AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifis_mjan_opreg_100.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 AATGTTATAAATTTTAAAAGAGTTTGTTAAAA 1 12 1 ATTTAAAGAG 0.760134 -54 TAAGTTGGTAAATTTTAACAAACTCTTTTAAA 1 24 0 AATTAACAAA 0.768652 -42 TCTTAAACATAAATGGAAAGAAGATTGAGACA 2 43 1 AATGAAAGAA 0.951564 -258 TTATCCACCCAAATCCAAAAAAACAGATTGTA 2 91 1 AATCAAAAAA 0.826968 -210 AAGAACCACTATCTGTAACAATTACTTTATCA 2 241 0 ATTGAACAAT 0.909565 -60 ATAAACTCCTAACTGAAAAGAACCACTATCTG 2 258 0 AATGAAAGAA 0.951563 -43 ATTTAAATAACTTTGCAAAGAACATACTTTGG 3 55 1 CTTGAAAGAA 0.95079 -110 TTTGCAGAGCCTCTGCAAATATCTCTATTAAA 3 93 1 CTTGAAATAT 0.814122 -72 GCAAATATCTCTATTAAAAAATACCTTTCAAT 3 107 1 CTTTAAAAAT 0.884628 -58 ATCAATAAATCTTTTAAAAGATGGTGGAGAGT 4 18 1 CTTTAAAGAT 0.823281 -283 AAAAAAAGTGATATGGAACAATATAAATCAAC 4 48 0 ATTGAACAAT 0.913396 -253 TTTATAACACATATGCAAAAATTGTAAGAGAC 4 77 1 ATTGAAAAAT 0.96784 -224 AAACATGGAAAATTGGAAATAATTATTGATTT 4 118 1 AATGAAATAA 0.817967 -183 TGAAGTTAGGCTATTTAAAAATGAAAATCCTG 4 153 1 CTTTAAAAAT 0.581196 -148 AATAATATTTAAGTTTAAAAAAGGAGAATTTA 4 189 1 AATTAAAAAA 0.907052 -112 TTAACCACAAATCTGAAAAAATTGATGTTATT 4 218 1 ATTGAAAAAT 0.964699 -83 TATTAGAATTATCTCAAAAAAAGTTAAATTAA 4 246 1 ATTCAAAAAA 0.880787 -55 AAAAAAAGTTAAATTAAAAGAGATAAAAGAAA 4 261 1 AATTAAAGAG 0.804127 -40 ** ** ****** Masking position 4 Map Score: 21.2253 Number of sites scoring better than the average of aligned sites = 1326 Number in coding regions = 1129 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 TCCCATTGCATCTCTGTGTTTT 2 2 0 TCCTGTGTTT 0.885385 -299 ATCGATACAATCTGTTTTTTTGGATTTGGGT 2 97 0 TCGTTTTTTT 0.947707 -204 AATTTGTGAATCCCTTTTTCTTCAGCAATTT 2 201 0 TCCTTTTTCT 0.98661 -100 TTGTTCCATATCACTTTTTTTATAACACATA 4 59 1 TCCTTTTTTT 0.99095 -242 GTGGTTAAATTCTCCTTTTTTAAACTTAAAT 4 195 0 TCCCTTTTTT 0.96676 -106 TCTTTTAATTTAACTTTTTTTGAGATAATTC 4 251 0 TACTTTTTTT 0.961606 -50 TTTTCTTTTATCTCTTTTAATTTAACTTTTT 4 263 0 TCCTTTTAAT 0.8288 -38 AACACATTAATAGCTTTTTCTTTTATCTCTT 4 278 0 TACTTTTTCT 0.943988 -23 ** ******** Masking position 7 Map Score: 7.5974 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 188 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 ATGGATTTAATAAATAAATTGGCAGATGTT 2 126 1 TAAATAAATT 0.828671 -175 AAGGGATTCACAAATTAATTGGCTTTGATA 2 216 1 CAAATTAATT 0.950536 -85 TTGGCTTTGATAAAGTAATTGTTACAGATA 2 234 1 TAAAGTAATT 0.814382 -67 CAAAGTTATTTAAATTAACTAAGGATGATT 3 40 0 TAAATTAACT 0.909236 -125 ATATAATATATACATTAATTAATGGGGTTG 3 140 1 TACATTAATT 0.935864 -25 TTATAAAATCAATAAATCTTTTAA 4 5 1 AAAATCAATA 0.844916 -296 TGGAACAATATAAATCAACTCTCCACCATC 4 37 0 TAAATCAACT 0.915634 -264 TAACTTCATCCAAATCAATAATTATTTCCA 4 131 0 CAAATCAATA 0.924672 -170 TAATTCTAATAACATCAATTTTTTCAGATT 4 227 0 AACATCAATT 0.852669 -74 CAAAAAAAGTTAAATTAAAAGAGATAAAAG 4 260 1 TAAATTAAAA 0.684086 -41 TTAACACATTAATAGCTTTTTCTT 4 287 0 CACATTAATA 0.876489 -14 ********** Masking position 4 Map Score: 7.17376 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 500 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 TTGGTAAATTTTAACAAACTCTTTTAAAAT 1 22 0 TTAACAAACT 0.873741 -44 TTTGTTAAAATTTACCAACTTATATAGGTA 1 34 1 TTTACCAACT 0.944869 -32 TTATCCCACCTATACCTATA 1 56 0 TTATCCCACC 0.948659 -10 ATAATGCCTGTTATCCACCCAAATCCAAAA 2 81 1 TTATCCACCC 0.960528 -220 AACAATTACTTTATCAAAGCCAATTAATTT 2 227 0 TTATCAAAGC 0.887573 -74 TAGAGGGAGTTTAATCATCCTTAGTTAATT 3 28 1 TTAATCATCC 0.749406 -137 TTTTCCAACCCCATTAATTA 3 155 0 TTTTCCAACC 0.98466 -10 TTATTTCCAATTTTCCATGTTTTAGAATGT 4 110 0 TTTTCCATGT 0.784627 -191 AAATTCTCCTTTTTTAAACTTAAATATTAT 4 190 0 TTTTTAAACT 0.678301 -111 ********** Masking position 2 Map Score: 2.47668 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 725 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AATTTTAACAAACTCTTTTAAAATTTATAACA 1 14 0 AACTCTTTAA 0.762497 -52 TTGTGATGATAACATCTGCCAATTTATTTATT 2 134 0 AACATCTCAA 0.969417 -167 TTATCATCACAACTCATACATAACCTATAAAA 2 154 1 AACTCATCTA 0.745013 -147 TTTCTTCAGCAATTTCTCTTAAATGTTTTGTT 2 184 0 AATTTCTTAA 0.835646 -117 GTTCAACTTCAACATCTCCATAAACTCCTAAC 2 277 0 AACATCTCTA 0.94921 -24 TATAATGAACTCCTTCTTAGAGGGAGTTT 3 8 1 AACTCCTCTA 0.967536 -157 AGGCTCTGCAAATACCATCCAAAGTATGTTCT 3 73 0 AATACCACAA 0.794986 -92 TCTATTAAAAAATACCTTTCAATAATATAATA 3 116 1 AATACCTTAA 0.851673 -49 TCAACTCTCCACCATCTTTTAAAAGATTTATT 4 21 0 ACCATCTTAA 0.686828 -280 TGTCTCTTACAATTTTTGCATATGTGTTATAA 4 78 0 AATTTTTCTA 0.585153 -223 TAAATAGCCTAACTTCATCCAAATCAATAATT 4 138 0 AACTTCACAA 0.903344 -163 ******* * ** Masking position 1 Map Score: 2.79901 Number of sites scoring better than the average of aligned sites = 1529 Number in coding regions = 1359 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 6 TCCCACCTATACCTATATAAGTTGGTAAAT 1 43 0 ACCTATATAA 0.93627 -23 AGATTGAGACACCAACAATAATGCCTGTTA 2 64 1 ACCAACAATA 0.843059 -237 CTCATACATAACCTATAAAACAAAACATTT 2 166 1 ACCTATAAAA 0.936269 -135 AATACCTTTCAATAATATAATATATACATT 3 126 1 AATAATATAA 0.729496 -39 AGTGATATGGAACAATATAAATCAACTCTC 4 44 0 AACAATATAA 0.945747 -257 AAAATCCTGAAACAATAATATTTAAGTTTA 4 176 1 AACAATAATA 0.903309 -125 ********** Masking position 5 Map Score: 0.00655172 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 427 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 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 Motif number 9 ********** 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