AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_mthe_reg_100.orf -o216_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH00518 35 M.thermo #2 RTH01836 222 M.thermo #3 RTH00222 184 M.thermo Motif number 1 TCACCGTGAACTCCATGTGAGAAGAAACCT 2 63 0 CTCCATGTGA 0.99647 -160 TCACATGGAGTTCACGGTGACATGAACATT 2 73 1 TTCACGGTGA 0.898966 -150 TCGCTGTGAACTCCATGTGAAATGTTCATG 2 93 0 CTCCATGTGA 0.99647 -130 TGGTGTTCATATCGCTGTGAACTCCATGTG 2 104 0 ATCGCTGTGA 0.941135 -119 GCGATATGAACACCATATGATGAACCTCAG 2 119 1 CACCATATGA 0.935582 -104 TGATGAACCTCAGAATGTGATATGCCGGTG 2 136 1 CAGAATGTGA 0.945836 -87 AGAATGTGATATGCCGGTGAAAGATATATA 2 147 1 ATGCCGGTGA 0.972489 -76 TGCCGCCCACCACCCTGTGACCTTTATATG 3 85 1 CACCCTGTGA 0.994783 -100 TTATCCATCACTGCAGGTGAAACC 3 171 1 CTGCAGGTGA 0.991737 -14 ********** Masking position 8 Map Score: 17.5347 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 601 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 CCATTACCGGTAATATGATCTGATAGGTTT 2 39 1 TAATATGATC 0.844567 -184 TTTCTTCTCACATGGAGTTCACGGTGACAT 2 66 1 CATGGAGTTC 0.983918 -157 GAACATTTCACATGGAGTTCACAGCGATAT 2 96 1 CATGGAGTTC 0.983918 -127 AGGTTCATCATATGGTGTTCATATCGCTGT 2 116 0 TATGGTGTTC 0.985879 -107 CATATCTAGATAATGAATTCAATTTTCAAC 3 22 0 TAATGAATTC 0.814298 -163 TGAGGACCTATATTAAGATCCTCAATCATA 3 48 0 TATTAAGATC 0.902165 -137 CTTAATTATATAAGGTGATCCCAACAATAG 3 134 1 TAAGGTGATC 0.976291 -51 ********** Masking position 2 Map Score: 7.13728 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 484 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 TCATGTCACCGTGAACTCCATGTGAGAAGA 2 68 0 GTGAACTCCA 0.994068 -155 TCATATCGCTGTGAACTCCATGTGAAATGT 2 98 0 GTGAACTCCA 0.994068 -125 TCACAGCGATATGAACACCATATGATGAAC 2 114 1 ATGAACACCA 0.982243 -109 ACACCATATGATGAACCTCAGAATGTGATA 2 128 1 ATGAACCTCA 0.983596 -95 TATCTAGATAATGAATTCAATTTTCAACAA 3 20 0 ATGAATTCAA 0.819677 -165 GACCTATATTAAGATCCTCAATCATATCTA 3 44 0 AAGATCCTCA 0.844123 -141 ATTATATAAGGTGATCCCAACAATAGTTAA 3 138 1 GTGATCCCAA 0.969222 -47 ********** Masking position 4 Map Score: 9.14328 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 458 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 ATCATATTACCGGTAATGGGAACAGGTGAG 2 28 0 CGGTAATGGG 0.978778 -195 TGTGATATGCCGGTGAAAGATATATATACT 2 151 1 CGGTGAAAGA 0.928499 -72 AAAGGTCACAGGGTGGTGGGCGGCAGATCC 3 80 0 GGGTGGTGGG 0.994425 -105 ATATAATTAAGAGTGGTGGATGGGCTGTGC 3 115 0 GAGTGGTGGA 0.986547 -70 GTTTCACCTGCAGTGATGGATAATCATTAA 3 164 0 CAGTGATGGA 0.989995 -21 ********** Masking position 4 Map Score: 3.99702 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 354 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 GCTGGAGGCCCCTTCAAATCAAAAAAAGAA 1 14 0 CCTTCAAATC 0.958993 -22 GAGAAGAAACCTATCAGATCATATTACCGG 2 45 0 CTATCAGATC 0.965889 -178 ATATCTTTCACCGGCATATCACATTCTGAG 2 144 0 CCGGCATATC 0.991833 -79 TTAAGATCCTCAATCATATCTAGATAATGA 3 36 0 CAATCATATC 0.948201 -149 AGGGTGGTGGGCGGCAGATCCTTTGAGGAC 3 71 0 GCGGCAGATC 0.981601 -114 ********** Masking position 6 Map Score: 1.69122 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 214 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 ********** No masking Map Score: -2.03625e-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: -2.03625e-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: -2.03625e-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