AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_tpal_reg_100.orf -o217_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00715 275 AE000520 #2 RTP00717 119 AE000520 Motif number 1 GCTCCTCTTCCCACGCGTGCATTCCTTCAA 1 15 1 CCACGCGTGC 0.836408 -261 ACTCGGCACTGCGCGCGTTCACGGTCATTG 1 42 0 GCGCGCGTTC 0.817035 -234 CGCTCCCCCTACTCGGCACTGCGCGCGTTC 1 52 0 ACTCGGCACT 0.750582 -224 GATCGCTCCGACGCGTTTCCCACGCTACCT 1 81 1 ACGCGTTTCC 0.944466 -195 TTCCCACGCTACCTGCCACTGATATGTTCC 1 97 1 ACCTGCCACT 0.898399 -179 CCCATGCGGAGCCTGCGTGCACGATTGCAG 1 130 0 GCCTGCGTGC 0.936067 -146 AAGGGTACCGACGTGGTAGTCACAAGCGGG 1 170 1 ACGTGGTAGT 0.912801 -106 GCAAACGCGTCCCCGCTTGTGACTACCACG 1 181 0 CCCCGCTTGT 0.97503 -95 ACAAGCGGGGACGCGTTTGCATCCATGTTT 1 191 1 ACGCGTTTGC 0.961889 -85 AGACATAGCGCCGTGCTTCTGGTATTGGCT 1 231 1 CCGTGCTTCT 0.921113 -45 GGTAATCTTTACCTGCGAGCCAATACCAGA 1 248 0 ACCTGCGAGC 0.966294 -28 ATAGTGACGAACGCGGTTGCC 2 2 0 ACGCGGTTGC 0.989296 -118 GCGAATAAGCACTCGGTAGCTCACCGCCCC 2 47 1 ACTCGGTAGC 0.934066 -73 AGCTCACCGCCCCCGGCACTTCCTGCCAGC 2 64 1 CCCCGGCACT 0.906208 -56 CCCCGGCACTTCCTGCCAGCTGATACGCGC 2 74 1 TCCTGCCAGC 0.829559 -46 GCCAGCTGATACGCGCTTCCTGTTCTTTTA 2 88 1 ACGCGCTTCC 0.991007 -32 ********** Masking position 5 Map Score: 22.9378 Number of sites scoring better than the average of aligned sites = 3431 Number in coding regions = 3155 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 ATTCCTTCAATGACCGTGAACGCGCGCAGTG 1 35 1 TACCGTGAAC 0.952881 -241 CGCGTCGGAGCGATCGCTCCCCCTACTCGGC 1 65 0 CATCGCTCCC 0.982637 -211 GTTTCCCACGCTACCTGCCACTGATATGTTC 1 95 1 CACCTGCCAC 0.871553 -181 TTCCTTCCTGCAATCGTGCACGCAGGCTCCG 1 123 1 CATCGTGCAC 0.978818 -153 GTACCCTTTCTTACCGTTCCCATGCGGAGCC 1 147 0 TACCGTTCCC 0.98825 -129 AACATGGATGCAAACGCGTCCCCGCTTGTGA 1 189 0 CAACGCGTCC 0.913648 -87 TCCATGTTTTTAACCGTCCAGACATAGCGCC 1 212 1 TACCGTCCAG 0.897082 -64 AATCGCATGGTAATCTTTACCTGCGAGCCAA 1 255 0 TATCTTTACC 0.521516 -21 GGCAACCGCGTTCGTCACTATTC 2 3 1 CACCGCGTTC 0.92657 -117 ACTCGGTAGCTCACCGCCCCCGGCACTTCCT 2 57 1 TACCGCCCCC 0.994161 -63 * ********* Masking position 3 Map Score: 6.82652 Number of sites scoring better than the average of aligned sites = 1231 Number in coding regions = 1127 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 TCTGGCTCCTCTTCCCACGCGTGCATTCCT 1 11 1 CTTCCCACGC 0.982873 -265 GGGAGCGATCGCTCCGACGCGTTTCCCACG 1 75 1 GCTCCGACGC 0.975693 -201 CTCCGACGCGTTTCCCACGCTACCTGCCAC 1 86 1 TTTCCCACGC 0.974826 -190 CTGCAATCGTGCACGCAGGCTCCGCATGGG 1 130 1 GCACGCAGGC 0.959282 -146 CTTTCTTACCGTTCCCATGCGGAGCCTGCG 1 143 0 GTTCCCATGC 0.989324 -133 GTAAGAAAGGGTACCGACGTGGTAGTCACA 1 164 1 GTACCGACGT 0.955637 -112 GGATGCAAACGCGTCCCCGCTTGTGACTAC 1 185 0 GCGTCCCCGC 0.672803 -91 GGACGCGTTTGCATCCATGTTTTTAACCGT 1 199 1 GCATCCATGT 0.837967 -77 TCTGGTATTGGCTCGCAGGTAAAGATTACC 1 248 1 GCTCGCAGGT 0.96625 -28 ********** Masking position 9 Map Score: 11.6167 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 911 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 TCTGGCTCCTCTTCCCACGCGTGCA 1 3 1 TGGCTCCCTC 0.991933 -273 GTCGGAGCGATCGCTCCCCCTACTCGGCACTGC 1 60 0 TCGCTCCCCC 0.998341 -216 GGGGGAGCGATCGCTCCGACGCGTTTCCCACGC 1 73 1 TCGCTCCACG 0.93753 -203 GACTACCACGTCGGTACCCTTTCTTACCGTTCC 1 158 0 TCGGTACCTC 0.964445 -118 ACCGCGTTCGTCACTATTCTGCCGTGGGCATTG 2 15 1 TCACTATCTC 0.898594 -105 GAGTGCTTATTCGCAATGCCCACGGCAGAATAG 2 28 0 TCGCAATCCC 0.98397 -92 TCACCGCCCCCGGCACTTCCTGCCAGCTGATAC 2 67 1 CGGCACTCCC 0.942726 -53 ******* ** * Masking position 1 Map Score: 2.33412 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 527 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 ********** No masking Map Score: -6.65478e-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 6 ********** No masking Map Score: -6.65478e-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: -6.65478e-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