AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_mthe_reg_300.orf -o293_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01746 83 M.thermo #2 RTH01824 300 M.thermo #3 RTH00437 20 M.thermo #4 RTH00902 142 M.thermo #5 RTH00250 30 M.thermo #6 RTH00057 21 M.thermo #7 RTH01659 205 M.thermo #8 RTH01211 72 M.thermo #9 RTH00503 300 M.thermo #10 RTH00097 230 M.thermo Motif number 1 TGTTAATTACCGGAAGGTGATTTTTC 1 68 1 CGGAGGTTTC 0.955223 -16 AAGGAAATAGGGGGTGCAGCTTCATCCACAGAGAAA 2 60 0 GGGGGGTTTC 0.996557 -241 GGGCTTCTGAGGGAAAAGGATACCTCTAAGGACCCG 2 103 0 GGGAAGTATC 0.631469 -198 TGGCGGATCCGGGATCAGGGGTTCCCGTGATAATCT 2 153 0 GGGACGGTCC 0.592307 -148 AGGTTTCCCTGGGAACAGCGTTTTTCAGGGGATAGG 2 263 1 GGGACCTTTC 0.963763 -38 CATAAATCTAGGAAGGTGGGTTAATC 5 15 1 GGAAGGTTTC 0.945106 -16 ATGGTGGTTTGGGGTGCTGTGTGGTCATGAATATGA 7 28 0 GGGGGGGTTC 0.990531 -178 CCTCCTCCAGGGGGAGGAGGTTGACCTCCATTTCGG 8 28 1 GGGGGGTTCC 0.995186 -45 TGGTGGATGTGAGGTCATGTTTAATCATCTCAATGG 9 42 0 GAGGCGTTTC 0.910501 -259 TTCTCTATCCGGTATGTGCTTTACTCTTTACTTCTC 9 199 0 GGTAGCTTTC 0.904337 -102 GAGTTATTGAGGGGGGTTCTCTATCCGGTATGTGCT 9 215 0 GGGGGCCTCC 0.928884 -86 ATGAAATTATGGTGGGCAGGTTATCCTACAAACTCC 10 36 0 GGTGGGTTCC 0.968554 -195 GGATGGAGAAGGGAACATGTTATCTCTGTTCCTTTA 10 108 0 GGGACGTATC 0.951718 -123 **** * * ** ** Masking position 16 Map Score: 16.4678 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 284 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 GGGATTTAAAGGAAATAGGGGGTGCAGCTTCAT 2 71 0 GGAAGGGGGT 0.886336 -230 GATACCTCTAAGGACCCGGGATTTAAAGGAAAT 2 88 0 AGGAGGGATT 0.940947 -213 TGGCGGATCCGGGATCAGGGGTTCCCGTGATAA 2 156 0 GGGAGGGGTT 0.982427 -145 GCGTTTTTCAGGGGATAGGAGGTTTTTTTAA 2 280 1 GGGGGGAGGT 0.984847 -21 TCATAAATCTAGGAAGGTGGGTTAATC 5 14 1 AGGATGGGTT 0.940947 -17 TCTTGACATGGTGGTTTGGGGTGCTGTGTGGTC 7 38 0 GTGGGGGGTG 0.941953 -168 ACTCTATAATAGGATAAGGGAGTATTTAAATCT 7 68 0 AGGAGGGAGT 0.971217 -138 GGCCTCCTCCAGGGGGAGGAGGTTGACCTCCAT 8 26 1 AGGGGGAGGT 0.986199 -47 AAGGAACTGGGAGGCCCTCCCGAA 8 59 0 AGGAGGGAGG 0.907359 -14 TGCCGTTGTGGTGGATGTGAGGTCATGTTTAAT 9 53 0 GTGGTGAGGT 0.888345 -248 CCACATGAACATGGTAGTGGAGTGGATTATTAT 9 134 0 ATGGTGGAGT 0.897408 -167 ACACTGAGTTATTGAGGGGGGTTCTCTATCCGG 9 223 0 ATTGGGGGTT 0.801918 -78 GGTTAAATGATGGGTATGGGTTTAAGGAGTTT 10 10 1 ATGGTGGGTT 0.940947 -221 GAATGAAATTATGGTGGGCAGGTTATCCTACAA 10 41 0 ATGGGCAGGT 0.752738 -190 **** ****** Masking position 9 Map Score: 12.8528 Number of sites scoring better than the average of aligned sites = 1769 Number in coding regions = 1647 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 GGTATCCTTTTCCCTCAGAAGCCCATGAGAA 2 115 1 TCCTCAGAAG 0.92416 -186 CCCTCAGAAGCCCATGAGAAGCATTAAAGAT 2 126 1 CCCTGAGAAG 0.960365 -175 GAATGGCGGATCCGGGATCAGGGGTTCCCGT 2 161 0 TCCGGATCAG 0.910583 -140 TACCATCATTTCCTGGAGGTATTCC 4 5 0 TCCGGAGGTA 0.88427 -138 AACCTCCTCCCCCTGGAGGAGGCCAGTGCTA 8 19 0 CCCGGAGGAG 0.990286 -54 CTGATAACGCCCCACAGGAGGGCCATGAGA 9 10 1 CCCACAGGAG 0.852812 -291 GCCATGAGAACCATTGAGATGATTAAACATG 9 32 1 CCATGAGATG 0.649488 -269 AGATAGAGAGCGCCTGAGAAGTAAAGAGTAA 9 184 1 CGCTGAGAAG 0.825913 -117 GGGTTCTCTATCCGGTATGTGCTTTACTCTT 9 207 0 TCCGTATGTG 0.765753 -94 CCTCCCGGTGTGCAGCAGGTGATATTGATCA 9 274 0 TGCGCAGGTG 0.920715 -27 AATTAGTTTTTCCGGGATCTGGATGGAGAAG 10 133 0 TCCGGATCTG 0.92186 -98 AAAGCATACATCCAGCAGATGTCTTAAAATC 10 188 1 TCCGCAGATG 0.968948 -43 CTCAACTCTCCTTGATGTGCTTGATTTTA 10 212 0 TCCTGATGTG 0.937838 -19 *** ******* Masking position 7 Map Score: 9.98269 Number of sites scoring better than the average of aligned sites = 2286 Number in coding regions = 2203 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 CAATAACTGCGGTTTCTCTGTGGATGAAGC 2 48 1 GGTTTCTCTG 0.908231 -253 TAGAGGTATCCTTTTCCCTCAGAAGCCCAT 2 111 1 CTTTTCCCTC 0.91345 -190 AACTCAAAGAGGTTTCCCTGGGAACAGCGT 2 254 1 GGTTTCCCTG 0.949555 -47 AGGTCAACCTCCTCCCCCTGGAGGAGGCCA 8 25 0 CCTCCCCCTG 0.767143 -48 GTGCCCGAGACGTCTCCATATACTGTTTGA 9 88 1 CGTCTCCATA 0.806021 -213 CTTCTCAGGCGCTCTCTATCTCTTTTCTTA 9 175 0 GCTCTCTATC 0.877793 -126 ATTGAGGGGGGTTCTCTATCCGGTATGTGC 9 216 0 GTTCTCTATC 0.914341 -85 GGTCTCCCTCCCGGTGTGCA 9 291 0 GGTCTCCCTC 0.986139 -10 AAGGGAACATGTTATCTCTGTTCCTTTAAT 10 106 0 GTTATCTCTG 0.842887 -125 AACATGTTCCCTTCTCCATCCAGATCCCGG 10 123 1 CTTCTCCATC 0.922065 -108 TTTAAAGTTAGTTATCTCTATTCCTTTAAT 10 161 0 GTTATCTCTA 0.644481 -70 ********** Masking position 3 Map Score: 5.28216 Number of sites scoring better than the average of aligned sites = 1281 Number in coding regions = 1235 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 TTATAATTAGAATTAATAGAGTTATCTATA 1 31 1 AATTAATAGA 0.757795 -53 AGGACCCGGGATTTAAAGGAAATAGGGGGT 2 81 0 ATTTAAAGGA 0.974183 -220 CTGATACTATTTTTAATGGATTATTTTATA 2 212 0 TTTTAATGGA 0.833039 -89 TAGTTTTTTCATTTAGAGGAGAAGATAAAA 10 76 0 ATTTAGAGGA 0.932421 -155 TGAAAAAACTAATTAAAGGAACAGAGATAA 10 95 1 AATTAAAGGA 0.974183 -136 CGGAAAAACTAATTAAAGGAATAGAGATAA 10 150 1 AATTAAAGGA 0.974183 -81 ********** Masking position 5 Map Score: 3.91769 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 27 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CAAGTTAGTTACCATCATTTCCTGGAGGTA 4 15 0 ACCATCATTT 0.984102 -128 AGCACCCCAAACCACCATGTCAAGATTTAA 7 46 1 ACCACCATGT 0.9805 -160 TAACTGGTTAACCATGATTTAGAGTTACAT 7 119 0 ACCATGATTT 0.934179 -87 GAGGAGGTTGACCTCCATTTCGGGAGGGCC 8 41 1 ACCTCCATTT 0.93946 -32 AATCCACTCCACTACCATGTTCATGTGGAG 9 139 1 ACTACCATGT 0.867096 -162 TAAACCCATACCCATCATTTAACC 10 5 0 CCCATCATTT 0.950118 -226 TAACCTGCCCACCATAATTTCATTCCATTT 10 49 1 ACCATAATTT 0.905448 -182 ********** Masking position 7 Map Score: 6.14378 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 59 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CGCTGCTAACCAGCTGAACAATAACTGCGG 2 30 1 CAGCTGAACA 0.949582 -271 TCTGTGGATGAAGCTGCACCCCCTATTTCC 2 64 1 AAGCTGCACC 0.862316 -237 CCTTTTCCCTCAGAAGCCCATGAGAAGCAT 2 120 1 CAGAAGCCCA 0.861326 -181 TTTATACAGACAACTGCACAATTTATCTAT 4 63 1 CAACTGCACA 0.88337 -80 GAATTTGTTTCTGAAGAACAGGTGAT 4 127 1 CTGAAGAACA 0.749879 -16 TGTGGTCATGAATATGAACAGCCAGTTATG 7 15 0 AATATGAACA 0.699107 -191 GGAGTGGATTATTATGCACAGTCTGAGGAA 9 119 0 ATTATGCACA 0.788857 -182 AAATAATCTCCACATGAACATGGTAGTGGA 9 146 0 CACATGAACA 0.893378 -155 TCATAAACTTAAGATGCACATACACTGAGT 9 247 0 AAGATGCACA 0.969225 -54 TCAATATCACCTGCTGCACACCGGGAGGGA 9 277 1 CTGCTGCACA 0.968036 -24 TTTGTAGGATAACCTGCCCACCATAATTTC 10 40 1 AACCTGCCCA 0.866951 -191 ATGTCTTAAAATCAAGCACATCAAGGAGAG 10 206 1 ATCAAGCACA 0.749553 -25 ********** Masking position 9 Map Score: 9.23473 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 354 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TTGTTAATTACCGGAAGGTGATTTTTC 1 67 1 CCGGAAGGTG 0.98165 -17 ATCATAAATCTAGGAAGGTGGGTTAATC 5 13 1 TAGGAAGGTG 0.79433 -18 ACCTCCATTTCGGGAGGGCCTCCCAGTTCC 8 51 1 CGGGAGGGCC 0.979079 -22 TAACGCCCCACAGGAGGGCCATGAGAACCA 9 15 1 CAGGAGGGCC 0.954066 -286 TCCACCACAACGGCAAGGTGCCCGAGACGT 9 71 1 CGGCAAGGTG 0.927964 -230 AAAGCACATACCGGATAGAGAACCCCCCTC 9 213 1 CCGGATAGAG 0.806547 -88 TGCTGCACACCGGGAGGGAGACC 9 288 1 CGGGAGGGAG 0.991904 -13 TTTCCGGGATCTGGATGGAGAAGGGAACAT 10 126 0 CTGGATGGAG 0.931887 -105 ********** Masking position 5 Map Score: 4.3127 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 536 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 GGTGCAGCTTCATCCACAGAGAAACCGCAG 2 54 0 CATCCACAGA 0.891978 -247 CCGGATCCGCCATTCACCGCACTTTTAGAT 2 177 1 CATTCACCGC 0.975465 -124 TATTCATGACCACACAGCACCCCAAACCAC 7 31 1 CACACAGCAC 0.8633 -175 TTTAGAGTTACATACACCGCCAGTATGGAA 7 102 0 CATACACCGC 0.990144 -104 CATGACCTCACATCCACCACAACGGCAAGG 9 59 1 CATCCACCAC 0.987094 -242 TTAAGATGCACATACACTGAGTTATTGAGG 9 239 0 CATACACTGA 0.840035 -62 TTAAAGCATACATCCAGCAGATGTCTTAAA 10 186 1 CATCCAGCAG 0.901631 -45 ********** Masking position 6 Map Score: 2.49926 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 323 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 10 GATCAGTAGCAATCAGTTTT 2 1 0 AATCAGTTTT 0.947095 -300 ACAGTATCAGAATTTGTTTCTGAAGAACAG 4 118 1 AATTTGTTTC 0.876323 -25 CTGTTCCTTTAATTAGTTTTTTCATTTAGA 10 89 0 AATTAGTTTT 0.968271 -142 CTATTCCTTTAATTAGTTTTTCCGGGATCT 10 144 0 AATTAGTTTT 0.968271 -87 ********** Masking position 7 Map Score: 0.344353 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 ********** No masking Map Score: 2.14117e-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 12 ********** No masking Map Score: 2.14117e-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: 2.14117e-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