AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mgen_reg_100.orf -o199_mgen_100.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMG00170 20 Mycoplasma RMG00177 16 Mycoplasma RMG05618 16 Mycoplasma RMG00824 22 Mycoplasma Input sequences: #1 RMG02265 300 Mycoplasma #2 RMG01247 55 Mycoplasma #3 RMG02280 28 Mycoplasma #4 RMG00179 51 Mycoplasma #5 RMG01278 257 Mycoplasma #6 RMG01371 192 Mycoplasma #7 RMG01372 45 Mycoplasma #8 RMG00290 89 Mycoplasma #9 RMG02403 63 Mycoplasma #10 RMG00320 239 Mycoplasma #11 RMG04493 22 Mycoplasma #12 RMG03467 59 Mycoplasma #13 RMG04478 44 Mycoplasma #14 RMG05623 23 Mycoplasma #15 RMG05622 40 Mycoplasma #16 RMG04471 151 Mycoplasma #17 RMG04456 38 Mycoplasma #18 RMG03425 36 Mycoplasma #19 RMG04443 58 Mycoplasma #20 RMG04419 89 Mycoplasma #21 RMG05538 78 Mycoplasma #22 RMG04418 88 Mycoplasma #23 RMG02908 119 Mycoplasma #24 RMG05363 169 Mycoplasma Motif number 1 TACTAAATAGAAATAAAAAAAGAACCTGTTTTTT 1 198 0 AAATAAAGAA 0.831204 -103 ATACTTAATAAAAATATAACTTTACTCAA 4 6 1 TAATAAATAA 0.885159 -46 AAAGTCCAATAATTAAACAGATAACAGCCATAAT 5 59 0 AATTAAATAA 0.940998 -199 CAAGAATTAAAAATAAAACTACTAAGATAAACAT 5 203 0 AAATAAACTA 0.886843 -55 GAATTTTTCTAAATAAGCTAACAAATTAAACC 6 9 0 AAATAAACAA 0.929579 -184 GAAAAATTCAAAATAAGCAAATTATAATTaGGTG 6 34 1 AAATAAATTA 0.948809 -159 GTTAATTCTAAATTAAGTTAATAACTATCTTTTT 7 14 0 AATTAAATAA 0.940993 -32 ACTAGTTAGTTAATAAATTGACTACGGATTTTGG 8 53 0 TAATAAACTA 0.660261 -37 CAAAAACCAAAAATAACGCTAAAATATCAATCCA 10 96 0 AAATAAAAAA 0.930872 -144 AAAAAGTTCAAAATAAATCTATTAATAAAACAGC 15 17 1 AAATAAATTA 0.947898 -24 TAGTTAATTTAATTAATTACATAAACCATTTGCT 16 28 1 AATTAAATAA 0.940998 -124 TTGCTTAACTAAATAAAGTTAAAATTCACAGAGT 16 57 1 AAATAAAAAA 0.930415 -95 AATATTAGATAAATAAGTATATTATC 17 3 0 AAATAAATTA 0.947898 -36 AATTAACAATAAAAATTAGACTTT 18 1 1 AATTAAAAAA 0.873087 -36 TTATAAAATTAAATAATCGAATTA 19 1 0 AAATAAATTA 0.948809 -58 GTTAGATAAATATTAATAAAATTACTCTGATTTA 22 20 1 TATTAAATTA 0.701918 -69 TATTGCAAGTAAATAATAACATAACTTGATAAAT 23 11 0 AAATAAATAA 0.968964 -109 TCGATAACTTTATTAAAGTTAAAAACTCGTTATT 23 56 0 TATTAAAAAA 0.622397 -64 AAATAAGGGAATGAAACTTAAGAA 24 1 1 AAATAAATGA 0.90062 -169 TGTTAATTTTAAATAAGTTTAAGATAAGCTGGAG 24 131 0 AAATAAAAGA 0.7959 -39 ACTTATTTAAAATTAACAACATAATTTAAACAA 24 147 1 AATTAAATAA 0.940998 -23 ****** **** Masking position 4 Map Score: 29.8999 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 133 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 AACTTCATTTGAAACCAAACATAAATTTAGT 1 66 0 GAAACCAAAA 0.90472 -235 ACCAGCTTCTAAATCTAAAGCATGATTACAA 1 117 0 AAATCTAAAC 0.879366 -184 GCAATGCATCCAATCCAAATAGTAATGTTCA 5 29 1 CAATCCAAAA 0.956469 -229 GATCTTTCGTAAAACCAAAGATAGGGGTTTT 5 151 1 AAAACCAAAA 0.978509 -107 ATCTTGGTGCAAAACTAAATATCAACCCAAG 5 233 0 AAAACTAAAA 0.943593 -25 GTATCAACTAAAAACTAAAGCGTTATGATTG 8 21 0 AAAACTAAAC 0.894122 -69 AAACCAAGCAAAAACCAAAAATAACGCTAAA 10 107 0 AAAACCAAAA 0.978509 -133 ATAATCACAACAAACCAAGCAAAAACCAAAA 10 118 0 CAAACCAAGA 0.800587 -122 TGGTGTACCTAGATCCAAAAAGACCGCTCCT 10 164 0 AGATCCAAAA 0.861091 -76 GATAATTTAAAATCGAAAACAC 11 10 1 AAATCGAAAC 0.858022 -13 ATTCAAGCTTCAATCTAAAAAACTGTTTTGA 13 18 1 CAATCTAAAA 0.889777 -27 GCTTAAAGAGAAATCGAAACAAGCGCATTTG 16 111 0 AAATCGAAAA 0.922906 -41 TACTTGCAATAAAACCAAAGAAAATAACGAG 23 34 1 AAAACCAAAA 0.978509 -86 ********* * Masking position 7 Map Score: 13.2492 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 176 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TTTACTAAATAGAAATAAAAAAAGAACCTGT 1 203 0 AGAAATAAAA 0.572125 -98 ACATTTTTGGAAAATTTTAAA 2 1 0 AAAATTTAAA 0.839034 -55 TATCAACCCAAGAATTAAAAATAAAACTACT 5 214 0 AGAATTAAAA 0.898602 -44 CTTATTTAGAAAAATTCAAAATAAGCAAATT 6 26 1 AAAATTAAAA 0.954463 -167 CGCTCCTCTAATAGTTAAAAAGATAATCACA 10 140 0 ATAGTTAAAA 0.778382 -100 GATAATTTAAAATCGAAAACAC 11 2 1 ATAATTAAAA 0.797294 -21 AAAGTTTCAAAACAGTTTTTT 13 34 0 AAAGTTCAAA 0.731925 -11 TTTGTTAAAAAGTTCAAAATAAATCTATT 15 9 1 AAAGTTAAAA 0.949282 -32 TTAACTAAATAAAGTTAAAATTCACAGAGTA 16 61 1 AAAGTTAAAT 0.60053 -91 AATTAACAATAAAAATTAGACTTTT 18 5 1 AACAATAAAA 0.685085 -32 AAAGTCTTATAAAATTAAATAATCGAATTA 19 10 0 AAAATTAATA 0.627353 -49 TTAATAATTAAACATTTTAAAAGTCTTATAA 19 29 0 AACATTTAAA 0.781927 -30 AGCCACTAACAGCGTTATAAAACGCATGCTA 20 36 0 AGCGTTTAAA 0.575148 -54 AGCGGATCAAAACATTAAAAAGCCACTAACA 20 56 0 AACATTAAAA 0.935142 -34 CAACATTGAAAAAAATAGCTAT 21 2 1 AACATTAAAA 0.935142 -77 TAACTTTATTAAAGTTAAAAACTCGTTATTT 23 55 0 AAAGTTAAAA 0.949282 -65 AAACTTATTTAAAATTAACAACATAATTTAA 24 145 1 AAAATTACAA 0.71389 -25 ****** **** Masking position 6 Map Score: 13.2249 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 168 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GATCTTTATCACTAAATTTATGTTTGGTTT 1 56 1 ACTAAATTTA 0.900844 -245 AAACTCATTGAGTAAAGTTATATTTTTATT 4 17 0 AGTAAAGTTA 0.955838 -35 TTGCTTGTGAACTAATTTTAAA 5 3 0 ACTAATTTTA 0.877051 -255 CAATCCAAATAGTAATGTTCATTATGGCTG 5 39 1 AGTAATGTTC 0.683059 -219 TGTTTATCTTAGTAGTTTTATTTTTAATTC 5 204 1 AGTAGTTTTA 0.812447 -54 ATAGTTATTAACTTAATTTAGAATTAACTA 7 20 1 ACTTAATTTA 0.709545 -26 CAAAATCCGTAGTCAATTTATTAACTAACT 8 54 1 AGTCAATTTA 0.777029 -36 CAAGAAAAGTTATTTATGCCAG 12 48 0 AGAAAAGTTA 0.649362 -12 TTTGATAAGTAATTTTAGAGAGG 14 7 0 AGTAATTTTA 0.945499 -17 AAAGCTCTATAGTTAATTTAATTAATTACA 16 19 1 AGTTAATTTA 0.855929 -133 TGCTTAACTAAATAAAGTTAAAATTCACAG 16 58 1 AATAAAGTTA 0.750449 -94 AAATTCACAGAGTAGTTTTATTTTTGACTA 16 78 1 AGTAGTTTTA 0.812447 -74 ATTAAATCAGAGTAATTTTATTAATATTTA 22 26 0 AGTAATTTTA 0.945499 -63 ATTTATCAAGTTATGTTATTATTTACTT 23 9 1 AGTTATGTTA 0.820451 -111 TTTTAACTTTAATAAAGTTATCGAGGATTT 23 66 1 AATAAAGTTA 0.750449 -54 GTTTGTTTTCACTAAATTTAAGTCCTTGAA 24 86 1 ACTAAATTTA 0.900844 -84 ********** Masking position 8 Map Score: 15.878 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 115 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 AGAACCTGAAAAAAACAGGTTCTTTTTTTAT 1 189 1 AAAAACAGTT 0.937084 -112 AACTTTTTGGAAAAACTCATTGAGTAAAGTT 4 28 0 AAAAACTATT 0.920466 -24 AAAAACTTTTTGGAAAAACTC 4 41 0 AAAAACTTTT 0.519323 -11 CAAAATCTAGTTCACTAGTTAG 8 78 0 AAAATCTGTT 0.816963 -12 CTTCAATCTAAAAAACTGTTTTGAAACTTT 13 25 1 AAAAACTTTT 0.803906 -20 AAAAGTATTTAAAAACAATTTAATAGAAGCG 21 34 0 AAAAACATTT 0.893491 -45 AATTTTAAATAAAAAGTATTTAAAAACAATT 21 45 0 AAAAAGTTTT 0.620037 -34 AATGGACTTAAAAAAGACATTGTTAATGCCT 22 53 1 AAAAAGAATT 0.669885 -36 TATTAAAGTTAAAAACTCGTTATTTTCTTTG 23 49 0 AAAAACTGTT 0.958938 -71 ******* *** Masking position 4 Map Score: 7.64399 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 195 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TCTTGATTATTTTATAAAAAAATGATACTA 1 14 0 TTTATAAAAA 0.737533 -287 ACCAGTACCATTTCCAAAAAACTGAGAACC 1 165 1 TTTCCAAAAA 0.965824 -136 TACTTGAACATTTACTAAATAGAAATAAAA 1 214 0 TTTACTAAAT 0.67534 -87 TTTAAAATTTTCCAAAAATGTGGGAGCT 2 9 1 TTTCCAAAAA 0.965824 -47 TCAATGAGTTTTTCCAAAAAGTTTTT 4 36 1 TTTCCAAAAA 0.965824 -16 CTTGGAGATCTTTCGTAAAACCAAAGATAG 5 145 1 TTTCGTAAAA 0.840892 -113 CTGTAAGATCTTTACAAAACCCCTATCTTT 5 167 0 TTTACAAAAC 0.854588 -91 TGTTAGCTTATTTAGAAAAATTCAAAATAA 6 20 1 TTTAGAAAAA 0.886492 -173 GGTGTCTTTCTTTACTAAAAATATGAAATT 6 64 1 TTTACTAAAA 0.920623 -129 ********** Masking position 7 Map Score: 7.10573 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 51 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 7 AAAGATCATGTGCTGATGTTCTTGATTATTTTAT 1 29 0 TGCTGTCTTG 0.973623 -272 TATGTTTGGTTTCAAATGAAGTTGGATTATAAAT 1 74 1 TTCTGAGTTG 0.913203 -227 TTGGATGCATTGCTTGTGAACTAATTTTAAA 5 8 0 TGCTGACTAA 0.935185 -250 AATCAAGGCATTCCTTTGGTCTTGATAAGTATTT 6 166 0 TTCTGTCTTG 0.958799 -27 TGCCTCTGAACTTGCTAGTGCAAT 10 1 1 TGCTGACTTG 0.99018 -239 AACCCCTTGCTTCCATTGCACTAGCAAGTTCAGA 10 15 0 TTCTGACTAG 0.958799 -225 TTAATAACCATTCTGGTGTACCTAGATCCAAAAA 10 174 0 TTCTGACCTA 0.868418 -66 ATAAAACGCATGCTAATGGACTTAATCACAGTTC 20 17 0 TGCTGACTTA 0.975255 -73 *** ** ***** Masking position 7 Map Score: 3.66769 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 GTTTCAAATGAAGTTGGATTATAAATCCTGCTTTA 1 82 1 AGTTGATTAA 0.971238 -219 ACCAAAAATAACGCTAAAATATCAATCCAAGTGAT 10 90 0 AGCTAATTAA 0.954414 -150 CAGTTTAGTCAAGCTTGATTATAAAACTTATCGCT 12 16 0 AGCTGATTAA 0.981672 -44 TTTTAGATTGAAGCTTGAATGTGAATT 13 3 0 AGCTGATTAA 0.981672 -42 GGATTATGTTGGAATATTAGATAAATAAGT 17 19 0 AGTTGATTAG 0.89969 -20 TTAACAATAAAAATTAGACTTTTAATTATTAGCT 18 13 1 AATTGATTAA 0.88537 -24 GACTTTTAAAATGTTTAATTATTAATATATAGCT 19 35 1 AGTTAATTAA 0.929576 -24 AAATTAACACTTAAATTTTAAATAAAAAGTA 21 58 0 AACTAATTAA 0.827251 -21 * *** ** * * ** Masking position 8 Map Score: 3.9235 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TTTTTTATAAAATAATCAAGAACATCAGCA 1 23 1 AATAATCAAG 0.941067 -278 TTCAACAAATACTTATCAAGACCAAAGGAA 6 160 1 ACTTATCAAG 0.972956 -33 ACTAATCAAGGCATTCCTTT 6 183 0 ACTAATCAAG 0.972956 -10 CGATAAGTTTTATAATCAAGCTTGACTAAA 12 18 1 TATAATCAAG 0.797548 -42 CTCTAAAATTACTTATCAAA 14 14 1 ACTTATCAAA 0.847697 -10 ATTTATCAAGTTATGTTATT 23 1 1 ATTTATCAAG 0.900508 -119 ********** Masking position 5 Map Score: 2.33872 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 35 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TATTAGTATCATTTTTTTATAAAAT 1 5 1 ATATCATTTT 0.944633 -296 GATCTTACAGATTATCATGTTTATCTTAGTA 5 187 1 ATATCATGTT 0.819263 -71 AGGGATATGCACTAGCATTTTACTTGCTAGT 6 124 1 ATAGCATTTT 0.906237 -69 TAAGTTAATAACTATCTTTTTTAG 7 4 0 ATATCTTTTT 0.964765 -42 GTTTGTTGTGATTATCTTTTTAACTATTAGA 10 134 1 ATATCTTTTT 0.964765 -106 TAACGCTGTTAGTGGCTTTTTAATGTTTTGA 20 50 1 ATGGCTTTTT 0.938264 -40 AGGCATTAACAATGTCTTTTTTAAGTCCATT 22 53 0 ATGTCTTTTT 0.964078 -36 GAAACTTAAGAATGTCTTTTGTGGTAAGGAA 24 23 1 ATGTCTTTTG 0.876978 -147 * ********* Masking position 1 Map Score: 4.75324 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TAAATTTATGTTTGGTTTCAAATGAAGTTG 1 68 1 TTTGGTTTCA 0.799573 -233 TTATTGGACTTTTGCTTTCTAACCATGGTT 5 81 1 TTTGCTTTCT 0.962225 -177 GGTTTAATTTGTTAGCTTATTTAGAAA 6 8 1 TTTGTTAGCT 0.664032 -185 GCACTAGCATTTTACTTGCTAGTTGTGCTT 6 132 1 TTTACTTGCT 0.886193 -61 ATTTTTGGTTTTTGCTTGGTTTGTTGTGAT 10 116 1 TTTGCTTGGT 0.781351 -124 CTCTTTAAGCTTTGCTTTCTTTTATTGGTA 16 132 1 TTTGCTTTCT 0.962225 -20 TATGTTATTATTTACTTGCAATAAAACCAA 23 22 1 TTTACTTGCA 0.84174 -98 TTAAAAACTCGTTATTTTCTTTGGTTTTAT 23 42 0 GTTATTTTCT 0.611343 -78 GGTAAGGAAAGTTGTTTTCATCAGCCAATA 24 45 1 GTTGTTTTCA 0.792005 -125 TTGGCAATTGTTTGTTTTCACTAAATTTAA 24 77 1 TTTGTTTTCA 0.898536 -93 ********** Masking position 6 Map Score: 3.10556 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 180 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 ********** No masking Map Score: -6.09402e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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 13 ********** No masking Map Score: -6.09402e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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 14 ********** No masking Map Score: -6.09402e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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