AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ilexA_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 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 GGTTAAAGGATAGTTATTAATTTGATGTTGAA 1 13 0 TAGTATTATT 0.849329 -288 GATACCATATTATATATTATTTTCGGTTTTTA 1 49 0 TATTATTTTT 0.967017 -252 TTATATATTCTTTTTATATATTCCCACAATAC 1 99 0 TTTTATAATT 0.966616 -202 CGTGTTTCATTTTTTATATATTCTTTTTATAT 1 112 0 TTTTATAATT 0.966616 -189 GCGCCACTTCTTTTTATTTTTTAATATCTATT 1 234 1 TTTTATTTTT 0.957063 -67 TATTTTTTAATATCTATTTACTATAAAACACG 1 248 1 TATTATTACT 0.918117 -53 CTTCAAACCTTTTATAATTATTATAAGGTTTG 4 38 0 TTTTAATATT 0.846354 -40 GGAAAGATATTATCTTTTCTTTTATTTTGGGT 6 29 1 TATTTTTTTT 0.742874 -29 CCTCCTCAATTATATATTTACTATTCTTAGGT 7 18 1 TATTATTACT 0.918117 -102 TATTCTTAGGTTTTTATAAATTCTCTTCTTTT 7 39 1 TTTTATAATT 0.966616 -81 CATATTTGACTATATAAAGATTTTGGTTTATA 7 87 0 TATTAAAATT 0.877292 -33 GGGACAATAGTTTAAATAATTTATTT 8 5 0 TTTAATATTT 0.686893 -34 TTTTTAACAATATTTATACTTTATTTATTTAT 9 40 1 TATTATATTT 0.966649 -49 ATACTTTATTTATTTATAATTTATACTTTTTA 9 55 1 TATTATATTT 0.966649 -34 *** **** *** Masking position 1 Map Score: 18.1841 Number of sites scoring better than the average of aligned sites = 1018 Number in coding regions = 607 Number in noncoding regions = 411 Number of orfs with sites within 600 bp upstream = 334 Fraction of orfs with sites within 600 bp upstream = 0.053646 Motif number 2 CATATTATATATTATTTTCGGTTTTTAGTAAGGTTA 1 40 0 ATATTTTTTT 0.976254 -261 ACTTCTTTTTATTTTTTAATATCTATTTACTATAAA 1 239 1 ATTTTTTTAT 0.661804 -62 TTGCACCTCCATAATTTCGTGTTTTATAGTAAATAG 1 261 0 ATATTTTTTA 0.80331 -40 AAAACCATTTTCATTCTAATTATTTGTCAAACCTT 4 10 1 TTATTCTTTT 0.696663 -68 ATATATCACCGTGTTTTCCTTCAAAC 4 62 0 ATTATCTTTT 0.936179 -16 AACTATCACCGTGTTTTAATCCAGTT 5 16 0 AATATCTTTT 0.573492 -16 ATTTATTTTACAATTTTTGGAAAGAT 6 1 1 ATTATTATTT 0.808272 -57 GAAAGATATTATCTTTTCTTTTATTTTGGGTGAGAA 6 30 1 ATTTTTTTTT 0.955311 -28 TTAGGTTTTTATAAATTCTCTTCTTTTTGAAACATA 7 44 1 ATAATTTTTT 0.979239 -76 TACTGTAGTTATAAACCAAAATCTTTATATAGTCAA 7 78 1 ATAACCTTTT 0.874223 -42 ACATCAATTGTCATATTTGACTATATAA 7 102 0 ATAATTTTTT 0.979135 -18 AAATAAATTATTTAAACTATTGTCCCCAAAAT 8 7 1 ATATTTTTTG 0.858248 -32 AATAAATTTGAAAATTTAATTAACTTA 9 2 1 ATAATTATTT 0.775499 -87 TGAAAATTTAATTAACTTAAGTTTTTAACAATATTT 9 19 1 ATAACTTTTT 0.924847 -70 TTATTTATTTATAATTTATACTTTTTAGTTGGTGAG 9 60 1 ATATTTTTTT 0.974918 -29 ** **** * *** Masking position 14 Map Score: 15.299 Number of sites scoring better than the average of aligned sites = 1131 Number in coding regions = 864 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 3 ATACCATATTATATATTATTTTCGGTTTTTA 1 49 0 ATATATTTTT 0.605852 -252 TATATATTCTTTTTATATATTCCCACAATAC 1 99 0 TTTTATAATT 0.94513 -202 GTGTTTCATTTTTTATATATTCTTTTTATAT 1 112 0 TTTTATAATT 0.94513 -189 CGCCACTTCTTTTTATTTTTTAATATCTATT 1 235 1 TTTTATTTTT 0.915647 -66 CTAATCACCTTCAATAATTTTTTGTTGAAT 2 38 0 TTCAATATTT 0.717212 -20 CCTTCAAACCTTTTATAATTATTATAAGGTT 4 40 0 TTTTATATTA 0.915648 -38 ATTTATTTTACAATTTTTGGAAAGAT 6 6 1 TTTTACATTT 0.89267 -52 ACCTCCTCAATTATATATTTACTATTCTTAG 7 17 1 TTATATATTA 0.812162 -103 ATTCTTAGGTTTTTATAAATTCTCTTCTTTT 7 40 1 TTTTATAATT 0.94513 -80 GGACAATAGTTTAAATAATTTATTT 8 5 0 TTAAATATTT 0.812162 -34 TTTTAACAATATTTATACTTTATTTATTTAT 9 41 1 ATTTATATTT 0.94513 -48 TACTTTATTTATTTATAATTTATACTTTTTA 9 56 1 ATTTATATTT 0.94513 -33 ******* *** Masking position 5 Map Score: 13.4462 Number of sites scoring better than the average of aligned sites = 1445 Number in coding regions = 986 Number in noncoding regions = 459 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 4 CCCACGCCTTGGCCGGGCTAGGCTACCTCC 1 153 0 GGCCGGGCTA 0.899083 -148 TTTGAACCCCCGCGGGGCAAAGCCCCATGG 1 193 0 CGCGGGGCAA 0.968344 -108 GTGGCGCGGAGGGGGGGATTTGAACCCCCG 1 211 0 GGGGGGGATT 0.848812 -90 ACGAAATTATGGAGGTGCAACCTTGACCGA 1 277 1 GGAGGTGCAA 0.974385 -24 AAAAATTATTGAAGGTGATTAG 2 46 1 GAAGGTGATT 0.88493 -12 AATATAAATTAAAGGTGAAACACT 3 12 1 AAAGGTGAAA 0.753443 -14 TGAAGGAAAACACGGTGATATAT 4 65 1 CACGGTGATA 0.959556 -13 TGGATTAAAACACGGTGATAGTT 5 19 1 CACGGTGATA 0.959556 -13 ATATAATTGAGGAGGTGTAAGC 7 3 0 GGAGGTGTAA 0.905432 -117 ********** Masking position 5 Map Score: 3.64899 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 158 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 GGATAGTTATTAATTTGATGTTGAAGT 1 6 0 TAATTTTGTT 0.971019 -295 ATATTATATATTATTTTCGGTTTTTAGTAAGG 1 43 0 TTATTTGGTT 0.917944 -258 GTTTCATTTTTTATATATTCTTTTTATATATT 1 109 0 TTATATTCTT 0.771446 -192 TTTTATTTTTTAATATCTATTTACTATAAAAC 1 245 1 TAATATATTT 0.656302 -56 TGCACCTCCATAATTTCGTGTTTTATAGTAAA 1 264 0 TAATTTTGTT 0.97102 -37 TCACCTTCAATAATTTTTTGTTGAATGTTATG 2 32 0 TAATTTTGTT 0.971019 -26 GTTTCACCTTTAATTTATATTT 3 1 0 TAATTTATTT 0.87157 -25 TGGAAAGATATTATCTTTTCTTTTATTTTGGG 6 28 1 TTATCTTCTT 0.73938 -30 ATCTTTTCTTTTATTTTGGGTGAGAAAC 6 40 1 TTATTTGGTG 0.678115 -18 AAACTTAAGTTAATTAAATTTTCAAATTTATT 9 11 0 TAATTATTTT 0.624547 -78 TATTTATTTATAATTTATACTTTTTAGTTGGT 9 61 1 TAATTTACTT 0.915236 -28 ****** **** Masking position 3 Map Score: 5.98212 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 505 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 6 ********** 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 7 ********** 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 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