AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___tpal_reg_300.orf -o190_tpal_300.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 RTP00381 170 AE000520 #2 RTP00767 126 AE000520 #3 RTP00768 96 AE000520 #4 RTP00769 125 AE000520 #5 RTP00770 34 AE000520 #6 RTP00771 204 AE000520 Motif number 1 TTTAAGATCACGGTGGTGGAGCGCGAGCGCAGCC 1 109 1 CGGGGGAGCC 0.993881 -62 AATGTGCTCGACGTGGCTGCGCTCGCGCTCCACC 1 123 0 ACGGGGCGCC 0.99061 -48 ATAGCCATCGACAGGGTGTTGCCCTGAGCAAACC 2 57 0 ACAGGTTGCC 0.942511 -70 TGTCTCGCGCCGAAAGGATAGCACC 2 112 1 CGAAGTAGCC 0.918022 -15 TACGCCAATGCAGTGGCCTTGCTCCGCCCAGACG 3 11 0 CAGGGTTGCC 0.992522 -86 AGACAGTCTCAAGGGGGTTCCCACCAGAAGGGGC 3 66 1 AAGGGTCCCC 0.920156 -31 GGGTTCCCACCAGAAGGGGCGCGCCGA 3 80 1 CAGAGGCGCC 0.993296 -17 CCGGCGGGTGTGCACGGCCATGCGC 4 2 1 CGGGGGTGCC 0.995812 -124 ATCTTTTTTGCAGAAGGAGTGCGCATGGCCGTGC 4 22 0 CAGAGGTGCC 0.994464 -104 TCCTTCTGCAAAAAAGATGAGCGCGCACAGCACG 4 38 1 AAAAGGAGCC 0.955135 -88 GTTCCAGTGTACCCGGTAGTGCGCACGTACTATG 4 94 0 ACCGGGTGCC 0.948941 -32 TGCGTTTTGAAAGAAGCGGAGGGCGGGGAAATCT 6 17 1 AAGAGGAGGC 0.865654 -188 GATCACCGACCAACAGATTTCCCCGCCCTCCGCT 6 31 0 CAAAGTTCCC 0.818396 -174 *** ** **** * Masking position 14 Map Score: 20.1924 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1125 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 TTACCTGAACAAAGAAGAACACCGGGACACG 1 60 1 AAAGAGAACA 0.942958 -111 TCTCGCGCCGAAAGGATAGCACC 2 114 1 AAAGGTAGCA 0.97013 -13 GTTCCCACCAGAAGGGGCGCGCCGA 3 82 1 GAAGGGCGCG 0.996413 -15 CTTTTTTGCAGAAGGAGTGCGCATGGCCGTG 4 23 0 GAAGGGTGCG 0.981562 -103 CTTCTGCAAAAAAGATGAGCGCGCACAGCAC 4 40 1 AAAGAGAGCG 0.990832 -86 GTGCGTTTTGAAAGAAGCGGAGGGCGGGGAA 6 16 1 AAAGAGCGGA 0.950854 -189 TATCCGAGTCAAAGGCGAGCAGCACGGTGGG 6 85 1 AAAGGGAGCA 0.993974 -120 ACGGGTGAGGAAAGGATCGCGGGTAGGGATA 6 152 1 AAAGGTCGCG 0.985146 -53 GGATAGGACGGAAGAAGCACATGTGACCGGT 6 178 1 GAAGAGCACA 0.955806 -27 ***** ***** Masking position 3 Map Score: 13.9704 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 543 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 AAAATACGCATCCGCCAGCGCCTGAAAGC 1 8 0 TCCCCGCGCC 0.986247 -163 CGAAAGCGTTTTCTCCGCCGTGTCCCGGTGTT 1 77 0 TTCCCCCGTG 0.985888 -94 GCGCTCGCGCTCCACCACCGTGATCTTAAACG 1 107 0 TCCCCCCGTG 0.995331 -64 GCAGTGGCCTTGCTCCGCCCAGACG 3 4 0 TGCCCCCCAG 0.932734 -93 CGCATGGCCGTGCACACCCGCCGG 4 3 0 TGCCACCGCC 0.98928 -123 GCAGAAGGAGTGCGCATGGCCGTGCACACCCG 4 15 0 TGCCAGGCCG 0.866435 -111 ATCACCCAATCTCTCATGCGCGCATAGTACGT 4 72 1 CTCCAGCGCG 0.888299 -54 ACCAACAGATTTCCCCGCCCTCCGCTTCTTTC 6 25 0 TTCCCCCCTC 0.948153 -180 ACGAAATCTCCCCACATCCCCGCACACAGAAA 6 116 0 CCCCACCCCG 0.984139 -89 CGCGATCCTTTCCTCACCCGTGCCTACGAAAT 6 141 0 TCCCACCGTG 0.994596 -64 TTCCGTCCTATCCCTACCCGCGATCCTTTCCT 6 159 0 TCCTACCGCG 0.979853 -46 TTCCTTACCGGTCACATGTGCTT 6 192 0 TCCTACGGTC 0.737637 -13 *** ** ***** Masking position 3 Map Score: 18.4069 Number of sites scoring better than the average of aligned sites = 1043 Number in coding regions = 948 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 ATTTTGAAAACGGATACACGTCAAATTACCTG 1 35 1 CGATCACGTC 0.98842 -136 AAGAAGAACACCGGGACACGGCGGAGAAAACG 1 71 1 CCGGCACGGC 0.987398 -100 GGAGCGCGAGCGCAGCCACGTCGAGCACATTA 1 126 1 CGAGCACGTC 0.992717 -45 CGTTCCGGGTCGTTTTCACCTGTTGGGGGAGT 2 19 1 CGTTCACCTG 0.908782 -108 CTGGGCGGAGCAAGGCCACTGCATTGGCGTAT 3 14 1 CAGGCACTGC 0.974682 -83 ACTGCATTGGCGTATCCACCTTTAGTGGAGTT 3 31 1 CGATCACCTT 0.823921 -66 CCGGCGGGTGTGCACGGCCATGCGCACT 4 7 1 GGGTCACGGC 0.968916 -119 TGCGCACTACCGGGTACACTGGAACGTGGAGC 4 103 1 CGGTCACTGG 0.978257 -23 ACGTACTTATCATTGACACTGCTGGCCGT 5 8 0 CATGCACTGC 0.929474 -27 GGGGAGATTTCGTAGGCACGGGTGAGGAAAGG 6 135 1 CGAGCACGGG 0.993946 -70 ** ** ****** Masking position 8 Map Score: 10.8326 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 452 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 CGCCGTGTCCCGGTGTTCTTCTTTGTTCAG 1 64 0 CGGTGTTCTT 0.368662 -107 TTTAAGATCACGGTGGTGGAGCGCGAGCGC 1 109 1 CGGTGGTGGA 0.655918 -62 TCGTTTTCACCTGTTGGGGGAGTATCTGTG 2 28 1 CTGTTGGGGG 0.971121 -99 GGGGGAGTATCTGTGGTTTGCTCAGGGCAA 2 43 1 CTGTGGTTTG 0.818503 -84 AACCCTTACGCTGTGTGTCTCGCGCCGAAA 2 97 1 CTGTGTGTCT 0.803024 -30 CGTCTGGGCGGAGCAAGGCC 3 1 1 CGTCTGGGCG 0.749322 -96 CGGCGCGCCCCTTCTGGTGGGAACCCCCTT 3 76 0 CTTCTGGTGG 0.717796 -21 CCGGCGGGTGTGCACGGCCAT 4 2 1 CGGCGGGTGT 0.964324 -124 GGTGATCGTGCTGTGCGCGCTCATCTTTTT 4 48 0 CTGTGCGCGC 0.749474 -78 CCAGTGTACCCGGTAGTGCGCACGTACTAT 4 95 0 CGGTAGTGCG 0.621369 -31 ATCATTGACACTGCTGGCCGT 5 2 0 CTGCTGGCCG 0.971221 -33 TTGAAAGAAGCGGAGGGCGGGGAAATCTGT 6 23 1 CGGAGGGCGG 0.947446 -182 GCGGGGAAATCTGTTGGTCGGTGATCGTAG 6 39 1 CTGTTGGTCG 0.963927 -166 ACCCACCGTGCTGCTCGCCTTTGACTCGGA 6 87 0 CTGCTCGCCT 0.708392 -118 GCGAGCAGCACGGTGGGTTTCTGTGTGCGG 6 99 1 CGGTGGGTTT 0.902783 -106 CGGTGGGTTTCTGTGTGCGGGGATGTGGGG 6 109 1 CTGTGTGCGG 0.955339 -96 ********** Masking position 1 Map Score: 10.2653 Number of sites scoring better than the average of aligned sites = 2518 Number in coding regions = 2248 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 6 TGTTCTTCTTTGTTCAGGTAATTTGACGTG 1 51 0 TGTTCAGGTA 0.807656 -120 CGTTTTCACCTGTTGGGGGAGTATCTGTGG 2 29 1 TGTTGGGGGA 0.983097 -98 ATCTGTGGTTTGCTCAGGGCAACACCCTGT 2 51 1 TGCTCAGGGC 0.90559 -76 CGTCTGGGCGGAGCAAGGCCACTG 3 5 1 TGGGCGGAGC 0.979856 -92 AAAGAAGCGGAGGGCGGGGAAATCTGTTGG 6 26 1 AGGGCGGGGA 0.982588 -179 GGAAATCTGTTGGTCGGTGATCGTAGAAAA 6 43 1 TGGTCGGTGA 0.968467 -162 TGGGTTTCTGTGTGCGGGGATGTGGGGAGA 6 112 1 TGTGCGGGGA 0.996159 -93 TGTGCGGGGATGTGGGGAGATTTCGTAGGC 6 122 1 TGTGGGGAGA 0.961783 -83 ********** Masking position 7 Map Score: 9.50914 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 286 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 GTCCCGGTGTTCTTCTTTGTTCAGGTAATTTG 1 56 0 TTCTTTGTTC 0.957388 -115 TGTATTCTTCGTTCCCTTAATGAT 1 157 0 TTCTTCGTTC 0.993162 -14 TGCTCCACGTTCCAGTGTACCC 4 114 0 TTCCACGTTC 0.981517 -12 TTCCCCGCCCTCCGCTTCTTTCAAAACGCACC 6 15 0 TGCTTCTTTC 0.910522 -190 ATCTACCTTCTTTTCTACGATCACCGACCAAC 6 51 0 TTCTACGATC 0.972848 -154 GACTCGGATATCATCTACCTTCTTTTCTACGA 6 63 0 TTCTACCTTC 0.97633 -142 * ********* Masking position 11 Map Score: 3.22697 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 27 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 CAGGCGCTGGCGGATGCGTATTTTGAAAACG 1 16 1 CGATGCGTAT 0.9365 -155 TGATCTTAAACGAAAGCGTTTTCTCCGCCGT 1 88 0 CGAAGCGTTT 0.988448 -83 CGATAGCCATCGACAGGGTGTTGCCCTGAGC 2 62 0 CGCAGGGTGT 0.988616 -65 AGACACACAGCGTAAGGGTTTGATCGATAGC 2 86 0 CGAAGGGTTT 0.99204 -41 ACCAGACAGTCTCAAGGGGGTTCCCACCAGA 3 63 1 CTAAGGGGGT 0.943316 -34 ** ******** Masking position 11 Map Score: 0.882555 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 70 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 ********** No masking Map Score: 1.65857e-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: 1.65857e-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 11 ********** No masking Map Score: 1.65857e-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