AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifis_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0111 65 protein translocase, subunit SECD (secD) #2 MJ0436 300 queuine tRNA-ribosyltransferase (tgtA) #3 MJ1253 164 protein translocase, subunit SECF (secF) #4 MJ1328 300 modification methylase, type II R/M system Motif number 1 TTTAACAAACTCTTTTAAAATTTATAACATT 1 12 0 TCTTTAAAAT 0.881701 -54 TTAAAAGAGTTTGTTAAAATTTACCAACTTA 1 25 1 TTGTTAAATT 0.545009 -41 GTCTCAATCTTCTTTCCATTTATGTTTAAGA 2 43 0 TCTTTCATTT 0.932734 -258 ACAATCTGTTTTTTTGGATTTGGGTGGATAA 2 91 0 TTTTTGATTT 0.733129 -210 GATAAAGTAATTGTTACAGATAGTGGTTCTT 2 242 1 TTGTTCAGAT 0.921336 -59 AGATAGTGGTTCTTTTCAGTTAGGAGTTTAT 2 259 1 TCTTTCAGTT 0.950391 -42 CAAAGTATGTTCTTTGCAAAGTTATTTAAAT 3 55 0 TCTTTCAAAG 0.941593 -110 CTTTGGATGGTATTTGCAGAGCCTCTGCAAA 3 81 1 TATTTCAGAG 0.909497 -84 TTAATAGAGATATTTGCAGAGGCTCTGCAAA 3 93 0 TATTTCAGAG 0.909497 -72 TTGAAAGGTATTTTTTAATAGAGATATTTGC 3 107 0 TTTTTAATAG 0.885854 -58 AATCAATAAATCTTTTAAAAGATGGTGGAGA 4 17 1 TCTTTAAAAG 0.85946 -284 TTGATTTATATTGTTCCATATCACTTTTTTT 4 49 1 TTGTTCATAT 0.894486 -252 TCTCTTACAATTTTTGCATATGTGTTATAAA 4 77 0 TTTTTCATAT 0.961444 -224 AATCAATAATTATTTCCAATTTTCCATGTTT 4 118 0 TATTTCAATT 0.767497 -183 AGGATTTTCATTTTTAAATAGCCTAACTTCA 4 153 0 TTTTTAATAG 0.885854 -148 ATAACATCAATTTTTTCAGATTTGTGGTTAA 4 218 0 TTTTTCAGAT 0.971792 -83 TAATTTAACTTTTTTTGAGATAATTCTAATA 4 246 0 TTTTTGAGAT 0.881014 -55 TTCTTTTATCTCTTTTAATTTAACTTTTTTT 4 261 0 TCTTTAATTT 0.840323 -40 ***** ***** Masking position 5 Map Score: 21.9145 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 1074 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 AAATGTTATAAATTTTAAAAGAGTTTGTTA 1 8 1 ATAATTTAAA 0.744857 -58 CTATACCTATATAAGTTGGTAAATTTTAACAAA 1 34 0 ATAGTTGTAA 0.669069 -32 TTATATAGGTATAGGTGGGATAA 1 53 1 ATAGTGGAAA 0.664824 -13 TCTTCTTTCCATTTATGTTTAAGATCCCTATTC 2 34 0 ATTATGTTAG 0.917316 -267 AGGCATTATTGTTGGTGTCTCAATCTTCTTTCC 2 57 0 GTTGTGTTAA 0.83197 -244 ACATCTGCCAATTTATTTATTAAATCCATCGAT 2 122 0 ATTATTTTAA 0.954339 -179 ATCAAAGCCAATTAATTTGTGAATCCCTTTTTC 2 212 0 ATTATTTTAA 0.954339 -89 ATCTGTAACAATTACTTTATCAAAGCCAATTAA 2 230 0 ATTCTTTTAA 0.797407 -71 AACCCCATTAATTAATGTATATATTATATTATT 3 136 0 ATTATGTTTA 0.877636 -29 TAAAAGATTTATTGATTTTATAA 4 1 0 ATTATTTAAA 0.900156 -300 CAATTTTTGCATATGTGTTATAAAAAAAGTGAT 4 68 0 ATAGTGTAAA 0.845045 -233 GTTTCAGGATTTTCATTTTTAAATAGCCTAACT 4 156 0 TTTATTTTAA 0.641364 -145 AAACTTAAATATTATTGTTTCAGGATTTTCATT 4 172 0 ATTTTGTTAG 0.585003 -129 AAACAATAATATTTAAGTTTAAAAAAGGAGAAT 4 185 1 ATTAAGTTAA 0.792405 -116 ATTTTTTCAGATTTGTGGTTAAATTCTCCTTTT 4 207 0 ATTGTGGTAA 0.934212 -94 ATCTGAAAAAATTGATGTTATTAGAATTATCTC 4 228 1 ATTATGTATA 0.75573 -73 AGAAAAAGCTATTAATGTGTTAA 4 288 1 ATTATGTTAA 0.979397 -13 *** **** * ** Masking position 2 Map Score: 13.2294 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 786 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 AATCTGTTTTTTTGGATTTGGGTGGATAACA 2 89 0 TTTGGATTTG 0.721377 -212 AGATTGTATCGATGGATTTAATAAATAAATT 2 115 1 GATGGATTTA 0.963003 -186 TTCTTTTCAGTTAGGAGTTTATGGAGATGTT 2 268 1 TTAGGAGTTA 0.899829 -33 TTATGGAGATGTTGAAGTTGAACCA 2 286 1 GTTGAAGTTA 0.952358 -15 CTCCCTCTAAGAAGGAGTTCATTATA 3 6 0 GAAGGAGTTA 0.980821 -159 CTCCTTCTTAGAGGGAGTTTAATCATCCTTA 3 20 1 GAGGGAGTTA 0.967739 -145 TATTGATTTGGATGAAGTTAGGCTATTTAAA 4 141 1 GATGAAGTTG 0.936465 -160 GTTTAAAAAAGGAGAATTTAACCACAAATCT 4 201 1 GGAGAATTTA 0.778758 -100 ********* * Masking position 6 Map Score: 2.67676 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 664 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 AAAACACAGAGATGCAATGG 2 1 1 AAAACACAGA 0.925056 -300 CCCAAATCCAAAAAAACAGATTGTATCGAT 2 98 1 AAAAAACAGA 0.966337 -203 TACATAACCTATAAAACAAAACATTTAAGA 2 170 1 ATAAAACAAA 0.835551 -131 ATGTGTTATAAAAAAAGTGATATGGAACAA 4 59 0 AAAAAAGTGA 0.941523 -242 CACTTTTTTTATAACACATATGCAAAAATT 4 70 1 ATAACACATA 0.603909 -231 TAGGCTATTTAAAAATGAAAATCCTGAAAC 4 159 1 AAAAATGAAA 0.686625 -142 TTTAAGTTTAAAAAAGGAGAATTTAACCAC 4 196 1 AAAAAGGAGA 0.892563 -105 CACAAATCTGAAAAAATTGATGTTATTAGA 4 223 1 AAAAAATTGA 0.713532 -78 AATTATCTCAAAAAAAGTTAAATTAAAAGA 4 252 1 AAAAAAGTTA 0.814546 -49 ATTAAAAGAGATAAAAGAAAAAGCTATTAA 4 273 1 ATAAAAGAAA 0.862892 -28 ********** Masking position 4 Map Score: 5.42266 Number of sites scoring better than the average of aligned sites = 1132 Number in coding regions = 969 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TTATCCCACCTATACCTATA 1 56 0 TTATCCCACC 0.986832 -10 ATAATGCCTGTTATCCACCCAAATCCAAAA 2 81 1 TTATCCACCC 0.986832 -220 AACAATTACTTTATCAAAGCCAATTAATTT 2 227 0 TTATCAAAGC 0.923051 -74 TTTTCCAACCCCATTAATTA 3 155 0 TTTTCCAACC 0.980605 -10 ********** Masking position 4 Map Score: 0.583856 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 31 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: 1.36667e-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 7 ********** No masking Map Score: 1.36667e-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 8 ********** No masking Map Score: 1.36667e-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