AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_aful_mthe_100.orf -o146_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG11206 49 Archaeoglobus_fulgidus #2 RAG10831 73 Archaeoglobus_fulgidus #3 RTH00407 249 M.thermo #4 RTH00771 24 M.thermo #5 RTH00911 35 M.thermo #6 RTH01399 41 M.thermo #7 RTH01500 55 M.thermo #8 RTH01705 40 M.thermo #9 RTH01266 139 M.thermo #10 RTH00772 30 M.thermo #11 RTH01355 147 M.thermo #12 RTH01016 118 M.thermo Motif number 1 CCATGTTTTCTCAAGTAGCATTTATTAAATTTTC 1 12 1 TCAGAATTTA 0.929806 -38 ATACTATCGATTTAGTAAAATTTATTAGTGTGTG 2 34 1 TTAGAATTTA 0.969386 -40 ACTCACCTTTTTTAAAAAGATTTATAT 3 233 1 TTAAAATTTA 0.879136 -17 CATGTTCTCATTCAGGATTATTTACGGGG 5 17 1 TTAGAATTTA 0.969196 -19 GTTTATGATAATAGAATCATTCCGG 6 2 1 TTATAATAGA 0.63467 -40 TGGAAGGGATTTAATCAGAAAAGAGGGGATTTA 7 33 1 TTATAAAAGA 0.811801 -23 TGAACTTCAATCAATAAAGAGCAAATGCTG 8 7 1 TCATAAAAGA 0.644782 -34 ATGAGGTCCATTAAGAAAGATTTATATATGGACC 9 101 1 TTAGAATTTA 0.969323 -39 GATCCCCTATTTTATTACGATTTATATAGAAAAC 11 65 1 TTATAATTTA 0.957405 -83 AACATGATTATTTATGATAATATAAAGTTTTCTA 11 91 0 TTATAATATA 0.897235 -57 CTCCCTTCTCTTTAGTACCAATAATTAACATGAT 11 117 0 TTAGAAATAA 0.628112 -31 CCACCTCACATCTAAAAACATATATCCATCTTTG 12 18 1 TCAAAATATA 0.675749 -101 ATATCCATCTTTGATTAACAGTTAAACAGATCTT 12 39 1 TTATAAGTTA 0.812575 -80 ATATTATAGATTAAGGACAAAAGATCTGTTTAAC 12 59 0 TTAGAAAAGA 0.856585 -60 TATATTTGAGTTCATGACTCTTTAACCTGGAGGC 12 90 1 TTATACTTTA 0.757442 -29 ** ** * ***** Masking position 7 Map Score: 14.3205 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 101 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 ACTGAAAATTTAATAAATGCTACTTGAGAA 1 19 0 TAATAAATGC 0.861072 -31 TTTTTTCATGTAATAAAGCTGAAATACTAT 2 11 1 TAATAAAGCT 0.906466 -63 AGCCACACACTAATAAATTTTACTAAATCG 2 41 0 TAATAAATTT 0.930612 -33 GAAGATTTAGTAATAAATTTTAAGGATTTT 3 97 0 TAATAAATTT 0.930612 -153 GATATCAGTAAAAAAAAGTTTCTGTAGAGA 3 144 1 AAAAAAAGTT 0.754294 -106 CAGATATTAGTAAAAAAGGCCATAATTTTA 3 180 1 TAAAAAAGGC 0.924368 -70 AAAGACCTCTTAATAAAATTATGGCCTTTT 3 193 0 TAATAAAATT 0.878104 -57 GAGTTAGACCTAAAAAAGACCTCTTAATAA 3 207 0 TAAAAAAGAC 0.844344 -43 TAAATCTTTTTAAAAAAGGTGAGTTAGACC 3 227 0 TAAAAAAGGT 0.956259 -23 TCCTGAAAAATAAAAAAATTGAAA 9 5 0 TAAAAAAATT 0.858402 -135 TGAGGTCCATTAAGAAAGATTTATATATGG 9 102 1 TAAGAAAGAT 0.780115 -38 CCTTAATCTATAATATATTTGAGTTCATGA 12 77 1 TAATATATTT 0.605293 -42 ********** Masking position 5 Map Score: 8.08591 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 143 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 AACCTCCAGGACATGATGGGGTGGGAAT 3 8 0 ACTGATGGGG 0.977446 -242 TTTTACTGATATCTGAAGGGTCCCTCTACAG 3 126 0 ATTGAAGGGT 0.847375 -124 AAGACATGATGTGGAATGAAAATG 7 4 1 ACTGATGTGG 0.882242 -52 GTGGAATGAAAATGGAAGGGATTTAATCAGA 7 21 1 AAGGAAGGGA 0.928161 -35 ATTTAATCAGAAAAGAGGGGATTTA 7 41 1 AAAGAGGGGA 0.972173 -15 TATCCATTATAACTGCGGGGGTCCTCAGCTG 9 47 1 AATGCGGGGG 0.964651 -93 ATGATTAAACACTTGAAGGGGAAGAGGCTGC 11 32 0 ACTGAAGGGG 0.987784 -116 AAATCGTAATAAAATAGGGGATCCGATGATT 11 57 0 AAATAGGGGA 0.753228 -91 ATTGGTACTAAAGAGAAGGGAGCTATAAA 11 129 1 AAAGAAGGGA 0.956571 -19 ATGTTTTTAGATGTGAGGTGGTGGGTGT 12 8 0 ATTGAGGTGG 0.907754 -111 ** ******** Masking position 1 Map Score: 8.05448 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 642 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 CCATCATGTCCTGGAGGTTCCTATGGAGTCA 3 20 1 CTGGAGGTCC 0.997144 -230 TTACTGATATCTGAAGGGTCCCTCTACAGAA 3 124 0 CTGAAGGTCC 0.993588 -126 TTACTAATATCTGGAGGTTTCTCTACAGAAA 3 162 0 CTGGAGGTTC 0.996917 -88 CCATTAACACCGGAATGATTCTATTATCATA 6 14 0 CGGAATGTTC 0.925321 -28 ACTCTTTAACCTGGAGGCTTTGA 12 106 1 CTGGAGGTTT 0.98412 -13 ******* *** Masking position 5 Map Score: 5.21873 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 64 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TTTTTAGGTCTAACTCACCTTTTTTAAAAA 3 221 1 TAACTCACCT 0.793054 -29 TCCATTTTCATTCCACATCATGTCTT 7 7 0 TTCCACATCA 0.88708 -49 TTCTTTACCTCAGCATTTGCTCTTT 8 26 0 TACCTCAGCA 0.9535 -15 TATAATGGATATCCTCACGTATTTCCTGAA 9 28 0 ATCCTCACGT 0.904843 -112 AACTGCGGGGGTCCTCAGCTGCCATGTAAA 9 57 1 GTCCTCAGCT 0.976851 -83 TTTCTTAATGGACCTCATGAAAACAGTACT 9 89 0 GACCTCATGA 0.819455 -51 ATCGTATATTCCACAGGTCCATATATAA 9 122 0 TTCCACAGGT 0.935375 -18 ACCTGTTAGATTCCTCATTTTA 10 3 0 TTCCTCATTT 0.879974 -28 AATTCCTCACCTGTTAGATTCC 10 19 0 TTCCTCACCT 0.986758 -12 ********** Masking position 7 Map Score: 5.45579 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 867 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 ATGTCCTGGAGGTTCCTATGGAGTCACATCCA 3 25 1 GGTTCCTTGA 0.98518 -225 TCCACTTACCGGTTTCTGTGAATATAATCACG 3 53 1 GGTTTCTTGA 0.969867 -197 ATATCTGAAGGGTCCCTCTACAGAAGATTTAG 3 117 0 GGTCCCTTAA 0.991687 -133 AATATCTGGAGGTTTCTCTACAGAAACTTTTT 3 156 0 GGTTTCTTAA 0.979521 -94 GTTTTCATGAGGTCCATTAAGAAAGATTTATA 9 95 1 GGTCCATAAA 0.871071 -45 ATATTCCACAGGTCCATATATAAATCTTTCTT 9 113 0 GGTCCATTAA 0.970187 -27 ATAATATAAAGTTTTCTATATAAATCGTAATA 11 77 0 GTTTTCTTAA 0.861192 -71 ******* ** * Masking position 12 Map Score: 5.95877 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 35 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 GCCATGTTTTCTCAAGTAGCATTTA 1 6 1 GTTTTCTCAA 0.833489 -44 ATGTCCTGGAGGTTCCTATGGAGTCACATC 3 25 1 GGTTCCTATG 0.978261 -225 TCCACTTACCGGTTTCTGTGAATATAATCA 3 53 1 GGTTTCTGTG 0.943316 -197 ATATCTGAAGGGTCCCTCTACAGAAGATTT 3 119 0 GGTCCCTCTA 0.981717 -131 AATATCTGGAGGTTTCTCTACAGAAACTTT 3 158 0 GGTTTCTCTA 0.983547 -92 ATAACTGCGGGGGTCCTCAGCTGCCATGTA 9 55 1 GGGTCCTCAG 0.90037 -85 ATATTCCACAGGTCCATATATAAATCTTTC 9 115 0 GGTCCATATA 0.743797 -25 ATAATATAAAGTTTTCTATATAAATCGTAA 11 79 0 GTTTTCTATA 0.868773 -69 ********** Masking position 7 Map Score: 3.34918 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 230 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GTCCCGAAGTCACAGCCACACACTAATAAAT 2 53 0 CCAGCCACAC 0.901336 -21 ATTCCCACCCCATCATGTCCTGGA 3 4 1 CCACCCCATC 0.93842 -246 CCTATGGAGTCACATCCACTTACCGGTTTCT 3 39 1 CCATCCACTT 0.982613 -211 CTCATCACCATTAACACCGGA 6 31 0 CCATCACCAT 0.9237 -11 CTGATTAAATCCCTTCCATTTTCATTCCACA 7 20 0 CCTTCCATTT 0.728526 -36 TTACGGCAGCCTCTTCCCCTTCAAGTGTTTA 11 27 1 CCTTCCCCTT 0.981457 -121 GTTTAATCATCGGATCCCCTATTTTATTACG 11 53 1 CGATCCCCTA 0.879127 -95 ACACCCACCACCTCACATCTAAAA 12 4 1 CCACCACCTC 0.964122 -115 * ********* Masking position 6 Map Score: 1.0466 Number of sites scoring better than the average of aligned sites = 1134 Number in coding regions = 1084 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 ********** No masking Map Score: 3.03645e-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: 3.03645e-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 11 ********** No masking Map Score: 3.03645e-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