AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_Ribosomal_Operon_8_mjan_reg_100.orf -o221_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ13714 300 M_jannaschii_chromosome #2 RMJ06988 57 M_jannaschii_chromosome #3 RMJ01689 25 M_jannaschii_chromosome #4 RMJ08498 23 M_jannaschii_chromosome #5 RMJ13016 22 M_jannaschii_chromosome #6 RMJ00809 60 M_jannaschii_chromosome #7 RMJ06364 110 M_jannaschii_chromosome Motif number 1 AGGATAGTTATTAATTTGATGTTGAAGT 1 6 0 TTAATTTTTT 0.970748 -295 ATATTATATATTATTTTCGGTTTTTAGTAAGGT 1 42 0 TTATTTTGTT 0.870065 -259 TTTTTATATATTCTTTTTATATATTCCCACAAT 1 101 0 TTCTTTTTTA 0.948267 -200 TGAAACGTGTTTCATTTTTTATATATTCTTTTT 1 116 0 TTCATTTTTA 0.955027 -185 TCCGCGCCACTTCTTTTTATTTTTTAATATCTA 1 231 1 TTCTTTTTTT 0.975345 -70 TTTTTATTTTTTAATATCTATTTACTATAAAAC 1 244 1 TTAATATATT 0.646958 -57 TTGCACCTCCATAATTTCGTGTTTTATAGTAAA 1 264 0 ATAATTTTTT 0.938914 -37 TGCTAAGTGTTTCATTTAATAAT 2 1 0 TTCATTTTAT 0.829356 -57 ATCACCTTCAATAATTTTTTGTTGAATGTTATG 2 32 0 ATAATTTTTT 0.938912 -26 TGTTTCACCTTTAATTTATATTT 3 1 0 TTAATTTATT 0.945108 -25 ATTTATTTTACAATTTTTGGAAAGA 6 3 1 TTATTTTATT 0.936966 -58 GAAAGATATTATCTTTTCTTTTATTTTGGGTGA 6 30 1 ATCTTTTTTA 0.894582 -31 AATAGTTGTTATCTTTTTGAATATTGTCGGGGA 7 81 0 ATCTTTTATA 0.814861 -30 ******* * ** Masking position 7 Map Score: 14.4463 Number of sites scoring better than the average of aligned sites = 1732 Number in coding regions = 1302 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 322 Fraction of orfs with sites within 600 bp upstream = 0.0517186 Motif number 2 CGCTCTGAAACGTGTTTCATTTTTTATATA 1 124 0 CGTGTTTCAT 0.995416 -177 TCCATAATTTCGTGTTTTATAGTAAATAGA 1 260 0 CGTGTTTTAT 0.986556 -41 TGTTATGCTAAGTGTTTCATTTAATAAT 2 9 0 AGTGTTTCAT 0.986556 -49 AGTGTTTCACCTTTAATTTA 3 16 0 AGTGTTTCAC 0.987533 -10 CGTGTTTTAATCCAGTTTAT 5 13 0 CGTGTTTTAA 0.966713 -10 CATGTTTCTCACCCAAAATA 6 51 0 CATGTTTCTC 0.899469 -10 ********** Masking position 5 Map Score: 9.13313 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 AATTAATAACTATCCTTTAACCTTACTAAA 1 23 1 TATCCTTTAA 0.984292 -278 TATAATATGGTATCCATTAATCATAACGTT 1 67 1 TATCCATTAA 0.888416 -234 CACTTCTTTTTATTTTTTAATATCTATTTA 1 238 1 TATTTTTTAA 0.887643 -63 ATGCTAAGTGTTTCATTTAATAAT 2 5 0 TTTCATTTAA 0.729209 -53 ACACTTAGCATAACATTCAACAAAAAATTA 2 24 1 TAACATTCAA 0.877688 -34 CTAATCACCTTCAATAATTTTTTG 2 44 0 TCACCTTCAA 0.918771 -14 AGTGTTTCACCTTTAATTTATATTT 3 10 0 TCACCTTTAA 0.940778 -16 GAAAAGATAATATCTTTCCAAAAATTGTAA 6 18 0 TATCTTTCCA 0.810478 -43 TACTTATTTCTATCCTTTAGGGGAAACAAC 7 37 1 TATCCTTTAG 0.921878 -74 AAACAACCACTAATTTTTAAATCCCCGACA 7 60 1 TAATTTTTAA 0.823256 -51 AGATAACAACTATTTTTAAAG 7 100 1 TATTTTTAAA 0.586053 -11 ********** Masking position 7 Map Score: 7.5355 Number of sites scoring better than the average of aligned sites = 1569 Number in coding regions = 1404 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 AAAACCGAAAATAATATATAATATGGTATC 1 51 1 ATAATATATA 0.958686 -250 GAGTATTGTGGGAATATATAAAAAGAATAT 1 97 1 GGAATATATA 0.982589 -204 ATATATAAAAAGAATATATAAAAAATGAAA 1 110 1 AGAATATATA 0.981231 -191 TTCGTGTTTTATAGTAAATAGATATTAAAA 1 252 0 ATAGTAAATA 0.883916 -49 TAAGTATAAGGGAGTATATAAATTTTATCA 7 13 0 GGAGTATATA 0.983853 -98 ********** Masking position 5 Map Score: 4.24891 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 76 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GGCTAGGCTACCTCCGCTCTGAAACGTGTTT 1 137 0 CCTCCGCTCG 0.983245 -164 CAGTCCCACGCCTTGGCCGGGCTAGGCTACC 1 156 0 CCTTGGCCGG 0.990279 -145 GGGATTTGAACCCCCGCGGGGCAAAGCCCCA 1 196 0 CCCCCGCGGG 0.74918 -105 GTTCAAATCCCCCCCTCCGCGCCACTTCTTT 1 216 1 CCCCCTCCGG 0.991038 -85 GGAGGTGCAACCTTGACCGAGAAT 1 287 1 CCTTGACCGG 0.983482 -14 ********* * Masking position 7 Map Score: 2.86401 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 1 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CTATCCTTTAACCTTACTAAAAACCGAAAA 1 32 1 ACCTTACTAA 0.914525 -269 ATTAATGGATACCATATTATATATTATTTT 1 58 0 ACCATATTAT 0.90721 -243 ATATATTCCCACAATACTCAACGTTATGAT 1 86 0 ACAATACTCA 0.972289 -215 AAAACCATTTTCATTCTAATTAT 4 4 1 ACCATTTTCA 0.957136 -20 TAAATCCCCGACAATATTCAAAAAGATAAC 7 77 1 ACAATATTCA 0.969025 -34 ********** Masking position 5 Map Score: 1.16448 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 100 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TTGAGTATTGTGGGAATATATAAAAAGAAT 1 95 1 TGGGAATATA 0.906735 -206 GGAGATCCCATGGGGCTTTGCCCCGCGGGG 1 186 1 TGGGGCTTTG 0.988831 -115 GGCGCGGAGGGGGGGATTTGAACCCCCGCG 1 209 0 GGGGGATTTG 0.992181 -92 TGAATATTGTCGGGGATTTAAAAATTAGTG 7 67 0 CGGGGATTTA 0.987956 -44 ********** Masking position 7 Map Score: 0.457086 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 65 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: 1.60826e-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: 1.60826e-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 10 ********** No masking Map Score: 1.60826e-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