTTCTCATTTAAAAAGGATCAAAATTTGTTT 28 178 1 TTAAAAAGTA 0.966721 -123 TGGAGAAATCTTAATAAAGATTAAACAAGTTTA 28 260 0 TTAATAAGTA 0.953697 -41 AGAAAAATAATGAAAAATGCTAAAGCTTTGTTT 31 43 0 TGAAAAAGTA 0.775547 -155 ******* * * * Masking position 3 Map Score: 14.5794 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 59 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTACTGTCACTGTTTGTTTTACCAGGAAAGTTCT 1 68 1 TTTTTTTACA 0.948754 -233 CTAGAATTTGTTTTTTCTTCATCAGTTAAATCTG 2 178 0 TTTTCTTACA 0.943944 -123 ATGCAATTGCTGTTTTATTTCGCACTAATATCAA 4 192 1 TTTTATTCCA 0.588934 -109 GTCTTTCAGGTATTTTTTTATGCAAAATTTGCCC 5 52 1 TTTTTTTTCA 0.847935 -83 ATCGCAAATATCTTTGATTTTGAAACGTTTAATC 9 200 1 TTTTATTTAA 0.459198 -101 GTCAAGCTGCTTTTTAATTAATAAACTTACTAAC 10 67 0 TTTTATTAAA 0.707973 -137 GGATAGCTGCTCTTTGTTTGAACAATCTCATGTC 10 98 0 TTTTTTTACA 0.948754 -106 TTTTATATTTACTTATTAATTATTTATGA 16 19 0 TTTTCTTTAA 0.575201 -19 TGACTACGTTTCTTTTTTTGAACAGGTAAATAAT 18 210 0 TTTTTTTACA 0.948754 -91 GCGCCAAACTTTTTTATTTGACTACGTTTCTTTT 18 228 0 TTTTTTTATA 0.68256 -73 ACCCTATATTCATTTTTTTCAGAAACTCTTTCCA 19 194 1 CTTTTTTAAA 0.519893 -107 CTTTCCAAATTCTTTTCTTAACCACTTTATTTTT 19 221 1 TTTTCTTACA 0.943943 -80 CAATTTAATTTCTTTCATTAAACATTTTTAAGGT 27 58 0 TTTTATTACA 0.91109 -32 TAATGGCAATCCTTTGTTTAATCATCGGTTTATT 30 71 1 CTTTTTTACA 0.802214 -203 CAAATTACGATGTTTATTTTAGTAGTGCTTTTTC 30 205 1 TTTTTTTATA 0.682539 -69 TAAAGTTTTGTCTTTAATTCAACAAACAAAGCTT 31 20 1 TTTTATTACA 0.91109 -178 CAGCGAGCAGTCTTTTCTTTACAATGTAAAGAAC 31 114 1 TTTTCTTAAA 0.818042 -84 TAGCAGCTTTTATTTCCTTTTGCAGTTGGGGAAT 33 32 0 TTTTCTTTCA 0.835303 -269 CAACGTTGCTAGTTTGTTTGAACAGTTTCAGCTA 33 184 1 ATTTTTTACA 0.59791 -117 * *** *** * ** Masking position 8 Map Score: 12.363 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 46 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 CTTTATCTACAAAAACAGCTTGTTCATTTTT 2 135 0 AAAACAGCTT 0.851727 -166 ATAAACCAAAACAACCACCTTAAGTGGGCTG 7 100 1 AAACCACCTT 0.946966 -58 GATAAAAAACACTACCAGCTTGGGCTCCATC 9 22 1 ATACCAGCTT 0.963872 -279 GTTGGTTATTAAAACCAGGTTAGTAAGTTTA 10 49 1 AAACCAGGTT 0.84545 -155 TTATTAATTAAAAAGCAGCTTGACATGAGAT 10 77 1 AAAGCAGCTT 0.967718 -127 GGAACTAATAAAAACCCGCTTTAATGTACCA 22 42 0 AAACCCGCTT 0.898278 -259 GCACTAATTCATAACCAGCTTGCTTTAAATC 22 140 1 AAACCAGCTT 0.980931 -161 CAGCGTCACGAATACCACCTTCGAAAAGGAA 23 97 1 ATACCACCTT 0.902543 -110 TGGTCTAGTTACTAGCACCTTACCAGTTTTA 23 185 1 ATAGCACCTT 0.843673 -22 CAAAGACAGTTTAAGCAGCTTTGCAGTTCTT 31 142 0 TAAGCAGCTT 0.776393 -56 TTGCAACTCTAAAACAAGCTTGCAAAGACAG 31 164 0 AAACAAGCTT 0.786823 -34 GGAAAATGTCATTAGCAGCTTTTATTTCCTT 33 47 0 ATAGCAGCTT 0.939568 -254 * ********* Masking position 4 Map Score: 12.2965 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 58 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AATTATTTTAATGGAAAGCGGTTGCGGAAA 3 39 0 ATGGAAAGCG 0.865865 -38 ACATGCTTTTTTTGAAAGCTAACTTAATTT 10 182 1 TTTGAAAGCT 0.893442 -22 TGTAAGGAGAATTTAAAGCGCCAAACTTTT 18 249 0 ATTTAAAGCG 0.818626 -52 AAGTTTAAAACTTCAAAGCTTTATTATTCA 19 159 0 CTTCAAAGCT 0.897064 -142 AAGCATTAACTTTGAAAGCGTATTAGCTTT 19 276 0 TTTGAAAGCG 0.94878 -25 CTTTGCCCAGATTCAAAGCGAAGTTTTCGA 20 122 0 ATTCAAAGCG 0.903119 -179 CGGAAGGGACTTGGAAAGCGGTCAATGGTA 22 223 1 TTGGAAAGCG 0.911937 -78 GTTTAAACTTTTTTAAAGCTAACTCTAAAT 23 38 0 TTTTAAAGCT 0.766215 -169 CAAATCTTGACCTGAAAGCGAAGCAAGTCC 30 130 0 CCTGAAAGCG 0.80369 -144 CTGTTAGATTTTAAAGCGCAAAATGAAA 30 256 0 TTTTAAAGCG 0.87865 -18 ATGTAAAGAACTGCAAAGCTGCTTAAACTG 31 137 1 CTGCAAAGCT 0.8297 -61 TTGCACTTCAAAGCTGTAACGTACC 33 286 0 CTTCAAAGCT 0.897064 -15 ********** Masking position 5 Map Score: 9.08511 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 77 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TCACCCCTTGACTGGGCTAATTTCTTATTTTGTT 7 33 0 ACGGGCTATC 0.854727 -125 TGATGAATAAACAGGGAATTCTCCTGGATTGTTT 9 128 1 ACGGGAATTC 0.956806 -173 TACTTGAAACACTGGGATAGCTGCTCTTTGTTTG 10 112 0 ACGGGATATC 0.956806 -92 TGTTTCAAGTACGGGGAAACAGGCAACCATAAAG 10 135 1 ACGGGAAAGC 0.98912 -69 CGGCTCCTAACCAGGGATTAGGGCAAATCTATAA 20 32 0 CCGGGATTGC 0.903685 -269 TTGTTCATTGACAGGGAAAATGTCATTAGCAGCT 33 58 0 ACGGGAAAGC 0.98912 -243 GTGCTTCTACACGGGGAATTTGACTTTGTTCATT 33 83 0 ACGGGAATGC 0.98266 -218 CGGGTTCAATACCGGGAAAAAGCCACTGCCCAAA 33 130 0 ACGGGAAAGC 0.98912 -171 ** ****** * * Masking position 6 Map Score: 6.55113 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TTCTGGGAAAAGCGCAAGATTTACTTGGAA 1 98 1 AGCGCAAGAT 0.742634 -203 CACCTCAATCAGAGAAAAAAATTTTTTTAA 2 76 0 AGAGAAAAAA 0.87607 -225 AAAGGTTCAAAGTGAAAAAACTATTGGTAA 4 142 1 AGTGAAAAAA 0.635565 -159 GTAAAAAACGAGCGAAAAATGCTGAAAAAA 5 15 1 AGCGAAAAAT 0.947623 -120 TACTGTGAATCGCGAAAAAACCTAA 15 6 0 CGCGAAAAAA 0.76509 -55 GACAGTTATTAGAGAAAAAATGAGGAC 18 8 0 AGAGAAAAAA 0.87607 -293 GAGATAAAGTAGAGAATAATACCTACAGCT 18 80 0 AGAGAATAAT 0.625837 -221 TTTAGATAGGAGCGAATAAATGTGTA 18 285 1 AGCGAATAAA 0.761321 -16 TCTATATGCTTGAGAAAGATATGGATAGGG 19 111 1 TGAGAAAGAT 0.595115 -190 TTGCGTGAAAAGCGAAAGATTGCGCAGAAG 23 133 1 AGCGAAAGAT 0.901317 -74 CCTTTTTAAATGAGAAAAAACTGGAGATTA 28 167 0 TGAGAAAAAA 0.715366 -134 TCTTTGGTTTTGCGAAAAATTTCCAAATCT 30 153 0 TGCGAAAAAT 0.865454 -121 TAGATTTTAAAGCGCAAAATGAAAAACTAA 30 250 0 AGCGCAAAAT 0.851099 -24 ********** Masking position 6 Map Score: 6.11749 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 74 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 10 CAAACAGTGACAGTAAACCAGCTAACACAT 1 54 0 CAGTAAACCA 0.861621 -247 ATCAGAAAGACAATTAACCAAACGCTTGTA 1 271 0 CAATTAACCA 0.84537 -30 TTTTTTAAATCAATTAAGCATATTTAATTT 2 54 0 CAATTAAGCA 0.713681 -247 TGAGCACATTTAACCGAAACCCAATT 4 7 1 CATTTAACCG 0.791635 -294 CAATTGCATCCTTTAAACCAGTGCCAAACT 4 171 0 CTTTAAACCA 0.730843 -130 AACTTATAATAAATAAACCAAAACAACCAC 7 88 1 AAATAAACCA 0.772222 -70 GAAGTAACGCAATTAAAGCAATTGTTAATT 11 33 0 AATTAAAGCA 0.680298 -21 TATTAACCTGCAATAAACCAAAGAAAATAA 17 30 1 CAATAAACCA 0.944533 -88 AAACATTTACAATTAAACCA 21 1 0 AATTAAACCA 0.823545 -51 TAAATGTTTGCCTTAAACCAAGGATGACCA 21 22 1 CCTTAAACCA 0.800971 -30 GTTACTGGTACATTAAAGCGGGTTTTTATT 22 37 1 CATTAAAGCG 0.843645 -264 AATTAACACACATTAAAGCATGGACGCAAT 30 24 1 CATTAAAGCA 0.914444 -250 GGTTGGATAGCAATAAACCGATGATTAAAC 30 86 0 CAATAAACCG 0.895796 -188 ********** Masking position 6 Map Score: 7.9592 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 117 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 CATAAAACAGTAAGGCAAAGAAGATCCCTGA 1 14 0 TAAGGAAAGA 0.866452 -287 AGAATAAAAATAAGAAAAATGAACAAGCTGT 2 121 1 TAAGAAAATG 0.8699 -180 AAAACGAAAGTAAGGAAAAGGTTCAAAGTGA 4 126 1 TAAGGAAAGG 0.943175 -175 CTAAAATCAATAAGACTAAGGG 8 2 0 TAAGATAAGG 0.914751 -44 GTGAAATCGGTAAGATAAAGGATTGTGATTT 9 81 0 TAAGAAAAGG 0.971393 -220 CTGATTTTAGTAAGAAAAAGAACGAAGTTTA 26 75 1 TAAGAAAAGA 0.929938 -64 AACCCTAAAATAAGAAAAAGCACTACTAAAA 30 221 0 TAAGAAAAGC 0.886179 -53 ATAAAAATCATAAGAAAAATAATGAAAAATG 31 57 0 TAAGAAAATA 0.723271 -141 ACATTGTCATTAAGAGTAAGGTACGTTACAG 33 267 1 TAAGATAAGG 0.914751 -34 ***** ***** Masking position 8 Map Score: 5.16547 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 31 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 GTTGAATTTCCGCAACCGCTTTCCATTAAA 3 33 1 CGCAACCGCT 0.948415 -44 TTTAATTTAACTCTAGCGCGCCA 6 4 0 CTCTAGCGCG 0.970531 -40 TTGCTGATAACTCTACCGCGTTTAATATCG 9 174 1 CTCTACCGCG 0.957665 -127 TCGCTTTTCACGCAAGCGCATTCCTTTTCG 23 118 0 CGCAAGCGCA 0.96399 -89 ATTTTTTAAGCGCAAGCGCGTTAGGTAATT 24 25 0 CGCAAGCGCG 0.989443 -24 ********** Masking position 5 Map Score: 0.775184 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 CTTGTAGAACTCAAAGTTTCTTTGGTATCAGT 1 245 0 TCAAAGTTTT 0.911034 -56 CGCACTAATATCAAAGTGAGTTTTACAAATCA 4 212 1 TCAAAGTATT 0.941266 -89 CTAATAACTATCAAAGTCATCT 7 146 1 TCAAAGTACT 0.716525 -12 CGTTTCAAAATCAAAGATATTTGCGATATTAA 9 195 0 TCAAAGAATT 0.911034 -106 ACTGGACAGCTCAAAGTTTATTGAAAAAAA 9 281 1 TCAAAGTTTT 0.911034 -20 TTTTCGCGATTCACAGTATATTATTATCTTAC 15 18 1 TCACAGTTTT 0.763884 -43 TTGTGCTATTGCAAAAATAATTTCTG 17 102 1 GCAAAAAATT 0.48185 -16 TAATACGCTTTCAAAGTTAATGCTTTTAGT 19 281 1 TCAAAGTATG 0.716525 -20 CTGGCCCGCATCAAAGACAATTTTGTCCCAAT 20 175 1 TCAAAGAATT 0.911034 -126 GAGAAATAGCTCAAAAAGTTTTAGTAGGTGGT 26 33 1 TCAAAAATTT 0.652883 -106 AGCTAACTAATCACAATAATTTCAGGTTAAAA 27 22 1 TCACAATATT 0.592723 -68 TTAAAAAGGATCAAAATTTGTTTTTAATAGTT 28 188 1 TCAAAATTTT 0.746419 -113 AAACAAGCTTGCAAAGACAGTTTAAGCAGCTT 31 152 0 GCAAAGAATT 0.763884 -46 ******* * ** Masking position 5 Map Score: 3.27806 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 90 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 ATTCAATTTTAGGGAATTGGGTTTCGGTTA 4 21 0 AGGGAATTGG 0.969895 -280 AAGATTAAGTGGGGAACTGGACAGCTCAAA 9 266 1 GGGGAACTGG 0.979612 -35 TCCCTCATGGGGGTAATTGGTGTAAGTAAT 18 111 1 GGGTAATTGG 0.916507 -190 CATTGATTTCGGGAAACTGGCCCGCATCAA 20 159 1 GGGAAACTGG 0.842907 -142 AACACGCGGAAGGGACTTGGAAAGCGGTCA 22 217 1 AGGGACTTGG 0.882729 -84 TTTGGTTTGAAGAGAATTGGTACAGCACTA 22 258 0 AGAGAATTGG 0.759521 -43 ACCAAAGACCGCGGAATTGTCAAAATTCTC 30 175 1 GCGGAATTGT 0.737705 -99 TTTTGCAGTTGGGGAATTGTTTCAAGTACA 33 19 0 GGGGAATTGT 0.950876 -282 GCTTCTACACGGGGAATTTGACTTTGTTCA 33 85 0 GGGGAATTTG 0.905987 -216 ********** Masking position 5 Map Score: 4.52556 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 59 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 15 GAAAAATGAACAAGCTGTTTTTGTAGATAAAG 2 134 1 CAGCTGTTTT 0.887219 -167 AACTACCCCACGGGGTGGTTTTAGTTAGTCTC 2 254 0 CGGGTGTTTT 0.882996 -47 AACCACCCCGTGGGGTAGTTTTTAATTTTAAG 2 266 1 TGGGTATTTT 0.845058 -35 TACAAATCAGCAAGGTACTTTTATTCCTGTAG 4 235 1 CAGGTATTTT 0.955655 -66 CCTGAAAGACTCAGGTATTTTTTCAGCATTTT 5 30 0 TAGGTATTTT 0.907028 -105 CCTGAGTCTTTCAGGTATTTTTTTATGCAAAA 5 47 1 TAGGTATTTT 0.907028 -88 TTGTTCATTCCGGGATAATTTTCCCGT 5 118 1 CGGATATTTT 0.573658 -17 AATCTCATGTCAAGCTGCTTTTTAATTAATAA 10 77 0 CAGCTGTTTT 0.887219 -127 TCCTTATAAGCGAGGTAGTTCTTTTGAAAGAC 20 263 1 CAGGTATTCT 0.881932 -38 CGCAAGCGCGTTAGGTAATTTTAAATTGTTGG 24 13 0 TAGGTATTTT 0.907028 -36 TAAAACTTTTTGAGCTATTTCTCCCAGCTTGT 26 24 0 TAGCTATTCT 0.663342 -115 ACTGTCTTTGCAAGCTTGTTTTAGAGTTGCAA 31 163 1 CAGCTTTTTT 0.664431 -35 * ***** **** Masking position 6 Map Score: 4.79773 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 53 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617