AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_tpal_reg_300.orf -o150_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 RTP00142 26 AE000520 #2 RTP00144 133 AE000520 #3 RTP00146 24 AE000520 #4 RTP01066 202 AE000520 #5 RTP00149 141 AE000520 #6 RTP00108 94 AE000520 #7 RTP00103 300 AE000520 #8 RTP00098 140 AE000520 #9 RTP00996 149 AE000520 #10 RTP00097 150 AE000520 Motif number 1 TCCCAGTGAAACACCCATACGCACCCTTCTCGCGC 2 12 0 AACCAACGCC 0.997068 -122 CGGTGCGTATTTTCGCAAACGCGGCTATGTCTCTG 2 60 1 TTCCAACGCC 0.907379 -74 CGTTTGGTAGATACTCAGACGCTTGTTTGTGCGTT 4 71 1 AACCAACGCG 0.994821 -132 TTGCACACAATCACAGAGAAGCTTCACC 5 4 0 TACGAAAGCC 0.793373 -138 TGCAGTACCTTCATACACACGCACCACGTGCCCTT 5 37 0 TATCAACGCC 0.920387 -105 CGTATGAAGAAAACTCAGACTCTTCTTGATAATCG 7 53 1 AACCAACTCC 0.979277 -248 ATGGATGTGTACACTGACACGCGTCGTGCGGCAGA 7 103 0 AACGAACGCC 0.995382 -198 TTTGGGGTACAAACAGACACTCTAGAT 9 3 0 AACGAACTCG 0.944171 -147 TAGGGCATACGGGGACGCTTGATCGCTTTGC 9 129 0 AACGGACGCG 0.985517 -21 ATCACACGCTATACATGCACCCTCCTGCAACTGAG 10 11 1 AACTGACCCC 0.800243 -140 GACCAACGAAAAATGCGCACGCCTCACTCCGTACA 10 45 1 AATCGACGCC 0.956679 -106 CATCATACGAAAACCCATTCGCCGCTTTCCTTATT 10 88 1 AACCATCGCC 0.970993 -63 TATTAATCCAAGACAGCGACCCTCGGAAAACACCA 10 119 1 AACGCACCCG 0.90942 -32 GACCCTCGGAAAACACCAACGCACG 10 136 1 AACCCACGCG 0.986616 -15 * ** ** **** * Masking position 12 Map Score: 20.4586 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 433 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 GCAACCTTACATGCGCGAGAAAATAA 1 5 1 CTAATGCGCG 0.973578 -22 CCCATACGCACCCTTCTCGCGCG 2 1 0 CTTTCGCGCG 0.829203 -133 CCGCGTTTGCGAAAATACGCACCGGTACACCAA 2 51 0 GAAACGCACC 0.733112 -83 GGTAGCAACACATGGGATGCGCAA 2 120 1 CGGATGCGCA 0.953701 -14 GCATCTGCTGGGCAGCTTGCGCCAACGCACAAA 4 96 0 GAGTTGCGCC 0.838498 -107 GGAGTACTGTCTTGGATTGCGCGTGAGTCAGCC 4 146 1 CGGTTGCGCG 0.956973 -57 CTACTCAATACGGAGTACGCACAGCCCCTGCTA 5 97 0 CAGACGCACA 0.904178 -45 CAAGCCGATTCGCTAAACGCACGTTCAAACCTT 7 182 1 CTAACGCACG 0.922649 -119 CATATCCGCGCAGAAATAGCGCA 8 1 0 CAATAGCGCA 0.872002 -140 GATATGCTCCCCCAATTTGCGCACCCTTAACTG 8 28 1 CAATTGCGCA 0.955671 -113 CCTGTTTCATCCCTGTAAGCGCGCCGCATCGGA 8 66 1 CTGAAGCGCG 0.913721 -75 GTACCCCAAACTGGATACGAGCCTCGTAACTCT 9 28 1 CGAACGAGCC 0.73845 -122 GGGGGCTTTACCAAACTCGCGCCGGTGATGACT 9 71 0 CAATCGCGCC 0.979381 -79 ATCACACGCTATACATGCACCCTCCTGCAAC 10 9 1 CTAATGCACC 0.89689 -142 CTGAGACCAACGAAAAATGCGCACGCCTCACTC 10 41 1 CAAATGCGCA 0.96952 -110 * ** ******* Masking position 9 Map Score: 14.0018 Number of sites scoring better than the average of aligned sites = 1780 Number in coding regions = 1674 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 CAGGAATCCTGTGCACCTCCGTTGT 4 6 0 GTGCACCTCC 0.975367 -197 CAACTGCAATCTGCATCTGCTGGGCAGCTT 4 111 0 CTGCATCTGC 0.965195 -92 AGTACTCCGTCTTCAACTGCAATCTGCATC 4 124 0 CTTCAACTGC 0.916804 -79 CACGCACCACGTGCCCTTGCACACAATCAC 5 25 0 GTGCCCTTGC 0.831973 -117 CCCCTGCTATTTTCCCCTCCCCAGGTACAC 5 76 0 TTTCCCCTCC 0.712674 -66 GGAGTACGCACAGCCCCTGCTATTTTCCCC 5 89 0 CAGCCCCTGC 0.9812 -53 GAATCTTAATGAGCTCCGGCGTAAATCCCA 7 23 1 GAGCTCCGGC 0.717539 -278 GAGAAGCGTTCTGCACTTGCCATTGTTGCT 7 246 0 CTGCACTTGC 0.957939 -55 GTGCAGAACGCTTCTCCTCATCAAGTACCA 7 260 1 CTTCTCCTCA 0.714984 -41 CCACGACGTTCAGCACCTCAGCAG 7 287 1 CAGCACCTCA 0.913144 -14 TCGACACCTCCTTCATCTCCGCGCATTCA 8 122 1 CTTCATCTCC 0.874738 -19 CCAAGCGAGTCATCACCGGCGCGAGTTTGG 9 64 1 CATCACCGGC 0.912753 -86 ATGCACCCTCCTGCAACTGAGACCAACGAA 10 25 1 CTGCAACTGA 0.846649 -126 ********** Masking position 4 Map Score: 11.4122 Number of sites scoring better than the average of aligned sites = 1595 Number in coding regions = 1460 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 CCATGTGTTGCTACCTCACGCTGCAAACGT 2 105 0 CTACCTCACG 0.938505 -29 ATGCTACCGGCTGACTCACGCGCAATCCAA 4 157 0 CTGACTCACG 0.982296 -46 AACAAAGTATATGCGTCTCGCATGCTACCG 4 178 0 ATGCGTCTCG 0.91287 -25 AAAAGATTTTCTGCCGCACGACGCGTGTCA 7 94 1 CTGCCGCACG 0.988864 -207 GATGTGTACACTGACACGCGTCGTGCGGCA 7 105 0 CTGACACGCG 0.927542 -196 TCTCTTCAAACTGACTCTCTGTCTTCACAT 7 137 1 CTGACTCTCT 0.92829 -164 GCTCTTTCCGATGCGGCGCGCTTACAGGGA 8 75 0 ATGCGGCGCG 0.950619 -66 AAACTGAAGGATGCCGCTCTTTCCGATGCG 8 90 0 ATGCCGCTCT 0.917654 -51 GAAAAGAGTTACGAGGCTCGTATCCAGTTT 9 35 0 ACGAGGCTCG 0.830823 -115 CGCGCCGGTGATGACTCGCTTGGAAAAGAG 9 57 0 ATGACTCGCT 0.916974 -93 GGGGCTTTACCAAACTCGCGCCGGTGATGA 9 73 0 CAAACTCGCG 0.666786 -77 AAAAATGCGCACGCCTCACTCCGTACAAAA 10 53 1 ACGCCTCACT 0.868868 -98 TCGGAAAACACCAACGCACG 10 141 1 CCAACGCACG 0.877354 -10 ********** Masking position 7 Map Score: 12.8705 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 1032 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TACTCCACGCAATGCGATACA 3 14 0 ACTCCACGCA 0.983693 -11 CCCCAGGTACACACCGTGCAGTACCTTCAT 5 58 0 ACACCGTGCA 0.976994 -84 TGGGGGAGCATATCCGCGCAGAAATAGCGC 8 12 0 TATCCGCGCA 0.976787 -129 ACCTCCTTCATCTCCGCGCATTCA 8 127 1 TCTCCGCGCA 0.995458 -14 CGCACGCCTCACTCCGTACAAAATACCGCA 10 60 1 ACTCCGTACA 0.963986 -91 ********** Masking position 10 Map Score: 3.82724 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 107 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 CAAACGTTGCCAGTCTTCAGAGACATAGCCGCGTTT 2 76 0 CGTCCAACAT 0.98575 -58 TAAAAAGTCGCTGTCAACAATTTCATTTTCGTTTGG 4 42 1 CGTCCATCAT 0.975146 -161 AGACAGTACTCCGTCTTCAACTGCAATCTGCATCTG 4 122 0 CGTCCAGCAA 0.912442 -81 GGATTTACGCCGGAGCTCATTAAGATTCTGCAGGAC 7 15 0 CGAGCAAGAT 0.814351 -286 CGACGCGTGTCAGTGTACACATCCATCTCTTCAAAC 7 112 1 CGTGCACCAT 0.986383 -189 AACTGACTCTCTGTCTTCACATCGATATTCCAGTCC 7 145 1 CGTCCACGAT 0.99514 -156 ATCGATATTCCAGTCCACAAGCCGATTCGCTAAACG 7 165 1 CGTCCACGAT 0.99514 -136 CAACAGCAGCCCATCAGCAAAGCGATCAAGCGTCCC 9 113 1 CATCCACGAT 0.958096 -37 * *** ** **** Masking position 9 Map Score: 6.35539 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 49 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 GGTACACCAATCGCTCCCAGTGAAACACCCATACGCACCCTTC 2 18 0 TCCCGAACCA 0.856836 -116 TGCTATTTTCCCCTCCCCAGGTACACACCGTGCAGTACCTTCA 5 59 0 CCCCGAACCC 0.99557 -83 ACTTATAATCCCCATTCGCGGTCCACGGCTCCCACAAAACAGC 6 17 1 CCTCGCACCC 0.99391 -78 GGCGTAAATCCCACGTATGAAGAAAACTCAGACTCTTCTTGAT 7 40 1 CCTAAAAACC 0.617676 -261 GCCGCACGACGCGTGTCAGTGTACACATCCATCTCTTCAAACT 7 106 1 GCTCTAACCC 0.870611 -195 CATCGATATTCCAGTCCACAAGCCGATTCGCTAAACGCACGTT 7 164 1 CCCCACGACA 0.565669 -137 AACCTTGCTTTCCTATCGCGATAGACAGCTGGCTTTCAGCAAC 7 209 1 TCTCGAACCC 0.971044 -92 GAACGCTTCTCCTCATCAAGTACCACGACGTTCAGCACCTCAG 7 265 1 CCTCGCACCC 0.994517 -36 TGTAAGCGCGCCGCATCGGAAAGAGCGGCATCCTTCAGTTTCC 8 79 1 CCTCAGGCCC 0.903745 -62 TGGTAAAGCCCCCTACCAAAAGCAACAGCAGCCCATCAGCAAA 9 91 1 CCCCACACCC 0.991031 -59 GTACAAAATACCGCATCATACGAAAACCCATTCGCCGCTTTCC 10 75 1 CCTCAAAACC 0.957476 -76 ATCCAAGACAGCGACCCTCGGAAAACACCAACGCACG 10 124 1 GCCCGAACCG 0.88612 -27 ** ** * * ** * * Masking position 19 Map Score: 6.28275 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 416 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AGAGACATAGCCGCGTTTGCGAAAATACGC 2 64 0 CCGCGTTTGC 0.987273 -70 TGAAGACTGGCAACGTTTGCAGCGTGAGGT 2 93 1 CAACGTTTGC 0.990951 -41 GATTTTAAGTCAACGTTTGCTGTTTTGTGG 6 48 0 CAACGTTTGC 0.990951 -47 GGCGTAAATCCCACGTATGAAGAAAACTCA 7 40 1 CCACGTATGA 0.968929 -261 GATAGGAAAGCAAGGTTTGAACGTGCGTTT 7 196 0 CAAGGTTTGA 0.894564 -105 GATCAAGCGTCCCCGTATGCCCTA 9 136 1 CCCCGTATGC 0.976512 -14 ********** Masking position 6 Map Score: 6.83313 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 62 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 GCGCGAGAAGGGTGCGTATGGGTGTTTCAC 2 12 1 GGTGCGTATG 0.902794 -122 AACAATTTCATTTTCGTTTGGTAGATACTC 4 57 1 TTTTCGTTTG 0.957772 -146 GACGCTTGTTTGTGCGTTGGCGCAAGCTGC 4 88 1 TGTGCGTTGG 0.985572 -115 CTGCTGTTGCTTTTGGTAGGGGGCTTTACC 9 92 0 TTTTGGTAGG 0.873675 -58 GCGTGCGCATTTTTCGTTGGTCTCAGTTGC 10 37 0 TTTTCGTTGG 0.979099 -114 GGCGAATGGGTTTTCGTATGATGCGGTATT 10 81 0 TTTTCGTATG 0.945703 -70 CGTGCGTTGGTGTTTTCCGA 10 141 0 CGTGCGTTGG 0.9615 -10 ********** Masking position 7 Map Score: 4.36935 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 113 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GTTGCAGGAATCCTGTGCACCTCCGTTGT 4 9 0 TCCTTGCACC 0.9361 -194 AATCTGCATCTGCTGGGCAGCTTGCGCCAAC 4 103 0 TGCTGGCAGC 0.979448 -100 TCACGCGCAATCCAAGACAGTACTCCGTCTT 4 141 0 TCCAGACAGT 0.940462 -62 CCATTCGCGGTCCACGGCTCCCACAAAACAG 6 28 1 TCCAGGCTCC 0.968285 -67 ATTAAGATTCTGCAGGACAACG 7 2 0 TGCAGACAAC 0.928232 -299 TCCTTCAGTTTCCTCGACACCTCCTTCATCT 8 109 1 TCCTGACACC 0.989421 -32 TCCTTATTAATCCAAGACAGCGACCCTCGGA 10 115 1 TCCAGACAGC 0.991855 -36 **** ****** Masking position 1 Map Score: 4.20567 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 107 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ********** No masking Map Score: 2.73092e-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 12 ********** No masking Map Score: 2.73092e-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 13 ********** No masking Map Score: 2.73092e-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