AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mgen_mpneu_300.orf -o294_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: RMG00144 20 Mycoplasma RMG05446 16 Mycoplasma RMP00287 27 Mycoplasma_pneumoniae RMP00673 25 Mycoplasma_pneumoniae Input sequences: #1 RMG01206 300 Mycoplasma #2 RMG01207 33 Mycoplasma #3 RMG00140 134 Mycoplasma #4 RMG00141 210 Mycoplasma #5 RMG01214 289 Mycoplasma #6 RMG02253 110 Mycoplasma #7 RMG01352 300 Mycoplasma #8 RMG00273 137 Mycoplasma #9 RMG02389 24 Mycoplasma #10 RMG03341 101 Mycoplasma #11 RMG04367 23 Mycoplasma #12 RMG05464 46 Mycoplasma #13 RMG04366 28 Mycoplasma #14 RMG04342 161 Mycoplasma #15 RMG04338 167 Mycoplasma #16 RMG05439 300 Mycoplasma #17 RMG01004 115 Mycoplasma #18 RMP00207 76 Mycoplasma_pneumoniae #19 RMP00208 300 Mycoplasma_pneumoniae #20 RMP00212 86 Mycoplasma_pneumoniae #21 RMP00268 300 Mycoplasma_pneumoniae #22 RMP00269 187 Mycoplasma_pneumoniae #23 RMP00272 103 Mycoplasma_pneumoniae #24 RMP00274 121 Mycoplasma_pneumoniae #25 RMP00288 42 Mycoplasma_pneumoniae #26 RMP00296 54 Mycoplasma_pneumoniae #27 RMP00624 300 Mycoplasma_pneumoniae #28 RMP00677 300 Mycoplasma_pneumoniae Motif number 1 TACTTGCTTTTTTTAGTTGGATGGCAATTGTTGGAATTC 1 73 1 TTTTATTATT 0.786522 -228 ATTCACAGCTTTTTAGTTGGAATTTTAGTTAATCATCAA 1 108 1 TTTTATTAAT 0.72813 -193 ATAACATACTTTTTACTTATTTTAAGTGTTTGATGATTA 1 137 0 TTTTATTTTT 0.948066 -164 CTAATAAAGCTTTTAATTTTTTTCTAATTACAgAGTATT 1 210 0 TTTTATTTTT 0.948062 -91 GGACTCaAAGTTTTAACTATTAGTTTTATTTGTGTTTGA 1 269 1 TTTTACTTAT 0.911784 -32 TTTATCAAATTTTTATCTATTTAATATTTAAGAAAGTCG 4 32 1 TTTTACTTTT 0.93438 -179 TTTCTTAGTTTTTTATTTGCTTAATGGTTAAAAAAGCGT 4 111 1 TTTTATTTTT 0.948066 -100 AAGCGTTAGTTTTTACCTTTATTTAATTAATAAACTTCG 4 144 1 TTTTACTATA 0.581712 -67 GCTTTCACATTTTTAGTTGTTAGGAGTTTTAACAAGTTG 5 29 0 TTTTATTTAT 0.929923 -261 GTTTTATGGCTTTTAGTTATTATCGAGTTTTATTGA 6 8 0 TTTTATTTAT 0.929923 -103 GTTTTGTGGTTTTTAGCTTGTTTATAACAATATTATTGC 6 51 1 TTTTACTTTA 0.873254 -60 AACGACAATCTTTTAGTTGATAAATACCTTTTATCAACC 7 110 0 TTTTATTTAT 0.929921 -191 AAACCTGATTTATTTTTATAGAAACAGTTACTTTGA 8 8 1 ATTTATTATA 0.348952 -130 TCATCAGTAAATTTATCTTCTTTTATCGAT 10 82 1 ATTTACTTTA 0.67448 -20 ACTTATTAAATTTTAATTCCTATATGCGTGAAGAAT 12 8 0 TTTTATTTAT 0.929923 -39 GTAACTTTATTTTTAACTAATAAAACAGTTTGTAGTGTT 14 14 1 TTTTACTTAT 0.911917 -148 TTAAGATAACTTTTACTTTCTTTTAAATTAGTTTTTAAT 15 79 1 TTTTATTTTT 0.948066 -89 TTAAATTAGTTTTTAATTATTAAAATATTTTTATTATGA 15 101 1 TTTTATTTAT 0.929922 -67 TTTGGTTTTAATTTAGTTAGTTTACCTGAGTCAATAGTA 16 53 1 ATTTATTTTA 0.726461 -248 CTATTTTCATTTTTAACTTTTTTGATGGTTGCATTTGCT 16 95 1 TTTTACTTTT 0.934394 -206 TCACTGATAAATTTAATTATTTTTATTCTGCTTAGTTTT 16 176 0 ATTTATTTTT 0.8459 -125 AGAACAATTATTTTAATAATTTTGGTAATTAATAATTTC 17 16 1 TTTTATATTT 0.589951 -100 cgaaaggtaattttattaaattgcggacttatttcac 18 50 1 ttttatattt 0.589951 -27 atgaaaacggttttaactcgataaatcta 21 1 0 ttttactata 0.581712 -300 taacaggaaaatttaatttttaagcctaatgctaatttc 21 73 0 atttatttaa 0.658766 -228 ggcgtagagtttttagtttttattgttgaaactttttaa 21 122 1 ttttatttaa 0.865233 -179 agcattggttttttagttgttttaagtatttgttatttc 21 256 1 ttttattttt 0.948066 -45 ttagttttaattactaaccacatatacaaggtt 22 5 1 ttttatttat 0.929747 -183 agcgtgcctgatttatttactagtagattaagcgtttat 22 60 0 atttatttat 0.799609 -128 cactttaagcatttaactgctaattgttaataattggta 22 146 1 atttacttaa 0.600988 -42 acaacccttcttttatctgcttattgaaagcctgt 23 7 0 ttttacttta 0.873216 -97 ***** ** ** * Masking position 5 Map Score: 40.4143 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 238 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 GTAATTAGAAAAAAATTAAAAGCTTTATTAGGAG 1 218 1 AAAAATTAAT 0.888572 -83 CAAACACAAATAAAACTAATAGTTAAAACTTtGA 1 273 0 TAAAACTAAT 0.863063 -28 AAATTTGATAAAAATCTAAAGCTTTTTTAACTA 4 10 0 AAAATCTAAT 0.793714 -201 CGACTTTCTTAAATATTAAATAGATAAAAATTTG 4 37 0 AAATATTAAA 0.706482 -174 TAAGCAAATAAAAAACTAAGAAAAATTTGCGACT 4 100 0 AAAAACTAAA 0.936955 -111 AAATAAAGGTAAAAACTAACGCTTTTTTAACCAT 4 134 0 AAAAACTAAT 0.918145 -77 AAGAATTATCTAAATTTAAATAGACTAGAATTAA 5 247 1 TAAATTTAAA 0.671123 -43 TTGAGCTGAGTAATACTAATTGCTCGAGGACTTA 7 74 1 TAATACTAAT 0.589949 -227 AGCACCAAGCAAAAATTAAGGACTATAGGTTTAA 7 252 1 AAAAATTAAT 0.888639 -49 CAGCTTGAAGTAAAATTAATCCTA 9 11 1 TAAAATTAAA 0.855443 -14 TTAAAATTTAAAATTATTGTGGTTAT 10 3 1 AAAATTTAAA 0.630882 -99 TATAGGAATTAAAATTTAATAAGTTTCTAAAAAT 12 23 1 AAAATTTAAT 0.732269 -24 TTTGTATTTAAAAATTAACAATATCTCACTAAA 15 10 1 AAAAATTAAA 0.913441 -158 ATATCTCACTAAATATTAATTAATGTTTAGCGCT 15 31 1 AAATATTAAT 0.644496 -137 TAATATCAGATAAATTTAAGATAACTTTTACTTT 15 64 1 TAAATTTAAA 0.671142 -104 TTTAATAATTAAAAACTAATTTAAAAGAAAGTAA 15 91 0 AAAAACTAAA 0.93645 -77 AAGCCAATGCAAATTCTAACGGGATTAATTTTTT 16 21 1 AAATTCTAAA 0.537319 -280 CTAACTAAATTAAAACCAAAAAAATTAATCCCGT 16 39 0 TAAAACCAAA 0.531943 -262 AAGCTAATGAAAAAACTAATGAAAGCAAATGCAA 16 123 0 AAAAACTAAA 0.936955 -178 TAATTGCATCTAAAACTAAGCAGAATAAAAATAA 16 165 1 TAAAACTAAA 0.893257 -136 TTTTCACTGATAAATTTAATTATTTTTATTCTGC 16 184 0 TAAATTTAAT 0.552767 -117 ATCTTATTAGTAATATTAAGCTTAGTGCAATAAT 17 64 1 TAATATTAAA 0.574919 -52 ttaaaccctaaaaaattaattggactcgctaatg 21 37 0 aaaaattaaa 0.913098 -264 cattaggcttaaaaattaaattttcctgttatgc 21 81 1 aaaaattaat 0.531847 -220 tttcaacaataaaaactaaaaactctacgccatc 21 119 0 aaaaactaat 0.918145 -182 gactattgaataaaactaaaacaatcgttattgt 27 72 1 taaaactaaa 0.893256 -229 ttgtccactgaaaaaccaaacgaaatctacacct 27 112 0 aaaaaccaaa 0.668693 -189 ttgcccaccgaaaaattaacaccttgacgttcga 27 149 1 aaaaattaat 0.888636 -152 ********* * Masking position 8 Map Score: 32.5511 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 310 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 TATCACAAAATGGTGTGATCTTATCAATAGCACTACTTGCTT 1 40 1 TTTTTCAACA 0.861961 -261 TTTTTCTAATTACAgAGTATTTGTTAATGCCATAATTGGAAA 1 189 0 TATTTTAACA 0.963972 -112 GAACTATTATTTGAAAAAAGTTATTAATTGCAAGTTGATAAA 5 182 1 TATTTTAACA 0.963968 -108 GCAGTAAAACTGCAATAATATTGTTATAAACAAGCTAAAAAC 6 59 0 TTTTTTATCA 0.920261 -52 TTCATCGCCTTTGTTTTGTCTTATTAATAGCAATGAAAAGTG 14 81 0 TTTTTTAACA 0.96397 -81 ACAAAGGCGATGAAAATCATTTATCAAGAACAACAGAATGAG 14 109 1 TATTTCAACA 0.861899 -53 ATTTAGTGAGATATTGTTAATTTTTAAATACAAA 15 3 0 AATTTTAACA 0.682439 -165 TTTTAATTATTAAAATATTTTTATTATGAACATAACGCCAAT 15 111 1 TTTTTTATCA 0.920263 -57 GTTTTTTCATTAGCTTCTTCTTTTTAATTGCATCTAAAACTA 16 141 1 TTTTTTAACA 0.963972 -160 AGCCTAAGTTTAACAAGTGCTTCTTAACTTCATTAATTAAAG 16 245 1 TGTTTTAACA 0.862094 -56 gattttaacttaagttgcttttgttaagttcgagttgtaatt 19 39 1 ttttttaacg 0.761056 -262 tttttagttgttttaagtatttgttatttccaaacaaatatt 21 265 1 tattttatca 0.920263 -36 ttagttttaattactaaccacatatacaaggt 22 1 1 tattctaaca 0.761054 -187 tcggtagtgttgctaaattatttttatttgcactttaagcat 22 116 1 ttttttatca 0.920263 -72 gttgtagtagtacagccctttttttattggcaccttagcctc 23 41 1 ttttttatca 0.920263 -63 catcgagctttgtttgcaaattattaaagacagcttgcagct 24 65 1 tattttaaca 0.963968 -57 taatatcgtttaaattgtaattcttaaaccaacgccctt 25 8 0 tattttaaaa 0.570242 -35 * * ** **** ** Masking position 11 Map Score: 14.549 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 97 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 4 GCTTTTTTTAGTTGGATGGCAATTGTTGGAATTC 1 78 1 GTTGTGGCTT 0.68641 -223 ATTCACAGCTTTTTAGTTGGAATTTTAGTTAATC 1 108 1 TTTTTTGGTT 0.672841 -193 TAACTATTAGTTTTATTTGTGTTTGAAGC 1 282 1 TTTTTTGTTT 0.849048 -19 CAAAACCAAGGTTTTATGGCTTTTAGTTATTATC 6 23 0 GTTTTGGCTT 0.873871 -88 TAAAACCTTGGTTTTGTGGTTTTTAGCTTGTTTA 6 41 1 GTTTTGGTTT 0.63093 -70 GTCCTTAATTTTTGCTTGGTGCTTACCTATTCTC 7 241 0 TTTGTGGTTT 0.530632 -60 AAAGCATGTTAAATTGCGTTTTT 11 8 1 GTTATTGCTT 0.858672 -16 CATTTTTCACTTTTCATTGCTATTAATAAGACAA 14 74 1 TTTTTTGCTT 0.957975 -88 TGATAAATGATTTTCATCGCCTTTGTTTTGTCTT 14 101 0 TTTTTCGCTT 0.768801 -61 TTAAGATAACTTTTACTTTCTTTTAAATTAGTTT 15 79 1 TTTTTTTCTT 0.501544 -89 AGCTTCTTCTTTTTAATTGCATCTAAAACTAAGC 16 152 1 TTTTTTGCCT 0.824731 -149 ATTAGCTCTATTTTCGTTGCCATTATTGCACTAA 17 85 0 TTTTTTGCTT 0.957975 -31 cgccaacgcctttaagttgctgttacattttgtg 18 18 0 tttattgctt 0.927103 -59 gggattttaacttaagttgcttttgttaagttcg 19 37 1 cttattgctt 0.633105 -264 ataatcacgctttattttgtcgttaacgtaggaa 19 188 0 tttattgttt 0.75834 -113 gctaaattatttttatttgcactttaagcattta 22 127 1 ttttttgctt 0.957975 -61 acagccctttttttattggcaccttagcctcatt 23 52 1 tttttggcct 0.749604 -52 tttaatatcgtttaaattgtaattcttaaaccaa 25 18 0 tttattgttt 0.75834 -25 gataaatcggtttatattgccattaatt 26 5 0 tttattgctt 0.927103 -50 **** **** ** Masking position 7 Map Score: 15.3944 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 173 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 GGTAAGGTTCAAAAAGGACTCaAAGTTTTAACTATTAGT 1 254 1 AACaAATTTT 0.957941 -47 AAAAAGCTTTAGATTTTTATCAAATTTTTATCTATTTAA 4 17 1 AACAAATTTT 0.957766 -194 TTTAATATTTAAGAAAGTCGCAAATTTTTATCAGTTTAT 4 51 1 AGCAAATTTT 0.949342 -160 TTTATTGGTCAAAGAAGTCGCAAATTTTTCTTAGTTTTT 4 85 1 AACAAATTTT 0.957954 -126 TGATTTGAACAATATGACCAACTTGTTAAAACTCCTA 5 9 1 AACAACTGTT 0.779351 -281 GACTAGAATTAAATTAAGACCAAAATGTTGC 5 269 1 AACAAATGTT 0.949382 -21 TTAGCACCAAACAAAAACGACAATCTTTTAGTTGATAAA 7 125 0 AACAATTTTT 0.743349 -176 GTAAGCTGTTACAAACACTACAAACTGTTTTATTAGTTA 14 27 0 AACAAATGTT 0.949382 -135 agcgtgattatagtttcactcaaaatgtttagtcgttcc 19 211 1 tgcaaatgtt 0.641213 -90 atttaattgaaaaactaccacaaacttttcaacacccat 21 168 0 aacaaatttt 0.957766 -133 acaaagctcgatgccagcttcaaagtttttgccaaaaaa 24 39 0 agcaaatttt 0.949382 -83 aaatttcaaaaaggcgaggtcaaaatttcgtcgatgtga 28 187 0 agcaaatttc 0.763022 -114 * * **** **** Masking position 12 Map Score: 7.42272 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 41 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTAACCTCCCCCAACCTCTATTTTCTGTTAC 2 5 1 CCCCCAACTT 0.968104 -29 AATGGTTATTCCTTCTCCAACTCCCCCTCCCCTTCTT 3 31 1 CCCCCAACCC 0.987157 -104 TGATTTAACCCCAACATTGATGTTAGAAAAA 3 114 0 TTCCCAACTT 0.807181 -21 ATAAACTTCGCCACCCCCATCACCGATTCTAAGGCTG 4 173 1 CCCCCATCCT 0.979953 -38 GATTGGGCTGTCTTCCCCAACTTTGCTTTCACATTTT 5 55 0 TCCCCAACTT 0.870134 -235 GTGGAAACACCTGGAACCATCCCGAACCCAGCAGTTA 7 171 1 CTACCATCCC 0.846322 -130 ataaaattacctttcgccaacgcctttaagttgctgt 18 29 0 ctcccaacct 0.988493 -48 gttaaaatcccttaacccaaagccaatttacacgagt 19 11 0 ctaccaaact 0.665336 -290 aactaaaaactctacgccatcactggcataacaggaa 21 103 0 tccccatccc 0.857808 -198 aattgtaattcttaaaccaacgccctt 25 1 0 ctaccaacct 0.965166 -42 aagtataaatctgtatccaacacaattccctaaaaat 27 14 1 ctaccaacct 0.965166 -287 gggggctggaccatcacaaacgcgatttaggtgggca 28 141 0 ccccaaacct 0.907965 -160 ** * ***** * * Masking position 9 Map Score: 6.81539 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 34 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 CTTtGAGTCCTTTTTGAACCTTACCCTCTCC 1 248 0 TTTTTGACCT 0.905195 -53 AACTAACGCTTTTTTAACCATTAAGCAAATA 4 124 0 TTTTTAACAT 0.800248 -87 AGACCATAGGTTTTTAAACCTATAGTCCTTA 7 268 0 TTTTTAACCT 0.976114 -33 ATAAACTTCTTTTTTATCCCTTATAAGCTAG 10 35 1 TTTTTATCCT 0.928128 -67 ACTTATTAAATTTTAATTCCTATATGCGTGA 12 16 0 TTTTAATCCT 0.871367 -31 TACAAAAATATTTCAAAACCTTTAATTAATG 16 275 0 TTTCAAACCT 0.833569 -26 tgctaatttcttttaaaccctaaaaaattaa 21 52 0 ttttaaacct 0.95543 -249 gaaaatttaatttttaagcctaatgctaatt 21 75 0 tttttaacct 0.976114 -226 ttgttgaaactttttaagcctttaatgggtg 21 144 1 tttttaacct 0.976114 -157 ******* *** Masking position 3 Map Score: 7.99202 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 33 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 TAATTGCAAGGCTAATGAACTTTTTAGTGT 1 12 0 GCTAATGAAC 0.856664 -289 TAACCATTAAGCAAATAAAAAACTAAGAAA 4 111 0 GCAAATAAAA 0.877085 -100 TTTATTTTTAACTAATAAAACAGTTTGTAG 14 19 1 ACTAATAAAA 0.686476 -143 TAGTTATCAAGCCAATGCAAATTCTAACGG 16 13 1 GCCAATGCAA 0.867222 -288 ACTAATGAAAGCAAATGCAACCATCAAAAA 16 113 0 GCAAATGCAA 0.858163 -188 TAATGAAAAAACTAATGAAAGCAAATGCAA 16 123 0 ACTAATGAAA 0.828686 -178 AAAAGAAGAAGCTAATGAAAAAACTAATGA 16 135 0 GCTAATGAAA 0.972079 -166 CGAAAATAGAGCTAATAAAAGAA 17 103 1 GCTAATAAAA 0.94033 -13 catgtttttagctaatgtaat 20 76 1 gctaatgtaa 0.830474 -11 aattggactcgctaatgaaaacggttttaa 21 24 0 gctaatgaaa 0.972079 -277 tgcttaaagtgcaaataaaaataatttagc 22 127 0 gcaaataaaa 0.877085 -61 aggctaaggtgccaataaaaaaagggctgt 23 52 0 gccaataaaa 0.885097 -52 ********** Masking position 5 Map Score: 13.1258 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 51 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 AGAAGTAGTAGAAGAAGAAGAAGAAGGGGAGGGG 3 54 0 GAAGAGAGAA 0.981044 -81 GAGTGGGGTAGAAGAGGAAGTAGAAGTAGTAGAA 3 75 0 GAAGAGAGAA 0.981044 -60 AGTTGATAAAGAAAATGAAGCAAAATAACAAGAA 5 214 1 GAAAAGAGAA 0.984233 -76 gtgaaacttggaaaaggaatgaaagcaaaaccta 19 122 0 gaaaagataa 0.906168 -179 ggttcaggaggaaaaagtagtaaaacggttaacg 20 14 1 gaaaagagaa 0.984233 -73 attcggcgatgaaaacgcagaacattttaatctc 28 99 1 gaaaagagaa 0.984233 -202 ***** * ** * * Masking position 9 Map Score: 3.70475 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 7 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 TATAAAAATAAATCAGGTTT 8 1 0 AATCAGGTTT 0.694742 -137 TTTAACTAATAAAACAGTTTGTAGTGTTTG 14 25 1 AAAACAGTTT 0.693566 -137 ttagcttgtgaaataggttttgctttcatt 19 109 1 aaataggttt 0.850186 -192 aaaaagtagtaaaacggttaacgattgtcc 20 25 1 aaaacggtta 0.780758 -62 ctcgctaatgaaaacggttttaactcgata 21 17 0 aaaacggttt 0.745173 -284 tatctgtgataaatcggtttatattgccat 26 16 0 aaatcggttt 0.736888 -39 atcacagataaaacaggttttaacttcgt 26 36 1 aaacaggttt 0.666285 -19 acggtttcacaattcggtttgtaacagtag 27 206 0 aattcggttt 0.859548 -95 ttgtggtaaaaacacggtttcacaattcgg 27 219 0 aacacggttt 0.86921 -82 ********** Masking position 8 Map Score: 2.96202 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 26 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 11 TTTAGGTTCGATTTTTCCAATTATGGCATTAAC 1 176 1 ATTTTCAATA 0.75801 -125 AGCTTTTAATTTTTTTCTAATTACAgAGTATTT 1 209 0 TTTTTCAATA 0.91998 -92 ATTAATGTAGTTATTTAAAAACATTTTTATCAT 5 116 0 TTATTAAAAA 0.455654 -174 AATTAATAACTTTTTTCAAATAATAGTTCGAAA 5 178 0 TTTTTCAATA 0.878234 -112 GTAACTTTATTTTTAACTAATAAAACAGTTTGT 14 14 1 TTTTACAATA 0.515741 -148 TAATAAAAATATTTTAATAATTAAAAACTAATT 15 104 0 ATTTTAAATA 0.500212 -64 ACTAAGCTTAATATTACTAATAAGATAGTAAAT 17 57 0 ATATTCAATA 0.711292 -59 aaaacatggattatttataatttaaattcggac 20 51 0 ttattaaatt 0.362039 -36 taagtatttgttatttccaaacaaatatttttc 21 278 1 ttattcaaaa 0.713641 -23 gattaagcgtttattgccaataaggcactcaac 22 41 0 ttattcaata 0.786799 -147 attctaccaattattaacaattagcagttaaat 22 156 0 ttattaaata 0.762968 -32 agcttcaaagtttttgccaaaaaagcgcttaaa 24 30 0 tttttcaaaa 0.71913 -92 catcgagctttgtttgcaaattattaaagacag 24 65 1 tgtttcaata 0.612002 -57 gttcgaggaattattaagaataattcctcctac 27 177 1 ttattaaata 0.664433 -124 cgtgacaatgtttttgcgaatttccattcgaca 28 226 1 tttttcaatt 0.669049 -75 ***** * *** * Masking position 9 Map Score: 4.2879 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 121 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 CTTTTTGAACCTTACCCTCTCCTAATAAAGCT 1 238 0 CTACCCCTCC 0.970267 -63 TTAACCTCCCCCAACCTCTATT 2 1 1 TTACCTCCCC 0.834666 -33 CCTTCTCCAACTCCCCCTCCCCTTCTTCTTCT 3 41 1 CTCCCCCCCC 0.996513 -94 ACTTCCTCTTCTACCCCACTCCCCACTTTTTC 3 88 1 CTCCCCCTCC 0.989752 -47 AATTAATAAACTTCGCCACCCCCATCACCGAT 4 168 1 CTCGCCCCCC 0.98783 -43 ATTTTTATCATTTCACCCCCCCACTATTTTCC 5 95 0 TTCACCCCCC 0.948734 -195 ** **** **** Masking position 2 Map Score: 1.63874 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 7 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 TTTGATGATTAACTAAAATTCCAACTAAAAAG 1 116 0 ACTAAAATCC 0.894041 -185 GAAAAATCGAACCTAAAATAACATACTTTTTA 1 161 0 ACTAAAATAC 0.956493 -140 TTACTGCATAATGTAAAATTACACAGC 6 94 1 AGTAAAATAC 0.761584 -17 ATTAGCACCAAACAAAAACGACAATCTTTTAG 7 133 0 ACAAAAACAC 0.789415 -168 TTTTAATTGCATCTAAAACTAAGCAGAATAAA 16 162 1 ACTAAAACAA 0.720481 -139 aagcaacttaagttaaaatcccttaacccaaa 19 27 0 attaaaatcc 0.593267 -274 ctatttcacaagctaaaattacggcgctggtt 19 93 0 actaaaatac 0.956493 -208 ttttgagtgaaactataatcacgctttatttt 19 204 0 actataatac 0.736383 -97 aataacaaatacttaaaacaactaaaaaacca 21 261 0 attaaaacac 0.83607 -40 tattgaataaaactaaaacaatcgttattgtg 27 75 1 actaaaacat 0.720481 -226 cgaaatctacacctaaaaccacaataacgatt 27 94 0 actaaaacac 0.967216 -207 * ******* ** Masking position 7 Map Score: 3.45828 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 92 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 CGAACCCAGCAGTTAAGCACAGTGGAGCTA 7 193 1 AGTTAAGCAC 0.974603 -108 TACTGAGAATAGGTAAGCACCAAGCAAAAA 7 237 1 AGGTAAGCAC 0.89966 -64 ACCAAGCAAAAATTAAGGACTATAGGTTTA 7 255 1 AATTAAGGAC 0.831461 -46 TAATAATTTAAATTAAGCACTCATACTAAT 8 58 1 AATTAAGCAC 0.96754 -80 AGTTTTAAAGAGTTAAGCAATCTAAAGGGA 8 95 0 AGTTAAGCAA 0.790009 -43 AGTTAAGAACAATTATTTTA 17 1 1 AGTTAAGAAC 0.810798 -115 aatcaggcacaaaatgtaac 18 1 1 aatcaggcac 0.932987 -76 gtttattgccaataaggcactcaaccttgt 22 36 0 aataaggcac 0.836181 -152 ctagtaaataaatcaggcacgctaatttag 22 76 1 aatcaggcac 0.932987 -112 ********** Masking position 5 Map Score: 2.65432 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 19 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 15 AAAAACCACAAAACCAAGGTTTTATGGCTTTTA 6 32 0 AACAGGTTTT 0.980815 -79 TAGGTTTAAAAACCTATGGTCTTTTTTTATTTA 7 277 1 AACAGGTCTT 0.971876 -24 TATCCCTTATAAGCTAGGGTTTTACTTTAGATG 10 49 1 AACAGGTTTT 0.980898 -53 TAACTTCATTAATTAAAGGTTTTGAAATATTTT 16 269 1 AATAGGTTTT 0.869472 -32 aattataaataatccatgtttttagctaatgta 20 62 1 aacagttttt 0.933371 -25 ccgaattgtgaaaccgtgtttttaccacaacca 27 219 1 aacggttttt 0.81163 -82 cgcggttacaaatcaatggtctttcagaaaacg 28 66 1 aacaggtctt 0.971875 -235 ** * * ****** Masking position 2 Map Score: 1.85048 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467