AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ilexA_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 MJ0189 300 SSU ribosomal protein S13P (rpsM) #2 MJ0190 57 SSU ribosomal protein S4P (rpsD) #3 MJ0191 25 SSU ribosomal protein S11P (rpsK) #4 MJ0193 77 LSU ribosomal protein L18E #5 MJ0194 31 LSU ribosomal protein L13P (rplM) #6 MJ0196 57 DNA-directed RNA polymerase, subunit N (rpoN) #7 MJ0869 119 DNA repair protein RAD51 (radA) #8 MJ0885 38 DNA polymerase B1 #9 MJ0888 88 conserved hypothetical protein Motif number 1 ACCGAAAATAATATATAATATGGTATCCAT 1 54 1 ATATATAATA 0.919138 -247 TATTGTGGGAATATATAAAAAGAATATATA 1 100 1 ATATATAAAA 0.966391 -201 TATAAAAAGAATATATAAAAAATGAAACAC 1 113 1 ATATATAAAA 0.966391 -188 ATAGATATTAAAAAATAAAAAGAAGTGGCG 1 235 0 AAAAATAAAA 0.863611 -66 AAATATAAATTAAAGGTGAA 3 1 1 AAATATAAAT 0.883356 -25 ACCTTATAATAATTATAAAAGGTTTGAAGG 4 41 1 AATTATAAAA 0.887301 -37 TCTTTCCAAAAATTGTAAAATAAAT 6 6 0 AATTGTAAAA 0.832539 -52 AAATAAAAGAAAAGATAATATCTTTCCAAA 6 26 0 AAAGATAATA 0.769418 -32 AGAATAGTAAATATATAATTGAGGAGGTGT 7 15 0 ATATATAATT 0.686819 -105 AAAGAAGAGAATTTATAAAAACCTAAGAAT 7 40 0 ATTTATAAAA 0.785662 -80 TAAATAAATAAAGTATAAATATTGTTAAAA 9 41 0 AAGTATAAAT 0.801535 -48 AAAAAGTATAAATTATAAATAAATAAAGTA 9 56 0 AATTATAAAT 0.533867 -33 ********** Masking position 7 Map Score: 15.1518 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 664 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 2 TAACCTTACTAAAAACCGAAAATAATATATAATATG 1 40 1 AAAAAAATAT 0.984332 -261 TATAAAAAGAATATATAAAAAATGAAACACGTTTCA 1 113 1 ATAAAAATAA 0.746036 -188 TTTATAGTAAATAGATATTAAAAAATAAAAAGAAGT 1 239 0 ATAAAAAAAT 0.806324 -62 CTATTTACTATAAAACACGAAATTATGGAGGTGCAA 1 261 1 TAAAAAATAT 0.861009 -40 AAGGTTTGACAAATAATTAGAATGAAAATGGTTTT 4 10 0 AAAAGAATAA 0.877402 -68 GTTTGAAGGAAAACACGGTGATATAT 4 62 1 AAAAGATAAT 0.872984 -16 ATATCTTTCCAAAAATTGTAAAATAAAT 6 3 0 AAAAAAAAAA 0.864614 -55 TTCTCACCCAAAATAAAAGAAAAGATAATATCTTTC 6 30 0 AAAAAAAAAT 0.959983 -28 TATGTTTCAAAAAGAAGAGAATTTATAAAAACCTAA 7 44 0 AAAAAATTAT 0.977097 -76 TTGACTATATAAAGATTTTGGTTTATAACTACAGTA 7 78 0 AAAAGGTTAT 0.825475 -42 TTATATAGTCAAATATGACAATTGATGT 7 102 1 AAAAAATTAT 0.977071 -18 ATTTTGGGGACAATAGTTTAAATAATTTATTT 8 7 0 CAAAAAATAT 0.901797 -32 TAAGTTAATTAAATTTTCAAATTTATT 9 2 0 AAATAATTAT 0.739769 -87 AAATATTGTTAAAAACTTAAGTTAATTAAATTTTCA 9 19 0 AAAAAGTTAT 0.918957 -70 CTCACCAACTAAAAAGTATAAATTATAAATAAATAA 9 60 0 AAAAAAATAT 0.984049 -29 *** * **** ** Masking position 3 Map Score: 17.0631 Number of sites scoring better than the average of aligned sites = 1570 Number in coding regions = 1171 Number in noncoding regions = 399 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 3 TTTAGTAAGGTTAAAGGATAGTTATTAATT 1 23 0 TTAAAGGATA 0.967581 -278 AACGTTATGATTAATGGATACCATATTATA 1 67 0 TTAATGGATA 0.842498 -234 ATTATTAAATGAAACACTTAGCAT 2 5 1 TTAAATGAAA 0.920642 -53 TAATTTTTTGTTGAATGTTATGCTAAGTGT 2 24 0 TTGAATGTTA 0.920133 -34 CAAAAAATTATTGAAGGTGATTAG 2 44 1 TTGAAGGTGA 0.969566 -14 AAATATAAATTAAAGGTGAAACACT 3 10 1 TTAAAGGTGA 0.952564 -16 GACAAATAATTAGAATGAAAATGGTTTT 4 9 0 TAGAATGAAA 0.768298 -69 TATAAAAGGTTTGAAGGAAAACACGGTGAT 4 54 1 TTGAAGGAAA 0.979314 -24 ********** Masking position 4 Map Score: 7.63057 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 454 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AGGATAGTTATTAATTTGATGTTGAAGT 1 6 0 TTAATTTGTT 0.949458 -295 CATATTATATATTATTTTCGGTTTTTAGTAAGG 1 43 0 ATTATTTGTT 0.975423 -258 TTGCACCTCCATAATTTCGTGTTTTATAGTAAA 1 264 0 ATAATTTGTT 0.979237 -37 ATCACCTTCAATAATTTTTTGTTGAATGTTATG 2 32 0 ATAATTTGTT 0.979237 -26 AAATATAAATTAAAGGTGAAACACT 3 5 1 ATAAATTGGT 0.789617 -21 ACCTTTTATAATTATTATAAGGTTTGACAAATA 4 31 0 ATTATTAGGT 0.759525 -47 TATCTTTTCTTTTATTTTGGGTGAGAAAC 6 39 1 TTTATTTGTG 0.786941 -19 AAATAAATTATTTAAACTATTGTCCCCAA 8 7 1 ATTATTTCTA 0.811219 -32 TAGTTAATTTTGGGGACAATAGTTTA 8 23 0 TTAATTTGGA 0.765843 -16 AGTTTTTAACAATATTTATACTTTATTTATTTA 9 38 1 AATATTTCTT 0.662636 -51 TTATTTATTTATAATTTATACTTTTTAGTTGGT 9 60 1 ATAATTTCTT 0.948373 -29 ******* *** Masking position 4 Map Score: 6.34116 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 436 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 5 CGCTCTGAAACGTGTTTCATTTTTTATATA 1 124 0 CGTGTTTCAT 0.990641 -177 TCCATAATTTCGTGTTTTATAGTAAATAGA 1 260 0 CGTGTTTTAT 0.980861 -41 TGTTATGCTAAGTGTTTCATTTAATAAT 2 9 0 AGTGTTTCAT 0.972801 -49 AGTGTTTCACCTTTAATTTA 3 16 0 AGTGTTTCAC 0.974753 -10 ATATATCACCGTGTTTTCCTTCAAACCTT 4 59 0 CGTGTTTTCC 0.944515 -19 AACTATCACCGTGTTTTAATCCAGTTTAT 5 13 0 CGTGTTTTAA 0.972801 -19 ATAACTACAGTATGTTTCAAAAAGAAGAGA 7 60 0 TATGTTTCAA 0.647394 -60 ********** Masking position 5 Map Score: 8.73234 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 21 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CCGGGCTAGGCTACCTCCGCTCTGAAACGTG 1 140 0 CTACCTCCGT 0.879127 -161 CAGTCCCACGCCTTGGCCGGGCTAGGCTACC 1 156 0 CCTTGGCCGG 0.977287 -145 GGGATTTGAACCCCCGCGGGGCAAAGCCCCA 1 196 0 CCCCCGCGGG 0.941162 -105 GTTCAAATCCCCCCCTCCGCGCCACTTCTTT 1 216 1 CCCCCTCCGG 0.991038 -85 GGAGGTGCAACCTTGACCGAGAAT 1 287 1 CCTTGACCGG 0.974684 -14 ATATATCACCGTGTTTTCCTTCA 4 65 0 ATATCACCGG 0.896162 -13 AACTATCACCGTGTTTTAATCCA 5 19 0 CTATCACCGG 0.98519 -13 ********* * Masking position 7 Map Score: 2.4149 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 8 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AGGGGGGGATTTGAACCCCCGCGGGGCAAA 1 202 0 TTGAACCCCC 0.988027 -99 TCGGTCAAGGTTGCACCTCCATAATTTCGT 1 277 0 TTGCACCTCC 0.99628 -24 GCTTACACCTCCTCAATTATAT 7 3 1 TTACACCTCC 0.989918 -117 ********** Masking position 5 Map Score: 1.30662 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 = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ********** No masking Map Score: 1.37435e-13 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: 1.37435e-13 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 10 ********** No masking Map Score: 1.37435e-13 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