AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_mgen_mpneu_300.orf -o199_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -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 = 0.36 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMG00170 20 Mycoplasma RMG00177 16 Mycoplasma RMG05618 16 Mycoplasma RMG05623 23 Mycoplasma RMG00824 22 Mycoplasma RMP00673 25 Mycoplasma_pneumoniae RMG04493 22 Mycoplasma RMG03453 300 Mycoplasma RMG04419 89 Mycoplasma RMP00178 84 Mycoplasma_pneumoniae RMP00396 22 Mycoplasma_pneumoniae RMP00371 18 Mycoplasma_pneumoniae RMP00605 22 Mycoplasma_pneumoniae Input sequences: #1 RMG02265 300 Mycoplasma #2 RMG01247 55 Mycoplasma #3 RMG02280 28 Mycoplasma #4 RMG00179 51 Mycoplasma #5 RMG00186 182 Mycoplasma #6 RMG02298 62 Mycoplasma #7 RMG02299 99 Mycoplasma #8 RMG01274 119 Mycoplasma #9 RMG01278 257 Mycoplasma #10 RMG01352 300 Mycoplasma #11 RMG00273 137 Mycoplasma #12 RMG02389 24 Mycoplasma #13 RMG01370 38 Mycoplasma #14 RMG01371 192 Mycoplasma #15 RMG01372 45 Mycoplasma #16 RMG00290 89 Mycoplasma #17 RMG02403 63 Mycoplasma #18 RMG00320 239 Mycoplasma #19 RMG03467 59 Mycoplasma #20 RMG04478 44 Mycoplasma #21 RMG05622 40 Mycoplasma #22 RMG04471 151 Mycoplasma #23 RMG04456 38 Mycoplasma #24 RMG03425 36 Mycoplasma #25 RMG04443 58 Mycoplasma #26 RMG05538 78 Mycoplasma #27 RMG04418 88 Mycoplasma #28 RMG02908 119 Mycoplasma #29 RMG05363 169 Mycoplasma #30 RMP00304 37 Mycoplasma_pneumoniae #31 RMP00305 117 Mycoplasma_pneumoniae #32 RMP00326 300 Mycoplasma_pneumoniae #33 RMP00327 92 Mycoplasma_pneumoniae #34 RMP00368 300 Mycoplasma_pneumoniae #35 RMP00387 300 Mycoplasma_pneumoniae #36 RMP00388 88 Mycoplasma_pneumoniae #37 RMP00389 20 Mycoplasma_pneumoniae #38 RMP00391 39 Mycoplasma_pneumoniae #39 RMP00394 116 Mycoplasma_pneumoniae #40 RMP00395 63 Mycoplasma_pneumoniae #41 RMP00590 273 Mycoplasma_pneumoniae #42 RMP00596 197 Mycoplasma_pneumoniae #43 RMP00597 24 Mycoplasma_pneumoniae #44 RMP00598 300 Mycoplasma_pneumoniae #45 RMP00604 56 Mycoplasma_pneumoniae #46 RMP00606 53 Mycoplasma_pneumoniae #47 RMP00607 28 Mycoplasma_pneumoniae #48 RMP00613 55 Mycoplasma_pneumoniae #49 RMP00617 275 Mycoplasma_pneumoniae #50 RMP00668 93 Mycoplasma_pneumoniae #51 RMP00669 246 Mycoplasma_pneumoniae #52 RMP00670 121 Mycoplasma_pneumoniae #53 RMP00671 153 Mycoplasma_pneumoniae #54 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 TTCAGTTTTGAAAAGAAAAGTTTAAATTAATGGTAAAATT 5 23 1 AAAAAATTAA 0.953807 -160 GAATTTTTTAAAATGAACTTCGAAATACAAACAGTATTGA 5 95 0 AAAAACAAAA 0.710188 -88 ACAATTTATGAAATTAAAAAAGACAATTAAATAACATATT 5 153 0 AAAAAAATAA 0.897116 -30 TTAAAAACAAAGCTGTAGTTGACACTTGTTTAT 7 4 1 AAAAAATTAC 0.834521 -96 ATTGATTAGAAAAACAACAACCTTGTAAAATTATTTAACT 7 42 1 AAAAACTAAA 0.853002 -58 CAAGAATTAAAAATAAAACTACTAAGATAAACATGATAAT 9 197 0 AAAAAATAAA 0.913196 -61 GTGAATCTTCAAAGTAACTGTTTCTATAAAAATAAATCAG 11 15 0 AAAAACTTAA 0.919284 -123 AACCAAGCAAAAACCAAAAATAACGCTAAAATATCAATCC 18 97 0 AAAAAAATAA 0.897116 -143 TAAAAAGTTCAAAATAAATCTATTAATAAAACAGC 21 16 1 AAAAAATTAA 0.953807 -25 TATTAGTCAAAAATAAAACTACTCTGTGAATTTTAACTTT 22 71 0 AAAAAATTAA 0.953807 -81 TACCAATAAAAGAAAGCAAAGCTTAAAGAGAAATCGA 22 125 0 AAAAAAATAA 0.897116 -27 CTTAAATTTTAAATAAAAAGTATTTAAAAACAATTTAATA 26 40 0 AAAAAATAAA 0.913196 -39 AACTTATTTAAAATTAACAACATAATTTAAACAA 29 146 1 AAAAACTTAA 0.919284 -24 aaattaaatcaatacaataataattggacg 31 1 1 aaaaaataaa 0.913196 -117 ttggttgcaaaaaagaaaactaaaaattaaattaagtttt 32 218 1 aaaaaaataa 0.897116 -83 ctatttatataaaagaaaattgttaattaaagcggagaaa 32 255 0 aaaaaattaa 0.953807 -46 ctaattcgccaaagaaactacgttctacaatgttacgttc 34 126 0 aaaaactaaa 0.853002 -175 aaggcgccagaaaccaaaacgctttttaaaggtttagaac 41 151 0 aaaaaattaa 0.953807 -123 gtaatcgtcgaaaataaaggaaaacgtcaaccccttaaca 44 29 0 aaaaaaataa 0.897116 -272 atgaaaatataaatcaaaagggtatttcaatgc 45 34 1 aaaaaattaa 0.953807 -23 tgatcatagcaaaaaaacatcttacaaaacttggtgattg 49 17 1 aaaaactaac 0.58631 -259 ggtccaaggaaaaagaaaaaataatcataagctttcacaa 49 206 1 aaaaaaaaaa 0.816268 -70 acaatcattcaaagaaaattgttaatttacccagaaaatt 51 65 1 aaaaaattac 0.834521 -182 attaaatcgaaaaacaaattagtcgttaaaggaaatatat 53 19 1 aaaaaattaa 0.953807 -135 *** *** * * ** Masking position 7 Map Score: 34.7694 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 151 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 CCTGAAAAAAACAGGTTCTTTTTTTATTTCTATTTAGTAAATGTT 1 193 1 AATTTTTTTT 0.938067 -108 AGTTTAATGAATAATTTTACCATTAATTTAAACTTTTCTTTTCAA 5 30 0 AATTTTTTTT 0.938067 -153 ATTATTCATTAAACTTTCCTTGTTAGTTGTAGTTTTCAATACTGT 5 60 1 AATTTTTGTT 0.929179 -123 CTAGATCTTTAAAATATGTTATTTAATTGTCTTTTTTAATTTCAT 5 141 1 AAATTTTGTT 0.717086 -42 CTATTAAGAAATTTTTGATCAGTTACTTTTACCTAGATAAATTTA 6 12 1 ATTTTTTTTA 0.57045 -51 TTTTACCTAGATAAATTTAAAGTTTATTTGTGGTA 6 38 1 AATTTTTTTA 0.745295 -25 TATTTAACTAAGTGATTATTACTTAATTGCACTTTAG 7 73 1 ATTTTTTGTT 0.85621 -27 TTAAACCTATAGTCCTTAATTTTTGCTTGGTGCTTACCTATTCTC 10 241 0 ATTTTTTGTT 0.85621 -60 AAGACACCtAATTATAATTTGCTTATTTTGAATTTTTCTAAATAA 14 27 0 ATATTTTTTT 0.57045 -166 CTAAAAAAGATAGTTATTAACTTAATTTAGAATTAACTAATGAC 15 10 1 AATTTTTTTT 0.938067 -36 TATTTGCTACAATCATAACGCTTTAGTTTTTAGTTGATACACCAA 16 12 1 ATTTTTTTTT 0.873003 -78 ACTTGGATTGATATTTTAGCGTTATTTTTGGTTTTTGCTTGGTTT 18 93 1 AATTATTTTT 0.59004 -147 AAATAAAGTTAAAATTCACAGAGTAGTTTTATTTTTGACTAATAC 22 67 1 AATGTTTTTT 0.537252 -85 GCTAATAATTAAAAGTCTAATTTTTATTGTTAATT 24 1 0 AATTTTTGTT 0.929165 -36 ATTAAAGTTAAAAACTCGTTATTTTCTTTGGTTTTATTGCAAGTA 28 34 0 AATTTTTTTT 0.938067 -86 tttggggagtatttattaattattcatttatatttt 30 12 1 attttttttt 0.87297 -26 tacaataataattggacgttatttggtttcttttattgctcaaaa 31 23 1 atatttttta 0.204174 -95 tttctttgatcaacttaataagttcattgatttttgcttgtgctt 32 120 0 catttttgtt 0.511689 -181 attaaagcggagaaaacttaatttaatttttagttttcttttttg 32 225 0 aaattttttt 0.745295 -76 ataaagtgaaaaaaattgcgaattgattgttctttctctaactga 34 167 0 aatttttgtt 0.929179 -134 gtcaattttaatttgtaagcgcttaattgctaataaatgcaaaat 35 252 0 attttttgta 0.534959 -49 gacaatctaaaatttcgcgttttactttttgattgggattttat 41 240 0 aatttttttt 0.938067 -34 tcgtcagaaaagaaatgttacatttcttgacgtttcgacgaattt 42 119 1 aatttttgtt 0.929179 -79 cgttcgaacaaaatctcaacgtttcgtttcaggttt 42 172 1 aatttttttt 0.938064 -26 gcattgaaatacccttttgatttatattttcatttctaa 45 28 0 tatttttttt 0.449401 -29 tgaacttgtgaaagcttatgattattttttctttttccttggacc 49 206 0 aattattttt 0.59004 -70 * * * ** *** ** Masking position 17 Map Score: 21.4926 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 141 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 TTTAAAATTTTCCAAAAATGTGGGAGCT 2 2 1 TTAATTTCAA 0.82864 -54 AAATTATTCATTAAACTTTCCTTGTTAGTTGTAGTTT 5 58 1 TTAATTTTGA 0.870441 -125 CAAATAAACTTTAAATTTATCTAGGTAAAAGTAACTG 6 31 0 TTAATTATGA 0.774369 -32 CAACAACCTTGTAAAATTATTTAACTAAGTGATTATT 7 56 1 GTAATTATAA 0.795097 -44 TTTAAAATTAGTTCACAAGCAATGCATC 9 2 1 TTAATTATAA 0.896802 -256 AGTATGAGTGCTTAATTTAAATTATTAGTAGTGAATC 11 48 0 CTAATTATAA 0.669766 -90 TTTGCTTATTTTGAATTTTTCTAAATAAGCTAACAAA 14 18 0 TTAATTTTAA 0.94448 -175 AAGCTCTATAGTTAATTTAATTAATTACATAAACCAT 22 20 1 GTAATTATAA 0.795097 -132 CTCTGTGAATTTTAACTTTATTTAGTTAAGCAAATGG 22 53 0 TTAATTTTAT 0.754619 -99 ATAACGAGTTTTTAACTTTAATAAAGTTATCGAGGAT 28 57 1 TTAATTTTAT 0.754619 -63 TCTTCAAGGACTTAAATTTAGTGAAAACAAACAATTG 29 81 0 CTAATTTTAA 0.798805 -89 CCAGCTTATCTTAAACTTATTTAAAATTAACAACATA 29 133 1 TTAATTATAT 0.61104 -37 TTGTTTAAATTATGTTGTTAATTTTAAATA 29 150 0 TTAATTATGA 0.774369 -20 tgctcaaaaattgaaattttttcaatagctcctaata 31 59 1 ttaattttaa 0.94448 -59 ctttgaaaagttaaaattttcccaatatttaactctt 36 54 1 ttaatttcaa 0.82864 -35 tgtaagcatggttaactttgattataaaactttcttt 40 17 0 gtaattttaa 0.883669 -47 ttacacacaattaaaatttgattacga 41 1 0 ttaattttaa 0.94448 -273 gaataacacagtgaaattttctgggtaaattaacaat 51 82 0 gtaattttga 0.749999 -165 ctttaatttgttgaagttttttcatcattggggcgaa 51 128 0 ttaattttaa 0.94448 -119 tattcggagattaaattttggcaaaaacctttgatta 52 42 0 ttaatttcaa 0.82864 -80 cctcgcctttttgaaatttcgtgacaatgtttttgcg 54 207 1 ttaattttaa 0.94448 -94 ** ** *** * * * Masking position 8 Map Score: 15.7346 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 113 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTAGCCATTCAGTTTTGAAAAGAAAAGTTTAA 5 16 1 AGTTTGAAAG 0.963833 -167 CAAAGATAGGGGTTTTGTAAAGATCTTACAGA 9 166 1 GGTTTGAAAG 0.960379 -92 TATTTATGCCAGTTTAGTCAAGCTTGATTATA 19 28 0 AGTTAGCAAG 0.752654 -32 AGCTTTCTAAAGCTCTATAGTT 22 1 1 AGTTTCAAAG 0.937696 -151 aatgaggagtgggttgctaaagcgaaattggt 32 191 1 ggttgcaaag 0.88443 -110 catgctaatgggctttgtaaagtttgctaca 33 10 0 ggtttgaaag 0.960379 -83 aaacgaacaaagtttgctcaagcaactcatgc 34 38 1 agttgccaag 0.794743 -263 ctgaaggggtaggcttggaaagcttatagatg 35 192 0 agcttgaaag 0.795396 -109 ggggaattaaagctttgaaaagttaaaatttt 36 42 1 agtttgaaag 0.963833 -47 gaaaaaagagcttacaaaagtgtaagcatg 40 44 0 agttacaaag 0.788774 -20 caggcgattgggatttggaaagcccaagttat 44 153 0 ggtttgaaag 0.960379 -148 aataatcataagctttcacaagttcatataag 49 225 1 agtttccaag 0.873832 -51 gtgacggtttgggtttgcaaattcttatatga 49 248 0 ggtttgaaat 0.596039 -28 atcagcaattagattggtaaagtgtgatacgt 54 28 1 agttggaaag 0.937101 -273 ** **** **** Masking position 10 Map Score: 13.3559 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 ATGGCTGTTATCTGTTTAATTATTGGACTTTTGC 9 62 1 TTTTTAATTT 0.879552 -196 TTAGTAGTTTTATTTTTAATTCTTGGGTTGATAT 9 212 1 TTTTTAATTT 0.879552 -46 TTAGCTCCACTGTGCTTAACTGCTGGGTTCGGGA 10 190 0 TTCTTAATCT 0.861687 -111 TTAAACCTATAGTCCTTAATTTTTGCTTGGTGCT 10 252 0 ATCTTAATTT 0.900611 -49 ATCCCTTTAGATTGCTTAACTCTTTAAAACTTCC 11 94 1 ATCTTAATTT 0.900675 -44 GTTGTGATTATCTTTTTAACTATTAGAGGAGCGG 18 138 1 TTTTTAATTT 0.879552 -102 AGACTTTTAAAATGTTTAATTATTAATATATAGC 25 34 1 ATTTTAATTT 0.861142 -25 TCTATTAAATTGTTTTTAAATACTTTTTATTTAA 26 38 1 TTTTTAATCT 0.814 -41 AAATTAACACTTAAATTTTAAATAAAAAG 26 60 0 ACCTTAATTT 0.699191 -19 cctcattacttttccttaattcttgagcttttct 32 164 0 ttcttaattt 0.911573 -137 gcaaactttgttcgtttaagttttcgtcaaaatc 34 21 0 tctttaattt 0.755351 -280 ttaatttgtaagcgcttaattgctaataaatgca 35 256 0 accttaatct 0.697706 -45 aaattttcccaatatttaactcttctctagca 36 67 1 attttaattt 0.860142 -22 aaagcatttttttccttaaattctat 46 3 0 ttcttaatct 0.861707 -51 tccgaataaaaatttttaagttttattcgtttat 52 71 1 attttaattt 0.861335 -51 * * ***** * ** Masking position 8 Map Score: 9.31516 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 106 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ATAATTTTACAAGGTTGTTGTTTTTCTAATCAATA 7 41 0 AAGTTTTTTT 0.738905 -59 AAACATCGTTAATGGCACTAGGTTTTTTATCAAGT 8 45 0 AAGCTGGTTT 0.863752 -75 TCGTAAAACCAAAGATAGGGGTTTTGTAAAGATCT 9 157 1 AAGTGGTTTT 0.965489 -101 TTATCAACTAAAAGATTGTCGTTTTTGTTTGGTGC 10 126 1 AAGTTGTTTT 0.948429 -175 AGCAAAAATTAAGGACTATAGGTTTAAAAACCTAT 10 259 1 AAGCTGGTTT 0.863753 -42 TTAAATAAAAAAAGACCATAGGTTTTTAAACCTAT 10 276 0 AAGCTGGTTT 0.862411 -25 CTTTTGTGGTAAGGAAAGTTGTTTTCATCAGCCAA 29 38 1 AAGATGTTTT 0.680628 -132 gttctagggtaatgttacgggttttgggcatgagt 34 62 0 aagtggtttt 0.967304 -239 tgttagatcaacggtttgcggtttatgaacttgg 34 277 0 aagtgggttt 0.956808 -24 cacatccccaaaaggtgtgcttttttaattgatac 35 15 1 aagtgttttt 0.819842 -286 gctctcgaaaagcgttaggtgtttttgcatgcgtg 35 86 0 aggtggtttt 0.789571 -215 aaacctttaaaaagcgttttggtttctggcgcctt 41 156 1 aaggtggttt 0.702799 -118 gacaatctaaaatttcgcgttttactttttgat 41 251 0 aaatggtttt 0.609916 -23 attttctttgaatgattgtcgttttttcgaggttc 51 49 0 aagttgtttt 0.948453 -198 acctttgattaaagatgggatttttctgatgaatt 52 18 0 aagtgttttt 0.819719 -104 acgagattaaaatgttctgcgttttcatcgccgaa 54 100 0 aagtggtttt 0.967305 -201 ** * * * ***** Masking position 13 Map Score: 11.8523 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 72 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 TAAAGCAGGATTTATAATCCAACTTCATTTGAAA 1 83 0 TTTTATCAAT 0.800145 -218 CCTTGTAAAATTATTTAACTAAGTGATTATTACT 7 62 1 TTATAACAAT 0.810728 -38 GGATGCATTGCTTGTGAACTAATTTTAAA 9 6 0 CTTTAACAAT 0.601285 -252 ATAAATACCTTTTATCAACCAATAAGTCCTCGAG 10 96 0 TTTTAACAAA 0.840694 -205 ATAAAAGGTATTTATCAACTAAAAGATTGTCGTT 10 115 1 TTTTAACAAA 0.840694 -186 AAAACTTCCCTTTATAATCAAATATCGCC 11 119 1 TTTTATCAAA 0.597684 -19 TCTAAACTTTTTGCAACTAATTAATTAGTTAA 13 9 1 TTTGAACAAT 0.915191 -30 TATTAGTTAACTAATTAATTAGTTGC 13 23 0 TTATAACAAT 0.810728 -16 CCGTAGTCAATTTATTAACTAACTAGTGAACTAG 16 60 1 TTTTAACAAT 0.934304 -30 CATAAACCATTTGCTTAACTAAATAAAGTTAAAA 22 47 1 TTGTAACAAT 0.658656 -105 GATAATATACTTATTTATCTAATATTCCAACATA 23 11 1 TTATATCAAA 0.30913 -28 ccaatttcgctttagcaacccactcctcattact 32 188 0 tttgaaccat 0.533647 -113 tagttttcttttttgcaaccaatttcgctttagc 32 206 0 tttgaacaat 0.915191 -95 ttggcatttctaaactaattaaccaattaa 38 7 1 ttttaacaat 0.934304 -33 taaagaaagttttataatcaaagttaaccatgct 40 16 1 ttttatcaat 0.800145 -48 aacattaccgttaggaaacaaattagtagccaaa 41 68 1 ttagaacaat 0.764717 -206 ctttttacgatttcgaaacaaacaacttaatttc 42 31 0 tttgaacaaa 0.800172 -167 accaatggactttctaaactacattggtcaggtt 49 143 0 ttttaacact 0.601285 -133 cttttgtcgatttggtaacaaagtggaccgtttg 53 111 1 tttgaacaat 0.915191 -43 *** * *** ** * Masking position 2 Map Score: 13.6646 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 126 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TATTAGTTAACTAATTAATTAGTTGCAA 13 21 0 AACTAATTAA 0.84305 -18 TAAATAAGCTAACAAATTAAACC 14 4 0 AACAAATTAA 0.920653 -189 ATTTATTTTGAACTTTTTAACAAA 21 5 0 AACTTTTTAA 0.563266 -36 TTAATAATTAAACATTTTAAAAGTCTTATA 25 30 0 AACATTTTAA 0.735864 -29 AGTATTTAAAAACAATTTAATAGAAGCGTA 26 32 0 AACAATTTAA 0.857506 -47 aaaatcaatgaacttattaagttgatcaaa 32 131 1 aacttattaa 0.713195 -170 attaagcgcttacaaattaaaattgaccca 35 270 1 tacaaattaa 0.552522 -31 ggcatttctaaactaattaaccaattaata 38 13 1 aactaattaa 0.84305 -27 accgttaggaaacaaattagtagccaaata 41 74 1 aacaaattag 0.785669 -200 tttcgaaacaaacaacttaatttctgtttt 42 25 0 aacaacttaa 0.730526 -173 aaaaaacttcaacaaattaaagttactaat 51 143 1 aacaaattaa 0.920653 -104 taaatcgaaaaacaaattagtcgttaaagg 53 21 1 aacaaattag 0.785669 -133 gaaaacgcagaacattttaatctcgtagtt 54 109 1 aacattttaa 0.735864 -192 ********** Masking position 2 Map Score: 6.94171 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 86 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GTAATGTTCATTATGGCTGTTATCTGTTTAATTATT 9 50 1 TTTGCTTTCG 0.90974 -208 AACTAAAAGATTGTCGTTTTTGTTTGGTGCTAATAT 10 131 1 TTTGTTTTTG 0.808761 -170 TCAGCCAATAATTTGGCAATTGTTTGTTTTCACTAA 29 65 1 ATTGCTTTTG 0.931657 -105 tgcggcccttttgtcgctgttagtggctttttactg 33 40 1 tttgcttgtg 0.90974 -53 ttactgttatttttagcccttttttgtacacga 33 70 1 tttgcttttg 0.977344 -23 ggaactgttattgtttcccttgttggttctagggta 34 86 0 ttttcttttg 0.808761 -215 cctttctataattttgcatttattagcaattaagcg 35 242 1 attgcttttg 0.931657 -59 aaagcccaagttatggccctttttcggtgacgggtt 44 131 0 tttgcttttg 0.977344 -170 cactgtgttattctagcggtttttcgccccaatgat 51 106 1 tttgcttttg 0.977344 -141 ** * ** ** ** * Masking position 10 Map Score: 4.55952 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 13 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 10 CATGGTTAGAAAGCAAAAGTCCAATAATTAA 9 77 0 AAGCAAAAGC 0.855081 -181 ACAACAAACCAAGCAAAAACCAAAAATAACG 18 112 0 AAGCAAAAAC 0.78662 -128 AAATAAGGGAATGAAACTTAAGAAT 29 5 1 AAGGGAATGA 0.655732 -165 tgagttttataaggaaaaagcacaagcaaaa 32 103 1 aaggaaaaac 0.889936 -198 gaaaaagcacaagcaaaaatcaatgaactta 32 116 1 aagcaaaaac 0.78662 -185 ctcaagaattaaggaaaagtaatgaggagtg 32 171 1 aaggaaaaga 0.927008 -130 tagaaccaacaagggaaacaataacagttcc 34 91 1 aagggaaaca 0.641939 -210 cgcctgaacgaagcgaaagtccagttctaaa 41 128 1 aagcgaaagc 0.812476 -146 atagaatttaaggaaaaaaatgctttttgt 46 10 1 aaggaaaaaa 0.888079 -44 ctcttggtccaaggaaaaagaaaaaataatc 49 201 1 aaggaaaaaa 0.888079 -75 ttgactgattaaggaatagaaaaaggtttga 51 206 0 aaggaataga 0.574743 -41 ttagtcgttaaaggaaatatatattttttcc 53 37 1 aaggaaataa 0.618415 -117 gcgaaagggaaaggaaatttgttcg 54 286 0 aagggaaaga 0.903154 -15 ********* * Masking position 6 Map Score: 4.88524 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 37 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 11 TTCTCAGTTTTTTGGAAATGGTACTGGTTACC 1 161 0 TTTGGATGGT 0.826013 -140 ATTTTGCTGTGGTACAAACGCTT 2 43 0 TTTTGGTGGT 0.884868 -13 AAGATAGGGGTTTTGTAAAGATCTTACAGATT 9 168 1 TTTTGAAGAT 0.611975 -90 TAACTGCTGGGTTCGGGATGGTTCCAGGTGTT 10 176 0 GTTCGATGGT 0.904451 -125 TTTTTGCTTGGTTTGTTGTGATTATCTTTTTA 18 124 1 GTTTGGTGAT 0.839267 -116 taacggtaatgtttgtaatgataaacttaacg 41 49 0 gtttgatgat 0.923917 -225 ttttattctttttcgtgatgattttatttgta 41 214 0 tttcgatgat 0.845651 -60 ttaatttctgttttgaaatggttttgtc 42 7 0 ttttgatggt 0.947018 -191 taagatgtttttttgctatgatcattcatg 49 9 0 ttttgatgat 0.918091 -267 cctaaatcgcgtttgtgatggtccagccccca 54 147 1 gtttgatggt 0.950897 -154 ***** ***** Masking position 3 Map Score: 1.87312 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 ATACTTAATAAAAATATAACTTT 4 4 1 CTTAATAAAA 0.69027 -48 ATCTAAAGGGATTAATATATTAGTATGAGT 11 76 0 ATTAATATAT 0.721809 -62 AAATAAATCTATTAATAAAACAGC 21 27 1 ATTAATAAAA 0.892089 -14 ATGTTTAATTATTAATATATAGCT 25 45 1 ATTAATATAT 0.721809 -14 TTAGATAAATATTAATAAAATTACTCTGAT 27 21 1 ATTAATAAAA 0.892089 -68 taaatgaataattaataaatactccccaaa 30 12 0 attaataaat 0.847122 -26 gtctttaataaaaacgttatcgt 31 105 0 tttaataaaa 0.724484 -13 taattaaccaattaataaaacagc 38 26 1 attaataaaa 0.892089 -14 tttctgccaaattaatataaacgaataaaa 52 91 0 attaatataa 0.791662 -31 tgtttttcgatttaataaatggaa 53 5 0 tttaataaat 0.639557 -149 ********** Masking position 5 Map Score: 2.98969 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 51 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 AGAACCTGAAAAAAACAGGTTCTTTTTTTATTTC 1 189 1 AAAAACTCTT 0.665209 -112 TTGCTGTGGTACAAACGCTTAATTAGCTCCCACA 2 29 0 ACAAACTATT 0.669826 -27 TGAAATTAAAAAAGACAATTAAATAACATATTTT 5 151 0 AAAGACTAAT 0.796931 -32 TTAGAAAGCAAAAGTCCAATAATTAAACAGATAA 9 69 0 AAAGTCTATT 0.654113 -189 TTTAGTAAAGAAAGACACCtAATTATAATTTGCT 14 49 0 AAAGACtATT 0.950513 -144 AAAAGTATTTAAAAACAATTTAATAGAAGCGTAT 26 31 0 AAAAACTAAT 0.739616 -48 AATTGTTTTTAAATACTTTTTATTTAAAATTTAA 26 45 1 AAATACTATT 0.713584 -34 TATTAAAGTTAAAAACTCGTTATTTTCTTTGGTT 28 46 0 AAAAACTATT 0.926467 -74 aaagacgctttattagagttggac 32 1 1 aaagactatt 0.950434 -300 tgattgttacaaaaatcgctgattttacgacaaa 49 51 1 aaaaattatt 0.458455 -225 aaattttggcaaaaacctttgattaaagatggga 52 33 0 aaaaactatt 0.932915 -89 tattaaatcgaaaaacaaattagtcgttaaagga 53 18 1 aaaaactagt 0.704751 -136 caaatcgacaaaagacgtttaattgaggggatct 53 91 0 aaagactatt 0.950513 -63 tcgttttctgaaagaccattgatttgtaaccgcg 54 66 0 aaagactatt 0.950526 -235 ****** * *** Masking position 3 Map Score: 8.02947 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 42 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 AAAATTATTTAACTAAGTGATTATTACTTAAT 7 68 1 ACAAGTGATT 0.896626 -32 TATCATGTTTATCTTAGTAGTTTTATTTTTAA 9 199 1 ACTAGTAGTT 0.721718 -59 CCTGCAAAGAAGCGCAGTAGTTATAGACAATA 18 54 1 ACCAGTAGTT 0.793548 -186 TAAAATATCAATCCAAGTGATTTTGTATTGTC 18 79 0 ACAAGTGATT 0.896831 -161 ggagttggttagcgaagtggtttaacacatca 34 247 0 acaagtggtt 0.977289 -54 acggagacttacccaagtggtttaagggggcg 35 120 0 acaagtggtt 0.976256 -181 ggggatacttacccaagtggctgaaggggtag 35 212 0 acaagtggct 0.95416 -89 aatcaacctgaccaatgtagtttagaaagtcc 49 139 1 acatgtagtt 0.820539 -137 aaccagcttcacctatgtggcttttcgcatca 50 34 1 acatgtggct 0.871673 -60 * * ******** Masking position 8 Map Score: 1.72406 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 22 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 CAAAACTAAATATCAACCCAAGAATTAAAA 9 225 0 TATCAACCCA 0.747146 -33 AAATACCTTTTATCAACCAATAAGTCCTCG 10 98 0 TATCAACCAA 0.872968 -203 AAAAGGTATTTATCAACTAAAAGATTGTCG 10 117 1 TATCAACTAA 0.863815 -184 TCTAAACTTTTTGCAACTAATTAATTAGTT 13 11 1 TTGCAACTAA 0.870635 -28 GAAGCACAACTAGCAAGTAAAATGCTAGTG 14 133 0 TAGCAAGTAA 0.819074 -60 GATTTTGGTGTATCAACTAAAAACTAAAGC 16 31 0 TATCAACTAA 0.863815 -59 TTTGGTTTTATTGCAAGTAAATAATAACAT 28 23 0 TTGCAAGTAA 0.672083 -97 aatttcgctttagcaacccactcctcatta 32 190 0 tagcaaccca 0.873801 -111 gttttcttttttgcaaccaatttcgcttta 32 208 0 ttgcaaccaa 0.879362 -93 ttgcatttattagcaattaagcgcttacaa 35 255 1 tagcaattaa 0.624028 -46 ********** Masking position 5 Map Score: 1.75851 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 56 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084